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PSMD1 and PSMD2 regulate HepG2 cell proliferation and apoptosis via modulating cellular lipid droplet metabolism. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-11-08 Yanjie Tan,Yi Jin,Xiang Wu,Zhuqing Ren
Obesity and nonalcoholic steatohepatitis (NASH) are well-known risk factors of hepatocellular carcinoma (HCC). The lipid-rich environment enhances the proliferation and metastasis abilities of tumor cells. Previous studies showed the effect of the ubiquitin–proteasome system (UPS) on tumor cell proliferation. However, the underlying mechanism of UPS in regulating the proliferation of lipid-rich tumor
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The effect of BACE1-AS on β-amyloid generation by regulating BACE1 mRNA expression. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-10-01 Fan Li,Yun Wang,Hui Yang,Yingying Xu,Xiaoyan Zhou,Xiao Zhang,Zhaohong Xie,Jianzhong Bi
The BACE1 antisense transcript (BACE1-AS) is a conserved long noncoding RNA (lncRNA). The level of BACE1-AS is significantly increased and the level of the BACE1 mRNA is slightly increased in subjects with AD. BACE1-AS exerts a significant moderating effect on the expression of the BACE1 mRNA and promotes the formation of Aβ. After the administration of Aβ1-42 to SH-SY5Y cells and C57/BL6J mice, we
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Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-09-23 Shivani Sharma,Gazaldeep Kaur,Anil Kumar,Varsha Meena,Jaspreet Kaur,Ajay Kumar Pandey
Hexaploid wheat is an important cereal crop that has been targeted to enhance grain micronutrient content including zinc (Zn) and iron (Fe). In this direction, modulating the expression of plant transporters involved in Fe and Zn homeostasis has proven to be one of the promising approaches. The present work was undertaken to identify wheat zinc-induced facilitator-like (ZIFL) family of transporters
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MiR-32-5p influences high glucose-induced cardiac fibroblast proliferation and phenotypic alteration by inhibiting DUSP1. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-08-22 Jie Shen,Wanhong Xing,Rui Liu,Yiying Zhang,Chunhong Xie,Fangqi Gong
The current study aimed to investigate the effects of miR-32-5p on cardiac fibroblasts (CFs) that were induced with high levels of glucose; we also aimed to identify the potential mechanisms involved in the regulation of DUSP1 expression. Human CFs were transfected with a miR-32-5p inhibitor or mimic and were treated with a normal concentration or a high concentration of glucose. Flow cytometry analysis
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Comparison of miRNA-101a-3p and miRNA-144a-3p regulation with the key genes of alpaca melanocyte pigmentation. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-08-14 Zhiwei Zhu,Yueyue Ma,Yuan Li,Zhixue Cheng,Huifeng Li,Lihuan Zhang,Dongmei Xu,Pengfei Li
Many miRNA functions have been revealed to date. Single miRNAs can participate in life processes by regulating more than one target gene, and more than one miRNA can also simultaneously act on one target mRNA. Thus, a complex regulatory network involved in many processes can be formed. Herein, the pigmentation regulation mechanism of miR-101a-3p and miR-144a-3p was studied at the cellular level by
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Correction to: A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-08-14 Neftali Vazquez,Lilia Sanchez,Rebecca Marks,Eduardo Martinez,Victor Fanniel,Alma Lopez,Andrea Salinas,Itzel Flores,Jesse Hirschmann,Robert Gilkerson,Erin Schuenzel,Robert Dearth,Reginald Halaby,Wendy Innis-Whitehouse,Megan Keniry
The original article [1] contains three erroneous mentions of usage of a restriction enzyme—BstZ17I—in the Methods section as displayed in the following sentences.
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Correction to: MicroRNA-325-3p protects the heart after myocardial infarction by inhibiting RIPK3 and programmed necrosis in mice. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-08-06 Dong-Ying Zhang,Bing-Jian Wang,Min Ma,Kun Yu,Qing Zhang,Xi-Wen Zhang
The original article [1] contains an error whereby Fig. 7 displays incorrect results; the correct version of Fig. 7 can be viewed ahead in this Correction article and should be considered in place of the original article’s version of Fig. 7.
