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https://www.readbyqxmd.com/read/29156779/selecting-lncrnas-in-gastric-cancer-cells-for-directed-therapy-with-bioactive-peptides-and-chemotherapy-drugs
#1
Wenyan Han, Rui Xiao, Chuanling Zhang, Qimuge Suyila, Xian Li, Xiulan Su
Selecting lncRNAs for directed therapy with bioactive peptides and chemotherapy drugs may be an effective approach to treating gastric cancer (GC). We show genome-scale identification and characterization of differentially expressed lncRNAs in GC cells treated with a novel anti-cancer bioactive peptide (ACBP) and the chemotherapy drug oxaliplatin (ASLB). A total of 17,897 lncRNAs were identified through pairwise comparison, including 2,074 novel lncRNAs. Of those, 1,386 lncRNAs were differentially expressed (over 1...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156757/a-pten-col17a1-fusion-gene-and-its-novel-regulatory-role-in-collagen-xvii-expression-and-gbm-malignance
#2
Xiaoyan Yan, Chuanbao Zhang, Tingyu Liang, Fan Yang, Haoyuan Wang, Fan Wu, Wen Wang, Zheng Wang, Wen Cheng, Jiangnan Xu, Tao Jiang, Jing Chen, Yaozhong Ding
Collagen XVII expression has recently been demonstrated to be correlated with the tumor malignance. While Collagen XVII is known to be widely distributed in neurons of the human brain, its precise role in pathogenesis of glioblastoma multiforme (GBM) is unknown. In this study, we identified and characterized a new PTEN-COL17A1 fusion gene in GMB using transcriptome sequencing. Although fusion gene did not result in measurable fusion protein production, its presence is accompanied with high levels of COL17A1 expression, revealed a novel regulatory mechanism of Collagen XVII expression by PTEN-COL17A1 gene fusion...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156689/implications-of-pi3k-akt-inhibition-on-rest-protein-stability-and-neuroendocrine-phenotype-acquisition-in-prostate-cancer-cells
#3
Ruiqui Chen, Yinan Li, Ralph Buttyan, Xuesen Dong
Treatment-induced neuroendocrine prostate cancer (t-NEPC) is an aggressive subtype of prostate cancer (PCa) that arises as a consequence of rigorous androgen receptor (AR) pathway inhibition (ARPI) therapies. While the PI3K/AKT pathway has been investigated as a co-therapeutic target with ARPI for advanced PCa, whether this strategy can prevent tumor progression to t-NEPC remains unknown. Here, we report that PI3K/AKT inhibition alone reduces RE-1 silencing transcription factor (REST) protein expression and induces multiple NE markers in PCa cells...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156685/whole-genome-and-transcriptome-analysis-reveal-maldi-tof-ms-and-sds-page-have-limited-performance-for-the-detection-of-the-key-outer-membrane-protein-in-carbapenem-resistant-klebsiella-pneumoniae-isolates
#4
Naina Adren Pinto, Roshan D'Souza, In Sik Hwang, Jongrak Choi, Yong Ha In, Hyung Soon Park, Choong-Min Ryu, Dongeun Yong, Kyungwon Lee
To detect the outer membrane protein (OMP), which plays a key role in carbapenem resistance, whole-genome and transcriptome analysis of the clinical carbapenem-resistant Klebsiella pneumoniae was carried out. The index strain lacked both OmpK35 and OmpK36, whereas the other strains lacked only OmpK35. After SDS-PAGE, the putative OMP bands were excised and identified as OmpA and OmpK36. MALDI-TOF MS showed peaks at ∼36 and ∼38 kDa that corresponded to OmpA and OmpK36, respectively. In all the strains except YMC2014/03/P345, the ∼38 kDa peaks were present...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156376/comparative-transcriptomic-analysis-of-endothelial-progenitor-cells-derived-from-umbilical-cord-blood-and-adult-peripheral-blood-implications-for-the-generation-of-induced-pluripotent-stem-cells
#5
Xiugong Gao, Jeffrey J Yourick, Robert L Sprando
Induced pluripotent stem cells (iPSCs) offer the potential to generate tissues with ethnic diversity enabling toxicity testing on selected populations. Recently, it has been reported that endothelial progenitor cells (EPCs) derived from umbilical cord blood (CB) or adult peripheral blood (PB) afford a practical and efficient cellular substrate for iPSC generation. However, differences between EPCs from different blood sources have rarely been studied. In the current study, we derived EPCs from blood mononuclear cells (MNCs) and reprogrammed EPCs into iPSCs...
