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Functional & Integrative Genomics

Roshan Kumar Singh, Shweta Shweta, Mehanathan Muthamilarasan, Rekha Rani, Manoj Prasad
Aquaporins are versatile proteins involved in several biological as well as molecular functions, and they have been extensively studied in various plant systems. Increasing evidences indicate their role in biotic and abiotic stresses, and therefore, studying these proteins in a naturally stress-tolerant crop would provide further insights into the roles of this important protein family. Given this, the present study was performed in foxtail millet (Setaria italica), a model plant for studying biofuel, stress tolerance, and C4 photosynthetic traits...
February 13, 2019: Functional & Integrative Genomics
Hongwen Cao, Renjie Gao, Chao Yu, Lei Chen, Yigeng Feng
This paper is to characterize the expression status of Fragile X Mental Retardation, Autosomal Homolog 1 (FXR1) in prostate cancer cells and understand its mechanistic involvement in the tumor biology of prostate cancer. The relative expression of FXR1 in prostate cancer cells was determined by real-time polymerase chain reaction and Western blotting. Cell proliferation in FXR1-deficient cells was evaluated by cell counting and MTT assays. The migrative and invasive capacities were measured by transwell assay...
February 11, 2019: Functional & Integrative Genomics
Shuli Liu, Xiaolong Kang, Claudia R Catacchio, Mei Liu, Lingzhao Fang, Steven G Schroeder, Wenli Li, Benjamin D Rosen, Daniela Iamartino, Leopoldo Iannuzzi, Tad S Sonstegard, Curtis P Van Tassell, Mario Ventura, Wai Yee Low, John L Williams, Derek M Bickhart, George E Liu
Duplicated sequences are an important source of gene evolution and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variations (CNVs) in the water buffalo (Bubalus bubalis). By aligning short reads of Olimpia (the reference water buffalo) to the UMD3.1 cattle genome, we identified 1,038 segmental duplications comprising 44.6 Mb (equivalent to ~1.73% of the cattle genome) of the autosomal and X chromosomal sequence in the buffalo genome...
February 7, 2019: Functional & Integrative Genomics
Joanna Zyla, Sylwia Kabacik, Grainne O'Brien, Salma Wakil, Najla Al-Harbi, Jaakko Kaprio, Christophe Badie, Joanna Polanska, Ghazi Alsbeih
Individual variability in response to radiation exposure is recognised and has often been reported as important in treatment planning. Despite many efforts to identify biomarkers allowing the identification of radiation sensitive patients, it is not yet possible to distinguish them with certainty before the beginning of the radiotherapy treatment. A comprehensive analysis of genome-wide single-nucleotide polymorphisms (SNPs) and a transcriptional response to ionising radiation exposure in twins have the potential to identify such an individual...
January 31, 2019: Functional & Integrative Genomics
M Sankari, H Hridya, P Sneha, C George Priya Doss, J Godwin Christopher, Jill Mathew, Hatem Zayed, Siva Ramamoorthy
The effect of salt stress on pigment synthesis and antioxidant enzyme activity as well as in the genes involved in the biosynthetic pathway of bixin was studied. The 14-day germinated seedlings of Bixa orellana were induced into the various NaCl concentration (0, 25, 50, 75, 100 mM). After 45 days, leaves were taken for pigment analysis, antioxidant assays, and gene expression analysis to study the response of salt stress. The pigment content such as chlorophyll level was increased upon salt stress with a reduction in total carotenoid clearly indicating the adaptability of plants towards the stressed state...
January 29, 2019: Functional & Integrative Genomics
Hengxing Ba, Datao Wang, Weiyao Wu, Hongmei Sun, Chunyi Li
Antler regeneration, a stem cell-based epimorphic process, has a potential as a valuable model for regenerative medicine. A pool of antler stem cells (ASCs) for antler development is located in the antlerogenic periosteum (AP). However, whether this ASC pool is homogenous or heterogeneous has not been fully evaluated. In this study, we produced a comprehensive transcriptome dataset at the single-cell level for the ASCs based on the 10× Genomics platform (scRNA-seq). A total of 4565 ASCs were sequenced and classified into a large cell cluster, indicating that the ASC resident in the AP are likely to be a homogeneous population...
January 23, 2019: Functional & Integrative Genomics
Rajesh Yarra, P B Kirti
Brinjal or eggplant (Solanum melongena L.) is an important solanaceous edible crop, and salt stress adversely affects its growth, development, and overall productivity. To cope with excess salinity, vacuolar Na+ /H+ antiporters provide the best mechanism for ionic homeostasis in plants under salt stress. We generated transgenic eggplants by introducing wheat TaNHX2 gene that encodes a vacuolar Na+ /H+ antiporter in to the eggplant genome via Agrobacterium-mediated transformation using pBin438 vector that harbors double35S:TaNHX2 to confer salinity tolerance...