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MicroRNA-325-3p protects the heart after myocardial infarction by inhibiting RIPK3 and programmed necrosis in mice. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-06-27 Dong-Ying Zhang,Bing-Jian Wang,Min Ma,Kun Yu,Qing Zhang,Xi-Wen Zhang
Receptor-interacting serine-threonine kinase 3 (RIPK3)-mediated necroptosis has been implicated in the progression of myocardial infarction (MI), but the underlying mechanisms, particularly whether microRNAs (miRNAs) are involved, remain largely unknown. A microarray analysis was used to screen for miR-325-3p expression in myocardial tissues from MI mice, and the expression was confirmed with qRT-PCR
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Giant group I intron in a mitochondrial genome is removed by RNA back-splicing. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-06-01 Sylvia Ighem Chi,Mikael Dahl,Åse Emblem,Steinar D Johansen
The mitochondrial genomes of mushroom corals (Corallimorpharia) are remarkable for harboring two complex group I introns; ND5-717 and COI-884. How these autocatalytic RNA elements interfere with mitochondrial RNA processing is currently not known. Here, we report experimental support for unconventional processing events of ND5-717 containing RNA. We obtained the complete mitochondrial genome sequences
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Exploration of carbohydrate binding behavior and anti-proliferative activities of Arisaema tortuosum lectin. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-05-07 Kshema Thakur,Tarnjeet Kaur,Manpreet Kaur,Rachna Hora,Jatinder Singh
Lectins have come a long way from being identified as proteins that agglutinate cells to promising therapeutic agents in modern medicine. Through their specific binding property, they have proven to be anti-cancer, anti-insect, anti-viral agents without affecting the non-target cells. The Arisaema tortuosum lectin (ATL) is a known anti-insect and anti-cancer candidate, also has interesting physical
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Characterization of cadmium-responsive MicroRNAs and their target genes in maize (Zea mays) roots. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-05-02 Jian Gao,Mao Luo,Hua Peng,Fabo Chen,Wenbo Li
Current research has shown that microRNAs (miRNAs) play vital roles in plant response to stress caused by heavy metals such as aluminum, arsenic, cadmium (Cd), and mercury. Cd has become one of the most hazardous pollutants in the environment. Maize can be a potential model to study phytoremediation of Cd-contaminated soil owing to its large biomass production. However, little is known about miRNAs
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Identification and validation of reference genes for real-time quantitative RT-PCR analysis in jute. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-04-29 Md Sabbir Hossain,Rasel Ahmed,Md Samiul Haque,Md Monjurul Alam,Md Shahidul Islam
With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene expression profiles of a target gene can provide valuable clues towards the understanding of its biological function. Reverse transcription quantitative real-time PCR (qRT-PCR) is the best method
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Small nucleolar RNA Sf-15 regulates proliferation and apoptosis of Spodoptera frugiperda Sf9 cells. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-04-11 Bo Wu,Lei Huang,Wujie Qiu,Xiao Liu,Yawen Shen,Yiping Lu,Zonglin Yang,Xinmei Li,Bin Cui,Shidong Xu,Huili Qiao,Reng Qiu,Lunguang Yao,Yunchao Kan,Dandan Li
Small nucleolar RNAs (snoRNAs) function in guiding 2′-O-methylation and pseudouridylation of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). In recent years, more and more snoRNAs have been found to play novel roles in mRNA regulation, such as pre-mRNA splicing or RNA editing. In our previous study, we found a silkworm C/D box snoRNA Bm-15 can interact with Notch receptor gene in vitro. To
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Key genes differential expressions and pathway involved in salt and water-deprivation stresses for renal cortex in camel. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-04-08 Yu Cao,Dong Zhang,Huanmin Zhou
Camels possess the characteristics of salt- and drought-resistances, due to the long-time adaption to the living environment in desert. The camel resistance research on transcriptome is rare and deficient, especially reabsorption in renal cortex. Non-coding RNAs are normally considered as the RNA molecules that are not translated into proteins, their current roles remain mostly in regulation of information
