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Functional & Integrative Genomics

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https://www.readbyqxmd.com/read/28480497/expression-analysis-of-genes-encoding-double-b-box-zinc-finger-proteins-in-maize
#1
Wenlan Li, Jingchao Wang, Qi Sun, Wencai Li, Yanli Yu, Meng Zhao, Zhaodong Meng
The B-box proteins play key roles in plant development. The double B-box (DBB) family is one of the subfamily of the B-box family, with two B-box domains and without a CCT domain. In this study, 12 maize double B-box genes (ZmDBBs) were identified through a genome-wide survey. Phylogenetic analysis of DBB proteins from maize, rice, Sorghum bicolor, Arabidopsis, and poplar classified them into five major clades. Gene duplication analysis indicated that segmental duplications made a large contribution to the expansion of ZmDBBs...
May 8, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28477104/using-scale-and-feather-traits-for-module-construction-provides-a-functional-approach-to-chicken-epidermal-development
#2
Weier Bao, Matthew J Greenwold, Roger H Sawyer
Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis...
May 5, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28470340/comprehensive-strategy-for-the-design-of-precision-drugs-and-identification-of-genetic-signature-behind-proneness-of-the-disease-a-pharmacogenomic-approach
#3
REVIEW
Preethi M Iyer, S Karthikeyan, P Sanjay Kumar, P K Krishnan Namboori
The proneness of diseases and susceptibility towards drugs vary from person to person. At present, there is a strong demand for the personalization of drugs. The genetic signature behind proneness of the disease has been studied through a comprehensive 'octopodial approach'. All the genetic variants included in the approach have been introduced. The breast cancer associated with BRCA1 mutation has been taken as the illustrative example to introduce all these factors. The genetic variants associated with the drug action of tamoxifen have been fully illustrated in the manuscript...
May 3, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28361233/rna-seq-analysis-for-transcriptome-profiling-in-response-to-classical-swine-fever-vaccination-in-indigenous-and-crossbred-pigs
#4
Shalu Kumari Pathak, Amit Kumar, G Bhuwana, Vaishali Sah, Vikramadiya Upmanyu, A K Tiwari, A P Sahoo, A R Sahoo, Sajjad A Wani, Manjit Panigrahi, N R Sahoo, Ravi Kumar
In present investigation, differential expression of transcriptome after classical swine fever (CSF) vaccination has been explored at the cellular level in crossbred and indigenous (desi) piglets. RNA Sequencing by Expectation-Maximization (RSEM) package was used to quantify gene expression from RNA Sequencing data, and differentially expressed genes (DEGs) were identified using EBSeq, DESeq2, and edgeR softwares. After analysis, 5222, 6037, and 6210 common DEGs were identified in indigenous post-vaccinated verses pre-vaccinated, crossbred post-vaccinated verses pre-vaccinated, and post-vaccinated crossbred verses indigenous pigs, respectively...
March 30, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28353203/gene-structure-of-the-pregnancy-associated-glycoprotein-like-pag-l-in-the-eurasian-beaver-castor-fiber-l
#5
Aleksandra Lipka, Marta Majewska, Grzegorz Panasiewicz, Martyna Bieniek-Kobuszewska, Bozena Szafranska
The pregnancy-associated glycoprotein-like family (PAG-L) is a large group of chorionic products, expressed in the pre-placental trophoblast and later in the post-implantational chorionic epithelium, and are involved in proper placenta development and embryo-maternal interaction in eutherians. This study describes identification of the PAG-L family in the genome of the Eurasian beaver (Castor fiber L.), named CfPAG-L. We identified 7657 bp of the CfPAG-L gDNA sequence (Acc. No. KX377932), encompassing nine exons (1-9) and eight introns (A-H)...
March 29, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28321518/identification-and-characterization-of-durum-wheat-micrornas-in-leaf-and-root-tissues
#6
Veronica Fileccia, Edoardo Bertolini, Paolo Ruisi, Dario Giambalvo, Alfonso Salvatore Frenda, Gina Cannarozzi, Zerihun Tadele, Cristina Crosatti, Federico Martinelli
MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs...
March 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28293806/morpho-physiological-and-transcriptome-profiling-reveal-novel-zinc-deficiency-responsive-genes-in-rice
#7
Tirthankar Bandyopadhyay, Poonam Mehra, Suboot Hairat, Jitender Giri
Intensive farming has depleted the soil zinc (Zn) availability resulting in decreased crop productivity. Here, we attempt to understand the Zn deficiency response in rice through temporal transcriptome analysis. For this, rice seedlings were raised under Zn-deficient conditions up to 4 weeks followed by Zn re-supply for 3 days. Zn-deficient plants developed characteristic deficiency symptoms such as leaf bronzing, decrease in biomass, total chlorophyll, PSII efficiency, decreased carbonic anhydrase activity and increased ROS production...
