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https://www.readbyqxmd.com/read/28110276/photosynthesis-in-c3-c4-intermediate-moricandia-species
#1
Urte Schlüter, Andrea Bräutigam, Udo Gowik, Michael Melzer, Pascal-Antoine Christin, Samantha Kurz, Tabea Mettler-Altmann, Andreas Pm Weber
Evolution of C4 photosynthesis is not distributed evenly in the plant kingdom. Particularly interesting is the situation in the Brassicaceae, because the family contains no C4 species, but several C3-C4 intermediates, mainly in the genus Moricandia Investigation of leaf anatomy, gas exchange parameters, the metabolome, and the transcriptome of two C3-C4 intermediate Moricandia species, M. arvensis and M. suffruticosa, and their close C3 relative M. moricandioides enabled us to unravel the specific C3-C4 characteristics in these Moricandia lines...
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110274/c4-photosynthesis-50-years-of-discovery-and-innovation
#2
EDITORIAL
Susanne von Caemmerer, Oula Ghannoum, Robert T Furbank
It is now over half a century since the biochemical characterization of the C4 photosynthetic pathway, and this special issue highlights the sheer breadth of current knowledge. New genomic and transcriptomic information shows that multi-level regulation of gene expression is required for the pathway to function, yet we know it to be one of the most dynamic examples of convergent evolution. Now, a focus on the molecular transition from C3-C4 intermediates, together with improved mathematical models, experimental tools and transformation systems, holds great promise for improving C4 photosynthesis in crops...
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110034/transcriptome-profiles-of-the-clam-meretrix-petechialis-hepatopancreas-in-response-to-vibrio-infection
#3
Fengjuan Jiang, Xin Yue, Hongxia Wang, Baozhong Liu
Microbial diseases have received much attention due to their enormous destruction of aquaculture, and Vibrio parahaemolyticus is one of the main pathogens that cause bacterial disease in the clam Meretrix petechialis. To better understand the molecular mechanisms of the immune response to Vibrio in M. petechialis, RNA-Seq was applied to explore global expression changes of hepatopancreas from this clam after Vibrio challenge. There were 199,318,966 clean reads obtained by Illumina sequencing, which were further assembled into 214,577 transcripts, and then 147,255 unigenes with an N50 of 1393 bp were identified...
January 18, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28109972/biological-responses-to-phenylurea-herbicides-in-fish-and-amphibians-new-directions-for-characterizing-mechanisms-of-toxicity
#4
Vicki L Marlatt, Christopher J Martyniuk
Urea-based herbicides are applied in agriculture to control broadleaf and grassy weeds, acting to either inhibit photosynthesis at photosystem II (phenylureas) or to inhibit acetolactate synthase acetohydroxyacid synthase (sulfonylureas). While there are different chemical formulas for urea-based herbicides, the phenylureas are a widely used class in North America and have been detected in aquatic environments due to agricultural run-off. Here, we summarize the current state of the literature, synthesizing data on phenylureas and their biological effects in two non-target animals, fish and amphibians, with a primary focus on diuron and linuron...
January 18, 2017: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
https://www.readbyqxmd.com/read/28109746/diversity-and-evolution-of-tir-domain-containing-proteins-in-bivalves-and-metazoa-new-insights-from-comparative-genomics
#5
Marco Gerdol, Paola Venier, Paolo Edomi, Alberto Pallavicini
The Toll/interleukin-1 receptor (TIR) domain has a fundamental role in the innate defence response of plants, vertebrate and invertebrate animals. Mostly found in the cytosolic side of membrane-bound receptor proteins, it mediates the intracellular signalling upon pathogen recognition via heterotypic interactions. Although a number of TIR-domain-containing (TIR-DC) proteins have been characterized in vertebrates, their evolutionary relationships and functional role in protostomes are still largely unknown. Due to the high abundance and diversity of TIR-DC proteins in bivalve molluscs, we investigated this class of marine invertebrates as a case study...
January 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28109431/proteogenomics-recycling-public-data-to-improve-genome-annotations
#6
A McAfee, L J Foster
Massively parallel sequencing is revealing species genomes faster than ever before, but the value of the raw sequence is limited unless the genes can be accurately annotated. This is typically achieved using gene prediction algorithms which, despite continual improvement, still require substantial verification and refinement. For example, in silico methods struggle with annotating splice isoforms accurately and empirical methods are needed to refine and verify the initial bioinformatic gene predictions. RNA-seq is an excellent way to confirm exon-exon boundaries and transcript termini, while mass spectrometry (MS) offers definitive proof that a gene is translated and a secondary means of confirming exon expression, protein termini, and posttranslational modifications...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109325/studying-hematopoiesis-using-single-cell-technologies
#7
REVIEW
Fang Ye, Wentao Huang, Guoji Guo
Hematopoiesis is probably the best-understood stem cell differentiation system; hematopoietic stem cell (HSC) transplantation represents the most widely used regenerative therapy. The classical view of lineage hierarchy in hematopoiesis is built on cell type definition system by a group of cell surface markers. However, the traditional model is facing increasing challenges, as many classical cell types are proved to be heterogeneous. Recently, the developments of new technologies allow genome, transcriptome, proteome, and epigenome analysis at the single-cell level...
