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Marco D'Aurora, Samantha Sperduti, Giovanna Di Emidio, Liborio Stuppia, Paolo Giovanni Artini, Valentina Gatta
The somatic component of follicular structure is a mixture of different cell types, represented by Granulosa cells (GCs) that are the paracrine regulators of the oocyte growth. GCs finely support this process by a continuous bidirectional talk with oocyte, which ensure oocyte quality and competence. Specific pathways are involved in the cross-talk and in both GCs and oocyte development. This review summarizes data from GCs gene expression analysis concerning both their physiological role and their interaction with oocyte...
October 18, 2016: Gynecological Endocrinology
Shanshan Xu, Lanlan Dong, Yingying Shi, Liujun Chen, Peipei Yuan, Shuang Wang, Zhi Li, Yan Sun, Song Han, Jun Yin, Biwen Peng, Xiaohua He, Wanhong Liu
Human foamy virus (HFV) is a complex and unique retrovirus with the longest genomes among retroviruses used as vectors for gene therapy. Long non-coding RNAs (lncRNAs) are regarded as key regulators that involved in diverse biological processes during viral infection. However, the role of lncRNAs in HFV infection remains unknown. In this study, we utilized next-generation sequencing to first characterize lncRNAs in 293T cells after HFV infection, evaluating length distribution, exon number distribution, volcano picture and lncRNA class distribution...
October 18, 2016: AIDS Research and Human Retroviruses
Hye Yeon Koh, Hyun Park, Jun Hyuck Lee, Se Jong Han, Young Chang Sohn, Sung Gu Lee
Psychrobacter sp. PAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzero temperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ 2 fold, p <0...
October 17, 2016: Environmental Microbiology
Weifang Wu, Qin Deng, Pibiao Shi, Jinghua Yang, Zhongyuan Hu, Mingfang Zhang
Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy...
2016: PloS One
Jian Huang, Lei Zhao, Ping Yang, Zhen Chen, Ni Tang, Xiong Z Ruan, Yaxi Chen
Hepatitis B virus (HBV) is a hepatocyte-specific DNA virus whose gene expression and replication are closely associated with hepatic metabolic processes. Thus, a potential anti-viral strategy is to target the host metabolic factors necessary for HBV gene expression and replication. Recent studies revealed that fatty acid translocase CD36 is involved in the replication, assembly, storage, and secretion of certain viruses, such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV). However, the relationship between CD36 and the HBV life cycle remains unclear...
2016: PloS One
Yong Yu, Jason C H Tsang, Cui Wang, Simon Clare, Juexuan Wang, Xi Chen, Cordelia Brandt, Leanne Kane, Lia S Campos, Liming Lu, Gabrielle T Belz, Andrew N J McKenzie, Sarah A Teichmann, Gordon Dougan, Pentao Liu
Innate lymphoid cells (ILCs) functionally resemble T lymphocytes in cytotoxicity and cytokine production but lack antigen-specific receptors, and are important regulators in immune response and tissue homeostasis(1, 2). ILCs are generated from common lymphoid progenitors (CLPs), which are subsequently committed to innate lymphoid lineages in the α lymphoid progenitor (αLP), early innate lymphoid progenitor (EILP), common helper innate lymphoid progenitor (CHILP) and innate lymphoid cell progenitor (ILCP) compartments(3, 4, 5, 6, 7, 8)...
September 29, 2016: Nature
A Harrod, J Fulton, V T M Nguyen, M Periyasamy, L Ramos-Garcia, C-F Lai, G Metodieva, A de Giorgio, R L Williams, D B Santos, P J Gomez, M-L Lin, M V Metodiev, J Stebbing, L Castellano, L Magnani, R C Coombes, L Buluwela, S Ali
Drugs that inhibit estrogen receptor-α (ER) activity have been highly successful in treating and reducing breast cancer progression in ER-positive disease. However, resistance to these therapies presents a major clinical problem. Recent genetic studies have shown that mutations in the ER gene are found in >20% of tumours that progress on endocrine therapies. Remarkably, the great majority of these mutations localize to just a few amino acids within or near the critical helix 12 region of the ER hormone binding domain, where they are likely to be single allele mutations...
