Tomas Jinnerot1*, Karin Malm1, Erik Eriksson1 and Jonas Johansson Wensman2
E-mail | [email protected]
...ith respiratory signs. A genome comparison program was used to select a suitable target DNA sequence. A PCR targeting the bfrZ gene was developed which showed no cross-reactivity in silico or when tested with a panel of bacterial isolates. The limit of detection was determined to 4x103 bacteria per mL of nasal swab sample and less than 10 copies of target DNA per PCR reaction. Out of 23 isolates of B. bronchisep...
Claudia Kohl*, Andreas Nitsche, Andreas Kurth
Email: [email protected]
...e. For instance, the metagenome of a lake would include all the fish, ducks, plants, fungi, bacteria and everything else that belongs to the lake. If we apply this approach to clinical samples we can identify the community of etiological pathogens, without any knowledge on the targets in advance. However, clinical specimens usually comprise an overwhelming amount of host nucleic acids, which by far exceeds the number of pathogen nucleic acids in the sample. Su...
Ummara Waheed Khan, Raza Ahmed, Irum Shahzadi and Mohmmad Maroof Shah
Email | [email protected]
...techniques, such as genome mapping, tissue culture, genetic transformation and in vitro regeneration offered new dimensions of research to improve important crop species including wheat. The tissue culture by itself has increased the crop improvement potential to develop new cultivars with desirable traits through somaclonal and gametoclonal selection. While successful tissue culture is critical for genetic transformation, it has been ...
Mohammed M. Islam1, 3 *, Damian F. J. Purcell2 and George Kannourakis1,3
...ast transcripts of viral genomes using suppression subtractive hybridization that can be adapted to unanimously identify viruses of diverse genetic backgrounds. ...
Zuhao Huang1, Feiyun Tu2 and Dianhua Ke1*
...e complete mitochondrial genome of Blue-throated Bee-eater M. viridis was determined. The mitogenome is a circular DNA molecule of 18,295 bp and comprises of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two control regions CR and CCR, which was first reported in the order Coraciiformes. The overall A+T content for the mitogenome is 52%, and the GC and AT skews are -0.4...
Zisha Liu1, Na Song1, Takashi Yanagimoto2, Zhiqiang Han3, Bonian Shui3 and Tianxiang Gao3*
...stify;">The complete mitogenomes of three species (O. lacepedii, O. rebecca and
Giselle R.R. Ayres* and Brandão P.E
...le-stranded positive RNA genome, corresponding to the largest known RNA genome, with about 27kb for AvCoV. The first 5’ two thirds of this genome, correspondent to a wide ORF1 (also called replicase gene), code for non-structural proteins (nsps) that are enrolled in viral transcription, replication and pathogenesis. The last 3’ one-third of the genome
Yaoguo Li1,2 and Maoxian He1*
...ustify;">The function of genome methylation in invertebrates has only recently been characterized in-depth. In this study, we firstly investigated the associations of genome methylation level and growth traits inpearl oyster, Pinctada fucata (P. fucata). The incidence of type II locus (hemi-methylation locus) was significantly correlated with the shell height and the shell length, with Pearson correlation coeff...
Neenish Rana, Nosheen Ehsan, Awais Ihsan and Farrukh Jamil*
...unctional by-products of genome evolution. However, it has been indicated by several lines of evidences that some pseudogenes are active. Using current data of NCBI we have retrieved 65 pseudogenes from the genome sequence of human pathogenic bacteria Helicobacter pylori (H. pylori) strain 26695. Computational analysis of the genome showed 6 transcriptionally active pseudogen...
Nirbhay Kushwaha, Achuit K Singh, Brotati Chattopadhyay and Supriya Chakraborty
Recent advances in geminivirus detection and future perspectives
...single-stranded (ss) DNA genomes (~2.7 kb size) and twined icosahedral virions (18 x 30 nm). Based on genome organization, host range and insect-vector, geminiviruses are divided into four genera:Mastrevirus, Curtovirus, Topocuvirus and Begomovirus. Begomoviruses are transmitted by whiteflies (Bemisia tabaci Gennadius) and usually possess a bipartite genome of twoDNAcomponents approximatel...
Baohua Chen1,2, Wenzhu Peng3, Jian Xu2, Jingyan Feng1,2, Chuanju Dong1,2 and Peng Xu2,3,*
...f members in common carp genome. Both sequences alignment and phylogenetic analysis exhibited that genes derived from the same GST class from different species share more similarity than genes of different classes in the same species. Copy number of GSTs examining showed that five classes of GST genes in common carp have undergone the gene duplications, including MGST1, GSTK, GSTM, GSTA and GSTT. Comparative genomics and syntenic analysis provided new evidence...
Nasar Khan1,2, Fahad Ali3,7, Sulaiman Bahadar5,*, Khalil ur Rahman3, Abdul Aziz3, Noor ul Akbar4, Muhammad Daud6, Azam Hayat5 and Mujaddad ur Rehman5
...p of 31 to 40 years. HBV genome was detected in 79.21% of HBsAg positive samples, showing that HBsAg on ELISA is much more sensitive than PCR as HBV shows chronic conditions and both of the tests are needed against HBV.
...
Yijin He1, Song Ma2, Bo Liu1,*, Ting Xue1, Qunlan Zhou1, Wu Jin1 and Kui Chen2,*
...een used as one of human genome model animal since mid-1990s. In this experiment, we cloned a pair of DNA fragment sequence including complete ORF (921bp) of taste receptor candidate gene T2R1 of T. fasciatus and studied the differential expression spectrum of tissues in combination with bioinformatics analysis so as to understand the possible functions in response to chemical sensation behavior of taste receptors. The receptors when compared wit...
Muhammad Abid1*, Tahir Yaqub2, Arslan Mehboob3 and Muhammad Zubair Shabbir4
...es for 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....
Zuhao Huang*, Meifang Li, Rujue Ruan and Jiawei Qin
... region of mitochondrial genome. To infer the organization and variation of Ardeidae mitochondrial DNA control region, the control region genes of 20 species were analyzed. All the Ardeidae species had duplicate control regions, except four species having only single region. The control region spans the region between the genes for tRNAGlu - tRNAPhe in the most Ardeidae species. The length of the control region sequences ranged from 1427 ...
Mushtaq Ahmad1,*, Mehboob Ahmed1,2 and Nasim Ahmad1
....
...
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,*
Syed Kashif Nawaz*, Faiza Zubair and Sidra Kanwal
...ntegral component of the genome. The present study investigated the various types of overlapping genes in human genome. Study was completed using genome assembly GRCh 38/ hg38 data was accessed using NCBI map viewer for the identification of exact loci of overlapping genes. It was noticed that maximum number (635) of overlapping genes were present on chromosome 1. Chromosome 21 carried the...
Yunjun Yan, Zhenming Lü, Tianming Wang, Yongjiu Chen, Jingwen Yang, Baoying Guo, Lihua Jiang, Changwen Wu and Liqin Liu*
...nce 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 a major long noncoding region (LNCR) of t...
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*
...tudies to elucidate full genome sequences of these isolates to better assess the disease transmission dynamics and future control strategies. ...
Sherin Reda Rouby
...extremely conserved with genome identities of at least 96% between SPPV, GTPV and LSDV. The LSDV is similar in antigenicity and in cultural characteristics to SPPV. The current study was delineated to identify capripoxviruses from different clinical samples and differentiate capripoxviruses 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 th...
Nadia Faqir1, Aish Muhammad2*, Ghulam Muhammad Ali2, Armghan Shehzad2, Hafeez Ur Rahman3, Farhatullah4 and Muhammad Zeeshan Hyder5
...dentity to the reference genome of ‘Khalas’ cultivar. While geranyl geranyl biphosphate reductase has 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. ...
