Ayesha Zahid,Ammara Muazzam, Sidra Mustafa, Saba Irshad*,Malik Siddique Mahmood and Rehman Shahzad
...otein was anticipated by bioinformatics tools, which manifest mild changes in overall charge but altered post translational modifications in a way which might have a deleterious effect on ion channels anatomy and on the whole, pave ways to the genesis of cataract.
...
Yijin He1, Song Ma2, Bo Liu1,*, Ting Xue1, Qunlan Zhou1, Wu Jin1 and Kui Chen2,*
...sues 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 with T. rubripes, there was 99.2% identity in two kinds ORF sequences, with only 7 bases different, and there were 5 amino acids different between speculated fusion proteins. Under bioinformatics analysis, the T2R1 gene without int...
Ghulam Abbas1,Asif Nadeem1,*, Masroor Ellahi Babar2, Tanveer Hussain2, Muhammad Sajid Tahir3, Wasim Shehzad1, Rajput Zahid Iqbal3, Muhammad Tayyab1 and Maryam Javed1
Pei-feng Yin1,2,Xiu-xiu Li1,Qi-wei Zeng3, Cheng-chen Shen1, Le Gao1 andJian-zhang Ton2,*
...y (MALDI-TOF-TOF MS) and bioinformatics technique were used for characterize the differential expressed proteins. Almost 78 patho-stress responsive proteins which expression level more than 1.5-fold were identified, where 50 proteins were up-regulated and 28 proteins were down-regulated; The identified proteins were categorized into 16 classes, which are mainly including energy metabolism, gene expression regulation, oxidation-reduction reaction, cellular comp...
Bin Wang1, 2, Qianji Ning1,*, Qian Wang2, Wei Peng2, Tong Hao2,*and Jinsheng Sun2,*
.... sinensis using the bioinformatics analysis method, which accounts for 91.9% of all un-localized proteins in the network. Subsequently, the molting interaction network was extracted from the global PPI, which contains 35 proteins and 32 interactions. By analyzing the subcellular annotation of the molting interaction network, the subcellular localization of 12 proteins was obtained. Half of these proteins located on the cell membrane, indicating the close ...
Guifen Liu1,2, Xiaomu Liu1,2, Khuram Shahzad3, Wei You1,2, Juan J. Loor3,* and Fachun Wan1,2,4,*
...ic impact approach (DIA) bioinformatics tool was used to uncover the most-affected biological pathways among the DEG. Ingenuity pathway analysis (IPA) software also was used to analyze upstream transcription regulators and gene networks. Bioinformatics analysis results indicated that 18 months being a key age for alterations in metabolism. The results of IPA analysis revealed that several transcription regulators related to ...
Fizza Anwar1, Muddassar Zafar1*, Zahid Anwar1, Raja Tahir Mehmood2
... were determined through bioinformatics tools.
...
Shahid Sherzada1,2,4,*, Muhammad Naeem Khan4, Masroor Ellahi Babar2, Muhammad Idrees3, Abdul Wajid2, Muhammad Nauman Sharif3, Muhammad Shahzad Iqbal3, Iram Amin3 and Muhammad Shahid3
... were evaluated by using bioinformatics tools. The average K2P conspecific, congenric and confamilial genetic distances were 0.22%, 6.71% and 12.33%, respectively. Findings of the present study revealed that DNA barcoding using COI gene is an efficient molecular technique for the exact identification of typical fish species.
...
Honghua Wang1,2, Summia Perveen1,2, Shucheng Shao1,2, Kun Wang1,2 and Fei Yin1,2,*
...were categorised using a bioinformatics approach. The results showed that 3,472 proteins were identified with a theoretical molecular weight of 11.53–610.90 kDa and an isoelectric point of 4.13–11.77. A total of 63.07% or 50.09% proteins were annotated by Kyoto Encyclopaedia of Genes and Genomes (KEGG) or Gene Ontology (GO) terms, respectively. These results highlight that mass material is transported and catabolised and growth- and death-related p...
Tong Feng, Zilu Zhang, Minghao Qu, Chan Luo, Laiba Shafique, Qingyou Liu and Kuiqing Cui*
...d analyzed by systematic bioinformatics. The result showed that the coding region of the MC1R gene of Nubian goat was 954 bp in length and encoded 317 amino acids. The results of multiple sequence comparison showed that the clones were 99%, 87%, 86%, 85%, 84%, 81%, and 77% similar to the published pig, cow, human, dog, sheep, mouse, and chicken, respectively. It showed that MC1R gene had a high conserved type among different species. The goat MC1R protein has ...