October 17, 2016: Oncogene
Michele Balsamo, Chandrani Mondal, Guillaume Carmona, Leslie M McClain, Daisy N Riquelme, Jenny Tadros, Duan Ma, Eliza Vasile, John S Condeelis, Douglas A Lauffenburger, Frank B Gertler
During tumor progression, alternative splicing gives rise to different Mena protein isoforms. We analyzed how Mena11a, an isoform enriched in epithelia and epithelial-like cells, affects Mena-dependent regulation of actin dynamics and cell behavior. While other Mena isoforms promote actin polymerization and drive membrane protrusion, we find that Mena11a decreases actin polymerization and growth factor-stimulated membrane protrusion at lamellipodia. Ectopic Mena11a expression slows mesenchymal-like cell motility, while isoform-specific depletion of endogenous Mena11a in epithelial-like tumor cells perturbs cell:cell junctions and increases membrane protrusion and overall cell motility...
October 17, 2016: Scientific Reports
Rachel A Johnston, Kristina L Paxton, Frank R Moore, Robert K Wayne, Thomas B Smith
The annual migration of a bird can involve thousands of kilometers of non-stop flight, requiring accurately timed seasonal changes in physiology and behavior. Understanding the molecular mechanisms controlling this endogenous programme can provide functional and evolutionary insights into the circannual biological clock and the potential of migratory species to adapt to changing environments. Under naturally-timed photoperiod conditions, we maintained captive Swainson's thrushes (Catharus ustulatus) and performed RNA sequencing (RNA-Seq) of the ventral hypothalamus and optic chiasma to evaluate transcriptome-wide gene expression changes of individuals in migratory condition...
October 16, 2016: Molecular Ecology
Jingchao Chen, Hongjuan Huang, Shouhui Wei, Zhaofeng Huang, Xu Wang, Chaoxian Zhang
Glyphosate is an important non-selective herbicide that is commonly used worldwide. However, evolved glyphosate-resistant (GR) weeds significantly affect crop yields. Unfortunately, the mechanisms underlying resistance in GR weeds, such as goosegrass (Eleusine indica L.), an annual weed found worldwide, have not been fully elucidated. In this study, transcriptome analysis was conducted to further assess the potential mechanisms of glyphosate resistance in goosegrass. The RNA-seq libraries generated 24,597,462 clean reads...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
Ru Zheng, Yue Li, Huiying Sun, Xiaoyin Lu, Bao-Fa Sun, Rui Wang, Lina Cui, Cheng Zhu, Hai-Yan Lin, Hongmei Wang
The syncytiotrophoblast (STB) plays a key role in maintaining the function of the placenta during human pregnancy. However, the molecular network that orchestrates STB development remains elusive. The aim of this study was to obtain broad and deep insight into human STB formation via transcriptomics. We adopted RNA sequencing (RNA-Seq) to investigate genes and isoforms involved in forskolin (FSK)-induced fusion of BeWo cells. BeWo cells were treated with 50 μM FSK or dimethylsulfoxide (DMSO) as a vehicle control for 24 and 48 h, and the mRNAs at 0, 24 and 48 h was sequenced...
October 14, 2016: Reproduction: the Official Journal of the Society for the Study of Fertility
Guillem Rigaill, Sandrine Balzergue, Véronique Brunaud, Eddy Blondet, Andrea Rau, Odile Rogier, José Caius, Cathy Maugis-Rabusseau, Ludivine Soubigou-Taconnat, Sébastien Aubourg, Claire Lurin, Marie-Laure Martin-Magniette, Etienne Delannoy
Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most of them are based on similar statistical frameworks after normalization, differing primarily in the choice of data distribution, mean and variance estimation strategy and data filtering. We propose an evaluation of the impact of these choices when few biological replicates are available through the use of synthetic data sets. This framework is based on real data sets and allows the exploration of various scenarios differing in the proportion of non-differentially expressed genes...
