keyword
MENU ▼
Read by QxMD icon Read
search

bioinformatics

keyword
https://www.readbyqxmd.com/read/28821760/a-database-of-breast-oncogenic-specific-sirnas
#1
Atul Tyagi, Manoj Semwal, Ashok Sharma
Breast cancer is a serious problem causing the death of women across the world. At present, one of the major challenges is to design drugs to target breast cancer specific gene(s). RNA interference (RNAi) is an important technique for targeted gene silencing that may lead to promising novel therapeutic strategies for breast cancer. Therefore, identification of such molecules having high oncogene specificity is the need of the hour. Here, we have developed a database named as Breast Oncogenic Specific siRNAs (BOSS, http://bioinformatics...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821614/multiple-circadian-transcriptional-elements-cooperatively-regulate-cell-autonomous-transcriptional-oscillation-of-period3-a-mammalian-clock-gene
#2
Ritsuko Matsumura, Makoto Akashi
Cell-autonomous oscillation in clock gene expression drives circadian rhythms. The development of comprehensive analytical techniques, such as bioinformatics and ChIP-sequencing, has enabled the genome-wide identification of potential circadian transcriptional elements that regulate the transcriptional oscillation of clock genes. However, detailed analyses using traditional biochemical and molecular-biological approaches, such as binding and reporter assays, are still necessary to determine whether these potential circadian transcriptional elements are actually functional and how significantly they contribute to driving transcriptional oscillation...
August 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28821562/gtse1-regulates-spindle-microtubule-dynamics-to-control-aurora-b-kinase-and-kif4a-chromokinesin-on-chromosome-arms
#3
Aaron R Tipton, Jonathan D Wren, John R Daum, Joseph C Siefert, Gary J Gorbsky
In mitosis, the dynamic assembly and disassembly of microtubules are critical for normal chromosome movement and segregation. Microtubule turnover varies among different mitotic spindle microtubules, dictated by their spatial distribution within the spindle. How turnover among the various classes of spindle microtubules is differentially regulated and the resulting significance of differential turnover for chromosome movement remains a mystery. As a new tactic, we used global microarray meta-analysis (GAMMA), a bioinformatic method, to identify novel regulators of mitosis, and in this study, we describe G2- and S phase-expressed protein 1 (GTSE1)...
August 18, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28820958/erratum-to-mass-spectrometric-detection-combined-with-bioinformatic-analysis-identified-possible-protein-markers-and-key-pathways-associated-with-bladder-cancer-gene-626c-2017-407-413
#4
Ziyu Wu, Sugui Wang, Fujin Jiang, Qiang Li, Chao Wang, Huanqiang Wang, Wei Zhang, Peng Xue, Shou-Lin Wang
No abstract text is available yet for this article.
August 15, 2017: Gene
https://www.readbyqxmd.com/read/28820485/disentangling-the-frames-the-state-of-research-on-the-alphavirus-6k-and-tf-proteins
#5
REVIEW
Jolene Ramsey, Suchetana Mukhopadhyay
For 30 years it was thought the alphavirus 6K gene encoded a single 6 kDa protein. However, through a bioinformatics search 10 years ago, it was discovered that there is a frameshifting event and two proteins, 6K and transframe (TF), are translated from the 6K gene. Thus, many functions attributed to the 6K protein needed reevaluation to determine if they properly belong to 6K, TF, or both proteins. In this mini-review, we reevaluate the past research on 6K and put those results in context where there are two proteins, 6K and TF, instead of one...
