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https://www.readbyqxmd.com/read/28324984/prediction-method-for-intronic-alternative-polyadenylation-sites
#1
Shanxin Zhang
Alternative Polyadenylation (APA) of mRNAs has been proven as a considerable mechanism for post-transcriptional gene regulation. The interplay between Intronic APA and splicing may affect the isoforms of mRNAs. In this paper, we have found four prevalent motifs, i.e. AATAAA, TTTTTTTT, CCAGSCTGG and RGYRYRGTGG surrounding the polyadenylation sites; then we proposed a new computational method to identify the Intronic APA sites in the human genome, which is based on a Support Vector Machine (SVM) with weighted degree string kernel...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28324890/regulation-of-itga3-by-the-dual-stranded-microrna-199-family-as-a-potential-prognostic-marker-in-bladder-cancer
#2
Takashi Sakaguchi, Hirofumi Yoshino, Masaya Yonemori, Kazutaka Miyamoto, Satoshi Sugita, Ryosuke Matsushita, Toshihiko Itesako, Shuichi Tatarano, Masayuki Nakagawa, Hideki Enokida
BACKGROUND: Based on the microRNA (miRNA) signature of bladder cancer (BC) by deep sequencing, we recently found that several double-stranded mature miRNAs derived from the same pre-miRNAs were sufficiently expressed and acted as tumour suppressors by regulating common target genes in BC. Our deep-sequencing signature of BC showed that all miR-199 family members (miR-199a-3p/-5p and miR-199b-3p/-5p) were also downregulated. We hypothesised that these miRNAs may function as tumour suppressors by regulating common target genes...
March 21, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28324845/pharmacological-effects-of-%C3%AE-d-mannuronic-acid-m2000-on-mir-146a-irak1-traf6-and-nf-%C3%AE%C2%BAb-gene-expression-as-target-molecules-in-inflammatory-reactions
#3
Seyed Shahabeddin Mortazavi Jahromi, Mehdi Malek Jamshidi, Ali Farazmand, Zahra Aghazadeh, Mehdi Yousefi, Abbas Mirshafiey
BACKGROUND: Impaired expression and function of microRNAs (miRNAs) are involved in the pathogenesis of many autoimmune and inflammatory diseases. Moreover, there is a close relationship between TLRs and miRNAs and impairment in regulating their expression which can play a vital role in the immunopathogenesis of many inflammatory reactions. This research aimed to study the pharmaceutical effects of M2000 (β-d-mannuronic acid) on the expression of miR-146a and its two target molecules (IRAK1 and TRAF6), and the transcription factor NF-κB in the HEK-Blue hTLR2 cell line...
January 24, 2017: Pharmacological Reports: PR
https://www.readbyqxmd.com/read/28324818/exogenous-malic-acid-alleviates-cadmium-toxicity-in-miscanthus-sacchariflorus-through-enhancing-photosynthetic-capacity-and-restraining-ros-accumulation
#4
Haipeng Guo, Houming Chen, Chuntao Hong, Dean Jiang, Bingsong Zheng
Malic acid (MA) plays an important role in the regulation of plant growth, stomatal aperture, nutrition elements homeostasis and toxic metals tolerance. However, little is known about the effects of exogenous MA on physiological and biochemical responses to toxic metals in plants. To measure the alleviation roles of exogenous MA against cadmium (Cd), we determined the effects of MA on plant growth, net photosynthetic rate (Pn), reactive oxygen species (ROS) accumulation and the activities of anti-oxidant enzymes in the leaves of Miscanthus sacchariflorus (M...
March 18, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28324774/methylation-changes-of-sirt1-klf4-dapk1-and-spg20-in-b-lymphocytes-derived-from-follicular-and-diffuse-large-b-cell-lymphoma
#5
Raffaele Frazzi, Eleonora Zanetti, Mariaelena Pistoni, Ione Tamagnini, Riccardo Valli, Luca Braglia, Francesco Merli
Diffuse large-B cell lymphomas (DLBCL) and follicular lymphomas (FL) are the most represented subtypes among mature B-cell neoplasms and originate from malignant B lymphocytes. Methylation represents one of the major epigenetic mechanisms of gene regulation. Silent information regulator 1 (SIRT1) is a class III lysine-deacetylase playing several functions and considered to be a context-dependent tumor promoter. We present the quantitative methylation, gene expression and tissue distribution of SIRT1 and some key mediators related to lymphoma pathogenesis in B lymphocytes purified from biopsies of follicular hyperplasias, FL and DLBCL...