Shuai Shang1,2, Honghai Zhang2,*, Xiaoyang Wu2, Qinguo Wei2, Jun Chen1, Huanxin Zhang1, Huaming Zhong2 and Xuexi Tang1,*
...l species based on their genome sequences and our previous study, including thirteen carnivorous species and one omnivorous species. Then, we constructed a phylogenetic tree using Tas2r genes sequences from these fifteen species. Phylogenetic analyses showed that most Tas2r genes of raccoon dogs were closed to other canid-species, indicating that the Tas2r genes were very conservative. Besides, we also detected positive selection in 11 int...
Baoying Guo*1, Yu Chen1, Chuan Zhang2, Zhenming Lv1, Kaida Xu3, Hongling Ping4 and Huilai Shi4
...plete mitochondrial (mt) genome of the kisslip cuttlefish, Sepia lycidas, made the comparison with the mt genomes of other cuttlefishes, and constructed phylogenetic trees estimating their relationships. The genome was 16,228 bp and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 long-noncoding regions [both in the control regions (CR)]. The co...
Yijiang Liu1, Kun Li2, Hui Zhang2, Khalid Mehmood2,3, Muhammad Shahzad3, Houqiang Luo1,*, Muhammad Asif Yaseen4 and Xiong Jiang2,5,*
...plete mitochondrial (mt) genome of the pet bamboo rat Rhizomys pruinosus, which had a problem in standing and walking in a Bamboo farm in Wenzhou, China was carried out, using its tibia. The mt genome (16,579 bp) is composed of 13 protein coding genes, 22 tRNA genes and 2 rRNA genes. The ratio of the bases of the mt genome of R. pruinosus from Wenzhou are A (32.31%), T...
G. Venkatesan* and Amit Kumar
...cated at termini of ORFV genome with their encoded products are attributed to host immune evasion, short-term immunity both in natural infection post-vaccination in target species and repeated host susceptibility. However, these genes are variable among ORFV isolates/strains as they are not located in central part of genome and some of them are either virus specific namely Viral interferon resistant (VIR) and GM-CSF/IL2 inhi...
Wei Meng1,3, Tianyan Yang2,*, Yunguo Liu1, Mahmut Halik1 and Tianxiang Gao2
...e complete mitochondrial genomes of G. dybowskii from Tarim River system (16, 677bp) and Ili River system (16, 667bp) were sequenced. Besides, their genetic characteristics were also identified and compared simultaneously. Genetic distance and sequence differentiation suggested that great genetic variation existed within species and the sample from Kaidu River in South Xinjiang might be a cryptic species or subspecies of G. dybowskii. The phyloge...
Ai Guo1,2,3, Jiaguang Xiao4, Binbin Shan4, Tianxiang Gao5 and Yongdong Zhou3,*
...e complete mitochondrial genomes of two lineages in Coilia mystus were compared. They were all typical circular double stranded DNA molecule with 17075 bp in C. mystus N and 16964 bp in C. mystus S, respectively, containing the standard metazoan set of 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and non-coding regions. The mitogenomes of C. mystus N and C. mystus S...
Muhammad Amir Maqbool1*, Muhammad Aslam1, Waseem Akbar2, Muhammad Waheed Anwar3 and Ehtisham Shakeel Khokhar1
... MtSIPs. Cicer arietinum genome comprised of 41 MIPs which were consisted of 10 CaPIPs, 12 CaTIPs, 15 CaNIPs and 4 CaSIPs protein sequences. Genome of Zea mays was carrying 36 ZmMIPs which were categorized into 12 ZmPIPs, 13 ZmTIPs, 8 ZmNIPs and 3 ZmSIPs. Phylogenetic trees were constructed separately for every sub-families of barrel medic, chickpea and maize. PIPs were consisted of two main groups for all of three crops whi...
Zisha Liu1, Na Song1, Takashi Yanagimoto2, Zhiqiang Han3, Bonian Shui3 and Tianxiang Gao3,*
...v>...
Iqra Arooj1,* and Shahida Hasnain2
...d pressure etc. Previous genome wide association studies have identified association of large number of loci with risk of CHD in different populations. The purpose of this study was to determine the association of 6q25.1/rs6922269 and 9p21.3/rs1333049 loci with risk of CHD in a population of Punjab province of Pakistan. A total of 645 subjects were included in this study of which 435 were patients visiting hospitals of Lahore and Gujranwala districts. All the ...
Rishen Liang*, Meng Zhou, Zhenxiang Lin, Guozhang Li, Yuan Chen, Xuan Lin and Zaohe Wu
..., complete mitochondrial genomes of the two species were first determined. The genomes were 16,546 bp (P. orientalis) and 16,545 bp (P. vittatus) in size, respectively, which both consisted of a typical structure of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one noncoding control region. Genomic composition, organization and gene order were similar to that obtained in most verteb...
Tazeen Jamil, Saba Ijaz, Rabia Arif*, Faiza Akram and Muhammad Saleem
... abundance in eukaryotic genomes and their insertion in coding regions leads to altered gene expression. We examined the diversity of retroelements in four consecutive generations of different strains of Sordaria fimicola. The parental strains werecollected from two contrasting environments of Evolution Canyon i.e. harsh South facing slope and neutral North facing slope. Retroelements profiles were generated in order to detect retrotransposons. S...
Zhengfei Wang*, Dan Tang, Xuejia Shi, Huayun Guo, Xiuping Chen, Daizheng Zhang and Boping Tang*
... PCGs from mitochondrial genomes of 48 Brachyura species and one Diogenidae species were examined. Each of the genes was investigated and compared to orthologous sequences using PAML, Datamonkey, and TreeSAAP. Nine mitochondrial PCGs (ATP6, ATP8, COX1, COX3, CYTB, ND1, ND2, ND4, and ND5) were validated to have undergone positive selection (i.e., directional selection) in vent crabs by at least two methods. A series of putatively selected codons w...
Muhammad Yasin1, Romana Shahzadi1, Muhammad Riaz2, Mahideen Afridi2, Wajya Ajmal3, Obaid Ur Rehman2, Nazia Rehman3, Ghulam Muhammad Ali1,3, Muhammad Ramzan Khan1,2,3*
...ing genes for developing genome edited plants to prevent yield losses in canola in future. ...
Jingchen Chen, Zhaochao Deng and Zhiqiang Han*
... the whole mitochondrial genome sequence of Ammodytes personatus, and compared with Sanger sequencing results. Three samples belonging to two lineages of A. personatus mitochondrial DNA (mtDNA) were used in the study. Based on the complete mtDNA sequence, the genetic distance between the two lineages is 0.064. Results show that the total sequence lengths of the three samples of A. personatus mitochondrial genome
Shaikh Abdul Lateef, Zhou Lin, Wu Jian, Junjie Qian, Jonathan Hartanto Tan and Zheng Shusen*
...Due to the complex viral genome of HBV, complete recovery from hepatitis is not achieved. Epidemiologically, it has been classified into infectious and serum hepatitis. The pattern of disease progression manifests liver inflammation, chronic hepatitis and hepatocellular carcinoma. In this article, we present a comprehensive review characterizing the viral architecture, life cycle, infectivity mechanisms, immune escape strategies, disease epidemiology and preve...
Hala Rajab1, Muhammad Sayyar Khan1*, Safdar Hussain Shah1 and Syed Mehar Ali Shah2
...egration into the plants genome was confirmed by PCR using the NtSAT4 gene specific primers. The positive transgenic lines were successfully acclimatized to soil and glass house conditions. The developed transgenic lines have the potential to overproduce high levels of cysteine and glutathione for enhanced stress tolerance especially against heavy metals. ...
