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Gene construction

Nanthini Jayabalan, Andrew Lai, Valeska Ormazabal, Stefanie Adam, Dominic Guanzon, Carlos Palma, Katherin Scholz-Romero, Ratana Lim, Thomas Jansson, Harold David McIntyre, Martha Lappas, Carlos Salomon
Context: Molecules produced by adipose tissue (AT) function as an endocrine link between maternal AT and fetal growth by regulating placental function in normal and gestational diabetes mellitus (GDM). Objective: We hypothesised that AT-derived exosomes from women with GDM carry a specific set of proteins that influences glucose metabolism in placenta. Design: Exosomes were isolated from omental AT-conditioned media from pregnant women with normal glucose tolerance (exo-NGT, n=65) and women with GDM (exo-GDM, n=82)...
December 3, 2018: Journal of Clinical Endocrinology and Metabolism
Lex Flagel, Yaniv Brandvain, Daniel R Schrider
Population-scale genomic datasets have given researchers incredible amounts of information from which to infer evolutionary histories. Concomitant with this flood of data, theoretical and methodological advances have sought to extract information from genomic sequences to infer demographic events such as population size changes and gene flow among closely related populations/species, construct recombination maps, and uncover loci underlying recent adaptation. To date most methods make use of only one or a few summaries of the input sequences and therefore ignore potentially useful information encoded in the data...
December 4, 2018: Molecular Biology and Evolution
Matheus Dias Cordeiro, Michele Bahia, Paulo Cesar Magalhães-Matos, Marcio Barizon Cepeda, Alexandro Guterres, Adivaldo Henrique Fonseca
This study aimed to perform a morphological, molecular and phylogenetic characterization of Borrelia theileri obtained from infected Rhipicephalus microplus in Brazil. Fifty engorged R. microplus females from cattle in the municipality of Seropédica, Rio de Janeiro, were analyzed for spirochetes by hemolymph smear. Macerated eggs and positive ticks, as well as blood from the bovine infested by these ticks, were analyzed the glpQ, flaB and hpt genes by PCR. The PCR products were purified and sequenced for analysis and construction of a phylogenetic tree...
October 2018: Revista Brasileira de Parasitologia Veterinária, Brazilian Journal of Veterinary Parasitology
Joel Pel, Amy Leung, Wendy W Y Choi, Milenko Despotovic, W Lloyd Ung, Gosuke Shibahara, Laura Gelinas, Andre Marziali
Targeted Next Generation Sequencing (NGS) is being adopted increasingly broadly in many research, commercial and clinical settings. Currently used target capture methods, however, typically require complex and lengthy (sometimes multi-day) workflows that complicates their use in certain applications. In addition, small panels for high sequencing depth applications such as liquid biopsy typically have low on-target rates, resulting in unnecessarily high sequencing cost. We have developed a novel targeted sequencing library preparation method, named Linked Target Capture (LTC), which replaces typical multi-day target capture workflows with a single-day, combined 'target-capture-PCR' workflow...
2018: PloS One
Wen Huang, Hongmei Li, Chuhang Cheng, Chunhua Ren, Ting Chen, Xiao Jiang, Kaimin Cheng, Peng Luo, Chaoqun Hu
Soil salinization erodes the farmlands and poses a serious threat to human life, reuse of the saline-alkali lands as cultivated resources becomes increasingly prominent. Pacific white shrimp (Litopenaeus vannamei) is an important farmed aquatic species for the development and utilization of the saline-alkali areas. However, little is known about the adaptation mechanism of this species in terms of high-pH stress. In the present study, a transcriptome analysis on the gill tissues of L. vannamei in response to high-pH stress (pH 9...
2018: PloS One
Saumya Agrawal, Austen R D Ganley
Ribosomal RNA gene repeats (rDNA) encode ribosomal RNA, a major component of ribosomes. Ribosome biogenesis is central to cellular metabolic regulation, and several diseases are associated with rDNA dysfunction, notably cancer, However, its highly repetitive nature has severely limited characterization of the elements responsible for rDNA function. Here we make use of phylogenetic footprinting to provide a comprehensive list of novel, potentially functional elements in the human rDNA. Complete rDNA sequences for six non-human primate species were constructed using de novo whole genome assemblies...
2018: PloS One
Zhelong Li, Xueying Zhou, Mengying Wei, Xiaotong Gao, Lianbi Zhao, Ruijing Shi, Wenqi Sun, Yunyou Duan, Guodong Yang, Lijun Yuan
In vitro and in vivo delivery of RNAs of interest holds promise for gene therapy. Recently, exosomes are considered as the rational vehicle for RNA delivery, especially miRNA and/or siRNA, while the loading efficiency is limited. In this study, we engineered the exosomes for RNA loading by constructing a fusion protein, in which the exosomal membrane protein CD9 was fused with RNA binding protein, while the RNAs of interest either natively harbors or is engineered to have the elements for the binding. By proof-of-principle experiments, we here fused CD9 with HuR, an RNA binding protein interacts with miR-155 with a relatively high affinity...
