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https://www.readbyqxmd.com/read/29150499/understanding-functional-roles-of-native-pentose-specific-transporters-for-activating-dormant-pentose-metabolism-in-yarrowia-lipolytica
#1
Seunghyun Ryu, Cong T Trinh
Pentoses including xylose and arabinose are the second-most prevalent sugars of lignocellulosic biomass that can be harnessed for biological conversion. Although Yarrowia lipolytica has emerged as a promising industrial microorganism for production of high-value chemicals and biofuels, its native pentose metabolism is poorly understood. Our previous study demonstrated that Y. lipolytica (ATCC MYA-2613) has endogenous enzymes for D-xylose assimilation, but inefficient xylitol dehydrogenase causes Y. lipolytica to assimilate xylose poorly...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29146447/in-the-ovary-of-ciona-intestinalis-type-a-immune-related-galectin-and-phenoloxidase-genes-are-differentially-expressed-by-the-follicle-accessory-cells
#2
Daniela Parrinello, Maria Antonietta Sanfratello, Maria Giovanna Parisi, Aiti Vizzini, Matteo Cammarata
Riboprobes (in situ hybridization) and antibodies (immunohistochemistry), previously used to show the upregulation of Ciona intestinalis (Type A) galectins (CiLgals-a, CiLgals-b) and phenoloxidase (CinPO2) immune-related genes, were tested on histological sections of the ovary. The ovarian follicles are composed of oocytes encased by follicular cells (FCs) and test cells (TCs). Results show the transcription upregulation of both CiLgals and CinPO2 genes in the vitellogenic FCs, conversely distinct cytolocalization of the proteins are shown...
November 13, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29146117/implications-of-disturbances-in-circadian-rhythms-for-cardiovascular-health-a-new-frontier-in-free-radical-biology
#3
REVIEW
Neelam Khaper, Craig D C Bailey, Nilesh R Ghugre, Cristine Reitz, Zikra Awosanmi, Ryan Waines, Tami A Martino
Cell autonomous circadian "clock" mechanisms are present in virtually every organ, and generate daily rhythms that are important for normal physiology. This is especially relevant to the cardiovascular system, for example the circadian mechanism orchestrates rhythms in heart rate, blood pressure, cardiac contractility, metabolism, gene and protein abundance over the 24-hour day and night cycles. Conversely, disturbing circadian rhythms (e.g. via shift work, sleep disorders) increases cardiovascular disease risk, and exacerbates cardiac remodelling and worsens outcome...
November 13, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29144837/evolution-of-alternative-adaptive-immune-systems-in-vertebrates
#4
Thomas Boehm, Masayuki Hirano, Stephen J Holland, Sabyasachi Das, Michael Schorpp, Max D Cooper
Adaptive immunity in jawless fishes is based on antigen recognition by three types of variable lymphocyte receptors (VLRs) composed of variable leucinerich repeats, which are differentially expressed by two T-like lymphocyte lineages and one B-like lymphocyte lineage. The T-like cells express either VLRAs or VLRCs of yet undefined antigen specificity, whereas the VLRB antibodies secreted by B-like cells bind proteinaceous and carbohydrate antigens. The incomplete VLR germline genes are assembled into functional units by a gene conversion-like mechanism that employs flanking variable leucine-rich repeat sequences as templates in association with lineage-specific expression of cytidine deaminases...
November 16, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/29144540/biosynthetic-energy-cost-of-potentially-highly-expressed-proteins-vary-with-niche-in-selected-actinobacteria
#5
Indrani Sarkar, Louis S Tisa, Maher Gtari, Arnab Sen
Amino acid and protein biosynthesis requires a number of high energy phosphate bonds and includes a dual energy cost for the synthesis of chemical intermediates during the fueling reactions and the conversion of precursor molecules to final products. One popular hypothesis is that the proteins encoded by putative highly expressed genes (hence called PHXPs) generally utilize low energy consuming amino acids to reduce the biosynthetic cost of the essential proteins. In our study, we found that this idea was not supported in the case of actinobacteria...