January 23, 2019: Functional & Integrative Genomics
Summi Dutta, Shailendra Kumar Jha, Kumble Vinod Prabhu, Manish Kumar, Kunal Mukhopadhyay
Significance of microRNAs in regulating gene expression in higher eukaryotes as well as in pathogens like fungi to suppress host defense is a well-established phenomenon. The present study focuses on leaf rust fungi Puccinia triticina (Pathotype 77-5) mediated RNAi to make wheat (Triticum aestivum L.) more susceptible. To reach such conclusions, we first confirmed the presence of argonaute (AGO) and dicer-like protein (DCL) family sequences in Puccinia. Bioinformatic tools were applied to retrieve the sequences from Puccinia genome followed by cloning and sequencing from P...
January 22, 2019: Functional & Integrative Genomics
Himanshu Dubey, Kanti Kiran, Rajdeep Jaswal, Priyanka Jain, Arvind M Kayastha, Subhash C Bhardwaj, Tapan Kumar Mondal, Tilak Raj Sharma
Cross-kingdom RNAi is a well-documented phenomenon where sRNAs generated by host and pathogens may govern resistance or susceptible phenotypes during host-pathogen interaction. With the first example of the direct involvement of fungal generated sRNAs in virulence of plant pathogenic fungi Botrytis cinerea and recently from Puccinia striiformis f. sp. tritici, we attempted to identify sRNAs in Puccinia triticina (P. triticina). Four sRNA libraries were prepared and sequenced using Illumina sequencing technology and a total of ~ 1-1...
January 7, 2019: Functional & Integrative Genomics
Neeta Lohani, Agnieszka A Golicz, Mohan B Singh, Prem L Bhalla
The global climate change-induced abiotic and biotic stresses are predicted to affect crop-growing seasons and crop yield. Heat stress transcription factors (Hsfs) have been suggested to play a significant role in various stress responses. They are an integral part of the signal transduction pathways that operate in response to environmental stresses. Brassica oleracea is one of the agronomical important crop species which consists of cabbage, cauliflower, broccoli, Brussels sprout, kohlrabi and kale. The identification and roles of Hsfs in this important Brassica species are unknown...
January 7, 2019: Functional & Integrative Genomics
Xiaomin Liu, Meijia Zhu, Xiuhua Li, Jiyou Tang
Kennedy's disease, resulted from the expansion of a CAG repeat in exon 1 of androgen receptor (AR) gene, is a motor neuron degenerative disease in the brainstem and spinal cord with the slow development of facial, bulbar, and limb muscle degeneration. To investigate the clinical manifestations and gene mutations in Han Chinese patients with Kennedy's disease. The clinical manifestations of 5 male Han Chinese patients including 2 probands and their relatives from 2 families and 1 sporadic case were retrospectively studied...
January 6, 2019: Functional & Integrative Genomics
Subodh Verma, Sabhyata Bhatia
Improvement of the quality and quantity of chickpea seed protein can be greatly facilitated by an understanding of the genic organization and the genetic architecture of the genes encoding seed storage proteins (SSPs). The aim of this study was to provide a comprehensive analysis of the chickpea SSP genes, putative co-expressing transcription factors (TFs), and to identify a seed-specific SSP gene promoter. A genome-wide identification of SSP genes in chickpea led to the identification of 21 non-redundant SSP encoding genes located on 6 chromosomes...
December 17, 2018: Functional & Integrative Genomics
Chon-Kit Kenneth Chan, Nedeljka Rosic, Michał T Lorenc, Paul Visendi, Meng Lin, Paulina Kaniewska, Brett J Ferguson, Peter M Gresshoff, Jacqueline Batley, David Edwards
Next-generation DNA sequencing technologies, such as RNA-Seq, currently dominate genome-wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies, a suitable reference genome is unavailable, especially for meta-transcriptome studies which assay gene expression from mixed populations of organisms. Where a reference is unavailable, it is possible to generate a reference by the de novo assembly of the sequence reads...
November 27, 2018: Functional & Integrative Genomics
Ratan K Choudhary, Shanti Choudhary, C S Mukhopadhyay, Devendra Pathak, Ramneek Verma
Although water buffaloes are the main milk-producing animals in Indian subcontinent, only limited attempts have been made to identify canonical pathways and gene regulatory networks operating within the mammary glands of these animals. Such information is important for identifying unique transcriptome signatures in the mammary glands of diseased animals. In this report, we analyzed the transcription profile of 3 prepubertal buffalo mammary glands and identified common genes (mean FPKM > 0.2 in all samples) operating in the glands...
