Sehrish Kanwal1, Ali Saeed1*, Muhammad Munir2, Memoona Arshad1
Life Sciences International Journal Issue 7 Volume 1
... samples. As high as 98% nucleotide sequences similarity was determined between the representative strains. Furthermore, these strains have shown homology with previously characterized strains from Pakistan (O/PAK Lahore), Afghanistan, Iran, India, Nepal and Bhutan. Phylogenetically, these strains clustered into PanAsian II lineage of FMD O serotype along with previously characterized strains of Pakistan. The network analysis of complete VP1 gene
Sehrish Kanwal, Ali Saeed, Muhammad Munir, Memoona Arshad
British Journal of Virology
... samples. As high as 98% nucleotide sequences similarity was determined between the representative strains. Furthermore, these strains have shown homology with previously characterized strains from Pakistan (O/PAK Lahore), Afghanistan, Iran, India, Nepal and Bhutan. Phylogenetically, these strains clustered into PanAsian II lineage of FMD O serotype along with previously characterized strains of Pakistan. The network analysis of complete VP1 gene
Sehrish Kanwal1, Ali Saeed1*, Muhammad Munir2, Memoona Arshad1
British Journal of Virology
... samples. As high as 98% nucleotide sequences similarity was determined between the representative strains. Furthermore, these strains have shown homology with previously characterized strains from Pakistan (O/PAK Lahore), Afghanistan, Iran, India, Nepal and Bhutan. Phylogenetically, these strains clustered into PanAsian II lineage of FMD O serotype along with previously characterized strains of Pakistan. The network analysis of complete VP1 gene
Gerald Misinzo1,*, Tebogo Kgotlele1, Epaphras A. Muse1, Jan Van Doorsselaere2, Mikael Berg3, and Muhammad Munir4
...ive for PPRV N gene. The nucleotide sequence and phylogenetic analysis clus- tered the PPRV from Tandahimba into lineages II and IV. The results give evidence of at least two separate introductions of PPRV into Southern Tanzania, underlining the transboundary nature of the disease, particularly in regions with uncontrolled livestock movements....
Christopher U Orji1*, Ignatius O Onyeocha2, Steven S Shaida3, Peter M Dede4, Bitrus Yakubu5, Elijah E Ella6 and Pam D Luka5
... haplotype diversity and nucleotide diversity for the two species. Based on combined loci of cytochrome oxidase II (COII) and cytochrome b (CytB), twelve haplotypes were generated for G. p. palpalis and five for G. m. submorsitans. Similarly, for the combined loci, haplotype diversity (Hd) was higher for G. p. palpalis (0.90) than G. m. submorsitans (0.68). Nucleotide diversity was homogenous for ...
Usman Ijaz1, Muhammad Sajid Tahir2, Khalid Abdul Majeed3*, Shahid Iqbal4, Iffat Huma5, S. Firyal6, Ijaz Ahmed7, Shahid Chohan8 and Aamir Riaz Khan9
...then observed for single nucleotide polymorphisms (SNPs). SNPs were observed on three loci of the COI gene as compared to reference sequence of Panthera pardus pardus. The specimens found in Pakistan were found to be closely related to Panthera pardus orientalis (Amur Leopard in South eastern Russia) and Panthera pardus japonensis (North Chinese Leopard), with all of these three speculated to be evolved from Panthera pardus pardus i...
Atul Sharma, Aruna Chandra Singh, Gautam Bacher, Sunil Bhand
...ingle stranded (ss) oligonucleotides (ss-RNA or DNA), which are developed by an in-vitro selection process known as “Systematic Evolution of Ligands by Exponential Enrichment (SELEX)” technique. Among the receptors available for biosensing, aptamer exhibit the advantages of high specificity, selectivity, stability, facile labelling and modification, which makes them ideal candidates for development of new biosensing applications for detection of sp...
Misbah Riaz1, Qaiser Mansoor2, Maleeha Akram1, Muhammad Ismail2, Parveen Akhtar3, Shakeel Mirza4, Mazhar Qayyum1, Afzaal Ahmed Naseem1, Faheem Tahir5 and Syed Shakeel Raza Rizvi1*
...on mutation of T to G at nucleotide position 123, which did not replace valine with any other amino acid. The other mutation determined at nucleotide position 101, was a missense mutation, which substituted serine with phenylalanine at 34th position of extracellular domain of GNRHR. The Ser34Phe mutation was manifested in phenotypic traits such as low concentrations of FSH, LH and T and delayed puberty. In conclusion, mutati...
Ali Raza Awan*, Sehrish Firyal, Muhammad Tayyab, Lala Rukh, M. Zia ul Haq, Shagufta Saeed and Muhammad Wasim
Sameera Akhtar1*, Muhammad Akram Muneer1, Khushi Muhammad1, Muhammad Yasin Tipu1, Muhammad Anees2, Imran Rashid1, Raza-ur-Rehman3 and Irshad Hussain1
..., based on F and HN gene nucleotide sequence analysis, the isolate clustered as genotype VII closely associated to those reported from Indonesia. Further sequence analysis of hyper-variable region within F gene revealed its clustering to sub-genotype VIIe. The inferred residue analysis of the virus revealed a number of substitution mutations in the structural and functional domains when compared to the representative strains of each genotype including the vacc...
Jakub Jan Skorupski
...ext-align: justify;">The nucleotide sequence, variation and gene-structure of the American mink (Neovison vison) growth hormone gene was analyzed. For this purpose set of 3 amplicons were sequenced, including 5’-UTR and all exons and introns. The study involved 389 animals. The sequencing results revealed the presence of 5 exons (10 bp, 161 bp, 117 bp, 162 bp, 201 bp) and 4 introns (245 bp, 171 bp, 176 bp, 290 bp), with a total length of 1745 bp. ...
Sadia Munir1a, Asif Nadeem1a*, Maryam Javed1, Masroor Ellahi Babar2, Tanveer Hussain2, Wasim Shehzad1, Rajput Zahid Iqbal3 and Sidra Manzoor1
...udy, a new set of single nucleotide polymorphisms (SNPs) were reported. Heterozygosity, allelic and genotypic frequencies of identified variants were also determined. Chi2 test was performed to evaluate the Hardy-Weinberg Equilibrium of each polymorphic site. Two loci were found to be in HWE. These identified alleles will be useful for animal selection at molecular level i.e. an ideal tool for marker-assisted selection of animals for future b...
Hussein Aly Hussein1*, Omneya Mohamed Khattab2, Shereen Mohamed Aly2, and Mohammed Abdel Mohsen Rohaim1
...ltiple alignments of the nucleotide sequences revealed that both isolates had nine nucleotide mutations in comparison with the local reference strain, LSDV-Egypt/89 Ismalia. Compared with the GPCR sequences of SPV and GPV strains, 21 nucleotide insertion and 12 nucleotides deletions were identified in the GPCR genes of our isolates and other LSDVs. The a...
Sidra Manzoor1,Asif Nadeem1,*, Masroor Ellahi Babar2, Wasim Shehzad1, Abu Saeed Hashmi1, Muhammad Imran1, Tanveer Hussain2, Abdul Wajid1 and Maryam Javed1
Ghulam Abbas1,Asif Nadeem1,*, Masroor Ellahi Babar2, Tanveer Hussain2, Muhammad Sajid Tahir3, Wasim Shehzad1, Rajput Zahid Iqbal3, Muhammad Tayyab1 and Maryam Javed1
...ally, aligned and single nucleotide polymorphisms were identified. Bioinformatics tools were applied for construction of phylogenetic tree and genetic diversity analysis. Lower genetic diversity was observed. The finding of this research is prerequisite for future research.
...
Carolina Torres Alejo1,2, Laila Andreia Rodrigues Beserra1,2, Paulo Eduardo Brandão1,2, Luis Ramiro Luna Espinoza1,2 and Fabio Gregori1,2*
...CR reactions followed by nucleotide sequencing and analysis. Twenty-nine pools (29/59; 49%) appeared positive for AAstV, 6 pools (6/59; 10%) were positive for RVD, forty-three pools (43/59; 72.8%) were positive for ACoV, and twenty-four pools (24/59; 40.67%) presented concomitant viral infections of two or three investigated agents. The relative high frequency of occurrence of the studied viruses both in single or concomitant infection emphasizes the need for ...
Yunjun Yan, Zhenming Lü, Tianming Wang, Yongjiu Chen, Jingwen Yang, Baoying Guo, Lihua Jiang, Changwen Wu and Liqin Liu*
... determined the complete nucleotide sequence of the mitochondrial genome of Octopus dollfusi (Robson, 1932) collected from the coast of Guangdong Province, China, and analyzed the phylogenetic relationship with other cephalopod species. The results show that the mitochondrial genome of O. dollfusi composed of 15843 nucleotide pairs and encodes 13 proteins, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and ...
Saba Rafique1,2,*, Khalid Naeem1, Naila Siddique1, Muhammad Athar Abbas1, Aamer Ali Shah2, Akbar Ali1, Abdul Rahim1 and Farooq Rashid1
...tic grouping and maximum nucleotide sequence identity values were used to identify the isolate that looked to be derived from recombination. It showed maximum nucleotide homology 99.5% with ck/CH/LHB/121010 (KP036503), India/IBV572 (KF809797) and Japan/JP/Wakayama-2/2004 (AB363951.2) and 99.3% with 4/91 vaccine (KF377577), Iran/491/08 (HQ842715) and 99.1% with India/NMK/72/VRI/10 (HM748585) and was least related to rest of I...
Muhammad Rasool1,*, Muhammad Zahid1, Muhammad Ismail Khan1, Qadeem Khan2 and Khalid Khan1
...as conducted to find out nucleotide variations in the pre-S2 region of the two clinically diagnosed Surface Antigen of Hepatitis B Virus (HBsAg). Pre-S2 region nucleotide sequence of the sample MR02 was found completely homologous with the Pre-S2 region of already reported subtype “adr4”. This sample showed 1.2 to 20% variation with the other reported sequences. Nucleotide sequ...
Qin Liu1,2, Feiwei Liu1, Xiuyue Zhang1, Nan Yang1 and Jianghong Ran1,*
...ere, 22 polymorphic tetranucleotide microsatellite markers were isolated from T. szechenyii using a next-generation sequencing technology. The allele number of these loci ranged from two to six in genotyped 35 individuals. Polymorphism information content ranged from 0.2735 to 0.7717 with an average of 0.5149. Observed and expected heterozygosities at each locus ranged from 0 to 0.879 and 0.332 to 0.814, respectively. These markers could be used to bett...
Selçuk Kaplan1,* and Sertaç Atalay2
...phism method. The single nucleotide polymorphism (SNP) in the regulatory region of the IGF1 gene was detected by amplification of the 294 bp region using specific primers and cleavage with the BfoI enzyme. Allele frequencies of A and B were found with 0.915 and 0.085 respectively. The genotype frequencies of IGF1 gene were 0.85 (AA), 0.13 (AB) and 0.02 (BB). The SNP in the exon 3 of the LEP gene was detected by amplification of the ...
Ali Haider Saleem1,*, Khalid Javed2, Masroor Ellahi Babar3, Tanveer Hussain3, Asad Ali2, Afzal Ali2, Nisar Ahmad2, Muhammad Zahid Farooq1 and Muhammad Dawood2
...analysis revealed single nucleotide polymorphism (T>A at position 483) and a sheterozygous condition (T>W at position 483). Generalized linear model was used to minimize the environmental effects. The variation i.e. “W” type heterozygous condition showed a higher average daily weight gain. Sequence analysis of LEP gene confirmed the presence of genetic variability among Lohi animals; this variation might be associated with other econom...
Sherin Reda Rouby
...differed in length by 21 nucleotides from those produced from SPPV either field or vaccinal strain. Among different LSD clinical samples, skin nodules and scabs are proved excellent sample material as they yield clear DNA bands that reflect the high concentrations of the virus. The results of the current study confirm the suitability of RP030 gene in differentiation of lumpy skin disease virus and sheep poxvirus in a single PCR assay without the necessity of p...
Ligia Neves Scuarcialupi, Laila Andreia Rodrigues Beserra, Julia Rosas Hochheim, Rodrigo Martins Soares, Fabio Gregori*
...ment of viral VP6-coding nucleotide sequence of each viral group. Amplicons were further submitted to genetic sequencing and analyzed by phylogenetic analysis. There were 5 RVF positive samples (5.15%) in 2 broilers, 1 laying hen and 2 breeders. Only one RVG sample (1.03%) was detected in laying hen, in coinfection with RVF. This data contributes to a better understanding of rotavirus distribution in Brazil.