August 18, 2017: Viruses
https://www.readbyqxmd.com/read/28820425/bioinformatics-analysis-of-phylogeny-and-transcription-of-taa-yuc-auxin-biosynthetic-genes
#6
Axel Poulet, Verena Kriechbaumer
Auxin is a main plant growth hormone crucial in a multitude of developmental processes in plants. Auxin biosynthesis via the tryptophan aminotransferase of arabidopsis (TAA)/YUCCA (YUC) route involving tryptophan aminotransferases and YUC flavin-dependent monooxygenases that produce the auxin indole-3-acetic acid (IAA) from tryptophan is currently the most researched auxin biosynthetic pathway. Previous data showed that, in maize and arabidopsis, TAA/YUC-dependent auxin biosynthesis can be detected in endoplasmic reticulum (ER) microsomal fractions, and a subset of auxin biosynthetic proteins are localized to the ER, mainly due to transmembrane domains (TMD)...
August 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28820312/architecture-of-the-atg2b-wdr45-complex-and-an-aromatic-y-hf-motif-crucial-for-complex-formation
#7
Jing-Xiang Zheng, Yan Li, Yue-He Ding, Jun-Jie Liu, Mei-Jun Zhang, Meng-Qiu Dong, Hong-Wei Wang, Li Yu
PtdIns3P signaling is critical for dynamic membrane remodeling during autophagosome formation. Proteins in the Atg18/WIPI family are PtdIns3P-binding effectors which can form complexes with proteins in the Atg2 family, and both families are essential for macroautophagy/autophagy. However, little is known about the biophysical properties and biological functions of the Atg2-Atg18/WIPI complex as a whole. Here, we demonstrate that an ortholog of yeast Atg18, mammalian WDR45/WIPI4 has a stronger binding capacity for mammalian ATG2A or ATG2B than the other 3 WIPIs...
August 18, 2017: Autophagy
https://www.readbyqxmd.com/read/28820135/bioinformatic-analyses-of-whole-genome-sequence-data-in-a-public-health-laboratory
#8
Kelly F Oakeson, Jennifer Marie Wagner, Michelle Mendenhall, Andreas Rohrwasser, Robyn Atkinson-Dunn
The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. However, the analysis of whole-genome sequence data depends on bioinformatic analysis tools and processes. Many public health laboratories do not have the bioinformatic capabilities to analyze the data generated from sequencing and therefore are unable to take full advantage of the power of whole-genome sequencing...
September 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28820125/fungal-genomes-and-insights-into-the-evolution-of-the-kingdom
#9
Jason E Stajich
The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28819440/microrna-204-5p-inhibits-invasion-and-metastasis-of-laryngeal-squamous-cell-carcinoma-by-suppressing-forkhead-box-c1
#10
Wei Gao, Yongyan Wu, Xiaoling He, Chunming Zhang, Meixia Zhu, Bo Chen, Qingqing Liu, Xukuan Qu, Weiyan Li, Shuxin Wen, Binquan Wang
Background and aim: Understanding the molecular biological mechanisms underlying laryngeal squamous cell carcinoma (LSCC) invasion and metastasis is crucial for diagnosis, treatment, and prognosis. We aimed to examine the expression of the tumor suppressor microRNA-204-5p (miR-204-5p) and its target gene, forkhead box C1 (FOXC1), in human LSCC and explore their roles in the malignant behaviors of LSCC Hep-2 and TU-177 cells. Methods: The regulatory effects of miR-204-5p on the 3' untranslated region of FOXC1 predicted by bioinformatics were tested by dual-luciferase reporter assay...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819415/szrd1-is-a-novel-protein-that-functions-as-a-potential-tumor-suppressor-in-cervical-cancer
#11
Ning Zhao, Guoying Zhang, Minwei He, He Huang, Lulu Cao, Ang Yin, Pingzhang Wang, Lu Wang
SZRD1 is a novel gene screened out by high-throughput platform, and so far there exists no systematic function reports. The purpose of our study is to discover the function and mechanism of this novel human gene. Bioinformatics analysis indicates that SZRD1 is a highly conserved intracellular protein. After overexpression of SZRD1, we found that SZRD1 could arrest the cell cycle in G2 phase and play a role in inhibiting cell proliferation and inducing apoptosis. In contrast, after knockdown of endogenous SZRD1, we concluded that it could promote cell proliferation...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819395/downregulation-of-abc-transporters-in-non-neoplastic-tissues-confers-better-prognosis-for-pancreatic-and-colorectal-cancer-patients