March 9, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28324702/the-cag-polymorphism-in-androgen-receptor-ar-gene-impacts-the-moral-permissibility-of-harmful-behavior-in-females
#6
Pingyuan Gong, Pengpeng Fang, Xing Yang, Wenzhao Ru, Bei Wang, Xiaocai Gao, Jinting Liu
The moral permissibility of harm is strikingly varied among individuals. In light of the connection between testosterone levels and utilitarian moral judgment, this study examined to what extent a CAG polymorphism in the androgen receptor gene, a genetic polymorphism with the ability to regulate testosterone function, contributes to individual differences in moral judgment. Four hundred and thirty-nine Chinese Han participants completed permissibility ratings of harm in moral dilemmas and moral transgression scenarios...
March 7, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28324682/gene-expression-analysis-in-untreated-absence-epilepsy-demonstrates-an-inconsistent-pattern
#7
Markus von Deimling, Robert Häsler, Verena Steinbach, Paul-Martin Holterhus, Sarah von Spiczak, Ulrich Stephani, Ingo Helbig, Hiltrud Muhle
OBJECTIVE: Childhood and Juvenile Absence Epilepsy account for 30% of all genetic generalized epilepsies with a strong genetic contribution. At the current state the genetic background remains to be resolved. The aim of this study was to identify disease associated transcripts pinpointing potential underlying disease mechanisms in patients with CAE and JAE. METHODS: We performed gene expression analysis from peripheral blood mononuclear cells (PBMCs) in 30 patients with newly-diagnosed absence epilepsy prior to initiating treatment and 30 healthy age - and gender-matched pediatric controls...
February 28, 2017: Epilepsy Research
https://www.readbyqxmd.com/read/28324652/positive-feedback-genetic-circuit-incorporating-a-constitutively-active-mutant-gal3-into-yeast-gal-induction-system
#8
Shintaro Ryo, Jun Ishii, Toshihide Matsuno, Yasuyuki Nakamura, Daiki Matsubara, Masahiro Tominaga, Akihiko Kondo
The GAL expression system is the most frequently used induction technique in the yeast Saccharomyces cerevisiae. Here we report a simple but powerful genetic circuit for use with the GAL induction system. Briefly, an artificial positive feedback circuit was incorporated into the GAL regulatory network. We selected green fluorescent protein (GFP) as a reporter of GAL1 induction, and designed a strain that expressed a constitutively active Gal3 mutant protein (Gal3(c)) under control of the GAL10 promoter. In the resulting strain, GAL1 and GAL10 promoters regulate the expression of GFP and GAL3(c), respectively...
March 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28324630/morphological-and-neurochemical-differences-in-peptidergic-nerve-fibres-of-the-mouse-vagina
#9
Christine Barry, Esther Ji, Harman Sharma, Lara Beukes, Pat Vilimas, Yvette DeGraaf, Dusan Matusica, Rainer V Haberberger
The vagina is innervated by a complex arrangement of sensory, sympathetic and parasympathetic nerve fibres that contain classical transmitters plus an array of neuropeptides and enzymes known to regulate diverse processes including blood flow and nociception. The neurochemical characteristics and distributions of peptide-containing nerves in the mouse vagina are unknown. This study used multiple labelling immunohistochemistry, confocal imaging and analysis to investigate the presence and colocalization of the peptides vasoactive intestinal polypeptide (VIP), calcitonin-gene related peptide (CGRP), substance P (SP), neuropeptide tyrosine (NPY) and the nitric oxide synthesizing enzyme neuronal nitric oxide synthase (nNOS) in nerve fibres of the murine vaginal wall...
March 21, 2017: Journal of Comparative Neurology
https://www.readbyqxmd.com/read/28324489/monitoring-mitochondrial-changes-by-alteration-of-the-pink1-parkin-signaling-in-drosophila
#10
Tsuyoshi Inoshita, Kahori Shiba-Fukushima, Hongrui Meng, Nobutaka Hattori, Yuzuru Imai
Mitochondrial quality control is a key process in tissues with high energy demands, such as the brain and muscles. Recent studies using Drosophila have revealed that the genes responsible for familial forms of juvenile Parkinson's disease (PD), PINK1 and Parkin regulate mitochondrial function and motility. Cell biological analysis using mammalian cultured cells suggests that the dysregulation of mitophagy by PINK1 and Parkin leads to neurodegeneration in PD. In this chapter, we describe the methods to monitor mitochondrial morphology in the indirect flight muscles of adult Drosophila and Drosophila primary cultured neurons and the methods to analyze the motility of mitochondria in the axonal transport of living larval motor neurons...