October 14, 2016: Briefings in Bioinformatics
Yi Zhou, Wenjuan Yu, Huan Zhong, Jianlin Li, Hongxia Li, Feng He, Jie Zhou, Yongkai Tang, Juhua Yu, Fan Yu
Common carp (Cyprinus carpio) is a widespread freshwater fish and economically important species in China and other East Asian countries. Recent studies suggest that insulin can alter the expression of immune genes and, thus, can be regarded as an immunomodulatory hormone. To understand the mechanism of the immune response to insulin, we performed a comparative RNA-seq transcriptome analysis using livers from common carp injected with insulin (5 μg/g bodyweight) or saline as a control. After filtering the low-quality reads and removing the adaptors, the clean raw reads were assembled into 60,421 unigenes with mean length of 746...
October 11, 2016: Fish & Shellfish Immunology
Otília Menyhárt, Hajnalka Harami-Papp, Saraswati Sukumar, Reinhold Schäfer, Luca Magnani, Oriol de Barrios, Balázs Győrffy
The hallmarks of cancer capture the most essential phenotypic characteristics of malignant transformation and progression. Although numerous factors involved in this multi-step process are still unknown to date, an ever-increasing number of mutated/altered candidate genes are being identified within large-scale cancer genomic projects. Therefore, investigators need to be aware of available and appropriate techniques capable of determining characteristic features of each hallmark. We review the methods tailored to experimental cancer researchers to evaluate cell proliferation, programmed cell death, replicative immortality, induction of angiogenesis, invasion and metastasis, genome instability, and reprogramming of energy metabolism...
October 11, 2016: Biochimica et Biophysica Acta
Federico Lopez-Osorio, Kurt M Pickett, James M Carpenter, Bryan A Ballif, Ingi Agnarsson
The phylogenetic relationships among genera of the subfamily Vespinae (yellowjackets and hornets) remain unclear. Yellowjackets and hornets constitute one of the only two lineages of highly eusocial wasps, and the distribution of key behavioral traits correlates closely with the current classification of the group. The potential of the Vespinae to elucidate the evolution of social life, however, remains limited due to ambiguous genus-level relationships. Here, we address the relationships among genera within the Vespinae using transcriptomic (RNA-seq) data...
October 11, 2016: Molecular Phylogenetics and Evolution
Ravi C Nirmal, Agnelo Furtado, Colin Wrigley, Robert J Henry
Puroindoline (Pina and Pinb) genes control grain texture or hardness in wheat. Wild-type/soft alleles lead to softer grain while a mutation in one or both of these genes results in a hard grain. Variation in hardness in genotypes with identical Pin alleles (wild-type or mutant) is known but the molecular basis of this is not known. We now report the identification of wheat genotypes with hard grain texture and wild-type/soft Pin alleles indicating that hardness in wheat may be controlled by factors other than mutations in the coding region of the Pin genes...
2016: PloS One
Uraipan Saetan, Unitsa Sangket, Panchalika Deachamag, Wilaiwan Chotigeat
The banana shrimp (Fenneropenaeus merguiensis) is one of the most commercially important penaeid species in the world. Its numbers are declining in the wild, leading to a loss of broodstock for farmers of the shrimp and a need for more successful breeding programs. However, the molecular mechanism of the genes involved in this shrimp's ovarian maturation is still unclear. Consequently, we compared transcriptomic profiles of ovarian tissue from females in both the vitellogenic stage and the non-vitellogenic stage...
2016: PloS One
A Bonizzato, E Gaffo, G Te Kronnie, S Bortoluzzi
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program...
October 14, 2016: Blood Cancer Journal
Chu-Yu Ye, Xingchen Zhang, Qinjie Chu, Chen Liu, Yongyi Yu, Weiqin Jiang, Qian-Hao Zhu, Longjiang Fan, Longbiao Guo
Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice...
October 14, 2016: RNA Biology
Linda Szabo, Julia Salzman
The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We review sources of experimental and bioinformatic biases that complicate the accurate discovery of circRNAs and discuss statistical approaches to address these biases...
October 14, 2016: Nature Reviews. Genetics
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