...
Nadia Faqir1, Aish Muhammad2*, Ghulam Muhammad Ali2, Armghan Shehzad2, Hafeez Ur Rahman3, Farhatullah4 and Muhammad Zeeshan Hyder5
...as one synonymous single nucleotide polymorphism in Qantar, Hamin wali, Kupra and Shakri, suggesting a lack of divergence in these genes in the studied cultivars. Tree plots generated showed inconsistencies in grouping of the cultivars thus showing no significant relationship of the plant morphology with the chemical composition of fruit. ...
Zhuanxia Chen1, Ningping Tao1,*, Xiao Qin1 and Dayong Liu2
...uch as free amino acids, nucleotides, trimethylamine oxide and betaine. Results showed that umami was the most prominent flavor. Compared with liver, IMP is the main flavor nucleotide in meat. However, the contents of the umami amino acids and betaine in liver are much higher than that of meat. Additionally, trimethylamine oxide is mainly found in the meat. After steaming, content of IMP in meat increased significantly. Comp...
Selçuk Kaplan
...nd sequenced to identify nucleotide variations in Anatolian water buffaloes. Sequence analysis were revealed seven polymorphic site (G1072A, T1081C, T1131G, T1143C, T1145G, T1151G and C1221T) and one monomorphic site (C1071T) in Anatolian water buffaloes. To the best of my knowledge, this is the first study that fully describes seven polymorphic sites of bubaline leptin gene in Anatolian water buffaloes.
...
Ahmed Zein Elabdeen Mahmoud1, Muaz Magzob Abdellatif2* and Mohamed Abdelsalam Abdalla3
Tanveer Hussain1,*, Masroor Ellahi Babar1, Marcos De Donato2, Abdul Wajid1, Asif Nadeem3, Zahoor Ahmad3, Waqas Ahmad Khan4, Sunday O. Peters5 and Ikhide G. Imumorin6
...y 26 individuals showing nucleotide changes. Only 5 point mutations were present in multiple individuals (SNP), but one was specific for indicine cattle. Two Lohani and 5 Nari Master cattle showed nucleotide changes specific to taurine cattle. Of the changes found, only three produced amino acid changes in the protein sequence. The UPGMA tree showed a clear differentiation between taurine and indicine cattle, except mitochon...
Wang-Dui Basang1, Tian-Wu An2, Luo-Bu Danjiu3, Yan-Bin Zhu1, Shi-Cheng He3, Xiao-Lin Luo2, Wei-Wei Ni4, Xiao Wang4, Shu-Zhu Cheng4, Jian Wang4 and Guang-Xin E4,*
...tes, including 54 single-nucleotide polymorphisms and 3 single-nucleotide copy number variants, and 59 haplotypes were detected. The number of haplotypes within the population ranged from 17 (SN and JL) to 28 (DX). The haplotype diversity ranged from 0.9420 (SN) to 0.9770 (NR). The highest nucleotide diversity was found in the JL population (0.01479), whereas the lowest was found in the SN...
Ai Guo1,2,3, Jiaguang Xiao4, Binbin Shan4, Tianxiang Gao5 and Yongdong Zhou3,*
...nd-specific asymmetry of nucleotide composition, but also the codon usage of genes. Whereas a significant variation among Coilia species was detected in length of the control region, mainly caused by the variable number of tandem repeats. Phylogenetic analysis was performed based on 13 concatenated mitochondrial protein-coding genes from 8 Coilia mitochondrial genomes. The results supported that C. lindmani at first clustered with C. na...
Fehmeeda Fatima, Asif Nadeem* and Maryam Javed
Sadaf Niaz1, Masroor Ellahi Babar2, Tanveer Hussain2, Asif Nadeem1, Misbah Hussain1, Riffat Mehboob3*, Fridoon Jawad Ahmad3
Mutation analysis of RING1 domain of Parkin in early onset of Parkinson’s disease in Pakistani patients-a pilot study
Faiz Muhammad1,2, Canfeng Dou1, Zhen-ming Lü1,*, Li Gong1, Xun Du1 and Muhammad Shafi3
...gh and low haplotype and nucleotide diversity observed. The data was further tested with AMOVA that validates 91.24% variation among populations and 8.76% within population. Genetic fixation index was also calculated as 0.91243*. The neighbor-joining phylogenetic analysis revealed three lineages. The Dongshan population distinctly has shown separate lineage. The haplotype networking has shown that Hap1 contributed 48.051% and appeared in six populations w...
Gangchun Xu1,2, Fukuan Du2, Yuyu Wang2, Yan Li2, Zhijuan Nie2 and Pao Xu1,2,*
... (AATAAA) was present 14 nucleotides upstream of the poly(A) tail in both the PTGES2aand thePTGES2bgene. The full-length genomic DNA sequence of PTGES2a is 3,222 bp long, and composed of seven exons and six introns. The full-length genomic DNA sequence of PTGES2b is 1,908 bp long, and composed of six exons and five introns. PTGES2a was strongly expressed in the gills and liver while PTGES2b was strongly expressed in th...
Liyan Zhang1,2, Zhidong Zhou1,3, Haiping Li1,2, Yanlong Qiao4, 5 and Yueping Zhang1,3,*
...ery management unit. The nucleotide mismatch distribution and neutrality test results indicated that the studied S. japonicus populations experienced a recent expansion event during the late Pleistocene. At present, S. japonicus resources show recessions and decreased mean ages due to overfishing, emphasizing the need to strengthen the management of corresponding fisheries and to develop and reasonably utilize S. japonicus resources to ach...
Madeeha Khalid and Amtul Jamil Sami*
...ilar and prone to single nucleotide variations. The sequence variation occurring in the non-coding region of the GH-1 gene leads to altered transcriptional regulation causing various developmental defects in humans. In this report, we have analyzed a short sequence of ~200-240 bp spanning the proximal promoter and exon 1 (proximal portion) of the GH-1 gene to analyze the SNPs and allele frequencies of respective SNPs. Genomic DNA from blood was extracted, and ...
Zhen-Yang Wu1, Guang-Xin E2,*, Hui Ran1, Da-Hui Wang1 and Tian-You Yang1
...s, including four single-nucleotide polymorphisms and 59 parsimony-informative sites, and 18 haplotypes were detected. The number of haplotypes within populations ranged from one (WS and DJ) to six (JK). Haplotype diversity ranged from 0.000 (DJ and WS) to 0.793 (JK). The largest amount of nucleotide diversity was found in the SQ population (0.03111 ), whereas the smallest amount was in the DJ and WS (0.00000) populations. P...
Amna Younus1,3, Mariam Faiz2 and Abida Yasmeen1,*
...I and TaqI single nucleotide polymorphisms (SNPs) genotypic frequency among different clinico-pathological features in Pakistani breast cancer patients. Newly diagnosed 300 breast cancer women from different areas of Punjab visiting Institute of Nuclear Medicine and Oncology Lahore were included in this study. Different clinico-pathological features were described. Vitamin D levels were determined and VDR FokI and TaqI SNPs were analyzed. ...
SiRui Wang1,2, Fekede Regasa Joka1,2, XiaoLong Wang1,2,* and SuYing Bai2,*
...performed. A total of 10 nucleotide sequences of the GED region of the Mx gene in wild birds were obtained, with a length of 231 bp, encoding 77 amino acids. The third locus in all tested amino acid sequences contains a Ser residue that corresponds to amino acid position 631, the virus resistance site, in the chicken Mx gene. The third locus in all tested amino acid sequences are Ser and corresponds to the chicken 631 amino acid position, the vir...
Bingbing Gao1, Na Song1, Zhonglu Li2, Tianxiang Gao3 and Liqin Liu3,*
...0.39–0.59) and low nucleotide diversity (0.00038–0.00073). The result of AMOVA and pairwise Fst values indicated weak or no genetic differentiation among different populations. Haplotype network and NJ phylogenetic trees revealed that there was no distinctly geographical distribution pattern among the haplotypes. Furthermore, the mismatch distribution of pairwise nucleotide and the negatively se...
Muhammad Yasin1, Romana Shahzadi1, Muhammad Riaz2, Mahideen Afridi2, Wajya Ajmal3, Obaid Ur Rehman2, Nazia Rehman3, Ghulam Muhammad Ali1,3, Muhammad Ramzan Khan1,2,3*
... size, respectively. The nucleotide alignments revealed 98% identity of BnSHP1-like and BnSHP2-like with BnSHP1 and BnSHP2 sequences. The sequence homology was estimated to be 95 and 96% at amino acid level for BnSHP1-like and BnSHP2-like genes, respectively. The phylogenetic reconstruction of SHP1 and SHP2 homologs from other species conglomerated BnSHP1-like and BnSHP2-like into their respective clades. Semi-quantitative RT-PCR revealed overlapping expressio...
Hala Mohamed Nabil Tolba1, Naglaa Fathy Saeed Awad1*, Gamelat Kotb Farag Kotb2, Amany Adel3
...n reaction (RT-PCR). The nucleotide and deduced amino acid sequences for VP2 hypervariable region of selected five IBDV field isolates were determined and compared to well characterized reference and vaccine strains worldwide. The IBD virus was detected in 9 out of 16 (56.25 %) investigated chicken flocks. Sequence analysis revealed that the analyzed Egyptian isolates identified as very virulent Infectious bursal disease virus (vvIBDV). The identity between th...
Farah Bilal*, Abdulmohsen Alhejaily, Shahida Husnain
...the prevalence of common nucleotide changes (E545K/E542K and H1047R/H1047L) occur in PIK3CA gene in non smoker patients of non-small cell lung cancer (NSCLC). Somatic mutational analysis was done by QMC-PCR following direct sequencing with sangers’ method. Only one sample detected p.E545K mutation at c.1633G>A. Another most common mutation was observed in PIK3CA exon 20 which leads to change A>G at codon 1047. This transition converts...
Sehrish Ashraaf1, Hafiz Muhammad Tahir1, Muhammad Akram Qazi2, Shaukat Ali1*
...ypothesis, variations in nucleotide frequency distribution in cytochrome c oxidase subunit I (COI) in spiders used as a marker to delimit species. Based on morphological identification and sequencing of CO1 gene, a total of 22 species of spiders belonging to five families were investigated and compared within each species and among families for nucleotide frequency distribution of all species c...
Nida Zia1, *, Ayesha Maqbool2, Muhammad Safdar3, Umm-I-Habiba1, Altaf Mehmood4, Muhammad Usman5, Zahid Iqbal6, Javed Iqbal6, Shahid Mehmood6, Amanullah Khan7 and Sajid Umar8
...d close proximity at the nucleotide level. The other cluster containing three strains belonged to the FAdV-D species and serotyped as FAdV-11. Furthermore, the sequencing analysis of detected field strains revealed the high similarity and close clustering with FAdV-4 and FAdV-11 strains isolated from neighboring countries, suggesting geographic and temporal relationships among these strains. This evidence emphasizes the need of further detailed and more system...
Gul Afshan1,2,*, Soumble Zulfiqar2, Sumaira Mehboob2, Muhammad Tahir Javed Khan1 and Abdul Rauf Shakoori2,*
...h other sequences showed nucleotide variations of HCV3a E2 compared with already reported sequences. A total of 140 (11%) point mutations were found in Pakistan’s gene sequence, out of which general and specific differences were 93 (9%) and 47 (4%), respectively. The general differences usually occur in common population while the specific differences are present only in some cases. The 3D structure of E2 was determined. Protein docking with appropriate ...
Jinfeng Liu1,2, Yanhong Cao3, Tong Feng1, Laiba Shafique1, Chan Luo1, Peng Zhu1,4,* and Qingyou Liu1,*
...ned. It consists of 1185 nucleotides that encodes 394 peptides bond. The BMP15 gene was observed to be expressed in cumulus tissue, granular tissue, hypophysis, genital ridge and tissues of ovary and testis. Moreover, QRT-PCR results showed that BMP15 was expressed in the whole process of embryogenesis and folliculogenesis, early high level and then down regulated. It was significantly expressed higher level in COCs of middle diameter sized folli...
Tasleem Akhtar1,2,Ghazanfar Ali1,*, Nuzhat Shafi2 and Abdul Rauf2
...e sequences. The average nucleotide length of 16S rRNA in 45 samples ranged from 1527 to 1552 bps. Five haplotypes (h) were observed, with haplotype diversity (Hd) 0.5323±0.080. Among 5 haplotypes, 2, 2 and 1 haplotype were detected in S. plagiostomus, S. niger and S. esocinus, respectively. Haplotype diversity was lowest and same in S. esocinus, S. niger and S. progastus (0.0001) and highest in S. plagiostomus (0.5436...