Peng Chen1,2, Zuhao Huang3,Chaoying Zhu1, Yuqing Han1, Zhifeng Xu1,
Guanglong Sun1, Zhen Zhang1, Dongqin Zhao4, Gang Ge1 and Luzhang Ruan1*
Huanxin Zhang1,2, Hongshuo Tang3, Jun Chen1, Yu Zang1,2, Xuexi Tang1,2,* and Ying Wang1,2,*
...re scared. The available genome sequence of African hunting dog offers us the way to examine the innate immunity of this endangered carnivore. 10 TLR genes (TLR1-10) were initially identified from the African hunting dog and lesser panda. The results showed that most of the TLR genes were very conservative in the African hunting dog. We found 6 of ten TLR genes had the evidence of positive selection, only a small proportion of sites show evidence of selection,...
Honghua Wang1,2, Summia Perveen1,2, Shucheng Shao1,2, Kun Wang1,2 and Fei Yin1,2,*
Sajida Rasool1, Saba Irshad1*, Neelam Saba1, Mehak Fiaz1, Muhammad Sajid Hussain2, MuhammadWajid Hussain3 and Peter Nürnberg2
Anand Kushwaha, Amit Kumar, Aparna Madhavan, Durga Goswami, Golmei Poulinlu and Gnanavel Venkatesan*
...ve 147 proteins in their genome, among which some of them are reported as potential immunogenic candidate genes. Selection and use of such candidate immunogenic proteins from an array of genes located at different structures of a mature virion are the real challenge and time consuming task for researchers. Nevertheless, identification of candidate gene(s) using advanced bioinformatic tools will ease the process and can select the suitable protein(s) to use in ...
Chuntao Li1, Hua Liu2, Jianqing Zhang1*, Jiaqiang Zhang1, Luming Dai1, Zhihuan Zhao1,Lizhou Fang1, Ling Liu1, Jingkui Shu1 and Jiagang Feng1
...s that the expression of genome-wide lncRNA in COPD blood samplesis different in comparison with healthy smokers by microarray analysis. LncRNA BMF-AS1 expression might potentially predict the apoptosis of COPD by regulating of BMF mRNA expression.
...
Samia Afzal*,Sadia Zahid, Iram Amin, Muhammad Shahid and Muhammad Idrees
...ntification of the viral genome. Thirty samples were found PCR positive and a subset of ten samples was direct sequenced. Sequence analysis showed 94% similarity to Stenotrophomonas maltophilia which is considered to be the second most prevalent bacterial species in mosquitoe’s midgut. This observation may lead towards the confusion that the outbreak is either of Dengue or Chikunguna virus. In conclusion, confirmatory molecular characterizat...
Olotu Titilayo Mabel*, Adeosun Idowu Jesulayomi, Kaka Mary Oluwatosin and Oladipo Elijah Kolawole
...nesis and disease. HIV-1 genome has nine genes; gag, pol, and env genes are common in all replication-competent retroviruses, and the pol gene is very unique encoding the enzymes for replication. Our objective is to describe the relatedness of these HIV-1 pol genes with each other and its antiviral drug susceptibility which will provide more information on its sensitivity and resistivity to each antiviral drug. Seventeen partial genome...
Asif Ali Khan*, Laiq Hassan*, Salim Ullah*
OPEN MP-BASED PARALLEL AND SCALABLE GENETIC SEQUENCE ALIGNMENT
...t task. Biologists align genome sequences to find
important similarities and dissimilarities in them. Multiple heuristics and dynamic programming based approaches
are available for sequence alignment. Smith-Waterman (SW), an exact algorithm for local alignment, is the most
accurate of them all. However, the space and time complexity of the SW algorithm is quadratic. It is imperative to
use parallelism and distributed computing techn...
important similarities and dissimilarities in them. Multiple heuristics and dynamic programming based approaches
are available for sequence alignment. Smith-Waterman (SW), an exact algorithm for local alignment, is the most
accurate of them all. However, the space and time complexity of the SW algorithm is quadratic. It is imperative to
use parallelism and distributed computing techn...
Muhammad Shahzad1, Arif Iqbal Umar1, Syed Hamad Shirazi1, Muhammad Tariq Pervez2*, Zakir Khan1, Waqas Yousaf1
HCDP: HEPATITIS C DATA BANK OF PAKISTAN
...nnotated database of HCV genome sequences allows the researcher to investigate the structural and genetic variability of the sequences efficiently and effectively. HCDP is a specialized database that mainly focuses on the HCV strain from Pakistani community. It helps virologists in drug designing and vaccine development....
Ming-Yan Shi2, Xu-Liang Yan1, Ping-Ping Han1, Yu-Jie Tang1 and Hui-Xia Li1*
Sehrish Firyal1,*, Ali Raza Awan1, Muhammad Umair Latif1, Muhammad Tayyab1, Muhammad Wasim1, Shagufta Saeed1 and Imaad Rashid2
...ormly 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 Cytb gene revealed Columbia livia as closest homologue of Pakistani Lathy pigeon with five novel SNPs. Phylogenetic analysis of domestic lathy pigeon indicated the monophyletic relati...
Moazam Ali1, Wajid Ali2, Ayhan Ceyhan2 and Zeeshan Ahmad Bhutta3*
Pigmentation Genome Influence in Animals and Human Interventions in its Course of Action
...scientists is working on genome sequences and mutations for getting a better and healthier pigmentation besides animal welfare. This review article contains a complete elaboration about the worth of pigmentation in animals, natural pigmentation process and new mutation and deviation in animal genome related to their pigmentation for human and animal welfare respectively....
Christian Marco Hadi Nugroho1 and Jeanne Adiwinata Pawitan2,3,4*
Production of Antibody for Direct Fluorescence Antibody Assay against Avian Influenza H9N2
...It has a minus sense RNA genome of eight segments. This fact makes the virus to easily re-assort, which might yield a new virus strain, and causes an outbreak in unimmunized humans or chickens. In reducing losses due to H9N2 infection, rapid diagnosis is an option to prevent further infections. Office International des Epizooties (OIE) suggested some methods for the detection of H9N2 infection including the immunofluorescence method that is commonly known as t...
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
...lopment in generation at genome editing level have made feasible to accurate mutations in human genome. A site oriented specific break in double stranded DNA is induced by CRISPR/Cas9, 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 edit...
Hong Hu1, 2, Li Qian1, Yuanlang Wang1, Chaodong Wu1, Xiaodong Zhang1, Yueyun Ding 1*, Li Wang1, Xudong Wu1, Wei Zhang1, Dengtao Li1, Jian Ding1, Min Yang1 and Zongjun Yin1*
Fan Sigang1, Guo Yihui1* and Xu Youhou2
Guofang Wu1,2, Xingxing Xue1, Wenjuan Shen1, Lei Wang1,2*, Yuhong Ma1 and Jiping Zhou1
...Sus scrofa reference genome (Sscrofa11.1) revealed that the L1-(GT)n microsatellite, which features a GT repeat motif, was located in the retinoic acid induced 2 gene (RAI2) on chromosome X in Sus scrofa (SSCX). Analysis further revealed that the L2-(AC)n locus, featuring AC repeats, and the L3-(TC)n locus, featuring TC repeats, were located in intergenic regions on SSC14 and SSC5, respectively. TGA repeats wi...