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
...h of further targets via bioinformatics tools help to predict gene target site. Keeping this in view, a study has been planned to investigate PDCD1 gene regulatory miRNA targets, their sequences and their seed location in human using online server miRDB. We have identified 26 specific miRNAs (hsa-miR-939-3p, hsa-miR-661, hsa-miR-2861, hsa-miR-23b-5p, hsa-miR-23a-5p, hsa-m...
Hui-Ying Chen1,2*, Ping-Chuan Yin1,2, Ya-Nan Lu1,2, Hai-Yun Li1,2*and Yang Shan3
Ming-Yan Shi2, Xu-Liang Yan1, Ping-Ping Han1, Yu-Jie Tang1 and Hui-Xia Li1*
...out using microarray and bioinformatics. The data revealed significant changes (>2-fold) in 29 out of 783 differentially expressed miRNAs, 12 of which were up-regulated and 17 were down-regulated. Bioinformatics analysis showed that 24 of these 29 miRNAs were involved in fat metabolism, cell differentiation and the development of the immune system in 315 potential target genes, while 39 target genes were associated with a...
Tai-hua Jin1, An-gang Lou2,Jiu-xiu Ji1, Cheng-dou Cui2, Long-zheng Yu2 andLi-zeng Guan1*
.../i>0.05). The results of bioinformatics analysis and double luciferase reporter gene system validation showed that miR-1468 targeted 3’UTR of cAMP responsive element binding protein 1 (CREB1). miR-1468 mimics could significantly inhibit the CREB1 mRNA and protein level (P<0.01), whereas miR-1468 inhibitor could significantly increase the CREB1 mRNA and protein level (P<0.01). This study demonstrated that miR-1468 ...
Amal Mahmoud1&2 and Medhat H. Hashem3
Hadeer M. Mossa, Ausama A. Yousif, Emad A. Aboelsoud, Mahmoud El Gamal, Ahmed El-
Sanousi
...nologies and
bioinformatics tools to directly represent the genetic content of entire communities of organisms in the
given harvest.
Results: In this study a 3rd generation sequencing (TGS) was applied using a Nanopore technology
(MinION) based on identification of DNA bases by measuring the changes in electrical conductivity
generated as DNA strands pass through a biological pore (nanopore). Its port...
Iram Liaqat1,*, Safdar Ali Mirza2, Sumera Sajjad3, Shaukat Ali1,*, Muhammad Faiz Qamar4 and Ikram Ul Haq5
Yanhong Hu* and Linkai Cui
...f the insect cells and a bioinformatics analysis. The result of immunofluorescence assay showed EpFAR to be localized to the cytoplasmic region, and the observed fluorescence pattern was characteristic of endoplasmic reticulum (ER) proteins. Comparative analysis of the prediction results showed EpFAR was localized to the ER membrane. These results, combined with the localization of other FARs, suggested the importance of ER as a related subcellular site of whi...
Junli Liu1, Tongfang Yang2 and Lisheng Wu3*
Lin Huang1, Ling Mai2, Keyan Zhong1 and Xinjun Chen3*
Pan Ziyi1, Ambreen Iqbal1, Gao Zhen1, Liu Juan1, Fang Xibi2, Jiang Ping1* and Zhao Zhihui1*
... It is predicted through bioinformatics analysis that bta-miR-12059 can bind to 3’UTR of the DHCR24 gene. Our results indicate that single nucleotide polymorphisms might be used as a molecular marker for marker-assisted selection in beef cattle breeding....
Fei Wang1, Xiaofen Hu1, Feng Wen2, Xiaoen Tang3, Shanshan Yang1, Shengwei Zhong1, Zuohong Zhou1, Xu Yuan1 and Yong Li1,*
...on between its molecular bioinformatics characteristics and biological function. After the desired RNA was extracted from the intestine of Wahui pigeons, the complete CDS of vasoactive intestinal peptide was obtained by PCR amplification and sequencing, in addition, a variety of bioinformatics analysis was performed to evaluate its structural characteristics. CDS of vasoactive intestinal peptide, encoding 132 amino acids, is...
Jiangbo Shao1, Donglai Zhu2, Shengqiang Zou1, Guohong Ge1 and Ju Huang1*
...ed through comprehensive bioinformatics analysis. We found that SOX9 mainly participated in heat stress response, protein folding as well as metabolism and biosynthesis of amino acid. SOX9 correlated with HSPA1B were negative to the progression in hepatocellular carcinoma patients. These results suggest that SOX9 participated in hepatocellular carcinoma progression through targeted regulation of HSPA1B that might provide novel insights in hepatocellular carcin...