Ali Mujtaba Shah1,2,3, Ali Raza Shah3, Muhammad Farooque Hassan2, Muhammad Yousif2, Zhisheng Wang1*
...rals, growth factors and nucleotides and its benefits to health of animals.
...
Detection and Phylogeny of Infectious Bursal Disease Virus (IBDV) during Field Outbreaks in Broilers
Umm-i-Habiba1,*, Ayesha Maqbool2, Muhammad Safdar3, Nida Zia1, Altaf Mehmood4, Muhammad Usman5, Mehwish Sharif6, Amanullah Khan7 and Sajid Umar8
...clusters on the basis of nucleotide sequences of hyper-variable region of the VP2 gene. According to phylogenetic analysis, 5 IBDV strains showed characteristic amino acid signatures in the VP2 gene (A222, I242, I256, I294, S299) and classified as vvIBDV. Furthermore, the sequencing analysis of detected field strains revealed the high similarity and close clustering with vvIBDV strains isolated from neighboring countries, sug...
Bibi Nazia Murtaza1, Mazhar Saeed Chaudry2, Shamaila Inayat Nadeem1, Muhammad Shahid Nadeem3 and Abdul Rauf Shakoori4,*
...sed by creating a single nucleotide mismatch at the 3′-end of primers to produce a BstNI recognition sequence at codon 12 while codon 13 was analysed by introducing HaeIII recognition sequence. By using RFLP and sequencing, point mutation substituting the glycine (GGC) to aspartic acid (GAC) was observed at codon 13. The p.G13D or cDNA.230G>A/ g.5590G>A is previously recognized as rs112445441 and being reported for the first time...
Peng Ren1, Xian-Qing Liu1, Chao-Wu Yang2,3, Hua-Rui Du2,3, Xiao-Song Jiang2,3 and Yi-Ping Liu1*
... gene expression. Single nucleotide polymorphisms (SNPs) in the coding regions (CDS) of the MyD88 gene have also been reported to be associated with inter-subject differences in responses to Salmonella Pullorum infection in chickens. However, whether the 3’-untranslated region (3’-UTR) of the MyD88 gene is associated with resistance to Salmonella Pullorum infection still remains unknown. In this study, a total of eight S...
Irfan Shahzad Sheikh, Masroor Ahmad Bajwa, Nadeem Rashid, Muhammad Zahid Mustafa, Mohammad Masood Tariq*, Majed Rafeeq, Abdul Samad, Tauseef M Asmat and Asad Ullah
...in E (200 mg/l), dietary nucleotides (100 mg/l) and DNA (100 mg/l) extracted from chicken liver were separately offered on days 1-21, 1-42 and 22-42 in experiments 1, 2 and 3, respectively. Under standard broiler management conditions, birds were divided into five treatment groups of 48 with four replicates. Commercial pre-starter feed, starter feed and finisher feed were offered on days 1-12, 13-25 and 26-42, respectively. Birds were vaccinated against Newcas...
Amna Shoaib*, Zoia Arshad Awan and Naureen Akhtar
...nd amplification of ISSR nucleotide sequences using three primers [P01 (AGAG)4 G, P02 (GTG)5, and P03 (GACA)4] confirmed that A. minisclerotigenes and A. flavus are two genetically distinct strains. Furthermore, both strains were qualitatively analyzed for aflatoxins (AFB1 and AFB2) production by thin-layer chromatography (TLC). A polyphasic strategy as adopted for the current study is a reliable and reproducible ...
Gulnaz Afzal1, Ghulam Mustafa2*, Shakila Mushtaq3 and Amer Jamil4
...uences were deposited in nucleotide database. A CO1 profile of all spider species was correctly assigned and 100% of subsequently analyzed specimens were identified up to their species levels. Such outcomes establish the potential of CO1 as a rapid identification tool and for phylogenetic relationships of spiders. Despite being sympatric species, the origin and diversification of Araneid fauna in wheat fields are remarkably distinguished which ma...
Muhammad Rizwan Ashraf1, Asif Nadeem1,2, Eric Nelson Smith3, Maryam Javed1, Utpal Smart3, Tahir Yaqub4, Abu Saeed Hashmi1 and Panupong Thammachoti3
.... Using the concatenated nucleotide data, Maximum likelihood and Bayesian phylogenetic trees were constructed that divided all Echis species into four groups. Saw-scaled viper in this study from Pakistan showed similarity and close relationship with Western India and UAE while showing difference from South Indian. Saw-scaled viper from South India is termed as Echis carinatus carinatus while that from Pakistan and Western India is Echis carinatus soc...
Peimin Yang*, Zongyun Hu, Yixin Liu, Guanghai Jin and Lei Wang
...h=0.8467) and low nucleotide diversity (Pi=0.0063). Genetic distances ranged from 0.0002 to 0.0149 within and 0.0007 to 0.0140 between populations. AMOVA analysis indicated significant genetic differentiation among populations (Fst=0.3202, P<0.01) and 68.98% of the total variation was resulted from intra-population differentiation. Pairwise Fst statistics also confirmed the presence of sign...
Aftab Shaukat1,*, Sana Hanif2, Irfan Shaukat3, Muhammad Ahsan Naeem4,5, Shadab Shaukat6, Rizwan Shukat8, Shahid Ali Rajput9, Imran Shaukat10, Mubashar Hassan4, Khalid Mehmood7, Saqib Umar11 and Muhammad Ali Jamil1
...RNAs comprising of 17-24 nucleotides that, targets in silencing of one or more genes. Despite their importance as gene regulator, computational strategies are still at its initial stages. Several computer based prediction databases remain the only foundation for rapid identification of putative microRNA target. By utilizing experimentally validated targets, the search of further targets via bioinformatics tools help to predict gene target site. Keeping this in...
Maria Khalid1, Tanveer Hussain1*, Zahid Farooq2, Kamran Abbas1 and Masroor Ellahi Babar1
...Edit software and single nucleotide polymorphisms (SNPs) were identified. The boot strapped Neighbor joining tree constructed from MEGA7 explained the genetic relationships of A.chukar with related members of Phasianidae family. The phylogenetic analysis also showed the genetic positioning of A. chukar with respect to other different reported species as well. The study gave us useful genomic information about genetic diversity in A. chukar...
Masroor Ellahi Babar*
...egions includes cysteine nucleotide deletion, AT bases insertion and transvertions (C>G; G>T). Deletion of A bases at c.1-1075 and hetrozygosity (CT) at the c1-1046 were analyzed along with some other SNPs are very important. These evidences points towards the change of expression of those protein which are nearest to the region of gene regulation and enhancer region. After observing taxas several distinct clads of camel breeds it was found that Kharani ...
Hui-Ying Chen1,2*, Ping-Chuan Yin1,2, Ya-Nan Lu1,2, Hai-Yun Li1,2*and Yang Shan3
...the PPI network: Guanine nucleotide-binding protein subunit β, ribosomal 60S subunit protein (RPL) 8A, RPL9A, RPL6B, ribosomal 40S subunit protein (RPS) 9B, RPL31B, RPL27B, RPS14B, RPL22B and RPL22A. In conclusion, the DEGs and Hub genes identified in the present study may further elucidate the molecular mechanisms of aspirin applied to redox-damaged yeast cells and may identify potential future biomarkers.
...
Mahvish Rajput1, Abdullah G. Arijo1, Muhammad Bachal Bhutto1, Rehana Shahnawaz Buriro2, Javaid Ali Gadahi1, Muhammad Naeem3 and Zubair Ahmed Laghari1*
...or further analysis. The nucleotide sequences from 6 isolates were further analyzed for sequence similarities and were used for constructing phylogenetic tree. The sequence and evolutionary relationship analysis indicate that all isolates were belong to the same species and were clustered together with Paramphistomum epiclitum. Taken together, this study provides the baseline data for the prevalence of rumen fluke infection in southeastern Pakistan and ...
Hafiz Muhammad Imran Javed* and Mushtaq Ahmed
...r phylogenetic analysis, nucleotide and deduced amino acid sequence analyses, and a comparison of three-dimensional protein structures. The N gene ORF was 1578 nucleotide long with a single open reading frame encoding 526 amino acids. Similarly, the ORF of F gene was 1641 nucleotide long which encoded 547 amino acids. Upon phylogenetic analysis of the country isolates with the vaccine stra...
Kajol, A. H. Bhat, Aasha and A. K. Chaubey
Biochemical and molecular characterization of Photorhabdus akhurstii associated with Heterorhabditis indica from Meerut, India
...-rDNA sequences showed 1 nucleotide base pair difference in aligned data with type description, however, no nucleotide base pair difference was seen in the D2D3 domain. The associated bacterial symbiont of the DH3 strain was identified as Photorhabdus akhurstii based on phenotypic, biochemical and 16S rDNA data. Most of the biochemical tests were negative and only three tests were found positive viz., Urease, Nitrogen reduct...
Muhammad Riaz1*, Naureen Akhtar1, Salik Nawaz Khan1, Muhammad Shakeel1,2 and Ateeq Tahir1
Neocosmospora rubicola: An Unrecorded Pathogen from Pakistan Causing Potato Stem Rot
...orphological characters, nucleotide sequences of internal transcribed spacer region (ITS) and partial beta tubulin gene. Phylogenetic analysis was also conducted to determine the phylogenetic relationship of this species with other reported species of this genus. Pathogenic potential of the isolate was verified by artificially inoculating the spores of pathogen in healthy plants. Appearance of same symptoms and re-isolation of N. rubicola from infected tissue ...
Muhammad Shahzad1, Arif Iqbal Umar1, Syed Hamad Shirazi1, Muhammad Tariq Pervez2*, Zakir Khan1, Waqas Yousaf1
HCDP: HEPATITIS C DATA BANK OF PAKISTAN
...pearance of protein/nucleotide sequences for analysis of different sites, visual representation of multiple sequence alignments using colour code along with motif finding/conserved region in the sequence and analysing of graphical structure of phylogenetic tree. With the help of Format converter/Fasta generator tool user can convert sequence with formats of PhyLip, NEXUS, MSF, CLUSTAL and PIR into standard FASTA. It is also observed that genotyp...
Mahak Fatima1, Memoona Syed1, Rabia Zeeshan2, Farah Rauf Shakoori3, Naveed Shahzad4, Moazzam Ali1 and Zeeshan Mutahir1*
...rsion of oxidized purine nucleotides to their monophosphate forms, thus preventing their incorporation into DNA and subsequently to oxidative damage. The present study explores the relationship between MTH1 gene silencing and its outcome on the growth of gemcitabine resistant breast cancer cells named MCF7-R. For this purpose, we transfected MCF7-R cells with MTH1 specific validated siRNA. Successful transfection of siRNA and consequent cytotoxic...
Sehrish Firyal1,*, Ali Raza Awan1, Muhammad Umair Latif1, Muhammad Tayyab1, Muhammad Wasim1, Shagufta Saeed1 and Imaad Rashid2
...ont-size: small;">Single nucleotide polymorphism (SNPs) analysis is a powerful tool for taxonomic and phylogenetic analysis. These are bi-allelic molecular markers, easy to interpret and uniformly distributed within genomes. In this study cytochrome b (Cytb) gene based SNPs analysis was employed to genetically characterize the Pakistani domestic breed Lathy pigeon. Cytb haplotype for local domestic breed was developed. Homology analysis of Cyt...
Aatif Amin1,*, Zakia Latif2, Arslan Sarwar1, Basit Zeshan1 and Mushtaq A. Saleem1
...the basis of merA nucleotide sequence confirmed 51-100% homology with the corresponding region of the merA gene of already reported mercury resistant Gram positive bacteria. Restriction fragment length polymorphism (RFLP) analysis was applied to the amplification products of 16S rRNA and merA genes and a specific restriction patterns was successfully obtained after treatment with different endonucleases. A small scale reservoir of Luria Be...
Ghulam Akbar1*, Ali Ahmad2, Neha Arooj1, Muhammad Anjum Zia1, Aamna Rafique1, Sania Riasat1, Mohsin Raza1, Mahpara Qamar1, Shahneela Nusrat1 and Shakila Hanif1
Critical Update for the Treatment of Anemia by using Advanced Genome Editing Crispr Cas Technology
..., whereas different oligonucleotides are provided to make accurate DNA template for genome correction. It is of importance to knowledge about types of CRISPR to treat anemia. Cas 9 showed one of best gene editing reactions than others. Recent data gives authentic applications of CRISPR use in anemia which provides potential for usage of gene editing technique for different types of anemia. In evaluation we defined currently developed genome editing device upda...
