Sehrish Kanwal1, Ali Saeed1*, Muhammad Munir2, Memoona Arshad1
Life Sciences International Journal Issue 7 Volume 1
...nd secretion. The direct sequencing and subsequent analysis of amplified PCR products for VP1 gene indicated the circulation of serotype O of FMD in studied areas. Moreover, using serotype-specific primers (SA(F)/SA(R)) which target the VP1 gene, serotype O was confirmed in all representative samples. As high as 98% nucleotide sequences similarity was determined between the representative strains. Furthermore, these strains have shown homology with previously ...
Sehrish Kanwal, Ali Saeed, Muhammad Munir, Memoona Arshad
British Journal of Virology
...nd secretion. The direct sequencing and subsequent analysis of amplified PCR products for VP1 gene indicated the circulation of serotype O of FMD in studied areas. Moreover, using serotype-specific primers (SA(F)/SA(R)) which target the VP1 gene, serotype O was confirmed in all representative samples. As high as 98% nucleotide sequences similarity was determined between the representative strains. Furthermore, these strains have shown homology with previously ...
Sehrish Kanwal1, Ali Saeed1*, Muhammad Munir2, Memoona Arshad1
British Journal of Virology
...nd secretion. The direct sequencing and subsequent analysis of amplified PCR products for VP1 gene indicated the circulation of serotype O of FMD in studied areas. Moreover, using serotype-specific primers (SA(F)/SA(R)) which target the VP1 gene, serotype O was confirmed in all representative samples. As high as 98% nucleotide sequences similarity was determined between the representative strains. Furthermore, these strains have shown homology with previously ...
Tomas Jinnerot1*, Karin Malm1, Erik Eriksson1 and Jonas Johansson Wensman2
E-mail | [email protected]
Claudia Kohl*, Andreas Nitsche, Andreas Kurth
Email: [email protected]
...ustify;">Next generation sequencing (NGS) opened up a plethora of new research possibilities in biology and medicine. Metagenomics is one of these emerging NGS applications and offers the opportunity to study i.e. whole ecosystems. Basically, the metagenomics approach is similar to well-known shotgun-sequencing, though on a much bigger scale. For instance, the metagenome of a lake would include all the fish, ducks, plants, f...
Christopher U Orji1*, Ignatius O Onyeocha2, Steven S Shaida3, Peter M Dede4, Bitrus Yakubu5, Elijah E Ella6 and Pam D Luka5
Usman Ijaz1, Muhammad Sajid Tahir2, Khalid Abdul Majeed3*, Shahid Iqbal4, Iffat Huma5, S. Firyal6, Ijaz Ahmed7, Shahid Chohan8 and Aamir Riaz Khan9
...of COI were subjected to sequencing, and 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 evo...
Misbah Riaz1, Qaiser Mansoor2, Maleeha Akram1, Muhammad Ismail2, Parveen Akhtar3, Shakeel Mirza4, Mazhar Qayyum1, Afzaal Ahmed Naseem1, Faheem Tahir5 and Syed Shakeel Raza Rizvi1*
...lymorphism (SSCP) and/or sequencing. No mutation was identified in GPR54 gene, while two mutations in GNRHR gene were observed in one sporadic case of isolated HH. The first was a synonymous substitution 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 extracellu...
Ali Raza Awan*, Sehrish Firyal, Muhammad Tayyab, Lala Rukh, M. Zia ul Haq, Shagufta Saeed and Muhammad Wasim
...or amplification and DNA sequencing of Cytb gene. The Phylogenetic analysis of the Cytb gene indicated that the Pakistani wild Rose ringed Parakeet was mono-phyletically claded with P. k. manillensis with a sequence similarity of 99.37%. Comparative analysis indicated 4 Single Nucleotide Polymorphism (SNPs) sites in the Pakistani wild Rose-ringed parakeet’s Cytb gene which tags the peculiarity to the Pakistani wild Rose-ringed parakeet. This is the first...