December 5, 2018: Nano Letters
Wen-Shyan Huang, Lin-Gwei Wei, Jhen-Kai Li, Keng-Yen Fu, Tai-Chun Huang, Pai-Shan Hsieh, Nien-Chi Huang, Lien-Guo Dai, Fung-Wei Chang, Shih-Hurng Loh, Yuan-Hao Chen, Bing-Heng Yang, Chia-Yang Shiau, Gwo-Jang Wu, Niann-Tzyy Dai
The pigment melanin is produced by melanocytes, is primarily responsible for skin color, and protects it against ultraviolet rays that can cause the destruction of genetic material within the keratinocytes. To elucidate the mechanisms of many diseases associated with melanocytes, such as melanoma and albinism, or burns with uneven pigment distribution, the disease model needs to be established first. In this study, we aimed to construct the melanocyte model from patients in a short period.Sandai virus vector containing 4 stemness genes (Oct4, Sox2, Klf4, c-Myc) was transfected into human adipose-derived stem cells to produce induced pluripotent stem cells (iPSCs)...
December 3, 2018: Annals of Plastic Surgery
Zhongyu Wang, Qian Song, Zuyi Yang, Jianing Chen, Jun Shang, Wen Ju
The kidney renal papillary cell carcinoma (KIRP) is a relatively rare type of kidney cancer. There has been no investigation to find a robust signature to predict the survival outcome of KIRP patients in the aspect of tumor immunology. In this study, 285 KIRP samples from The Cancer Genome Atlas (TCGA) were randomly divided into training and testing set. A total of 1534 immune-related genes from The Immunology Database and Analysis Portal (ImmPort) were used as candidates to construct the signature. Using univariate Cox analysis, we evaluated the relationship between overall survival and immune-related genes expression and found 272 immune-related genes with predicting prognostic ability...
December 5, 2018: Cancer Medicine
Jin-Seong Cho, Hyung-Woo Jeon, Min-Ha Kim, The K Vo, Jinsoo Kim, Eung-Jun Park, Young-Im Choi, Hyoshin Lee, Kyung-Hwan Han, Jae-Heung Ko
With the exponential growth of the human population and industrial developments, research on renewable energy resources is required to alleviate environmental and economic impacts caused by the consumption of fossil fuels. In this study, we present a synthetic biological application of a wood forming tissue-specific bicistronic gene expression system to improve both the quantity and quality of woody biomass to minimize undesirable growth penalties. Our transgenic poplars, designed to express both PdGA20ox1 (a GA20-oxidase from Pinus densiflora producing bioactive gibberellin, GA) and PtrMYB221 (a MYB transcription factor negatively regulating lignin biosynthesis) under the developing xylem (DX) tissue-specific promoter (i...
December 5, 2018: Plant Biotechnology Journal
Wen-Yi Geng, Feng-Jiao Yao, Ting Tang, Shan-Shan Shi
The selection of a suitable reference gene is an important prerequisite for the precise analysis of target gene expression by real-time quantitative PCR (qPCR). The present study aims to explore the expression pattern of the Macrobrachium nipponense (M. nipponense) β-actin gene under Aeromonas hydrophila bacterial infection conditions. The complete sequence of the β-actin gene from M. nipponense was cloned by PCR. Identified and named β-actin genes were searched in the NCBI database, and the characteristics of the β-actin gene were analyzed using bioinformatics methods...
December 4, 2018: Molecular Biology Reports
Adugna Abdi Woldesemayat, Monde Ntwasa
Drought alone or in combination with other stresses forms the major crop production constraint worldwide. Sorghum, one of the most important cereal crops is affected by drought alone or in combination with co-occurring stresses; notwithstanding, sorghum has evolved adaptive responses to combined stresses. Furthermore, an impressive number of sorghum genes have been investigated for drought tolerance. However, the molecular mechanism underling drought response remains poorly understood. We employed a systems biology approach to elucidate regulatory and broad functional features of these genes...
2018: Frontiers in Genetics
Yuhan Zhang, Ruxin Liu, Kaiyue Tian, Zeng Wang, Xia Yang, Dongsheng Gao, Youming Zhang, Jun Fu, Hailong Wang, Jun Zhao
Since May 2015, outbreaks of hydropericardium-hepatitis syndrome (HHS) caused by fowl adenovirus 4 (FAdV-4) with a novel genotype have been reported in China, causing significant economic losses to the poultry industry. A previous comparative analysis revealed that highly virulent FAdV-4 isolates contain various genomic deletions and multiple distinct mutations in the major structural genes fiber2 and hexon. To identify the genes responsible for the virulence of HHS-associated novel FAdV-4 isolates, FAdV-4 infectious clones were constructed by directly cloning the whole genome of a highly pathogenic FAdV-4 isolate (CH/HNJZ/2015) and that of a nonpathogenic strain (ON1) into a p15A-cm vector using the ExoCET method...