Nosheen Basharat1, Usman Waheed2,3*, Muhammad Arshad1, Noor e Saba4, Iram Masood1, Akhlaaq Wazeer1, Ahmad Farooq1, Sadaf Moneeba1, Abdul Rauf5 and Hasan Abbas Zaheer2,3
...anded negative-sense DNA genome. TTV represents the first circovirus-like virus found in humans. The study was conducted to assess the molecular epidemiology of TTV in healthy blood donors and find its relationship with hepatitis B and hepatitis C seropositivity. The study was conducted at the Department of Pathology and Transfusion Medicine, Shaheed Zulfiqar Ali Medical University, Islamabad, from November 2016 to June 2017. Total 282 samples were selected af...
Dilara Devranoglu, Ilksen Tavaci, Gonul Filoglu and Ozlem Bulbul*
...tic 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 electrophoresis were performed. The multinomial logistic regression model statistics is app...
Saad A. Moussa1, Ahmed F. Afify1*, Suzan Salah2 and Ayman Hamed3
...te and stability of BCoV genome....
Arsalan Rasheed1, Tahir Usman2,*, Sadaf Niaz1, Irfan Khattak2, Saira Gul2, Nawab Ali1,Naimat Ullah Khan2, Hazrat Ali2, and Mian Saeed Sarwar2
Muhamamd Rizwan1*, Muhammad Arshad2, Muhammad Kashif3, Aneela Zameer Durrani4, Asghar Abbas5, Tanveer Ahmad6, Muhammad Nadeem7 , Kinza Khan8
...system and there role in genome editing, bacterial virulence and antibiotics resistance. CRISPR Cas system is an integral part of prokaryotic (Bacteria and Archaea) immune system that provides protection against viral infection. When bacteria recognize viral DNA inside it, bacteria incorporate small fragment of viral DNA into its genome at specific site termed as CRISPR locus. Insertion of viral DNA at CRISPR locus allows to...
Ahmed F. Afify1, Mohamed A. Shalaby2, Ahmed A. El-Sanousi2 and Amal S. Gaber1
...lecular detection of EAV genome was performed only on 8 selected semen and
EDTA-blood samples which were giving highly distinct positive reaction in the
indirect ELISA. All samples were found negative to the presence of EAV genome by
real time RT-PCR. Trials of isolation on different types of cell cultures were done on
the 4 described semen samples; RK-13, VERO-1008, BHK-21 AND...
Ala’audin Hakami,1AusamaA Yousif,2* Mohamed Zaki,3 Mahmoud Ismail,4,5 Ahmed Al-Ali,5 Abdu-Rahman Al-Ankari5
...3 bp region of the viral genome. PBFDV was detected in
31.6% of clinical cases (3.5% of samples). Two positive samples were
collected during 2008, three during 2009, and one during 2010. Positive
samples were from clinical cases. Negative samples tested positive for bird
rDNA. In positive cases, feathers not blood, consistently tested positive.
Four of the positive samples were collected from African ...
Abeer A. Feisall; B.A. Othman2; Kh.A. El-Dougdoug2 and H.S. Shalaby1
...mHI, XhoI and EcoRI. The genome size of the
phage was estimated to be 18 kbp.
...
Nashwa M. Helmy1 and Ahmed S. A.2
...s antigen or
genome. So, the vesicular epithelial tissues collected from infected cattle from Sharkia
(7) and Fayoum (5) governorates were subjected to antigen ELISA and RT-PCR. 8
epithelial tissues were identified by Indirect sandwich ELISA. The results were 5 and 3
positive from Sharkia and Fayoum respectively, while 12 samples were positive by RTPCR.
In conclusion, this study demonstrates that real...
Aya El-Turkey1, A. K. El-Attar1, A. E. Aboulata1, B. Othman2 and K. A. El-dougdoug2
...s 2 (HSV) is a DNA-viral genome and cause infection for both human and animal. HSV-1 and HSV-2 are causing infection to human. HSV-2 is a sexually-transmitted virus. HSV-2 is prevalence in European countries and also in Egyptian-closed societies like Upper Egypt. Egyptian isolate of HSV-2 was isolated and Glycoprotein D (HSV-2gD) subunit was amplified using specific PCR primers.PCR product was molecularly cloned in t E.coli cells using PCR2.1/TOPO/ TA cloning ...
Amro A. Farrag1; Ahmed K. El-Attar1; Om-Hashem M. El-Banna2; Ibrahim A. I.2; H.
M. Mazyad1
...the
complete genome of the virus was as follow, DNA-A (2667 bp) and DNA-B (2621 bp).
The obtained sequences were submitted into the GenBank with accession numbers
KJ624994 and KJ579954.The full nucleotide sequence of DNA-A, DNA-B and all open
reading frames (ORF) of the SLCV-bean was aligned and compared with eleven different
isolates of the SLCV available in the GenBank. The phylogenetic analysis of ...
Amel, S.M. Abo-Senna1; M.A. Nasr-Eldin2; B.A. Othman3 and A.A. Megahed4
...ding region of the virus genome. The cytopathological effects of ZYMV on the infected cells were completely chloroplasts destruction, and deformation of vascular bundles. The effect of late ZYMV infection decreased fresh weight and yield of squash plants....
Aly M. Abdel-Salam
...se,
RT/RNase genome regions of ORF III detected the virus in infected sugarcane leaves
and in its vector Saccharicoccus sacchari and in another unidentified
Pseudococcidae- mealybug. Amplicons for the RT/RNaseH motifs of the two virus
isolates were cloned, sequenced, and submitted to the GenBanak. Pair-wise nucleotide
identity indicated 86% identity between the Giza and Assiut isolates. NCBI-blastn
AdlyAbd-Alla1,2, MahaNada3, Francois Cousserans1, and Max Bergoin1
.../div>
ssRNA linear genome and analysis of capsids showed two major proteins of 31 and 32 kDa
and a minor 78 kDa protein. Infection of third instar nymphs by feeding on contaminated food
induced similar disease symptoms and bioassay experiment confirmed virus concentration
response mortality. Injection of a purified virus suspension to third instar larvae of Galleria
melonella and Spodopteralittoralis failed...
Sahar Abd El Rahman1; Mohamed Eladl2 and Mohamed M. El-Diasty3
... characterization of its genome. Infection by the bovine ephemeral fever virus (BEFV) was noticed in Dakahlyia governorates during the summer season of 2015. Twelve samples of buffy coats were collected from dairy farms suspected from clinical investigations to be infected by bovine ephemeral fever virus. The virus was isolated intracerebrally in suckling mice then successfully identified by indirect immunofluorescence technique in the brain sections of positi...
Sahar A. Youssef1; Manal A. El-Shazly1,2; Azza G.Farag1,3; Eman A. Khattab1,2
...s to be portion of PNRSV genome. These results indicate that the virus in rose is an isolate of PNRSV from Taif, KSA....
Hadeer M. Mossa, Ausama A. Yousif, Emad A. Aboelsoud, Mahmoud El Gamal, Ahmed El-
Sanousi
...ved areas all over their genomes
remain to be addressed to fully exploit the potential of the nanopore technology, together with some
other conventional testing before judging the sample.
...
Yongmin Li1,2, Huabin Zhang1, Xiaoyou Wu1, Dongwei Li 2, Peng Yan1 and Xiaobing Wu1*
...plete mitochondrial (mt) genome of Rhacophorus dennysi (family Rhacophoridae). The R. dennysi mitogenome (18,052 bp) contained the 37 genes and a single control region (CR) typically found in neobatrachian mtDNAs. In the new mt genome, the ND5 gene and a TLPF tRNA cluster (tRNAThr, tRNALeu(CUN), tRNAPro and tRNAPhe) we...