Aiza Tahir, Muhammad Asif, Zaigham Abbas and Shafiq ur Rehman*
...cterization and 16S rRNA sequencing indicated that two strains were S. aureus, while all others were different coagulase negative Staphylococci. Their sensitivity against three phages indicated broad host range of phages SANF and SA2, and relatively narrow host range of phage SA. Phage SNAF showed an effective growth reduction of S. aureus RP isolate, compared with other bacteriophages. The bacterial challenge test in milk indicated that proliferation of S. au...
Fukuan Du1,2, Yan Li2, Zhixin Wen1, Ruguo Chen1 and Pao Xu2*
... performed transcriptome sequencing of six libraries from hepatopancreas samples in E. sinensis. After removing low-quality reads, short reads and reads belonging to mitochondria, a total of 278,260,960 clean reads corresponding to mRNAs were obtained, these reads covered a total of 34,780,598,273 bases. A total of 48,657 SSR loci were recognized, of which 10,310 unigene sequences contain more than one SSR. These genetic markers are ideal molecular markers for...
Iram Liaqat1*, Najma Arshad2, Muhammad Arshad3, Safdar Ali Mirza4, Nazish Mazhar Ali1 and Ammara Shoukat1
...haracterization. 16SrRNA sequencing was performed to identify three highly resistant strains at species level. Antimicrobial activity of aqueous and methanolic plant extracts of Camellia sinensis (Green tea), Syzygium aromaticum (Clove) and Mentha piperita (Peppermint) was evaluated against identified isolates. Agar well diffusion assay was used to monitor the antimicrobial activity of these strains both in mono culture and mixed culture. Streptomycin sulphate...
Sameera Akhtar1*, Muhammad Akram Muneer1, Khushi Muhammad1, Muhammad Yasin Tipu1, Muhammad Anees2, Imran Rashid1, Raza-ur-Rehman3 and Irshad Hussain1
...aluation. In this study, sequencing and molecular analysis of fusion (F) and hemagglutinin (HN) genes of NDV strain isolated from an outbreak in a peacock flock was undertaken. Proteolytic cleavage site of F0 showed a cleavage motif (112RRQKR↓F117), representative of a velogenic serotype. Moreover, based on F and HN gene nucleotide sequence analysis, the isolate clustered as genotype VII closely associated to those reporte...
Jiancheng Zhai, Li Gao, Yanling Xia and Heping Li*
...gh recovery, cloning and sequencing. Three of them (Af1, Ce1, Ci2) presented a higher expression in antler mesenchyme of female reindeer, but the other two (Ae1, Af3) were the opposite. The results of Blast in GenBank showed that they shared high homologies with SMAD5 (95%), COL6A3 (95%), SLC17A5 (93%), TPM4 (99%) and HMGB1 (98%), respectively. Quantitative RT-PCR validation of gene COL6A3 showed that the expression in both sexes was consistent with the result...
Sung Kwon Park1a, Jin Young Jeong2a, Eun Seok Cho3, Yong Dae Jeong3 and Chang Seok Park4*
... transcriptomes with RNA sequencing (RNA-seq) in peripheral blood mononucleated cell (PBMC) of piglets, Large White x Landrace crossbreds, infected with live strain PED virus (PEDV). Several gene ontology (GO) and differentially expressed gene (DEG) are also identified by RNA-seq. The analyzed transcriptome provides the 1805 DEGs and gene networks involving cellular processes. Between vaccinated and unvaccinated groups, there were 13 and 17 up- and down-regula...
Yi-qiang Ouyang1, Zhen-xin Liang1, Shi-wen Huang2, Ying Zhang3, Shao-shi Luo1, Jin-ning Liang1, Jia-fu Li1, Yu He4 and Song-chao Guo1,*
... we used high-throughput sequencing to analyze changes in the hippocampal transcriptome induced by injection of the three AD agents. These results open the door to new small-animal studies of AD that complement and extend studies in rodents and primates.
...
Jakub Jan Skorupski
...nvolved 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. Fourteen polymorphic variable sites were identified: 12 SNP substitutions, one single nucleotide deletion and one ins/del polymorphism. The assessment of informativeness and conclusiveness of the identified variable sitesshows that the highest ability to differentiat...