December 5, 2018: Emerging Microbes & Infections
Jiantao Sun, Jiemei Yang, Jing Chi, Xue Ding, Nan Lv
BACKGROUND: Cardiac hypertrophy and acute myocardial infarction (AMI) are two common heart diseases worldwide. However, research is needed into the exact pathogenesis and effective treatment strategies for these diseases. Recently, microRNAs (miRNAs) have been suggested to regulate the pathological pathways of heart disease, indicating a potential role in novel treatments. RESULTS: In our study, we constructed a miRNA-gene-drug network and analyzed its topological features...
December 4, 2018: Human Genomics
Annabelle Monnier, Rachel Boniface, Régis Bouvet, Amandine Etcheverry, Marc Aubry, Tony Avril, Véronique Quillien, Eric Chevet, Jean Mosser
BACKGROUND: Glioblastoma (GB) is a highly invasive primary brain tumor that nearly always systematically recurs at the site of resection despite aggressive radio-chemotherapy. Previously, we reported a gene expression signature related to tumor infiltration. Within this signature, the EMX2 gene encodes a homeodomain transcription factor that we found was down regulated in glioblastoma. As EMX2 is reported to play a role in carcinogenesis, we investigated the impact of EMX2 overexpression in glioma-related cell lines...
December 4, 2018: BMC Cancer
Gregory A Taylor, Heather Kirk, Lauren Coombe, Shaun D Jackman, Justin Chu, Kane Tse, Dean Cheng, Eric Chuah, Pawan Pandoh, Rebecca Carlsen, Yongjun Zhao, Andrew J Mungall, Richard Moore, Inanc Birol, Maria Franke, Marco A Marra, Christopher Dutton, Steven J M Jones
The grizzly bear ( Ursus arctos ssp. horribilis ) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96...
November 30, 2018: Genes
Hongsen Xu, Jing Xing, Xiaoqian Tang, Xiuzhen Sheng, Wenbin Zhan
Outer membrane protein K (OmpK) is an immunogenic protein that could act as subunit vaccine candidate for Vibrio anguillarum. In this study, a DNA vaccine encoding the OmpK gene of V. anguillarum was constructed and confirmed to express OmpK in vitro and in vivo. To evaluate the potential of pcDNA3.1-OmpK (pOmpK) as vaccine candidate, the humoral and cellular immune response, and protective effects were analyzed in flounder model. The results showed that the transcription and translation of OmpK gene occurred in both transfected hirame natural embryo (HINAE) cells and injected fish muscles, indicating the functionality of pOmpK to express OmpK...
December 1, 2018: Fish & Shellfish Immunology
Abigail N Leistra, Nicholas C Curtis, Lydia M Contreras
Non-coding RNAs (ncRNAs) are versatile and powerful controllers of gene expression that have been increasingly linked to cellular metabolism and phenotype. In bacteria, identified and characterized ncRNAs range from trans-acting, multi-target small non-coding RNAs to dynamic, cis-encoded regulatory untranslated regions and riboswitches. These native regulators have inspired the design and construction of many synthetic RNA devices. In this work, we review the design, characterization, and impact of ncRNAs in engineering both native and exogenous metabolic pathways in bacteria...
December 1, 2018: Metabolic Engineering
Timothy P Maus, Joel P Felmlee, Mark D Unger, Andreas S Beutler
BACKGROUND: Development of new analgesic drugs or gene therapy vectors for spinal delivery will be facilitated by "hyperlocal" targeting of small therapeutic injectate volumes if spine imaging technology can be used that is ready for future clinical translation. NEW METHOD: This study provides methods for MRI-guided drug delivery to the periganglionic epidural space and the dorsal root ganglion (DRG) in the Yucatan swine. RESULTS: Phantom studies showed artifact-corrected needle localization with frequency encoding parallel to the needle shaft, while maximizing bandwidth (125 KHz) minimized needle artifact...
December 1, 2018: Journal of Neuroscience Methods
Zhiyun Shi, Juan Xu, Xuemei Jia
OBJECTIVE: To study the effect of Wdr1 deletion in germ cells on ovarian function of mice. METHODS: Oocyte-specific gene knockout mouse model was constructed by crossing Wdr1fl/fl female mice with Cre recombinase transgenic male mice which was driven by a germ cell-specific promoter. Wdr1fl/- ; Ddx4-Cre mice and control mice were sacrificed at 14 days, 28 days and 4 months after birth, whose ovaries were subjected to photography, paraffin sectioning and Hematoxylin-Eosin (HE) staining...
December 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
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