Guan-bao Ning1, Sheng Niu1, Yue-jian Li1,2, Xiao-xiao Lu1,3, Shi-xiong Yang1, Ali-Raza Jahejo1, Ding Zhang1, Wei-fang Hao4, Wen-wei Gao1, Yu-jun Zhao1, Jian-hui Li1, Fang Yan1, Rong-kun Gao1, Yu-hai Bi1,5, Wen-xia Tian1* and Ling-xia Han6*
...ed against the reference genome (Gallusgallus 5.0). A significant differential pattern of the immune response of chicken erythrocytes was identified by the GO and KEGG databases between the two phases of MDV infection. The results indicated that cytokine-cytokine receptor interaction, toll-like receptor signaling pathway, mitogen-activated protein kinases (MAPK) signaling pathway, Janus kinase/signal transducers and activators of transcription (JAK-STAT) signa...
Jie Gao1, Guannan Wang1, Chuang Zhou1, Megan Price2, Jinnan Ma1, Xiaohong Sun1, Benping Chen3, Xiuyue Zhang2 and Bisong Yue1*
...e complete mitochondrial genome of F. cinereiceps is lacking although there has been considerable phylogenetic research on babblers. Therefore, we aimed to determine F. cinereiceps’ mitogenome and investigate its phylogenetic relationships within the babblers and superfamily Sylvioidea. F. cinereiceps’ mitogenome is typically circular, 16,969 bp in size wit...
Chaochao Hu1,2, Xue Xu1, Wenjia Yao1, Wei Liu3, Deyun Tai1, Wan Chen4 and Qing Chang1*
...termine the complete mitogenome sequence of H. ostralegus, and illustrating mitogenomes structure and investigating their evolutionary relationship by comparing 31 species in Charadriiformes.The complete mitochondrial genome of H. ostralegus is a circular molecule of 16,798 bp in length and the overall nucleotide composition of H-strand was A: 31.45%, T: 23.46%, C: 31.30%, G:...
Iqra Mobeen1*, Rabia Arif1*,Maimoona Ilyas1, Siu Fai Lee2 and Muhammad Saleem1
...r 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 RKM1 gene and nine in RKM4 gene were identified. A subset of SNPs were unique in SFS strains and other...
Rehman Shahzad1, Saba Irshad1* and Faisal Amin2
...surveillance of evolving genome of H9N2 virus prevailing in the country to combat the future challenges of avian influenza out breaks in Pakistan....
Mustafa Ozan Atasoy
...he manipulation of viral genomes, thereby gaining a better understanding of the molecular insights of viral diseases. These have spurred the development of safer and efficient vector vaccines, which convey immunogenic genes of interest obtained from vitally important diseases. Herpesvirus of turkeys (HVT) has long been considered a versatile tool owing to its non-pathogenic characteristic, relatively higher transgenic capacity, and enabling the DIVA strategy. ...
Lin Huang1, Ling Mai2, Keyan Zhong1 and Xinjun Chen3*
... basis, SeFABP was whole-genome synthesized and cloned into prokaryotic expression vector. The recombinant plasmid pET-30a(+)-SeFABP was constructed, then transformed into E. coli BL21 (DE3) and induced by IPTG. The purified SeFABP was obtained by Ni-IDA resins affinity chromatography, and were finally confirmed by SDS-PAGE and Western blot. The results showed that SeFABP, a stable intracellular protein without signal peptide and transmembrane region, was comp...
Alexander Tsybulsky1*, Tatyana Tabakaeva1, Anna Klimovich2, Michail Shchelkanov1, Eduard Kostetsky1, Maksim Aliev1, Anton Degtyarenko3
...r guard factors for cell genome integrity evaluation (p53, etc.). Methods. In domestic cats with a previously established diagnosis of «FeLV-infection and chronic leukaemia» (n = 10) and healthy control cats (n = 6), we examined the following: 1) Haematological parameters of the blood; 2) Biochemical blood indicators of the physiological characteristics of the kidneys and liver, whose disorders are most critical in the progression of the leukaemic ...
Zhang Dong-jie1, He Xin-miao1,2, Wang Wen-tao1,2 and Liu Di1,2*
...In this study, the whole genomes of ten Min pigs and four Northeast wild boars were sequenced and the analysis yielded 8,988,338 non-redundant SNPs plus 1,231,680 InDels. A phylogenetic tree was constructed and a principal component analysis (PCA) was performed based on previously published SNP data from 66 individual pigs. Both analyses indicated the Min pig fell between the European and Asian pigs, while the Northeast wild boar was closely related to the Asi...
Sana Khalid1,2*, Muhammad Zia-ur-Rehman2,3, Usman Hameed2,4, Shabnum Shaheen1, Muhammad Naveed Shahid5, Khajista Jabeen1, Farah Khan1, Muhammad Saleem Haider1
... CP gene and full length genome of viruses for authentication of results. So, it has been confirmed that whiteflies were not responsible for transmission of CpCDV and MCV from diseased to healthy plants....
Hua Liu, Wei Hou, Li Peng, Changjun Peng, Yansen Cai and Jing Li*
...cies. 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 structure of three populations of M. thibetana were estimated. Our results showed the novel SNP loci were polymorphic and bi-allelic. The observed and expected heterozygosity across 38 individuals varied from 0.184-0.605 and 0.405-0.506, respectively. The minor al...
Guo-dong Zhao1,2*, He-ying Qian1,2, Yi-ling Zhang1,2, Gang Li1, 2, Jian Tang1, 2 and An-ying Xu1,2*
Muhammad Altaf1* Arshad Mahmood Abbasi2, Muhammad Shoaib Amjad3, Sadia Naseer1 and Muhammad Umair4
...d and RNA virus, largest genome among all RNA viruses and has 4 proteins i.e. envelope, spike, nucleocapsid and membrane. Coronaviruses are classified into 4 genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. Betacoronavirus most probably originated from bats and the virus may have jumped to avian species and evolved as Deltacoronavirus group. The avian coronaviruses jumped among other avian species, giving rise to Gammacoronavir...
Ghassan Zahid1, 2*, Sara Iftikhar3, Muhammad Umer Farooq4 and Shakeel Ahmed Soomro5
...at specific loci and the genome level. This review focuses on exploring the application, recent advancements and future implications of DNA-based molecular markers with the context of their role in the genetic improvement of fruit germplasm that is widely grown in Pakistan like citrus, apples, mangoes, guavas, bananas, date palms and peaches, etc. Furthermore, by offering a piece of scientific information and addressing developments, notably in DNA-based molec...
Mostafa El-Sebelgy1*, Hanafy Madbouly2, Sabry Tamam2, Nagwa Ata1, Kawther Zaher1
... AHSV and EEV within BTV genome.
Keywords | African Horse Sickness Virus, Equine Encephalosis Virus, shotgun proteomics, Bluetongue Virus, Egypt.
...
Omnia Mohamed Khattab1*, Hala Kamel Abdelmegeed2, Mohamed Mahmoud Mashaly1, Mervat Hamdy1*, Naglaa Hagag1, Ayman Hamed3, Hanan Aly Fahmy3, Essam Ibrahim4, Momtaz Abdelhady Shahein2, Elsayyad Mohamed Ahmed2
...cal investigation. Whole-genome sequencing is required to address any genetic recombination in EHV-4 associated with abortion cases.
Keywords | EHV-4, Equine, rt-PCR, n-PCR, Sequencing, Phylogenetic analysis, Outbreak
...
Alexander Tsybulsky1*, Eduard Kostetsky1, Anton Degtyarenko2, Michail Shchelkanov1,2,3
...e health of the cellular genome. Evaluation of the expression levels of this spectrum of genes, especially the gadd45g and ifnλ1 genes, may be useful as an additional criterion for the differential diagnosis of benign and malignant breast diseases in cats.