Gautam Patra1*, Ana Sahara2, Sonjoy Kumar Borthakur1, Parthasarathi Behera3, Subhamoy Ghosh1, Apurba Debbarma4 and Seikh Sahanawaz Alam5
...d. The obtained complete nucleotide sequences of cyt b gene from P. relicum revealed100% identity among themselves while the other sequences registered in Gen Bank showed 95% to 99% similarity. In the phylogenetic analysis all the isolates of P. relictum formed a separate clade with high bootstrap values. It can be inferred from the study that P. relictum is fairly common in wild birds and the cyt b gene is highly conserved among di...
Yifan Ni1, Jian Liu1, Fen Wu1, Jianfeng Cai1, Jinzhi Zhang1*, Jianqing Hua2 and Jiping Fu2
...o investigate the single-nucleotide polymorphisms (SNP) of the Multiple Drug Resistance Gene 1(MDR1) and the Porcine Osteopotin (OPN) gene and their association with reproductive traits in Landrace, Large Yorkshire and Jinhua sows. A total of 316 sows of three different breeds were used to examine the genotypes, and DNA sequencing method was employed to detect the potential SNPs in this study. There were two SNP loci found in these ...
Muhammad Iqbal1, Muhammad Ehetisham ul Haq1*, Muhammad Kamran1, Muhammad Idrees1, Shahid Nazir2, Ihsan Ullah3, Sumera Naz1, Shaukat Ali1 and Muhammad Zafar Iqbal2
Morpho-Molecular Characterization of Xanthomonas Axonopodis Pv. Citri Associated with Kinnow (Mandarin) and its Management
... 100% similarity with 40 nucleotide sequences of X. axonopodis pv. citri submitted in NCBI. Relative efficacy of six antibiotics (Streptomycin sulphate, Oxytetracycline, Cefalexin, Kasugamycin, Kanamycin and Levofloxacin USP) against colony growth of X. axonopodis pv. citri was evaluated at 50, 100 and 150 ppm using disc sensitivity technique. Streptomycin sulphate was found most effective to inhibit the colony growth of the bacterium. Streptomycin sulphate an...
Haseeb Nisar1, Usman Pasha1, Kiran Hanif1, Rizwan Abid1, Rehan Ahmad Khan Sherwani2, Haja N. Kadarmideen3 and Saima Sadaf1*
... of single- and multiple nucleotide polymorphisms in larger cohorts, originating from diverse ethnic groups, are imperative to ascertain the genetic contributors of RA in a specific population.
...
Zhilong Tian1, 2, Yuqin Wang2, Jishun Tang1,3 and Mingxing Chu1*
...sampled to detect single nucleotide polymorphism (SNP), and Sequenom Mass ARRAY®SNP assay was applied to genotype SNP loci of the SYNE2 gene. In this study, four SNPs were identified and that SNPs were identified that involved in amino acid changes. Population genetic analysis indicated that SYNE2 gene g.73310578G>A, g.73312791A>G showed moderate polymorphism (0.25<PIC<0.5) in Small Tail Han sheep. Furthermore, g.733105...
Q. Sun1, Q. Liu1, R. Di1, Y. Wang1, S. Gan2, S. Liu2, X. Wang1, W. Hu1, X. Cao1, Zh. Pan1, X. Guo1, Y. Yang3, H.E. Rushdi4* and M. Chu1*
...Identification of single nucleotide polymorphisms (SNPs) of sheep THRSP gene and their association with fat deposition were investigated using Altay and White Suffolk sheep. In addition, the messenger RNA expression profiling of THRSP in fat-tailed and thin-tailed breeds was compared among 8 different tissues. Four SNPs have been detected in position g. 205A>C, c. 52C>T, c. 364A>T and c. 1031C>T of THRSP gene. Genotyping method...
Qin Liu1,2, Bin Wang1,3, Yu Xu1,4, Xiuyue Zhang1, Tao Zeng1* and Jianghong Ran1*
...dy, we isolated 17 tetra-nucleotide microsatellite loci to test parentage and kinship for a wild population with 29 individuals from 10 different families (A-J). The 17 loci with the mean polymorphic information content (PIC) of 0.566 and the combined probability of exclusion for the second parent (CPE2 = 99.98%) met the minimum standard of international human paternity test. Among all 18 identified birdlings and helpers, bi-parents of eight offspring were suc...
Iftikhar Hussain1, Sardar Azhar Mehmood1, Muzafar Shah2*, Mohammad Salim3, Shabir Ahmed1, Sana Ullah1,Sidra Batool4, Nadia Saeed1 and Khalid Usman1
...inx were 0.011%. The nucleotide composition of the sequences showed higher concentration of A+T as compared to G+C. The A+T contents were 53.1% and C+G were 46.8%. In phylogenetic tree the sequences of C. sphinx clustered together with 100% bootstrap support. The relationship between C. sphinx and C. horsefield was supported by 83% bootstrap value. The relationship between C. titthaecheilus and C
Dilara Devranoglu, Ilksen Tavaci, Gonul Filoglu and Ozlem Bulbul*
...ont-size: small;">Single nucleotide polymorphisms (SNPs) are the most abundant genetic markers in the human genome. SNPs are used in forensics for predicting the externally visible characteristics of a given individual based on a sample of DNA alone. In this study, we tested degraded DNA samples to determine the eye color prediction accuracy of the IrisPlex system. We used five years old bloodstains and UVC exposed (30 and 60 min) DNA samples. PCR and electrop...
Yongyun Zhang1, 2, Xinyang Fan1, Fangting Zhou1, Weizhen Li3, Yina Ouyang1,4 and Yongwang Miao1*
...gth, which contained 645 nucleotides and encoded a peptide composing of 214 residues. A total of 5 single nucleotide polymorphisms (SNPs) was identified in two types of buffalo. Among them, c.516T>C and c.578C>T were observed only in river buffalo, while c.175A>G, c.580T>C and c.609T>G were found only in swamp buffalo. The c.175A>G, c.578C>T and c.580T>C were non-synonymous, which led to substitutions...
Saad A. Moussa1, Mohammed Ahmed Mahmoud Abdullah2*, Mahmoud Saied1, Mustafa Saleh1, Mohamed A. Soliman2 and Ali Mahmoud Zanaty2
.../SDWF07/2011 strain with nucleotide identity percentage (99.3% -100%). The main causative agent of recent ND outbreaks in vaccinated broiler flocks in Menofia governorate, Egypt was found to belong to very virulent genotype VII. This strain was genetically identical to Egyptian genotype VII isolates isolated in the last period.
...
Muhammad Naveed1, Asif Nadeem1,2*, Maryam Javed1, Muhammad Fahad Bhutta3 and Ruqayya Bint Khalid1
...lyzed to identify single nucleotide polymorphisms and its effect on evolutionary divergence. Nine polymorphisms, six in intronic and three in exonic regions, were identified in STAT5A gene. One exonic polymorphism G→A, in exon 5, was significant that causes a non-synonymous amino acid change from Serine (S) to Asparagine (N). Further, 64 genetic variants were also identified in STAT5A gene and these variants were due to cattle and buffalo di...
Amreen Zahra1, Mushtaq A. Saleem1*, Hasnain Javed2, Muhammad Azmat Ullah Khan3, Muhammad Naveed1 and Abdul Rauf Shakoori4
Ahmed A. Kheder
...howed 65.9 – 99.5% nucleotide similarity with available homologous sequences from other crops. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay which is one of the most promising molecular diagnostic techniques was applied. The amplified products were analyzed using amplification curves and electrophoresis. In this study SLRSV was characterized and detected with DAS-ELISA and molecular diagnostic techniques the obtained result...
Ala’audin Hakami,1AusamaA Yousif,2* Mohamed Zaki,3 Mahmoud Ismail,4,5 Ahmed Al-Ali,5 Abdu-Rahman Al-Ankari5
Mai A. Kilany1; Hanaa H.A. Gomaa1; Yousry E. Abo El-magd2 and Nermin Raafat2.
...adicals. Val16Ala single nucleotide polymorphism (SNP) is one of the most widely investigated SNPs in the MnSOD gene, where C to T transition resulting in the con-version of valine to alanine at amino acid 16 within the mitochondrial signaling se-quence. This study was designed to investigate the association of MnSOD gene SNP (Val16Ala) with HCV and HCV-related HCC to elucidate its possible role in patho-genesis of HCC. The study included sixty individuals; th...
Amal Mahmoud1&2 and Medhat H. Hashem3
...ogenetic analysis of the nucleotide sequence and the amino acid of the pol or env genes revealed that 7 out of the 8 isolates were closely related to genotype D. Only Sohag 1-HCC isolate was clustered with genotype C which is known as risk factor of HCC. Multiple sequence alignment resulted in unique amino acid substitutions (V320→L and N464→T) and (I284→L, T300→I and K334→R) in pol and env genes respectively. Further prospective studi...
Nader M. Sobhy,1 Sunil K. Mor,2 Mohammed E.M. Mohammed,1
Iman M. Bastawecy,3 Hiam M. Fakhry,4 and Sagar M. Goyal2
... serotypes O, A and SAT2 nucleotide sequence. In this work FMDV serotype O, A and SAT2 were isolated from cattle clinical samples (foot lesions). RNA extracted from clinical samples was subjected to reverse transcriptase polymerase chain reaction( Rt. PCR) nucleotide of FMDV ID and 3D genes were determined using standard automated sequencing technique. Phylogenetic analysis of FMD / SAT-2 /3D/Egypt/Sharkia/2013/ FMD / (KJ210...
Yanni, M. I1; Hanaa A. Ahmed2; Lamyaa, A. Ahmed1; Hanan, A. Fahmy3 and Ibrahim, E.M.4 Aggour, M. G.3
... was conducted. The % of nucleotide identities of the Egyptian recent isolate (Egy/cairo /2014) with three previous Egyptian isolates were 98.4-98 and 98.4% respectively. Egy/cairo/14 share nucleotide identity with the vaccinal strain flury LEP and kelev with a percentage of (93.1% and 98% respectively). All Egyptian isolates have a common origin. In conclusion ,further epizootological study on a molecular basis is needed.
Fawzy Rania1, AboElkhair M.1, Bazid A.M.1, Sultan H.2, Hussien A.H.3
...itive for IBVs. Multiple nucleotide and amino acids alignments revealed prominent nucleotide substitutions which affect amino acids composition of HVR3 of S1 subunit. Phylogenetic analysis revealed that seven strains were belonging to variant 2 group of IBV of great similarity with Israeli IB strains, two strains were belonging to IS/1494/06 group like and one strain was belonging to 4/91 group like. This study reports the c...
Amro A. Farrag1; Ahmed K. El-Attar1; Om-Hashem M. El-Banna2; Ibrahim A. I.2; H.
M. Mazyad1
...nerate and specific oligonucleotide primers. SLCV (bean isolate) was
transmitted from naturally infected common bean onto twenty two species and varieties
belonging to six different families i.e. Moraceae, Solanaeae, Cucurbitaceae,
Leguminoceae, Chenopodiaceae, and Malvaceae using viruliferous whitefly (Bemisia
tabaci). Results revealed that SLCV could be transmitted to 16 out of 22 species and
positi...
K.A. El-Dougdoug1, A.R. Sofy2, A.A. Mousa2 and E.E. Refaey2
...es and Lady Rosetta. The nucleotide sequence
of Ryadg of cultivars Dita, Execusa and Lady Rosetta was aligned with other recommended PVY
strains registered in GenBank. A phylogenetic tree of Ryadg gene based on nucleotide sequence
revealed 93% a moderate degree of similarity to Potato gene Y-1 isolated from Solanum
tuberosum subsp. andigenum
...
Aly M. Abdel-Salam1, Rehab A. Dawoud2, Amira M.E.Aly2, and Salama M. El-Saghir2
...
accessions showed nucleotide-pairwise identity between 76-82% and amino acid
similarity between 29-63% indicating high diversity. In addition, the four BSV
isolates showed nucleotide identity between 64-88% with four BSV accessions,
retrieved from the GenBank. Phylogenetic analysis based on the partial RT/RNaseHsequence
showed that the four Egyptian BSV isolates clustere...