March 22, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324206/indeterminate-domain-protein-binding-sequences-in-the-5-untranslated-region-and-promoter-of-the-scarecrow-gene-play-crucial-and-distinct-roles-in-regulating-scarecrow-expression-in-roots-and-leaves
#11
Atsushi Kobayashi, Satoshi Miura, Akiko Kozaki
SCARECROW (SCR) and SHORT-ROOT (SHR), which belong to the GRAS transcription factor family, are key regulators of root and leaf growth and development. Despite the importance of SCR expression for proper plant development, the mechanism of SCR regulation has not been clarified. A previous study showed that an INDETERMINATE DOMAIN transcription factor, JACKDAW (JKD), is essential for the expression of SCR in combination with SCR and SHR. In this study, we characterized possible binding sequences of INDETERMINATE DOMAIN PROTEIN in the 1...
March 21, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28324176/bhlha9-regulates-apical-ectodermal-ridge-formation-during-limb-development
#12
Kensuke Kataoka, Takahide Matsushima, Yoshiaki Ito, Tempei Sato, Shigetoshi Yokoyama, Hiroshi Asahara
Split hand/foot malformation (SHFM) and SHFM combined with long-bone deficiency (SHFLD) are congenital dysgeneses of the limb. Although six different loci/mutations (SHFM1-SHFM6) have been found from studies on families with SHFM, the causes and associated pathogenic mechanisms for a large number of patients remain unidentified. On the basis of the identification of a duplicated gene region involving BHLHA9 in some affected families, BHLHA9 was identified as a novel SHFM/SHFLD-related gene. Although Bhlha9 is predicted to participate in limb development as a transcription factor, its precise function is unclear...
March 21, 2017: Journal of Bone and Mineral Metabolism
https://www.readbyqxmd.com/read/28324173/effect-of-oaz1-overexpression-on-goose-ovarian-granulosa-cells
#13
Bo Kang, Dongmei Jiang, Hui He, Rong Ma, Ziyu Chen, Zhixin Yi
Ornithine decarboxylase antizyme 1 (OAZ1) regulates both polyamine biosynthesis and transport and acts as a tumor suppressor because of its functions in the regulation of cell proliferation, apoptosis and growth. However, the roles of OAZ1 in the regulation of polyamine metabolism, cell proliferation, apoptosis and hormone receptor expression in granulosa cells (GCs) from geese have not been determined. To define the roles of OAZ1 in primary GCs, we constructed and transfected an Oaz1 overexpression vector with a thymidine deletion into primary GCs...
March 21, 2017: Amino Acids
https://www.readbyqxmd.com/read/28324111/arap1-deficiency-causes-photoreceptor-degeneration-in-mice
#14
Ala Moshiri, Devin Humpal, Brian C Leonard, Denise M Imai, Addy Tham, Lynette Bower, Dave Clary, Thomas M Glaser, K C Kent Lloyd, Christopher J Murphy
Purpose: Small guanosine triphosphatase (GTPase) ADP-ribosylation factors (Arfs) regulate membrane traffic and actin reorganization under the control of GTPase-activating proteins (GAPs). Arap1 is an Arf-directed GAP that inhibits the trafficking of epidermal growth factor receptor (EGFR) to the early endosome, but the diversity of its functions is incompletely understood. The aim of this study was to determine the role of Arap1 in the mammalian retina. Methods: Genetically engineered Arap1 knockout mice were screened for ocular abnormalities in the National Institutes of Health Knockout Mouse Production and Phenotyping (KOMP2) Project...
March 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28324069/glucose-homeostasis-regulation-by-peripheral-circadian-clocks-in-rodents-and-humans
#15
Frederic Gachon, Ursula Loizides-Mangold, Volodymyr Petrenko, Charna Dibner
Most organisms, including humans, have developed an intrinsic system of circadian oscillators, allowing the anticipation of events related to the rotation of the Earth around its own axis. The mammalian circadian timing system orchestrates nearly all aspects of physiology and behavior. Together with systemic signals, emanating from the central clock which resides in the hypothalamus, peripheral oscillators orchestrate tissue-specific fluctuations in gene expression, protein synthesis, and posttranslational modifications, driving overt rhythms in physiology and behavior...