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Development of a novel selection/counter-selection system for chromosomal gene integrations and deletions in lactic acid bacteria. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-03-29 Winschau F Van Zyl,Leon M T Dicks,Shelly M Deane
The underlying mechanisms by which probiotic lactic acid bacteria (LAB) enhance the health of the consumer have not been fully elucidated. Verification of probiotic modes of action can be achieved by using single- or multiple-gene knockout analyses of bacterial mutants in in vitro or in vivo models. We developed a novel system based on an inducible toxin counter-selection system, allowing for rapid
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Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-03-25 Renjun Qu,Yujing Miao,Yingjing Cui,Yiwen Cao,Ying Zhou,Xiaoqing Tang,Jie Yang,Fangquan Wang
Isatis indigotica, a traditional Chinese medicine, produces a variety of active ingredients. However, little is known about the key genes and corresponding expression profiling involved in the biosynthesis pathways of these ingredients. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful, commonly-used method for gene expression analysis, but the accuracy of the quantitative data
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MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-03-18 Yujuan Xiong,Lin Wang,Wenyi Jiang,Lihua Pang,Weihua Liu,Aiqun Li,Yun Zhong,Wenchao Ou,Benrong Liu,Shi-Ming Liu
Myocyte enhancer factor 2A (MEF2A) plays an important role in cell proliferation, differentiation and survival. Functional deletion or mutation in MEF2A predisposes individuals to cardiovascular disease mainly caused by vascular endothelial dysfunction. However, the effect of the inhibition of MEF2A expression on human coronary artery endothelial cells (HCAECs) is unclear. In this study, expression
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Transcriptomic responses to grazing reveal the metabolic pathway leading to the biosynthesis of domoic acid and highlight different defense strategies in diatoms. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-02-26 Sara Harðardóttir,Sylke Wohlrab,Ditte Marie Hjort,Bernd Krock,Torkel Gissel Nielsen,Uwe John,Nina Lundholm
A major cause of phytoplankton mortality is predation by zooplankton. Strategies to avoid grazers have probably played a major role in the evolution of phytoplankton and impacted bloom dynamics and trophic energy transport. Certain species of the genus Pseudo-nitzschia produce the neurotoxin, domoic acid (DA), as a response to the presence of copepod grazers, suggesting that DA is a defense compound
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RNA sequencing, selection of reference genes and demonstration of feeding RNAi in Thrips tabaci (Lind.) (Thysanoptera: Thripidae). BMC Molecular Biol. (IF 4.619) Pub Date : 2019-02-18 Satnam Singh,Mridula Gupta,Suneet Pandher,Gurmeet Kaur,Neha Goel,Pankaj Rathore,Subba Reddy Palli
Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this insect, RNA was sequenced; de novo transcriptome assembly and analysis were performed. The RNAseq data was used to identify reference and RNAi pathway genes in this insect. Additionally, feeding
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A fragment activity assay reveals the key residues of TBC1D15 GTPase-activating protein (GAP) in Chiloscyllium plagiosum. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-02-12 Yangyang Jin,Guodong Lin,Yanna Chen,Yinghua Ge,Ruofeng Liang,Jia Wu,Jianqing Chen,Dan Wang,Hengbo Shi,Hui Fei,Zhengbing Lv
GTPase-activating proteins (GAPs) with a TBC (Tre-2/Bub2/Cdc16) domain architecture serve as negative regulators of Rab GTPases. The related crystal structure has been studied and reported by other members of our research group in 2017 (Chen et al. in Protein Sci 26(4):834–846, 2017). The protein crystal structure and sequencing data accession numbers in Protein structure database (PDB) are 5TUB (Shark
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HexA is required for growth, aflatoxin biosynthesis and virulence in Aspergillus flavus. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-02-11 Jun Yuan,Ding Li,Ling Qin,Jiaojiao Shen,Xiaodong Guo,Elisabeth Tumukunde,Mingzhu Li,Shihua Wang
Woronin bodies are fungal-specific organelles whose formation is derived from peroxisomes. The former are believed to be involved in the regulation of mycotoxins biosynthesis, but not in their damage repair function. The hexagonal peroxisome protein (HexA or Hex1) encoded by hexA gene in Aspergillus is the main and the essential component of the Woronin body. However, little is known about HexA in