Aly M. Abdel-Salam
... the GenBanak. Pair-wise nucleotide
identity indicated 86% identity between the Giza and Assiut isolates. NCBI-blastn
analysis for the two isolates with four SCBV accessions retrieved from the GenBank
indicated identity range of 66-91%. Phylogenetic analysis based on amino acid
sequence identity indicated the clustering of the two SCBV in a separate branch from
the other known SCBV; indicating the spe...
Abd El-Hamid, M.I1, Seham, A.El-Zeedy1, El-Sanousi, A.A2, Reda, I.M2, Nehal, S. Saleh1, Abbas, A.M1
...lignment revealed single nucleotide substitution at the base pair number 121 from the start codon which give lead to single Amino Acid Substitution from CAG (Glutamine(Gln/Q)) which is considered as a polar Amino Acid to AAG (Lysine(Lys/K)) which is a basic Amino Acid, then the sequenced product of the local isolate was cloned Into PET 151 D topo plasmid with an N-terminal tag containing the V5 epitope and a 6xHis tag and transformed into Top 10 Ecoli cells ju...
Abd El-Hamid, M.I1; Seham, A. ElZeedy1; El-Sanousi A.A2, Reda, I.M2, Nehal, S. Saleh1., Abbas, A.M1
...lignment revealed single nucleotide substitution at the base pair number 121 from the start codon which give lead to single Amino Acid Substitution from CAG (Glutamine(Gln/Q)) which is considered as a polar Amino Acid to AAG (Lysine(Lys/K)) which is a basic Amino Acid which is very characteristic for the local isolate than the rest of isolate and strains....
A. A. Rezk1,3, K. A. Alhudaib2 and A. M. Soliman2,3
...n reaction (RT-PCR). The nucleotide sequence for the coat protein (CP) gene was carried out and submitted in GenBank under accession number JN083790. The phylogenetic tree showed that there are two big clusters and the identity between them 90%. The isolated CYSDV in this study is located in the second cluster with the isolates from Sudan, Iran and the other isolate from Saudi Arabia. The analysis showed that the highest nucleotide
Sahar A. Youssef1; Manal A. El-Shazly1,2; Azza G.Farag1,3; Eman A. Khattab1,2
Ehab M. El-Nahas1, Hemat S. El-Sayed2, Sawsan S. El-Basuni3, Gabr F. El-Bagoury1
... prototypes. Comparisons nucleotide and amino acid sequence of partial S1 gene showed that the recent isolate had 98.2% and 95.2% nucleotide similarities and 96.8% and 91.4% amino acid similarities with the commonly used IBV vaccine Massachusetts strains H120 and M41 respectively. Egypt/Qal/014p had a unique amino acid substitution at residues 39 (Serine), 40 (Tyrosine), 41 (Lysine), 64 (Glutamate) and 69 (Valine) of the S1 ...
Ayman S. El-Habbaa 1, Gabr F. El-Bagoury1, Samar F. El-Adaway2, and Susan S. El-Mahdy2
...-PCR) then subjected for nucleotide and amino acid sequence detection. Results: NDV Giza 2014 isolate and NDV Qualubiya 2014 were characterized as velogenic and lentogenic strains, respectively using Mean Death Time (MDT), Intracerebral Pathogenicity Index (ICPI) and studying amino acid motif of the F protein cleavage site. Phylogeny put NDV Giza 2014 in a separate branch independent from other Egyptian isolates, however it is more related to Lasota (genotype ...
Rasha M. Mahrous1,4, Ahmed K. El-Attar2, Ahlam A. AlWatban1, Sohair I. EL-Afifi3,
Nagwa M. Aref1,3
... from 16S rRNA gene. The nucleotide sequences were published to the
GenBank as Lemon Witches' broom-Egyptian strain (LWB-Eg strain) with accession number
“KJ948653”. Phylogenetic analysis showed a high similarity (99%) with Oman isolate.
Conclusion: Phytoplasma strain of LWB-Eg Candidatus Phytoplasma that reported as a natural causal
agent from Lime WB strain in Egypt was classified as 16SrII subgroup...
Akram I. Aboelkhair1, Ayman H. El-Deeb2, Momtaz A. Shahin1 and Hussein A. Hussein2
...iv>presence of LSDV . By nucleotide sequences and genetic characterization was conducted on (G-PCR)
gene segment of these isolates.
Results: 93 samples were positive for LSDV by using conventional PCR direct from nodular lesion, 4
positive samples were inoculated on CAM showed characteristic pock lesion, formerly after passaging
of samples on MDBK cell line revealed characteristic cytopathic effect of LSDV, as we...
Hanaa A. Elsamadony1, Laila A. Tantawy1, Sabry E. Omar2 and Heba A. Abd Alah1
...dentity with
nucleotides of Indian and Japan strains, 97% amino acid identity with the same strains. Our circulating
strain has low nucleotides identity 37%, 38% and amino acid identity 15% for both with vaccinal
strains (Cux-1N/Germany and CAV/Nobilis®P4) respectively. The high percentage of similarity of
nucleotides identity with Egypti...
Ayman S. El-Habbaa1 and Mervat E. Radwan2
... showed
100% nucleotide homology with BEF virus from Egypt 2014 but nucleotide and deduced amino acid
substitution generates were showed with other BEF viruses that reduced this homology. Phylogeny
showed that BEF viruses from Egypt 2014 and 2017 had close homology to BEF virus circulated in
Israel during the same period suggesting that the virus was circulated in middle east.<...
Ahmed K. El-Attar1, Samah A. Mokbel1 and Om-Hashem M. EL-Banna2
...anscription (RT)-PCR and nucleotide
sequence determination. Ultra-structural responses of basil leaf cells infected with a
morphologically distinct RNA virus, AMV, were studied. Molecular characterization and
phylogenetic analysis were performed for the AMV coat protein (CP) gene. An amplicon of the
predicted size (∼666 bp) derived from O. basilicum isolate was purified and cloned in E.Coli
into p...
Ahmed M. Soliman
... The CMV isolates showed nucleotide sequences similarity between them ranged from 97%-99%. Conclusion: This study revealed the existence of CMV in some vegetable crops in Al-Ahsaa at Eastern Province of Saudi Arabia. High nucleotide sequence similarity between the four isolates of CMV suggesting no genetic diversity. The four CMV isolates located in one cluster, belonging to subgroup IA.
...
Ewa Czerniawska-Piątkowska1, Iwona Szatkowska1, Daniel Zaborski2*, Wilhelm Grzesiak2, Sara Tabor-Osińska1, Małgorzata Wasielewska1, Witold S. Proskura1, Wojciech Kruszyński3 and Edward Pawlina3
Chaochao Hu1,2, Xue Xu1, Wenjia Yao1, Wei Liu3, Deyun Tai1, Wan Chen4 and Qing Chang1*
...n length and the overall nucleotide composition of H-strand was A: 31.45%, T: 23.46%, C: 31.30%, G: 13.79%. In Charadriiformes mitogenomes, AT skews values were positive, while the values of GC skew were negative. We found a significant negative correlation between CBI and ENC, and a significant positive correlation was found between CBI and G + Cc and G + C3s. The ratio of Ka/Ks of all PCGs indicated that all these genes evolved under purifying selection. Evi...
Zhongyong Wu1, Wenzhu Li2, Chunxia Ni1, Zhuolin He1, Xiao Hou1 and Wanxia Pu1*
...) method with three oligonucleotide primers. In total, 177 Staphylococcus aureus isolates were obtained from dairy farms in 5 different provinces in China, including Guizhou, Inner Mongolia, Shanghai, Sichuan, and Gansu. The results showed that the amplified product bands with three primers per isolate ranged from 1~9 and the product sizes from 240 to 4,500 bp. Primer OLP13 had the highest discriminant coefficient. The Staphylococcus aureus strai...
Rizwana Sultan1, Asim Aslam1, Muhammad Yasin Tipu1, Habib ur Rehman2, Saba Usman1, Ahsan Anjum1,*, Muhammad Saeed Imran1, Muhammad Usman3 and Muhammad Zahid Iqbal3
...omology index of 99.82% (nucleotide level) and 99.47% (amino acid level) with each other. The maximum similarity percentage indicated that RSI and RSII isolates were closely related to strains reported from India and China. This study is the first report on molecular characterization of E. tenella in Pakistan highlighting the pathological potential and distribution of E. tenella.
...
Iqra Mobeen1*, Rabia Arif1*,Maimoona Ilyas1, Siu Fai Lee2 and Muhammad Saleem1
...ont-size: small;">Single nucleotide polymorphisms (SNPs) are one of the most common and abundant class of molecular markers present in the genome of many organisms. The current study represents the first attempt to investigate the natural variations in the RK-MTases genes; Ribosomal N-lysine methyltransferase1 (RKM1) and Ribosomal N-lysine methyltransferase4 (RKM4) in Sordaria fimicola using SNP markers. A total seven SNPs in the
Shaokun Lu1,2, Ronghua Li1,2*, Chunlin Wang1,2, Changkao Mu1,2 and Weiwei Song1
...udy, sixteen SNP (single nucleotide polymorphism) markers were developed from EST (expressed sequence tag) database of Portunus trituberculatus. Polymorphism evaluation was tested on 30 wild individuals of P.trituberculatus collected from Xiangshan, Zhejiang province, China. The minor allele frequency ranged between 0.292 and 0.500, with an average of 0.384. The expected and observed heterozygosities (He and Ho) ranged from 0.422 to 0.545 and from 0.000 to 1.0...
Muhammad Abdullah1, Sana Zahoor1*, Akhtar Ali2 and Masroor Ellahi Babar3
... was to look into single nucleotide polymorphism in upstream region of -238TNF-α and -308 by ARMS PCR technique in asthmatic and control group. It was a prospective study constituting 17 clinical diagnosed asthmatic patients (Diseased) and 19 non-asthmatic patients (Control). The female was 6 (31.6%) and males were 13 (68.4%) in control group while females were 9 (52.9%) and male were 8 (47.1%) in asthmatic group. Mean age (49.59±15.82 year) and B...
Hadia Gul1, Abdul Haleem Shah1, Ricardo Harripaul2, Anna Mikhailov2, Ejaz Ullah Khan3, Wasim Shah3, Nisar Ahmad3, John B Vincent2,4 and Muzammil Ahmad Khan3*
...er includes few intronic nucleotides or skip exon-20 in the mature mRNA. Our study further supports the evidence of high incidence of OCA2 gene mutations in Pakistani families....
Farheen Aslam*, Hira Lodhi, Rasheeda Bashir, Faiza Saleem and Shagufta Naz
Shahid Sherzada1,2*, Muhammad Naeem Khan1 and Masroor Ellahi Babar2
...pes. Mean haplotypes and nucleotide diversity was 0.42 and 0.0018, respectively. The mean intraspecific and intragenric K2P genetic distances were 0.2% and 1.2%, respectively. Rate of transitional and transversional substitution was 16.68% and 4.16%, respectively. The transition/transversion bias value R was 1.25. The negative values of Tajima D test as well as Fu and Li D and F tests supported the process of population expansion with excess of rare alleles. T...
Aly M. Ghetas1*, Dalia M. Sedeek1, Hanaa S. Fedawy1, M.A. Bosila1, Asmaa M. Maatouq1, Hoda M. Mekky1, Kh. M. Elbayoumi1,2, Mohamed M. Amer3
...V (vvIBDV). The obtained nucleotide sequences of partial portion of VP2 gene of 2 isolates revealed 97.0 - 100% and 91.2-92.5% identity with the Egyptian strains and vaccine strains respectively. Finally, significant genetic changes in our IBDV isolates were observed as comparing to vaccine strains. Thus, continuous monitoring of IBDV outbreaks in vaccinated chickens and evaluation of the used vaccines are required.
Keywords | I...
Ly Thi Thu Lan1, Nguyen Thi Anh Thu1, Lam Thai Hung2, Nguyen Thi Hong Nhan3, Le Thanh Phuong4, Nguyen Trong Ngu3*
.... For determining single nucleotide polymorphisms, the PCR-RFLP method was used with the help of AcyI restriction enzyme. A polymorphic site was found in the population, with the frequencies of 11, 12, and 22 genotypes being 0.18, 0.67, and 0.15, respectively. At the end of the experiment, better body weight (965-976 g/bird) and daily weight gain (10.5-10.6 g/bird/day) were found in chickens with 11 and 12 genotypes. Carcass parameters were superior in chicken...
Pan Ziyi1, Ambreen Iqbal1, Gao Zhen1, Liu Juan1, Fang Xibi2, Jiang Ping1* and Zhao Zhihui1*
...lts indicate that single nucleotide polymorphisms might be used as a molecular marker for marker-assisted selection in beef cattle breeding....