Man Wang1 and Fengmei Yang2*
...of liver cancer based on bioinformatics analysis. GEPIA, UALCAN, cbioportal and other tools were used to analyze the correlation between TOP2A gene expression and methylation, prognosis and immune cell infiltration in databases. The expressions of TOP2A gene and protein in tumor tissues were higher than those in normal tissues, and the differences were statistically significant (P<0.05); TOP2A gene expression was positively correlated with immune cells infi...
Dong-Min Hou1, Ting Jia2, Hui-Juan Wang1, Zheng-Kun Wang1 and Wan-Long Zhu1*
...ism were screened out by bioinformatics analysis. The results showed that there were significant differences in the expression of 2879 genes in cold acclimation group compared with that of control group, 1181 were up-regulated and 1698 were down-regulated in cold acclimation group. Pathway analyses showed that the differentially expressed genes were significantly enriched in oxidative phosphorylation, steroid biosynthesis, glycerophospholipid and fatty acid me...
Saba Rehman1, Faisal Salih Hayat1, Sadia Norin2, Abdul Aziz1, Siddiq Ur Rahman1* and Noor ul Haq1*
...s been predicted through bioinformatics tools and several databases have been used to identify suitable natural inhibitors. The OMICRON variant was analyzed to identify suitable vaccine candidates by identifying B-Cell epitopes. To design a drug, REPAGLINIDE and ENT-NATEGLINIDE were identified as natural inhibitors based on docking score. To design a vaccine the B-cell epitope i.e., CLIGAEYVNNSYECD was found to the highest antigenicity score. The present study...
Chunlan Shan1, Chaoying Liu1, Qin Lu1, Guowen Fu2, Syed Aftab Hussain Shah3, Rana Waseem Akhtar4, Ru Zhao2, Libo Gao2, Chang Liu2, Shushu Miao2, Hongdan Wang2 and Hong Gao2*
...es, were predicted using bioinformatics tools. These proteins had differences in random curls, α-helix and slight amount of β-sheet. After validation, 10 iron deficient isolates expressed the ferritin HMWPs similar to those of Yersinia. Later on, Kunming mice were infected with E. coli HPI+ and HPI- strains, respectively for the histopathology examination. The higher organ damage was observed by E. coli HPI+ than HPI- strain in mice. This study post...
Jian-Cheng Zhai1,2, Sheng-Nan Wang1,3, Qiang-Hui Wang1, Yan-Ling Xia1, Wei-Shi Liu1, Ya-Jie Yin4 and He-Ping Li1*
..., respectively. Based on bioinformatics analysis, the regions of IGF1 (-50bp ~ +615bp), KGF (-285bp ~ +207bp) and NGF (-388bp ~ +109bp) were selected for studying the methylation status. The antler mesenchyme of male reindeer was the only methylation sample in IGF1 (2.23 ± 0.92%), significantly higher in methylation level than that of female reindeer and sika deer (0.01<P<0.05). Methylation levels of KGF in antler mesenchyme were highly significan...
Wuritunashun*, Burenbatu, Narenqiqige, Jiuguniang, Eerdunduleng, Shuanglian Wang, Cuiqin Gong, Hashengaowa, Huizhi Jin, Baiwurihan and Chunhaizi
Jie Wang1, Di Fang1, Jianqing Zhao1, Fei Huang2, Bo Liu2, Weikun Tao2, Baoshan Cui2 and Qinghua Gao1,2,3*
...l annotation and related bioinformatics analysis. We found that Q30 percentage range of eight samples was 91.79-92.37%. The filtration sequence was 44106250-54234844. Compared 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...
Qingjin Li1,2, Zhiyuan Sui1,2, Jihu Zhang1,2, Zhishuai Zhang1,2 and Feng Xing1,2*
Di Zhou1, Qingmeng Long1*, Rong Yang1, Xiaoshan Tan1, Jun Li1, Mingyan Tang1, Zhonghai Zhao3, Ye Ao2, Zhinan Zhou1 and Changxue Chen1
...alyzed the results using bioinformatics and qRT-PCR. We found 8120 differentially expressed genes (DEGs) in ovarian tissues (3205 up- and 4915 down-regulated), 5255 DEGs in the fallopian tubes (1317 up- and 3888 down-regulated) and 5180 DEGs in uterine tissue (2597 up- and 2583 down-regulated). The biological processes associated with these DEGs were primarily cell differentiation, reproduction and biological regulation. The associated gene functions were rela...