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Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-01-15 Yanhong Zhao,Anmin Zhang,Yanfang Wang,Shuping Hu,Ruiping Zhang,Shuaiwei Qian
Physical exercise can improve brain function by altering brain gene expression. The expression mechanisms underlying the brain’s response to exercise still remain unknown. miRNAs as vital regulators of gene expression may be involved in regulation of brain genes in response to exercise. However, as yet, very little is known about exercise-responsive miRNAs in brain. We constructed two comparative small
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MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-01-03 Berna I G Kappeler,Luciana C A Regitano,Mirele D Poleti,Aline S M Cesar,Gabriel C M Moreira,Gustavo Gasparin,Luiz L Coutinho
MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great
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Graphene oxide down-regulates genes of the oxidative phosphorylation complexes in a glioblastoma. BMC Molecular Biol. (IF 4.619) Pub Date : 2019-01-03 Maciej Szmidt,Adrian Stankiewicz,Kaja Urbańska,Sławomir Jaworski,Marta Kutwin,Mateusz Wierzbicki,Marta Grodzik,Beata Burzyńska,Monika Góra,André Chwalibog,Ewa Sawosz
Recently different forms of nanographene were proposed as the material with high anticancer potential. However, the mechanism of the suppressive activity of the graphene on cancer development remains unclear. We examined the effect of oxygenated, reduced and pristine graphene on the gene expression in glioblastoma U87 cell line. Conducting microarrays and RT-qPCR analysis we explored that graphene
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The Dictyostelium discoideum homologue of Twinkle, Twm1, is a mitochondrial DNA helicase, an active primase and promotes mitochondrial DNA replication. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-12-19 Ashley Harman,Christian Barth
DNA replication requires contributions from various proteins, such as DNA helicases; in mitochondria Twinkle is important for maintaining and replicating mitochondrial DNA. Twinkle helicases are predicted to also possess primase activity, as has been shown in plants; however this activity appears to have been lost in metazoans. Given this, the study of Twinkle in other organisms is required to better
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Matrix association region/scaffold attachment region (MAR/SAR) sequence: its vital role in mediating chromosome breakages in nasopharyngeal epithelial cells via oxidative stress-induced apoptosis. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-12-04 Sang-Nee Tan,Sai-Peng Sim,Alan S B Khoo
Oxidative stress is known to be involved in most of the aetiological factors of nasopharyngeal carcinoma (NPC). Cells that are under oxidative stress may undergo apoptosis. We have previously demonstrated that oxidative stress-induced apoptosis could be a potential mechanism mediating chromosome breakages in nasopharyngeal epithelial cells. Additionally, caspase-activated DNase (CAD) may be the vital
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Molecular analysis of NPAS3 functional domains and variants. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-12-03 Leiah M Luoma,Fred B Berry
NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to cause alterations in neurodevelopment, as well as a marked reduction in neurogenesis in the adult mouse hippocampus. This neurogenic deficit, alongside the reduction in cortical interneuron number, likely contributes to the behavioral
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Integration of transcriptome and proteome profiles in glioblastoma: looking for the missing link. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-11-21 Jean-Michel Lemée,Anne Clavreul,Marc Aubry,Emmanuelle Com,Marie de Tayrac,Jean Mosser,Philippe Menei
Glioblastoma (GB) is the most common and aggressive tumor of the brain. Genotype-based approaches and independent analyses of the transcriptome or the proteome have led to progress in understanding the underlying biology of GB. Joint transcriptome and proteome profiling may reveal new biological insights, and identify pathogenic mechanisms or therapeutic targets for GB therapy. We present a comparison
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Analyses of changes in myocardial long non-coding RNA and mRNA profiles after severe hemorrhagic shock and resuscitation via RNA sequencing in a rat model. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-11-01 Lin Lin,Zhengfei Yang,Guanghui Zheng,Yongxun Zhuansun,Yue Wang,Jianguo Li,Rui Chen,Wanchun Tang