Amira M. Nowier1, Hassan R. Darwish2, Sherif I. Ramadan3, Nadia A. Abo El-Maaty2 and Othman E. Othman2*
...t; CCG Pro) at the sixth nucleotide of α-lactalbumin gene exon III. Barki breed showed the highest heterozygosity (0.260) and effective number of alleles (1.345). The T>C SNP showed non-significant association with body weight traits. Body weights at birth, 3 months and 12 months in Damascus goat were significant and higher than those in Zaraibi. Kids born single were heavier than twins and triplets at birth age. The highest milk yield was recorded fo...
Hua Liu, Wei Hou, Li Peng, Changjun Peng, Yansen Cai and Jing Li*
...genotyping error, single nucleotide polymorphism (SNPs) are considered to be preferable molecular markers for genetic population analysis. SNP markers that are suitable for non-invasive samples are important to wild population investigations in endangered species. Based on the whole genome sequences of Macaca thibetana, we successfully developed 26 SNP loci that were sensitive to non-invasive samples, then based on which, genetic diversity and population struc...
Muhammad Altaf1* Arshad Mahmood Abbasi2, Muhammad Shoaib Amjad3, Sadia Naseer1 and Muhammad Umair4
...rsion and viral specific nucleotide positive documented in all COVID-19 patients tested provides confirmation of a link between the presence of this virus and the disease....
Ahmed M. Darwish1*, Hassan R. Darwish1, Dalia M. Mabrouk1, Mohamed A. Abdelhafez1, Ahmed M. Abdel-Salam2, Ibrahim E. Mohamed3, Ibrahim M. Farag1
...otype without any single nucleotide polymorphism (SNP) while the LEP gene has two genotypes (CC and CT) with one SNP at position 194 C>T. The statistical analysis of milk and genotypes data showed that the β-LG gene has not any effect in the measurement of milk composition in Zaraiby and Damascus goats, while the CT genotype of the LEP gene causes an insignificant reduction in protein percentage and insignificant increase in fat percentage in Damascus ...
Aml M. Ragab1*, Maha R. Basyoni1, Enas A.I. Khoris2, Nadia A. Abd Elghany3
...e identical to others in nucleotide sequence similarity, ranging from 98% to 100%. The topology of the groEL- based trees was comparable to that of the phylogenetic tree from B. cereus group strains. Three subclusters could be identified, (nhe) and (cytK) could be detected in all of the B. cereus isolates, (hbl) could be detected in 50% , and (ces) gene could be detected only in 25%. During the experimental period, the high mortality rate was (80%) in the grou...
Weidong Huang1,2,3, Xinyue Liang1,2,3, Xiufeng Xie4, Xingmin Wang2, 3 and Xiaosheng Chen1,2,3*
...02) and the low level of nucleotide diversity (Pi = 0.004). In addition, the number of haplotypes was 17 and the same elytral color patterns of M. sexmaculatus didn’t share the same haplotype. Furthermore, phylogenetic analyses showed all M. sexmaculatus samples formed a single clade, but the identical elytral pattern individuals do not cluster together as no special relationships among different phenotypes individuals. Our systematic analyses illustrate...
Maria Qibtia1, Sehrish Faryal1, Muhammad Wasim1, Farzana Chowdhary1, Muhammad Tayyab1, Ahmed Mansovuri2, Zeeshan Ahmed2, Muhammad Hamid3 and Ali Raza Awan1,*
Hend K. Sorour, Mohammed A. M. Saleh, Azhar G. Shalaby*
Muneeza Zafar1,2,3, Fazli Rabbi Awan2,*, Munazza Raza Mirza3,*, Sumaira Nishat2,4, Sajid Ali Rajput5 and Imran Riaz Malik1,*
...se and non-coding single nucleotide polymorphisms (SNPs) of APOB retrieved from dbSNP using 17 different computational tools and further evaluated the structural impact of these convergent deleterious SNPs on APOB through HOPE. We found 9 missenses, 15 intronic or regulatory region SNPs and 2 were found in miRNA target sites of APOB. Out of these variant, the rs13306194 (Arg532Trp) was found in the conserved region of protein domain, which can potentially disr...
Heba Abdo Basha1, Walaa Slouma Hamouda Abd El Naby2*, Samya Erian Ibrahim3, Abeer Fikry Elnahas2
...e turkey with the single nucleotide polymorphism in the coding region of the MSTN gene and IGF-2 (3’-UTR), using DNA sequencing. Fifty turkeys were categorized into high and low body weight. Blood samples were collected from each bird for DNA extraction. Four birds were selected randomly/group to be slaughtered for carcass traits. In MSTN, only six non-synonymous SNPs were recorded leading to four amino acid substitution in exon 1 and 2 amino acids subst...
Basel A. Abokhadra, Samah M. Mosad, Sahar Abd El Rahman*
...t from our isolate by 25 nucleotide substitutions, which led to five amino acid substitutions ( E316D, A378T, S410G, I425T, E429G).
Keywords | Bovine alphaherpesvirus 1, Glycoprotein B, Immunoflourescent technique, Phylogenetic tree, Nucleotide and amino acid substitution
...
A. El-Shemy1*, Hoda M. Mekky2, M. A. Bosila2, A. M. Allam1, Kh. M. Elbayoumi2, M. M. Amer3
...es had 77.4%–80.2% nucleotide similarities with the most frequently used DHAV-1 vaccine in Egypt. However, the phylogenetic relationship using the partial 3D protein revealed that the isolated Egyptian strains in this study were distant from the vaccine strain used in Egypt. In conclusion, three isolates of DHAV-1 were characterized from the examined duck flocks. Phylogenetic analysis of these isolates revealed the occurrence of differentiation between o...
Ngoc Tan Nguyen1*, Minh Thanh Tram1, Thi Thu Pham1, Tan Loi Le1, Thi Khanh Ly Nguyen1, Tuan Thanh Hoang2, Cong Thieu Pham3, Nguyen Khang Duong4
...by sequencing to analyze nucleotide polymorphism, haplotype diversity and genetic distance to construct a phylogram. Results showed that the fragment of 687 bp was successfully amplified. Examination of 49 sequence variants in 599 bp of the control region revealed the nucleotide composition was Adenine (A) = 32.55%, Thymine (T) = 28.33%, Guanine (G) = 14.67%, Cytosine (C) = 24.87% and G+C content was 39.12%. Out of a total o...
Ngoc Tan Nguyen1*, Pham Kim Ngan Nguyen1, Thao Huong Phan1, Tan Loi Le1, Thi Khanh Ly Nguyen1, Tuan Thanh Hoang2, Cong Thieu Pham3, Cong Dinh Nguyen3, Nguyen Khang Duong4
...ions of Vietnam based on nucleotide sequence in a displacement loop (D-loop) of mitochondrial DNA (mtDNA). Thirty-one blood samples that were collected from three native buffalo populations such as Bao Yen (BY: 7 samples), LangBiang (LB: 7 samples) and Thanh Chuong (TC: 7 samples) and two imported buffaloes from Thailand (T: 5 samples) and India (Murrah – M: 5 samples) were extracted for total DNA and amplified about 760 bp mtDNA fragment, with 576 bp in...
Anara Ryskeldina, Indira Iskakova, Nurgul Sarina , Alexander Shevtsov , Laura Syzdykova, Alexander Shustov, Yerlan Ramankulov, Marat Kuibagarov*
...NA and are reporting its nucleotide sequence. Bacterial expression of a portion of the natural gene encoding a mature form of boPAG1 failed. But a fusion protein made up of E. coli thioredoxin and boPAG1 was efficiently expressed in E. coli. Using the recombinant protein as an antigen, mAbs were generated. One mAb reacted with a protein present in extracts from cow placenta. The described results are useful for creating immunological reagents to detect pregnan...
Muhammad Ismail1, Jabbar Khan1*, Zahid Rauf2, Khalid Khan3 and Muhammad Rafi1
...esed to visualize single nucleotide polymorphisms (SNPs); rs9340799 (G>A) and rs2234693 (C>T) in ESR1 gene. The amplified product of 524bp of rs9340799 sequence of ESR1 gene was treated with Xbal restriction enzyme while amplified product of 451bp of rs2234693 sequence was treated with PvuII restriction enzyme. Nine patients were found homozygous and 8 were heterozygous for minor allele while 1 patient was carrying major allele. For rs2234693, all the pa...
Alicja Kowalczyk1*, Inga Kowalewska-Łuczak2, Ewa Czerniawska-Piątkowska3*, Jesús Juan Cantalapiedra4, Joaquim Orlando Lima Cerqueira5,6 and José Pedro Pinto de Araújo5,7
... evaluate whether single nucleotide substitutions within exon 4 of the quality of AQP7 gene may affect the sperm cells of Polish Holstein-Friesian bulls. The research material was biological material (semen and blood) collected from 60 Holstein-Friesian bulls of the same age. The nucleotide substitutions analyzed are located in exon 4 of the AQP7 gene and are responsible for missense mutations. Individual genotypes were dete...
Xin Xing Dong1*, Gai Cui Bai2, Ming Li Li1, Guo Xiang Lan1, Da Wei Yan1, Xiao Yi Wang1, Qiang Chen1 and Shao Xiong Lu1*
...stigate the novel single nucleotide polymorphisms (SNPs) at GHRL gene in three different pig breeds, including Duroc, Yorkshire and Landrace, and the association of the novel SNPs with growth traits. PCR-SSCP and sequencing were used to detect the GHRL gene polymorphisms in the present study. Three SNPs were detected, one in the exon 1 (g.3734 G>T), which was synonymous, and two SNPs in intron 4 (g.7691 A>C and g.8523 T>C). The sites g.3734 G>T and...
Tinda Afriani*, Endang Purwati, Yurnalis, Jaswandi, Mangku Mundana, Adisti Rastosari, Anna Farhana
...attle to identify single nucleotide polymorphisms (SNP). The samples used in this study were blood samples (n= 70) collected from Pesisir cattle (aged 2-5 years). DNA was isolated and the targeted region was amplified using the polymerase chain reaction (PCR) technique. Then the amplified products were sequenced. The results showed that the population of Pesisir cattle used in this study was polymorphic. There were 5 polymorphisms in the exon 9 and intron 9 re...
Jie Yang1, Wenjun Zhou2, Qi Zhang2, Lei Chu2, Zhenshi Chen1, Xiajun Zhang2, Weidong Wu3*, Shaoru Zhang1* and Lihui Wang1*
...at there were single (A) nucleotide deletion mutation in mtrR promoter region, G45D mutation in mtrR coding region, G70 mutation in rplD and A2047G mutation in 23s rRNA allele, but no mutation was found in rplV. A total of 8 different STs were identified in 5 AZM-R strains, of which two ST1866 isolates showed a high level of AZM-R. The clinical isolates of N. gonorrhoeae in Danyang have high genetic diversity. ST1866 isolates showed a high level of AZM-R, Ther...
Ty Nguyen, Giang Thi Huong Phung, Lan Le Thuy Hoang and Giang Van Tran*
...e ratio of four types of nucleotides is A: 23.38%; T: 32.62%; G:18.15%; C: 25.85%. The rate of difference in CO1 sequences of the 2 samples is low compared to previous studies. The similarity coefficient of M. cunnesius in the two areas of Tam Giang lagoon is very high (0.9953).
Novelty Statement | The paper presented detailed morphological features and genetic diversity of Moolgarda cunnesius (...
Abdul Kabir1, Muhammad Rasheed2, Hubdar Ali Kaleri5, Depeesh Kumar Bhuptani3, Mithan Kumar4, Raza Ali Mangi6, Abdul Wahid Solangi4, Sheva Dari1, Saqib Kakar4, Panah Munir4, Ekra Akbar4 and Rameez Raja Kaleri4,5*
...udy also showed that the nucleotide sequence of human corona virus (SARS Cov-2 virus) is 87.5 percent to 96.3 percent identical to bat-borne corona viruses. Factory closures, IT parks, restaurants, shopping centers, and multiplexes are relatively easy to close during lockdowns, but agriculture and animal husbandry are more difficult to close; these industries will continue to produce. In order to manage our agriculture and livestock sectors in the best interes...