#12
Pavel Dvorak, Viktor Hlavac, Beatrice Mohelnikova-Duchonova, Vaclav Liska, Martin Pesta, Pavel Soucek
Transport of a wide variety of substrates, including xenobiotics, is one of the main functions attributed to human ATP-binding cassette (ABC) proteins. Overexpression of ABC genes is considered to be an important mechanism facilitating the development of chemoresistance. Relationships between the expression levels of ABC genes in tumor tissues and established clinicopathological features were extensively studied previously. The current study tested our hypothesis that the expression levels of ABC genes in non-neoplastic (control) tissues also provide important information in relation to the relevant tumor progression...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819321/sh3bp4-a-novel-pigmentation-gene-is-inversely-regulated-by-mir-125b-and-mitf
#13
Kyu-Han Kim, Tae Ryong Lee, Eun-Gyung Cho
Our previous work has identified miR-125b as a negative regulator of melanogenesis. However, the specific melanogenesis-related genes targeted by this miRNA had not been identified. In this study, we established a screening strategy involving three consecutive analytical approaches-analysis of target genes of miR-125b, expression correlation analysis between each target gene and representative pigmentary genes, and functional analysis of candidate genes related to melanogenesis-to discover melanogenesis-related genes targeted by miR-125b...
August 18, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28819315/mce-domain-proteins-conserved-inner-membrane-lipid-binding-proteins-required-for-outer-membrane-homeostasis
#14
Georgia L Isom, Nathaniel J Davies, Zhi-Soon Chong, Jack A Bryant, Mohammed Jamshad, Maria Sharif, Adam F Cunningham, Timothy J Knowles, Shu-Sin Chng, Jeffrey A Cole, Ian R Henderson
Bacterial proteins with MCE domains were first described as being important for Mammalian Cell Entry. More recent evidence suggests they are components of lipid ABC transporters. In Escherichia coli, the single-domain protein MlaD is known to be part of an inner membrane transporter that is important for maintenance of outer membrane lipid asymmetry. Here we describe two multi MCE domain-containing proteins in Escherichia coli, PqiB and YebT, the latter of which is an orthologue of MAM-7 that was previously reported to be an outer membrane protein...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819133/combined-transcriptome-and-metabolome-analyses-of-metformin-effects-reveal-novel-links-between-metabolic-networks-in-steroidogenic-systems
#15
Sameer S Udhane, Balazs Legeza, Nesa Marti, Damian Hertig, Gaëlle Diserens, Jean-Marc Nuoffer, Peter Vermathen, Christa E Flück
Metformin is an antidiabetic drug, which inhibits mitochondrial respiratory-chain-complex I and thereby seems to affect the cellular metabolism in many ways. It is also used for the treatment of the polycystic ovary syndrome (PCOS), the most common endocrine disorder in women. In addition, metformin possesses antineoplastic properties. Although metformin promotes insulin-sensitivity and ameliorates reproductive abnormalities in PCOS, its exact mechanisms of action remain elusive. Therefore, we studied the transcriptome and the metabolome of metformin in human adrenal H295R cells...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818754/daily-thanatomicrobiome-changes-in-soil-as-an-approach-of-postmortem-interval-estimation-an-ecological-perspective
#16
Joe Adserias-Garriga, Marta Hernández, Narciso M Quijada, David Rodríguez Lázaro, Dawnie Steadman, Jesús Garcia-Gil
Understanding human decomposition is critical for its use in postmortem interval (PMI) estimation, having a significant impact on forensic investigations. In recognition of the need to establish the scientific basis for PMI estimation, several studies on decomposition have been carried out in the last years. The aims of the present study were: (i) to identify soil microbiota communities involved in human decomposition through high-throughput sequencing (HTS) of DNA sequences from the different bacteria, (ii) to monitor quantitatively and qualitatively the decay of such signature species, and (iii) to describe succesional changes in bacterial populations from the early putrefaction state until skeletonization...
