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https://www.readbyqxmd.com/read/28346800/using-chemoinformatics-bioinformatics-and-bioassay-to-predict-and-explain-the-antibacterial-activity-of-nonantibiotic-food-and-drug-administration-drugs
#1
Nour Aldin Kahlous, Muhammad Al Mohdi Bawarish, Muhammad Arabi Sarhan, Manfred Küpper, Ali Hasaba, Mazen Rajab
Discovering of new and effective antibiotics is a major issue facing scientists today. Luckily, the development of computer science offers new methods to overcome this issue. In this study, a set of computer software was used to predict the antibacterial activity of nonantibiotic Food and Drug Administration (FDA)-approved drugs, and to explain their action by possible binding to well-known bacterial protein targets, along with testing their antibacterial activity against Gram-positive and Gram-negative bacteria...
March 27, 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28346717/characterization-of-two-novel-antimicrobial-peptides-from-the-cuticular-extracts-of-the-ant-trichomyrmex-criniceps-mayr-hymenoptera-formicidae
#2
Nagachaitanya Bhagavathula, Venkateshwarlu Meedidoddi, Simon Bourque, Reshmy Vimaladevi, Santoshkumar Kesavakurup, Dayanandan Selvadurai, Sameer Shrivastava, Chandrashekara Krishnappa
Antimicrobial peptides (AMPs) from cuticular extracts of worker ants of Trichomyrmex criniceps (Mayr, Hymenoptera: Formicidae) were isolated and evaluated for their antimicrobial activity. Eight peptides ranging in mass from 804.42 to 1541.04 Da were characterized using a combination of analytical and bioinformatics approach. All the eight peptides were novel with no similarity to any of the AMPs archived in the Antimicrobial Peptide Database. Two of the eight novel peptides, the smallest and the largest by mass were named Crinicepsin-1 and Crinicepsin-2 and were chemically synthesized by solid phase peptide synthesis...
March 27, 2017: Archives of Insect Biochemistry and Physiology
https://www.readbyqxmd.com/read/28346370/de-novo-assembly-annotation-and-characterization-of-root-transcriptomes-of-three-caladium-cultivars-with-a-focus-on-necrotrophic-pathogen-resistance-defense-related-genes
#3
Zhe Cao, Zhanao Deng
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346358/genomic-evidence-for-bacterial-determinants-influencing-obesity-development
#4
Raphael D Isokpehi, Shaneka S Simmons, Matilda O Johnson, Marinelle Payton
Obesity is a major global public health problem requiring multifaceted interventional approaches including dietary interventions with probiotic bacteria. High-throughput genome sequencing of microbial communities in the mammalian gastrointestinal system continues to present diverse protein function information to understand the bacterial determinants that influence obesity development. The goal of the research reported in this article was to identify biological processes in probiotic bacteria that could influence the mechanisms for the extraction of energy from diet in the human gastrointestinal system...
March 26, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28346351/in-vitro-and-in-vivo-studies-on-the-structural-organization-of-chs3-from-saccharomyces-cerevisiae
#5
Simon Gohlke, Subbaratnam Muthukrishnan, Hans Merzendorfer
Chitin biosynthesis in yeast is accomplished by three chitin synthases (Chs) termed Chs1, Chs2 and Chs3, of which the latter accounts for most of the chitin deposited within the cell wall. While the overall structures of Chs1 and Chs2 are similar to those of other chitin synthases from fungi and arthropods, Chs3 lacks some of the C-terminal transmembrane helices raising questions regarding its structure and topology. To fill this gap of knowledge, we performed bioinformatic analyses and protease protection assays that revealed significant information about the catalytic domain, the chitin-translocating channel and the interfacial helices in between...