He-Cai Zhang, Tian-Ge Hu, Chang-Ying Shi, Guang-Wen Chen* and De-Zeng Liu
...otype diversity (Hd) and nucleotide diversity (π) were 0.961 and 0.00157, respectively. The phylogenetic relationship and haplotype network analysis indicated that there was no obvious correspondence between the haplotypes and the geographical locations, revealing no obvious phylogeographic pattern. Analysis of molecular variance (AMOVA) suggested that the genetic differentiation of D. japonica in Taihang Mountains was very great (FST=0.405, P<0.01). Thi...
Abdurakhim E. Kuchboev1*, Mehmonjon Kh. Egamberdiyev2
...trongylids. Based on the nucleotide sequence data, three species of nematode larvae Protostrongylus rufescens, Muellerius capillaris, and Cystocaulus ocreatus were identified. According to the morphological characteristics of the studied land mollusсs, the shell structure was identified as six different morphotypes. After molecular genetics and morphological analyzes, these land molluscs belonged to 8 different species: Angiomphallia regeliana, Pseudonapaeus ...
Xiao Zhang1, Guoqing Shen1, Yang Wang1, Pengdan Huang1,2, Yan Shui2, Zenghong Xu2 and Huaishun Shen1, 2*
... the most common type di-nucleotide repeat motifs (49.94%). The second most common repeats were the tri-nucleotide ones (131,405, 39.09%). A total of 312,454 microsatellite loci had flanking sequences. A subset of 56 primer pairs was randomly selected for the PCR experiments to validate the SSRs that had been identified. Forty-six primer pairs (80%) had PCR products that matched the sizes expected, and the products from 40 p...
Istkhar† and A. K. Chaubey†
...d comparative account on nucleotides analyses based on ITSs study confirmed the
present specimens as isolates of S. abbasi. The nucleotide composition resemblance within 5.8S gene with other
Steinernema species evident the less polymorphism and highly conserved nature of this region as compared to ITS1
and ITS2 and delimit the relationship of steinernematid nematodes.
...
F. Shahina† and G. Mehreen
...estimated by
nucleotide sequences using three molecular makers viz; ITS-1, 5.8S and ITS-2 rDNA (seventy nine); D2-D3 and
28S (LSU) sequences of rDNA region (fifteen) and 12S rDNA mitochondrial gene (twenty nine) to investigate the
genetic diversity. Phylogenetic trees were constructed using two different methods maximum parsimony (MP) and
Bayesian inference (BI) in which most of them form highly to moderately sup...
Ayesha Ahsan1, Rabia Arif2*, Samina Nazir1, Muhammad Saleem2 and Memunna G. Shahid1
...netic variations in four nucleotides were observed for PKC gene i.e. C (150) T; C (186) A; C (429) G and T (521) A which were common for S1, S2 and S3 strains, while point mutation C (497) G was detected only in S2 and S3 strains. Post translational modifications (PTMs) of both proteins were predicted and compared with the reference sequences of Neurospora crassa and Sordaria macrospora by using different PTMs predictor servers. Phosphorylation and glycosylati...
M. A. Abou El- Nasr1, Kh. A. Dougdoug1, Hayam S. Abdelkader2, and Rehab A.
Dawoud2
...dlings. Degenerated oligonucleotide primers were designed to amplify the N-terminal portion of the capsid protein of PPV. The amplified products were cloned into pGEM-T-Easy vector and hybridized to PPV DNA specific probe labeled with Dig-I 1dUTP. DNA sequencing using fluorescent dideoxy nucleotides showed that the capsid protein region of PPV-EA strain had about 65% sequence homology with other strains of PPV and 45% simila...
M. A. Amer1; M. H. El-Hammady2; H. M. Mazyad1; A. A. Shalabyl and F. M. Abo-El-abbas
... western blot assay. The nucleotide sequence of the Egyptian isolate of PVY CP gene was determined to be 801 nucleotides in length encoding a deduced 267 amino acid. Nucleotide sequence analysis revealed a range of 96- 99.5 % sequence identity among the PVYNTN isolate (PVY-T, PVY SWS, PVY II and PVY NTN)....
Om-Hashem M. EI-Banna1, M. A. S El-Kady2, E. A Salama1 and Salwa N. Zein2
...ains. On the Other hand, nucleotide, and amino acid sequences of the two strains revealed differences in the 5' untranslated region (UTR) between the coat protein and ꞵb gene. It was clear that five bases, and 18 out of 1 16 amino acids were found different. three amino acids insertion, and one amino acid deletion. Little differences were also observed regarding the 5' UTR of RNA γa as six nucleotides were changed. 1...
E. K. Allam.1; B. A. Othman.1; Hayam S. Abdelkader2; and Noher A. Mahmoud2
Sahar. A. Shoman1 and B. A. Othman2
... was sequenced, and this nucleotide sequence was analyzed using a software program. Sequence analysis of the amplified fragment revealed a high conserved sequence homology located at the 3'-terminal region of the 126KDa (ORF1) sequence of the published TMV strains. Detection of the TMV-E using RT-PCR raises the availability of species-specific primers for the TMV-E that will be helpful for diagnosis in mixed infection. In addition, it will be helpful in ...
Zhao Fulin1,2, Liang Chen2, Tao Lin1, Jiang Yanting3, Ouyang Yina3, Hong Qionghua3* and Chu Mingxing1*
...sociation between single nucleotide polymorphisms (SNPs) in the FGFR1 and EBP41L5 genes and kidding performance of goats. Mass ARRAY®SNP typing technology was applied to genotype the SNPs of FGFR1 and EBP41L5 genes, of which the genetic characteristics of Yunshang Black goat (YS, n=544), Jining Grey goat (JN, n=133) and Liaoning Cashmere goat (LN, n=91) were explored. Then the association was analyzed between FGFR1 and EBP41L5 and kidding performance (litt...
Fakhra Nazir1*, Sahar Fazal1 and Fakhar-i-Abbas2
... of family Corvidae. The nucleotide sequences were submitted to the Barcode of Life Data System (BOLD) and the eligible sequences were assigned the Barcode Index Numbers (BINs). The COI gene sequence data of 8 species of family Corvidae were retrieved from GenBank (NCBI) database and phylogenetic relationship was established in these 13 barcodes. K2-parameter distances were calculated on MEGA7 software with overall average distance of 0.141 calculated at 1000 ...
Ying Liu1,2, Ji-Yong Fang2, Na Zheng3 and Hai-Long Wu1*
...OI sequences show 59.31% nucleotide divergence with Seuratascaris numidica (Seurat, 1917) (GenBank acc. no. MG434691 and MG434692). Through morphological and molecular characterization of S. schmackeri sp. nov., we generated new data on the Seuratascaris genus, providing a crucial scientific basis for future studies on the genus. ...
Muhammad Salman Ikram1, Tahir Mehmood1,2*, Sehrish Firyal3, Huma Sattar4, Shagufta Saeed3, Fareeha Nadeem3 and Muhammad Imran Mahmood Khan5
...at (Y-STR) and Y- Single nucleotide polymorphism (Y-SNP), and reveal the importance of next generation sequence (NGS) as an advanced technology in forensic genetics. This manuscript also demonstrates the unique features of Y-STR markers and their different application in forensic like significance of population genetics and genealogical pattern of Y-chromosome STRs diversity in different regions of world which helps to understand the pattern of variation in DN...
Umer Farooq1,2, Nimra Murtaza2, Abubakar Siddique1, Bilal Saleem1, Obaid Ur Rehman1, Nageen Zahra1, Muhammad Uzair1, Muhammad Naeem Riaz1,3* and Muhammad Ramzan Khan1*
...h 25,469,157 were single nucleotide polymorphisms (SNPs) and 3,563,505 were Insertion/Deletions (InDels). Functional annotation identifies 122,943 missense SNPs that may possibly affect economically important traits. Using sequence and structure based computational tools SIFT, we identified 154 deleterious variants in 134 genes. Gene enrichment highlighted the presence of these genes in different biological processes including developmental, signaling, transpo...
Ni Putu Sarini1*, I Gde Suranjaya1, I Gusti Agung Arta Putra1, I Wayan Suarna1, Lindawati Doloksaribu1, I Ketut Puja2, I Ketut Gde Natakesuma3, I Gusti Ngurah Bagus Rai Mulyawan4
...the 10 Bali cattle has a nucleotide variation of 0.31% generated from Bos taurus and 0.21% generated from Bos indicus. While the nucleotide variation of the MC1R gene from cattle with color pattern deviations to the Bali cattle, namely 1.36% albino, 0.21% injin, and 0.10% poleng Bali cattle. ...
Asifa Majeed*, Amir Rashid, Palvasha Waheed, Asma Faryal, Aden Razaq and Ayesha Maryam
... a pattern of the normal nucleotide sequence in all subjects of three groups with no pathogenic genetic variation. Thus, exon 3 of the ABCG1 gene and exons 2 and 3 of the APOA1 gene do not contribute to the onset of dyslipidemia in type 2 diabetes patients....
Arnold Christian Tabun*, Ferdinan Suharjono Suek, Cardial L Leo Penu, Johanis A. Jermias, Thomas Lapenangga
...ication of DNA sequences nucleotide. Bali cows with sorrel, black and white coat colors are used with an age range of 3-5 years. DNA sequencing conducted multiple alignments, the identification of the genetic distance, and the preparation of phylogenetic trees using the software Mega X. The results of PCR sequencing of Bali cows with different coat colors in Kupang were 464 bp. Identification of single nucleotide polymorphis...
Muhammad Haseeb Malik2, Muhammad Moaeen-ud-Din1*, Ghazal Kaukab Raja2 and Feroza Hamid Wattoo2
...were converted to single nucleotide polymorphism markers for high throughput genotyping. The allele frequencies in both breeds were determined for discrimination ability using AFLP. The probability of identifying Sahiwal breed was 0.86 and probability of misjudgment was 0.021 using single selected marker. However, probabilities for judgment and misjudgment with two markers and combined with three markers were 0.745, 0.367 and 0.964, 0.376 respectively. The res...
Wei Fang1,2,3, Jiawei Hong1,2,3,4, Zhengyi Fu1,2,3, Jing Hu1,2,3, Gang Yu1,2,3, Zhenhua Ma1,2,3* and Humin Zong5*
...tant repeat type was mononucleotide repeats (7,840, accounting for 51.31%), followed by dinucleotide repeats (4,007, accounting for 26.22%), while the number of tetranucleotide, pentanucleotide and hexanucleotide repeat was relatively small. Through the above analysis, it could be concluded that the difference in gene ...
Mervat M. Fath- Allah, Amal A. Ahmed, Hala A. Amin
...LISA results. The
nucleotide sequence analysis of the polyprotein gene of PVY-ME2 (the present Egyptian isolate)
showed 98% homology with the PVY-isolate strain N of Poland. In turn the PVY-ME2 showed low
homology with the other characterized Potyvirus members. Furthermore the PVY-ME2 had much
more distantly related (91%) to the previously published Egyptian and France isolates. The WMVME2
isolate (Egyptian isolate) has a hig...
nucleotide sequence analysis of the polyprotein gene of PVY-ME2 (the present Egyptian isolate)
showed 98% homology with the PVY-isolate strain N of Poland. In turn the PVY-ME2 showed low
homology with the other characterized Potyvirus members. Furthermore the PVY-ME2 had much
more distantly related (91%) to the previously published Egyptian and France isolates. The WMVME2
isolate (Egyptian isolate) has a hig...
Nguyen Thi Thu Hien1, Dong Huu Rin2, Nguyen Xuan Hoa1, Le Viet Tuan Khanh2, Phung Thang Long1*, Dinh Thi Bich Lan1
...99.07% similarity to the nucleotide sequence of P36 gene from strain M. hyopneumoniae 7448 recorded in GenBank (accession No. AE017244.1), corresponding to 144 amino acids. Expression of this protein in E. coli BL21 produced a fusion protein with molecular weight of approximately 20 kDa. Moreover, the antibodies against M. hyopneumoniae in sera taken from pigs that were immunized with the PEP inactivated vaccine (HYOGEN®) strong detected the recombinant M....
Michelle Anne Diano1,2, Loel Dalan1,2, Neil Pep Dave Sumaya3 and Nanette Hope Sumaya1,2*
...239), do not exhibit any nucleotide differences with each other or with previously described populations of C. briggsae from China (MN519141), Germany (EF417140), and the USA (AY604481, JN636061); therefore, they are conspecific. This is the first report of C. briggsae isolated from L. fulica in the southern Philippines. This study provides an additional account of C. briggsae to existent worldwide descriptions, thereby extending its geographic distribution an...