Ischemia–reperfusion injury has been proven to induce organ dysfunction and death, although the mechanism is not fully understood. Long non-coding RNAs (lncRNAs) have drawn wide attention with their important roles in the gene expression of some biological processes and diseases, including myocardial ischemia–reperfusion (I/R) injury. In this paper, a total of 26 Sprague–Dawley (SD) rats were randomized
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Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-08-01 Paola M Boggiatto,Daniel Fitzsimmons,Darrell O Bayles,David Alt,Catherine E Vrentas,Steven C Olsen
Brucella melitensis bacteria cause persistent, intracellular infections in small ruminants as well as in humans, leading to significant morbidity and economic loss worldwide. The majority of experiments on the transcriptional responses of Brucella to conditions inside the host have been performed following invasion of cultured mammalian cells, and do not address gene expression patterns during long-term
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Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-07-27 Aleksandra Brzek,Marlena Cichocka,Jakub Dolata,Wojciech Juzwa,Daniel Schümperli,Katarzyna Dorota Raczynska
Core canonical histones are required in the S phase of the cell cycle to pack newly synthetized DNA, therefore the expression of their genes is highly activated during DNA replication. In mammalian cells, this increment is achieved by both enhanced transcription and 3′ end processing. In this paper, we described positive cofactor 4 (PC4) as a protein that contributes to the regulation of replication-dependent
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Evaluation of suitable reference genes for qRT-PCR normalization in strawberry (Fragaria × ananassa) under different experimental conditions. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-06-22 Yunting Zhang,Xiaorui Peng,Yi Liu,Yali Li,Ya Luo,Xiaorong Wang,Haoru Tang
Strawberry has received much attention due to its nutritional value, unique flavor, and attractive appearance. The availability of the whole genome sequence and multiple transcriptome databases allows the great possibility to explore gene functions, comprehensively. Gene expression profiles of a target gene can provide clues towards the understanding of its biological function. Quantitative real-time
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Laser capture microdissection for transcriptomic profiles in human skin biopsies. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-06-19 Silvia Santoro,Ignazio Diego Lopez,Raffaella Lombardi,Andrea Zauli,Ana Maria Osiceanu,Melissa Sorosina,Ferdinando Clarelli,Silvia Peroni,Daniele Cazzato,Margherita Marchi,Angelo Quattrini,Giancarlo Comi,Raffaele Adolfo Calogero,Giuseppe Lauria,Filippo Martinelli Boneschi
The acquisition of reliable tissue-specific RNA sequencing data from human skin biopsy represents a major advance in research. However, the complexity of the process of isolation of specific layers from fresh-frozen human specimen by laser capture microdissection, the abundant presence of skin nucleases and RNA instability remain relevant methodological challenges. We developed and optimized a protocol
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Targeting miR-9 in gastric cancer cells using locked nucleic acid oligonucleotides. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-06-07 Joana Filipa Lima,Joana Carvalho,Inês Pinto-Ribeiro,Carina Almeida,Jesper Wengel,Laura Cerqueira,Céu Figueiredo,Carla Oliveira,Nuno Filipe Azevedo
Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recently, it has been demonstrated that gastric cancer cells display a specific miRNA expression profile, with increasing evidence of the role of miRNA-9 in this disease. miRNA-9 upregulation has been shown to influence the expression of E-cadherin-encoding gene, triggering cell motility and invasiveness. In this study
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Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-03-27 Yiming K Chang,Zheng Zuo,Gary D Stormo
BATF family transcription factors (BATF, BATF2 and BATF3) form hetero-trimers with JUNB and either IRF4 or IRF8 to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the hetero-trimer has a distinct role, some degree of cross-compensation was observed. The basis for the differential actions of IRF4 and IRF8 with BATF factors and JUNB is still unknown. We propose that
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pH-mediated upregulation of AQP1 gene expression through the Spi-B transcription factor. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-03-20 Yihui Zhai,Hong Xu,Qian Shen,Franz Schaefer,Claus P Schmitt,Jing Chen,Haimei Liu,Jialu Liu,Jiaojiao Liu