January 21, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28109288/long-intergenic-non-coding-rna-00152-promotes-lung-adenocarcinoma-proliferation-via-interacting-with-ezh2-and-repressing-il24-expression
#8
Qin-Nan Chen, Xin Chen, Zhen-Yao Chen, Feng-Qi Nie, Chen-Chen Wei, Hong-Wei Ma, Li Wan, Shuai Yan, Sheng-Nan Ren, Zhao-Xia Wang
BACKGROUND: Numerous studies have shown that long non-coding RNAs (lncRNAs) behave as a novel class of transcript during multiple cancer processes, such as cell proliferation, apoptosis, migration, and invasion. LINC00152 is located on chromosome 2p11.2, and has a transcript length of 828 nucleotides. The biological role of LINC00152 in LAD(lung adenocarcinoma) remains unknown. METHODS: Quantitative reverse transcription PCR(qRT-PCR) was used to detect LINC00152 expression in 60 human LAD tissues and paired normal tissues...
January 21, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28109190/qtl-mapping-and-candidate-genes-for-resistance-to-fusarium-ear-rot-and-fumonisin-contamination-in-maize
#9
Valentina Maschietto, Cinzia Colombi, Raul Pirona, Giorgio Pea, Francesco Strozzi, Adriano Marocco, Laura Rossini, Alessandra Lanubile
BACKGROUND: Fusarium verticillioides is a common maize pathogen causing ear rot (FER) and contamination of the grains with the fumonisin B1 (FB1) mycotoxin. Resistance to FER and FB1 contamination are quantitative traits, affected by environmental conditions, and completely resistant maize genotypes to the pathogen are so far unknown. In order to uncover genomic regions associated to reduced FER and FB1 contamination and identify molecular markers for assisted selection, an F2:3 population of 188 progenies was developed crossing CO441 (resistant) and CO354 (susceptible) genotypes...
January 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28108965/transcriptomic-and-hormone-analyses-reveal-mechanisms-underlying-petal-elongation-in-chrysanthemum-morifolium-jinba
#10
Jingjing Wang, Haibin Wang, Lian Ding, Aiping Song, Feng Shen, Jiafu Jiang, Sumei Chen, Fadi Chen
Auxin regulates chrysanthemum petal elongation by promoting cell elongation. Transcriptomic analysis shows that auxin signal transduction may connect with other transcription factors by TCPs to regulate chrysanthemum petal elongation. As an ornamental species, Chrysanthemum morifolium has high ornamental and economic value. Petal size is the primary factor that influences the ornamental value of chrysanthemum, but the mechanism underlying the development of C. morifolium petals remains unclear. In our study, we tracked the growth of petals and found that the basal region of 'Jinba' petals showed a higher elongation rate, exhibiting rapid cell elongation during petal growth...
January 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28108736/long-non-coding-rnas-a-rising-biotarget-in-colorectal-cancer
#11
Jian Luo, Jian Qu, Dong-Kai Wu, Zhi-Li Lu, Yue-Sheng Sun, Qiang Qu
Colorectal cancer (CRC) is a common gastrointestinal cancer, with a high incidence and high mortality. Long non-coding RNAs (lncRNAs) are involved in the development, invasion and metastasis, early diagnosis, prognosis, the chemoresistance and radioresistance of CRC through interference with mRNA activity, directly combining with proteins to regulate their activity or alter their localization, influencing downstream gene expression by inhibiting RNA polymerase and regulating gene expression as competing endogenous RNAs...
January 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28108659/yamat-seq-an-efficient-method-for-high-throughput-sequencing-of-mature-transfer-rnas
#12
Megumi Shigematsu, Shozo Honda, Phillipe Loher, Aristeidis G Telonis, Isidore Rigoutsos, Yohei Kirino
Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108657/risearch2-suffix-array-based-large-scale-prediction-of-rna-rna-interactions-and-sirna-off-targets
#13
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck, Peter F Stadler, Ivo L Hofacker, Jan Gorodkin
Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108623/tumor-induced-stromal-stat1-accelerates-breast-cancer-via-deregulating-tissue-homeostasis
#14
Victoria R Zellmer, Patricia M Schnepp, Sarah L Fracci, Xuejuan Tan, Erin N Howe, Siyuan Zhang
: The tumor microenvironment (TME) is a dynamic tissue space in which the tumor exists, plays a significant role in tumor initiation, and is a key contributor in cancer progression; however, little is known about tumor-induced changes in the adjacent tissue stroma. Herein, tumor-induced changes in the TME were explored at the morphological and molecular level to further understand cancer progression. Tumor-adjacent mammary glands (TAGs) displayed altered branching morphology, expansion of myofibroblasts, and increased mammosphere formation, broadly suggesting a tumor-induced field effect...