Javeria1, Masroor Ellahi Babar2,*, Tanveer Hussain2, Rashid Saif2, Sadaf Rashid3, Hanan Sarfraz4, Abbas Ali Shah3, Muhammad Wasim1 and Muhammad Abdullah1
Sidra Manzoor1,Asif Nadeem1,*, Masroor Ellahi Babar2, Wasim Shehzad1, Abu Saeed Hashmi1, Muhammad Imran1, Tanveer Hussain2, Abdul Wajid1 and Maryam Javed1
...gn: justify;">Nucleotide sequencing of bovine osteopontin gene showed a novel DNA polymorphism 37421762 (C>A) in the 3’-untranslated region (3’-UTR) of the gene. Association test was performed to analyze its relation with milk composition but it was found non-significant in all analyzed traits. So, it was inferred that it might be due to environmental or epigenetic effect, sampling number or a breed difference. To know the functional consequence...
Muhammad Abid1*, Tahir Yaqub2, Arslan Mehboob3 and Muhammad Zubair Shabbir4
...analysis of whole genome sequencing of prevailing H9N2 viruses in Pakistan which may further contribute towards the better understanding of the genetic nature and evolutionary behavior of these viruses in the country....
Mehran Kausar1,2, Naveed Ashraf3, Farzana Hayat4, Asraf Hussain Hashmi1, Saima Siddiqi1,* and Mariam Anees2
...nds. We performed direct sequencing of CTSK for five members of the family to find out the causative mutation. All coding exons of CTSK gene were amplified and sequenced in the affected and unaffected individuals of a consanguineous Pakistani family consisting of five members, three affected brothers, one unaffected sister and the unaffected mother. We identified a known missense mutation c.136 C>T in the third exon of CTSK changing arg...
Kulsoom Akhter1, Tahseen Ghous1,2,Saiqa Andleeb3,*, Faiz-ul-Hassan Nasim4, Samina Ejaz5, Zain-ul-Abdin1, Bilal Ahmed Khan1 and Muhammed Naeem Ahmed1
...ochemical, 16S rRNA gene sequencing, the isolates were identified as B. cereus BDBC01, B. cereus AVP12 and B. cereus NC7401. At maximum studied concentration of metal ions (250 mgl-1), in above sequence, the strains accumulated 118.2, 121.87 and 90 mg/g Cr (VI), 135, 127.5 and 146.25 mg/g Ni (II) and 120, 129.37, 135 mg/g Cd(II). Langmuir and Freundlich models were applied and found suitable to describe biosorption of selected m...
Carolina Torres Alejo1,2, Laila Andreia Rodrigues Beserra1,2, Paulo Eduardo Brandão1,2, Luis Ramiro Luna Espinoza1,2 and Fabio Gregori1,2*
...s 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 continued m...
Saba Manzoor1,*, Ali Raza Awan1, Abdul Wajid1, Sehrish Firyal1, Muhammad Tayyab1, Muhammad Mansha2, Asim Khalid Mahmood3, Abu Saeed Hashmi1 and Muhammad Wasim1,*
...re analyzed using Sanger sequencing method and RT-qPCR for the mutation and expression profiling of c-Myc gene. The coding region of c-Myc gene (exon2 and 3) did not show any variation in both species. While expression of c-Myc gene was found to be up regulated in different canine (62.5% in mammary adenocarcinoma, 75% in oral squamous cell carcinoma, 66.6% in peri-anal sac adenocarcinoma, 80% in mast cell tumor and 100% in soft tissue sarc...
Zahid Latif1,*, Kathrin Blasius2-4, Tufail Hussain Tahir7, Muhammad Nasim Khan1, Ghazanfar Ali5, Ansar Ahmed Abbasi6, Abdul Rauf1, Hao Hu8 and Angela M. Kaindl2,3,4
... and confirmed by Sanger sequencing. This family showed a homozygous c.2536G>A mutation in CRB1 gene as an underlying pathogenic variant for non-syndromic autosomal recessive retinitis pigmentosa.
...