Bicarbonate-based peritoneal dialysis (PD) fluids enhance the migratory capacity and damage-repair ability of human peritoneal mesothelial cells by upregulating AQP1. However, little is known about the underlying molecular mechanisms. Here we used HEK-293T cells to investigate the effect of pH on AQP1 gene transcription levels. We found that AQP1 mRNA levels increases with pH. Transfection of HEK-293T
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A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-03-14 Neftali Vazquez,Lilia Sanchez,Rebecca Marks,Eduardo Martinez,Victor Fanniel,Alma Lopez,Andrea Salinas,Itzel Flores,Jesse Hirschmann,Robert Gilkerson,Erin Schuenzel,Robert Dearth,Reginald Halaby,Wendy Innis-Whitehouse,Megan Keniry
Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employed as genome editing tools in wide ranging organisms. Here, we provide a detailed protocol to truncate genes in mammalian cells using CRISPR Cas9 editing. We describe custom donor vector construction
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Recommendations for mRNA analysis of micro-dissected glomerular tufts from paraffin-embedded human kidney biopsy samples. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-03-13 Clemens L Bockmeyer,Juliane Wittig,Karen Säuberlich,Philipp Selhausen,Marc Eßer,Philip Zeuschner,Friedrich Modde,Kerstin Amann,Christoph Daniel
Glomeruli are excellent pre-determined natural structures for laser micro-dissection. Compartment-specific glomerular gene expression analysis of formalin-fixed paraffin-embedded renal biopsies could improve research applications. The major challenge for such studies is to obtain good-quality RNA from small amounts of starting material, as applicable for the analysis of glomerular compartments. In
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Nutrient depletion and TOR inhibition induce 18S and 25S ribosomal RNAs resistant to a 5'-phosphate-dependent exonuclease in Candida albicans and other yeasts. BMC Molecular Biol. (IF 4.619) Pub Date : 2018-01-19 Jacob Fleischmann,Miguel A Rocha
Messenger RNA (mRNA) represents a small percentage of RNAs in a cell, with ribosomal RNA (rRNA) making up the bulk of it. To isolate mRNA from eukaryotes, typically poly-A selection is carried out. Recently, a 5´-phosphate-dependent, 5´→3´ processive exonuclease called Terminator has become available. It will digest only RNA that has a 5´-monophosphate end and therefore it is very useful to eliminate
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An optimized rapid bisulfite conversion method with high recovery of cell-free DNA. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-12-19 Shaohua Yi,Fei Long,Juanbo Cheng,Daixin Huang
Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. However
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Sumoylation in p27kip1 via RanBP2 promotes cancer cell growth in cholangiocarcinoma cell line QBC939. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-09-07 Jun Yang,Yan Liu,Bing Wang,Hongzhen Lan,Ying Liu,Fei Chen,Ju Zhang,Jian Luo
Cholangiocarcinoma is one of the deadly disease with poor 5-year survival and poor response to conventional therapies. Previously, we found that p27kip1 nuclear-cytoplasmic translocation confers proliferation potential to cholangiocarcinoma cell line QBC939 and this process is mediated by crm-1. However, no other post-transcriptional regulation was found in this process including sumoylation in cholangiocarcinoma
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An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-08-23 Parisa Amini,Julia Ettlin,Lennart Opitz,Elena Clementi,Alexandra Malbon,Enni Markkanen
Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA–protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e.g. when performing Laser-capture microdissection
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Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-08-09 Gorantla Venkata Raghuram,Deepika Gupta,Siddharth Subramaniam,Ashwini Gaikwad,Naveen Kumar Khare,Malcolm Nobre,Naveen Kumar Nair,Indraneel Mittra
We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular
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Interaction between NFATc2 and the transcription factor Sp1 in pancreatic carcinoma cells PaTu 8988t. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-08-03 Manuela Malsy,Bernhard Graf,Katrin Almstedt
Nuclear factors of activated T-cells (NFATs) have been mainly characterized in the context of immune response regulation because, as transcription factors, they have the ability to induce gene transcription. NFAT proteins are found in several types of tumors, for instance, pancreatic carcinoma. The role of NFATs in carcinogenesis is regulating central genes in cell differentiation and cell growth.