March 14, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28285413/comprehensive-assessment-of-the-genes-involved-in-withanolide-biosynthesis-from-withania-somnifera-chemotype-specific-and-elicitor-responsive-expression
#8
Aditya Vikram Agarwal, Parul Gupta, Deeksha Singh, Yogeshwar Vikram Dhar, Deepak Chandra, Prabodh Kumar Trivedi
Withania somnifera (L.) Dunal (Family, Solanaceae), is among the most valuable medicinal plants used in Ayurveda owing to its rich reservoir of pharmaceutically active secondary metabolites known as withanolides. Withanolides are C28-steroidal lactones having a triterpenoidal metabolic origin synthesised via mevalonate (MVA) pathway and methyl-D-erythritol-4-phosphate (MEP) pathway involving metabolic intermediacy of 24-methylene (C30-terpenoid) cholesterol. Phytochemical studies suggest differences in the content and/or nature of withanolides in different tissues of different chemotypes...
March 11, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28251419/transcriptome-profile-of-the-human-placenta
#9
Marta Majewska, Aleksandra Lipka, Lukasz Paukszto, Jan Pawel Jastrzebski, Kamil Myszczynski, Marek Gowkielewicz, Marcin Jozwik, Mariusz Krzysztof Majewski
The human placenta is a particular organ that inseparably binds the mother and the fetus. The proper development and survival of the conceptus relies on the essential interplay between maternal and fetal factors involved in cooperation within the placenta. In our study, high-throughput sequencing (RNA-seq) was applied to analyze the global transcriptome of the human placenta during uncomplicated pregnancies. The RNA-seq was utilized to identify the global pattern of the gene expression in placentas (N = 4) from women in single and twin pregnancies...
March 1, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28247088/characterization-of-mir061-and-its-target-genes-in-grapevine-responding-to-exogenous-gibberellic-acid
#10
Mengqi Wang, Xin Sun, Chen Wang, Liwen Cui, Lide Chen, Chaobo Zhang, Lingfei Shangguan, Jinggui Fang
MicroRNAs (miRNAs), as an important growth regulator, are also involved in gibberellic acid (GA) signaling, revealing much relationship between miRNAs and GA in various plant responses. Grape is highly sensitive to GA3, which plays a significant regulatory role in regulation of flower development, berry expansion, berry set, berry ripening, and seedlessness induction; further, it was found that grapevine miR061 (VvmiR061) is a GA3 responsive miRNA. In this study, grapevine REV (VvREV) and HOX32 (VvHOX32), two target genes of VvmiR061, were predicted, verified, and cloned; homologous conservation was analyzed in various plants...
February 28, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28236275/gene-expression-profiles-predictive-of-cold-induced-sweetening-in-potato
#11
Jonathan Neilson, M Lagüe, S Thomson, F Aurousseau, A M Murphy, B Bizimungu, V Deveaux, Y Bègue, J M E Jacobs, H H Tai
Cold storage (2-4 °C) used in potato production to suppress diseases and sprouting during storage can result in cold-induced sweetening (CIS), where reducing sugars accumulate in tuber tissue leading to undesirable browning, production of bitter flavors, and increased levels of acrylamide with frying. Potato exhibits genetic and environmental variation in resistance to CIS. The current study profiles gene expression in post-harvest tubers before cold storage using transcriptome sequencing and identifies genes whose expression is predictive for CIS...
February 24, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28236274/comparative-pan-genome-analysis-of-oral-prevotella-species-implicated-in-periodontitis
#12
Maziya Ibrahim, Ahalyaa Subramanian, Sharmila Anishetty
Prevotella is part of the oral bacterial community implicated in periodontitis. Pan genome analyses of eight oral Prevotella species, P. dentalis, P. enoeca, P. fusca, P. melaninogenica, P. denticola, P. intermedia 17, P. intermedia 17-2 and P. sp. oral taxon 299 are presented in this study. Analysis of the Prevotella pan genome revealed features such as secretion systems, resistance to oxidative stress and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems that enable the bacteria to adapt to the oral environment...