Guang-Xin E1, Yong-Ju Zhao1, Yue-Hui Ma2, Ming-Xing Chu2, Jia-Hua Zhang1, Zhong-Quan Zhao1, Hui-Jiang Gao2, Huai-Zhi Jiang3, Di Liu4, Li Liu5, Yan-Bin Zhu6, Wang-Dui Basang6, Luo-Bu Danjiu7, Tian-Wu An8, Xiao-Lin Luo8, Shi-Cheng He7 and Yong-Fu Huang1,*
...ough Illumina paired-end sequencing, and their mapping rate was 84.99% and 84.47%, respectively. A total of 12577 differentially expressed genes (DEGs) were identified, including 6009 upregulated and 6568 downregulated genes in dominant follicles compared with nondominant follicles of goat. Of the 1026 significantly differentially expressed, long noncoding RNAs (lncRNAs) found, 419 were upregulated and 607 were downregulated. The DEGs related to 56 GO categori...
Gut Microbe Analysis between Asthma Patients and Healthy Volunteers in Shaanxi Province, Xian, China
Hafiz Muhammad Ishaq1, Muhammad Shahzad2, Xiaokang Wu3, Chaofeng Ma4 and Jiru Xu1,*
RuiHua Zhang, YongFang Jia, TingTing Liang, QianWen Yang, QiYan Du and ZhongJie Chang*
...ences from transcriptome sequencing data of carp: CcSox5, CcSox6 and CcSox13 (Cyprinus carpio SoxD).These genes were verified by sequencing, blast and homology alignment. CcSoxD have two to four exons and encode a 780, 784 and 602 amino acid protein, respectively. Chromosome synteny analyses revealed that CcSox5 and CcSox13 weretightly linked with the etnk gene, which w...
Iracema Nunes de Barros1,2, Luciane Dubina Pinto3, Rosely Bianca dos Santos Kuroda1, Sheila Oliveira de Souza Silva1, Leonardo José Richtzenhain1,2, Cláudio Wageck Canal3 and Paulo Eduardo Brandão1,2*
...ere subjected to partial sequencing for the membrane (M), spike (S), nucleocapsid (N) and non-structural protein 3b genes. Out of the samples collected, 40.17% were positive for CCoV; 57.45% of CCoV-infected animals showed enteritis and most of these (76%) were younger than 3 months and unvaccinated. Distance genealogy using CCoV sequences from GenBank for M gene showed that eight strains were CCoV-II twenty-six were CCoV-I. These findings show some genetic fe...
Saba Rafique1,2,*, Khalid Naeem1, Naila Siddique1, Muhammad Athar Abbas1, Aamer Ali Shah2, Akbar Ali1, Abdul Rahim1 and Farooq Rashid1
... subjected to Spike gene sequencing covering the amino-terminus region of 01 to 974 base pairs. The S protein sequence was submitted to the GenBank with accession number KU145467. Phylogenetic 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 (AB...
Qin Liu1,2, Feiwei Liu1, Xiuyue Zhang1, Nan Yang1 and Jianghong Ran1,*
... 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 better understand the breeding system and protection manage of this species.
...
Dildar Hussain Kalhoro1,2,, Shan Liang1, Muhammad Saleem Kalhoro2, Shoaib Ahmed Pirzado2, Nasir Rajput2, Muhammad Naeem2, Fahmida Parveen2 andYongjie Liu1*
Basit Zeshan1,2,*, Mushtaq A. Saleem2,Javed Iqbal Wattoo2, Mohd Mokhtar Arshad1 and Maizan Mohamed1
...nfirmed the construct by sequencing. The recombinant plasmid was identified by restriction enzyme and sequencing analysis. The in vitro expression of the truncated protein was analyzed in E. coli with a molecular weight of 38kDa determined through SDS-PAGE and confirmed by Western blotting. The recombinant truncated protein was then purified from the culture media. The immunogenicity of the protein was st...
Sherin Reda Rouby
...without the need of gene sequencing. A total of 16 lumpy skin disease clinical samples (skin nodules, scabs, buffy coat, lymph aspirate and engorged ticks) and three sheep pox biopsy skin samples were subjected to DNA extraction followed by 30 kDa RNA polymerase subunit gene-based polymerase chain reaction (PCR) (RPO30) together with tissue culture-adapted cattle LSDV/Ismailyia88 strain and two Sheep poxvirus vaccinal strains as control. LSDV yield amplic...