November 7, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29156228/effect-of-abiotic-and-biotic-stress-factors-analysis-using-machine-learning-methods-in-zebrafish
#6
Rajasekar Gutha, Suresh Yarrappagaari, Lavanya Thopireddy, Kesireddy Sathyavelu Reddy, Rajeswara Reddy Saddala
In order to understand the mechanisms underlying stress responses, meta-analysis of transcriptome is made to identify differentially expressed genes (DEGs) and their biological, molecular and cellular mechanisms in response to stressors. The present study is aimed at identifying the effect of abiotic and biotic stress factors, and it is found that several stress responsive genes are common for both abiotic and biotic stress factors in zebrafish. The meta-analysis of micro-array studies revealed that almost 4...
November 11, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29156217/characterization-of-udp-glucosyltransferase-from-indigofera-tinctoria
#7
Shintaro Inoue, Toshiki Moriya, Rihito Morita, Keiko Kuwata, Sanjog T Thul, Bijaya K Sarangi, Yoshiko Minami
Indican is a secondary metabolite in Indigofera tinctoria; its synthesis from indoxyl and UDP-glucose is catalyzed by a UDP-glucosyltransferase (UGT). In this study, we partially purified UGT extracted from I. tinctoria leaves and analyzed the protein by peptide mass fingerprinting. We identified two fragments that were homologous to UGT after comparison with the transcriptomic data of I. tinctoria leaves. The fragments were named itUgt1 and itUgt2 and were amplified using rapid amplification of cDNA ends polymerase chain reaction to obtain full-length cDNAs...
November 6, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29155974/transcript-profiling-of-a-bitter-variety-of-narrow-leafed-lupin-to-discover-alkaloid-biosynthetic-genes
#8
Ting Yang, Istvan Nagy, Davide Mancinotti, Sophie Lisa Otterbach, Trine Bundgaard Andersen, Mohammed Saddik Motawia, Torben Asp, Fernando Geu-Flores
Lupins (Lupinus spp.) are nitrogen-fixing legumes that accumulate toxic alkaloids in their protein-rich beans. These anti-nutritional compounds belong to the family of quinolizidine alkaloids (QAs), which are of interest to the pharmaceutical and chemical industries. To unleash the potential of lupins as protein crops and as sources of QAs, a thorough understanding of the QA pathway is needed. However, only the first enzyme in the pathway, lysine decarboxylase (LDC), is known. Here, we report the transcriptome of a high-QA variety of narrow-leafed lupin (L...
November 16, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29155939/group-b-streptococcus-activates-transcriptomic-pathways-related-to-premature-birth-in-human-extraplacental-membranes-in-vitro
#9
Hae-Ryung Park, Sean M Harris, Erica Boldenow, Richard C McEachin, Maureen Sartor, Mark Chames, Rita Loch-Caruso
Streptococcus agalactiae (group B streptococcus, GBS) infection in pregnant women is the leading cause of infectious neonatal morbidity and mortality in the United States. Although inflammation during infection has been associated with preterm birth, the contribution of GBS to preterm birth is less certain. Moreover, the early mechanisms by which GBS interacts with the gestational tissue to affect adverse pregnancy outcomes are poorly understood. We hypothesized that short term GBS inoculation activates pathways related to inflammation and premature birth in human extraplacental membranes...
November 16, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29155926/codon-usage-and-codon-pair-patterns-in-non-grass-monocot-genomes
#10
Purabi Mazumdar, RofinaYasmin Binti Othman, Katharina Mebus, N Ramakrishnan, Jennifer Ann Harikrishna
Background and Aims: Studies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots. Methods: First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available...