November 16, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/29143709/acute-and-chronic-cold-exposure-differentially-affects-the-browning-of-porcine-white-adipose-tissue
#6
Y Gao, N R Qimuge, J Qin, R Cai, X Li, G Y Chu, W J Pang, G S Yang
Piglets are characteristically cold intolerant and thus susceptible to high mortality. However, browning of white adipose tissue (WAT) can induce non-shivering thermogenesis as a potential strategy to facilitate the animal's response to cold. Whether cold exposure can induce browning of subcutaneous WAT (sWAT) in piglets in a similar manner as it can in humans remains largely unknown. In this study, piglets were exposed to acute cold (4°C, 10 h) or chronic cold exposure (8°C, 15 days), and the genes and proteins of uncoupling protein 1 (UCP1)-dependent and independent thermogenesis, mitochondrial biogenesis, lipogenic and lipolytic processes were analysed...
November 16, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29143658/a-key-enzyme-of-animal-steroidogenesis-can-function-in-plants-enhancing-their-immunity-and-accelerating-the-processes-of-growth-and-development
#7
George V Shpakovski, Svetlana G Spivak, Irina N Berdichevets, Olga G Babak, Svetlana V Kubrak, Alexander V Kilchevsky, Andrey V Aralov, Ivan Yu Slovokhotov, Dmitry G Shpakovski, Ekaterina N Baranova, Marat R Khaliluev, Elena K Shematorova
BACKGROUND: The initial stage of the biosynthesis of steroid hormones in animals occurs in the mitochondria of steroidogenic tissues, where cytochrome P450SCC (CYP11A1) encoded by the CYP11A1 gene catalyzes the conversion of cholesterol into pregnenolone - the general precursor of all the steroid hormones, starting with progesterone. This stage is missing in plants where mitochondrial cytochromes P450 (the mito CYP clan) have not been found. Generating transgenic plants with a mitochondrial type P450 from animals would offer an interesting option to verify whether plant mitochondria could serve as another site of P450 monooxygenase reaction for the steroid hormones biosynthesis...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143545/taz-responds-to-fluid-shear-stress-to-regulate-the-cell-cycle
#8
Hyun Jung Lee, Adesuwa Ewere, Miguel F Diaz, Pamela L Wenzel
Physical forces associated with tumor growth and drainage alter cancer cell invasiveness and metastatic potential. We previously showed that fluid frictional force, or shear stress, typical of lymphatic flow induces YAP1/TAZ activation in prostate cancer cells to promote motility dependent upon YAP1 but not TAZ. Here, we show that shear stress elevates TAZ protein levels and promotes TAZ nuclear localization. Increased TAZ activity drives increased DNA synthesis and induces AMOTL2, ANKRD1, and CTGF gene transcription independently of YAP1...
November 16, 2017: Cell Cycle
https://www.readbyqxmd.com/read/29141788/interleukin-1-receptor-antagonist-and-2-5-oligoadenylate-synthetase-like-molecules-as-novel-biomarkers-for-multiple-sclerosis-patients-in-bahrain
#9
Moudi Al-Nashmi, Safa Taha, Isa Alsharoqi, Moiz Bakhiet
BACKGROUND: Multiple sclerosis (MS) is a multi-factorial disease of the Central Nervous System (CNS) affecting young adults leading to significant disabilities over time. MS is now believed to be prevalent in Arabian Gulf area with high incidence due to environmental factors and unknown genetic variations. The objectives of this study was to detect up-regulated potential genes that might be involved in neuroinflammatory process in MS patients in Bahrain and to measure the protein levels of the expressed genes...
November 2017: Multiple Sclerosis and related Disorders
https://www.readbyqxmd.com/read/29141593/bidirectional-alteration-of-cav-1-expression-is-associated-with-mitogenic-conversion-of-its-function-in-gastric-tumor-progression
#10
Byung-Kyu Ryu, Min-Goo Lee, Nam-Hoon Kim, Kil Yeon Lee, Shin-Ju Oh, Jung-Rock Moon, Hyo Jong Kim, Sung-Gil Chi
BACKGROUND: Expression of caveolin-1 (Cav-1) is frequently altered in many human cancers and both tumor suppression and promotion functions of Cav-1 have been suggested based on its expression status. However, it remains unanswered how Cav-1 provokes opposite effects in different cancers or different phases of tumor progression. METHODS: To explore the implication of Cav-1 alteration in gastric tumorigenesis, the expression and mutational status of Cav-1 and its effects on tumor cell growth were characterized...