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Splicing arrays reveal novel RBM10 targets, including SMN2 pre-mRNA. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-07-20 Leslie C Sutherland,Philippe Thibault,Mathieu Durand,Elvy Lapointe,Jose M Knee,Ariane Beauvais,Irina Kalatskaya,Sarah C Hunt,Julie J Loiselle,Justin G Roy,Sarah J Tessier,Gustavo Ybazeta,Lincoln Stein,Rashmi Kothary,Roscoe Klinck,Benoit Chabot
RBM10 is an RNA binding protein involved in message stabilization and alternative splicing regulation. The objective of the research described herein was to identify novel targets of RBM10-regulated splicing. To accomplish this, we downregulated RBM10 in human cell lines, using small interfering RNAs, then monitored alternative splicing, using a reverse transcription-PCR screening platform. RBM10 knockdown
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Growth arrest specific gene 2 in tilapia (Oreochromis niloticus): molecular characterization and functional analysis under low-temperature stress. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-07-17 ChangGeng Yang,Fan Wu,Xing Lu,Ming Jiang,Wei Liu,Lijuan Yu,Juan Tian,Hua Wen
Growth arrest specific 2 (gas2) gene is a component of the microfilament system that plays a major role in the cell cycle, regulation of microfilaments, and cell morphology during apoptotic processes. However, little information is available on fish gas2. In this study, the tilapia (Oreochromis niloticus) gas2 gene was cloned and characterized for the first time. The open reading frame was 1020 bp
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Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-06-27 Daniyah H Bay,Annika Busch,Fred Lisdat,Keisuke Iida,Kazunori Ikebukuro,Kazuo Nagasawa,Isao Karube,Wataru Yoshida
G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD
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Mitochondrial RNA processing in absence of tRNA punctuations in octocorals. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-06-17 Gaurav G Shimpi,Sergio Vargas,Angelo Poliseno,Gert Wörheide
Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which
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Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-06-06 Bingying Deng,Xiang Cheng,Haoming Li,Jianbing Qin,Meiling Tian,Guohua Jin
The denervated hippocampus provides a proper microenvironment for the survival and neuronal differentiation of neural progenitors. While thousands of lncRNAs were identified, only a few lncRNAs that regulate neurogenesis in the hippocampus are reported. The present study aimed to perform microarray expression profiling to identify long noncoding RNAs (lncRNAs) that might participate in the hippocampal
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Early growth response protein 1 regulates promoter activity of α-plasma membrane calcium ATPase 2, a major calcium pump in the brain and auditory system. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-05-22 Rebecca R Minich,Jin Li,Bruce L Tempel
Along with sodium/calcium (Ca2+) exchangers, plasma membrane Ca2+ ATPases (ATP2Bs) are main regulators of intracellular Ca2+ levels. There are four ATP2B paralogs encoded by four different genes. Atp2b2 encodes the protein pump with the fastest activation, ATP2B2. In mice, the Atp2b2 transcript has several alternate transcriptional start site variants: α, β, µ and δ. These variants are expressed in
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hSSB1 associates with and promotes stability of the BLM helicase. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-05-15 Laura V Croft,Nicholas W Ashton,Nicolas Paquet,Emma Bolderson,Kenneth J O'Byrne,Derek J Richard
Maintenance of genome stability is critical in human cells. Mutations in or loss of genome stability pathways can lead to a number of pathologies including cancer. hSSB1 is a critical DNA repair protein functioning in the repair and signalling of stalled DNA replication forks, double strand DNA breaks and oxidised DNA lesions. The BLM helicase is central to the repair of both collapsed DNA replication
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Selective measurement of α smooth muscle actin: why β-actin can not be used as a housekeeping gene when tissue fibrosis occurs. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-04-27 Apor Veres-Székely,Domonkos Pap,Erna Sziksz,Eszter Jávorszky,Réka Rokonay,Rita Lippai,Kálmán Tory,Andrea Fekete,Tivadar Tulassay,Attila J Szabó,Ádám Vannay
Prevalence of fibroproliferative diseases, including chronic kidney disease is rapidly increasing and has become a major public health problem worldwide. Fibroproliferative diseases are characterized by increased expression of α smooth muscle actin (α-SMA) that belongs to the family of the six conserved actin isoforms showing high degree homology. The aim of the present study was to develop real-time