Keywords | Breast cancer, Mastopathy, Interferon genes, Tumour-suppressor genes, Expression
...
Ali Wahdan1*, Mahmoud Ezzat1, Fatma Youssef2, Manal Munier2, Elsayyad M. Ahmed3, Marwa Abo Hashem1
...ere sequenced with other genome sequences retrieved from the GenBank. Ten samples (9.17%) were S. aureus from human, while 3 samples (1.24%) were S. aureus and 2 samples (0.83%) were coagulase negative staphylococcus (CONS) from animal sources. The multiple sequences alignments (MSA) and phylogenetic tracking proved the genetic similarity among A9, A12 and A13 from (human, animal, food of animal origin respectively) reached to 94 %. In conclusion, although the...
Muhammad Ikram Ullah
...enomic DNA extraction. A genome-wide scan was carried out on four affected members to establish homozygosity linkage. The analysis for genotype assessment was carried out, and three homozygous regions were identified. Whole exome sequencing was carried out to identify the mutation in putative gene/s. The data was arranged, and MAN2B1 was selected for the DNA sequencing. Protein homology was analyzed by the pymol tool to predict the effect on the mutant protein...
Othman E. Othman1*, Lingjiang Min2, Amira M. Nowier3
...le using WGBS. The whole genome DNA was extracted from ovaries of Zaraibi goats belonging to two different fertility groups: high (HFG) and low (LFG) fertility groups. The extracted DNA was subjected to WGS after treatment with bisulfite. The findings declared that a small difference in the DNA methylation levels is present among high and low fertility groups. The methylated C frequencies in contexts: CG, CHG and CHH were 89.89%, 2.39%, 7.72% and 90.19, 2.34%,...
Muhammad Tariq Navid1,2*, Mian Muhammad Awais2*, Muhammad Irfan Anwar2 and Masood Akhtar2
...ectly to detect AI viral genome through RT-PCR while other segment was used for viral inoculation into the embryonated chicken eggs. The direct detection through RT-PCR confirmed H9 gene from cloacal swab samples in 6.9% of the seropositive sample while we could not confirm any of the oro-pharyngeal samples for H9 gene through direct molecular detection. The cultivated oro-pharyngeal and cloacal swab samples were not found positive upon re-confirmation from al...
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*
...ulty in breathiness. Its genome sequence homology study 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 a...
Xiao Zhang1, Guoqing Shen1, Yang Wang1, Pengdan Huang1,2, Yan Shui2, Zenghong Xu2 and Huaishun Shen1, 2*
...ighly polymorphic in the genome. However, the microsatellite markers available for the red swamp crayfish Procambarus clarkii are limited. In this study, a sizeable number of microsatellites were identified using the data of the P. clarkii genome survey generated from Illumina Hi-Seq PE sequencing. A total length of 1,625 Mb genomic sequences of P. clarkii were assembled based on 124 Gb raw sequencing data. Based on a Kmer a...
Saleh Aljubran, Shaker Al-Suwaiegh, Yousef Alyousef, Sulaiman Alhajri, Mohammed Alghareeb, Abd El-Nasser Ahmed Mohammed*
...m cells and embryos, and genome resource banking for mammalian species. Such biotechnologies allow more offspring to be obtained from selected parents to increase milk and meat productivity, reduce the interval between generations, therapy of diseases and conservation of endangered mammalian species. Practically, current reproductive biotechnologies are species-specific because of differences in estrous cycle, seasonality, structural anatomy, gamete physiology...
Aqleem Abbas1, Mustansar Mubeen2, Yasir Iftikhar2, Qaiser Shakeel3*, Hafiz M. Imran Arshad4, Maria del Carmen Zuñiga Romano5 and Sarfaraz Hussain6
...ers, gene silencing, and genome editing are also summarized. Finally, the expression of resistant-related genes in rice crops and biological agent mechanisms of action are discussed....
Muhammad Afzal1,3*, Shafqat Saeed1, Hasan Riaz1, Muhammad Ishtiaq1, M. Habib ur Rahman2
...cultivars and editing of genome are some of the good practices contributing to suppress this disease. The study is helpful in understanding population dynamics of whitefly cryptic species interaction with the begomoviruses and alternative host plants which is imperative to devise effective management strategies for CLCuD and its vector whitefly....
Syeda Fakhra Waheed1, Asim Aslam1*, Muti-ur-Rehman Khan1, Kamran Ashraf2 and Beenish Zahid3
Zhe Lin1, Yumo Li1, Yuchen Wang1, Yuechen Li1, Ke Pei1, Guangfu Lv2, He Lin1* and Zhun Yu3*
Omnia M. Khattab1, Morcos I. Yanni2, Hala K. Abdelmegeed2, Mahmoud Eliwa1, Naglaa M. Hagag1, Sara M. Elnomrosy1
...red to the published FPV genome, which could imply that FPV appears to be in genomic stasis as compared to other Parvoviruses. Genomic stasis appears among the three Egyptian samples in this study under the GenBank accession number OP594200, OP574201, and OP574202, in addition to the high similarity of the isolates the vaccine strains of EU498680 and EU498681.No amino acid substitution was detected.
Keywords | Feline Pan-leucopen...
A.Y. Ahmad1, M. A. Amer2, T. A. Mostafa1, F. M. Abo El-Abbas1, and M. El-Hammady1
...and PI gene from the PVY genome. PCR products yielded by one primers pair reached 835 bp. while reached about 1 kb (974, 926 bp) by the other primers. Partial sequencing or fragment 835 bp was performed. Comparing with standard PVY strains showed highest similarity with PVY NTN -H followed by PVY NTN-Tu660, PVYN-Jg. PVY Wi and PVYN-Fre in rate of 98.8, 90.0, 89.9, 83.9, and 70.1 % respectively using DNASTAR software....
Sahar. A. Shoman1 and B. A. Othman2
...3836 bp of the whole TMV genome. The intensity of these RT-PCR amplified products was estimated, and it indicated relatively to the amount of the virus in the infected plant, The specificity of amplification was verified using internal primers through nested—PCR (n-PCR) to demonstrate the specificity of this technique. the n-PCR-expected product (869bp) was sequenced, and this nucleotide sequence was analyzed using a software program. Sequence analysis o...
Asmaa A. M. Abdel-Ghany1, Ahmed N. El Taweel2, Yassmin Moatasim2, Nagwa S. Ata1, Amany Adel3, Ayman Hany El-Deeb4, Ahmed Kandeil2, Mohamed A. Ali2*, Hussein Ali Hussein4*
...e were subjected to full genome sequencing and genetic analysis. Although both of H5N8 viruses were closely related to clade 2.3.4.4b, they were genetically distinct and had genetically different constellation forms. This study highlights the need of active surveillance of AIVs in backyard production sector for assessing the epidemiology, evolution, and diversity of currently circulating viruses in Egypt.
...
...
Mati Ullah1*, Muhammad Rizwan2, Ali Raza3, Xianlin Zhao4, Yanling Sun4, Sarah Gul5, Muhammad Ihtesham Waheed6, Muhammad Nadeem Khan7, Alvina Gul8, Sami Ullah Jan9* and Chao Huang4*
...mparatively analysed the genomes of three strains (Lactobacillus rhamnosus ATCC 53103, Lactobacillus casei L9, and Lactobacillus paracasei W56) of LCG isolated from traditional yogurt samples using the next-generation sequencing approach. The GC contents of the characterized strains were in the range of 46.03 to 46.52% while the protein-coding sequences (CDS) were in the range of 2544 to 2888. The pan-genome analysis of the ...