Ligia Neves Scuarcialupi, Laila Andreia Rodrigues Beserra, Julia Rosas Hochheim, Rodrigo Martins Soares, Fabio Gregori*
...her 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.
...
Ayesha Munir, Hafiz Muhammad Umer, Anjum Nasim Sabri and Imran Sajid*
...ication by 16S rRNA gene sequencing confirmed that caries isolates are pathogenic S. mutans and soil isolates belong to the genus Streptomyces. The antibiotic resistance profile of S. mutans illustrated resistance to optochin. The antimicrobial screening of Streptomyces against S. mutans showed that these strain are the prolific producers of active agents to inhibit the growth of caries causing S. mutans. The natural e...
Yijiang Liu1, Kun Li2, Hui Zhang2, Khalid Mehmood2,3, Muhammad Shahzad3, Houqiang Luo1,*, Muhammad Asif Yaseen4 and Xiong Jiang2,5,*
... industry.
...
Xiangbin Meng1,Tianxiang Gao2, Chunhou Li3, Na Song1, Lu Liu1, Liqin Liu2 and Xiumei Zhang1,*
...erformed next-generation sequencing and de novo assembly to obtain potential useful microsatellite markers for S. esculenta. Among 80 tested microsatellite markers, 19 showed polymorphism among S. esculenta individuals. The allele number of all polymorphic microsatellite markers ranged from 6 to 10. Expected and observed heterozygosity varied from 0.260 to 0.904 and from 0.292 to 0.861, with an average of 0.741 and 0.607, respectively. The...
Jun Chen1, Shuai Shang2, Xiaoyang Wu1, Jiakuo Yan1, Huaming Zhong1, Huanxin Zhang2, Weilai Sha1, Wanchao Zhu1 and Honghai Zhang1,*
...high-throughput Illumina sequencing technology. We analyzed 100,180 high-quality sequences of the 16S rRNA gene obtained from fecal samples from three cape oryx animals, one female and two males. At the 3% level in our research, we found 3959, 4553, and 3930 operational taxonomical units (OTUs). Additionally, the three samples have 754 OTUs in common, which comprised 19.59%, 16.55%, and 19.81% of the reads in C1, C2 and C3. We identified 18 prokaryotic phyla i...
Danyu Zhang1, Ying Liu1, Qinxin Shi1, Zhiwei Peng1, Yan Hua1 and Zhijun Hou1,2,*
...d NaCl floating and next sequencing methods. The parasites were Capillaria sp., Baylisascaris devosi, Echinochasmus sp., and two Coccidianspecies. The Echinochasmus sp. andtwo Coccidian species were first time found either in sable or in other martens. The 434 genus of bacteria, belong to 30 phylum, the more popular bacteria were Proteobacteria (33.54%), following by Firmicutes (18.58), Acidobacter...
Abdul Wajid1,*, Asma Basharat2, Muhammad Akbar Shahid3, Sidra Tul Muntaha1, Abdul Basit4, Tanveer Hussain5, Muhammad Farooq Tahir6, Muhammad Azhar7, Masroor Ellahi Babar1 and Shafqat Fatima Rehmani2
...analysis based on direct sequencing of hypervariable region of hexon gene grouped these sequences into two distinct groups, three FAdV isolates were clustered together belonging to fowl adenoviruses C species and serotype FAdV-4. The similar viruses have been commonly isolated since late 1980s from the poultry flocks. In addition, seven genetically related FAdV isolates were from fowl adenovirus type 11 in D species. To our knowledge, this is the first report ...
Maryam Javed*, Farwa Saghir, Naveera Aziz, Maham Saeed, Asif Nadeem and Wasim Shehzad
...er’s method of DNA sequencing was used. Multiple sequence alignment demonstrated that sheep and goat were having the wild base Guanine against which the cattle and buffalo depicted the mutant form Adenine. Results of this study illustrated the genetic tendency of large domestic bovines towards aggression and attack, so they should be handled with great caution.
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