Irfan Safdar Durrani*, Noreen Asim and Ammar Sohail
Kristina Morkūnienė*, Rūta Insodaitė, Laimutis Kučinskas, Renata Bižienė
...notyped for three single nucleotide polymorphisms (SNP) using the real-time polymerase chain reaction method. Statistical analysis was performed with SPSS Statistics 20 and PLINK software. SNP at position 7454459 (Asn → Thr) of Mblk-1 gene mutant allele A was more common in untreated domestic and wild honey bees (18.90% and 8.14% respectively; p=0.001) compared to treated domestic bees which persistently infected with the disease. Regression analysis show...
Muhammad Nauman Arif1, Muhammad Mansha1* and Tanveer Hussain2
...he sequences, and single nucleotide polymorphisms (SNPs) were evaluated. The MEGA X-based maximum likelihood method was employed to study the genetic relatedness between sequenced samples and reference sequence as well as other deer. Among query sequences, the greatest genetic distance was observed between #B2_N1 and #H2_N7 i.e., 0.1184 and smallest genetic distance is seen between #C2_N2 and #G2_N6 i.e., 0.0210. The genetic distance between query samples and ...
Shudong Liu1,2, Shuai Wang1,2, Haoran Cui1 and Genyuan Chen1,2*
...aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ACMS in the Chinese Merino sheep population. To identify the genetic risk factors of alopecia in Chinese Merino sheep population, we carried out a genome-wide association study (GWAS). The 60 Chinese Merino sheep alopecia cases and the 190 Chinese Merino sheep controls were from the same livestock farm. DNA was extracted from ear tissue using the saturated phe...
Morcos Ibrahim Yanni1* and Eid Elsaid Abdelaziz2
...nt of their influence on nucleotide and amino acids variation of rabies virus isolates from the brain tissues of three dogs from 2017 to 2019 at the genetic level of the N and P genes from three governorates of Delta region in Egypt with earlier isolates, locally used vaccinal strains and other used strains internationally. Ten brain tissues from confirmed rabid cases in three governorates; Dakahleya (3), Alexandria (4); and Beheira (3) were diagnosed using vi...
Omaima Khamiss
...imilar and share overall nucleotide sequence identities in excess of 95%. This work focuses on the comparative essential basis studies to better know complex interactions between baculoviruses infecting the pest in question (Spodoptera littoralis) in relation to stability or mechanism of infection in the same host multiple nucleopolyhedroviruses (MNPVs) Spli MNPV, and granulovirus SpliGV. Mixed infection of the tow viruses was carried out in vivo and in...
Hemeida, A. A., Osman, M., El-Shahat, Mohamed, Hashem, Medhat H., Mahmoud, Amal and Dahi, Hosni
...tions. Sequencing of 223 nucleotide of 5'-untranslated region (5'-UTR) was performed. In the phylogenetic analysis, the three sequences and 80 sequences of HCV different genotypes from GenBank were used. Nucleotide variations were found in 7 (3.14%) of the 223 nucleotide positions analyzed. The variations were observed in the nucleotides (74, 92, 112, 11...
Elkalamawyl, I.M.; Elhddadl, S.; Swelim2, M.A.; Hamdy2, S.M. and Fahmy3, Hanan A.•
... based on I-BsAg partial nucleotide sequence was displayed. In conclusion, by understanding the HBsAg major immunodominant region nucleotide sequence, highly sensitive diagnostic assays can be achieved for detection of HBV in clinical specimens. Control of these EBV mutants, which will require new drugs, vaccines, and treatment strategies, will become the next major challenge on the path to eventual elimination of HBV infect...
Zaghloull , A.H.; Mahmoud2, Amal; Hassanl , H.Y.; Hemeida2, A.A.; Nayell , M. A. and Zaghawal , A.A.
... designed to amplify 438 nucleotide fragments from the glycoprotein G gene allowed specific amplification of BEFV-cell culture isolates from Egypt (Menoufia and Alexandria Governorates) and Japan. The PCR product was sequenced and analyzed. PCR product of Alexandria isolate was cloned and labeled with digoxigenin and used as diagnostic probe for BEF virus infection using dot-blot hybridization. Thirty six samples were collected from Menoufia Governorate (Berke...
El-Absawy, E.A.; Mahmoud, Amal; Hemeida, A.A. and Helmy, M.
...ated to PVY strains. Ten nucleotide substitutions resulted in 3 conserved amino acid substitutions (VI*I, G7*E, M or V and S8*G) and were able to differentiate between both groups. The partial coat protein region was more diverse than that of the 3'UTR (92.6-100% and (97.7-100% identity, respectively). The 3'UTR of the Egyptian isolate showed RNA secondary structures different from those of the 5 PVY strains....
Elbeshehy, E. K.F. and Sallaml, A.A.A.
... (AJ810260). The partial nucleotide sequence alignment, showed (95%) homology between CMV New Zealand isolate and CMV-Egyptian isolate. The sequence alignment also indicated that the CMV isolate is far from similarity with India CMV, showing (92%) according to the phylogenetic homology tree , which were 92 to 99% identical to those of CMV- Egypt isolate....
Nassarl , Entsar A.; El-Dougdoug , Kh. A.; Osmanl , M.E; Dawoud3, Rehab
A. and Kinawy l , Aliaa H.*
...h-EG/CP- gene showed 89% nucleotide sequence homology with other published strains of TMV in GenBank and 81% amino acid sequence homology. Tissue culture approach was used to pemit the recovery of TMV-Ch-free micropropagated shoots via application of 20 mg/l virazole followed by thermotherapy at 380C for two weeks and early screening to facilitate the efficient production of virus free tissue culture derived propagules using the produced antiserum against TMV-...
Soliman*, Ahmed M.; Mahmoud**, Sabry Y. M. and Dawood*, Rehab A.
...ained and sequenced. The nucleotide sequences were compared with corresponding viral nucleotide sequences reported in GenBank. The sequence analysis showed that; nucleotide sequence of OYDV-EG [Egyptian isolate (HM473189)] had 82-96% similarity compared with ten reported OYDV isolates. Thus, a method of identification and detection by RT-PCR of OYDV was established. This study also aimed t...
El-Dougdoug, Kh.A.; Rezk , A.A.; Dawoud, Rehab A. and Sofy, A.R.
Sharawil , S.S.A. and Abd El-Rahim2, I.H.A.•
... analyze for their nucleotide sequences of this F protein gene and phylogenic analysis properties, by matching with other reference world recorded isolates. The gene sequenced a 322 nucleotide cDNA fragment of the fusion protein gene was obtained. The isolates showed unique phylogenic analysis had not previously been identified internationally and defined as Egypt 2009. In addition; by using the obtained sequences gene...
*El-Helaly, Sahar H.; ** Ahmed, Amal A.; * Awad, M.A. and ** Soliman, A.M.'
...ained and sequenced. The nucleotide sequences were compared with corresponding viral nucleotide sequences reported in GenBank. The analysis showed that nucleotide sequence of the Egyptian isolate of AMV (GenBank Accession No. HQ288892) had percentage of similarity ranged from 97-98% with eight reported AMV isolates. Thus, a method of identification and detection by RT-PCR of AMV was establ...
Hussein, HA; sultan, HA. Al Deeb AH and AA. El-Sanousi
...re sequenced. Results of nucleotide sequence analysis of I I detected viruses confirm the existence and circulation of the H5Nl in Sharkia governorate along the period of study and no H7 viruses were detected. The serum samples collected from different farms were divided into 4 groups based on the date of collection. HI results showed that in the first group (samples collected between December 2006 to March2007) 43% of the tested samples were of HI titers of 6...
El-Tarabili M. M., El-Shahidy M. S., Rifaat M. M., Kania S. A. and Abdelwahab Shahira A.
S.A. Sidaros, S.A. El-Kewey , Hala A. Amin;Eman A.H. Khatab , A.A. Emeran l , Samaa Abd El-Khalilk and M.A.S. El-Kady
...ison of the CP ORF nucleotide sequence of Egyptian isolate (PMMoV-E2) with those of another isolates revealed 'that it was very close to the Brazilian and Japanese isolates (99 % and 98% respectively). Whereas the cp of PMM0V-E2 isolate was closely related to TMV-CP (99 & 97%) of Japan and Korea isolates, respectively. In the meantime it appeared far from Tropica Soda Apple Mosaic Virus-CP (TSAMV-CP) Florida isolate (USA) of Tobomovirus...
*Amal Abou El-Ela A., M. A. Amer and Eman A. H. Khatab,
...nt using degenerate oligonucleotide primers specific for detection of Potyvirus group. Amplification of total RNA extracted from infected carnation suggesting the presence of one Potyvirus in the tested carnation plant. Nucleic acid spot hybridization assay also was used to confirm identification of the present virus as one of the Potyvirus group using DIG labeled general cDNA probe for detection of potyviruses group, It showed high levels of hybridization sig...
Seham A. El-Zeedy1, Dalia A. Abd El-Moaty1, H. A. Hussein2 and M. A. Shalaby2
...highest identity on both nucleotide and amino acid levels 99.4% and 98.8% to the classical strains Cu-l, D78, and PBG-98, while Giza/2000 has the highest identity 98.3-98.1% on nucleotide level and 98.3% on a.a level to the vvIBDV. The multiple alignment of the two Egyptian isolates with different IBDV serotype I strains showed that isolate shared three unique a.a residues at positions 222A, 256I, and 294Ile that were found ...
A. A. El-Kholy1, S. Vilcek2 and A. M. Daoud1
...cons revealed an extreme nucleotide sequence homology (≥ 98%) among all tested Egyptian isolates versus the local vaccine strain. sequence alignments showed variable identity (74% - 93%) of the Egyptian vaccinal strain versus reference laboratory and vaccinal strains of BVDV. Clustering and phylogenetic analyses suggested that these Egyptian vaccinal and field BVDVs are low-Kinetic variants of reference BVDV-Ia. particularly the NADL, represented as a disti...
Nurlan Akhmetsadykov1*, Tanatar Kydyrov2, Moldir Akhmetzhanova1, Gulnazi Akhmetova3, Maxat Berdikulov4
...everse translated to the nucleotide sequence, after which the gene was synthesized using solid-phase method. The gene fragment, encoding the GM6 protein, was inserted or cloned into the pET28 expression vector after synthesis. The obtained sequences were checked by sequencing for correspondence to the matrix molecule. For transformation E. coli BL21 (DE3) strain was used. To assess the efficacy of the antigen, immunoassay analysis and blot-hybridization techni...
Zhengfei Wang1*, Chenchen Shen1,2, Yiping Zhang1, Dan Tang1,3, Yaqi Luo1, Yaotong Zhai1, Yayun Guan1, Yue Wang1 and Xinyu Wang1
...athway, including Cyclic nucleotide-gated cation channel beta-1, Adenylyl cyclase III, Calcium/calmodulin-dependent protein kinase II and Na+/Ca2+ exchanger. As a whole, our study laid a solid foundation for further functional elucidations of olfactory molecular mechanism in Procambarus clarkii, and provided further insight for a better understanding of olfaction molecular mechanism in crustaceans....
Fadime Eroglu1*, Altan Akineden2, Cemal Cicek3, Selcuk Turkel2
...37/310) in 120 bp-200 bp nucleotide. Our study shows that in addition to diseases such as diabetes and hypertension, intestinal protozoan infections can be a comorbidity with COVID-19 disease and increase the mortality rate of COVID-19 disease. In addition, our study shows that C. parvum var 1 may be the cause in recurrent COVID-19 disease. Therefore, it is useful to consider intestinal protozoan infections in the follow-up and treatment processes of COVID-19 ...
Perinçek Seçkinozan Seker
...vin had a relatively low nucleotide diversity and high haplotype diversity. A total of two haplotypes were identified for cyt b, while three haplotypes were identified for COI. Of the haplotypes detected, two cyt b and two COI haplotypes were specific to Turkey. Molecular phylogenetic analyses; Maximum Likelihood (ML), Bayesian Inference (BI), and Network revealed topologies and evolutionary networks which were not definitely resolved. Consequently, Turkish ro...
Aatif Masood Ahmad Khan1, Masood Rabbani1*, Arfan Ahmad1, Muhammad Wasim2 and Sohail Raza1
...d nicotinamide adenine dinucleotide phosphate (NAD) for their growth. The isolates were typical for Av. paragallinarum as they were not able to ferment neither galactose nor trehalose. Performing PCR of direct swab samples provided higher detection level as compared to the PCR from isolated colonies following conventional diagnostic procedure. In the current study, page serotyping demonstrated that all isolated Av. paragallinarum belonged to page serovars B. A...