November 16, 2017: Annals of Botany
https://www.readbyqxmd.com/read/29155830/molecular-characterization-of-tsetse-s-proboscis-and-its-response-to-trypanosoma-congolense-infection
#11
Erick O Awuoche, Brian L Weiss, Aurélien Vigneron, Paul O Mireji, Emre Aksoy, Benson Nyambega, Geoffrey M Attardo, Yineng Wu, Michelle O'Neill, Grace Murilla, Serap Aksoy
Tsetse flies (Glossina spp.) transmit parasitic African trypanosomes (Trypanosoma spp.), including Trypanosoma congolense, which causes animal African trypanosomiasis (AAT). AAT detrimentally affects agricultural activities in sub-Saharan Africa and has negative impacts on the livelihood and nutrient availability for the affected communities. After tsetse ingests an infectious blood meal, T. congolense sequentially colonizes the fly's gut and proboscis (PB) organs before being transmitted to new mammalian hosts during subsequent feedings...
November 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29155818/snail1-mediated-downregulation-of-foxa-proteins-facilitates-the-inactivation-of-transcriptional-enhancer-elements-at-key-epithelial-genes-in-colorectal-cancer-cells
#12
Sabine Jägle, Hauke Busch, Vivien Freihen, Sven Beyes, Monika Schrempp, Melanie Boerries, Andreas Hecht
Phenotypic conversion of tumor cells through epithelial-mesenchymal transition (EMT) requires massive gene expression changes. How these are brought about is not clear. Here we examined the impact of the EMT master regulator SNAIL1 on the FOXA family of transcription factors which are distinguished by their particular competence to induce chromatin reorganization for the activation of transcriptional enhancer elements. We show that the expression of SNAIL1 and FOXA genes is anticorrelated in transcriptomes of colorectal tumors and cell lines...
November 20, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29155729/sample-preparation-and-analysis-of-rnaseq-based-gene-expression-data-from-zebrafish
#13
Timothy L Hostelley, Jessica E Nesmith, Norann A Zaghloul
The analysis of global gene expression changes is a valuable tool for identifying novel pathways underlying observed phenotypes. The zebrafish is an excellent model for rapid assessment of whole transcriptome from whole animal or individual cell populations due to the ease of isolation of RNA from large numbers of animals. Here a protocol for global gene expression analysis in zebrafish embryos using RNA sequencing (RNASeq) is presented. We describe preparation of RNA from whole embryos or from cell populations obtained using cell sorting in transgenic animals...
October 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155718/the-murine-choline-deficient-ethionine-supplemented-cde-diet-model-of-chronic-liver-injury
#14
Jully Gogoi-Tiwari, Julia Köhn-Gaone, Corey Giles, Dirk Schmidt-Arras, Francis D Gratte, Caryn L Elsegood, Geoffrey W McCaughan, Grant A Ramm, John K Olynyk, Janina E E Tirnitz-Parker
Chronic liver diseases, such as viral hepatitis, alcoholic liver disease, or non-alcoholic fatty liver disease, are characterized by continual inflammation, progressive destruction and regeneration of the hepatic parenchyma, liver progenitor cell proliferation, and fibrosis. The end-stage of every chronic liver disease is cirrhosis, a major risk factor for the development of hepatocellular carcinoma. To study processes regulating disease initiation, establishment, and progression, several animal models are used in laboratories...
October 21, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155478/alternative-polyadenylation-is-involved-in-auxin-based-plant-growth-and-development
#15
Liwei Hong, Congting Ye, Juncheng Lin, Haihui Fu, Xiaohui Wu, Qingshun Q Li
Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, impact of auxin on pre-mRNA posttranscriptional regulation is mostly unknown. By using a poly(A) tag (PAT) sequencing approach, mRNA alternative polyadenylation (APA) profiles after auxin treatment were revealed. We showed that hundreds of poly(A) site clusters (PACs) are affected by auxin at the transcriptome level, where auxin reduces PAC distribution in 5'UTR, but increases in 3'UTR...