February 24, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28236273/developmental-processes-and-responses-to-hormonal-stimuli-in-tea-plant-camellia-sinensis-leaves-are-controlled-by-grf-and-gif-gene-families
#13
Zhi-Jun Wu, Wen-Li Wang, Jing Zhuang
Tea plant (Camellia sinensis (L.) O. Kuntze) is an important leaf-type woody crop used for producing of non-alcoholic beverages worldwide. The GROWTH-REGULATING FACTOR (GRF) transcription factors cooperated with GRF-INTERACTING FACTOR (GIF) transcriptional coactivators positively regulate leaf development. In the present study, six GRF and two GIF genes were identified and characterized in the leaf transcriptome of C. sinensis, respectively. The alignment results showed that the feature structures of the predicted homologous GRF and GIF proteins of C...
February 24, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28386681/addition-to-special-issue-mirna-in-model-and-complex-organisms
#14
(no author information available yet)
No abstract text is available yet for this article.
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27665284/abiotic-stress-mirnomes-in-the-triticeae
#15
REVIEW
Burcu Alptekin, Peter Langridge, Hikmet Budak
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27541609/mir-216-and-mir-217-expression-is-reduced-in-transgenic-mouse-models-of-pancreatic-adenocarcinoma-knockout-of-mir-216-mir-217-host-gene-is-embryonic-lethal
#16
Ana Clara P Azevedo-Pouly, Dhruvitkumar S Sutaria, Jinmai Jiang, Ola A Elgamal, Foued Amari, David Allard, Paul J Grippo, Vincenzo Coppola, Thomas D Schmittgen
Mice harboring a G12D activating Kras mutation are among the most heavily studied models in the field of pancreatic adenocarcinoma (PDAC) research. miRNAs are differentially expressed in PDAC from patients and mouse models of PDAC. To better understand the relationship that Kras activation has on miRNA expression, we profiled the expression of 629 miRNAs in RNA isolated from the pancreas of control, young, and old P48(+/Cre);LSL-KRAS(G12D) as well as PDX-1-Cre;LSL-KRAS(G12D) mice. One hundred of the differentially expressed miRNAs had increased expression in the advanced disease (old) P48(+/Cre);LSL-KRAS(G12D) compared to wild-type mice...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27068847/in-silico-search-and-biological-validation-of-micrornas-related-to-drought-response-in-peach-and-almond
#17
Fazileh Esmaeili, Behrouz Shiran, Hossein Fallahi, Neda Mirakhorli, Hikmet Budak, Pedro Martínez-Gómez
Plant responses to drought stress are regulated at the transcriptional and post-transcriptional levels through noncoding endogenous microRNAs. These microRNAs play key roles in gene expression, mainly by down-regulating target mRNAs. In this work, an in silico search and validation for microRNAs related to drought response in peach ('G.H. Hill'), almond ('Sefied') and an interspecific peach-almond hybrid ('GN 15') has been performed. We used qPCR to analyse the gene expression of several miRNAs described as being related to drought response in peach, including miR156, miR159, miR160, miR167, miR171, miR172, miR398, miR403, miR408, miR842 and miR2275 under mild and severe water deficit...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27032785/wheat-mirna-ancestors-evident-by-transcriptome-analysis-of-a-b-and-d-genome-donors
#18
Burcu Alptekin, Hikmet Budak
MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28224250/abscisic-acid-sucrose-and-auxin-coordinately-regulate-berry-ripening-process-of-the-fujiminori-grape
#19
Haifeng Jia, Zhenqiang Xie, Chen Wang, Lingfei Shangguan, Ning Qian, Mengjie Cui, Zhongjie Liu, Ting Zheng, Mengqi Wang, Jinggui Fang
The aim of this study was to examine the effect of abscisic acid (ABA), sucrose, and auxin on grape fruit development and to assess the mechanism of these three factors on the grape fruit ripening process. Different concentrations of ABA, sucrose, and auxin were used to treat the grape fruit, and the ripening-related indices, such as physiological and molecular level parameters, were analyzed. The activity of BG protein activity was analyzed during the fruit development. Sucrose, ABA, and auxin influenced the grape fruit sugar accumulation in different ways, as well as the volatile compounds, anthocyanin content, and fruit firmness...
February 21, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28220336/micrornas-in-model-and-complex-organisms
#20
EDITORIAL
Hikmet Budak, Baohong Zhang
Non-coding RNAs such as microRNAs (miRNAs) are very tiny ribonucleotides having an essential role in gene regulation at both post-transcriptional and translational levels. They are very conserved and expressed in worms, flies, plants, and mammals in a sequence-specific manner. Furthermore, it is now possible to clone miRNAs using the new genome editing tool CRISPR/cas9, which shows benefit in control of untargeted effect. In this special issue, we tried to cover researches associated with functional roles of miRNAs accross model and complex organisms...
February 20, 2017: Functional & Integrative Genomics
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