August 7, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28818599/a-new-cost-and-time-effective-method-for-multilocus-microsatellite-typing-mlmt-studies-application-of-leishmania-tropica-isolates-and-clinical-samples-from-turkey
#17
Mehmet Karakuş, Bahtiyar Yılmaz, Yusuf Özbel, Seray Töz
Molecular techniques are widely used in the field of parasitology to identify the genetic profile of the microbiological agents. Microsatellite typing studies are comprised of the amplification of polymorphic markers to analyze the fragment sizes using bioinformatics tools. Current methods need fluorescently labeled primers and size markers to obtain fragment peaks in ABI PRISM® systems and due to low discrimination power of gel-electrophoresis, it is not possible to differentiate primer-dimers from small fragments In the present study, we designed a new method for fragment analysis studies, which reduce the time by eliminating the classical PCR, the gel-electrophoresis and the preparation steps of fragment analysis...
August 14, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28818578/can-exercise-training-counteract-doxorubicin-induced-oxidative-damage-of-testis-proteome
#18
José Magalhães, António Ascensão, Ana I Padrão, Inês M Aleixo, Estela Santos-Alves, Sílvia Rocha-Rodrigues, André Ferreira, Luis Korrodi-Gregório, Rui Vitorino, Rita Ferreira, Margarida Fardilha
The use of the chemotherapeutic drug doxorubicin (DOX) is limited by its toxicity in several organs such as testes. So, we analyzed the effect of endurance treadmill exercise training (EX) performed before sub-chronic DOX treatment on sperm count and motility, testes markers of oxidative damage and apoptosis. Tissue profiling of proteins more susceptible to oxidation was made to identify the molecular pathways regulated by oxidative modifications, as nitration and carbonylation. Twenty-four adult male rats were divided into four groups (n=6/group): sedentary saline (SED+SAL), sedentary sub-chronically injected with DOX (2mg-kg-1 per week, during 7 weeks; SED+DOX), 12 weeks trained saline (EX+SAL) and trained treated with DOX (EX+DOX)...
August 14, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28818574/antimicrobial-resistance-determinants-and-susceptibility-profiles-of-pneumococcal-isolates-recovered-in-trinidad-and-tobago
#19
Paulina A Hawkins, Patrick E Akpaka, Michele Nurse-Lucas, Rebecca Gladstone, Stephen D Bentley, Robert F Breiman, Lesley McGee, William H Swanston
INTRODUCTION: In Latin America and the Caribbean, pneumococcal infections were estimated to account for 12,000-18,000 deaths, 327,000 cases of pneumonia, 4,000 cases of meningitis and 1,229 cases of sepsis each year in children under five years old. Resistance of pneumococci to antimicrobial agents has evolved into a worldwide health problem in the last few decades. OBJECTIVE: The aim of this study was to determine the antimicrobial susceptibility profiles of 98 pneumococcal isolates collected in Trinidad and Tobago and associated genetic determinants...
August 14, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28817829/altered-expression-profile-of-circular-rnas-in-the-serum-of-patients-with-diabetic-retinopathy-revealed-by-microarray
#20
Yonghao Gu, Genjie Ke, Lin Wang, Enliang Zhou, Kai Zhu, Yingying Wei
PURPOSE: Diabetic retinopathy (DR) is the leading cause of blindness among working age adults. Circular RNAs (circRNAs) are a kind of noncoding RNAs that are involved in the development of some diseases. Here, we aimed to determine the possible role of circRNAs in the pathogenesis of DR by determining the expression profile of circRNAs in the serum of DR patients. METHODS: Nineteen subjects with type 2 diabetes mellitus with proliferative DR (T2DR), 15 subjects with type 2 diabetes mellitus without DR (T2DM), and 21 age-matched nondiabetic control subjects were included in the study...
August 18, 2017: Ophthalmic Research
keyword
keyword
6050
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"