November 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29155438/circular-rnas-mediated-by-transposons-are-associated-with-transcriptomic-and-phenotypic-variation-in-maize
#16
Lu Chen, Pei Zhang, Yuan Fan, Qiong Lu, Qing Li, Jianbing Yan, Gary J Muehlbauer, Patrick S Schnable, Mingqiu Dai, Lin Li
Circular RNAs (circRNAs) are covalently closed RNA molecules. Recent studies have shown that circRNAs can arise from the transcripts of transposons. Given the prevalence of transposons in the maize genome and dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. We performed circRNA-Seq on B73 seedling leaves and uncovered 2804 high-confidence maize circRNAs, which show distinct genomic features...
November 20, 2017: New Phytologist
https://www.readbyqxmd.com/read/29155150/enhancement-of-cutaneous-immunity-during-ageing-by-blocking-p38-mapkinase-induced-inflammation
#17
Milica Vukmanovic-Stejic, Emma S Chambers, Mayte Suarez- Farinas, Daisy Sandhu, Judilyn Fuentes-Duculan, Neil Patel, Elaine Agius, Katie E Lacy, Carolin T Turner, Anis Larbi, Veronique Birault, Mahdad Noursadeghi, Neil A Mabbott, Malcolm H A Rustin, James Krueger, Arne N Akbar
BACKGROUND: Immunity declines with age that leads to re-activation of varicella zoster virus (VZV). In humans, age associated immune changes are usually measured in blood leukocytes however this may not reflect alterations in tissue-specific immunity. OBJECTIVES: We used a VZV antigen challenge system in the skin to investigate changes in tissue specific mechanisms involved in the decreased response to this virus during ageing. METHODS: We assessed cutaneous immunity by the extent of erythema and induration after intradermal VZV antigen injection...
November 16, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29155030/transcriptome-analysis-and-discovery-of-genes-involved-in-immune-pathways-from-coelomocytes-of-onchidium-struma-after-bacterial-challenge
#18
Mingming Zhang, Guo Qiao, Qiang Li, De-Hai Xu, Zhitao Qi, Aiming Wang, Mengyao Xu, Jintian Huang
Onchidium struma widely distributes in subtidal and low-tidal zones, which is considered to be an economical species with rich nutrition, a valuable biomonitor for heavy metal pollution and a representative species for evolution from ocean to land. However, there is limited genetic information available for O. struma development. This study compared transcriptomic profiles of coelomocytes from normal and bacteria infected O. struma by Illumina-based paired-end sequencing to explore the molecular immune mechanism of O...
November 15, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29154989/targeting-bromodomain-and-extraterminal-proteins-in-breast-cancer
#19
REVIEW
Jennifer M Sahni, Ruth A Keri
Breast cancer is a collection of distinct tumor subtypes that are driven by unique gene expression profiles. These transcriptomes are controlled by various epigenetic marks that dictate which genes are expressed and suppressed. During carcinogenesis, extensive restructuring of the epigenome occurs, including aberrant acetylation, alteration of methylation patterns, and accumulation of epigenetic readers at oncogenes. As epigenetic alterations are reversible, epigenome-modulating drugs could provide a mechanism to silence numerous oncogenes simultaneously...
November 15, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29154927/integrative-transcriptome-and-proteome-analyses-define-marked-differences-between-neospora-caninum-isolates-throughout-the-tachyzoite-lytic-cycle
#20
P Horcajo, D Xia, N Randle, E Collantes-Fernández, J Wastling, L M Ortega-Mora, J Regidor-Cerrillo
Neospora caninum is one of the main causes of transmissible abortion in cattle. Intraspecific variations in virulence have been widely shown among N. caninum isolates. However, the molecular basis governing such variability have not been elucidated to date. In this study label free LC-MS/MS was used to investigate proteome differences between the high virulence isolate Nc-Spain7 and the low virulence isolate Nc-Spain1H throughout the tachyzoite lytic cycle. The results showed greater differences in the abundance of proteins at invasion and egress with 77 and 62 proteins, respectively...
November 14, 2017: Journal of Proteomics
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