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Erratum to: RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-04-21 Shubham Goyal,Takahiro Suzuki,Jing-Ru Li,Shiori Maeda,Mami Kishima,Hajime Nishimura,Yuri Shimizu,Harukazu Suzuki
The original article [1] contained an error in the title whereby the word ‘of’ was mistakenly inserted between ‘independent’ and ‘active’ during the article’s production. As such, the original article title has now been updated to reflect the correct title. 1. Goyal S, Suzuki T, Li J-R, Maeda S, Kishima M, Nishimura H, Shimizu Y. Suzuki H RUNX1 induces DNA replication independent active DNA demethylation
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Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-04-05 Tianyi Li,Hongying Diao,Lei Zhao,Yue Xing,Jichang Zhang,Ning Liu,Youyou Yan,Xin Tian,Wei Sun,Bin Liu
Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not received sufficient attention in related studies. The objective of this
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RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-04-04 Shubham Goyal,Takahiro Suzuki,Jing-Ru Li,Shiori Maeda,Mami Kishima,Hajime Nishimura,Yuri Shimizu,Harukazu Suzuki
SPI1 is an essential transcription factor (TF) for the hematopoietic lineage, in which its expression is tightly controlled through a −17-kb upstream regulatory region and a promoter region. Both regulatory regions are demethylated during hematopoietic development, although how the change of DNA methylation status is performed is still unknown. We found that the ectopic overexpression of RUNX1 (another
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Immunoglobulin T from sea bass (Dicentrarchus labrax L.): molecular characterization, tissue localization and expression after nodavirus infection. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-03-15 Francesco Buonocore,Valentina Stocchi,Noelia Nunez-Ortiz,Elisa Randelli,Marco Gerdol,Alberto Pallavicini,Angelo Facchiano,Chiara Bernini,Laura Guerra,Giuseppe Scapigliati,Simona Picchietti
Immunoglobulins (Igs) are fundamental components of the adaptive immune system of vertebrates, with the IgT/IgZ isotype specific of Teleosts. In this paper we describe the identification of an IgT heavy chain from the European sea bass (Dicentrarchus labrax L.), its molecular characterization and tissue mRNA localization by in situ hybridization. Sea bass IgT consists of 552 aa (Accession Number KM410929)
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Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-03-09 Toshiki Aiba,Toshiyuki Saito,Akiko Hayashi,Shinji Sato,Harunobu Yunokawa,Toru Maruyama,Wataru Fujibuchi,Hisaka Kurita,Chiharu Tohyama,Seiichiroh Ohsako
It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries
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Properties of STAT1 and IRF1 enhancers and the influence of SNPs. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-03-09 Mohamed Abou El Hassan,Katherine Huang,Manoja B K Eswara,Zhaodong Xu,Tao Yu,Arthur Aubry,Zuyao Ni,Izzy Livne-Bar,Monika Sangwan,Mohamad Ahmad,Rod Bremner
STAT1 and IRF1 collaborate to induce interferon-γ (IFNγ) stimulated genes (ISGs), but the extent to which they act alone or together is unclear. The effect of single nucleotide polymorphisms (SNPs) on in vivo binding is also largely unknown. We show that IRF1 binds at proximal or distant ISG sites twice as often as STAT1, increasing to sixfold at the MHC class I locus. STAT1 almost always bound with
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Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae). BMC Molecular Biol. (IF 4.619) Pub Date : 2017-02-16 Kang-Sheng Ma,Fen Li,Ying Liu,Ping-Zhuo Liang,Xue-Wei Chen,Xi-Wu Gao
MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have been investigated, there is as yet an absence of studies about the regulatory roles of miRNAs involved in the metabolism of plant allelochemicals in insects. We constructed five small RNA libraries
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Binding affinity of five PBPs to Ostrinia sex pheromones. BMC Molecular Biol. (IF 4.619) Pub Date : 2017-02-07 Tiantao Zhang,Yaqi Sun,Kevin W Wanner,Brad S Coates,Kanglai He,Zhenying Wang
Pheromone binding proteins (PBPs) of male Lepidoptera function in chemical communication, mate attraction and recognition. Directional selection was previously predicted between PBP3 orthologs of Ostrinia furnacalis and Ostrinia nubilalis were interpreted as being involved in sexual isolation. In vitro assays show that recombinant male OfurPBP3 bound O. furnacalis sex pheromones, Z-12-tetradecenyl