March 25, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28345463/computational-and-mechanistic-studies-on-the-effect-of-galactoxyloglucan-imatinib-nanoconjugate-in-imatinib-resistant-k562-cells
#6
Alphy Rose James, B S Unnikrishnan, R Priya, Manu M Joseph, T K Manojkumar, K Raveendran Pillai, R Shiji, G U Preethi, P Kusumakumary, T T Sreelekha
Imatinib mesylate, a BCR/ABL fusion protein inhibitor, is the first-line treatment against chronic myelogenous leukemia. In spite of its advantageous viewpoints, imatinib still has genuine impediments like undesirable side effects and tumor resistance during chemotherapy. Nanoparticles with sustainable release profile will help in targeted delivery of anticancer drugs while minimizing deleterious side effects and drug resistance. The use of biopolymers like galactoxyloglucan (PST001) for the fabrication of imatinib mesylate nanoparticles could impart its use in overcoming multidrug resistance in chronic myelogenous leukemia patients with minimal side effects...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28345460/coactivator-associated-arginine-methyltransferase-1-promotes-cell-growth-and-is-targeted-by-microrna-195-5p-in-human-colorectal-cancer
#7
Meifeng Zhang, Wei Wu, Ming Gao, Jie Zhang, Xinde Ding, Ronghua Zhu, Haiqun Chen, Zhewei Fei
The pathogenesis of colorectal cancer remains poorly understood. Here, we show that coactivator-associated arginine methyltransferase 1 is frequently upregulated in colorectal cancer tissues and promotes cell growth in vitro and in vivo. Using bioinformatics-based prediction and luciferase reporter system, we found that coactivator-associated arginine methyltransferase 1 is post-transcriptionally targeted by microRNA-195-5p in colorectal cancer. Ectopic expression of microRNA-195-5p led to the suppression of the coactivator-associated arginine methyltransferase 1 3'-untranslated regions activity and downregulation of the endogenous coactivator-associated arginine methyltransferase 1 protein in colorectal cancer cells...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28344583/rbm25-mediates-abiotic-responses-in-plants
#8
Chunhong Cheng, Zhijuan Wang, Bingjian Yuan, Xia Li
Alternative splicing (AS) of pre-mRNAs is one of the most important post-transcriptional regulations that enable a single gene to code for multiple proteins resulting in the biodiversity of proteins in eukaryotes. Recently, we have shown that an Arabidopsis thaliana RNA recognition motif-containing protein RBM25 is a novel splicing factor to modulate plant response to ABA during seed germination and post-germination through regulating HAB1 pre-mRNA AS. Here, we show that RBM25 is preferentially expressed in stomata and vascular tissues in Arabidopsis and is induced by ABA and abiotic stresses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28343438/hsa-mir-27b-is-up-regulated-in-cytomegalovirus-infected-human-glioma-cells-targets-engrailed-2-and-inhibits-its-expression
#9
Linqian Wang, Ming Yang, Shijing Liao, Wei Liu, Gan Dai, Guojun Wu, Liyu Chen
Human cytomegalovirus (HCMV) dormant infection can alter the expression of the hosts' microRNAs (miRNAs) and impact on the regulation of target genes. To investigate the differentially expressed miRNAs induced by HCMV in human glioma U251 cells, a comprehensive miRNA screen was performed. As a result, 19 up-regulated and 14 down-regulated miRNAs were determined. Of these, hsa-miR-27b (miR-27b) attracted our attention. MiR-27b levels in U251 cells increased 7.70-fold, 8.64-fold, and 4.78-fold, respectively, post 24 h, 48 h, and 72 h HCMV infection, compared to those in the mimic-infected cells, and this up-regulation was further confirmed by quantitative RT-PCR...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28342423/a-bioinformatics-approach-to-designing-a-zika-virus-vaccine
#10
Sumanta Dey, Ashesh Nandy, Subhash C Basak, Papiya Nandy, Sukhen Das
The Zika virus infections have reached epidemic proportions in the Latin American countries causing severe birth defects and neurological disorders. While several organizations have begun research into design of prophylactic vaccines and therapeutic drugs, computer assisted methods with adequate data resources can be expected to assist in these measures to reduce lead times through bioinformatics approaches. Using 60 sequences of the Zika virus envelope protein available in the GenBank database, our analysis with numerical characterization techniques and several web based bioinformatics servers identified four peptide stretches on the Zika virus envelope protein that are well conserved and surface exposed and are predicted to have reasonable epitope binding efficiency...