January 20, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28108512/constitutive-notch3-signaling-promotes-the-growth-of-basal-breast-cancers
#15
Lisa Choy, Thijs Hagenbeek, Margaret Solon, Dorothy M French, David Finkle, Amy Shelton, Rayna Venook, Matthew J Brauer, Christian W Siebel
Notch ligands signal through one of four receptors on neighboring cells to mediate cell-cell communication and control cell fate, proliferation and survival. Although aberrant Notch activation has been implicated in numerous malignancies, including breast cancer, the importance of individual receptors in distinct breast cancer subtypes and the mechanisms of receptor activation remain unclear. Using a novel antibody to detect active NOTCH3, we report here that NOTCH3 signals constitutively in a panel of basal breast cancer cell lines and in more than one-third of basal tumors...
January 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28108505/comparative-transcriptomics-of-buzura-suppressaria-lepidoptera-geometridae-assembled-de-novo-yield-insights-into-response-after-buzura-suppressaria-nuclear-polyhedrosis-virus-infection
#16
Ji Luo, Yating Zhong, Jiyu Zhu, Guoying Zhou, Huayan Huang, Yaojun Wu
Buzura suppressaria Guenee (Lepidoptera: Geometridae) is a defoliator that seriously harms eucalyptus trees in South China. Buzura suppressaria nuclear polyhedrosis virus (BsNPV) is a baculovirus that infects B. suppressaria with high specificity and efficiency. Transcriptomes of B. suppressaria were sequenced before and after BsNPV infection using an Illumina-based platform to probe for differentially expressed genes (DEGs) of B. suppressaria after viral infection. On average, ∼57.4 million high-quality clean reads were generated and assembled de novo into 69,761 unigenes...
January 20, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28108491/transcriptome-analysis-identifies-multifaceted-regulatory-mechanisms-dictating-a-genetic-switch-from-neuronal-network-establishment-to-maintenance-during-postnatal-prefrontal-cortex-development
#17
Yvet Kroeze, Martin Oti, Ellen van Beusekom, Roel H M Cooijmans, Hans van Bokhoven, Sharon M Kolk, Judith R Homberg, Huiqing Zhou
The prefrontal cortex (PFC) is one of the latest brain regions to mature, which allows the acquisition of complex cognitive abilities through experience. To unravel the underlying gene expression changes during postnatal development, we performed RNA-sequencing (RNA-seq) in the rat medial PFC (mPFC) at five developmental time points from infancy to adulthood, and analyzed the differential expression of protein-coding genes, long intergenic noncoding RNAs (lincRNAs), and alternative exons. We showed that most expression changes occur in infancy, and that the number of differentially expressed genes reduces toward adulthood...
January 19, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28108400/overexpression-of-a-three-gene-conidial-pigment-biosynthetic-pathway-in-aspergillus-nidulans-reveals-the-first-nrps-known-to-acetylate-tryptophan
#18
Calvin T Sung, Shu-Lin Chang, Ruth Entwistle, Green Ahn, Tzu-Shyang Lin, Vessela Petrova, Hsu-Hua Yeh, Mike B Praseuth, Yi-Ming Chiang, Berl R Oakley, Clay C C Wang
Fungal nonribosomal peptide synthetases (NRPSs) are megasynthetases that produce cyclic and acyclic peptides. In Aspergillus nidulans, the NRPS ivoA (AN10576) has been associated with the biosynthesis of grey-brown conidiophore pigments. Another gene, ivoB (AN0231), has been demonstrated to be an N-acetyl-6-hydroxytryptophan oxidase that putatively acts downstream of IvoA. A third gene, ivoC, has also been predicted to be involved in pigment biosynthesis based on publicly available genomic and transcriptomic information...
January 17, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28108348/epigenetic-basis-of-cancer-health-disparities-looking-beyond-genetic-differences
#19
REVIEW
Aamir Ahmad, Shafquat Azim, Haseeb Zubair, Mohammad Aslam Khan, Seema Singh, James E Carter, Rodney Rocconi, Ajay P Singh
Despite efforts at various levels, racial health disparities still exist in cancer patients. These inequalities in incidence and/or clinical outcome can only be explained by a multitude of factors, with genetic basis being one of them. Several investigations have provided convincing evidence to support epigenetic regulation of cancer-associated genes, which results in the differential transcriptome and proteome, and may be linked to a pre-disposition of individuals of certain race/ethnicity to early or more aggressive cancers...
January 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28108340/rna-seq-transcriptome-analysis-of-the-olive-flounder-paralichthys-olivaceus-kidney-response-to-vaccination-with-heat-inactivated-viral-hemorrhagic-septicemia-virus
#20
Jee Youn Hwang, Mun Gyeoung Kwon, Sung-Hee Jung, Myoung Ae Park, Dong-Wook Kim, Wang Sik Cho, Jeong Woo Park, Maeng-Hyun Son
Viral hemorrhagic septicemia (VHS) is a highly contagious disease of cultured flounder caused by VHS virus (VHSV). To develop effective VHSV vaccines, it is essential to understand the molecular mechanisms underlying the host's protective response against VHSV. The purpose of this study is to clarify which genes are involved in the protective response of olive flounder after VHSV vaccination. We first injected olive flounder intraperitoneally with 10(7) TCID50 heat-inactivated VHSV vaccine and evaluated the vaccine efficacy at 20 °C...
January 17, 2017: Fish & Shellfish Immunology
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