November 15, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29141555/evaluation-of-antineoplastic-effects-of-nf-%C3%AE%C2%BAb-inhibition-by-dhmeq-dehydroxymethylepoxyquinomicin-in-medulloblastoma-cell-lines
#11
Priscila Maria Manzini Ramos, Julia Alejandra Pezuk, Angel Mauricio Castro-Gamero, Harley Francisco de Oliveira, Carlos Alberto Scrideli, Kazuo Umezawa, Luiz Gonzaga Tone
PURPOSE: NF-κB is a transcription factor involved in the transcriptional regulation of a large number of genes related to tumorigenesis in several cancer cell types, and it's inhibition have been related to anticancer effect. DHMEQ (Dehydroxymethylepoxyquinomicin) is a compound that blocks the translocation of NF-κB from the cytoplasm to the nucleus, thus inhibiting its activity as a transcriptional activator. Several studies have shown the antineoplastic effects of DHMEQ in numerous tumor types, however, there are no surveys that tested their effects in MB...
November 13, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/29141455/methionine-adenosyltransferases-in-cancers-mechanisms-of-dysregulation-and-implications-for-therapy
#12
Lauren Y Maldonado, Diana Arsene, José M Mato, Shelly C Lu
Methionine adenosyltransferase genes encode enzymes responsible for the biosynthesis of S-adenosylmethionine, the principal biological methyl donor and precursor of polyamines and glutathione. Mammalian cells express three genes - MAT1A, MAT2A, and MAT2B - with distinct expression and functions. MAT1A is mainly expressed in the liver and maintains the differentiated states of both hepatocytes and bile duct epithelial cells. Conversely, MAT2A and MAT2B are widely distributed in non-parenchymal cells of the liver and extrahepatic tissues...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/29139179/involvement-of-lemrp-an-atp-binding-cassette-transporter-in-shikonin-transport-and-biosynthesis-in-lithospermum-erythrorhizon
#13
Yu Zhu, Shu-Juan Chu, Yue-Lin Luo, Jiang-Yan Fu, Cheng-Yi Tang, Gui-Hua Lu, Yan-Jun Pang, Xiao-Ming Wang, Rong-Wu Yang, Jin-Liang Qi, Yong-Hua Yang
·Shikonin and its derivatives are important medicinal secondary metabolites accumulating in the roots of Lithospermum erythrorhizon. Although some membrane proteins have been identified as transporters of secondary metabolites, the mechanisms underlying shikonin transport and accumulation in L. erythrorhizon cells still remain largely unknown. ·In this study, we isolated a cDNA encoding LeMRP, an ATP-binding cassette transporter from L. erythrorhizon and further investigated its functions in the transport and biosynthesis of shikonin with the yeast transformation and transgenic hairy root method, respectively...
November 15, 2017: Plant Biology
https://www.readbyqxmd.com/read/29138847/srpk1%C3%A2-sirna-suppresses-k562-cell-growth-and-induces-apoptosis-via-the-parp%C3%A2-caspase3-pathway
#14
Hailian Wang, Wei Ge, Wen Jiang, Dong Li, Xiuli Ju
Serine-arginine protein kinase 1 (SRPK1) has been used as an important signal mediator, and is associated with cancer development. However, studies have yet to determine whether SRPK1 suppresses leukemia cell growth and induces apoptosis. Studies have also yet to reveal the underlying mechanisms. In the present study, the effects of downregulating SRPK1 gene expression on chronic myeloid leukemia cell lines (K562 cells) were investigated through RNA interference (RNAi) and the proliferation inhibition and apoptosis induction of SRPK1 in K562 cells were analyzed...
November 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29138319/frequent-nonallelic-gene-conversion-on-the-human-lineage-and-its-effect-on-the-divergence-of-gene-duplicates
#15
Arbel Harpak, Xun Lan, Ziyue Gao, Jonathan K Pritchard
Gene conversion is the copying of a genetic sequence from a "donor" region to an "acceptor." In nonallelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250 bp and a probability of [Formula: see text] per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate)...