March 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28342076/schizosaccharomyces-pombe-rsv1-transcription-factor-and-its-putative-homologues-preserved-their-functional-homology-and-are-evolutionarily-conserved
#11
Emese Pataki, Matthias Sipiczki, Ida Miklos
Environmental glucose is an important regulator of biological processes, as it can launch different cell processes depending on its concentration. Thus, low glucose concentration can induce entry into quiescence, which ensures long-term viability for the cells or in other cases mycelial growth in the dimorphic species, which, in turn, provides the cells with fresh nutrients. Several genes, such as the genes of cAMP cascade, are involved in glucose sensing and response. Since this signal transduction pathway seemed to be an evolutionarily conserved process, we assumed that its genes were also conserved and preserved their functional homology...
March 24, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28341855/mir-503-promotes-bone-formation-in-distraction-osteogenesis-through-suppressing-smurf1-expression
#12
Yuxin Sun, Jia Xu, Liangliang Xu, Jinfang Zhang, Kaiming Chan, Xiaohua Pan, Gang Li
Distraction osteogenesis (DO) is a unique technique for promoting bone formation in clinical practice. However the underlying mechanism remains elusive. As epigenetic mediators, microRNAs have been reported to play important roles in regulating osteogenesis. In this study, after successfully established the DO model of rats, a microRNA microarray was performed to find molecular targets for DO. Total 100 microRNAs were identified as differently expressed, with miR-503 being one of the most significantly up-regulated miRNAs in DO...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28341809/structural-basis-of-molecular-recognition-of-helical-histone-h3-tail-by-phd-finger-domains
#13
Alessio Bortoluzzi, Anastasia Amato, Xavier Lucas, Manuel Blank, Alessio Ciulli
The plant homeodomain (PHD) fingers are amongst the largest family of epigenetic domains, first characterized as readers of methylated H3K4. Readout of histone post-translational modifications by PHDs has been the subject of intense investigation, however less is known about the recognition of secondary structure features within histone tail itself. We solved the crystal structure of the PHD finger of the bromodomain adjacent to zinc finger 2A (BAZ2A, also known as TIP5) in complex with unmodified N-terminal histone H3 tail...
March 24, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28341746/leveraging-sequence-based-faecal-microbial-community-survey-data-to-identify-a-composite-biomarker-for-colorectal-cancer
#14
Manasi S Shah, Todd Z DeSantis, Thomas Weinmaier, Paul J McMurdie, Julia L Cope, Adam Altrichter, Jose-Miguel Yamal, Emily B Hollister
OBJECTIVE: Colorectal cancer (CRC) is the second leading cause of cancer-associated mortality in the USA. The faecal microbiome may provide non-invasive biomarkers of CRC and indicate transition in the adenoma-carcinoma sequence. Re-analysing raw sequence and metadata from several studies uniformly, we sought to identify a composite and generalisable microbial marker for CRC. DESIGN: Raw 16S rRNA gene sequence data sets from nine studies were processed with two pipelines, (1) QIIME closed reference (QIIME-CR) or (2) a strain-specific method herein termed SS-UP (Strain Select, UPARSE bioinformatics pipeline)...
March 24, 2017: Gut
https://www.readbyqxmd.com/read/28341704/structural-landscape-of-base-pairs-containing-post-transcriptional-modifications-in-rna
#15
Preethi P Seelam, Purshotam Sharma, Abhijit Mitra
Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts towards understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures, and most commonly involve guanine or uridine modifications...