March 15, 2017: Endocrinology
https://www.readbyqxmd.com/read/28324053/hepatic-insulin-resistance-and-altered-gluconeogenic-pathway-in-premature-baboons
#16
Lisa McGill-Vargas, Amalia Gastaldelli, Hanyu Liang, Diana Anzueto Guerra, Teresa Johnson-Pais, Steven Seidner, Donald McCurnin, Giovanna Muscogiuri, Ralph DeFronzo, Nicolas Musi, Cynthia Blanco
Premature infants have altered glucose regulation early in life and increased risk for diabetes in adulthood. Although prematurity leads to an increased risk of diabetes and metabolic syndrome in adult life, the role of hepatic glucose regulation and adaptation to an early extra-uterine environment in preterm infants remain unknown. The purpose of this study was to investigate developmental differences in glucose metabolism, hepatic protein content and gene expression of key insulin signaling/gluconeogenic molecules...
January 17, 2017: Endocrinology
https://www.readbyqxmd.com/read/28324048/demonstration-of-a-functional-kiss-kissr-system-in-amphioxus-with-implications-for-origin-of-neuroendocrine-regulation
#17
Peng Wang, Meng Wang, Guangdong Ji, Shuangshuang Yang, Shicui Zhang, Zhenhui Liu
Amphioxus belongs to the Cephalochordata, which is the most basal subphylum of the chordates. Despite many studies on the endocrine system of amphioxus, key information about its regulation remains ambiguous. Here we clearly demonstrated the presence of a functional kisspeptin/kisspeptin receptor (Kiss-Kissr) system, which is involved in the regulation of reproduction in amphioxus. Evolutionary analyses revealed large expansion of Kiss and Kissr (gpr54) genes in amphioxus and they might represent the ancestral type of the Kiss/gpr54 genes in chordates...
January 24, 2017: Endocrinology
https://www.readbyqxmd.com/read/28324044/inverse-regulation-of-dht-synthesis-enzymes-5%C3%AE-reductase-types-1-and-2-by-the-androgen-receptor-in-prostate-cancer
#18
Étienne Audet-Walsh, Tracey Yee, Ingrid S Tam, Vincent Giguère
5α-reductase types 1 and 2, encoded by SRD5A1 and SRD5A2, are the two enzymes that can catalyze the conversion of testosterone to dihydrotestosterone, the most potent androgen receptor (AR) agonist in prostate cells. 5α-reductase type 2 is the predominant isoform expressed in the normal prostate. However, its expression decreases during prostate cancer (PCa) progression, while SRD5A1 increases and the mechanism underlying this transcriptional regulatory switch is still unknown. Interrogation of SRD5A mRNA expression in three publicly available datasets confirmed that SRD5A1 is increased in primary and metastatic PCa compared to non-tumoral prostate tissues, while SRD5A2 is decreased...
January 23, 2017: Endocrinology
https://www.readbyqxmd.com/read/28324027/follistatin-targets-distinct-pathways-to-promote-brown-adipocyte-characteristics-in-brown-and-white-adipose-tissues
#19
Rajan Singh, Melissa Braga, Srinivasa T Reddy, Se-Jin Lee, Meher Parveen, Victor Grijalva, Laurent Vergnes, Shehla Pervin
We previously demonstrated that Fst expression is highest in brown adipose tissue (BAT) and skeletal muscle, but is also present at substantial levels in epididymal (Epi) and subcutaneous (SC) white adipose tissues (WAT). Fst promotes mouse brown preadipocyte differentiation and promotes browning during differentiation of mouse embryonic fibroblasts (MEFs). Fst-transgenic (Fst-Tg) mouse show significant increase in circulating Fst levels and increased brown adipose mass. BAT of Fst-Tg mice had increased expression of brown adipose-associated markers including uncoupling protein 1 (UCP1), PRDM16, PGC-1α and Glut4...
January 16, 2017: Endocrinology
https://www.readbyqxmd.com/read/28324024/thyroid-hormone-receptor-%C3%AE-controls-developmental-timing-and-regulates-the-rate-and-coordination-of-tissue-specific-metamorphosis-in-xenopus-tropicalis
#20
Luan Wen, Yuki Shibata, Dan Su, Liezhen Fu, Nga Luu, Yun-Bo Shi
Thyroid hormone (T3) receptor (TR) mediates the effects of T3 on organ metabolism and animal development. There are two TR genes, TRα and TRβ, in all vertebrates. During animal development, TRα expression is activated earlier than zygotic T3 synthesis and secretion into the plasma, implicating a developmental role of TRα both in the presence and absence of T3. Using T3-dependend amphibian metamorphosis as a model, we have previously proposed a dual functional model for TRs, in particular TRα, during development...
March 14, 2017: Endocrinology
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