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*
...L to obtain Unigene, and bioinformatics methods were then adopted to perform functional annotation classification, metabolic pathways and SSR feature analysis. The results showed that a total of 42.40 Gb data were obtained from transcriptome sequencing, and 38,817 Unigenes were obtained after assembly and de-redundancy; Using BLAST to annotate the assembled unigenes with seven functional databases (NR, NT, GO, COG, KEGG, Swissprot and Interpro), a total of 23,...
Qiangsheng Wu1, Yumei Yin2, Hui Gao1, Baoding Chen3, Jianjun Yu2, Jian Zhang4, Donglai Zhu5, Fang Liu6, Guohong Ge7 and Ya-Mei Dang8*
...ma were analyzed through bioinformatics analysis. The results showed that the functions of these 1495 differently expressed genes enriched in cell cycle, oxidation-reduction and drug metabolic process. Additionally, the top 10 core genes of these differently expressed genes were mainly participated in cell cycle and strongly correlated with worse prognosis of survival, which may be potential diagnostic and therapeutic targets of HCC....
Irfan Safdar Durrani*, Noreen Asim and Ammar Sohail
...ultivar Dilrosh-97 using bioinformatics approach. The possible cis-acting regulatory elements were analyzed using PlantCARE and PlantPAN3.0. Phylogenetic tree was constructed using MEGA7 and docking of regulatory elements with the corresponding Transcription factors was performed using pyDockDNA. The OsGLP12-3 promoter region (1863bp) was PCR amplified using genomic DNA from Indica rice cultivar Dilrosh-97 and subsequently purified and sequenced. Sequence anal...
Faiza Naeem1, Muhammad Farooq Sabar1, Muhammad Usman Ghani2,*, Qurat Ul Ain1 and Qurat-ul-Ain Zafar1
...athway Connector (http://bioinformatics.cing.ac.cy/PathwayConnector) was used to analyze the pathways associated with genes as well as novel pathways through complimentary network analysis. Protein-protein interaction studies were conducted using String (https://string-db.org/) and genes were ranked on a centrality score basis using Cytoscape (https://cytoscape.org/index.html). IL4, IL13, IL10, IL27, ADAM33, TBXA2R, FCER1β, ORMDL3, IKZF3, LRRC3C, GSDMA, G...
Hualong Jiang1, Tao Li2,3*, Jing Xiang3, Hanqing Yang3 and Maolin He3
...eneration sequencing and bioinformatics analyses were performed to compare changes of microeukaryotic communities in local sediments influenced by sea-crossing bridge construction. Relatively low levels of alpha diversity and high levels of beta diversity were observed in samples influenced by bridge construction (group EG). The decreased abundance of Chloroplastida and increased abundance of Animalia in group EG suggested that engineering activities induced e...
Sofyl *, A.R.; Soliman , A.M.; Mousal, A.A. and El-Dougdoug , Kh.A.
Sijie Jian1,2,3,4, Wei Sun1,3, Jia Chao1,2, Na Rong1,4, Xiang Liu1,2,3,4* and Chen Chen1,2,3,4*
...ns in fish vaccines. Slp bioinformatics analysis showed that anti-Slp serum might provide cross-protection to resist bacterial infection in fish. Slp was obtained by molecular cloning, expression and purification, and the expression conditions were optimized. In mice immunized with Slp, the immune-related factors of LZM and AKP were enhanced (p < 0.05), and a specific antiserum titer (1: 3200) was obtained that had immune recognition effects for A. hydrophi...
Cis-acting regulatory elements and transcription factors as a key regulator in plant gene expression
HIRA MUBEEN1, 2*, AMMARA NASEEM1, AMMARA MASOOD2, SHAHID RAZA3 & NAUREEN NAEEM3
... Furthermore, the use of bioinformatics approach for identification of transcription factors and putative motifs within the promoter region has gained much success for studying DNA-protein interactions. These findings promote the importance of CRE and TF inactivation of transcriptional networks for enhanced gene expression studies in plants....
*SHAJAHAN BAIG1, MUSHTAQ AHMAD SALEEM1, MUHAMMAD AZMAT ULLAH KHAN1 ZEESHAN NADEEM2, SUFIAN AHMED2, MEMUNA GHAFOOR SHAHID3 & TANZEEM AKBAR CHEEMA3
...are needed. Furthermore, bioinformatics studies may be quite useful for the successful application of these profiling methods to analyze the safety of genetically modified (GM) foods. These bioinformatic methods employ the comparison of different linked databases which may cover all the information significant for profiling. These methods are also significant in identifying the changes at various stages of development under diverse environmental conditions.