November 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29138277/coupling-shrna-screens-with-single-cell-rna-seq-identifies-a-dual-role-for-mtor-in-reprogramming-induced-senescence
#16
Marieke Aarts, Athena Georgilis, Meryam Beniazza, Patrizia Beolchi, Ana Banito, Thomas Carroll, Marizela Kulisic, Daniel F Kaemena, Gopuraja Dharmalingam, Nadine Martin, Wolf Reik, Johannes Zuber, Keisuke Kaji, Tamir Chandra, Jesús Gil
Expression of the transcription factors OCT4, SOX2, KLF4, and cMYC (OSKM) reprograms somatic cells into induced pluripotent stem cells (iPSCs). Reprogramming is a slow and inefficient process, suggesting the presence of safeguarding mechanisms that counteract cell fate conversion. One such mechanism is senescence. To identify modulators of reprogramming-induced senescence, we performed a genome-wide shRNA screen in primary human fibroblasts expressing OSKM. In the screen, we identified novel mediators of OSKM-induced senescence and validated previously implicated genes such as CDKN1A We developed an innovative approach that integrates single-cell RNA sequencing (scRNA-seq) with the shRNA screen to investigate the mechanism of action of the identified candidates...
November 14, 2017: Genes & Development
https://www.readbyqxmd.com/read/29137993/characterization-of-cold-adapted-and-ethanol-tolerant-%C3%AE-glucosidase-from-bacillus-cellulosilyticus-and-its-application-for-directed-hydrolysis-of-cellobiose-to-ethanol
#17
Jian Wu, Alei Geng, Rongrong Xie, Hongcheng Wang, Jianzhong Sun
A β-glucosidase gene from Bacillus cellulosilyticus was expressed in Escherichia coli BL21 and characterized. The recombinant enzyme (BcBgl1A) showed the optimal activity at 40°C, and the half-life of BcBgl1A activity at 40 °C was 24 h. BcBgl1A was sensitive to heat and exhibited obvious cold-adapted activity, retained 27.2% and 46.5% of the optimal activity at 4 and 20°C, respectively. The best activity was observed at pH 7.0 and stable over the range of pH 6.0-8.0. The activity was significantly enhanced by Fe(2+), Fe(3+) and Mn(2+), also showed a high level of NaCl tolerance...
November 11, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29137634/profiling-of-saccharomyces-cerevisiae-transcription-factors-for-engineering-the-resistance-of-yeast-to-lignocellulose-derived-inhibitors-in-biomass-conversion
#18
Guochao Wu, Zixiang Xu, Leif J Jönsson
BACKGROUND: Yeast transcription factors (TFs) involved in the regulation of multidrug resistance (MDR) were investigated in experiments with deletion mutants, transformants overexpressing synthetic genes encoding TFs, and toxic concentrations of lignocellulose-derived substances added to cultures as complex mixtures or as specific compounds, viz. coniferyl aldehyde, 5-hydroxymethylfurfural, and furfural. RESULTS: In the presence of complex mixtures of toxic substances from spruce wood, transformants overexpressing YAP1 and STB5, TFs involved in oxidative stress response, exhibited enhanced relative growth rates amounting to 4...
November 14, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29137598/gff3sort-a-novel-tool-to-sort-gff3-files-for-tabix-indexing
#19
Tao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo, Rui Zhang
BACKGROUND: The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse. RESULTS: We developed GFF3sort, a script to sort GFF3 files for tabix indexing...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29137219/functional-characterization-of-lysine-specific-demethylase-2-lsd2-kdm1b-in-breast-cancer-progression
#20
Lin Chen, Shauna N Vasilatos, Ye Qin, Tiffany A Katz, Chunyu Cao, Hao Wu, Nilgun Tasdemir, Kevin M Levine, Steffi Oesterreich, Nancy E Davidson, Yi Huang
Flavin-dependent histone demethylases govern histone H3K4 methylation and act as important chromatin modulators that are extensively involved in regulation of DNA replication, gene transcription, DNA repair, and heterochromatin gene silencing. While the activities of lysine-specific demethylase 1 (LSD1/KDM1A) in facilitating breast cancer progression have been well characterized, the roles of its homolog LSD2 (KDM1B) in breast oncogenesis are relatively less understood. In this study, we showed that LSD2 protein level was significantly elevated in malignant breast cell lines compared with normal breast epithelial cell line...
October 10, 2017: Oncotarget
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