March 24, 2017: RNA
https://www.readbyqxmd.com/read/28341602/cytosolic-yb-1-and-nsun2-are-the-only-proteins-recognizing-specific-motifs-present-in-mrnas-enriched-in-exosomes
#16
Olga A Kossinova, Alexander V Gopanenko, Svetlana N Tamkovich, Olga A Krasheninina, Alexey E Tupikin, Elena Kiseleva, Darya D Yanshina, Alexey A Malygin, Alia G Ven'yaminova, Marsel R Kabilov, Galina G Karpova
Exosomes, membranous vesicles secreted by various cells, are involved in intercellular communication and carry vast repertoires of RNAs and proteins. Processes mediating RNA sorting into exosomes are currently poorly understood. Using bioinformatics approaches, three structural motifs ACCAGCCU, CAGUGAGC and UAAUCCCA have been discovered as enriched in exosomal mRNAs and long noncoding RNAs. Here, utilizing short RNA hairpins, each containing one of the motifs, in a pull-down assay of cytosolic extract of human embryonic kidney 293 (HEK293) cells, we prove that multifunctional RNA-binding protein YB-1 specifically interacts with all three motifs, whereas methyltransferase NSUN2 recognizes only the motif CAGUGAGC...
March 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28341418/a-novel-y-chromosome-microdeletion-potentially-associated-with-defective-spermatogenesis-identified-by-custom-array-comparative-genome-hybridization
#17
Tianwen He, Xiangzhong Zhang, Hua Deng, Weiping Zhou, Xin Zhao, Hui Zhao, Jian Lu, Yichun Zheng, Changbin Zhang, Liang Zhang, Aihua Yin
Male infertility is a major health problem worldwide. Oligospermia and azoospermia are the most common symptoms of this disorder. Despite recent advances, the aetiopathogenesis of defective spermatogenesis remains largely uncertain. The aim of this study is to discover unknown or novel chromosome aberrations associated with male reproductive failure. We developed a high-resolution custom array comparative genomic hybridization for initial screening of copy number variations in 10 patients with idiopathic oligozoospermia and azoospermia and eight normal fertile men...
January 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/28341036/advanced-methodologies-in-high-throughput-sequencing-of-immune-repertoires
#18
REVIEW
Simon Friedensohn, Tarik A Khan, Sai T Reddy
In recent years, major efforts have been made to develop sophisticated experimental and bioinformatic workflows for sequencing adaptive immune repertoires. The immunological insight gained has been applied to fields as varied as lymphocyte biology, immunodiagnostics, vaccines, cancer immunotherapy, and antibody engineering. In this review, we provide a detailed overview of these advanced methodologies, focusing specifically on strategies to reduce sequencing errors and bias and to achieve high-throughput pairing of variable regions (e...
March 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28340577/gene-and-protein-analysis-reveals-that-p53-pathway-is-functionally-inactivated-in-cytogenetically-normal-acute-myeloid-leukemia-and-acute-promyelocytic-leukemia
#19
Julia Abramowitz, Tzahi Neuman, Riki Perlman, Dina Ben-Yehuda
BACKGROUND: Mechanisms that inactivate the p53 pathway in Acute Myeloid Leukemia (AML), other than rare mutations, are still not well understood. METHODS: We performed a bioinformatics study of the p53 pathway function at the gene expression level on our collection of 1153 p53-pathway related genes. Publically available Affymetrix data of 607 de-novo AML patients at diagnosis were analyzed according to the patients cytogenetic, FAB and molecular mutations subtypes...
March 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28340574/myocyte-enhancer-factor-2d-provides-a-cross-talk-between-chronic-inflammation-and-lung-cancer
#20
Hai-Xing Zhu, Lin Shi, Yong Zhang, Yi-Chun Zhu, Chun-Xue Bai, Xiang-Dong Wang, Jie-Bai Zhou
BACKGROUND: Lung cancer is the leading cause of cancer-related morbidity and mortality worldwide. Patients with chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), are exposed to a higher risk of developing lung cancer. Chronic inflammation may play an important role in the lung carcinogenesis among those patients. The present study aimed at identifying candidate biomarker predicting lung cancer risk among patients with chronic respiratory diseases. METHODS: We applied clinical bioinformatics tools to analyze different gene profile datasets with a special focus on screening the potential biomarker during chronic inflammation-lung cancer transition...
March 24, 2017: Journal of Translational Medicine
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