Umer Farooq1,2, Nimra Murtaza2, Abubakar Siddique1, Bilal Saleem1, Obaid Ur Rehman1, Nageen Zahra1, Muhammad Uzair1, Muhammad Naeem Riaz1,3* and Muhammad Ramzan Khan1*
...ic disease. We performed genome wide reference-based sequence alignment and functional annotation to identify deleterious non-synonymous SNPs (nsSNPs) in cattle breeds of Pakistan. For this purpose, genomic data of four different purpose cattle breeds including Bhagnari, Cholistani, Sahiwal and Red Sindhi was analyzed. Comparison with taurine reference genome ARS-UCD.1.2.99 discovered 29,032,662 genomic variations of which 2...
Jie Wang1, Di Fang1, Jianqing Zhao1, Fei Huang2, Bo Liu2, Weikun Tao2, Baoshan Cui2 and Qinghua Gao1,2,3*
...pared with the reference genome by TopHat software, the net reading ratio of the bovine reference gene at each stage was 93.17-9 4.23%, the ratio of sequence numbers to multiple sites of the genome was 2.99-4.89. The DEG was identified by using the fold change ≥2 and FDR <0.01 as cut-off values. There were 525 differentially expressed genes. GO and KEGG analysis showed that “cell part”, “organelle&rdq...
Amthal Ahmed Fouad1, Basem Mohamed Ahmed2, Momtaz Abdelhady Shahein1, Hussein Aly Hussein2*
...ic data -including whole genomes- from Egypt are clustered within a unique lineage (Africa-4 lineage of the cosmopolitan clade), no report provided detailed description of this lineage genome and the last published whole genome dates back to 2009. In this context, a complete RABV genome (5EG-QH19) was obtained from a stray dog, analyzed, and compared to ...
Lichun Jiang1,2*, Lan Zhu1, Meiqi Li1, Xinyue Bao1, Zhenkun Zhao2, Haifen Qin2 and Wei Chen3*
...uclear and mitochondrial genomes and their phylogenetic position within the family Cervidae. In this study, we have determined the complete sequence of the mitochondrial genome of the tufted deer, by using a long polymerase chain reaction (PCR) technique. The entire mtDNA sequence is 16,196 bp in length, which compared with previous studies is the least, containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfe...
Sri Rahayu*, Muhaimin Rifa’i and Widodo
Peng Chen1, Jiaqi Li1, Hongbo Li2, Qin Lu3, Wei Liu1,4,5* and Jianliang Zhang1*
...ategy. The mitochondrial genome (mitogenome) of Mergus serrator was 16,627 bp in length, and its structure was circular. The structure and gene arrangement of the genome were basically the same as those of Anseriformes species. The mean base composition of the mitogenome of Anseriformes was T (22.31 ± 0.51%), C (32.63 ± 0.64%), A (29.36 &pl...
Asifa Majeed*, Amir Rashid, Palvasha Waheed, Asma Faryal, Aden Razaq and Ayesha Maryam
...h Tool against the human genome database to find any genetic variation. It has been found that ABCG1 gene and APOA1 gene exhibited 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....
The Complete Mitogenome of the Lophius litulon (Lophioidei: Lophiidae) and Phylogenetic Implications
Lu Liu1, Xiang Zhao2, Yue Qin2, Tianxiang Gao3 and Tianyan Yang3*
...e complete mitochondrial genome of Lophius litulon was sequenced and assembled by next-generation sequencing techniques. The complete mitochondrial genome of Lophius litulon contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. The total length of the mitochondrial genome of L. litulon was 16,430 bp, and the overall base composit...
Qi Jiayi1, Huang XuMiao2, Lin Wei3, Ao YaHui3, Zhao Wenting2* and Cao Chunhao3*
Hafiz Nawaz1*, Kashaf Nawaz2, Attiq ur Rehman1, Muhammad Bashir3, Mussera Hira2 and Mariyam Nawaz4
...e up its single-stranded genome. The virus’s virulence and symptoms need both components. The sequencing of both components showed considerable variation between old-world and new-world viruses. Cultural practices, insecticides, and virus-resistant mungbean cultivars may help suppress the disease. MYMD-resistant NIAB mungbean lines include 1429, 3198, 3845, 3850, 3854, and 3881 (Schreinemachers et al., 2019). A recent study has revealed resistant varieti...
Shudong Liu1,2, Shuai Wang1,2, Haoran Cui1 and Genyuan Chen1,2*
...lation, 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 phenol-chloroform method. The DNA was genotyped using the Illumina Ovine SNP50 Bead Chip. After quality control, we detected 4,8335 SNPs, which included four SNPs that are significantly associated with the ACMS of sheep. We ide...
Omaima Khamiss
...height:107%">Baculovirus genomes from different virus species generally exhibit a considerable degree of structural diversity. However, some sequenced baculovirus genomes from closely related viruses are structurally very similar 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 th...
Soliman*, Ahmed M.; Mahmoud**, Sabry Y. M. and Dawood*, Rehab A.
... fragment from the viral genome using RT-PCR from infected garlic plants, such fragnent were not obtained from healthylooking plants and/or virus-free seedlings of shoot-tips. The amplified products of OYDV was cloned into pGEM@-T Easy vector, and transformed into Escherichia coli (E. coli) strain DH5a. The recombinant plasmids were obtained and sequenced. The nucleotide sequences were compared with corresponding viral nucleotide sequences reported in GenBank....
El-Sayed • l , Eman H; Mahfouze , Sherin A.; Shaltout ,A. D.; El-Dougdoug3 ,Kh. A. and Sayed1 , R. A.
... create mutations in the genome of plants. Selection of plant mutants is based on morphological and ISSR-PCR markers. The DNA based marker is reliable and reproducible for mutant selection for BBTV and BMV resistance banana plants used in the study. Explants from shoot apical meristem were cultured on MS-medium supplemented with different concentrations of 2, 4-D (2, 4 and 6 mg/l) 6-Benzylaminopurine (6, 7 and 8 mg/l), and Sodium Aide ranging from (1, 2 and 3 ...
El-Tabakh, SAA l ; Abdel Wahab, KSE; Badr, AF and Helal, IG
...f infection (MOL) of one genome copy per 103 cells. Stock HepG2 cell cultures were grown in Dulbecco modified minimum essential medium (DMMM) as growth medium with 10% fetal calf serum and antibiotic mixture (IOOU penicillin and 100 mgm streptomycin/ml) and subcultured at 3-4 days. HepG2 cells were maintained throughout the experiment in Ham F-12 medium maintenance medium with 2% fetal calf serum; 1000 IU penicillin and 1000 mgm streptomycin antibiotic mixture...
*Amal Abou El-Ela A., M. A. Amer and Eman A. H. Khatab,
...conserved regions in the genome of potyviruses was designed to amplify a 335 bp cDNA fragment from infected plant 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 usin...
M.R. Abd-El Wahab l, H.A. Hussein2, T.M. Asfourl and M.A. Shalaby2
...ranslated region of BVDV genome to detect BVDV RNA in some buffy coat samples, collected from the cohoused camels in the area where dead camels were found (BVDV-positive). revealed positive results. However. genotyping of such positive samples using RT-PCR genotyping based assay revealed negative for the presence of BVDV type I, II, and border disease virus. After 3 passages of the detected positive buffy coats on MDBK cells. no CPE was detected suggesting tha...
Yongtao Xu1, Dandan Wang1, Xiaolong Hu1, Minling Li1, Ming Tang1, Wuhua Liu2, Jianwen Zhan2 and Weiwei Zhang1*
...gions of the chloroplast genome from 30 fecal samples of Taohongling sika deer were amplified with universal primers and sequenced by high-throughput. We found that 28 out of 30 valid samples had a total of 677,856 valid amplified sequences with an average valid sequence of 24,209.14±323.83. A total of 326 OTUs were obtained from 28 valid samples, and the MP, SS, and NJS groups shared 222 OTUs, accounting for 68.09% of the total OTUs. OTUs alignment ind...