November 23, 2018: Functional & Integrative Genomics
Ranjeet R Kumar, Khushboo Singh, Sumedha Ahuja, Mohd Tasleem, Indra Singh, Sanjeev Kumar, Monendra Grover, Dwijesh Mishra, Gyanendra K Rai, Suneha Goswami, Gyanendra P Singh, Viswanathan Chinnusamy, Anil Rai, Shelly Praveen
Terminal heat stress has detrimental effect on the growth and yield of wheat. Very limited information is available on heat stress-associated active proteins (SAAPs) in wheat. Here, we have identified 159 protein groups with 4271 SAAPs in control (22 ± 3 °C) and HS-treated (38 °C, 2 h) wheat cvs. HD2985 and HD2329 using iTRAQ. We identified 3600 proteins to be upregulated and 5825 proteins to be downregulated in both the wheat cvs. under HS. We observed 60.3% of the common SAAPs showing upregulation in HD2985 (thermotolerant) and downregulation in HD2329 (thermosusceptible) under HS...
November 22, 2018: Functional & Integrative Genomics
Yan Tian, Yu Xu, Huawei Wang, Ruo Shu, Liang Sun, Yujian Zeng, Fangyou Gong, Yi Lei, Kunhua Wang, Huayou Luo
Increasing data demonstrate that circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) play important roles in tumorigenesis. However, the mechanisms in colorectal cancer (CRC) remain unclear. Here, hundreds of significantly expressed circRNAs, and thousands of lncRNAs as well as mRNAs were identified. By qRT-PCR, one abnormal circRNA, lncRNA, and three mRNAs were verified in 24 pairs of tissues and blood samples, respectively. Then, by GO analysis, we found that the gene expression profile of linear counterparts of upregulated circRNAs in human CRC tissues preferred positive regulation of GTPase activity, cellular protein metabolic process, and protein binding, while that of downregulated circRNAs of CRC preferred positive regulation of cellular metabolic process, acetyl-CoA metabolic process, and protein kinase C activity...
November 16, 2018: Functional & Integrative Genomics
Sergio Gálvez, Rosa Mérida-García, Carlos Camino, Philippa Borrill, Michael Abrouk, Ricardo H Ramírez-González, Sezgi Biyiklioglu, Francisco Amil-Ruiz, Gabriel Dorado, Hikmet Budak, Victoria Gonzalez-Dugo, Pablo J Zarco-Tejada, Rudi Appels, Cristobal Uauy, Pilar Hernandez
Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought responses in the field remain largely unknown. Here, we addressed this by utilizing an interdisciplinary approach involving field water status phenotyping, sampling, and gene expression analyses...
November 16, 2018: Functional & Integrative Genomics
Min Zhou, Shigang Zheng, Rong Liu, Jing Lu, Lu Lu, Chihong Zhang, Zehou Liu, Congpei Luo, Lei Zhang, Yu Wu
Wheat, one of the most broadly cultivated and consumed food crops worldwide, can accumulate high Cd contents in their edible parts, which poses a major hazard to human health. Cd accumulation ability differs among varieties in wheat, but the underlying molecular mechanism is largely unknown. Here, key genes responsible for Cd accumulation between two contrasting wheat genotypes (low-Cd accumulation one L17, high-Cd accumulation one H17) were investigated. Total 1269 were differentially expressed genes (DEGs) in L17 after Cd treatment, whereas, 399 Cd-induced DEGs were found in H17...
November 15, 2018: Functional & Integrative Genomics
JunLong Sun, LiuLan Zhao, Hao Wu, WenQiang Lian, Can Cui, ZongJun Du, Wei Luo, MingZhou Li, Song Yang
Water temperature affects the survival, growth, immunity, reproduction, and productivity of farmed fish. The temperature beyond suitable range will disrupt the normal physiological activity. Common carp (Cyprinus carpio L.) is a representative eurythermic fish; they are able to sense and respond to changes in water temperature by adjusting their physiology. To investigate the miRNAs in common carp at different temperatures, nine liver small-RNA libraries (5 °C, 17 °C, and 30 °C, each group have three biological repetitions) were constructed and sequenced using high-throughput sequencing...
November 15, 2018: Functional & Integrative Genomics
Vishnu Sukumari Nath, Sayuj Koyyappurath, Teena Elizabeth Alex, Kiran Ayyanperumal Geetha, Lesly Augustine, Alka Nasser, George Thomas
Transcription factors (TFs) fine-tune the host defense transcriptome in response to pathogen invasions. No information is available on Zingiber zerumbet (Zz) TFs involved in defense response against Pythium myriotylum. Here, we provide a global identification, characterization, and temporal expression profiling of Zz TFs following an incompatible interaction with P. myriotylum using a transcriptome sequencing approach. We identified a total of 903 TFs belonging to 96 families based on their conserved domains...
November 11, 2018: Functional & Integrative Genomics
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