Zhenglei Qiao*, Jie Xing and Fang Li
... the whole mitochondrial genome sequence of Pethia stoliczkana was obtained using high-throughput sequencing technology, and its structure and characteristics were analyzed. The P. stoliczkana mitochondrial genome contained a total of 16,966 base pairs, including 13 protein-coding genes, 22 transport RNA genes, two ribosomal RNA genes, and one control region. The A+T content (59.7%) of the whole mitochondrial
Zhenkun Zhao1,2, Ziniu Alimo2, Xinyue Zhao2, Haifen Qin1, Buddhi Dayananda3, Lichun Jiang1,2* and Wei Chen4*
... justify;">Mitochondrial genome is a very useful marker for determining the phylogenetic relationships. Hence in this study, the complete mitochondrial genome of Turdus merula was sequenced, described, and analyzed with Sanger sequencing technology. The complete mitochondrial genome of T. merula was 16,734 bp in length and encoded 37 genes, including 13 protein-coding genes, 22 tRNAs, 2 rR...
Yuping Liu, Sige Wang and Tianyan Yang*
...e complete mitochondrial genome (16607 bp) of A.cernua was sequenced by high-throughput sequencing technology, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, a control region (CR) and a L-strand replication origin (OL), and its gene composition and order were similar to those of most teleosts. The A + T content of the whole mtDNA was 55.39 %, suggesting an obvious anti-G bias (16.64 %). The positive AT-skew (0.01) and negative GC-skew (...
Abdul Rahman Sesay1,2, Muhammad Saif-ur-Rehman1*, Faisal Ramzan1 and Faisal Saeed Awan3
...ations at the individual genome level. The study aimed to discover and analyze potential indicators of recent selection in Sahiwal cattle, specifically identifying the genes and quantitative trait loci associated with these selection indicators. The study utilized a sample size of 98 Sahiwal bulls. The genotyping of all animals was conducted using the BovineHD140k BeadChip. After undergoing quality control measures, 87 samples as well as 74,070 SNPs located th...
Yasameen Waleed Al-Abedi1, Murtadha Kadhim Hasan2*, Alaa Abdalhadi Halboti3, Ali Abdulhussein Saleh Alsaeedi3, Rafed Abbas Kadhum1
...align: justify;">Precise genome editing, which is the foundation of modern biotechnology, is uniquely capable of introducing highly specified genetic modifications into DNA with a high level of accuracy. This study is tailored to demonstrating applicability of antiviral system (Clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins (CRISPR-Cas) for carrying out site-specific epigenetic alterations and so uncovering th...
Pavana Jyothi Vanjavaka1, Mouradam Veerasami2, Mohana Subramanian Bhaskaran2*, Vijay A.K.B. Gundi1*
...quence variations in the genomes.
Keywords | Canine parvovirus, Hemorrhagic enteritis, VP2 gene, Maternal antibodies, CPV variants, Immunisation
...
Mati Ullah1*, Muhammad Rizwan2, Ali Raza3, Xianlin Zhao4, Yanling Sun4, Sarah Gul5, Muhammad Ihtesham Waheed6, Muhammad Nadeem Khan7, Alvina Gul8, Sami Ullah Jan9* and Chao Huang4*
...rehensively analyzed the genome of Lactobacillus delbrueckii subsp. bulgaricus NDO2 isolated from traditional yogurt samples using the next-generation sequencing approach. The GC contents of the selected genome were 45.3%. Among the total 2284 genes identified, 970 genes similar in three genomes make the core genome portion. The subsystems, category dist...
Yujun Shuai and Jinhong Zhao*
...sis of the mitochondrial genome of Anisakis simplex, the results revealed a full-length genome with 13,903 bp, including 12 protein-coding genes, 2 rRNAs and 22 tRNAs. There was no encoding gene of atp8, which was consistent with the genome characteristics of Anisakis nematodes. Additionally, 25 related nematodes belonged to 5 different families served as study subjects for the constructio...
Xiaoping Gao1, Yanping Li2*, Renyi Zhang3, Yunyun Lv2, Yongming Wang2, Jinrong Shi2, Jiang Xie2, Chiping Kong1 and Lekang Li1
...ermined the complete mitogenome of S. cyphotergous using an Illumina Hiseq X Ten sequencer. This mitogenome’s structure is typical circular with 16,611 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The overall base composition of S. cyphotergous is 31.33% A, 25.89% T, 26.49% C, and 16.29% G with a slight AT bias of 57.22%. Most mitochondrial gen...
Haifen Qin1,2, Yujia Liu1, Yujie Zhang1, Jingfeng Liu1, Zhenkun Zhao1,2 and Lichun Jiang1,2*
... justify;">Mitochondrial genomes are important markers using to reconstruct phylogenetic status and reveal insect molecular evolution. In this study, the mitochondrial genome (mitogenome) of Anoplophora horsfieldi (Coleoptera: Chrysomelidae) was determined using high-throughput sequencing. The size of circular mitogenome is 15,796 bp and it includes a ty...
Ye-Ling Lao, Jin-Long Huang, Cheng-He Sun, Xiao-Ying Huang, Ting Wu and Qun Zhang*
...n complete mitochondrial genome determination, researchers have published the mitogenomes of many New World cichlids. However, few phylogenetic analyses of New World cichlids have been conducted. In this study, we determined the complete mitogenome of Mikrogeophagus altispinosus. After sequencing with the Illumina HiSeq 4000 platform, SPAdes v3.10.1 was used for assembly, and MITOS2 and Mi...
Shibao Guo1, Junhua Chen1, Nan Song2, Fangmei Zhang1*
...e complete mitochondrial genome of Sphaeniscus atilius was characterized and annotated in this study. The mitogenome was 16,854 bp in length and encoded 37 typical mitochondrial genes, including 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control regions. The total length of the 13 PCGs was 11,140 bp, and the AT content was 79.8%. There were five types of start codons, ATT (nad2, nad3, nad5, and nad6...
Pakistan Journal of Zoology
October
Featuring
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Molecular Detection and Genetic Characterization of Peste des Petits Ruminant Virus in Punjab, Pakistan
Javeria, Mudasser Habib and Muhammad Salahuddin Shah
Pakistan J. Zool., Vol. 56, Iss. 6, pp. 2997-3000
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TGF-β Mediates the Role of P53 and microRNA-Related Signaling Pathways in the Pathogenesis of Diabetic Nephropathy in Rats
Yonghong Ma, Jinlan Ma, Qifu Zhang, Huajie Zou and Shenghua Ma
Pakistan J. Zool., Vol. 56, Iss. 6, pp. 2993-2996
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Latrine Site Selection by the Asian Badger (Meles leucurus) in a Temperate Forest of South Korea
Ho-Kyoung Bae, Jae-Kang Lee, Tae-Kyung Eom, Dong-Ho Lee, Hyeongyu Ko, Joo-Hee Kim, Sung-Hyun Ahn and Shin-Jae Rhim
Pakistan J. Zool., Vol. 56, Iss. 6, pp. 2989-2992
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Growth Performance of Labeo rohita Fingerlings Fed with Lactobacillus rhamnosus Supplemented Canola Meal and Corn Gluten-Based Feeds
Sadaf Aman, Yung Fu Chang, Javed Iqbal Qazi, Rahman Ullah and Farah Aman
Pakistan J. Zool., Vol. 56, Iss. 6, pp. 2985-2988
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