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61.
High density genetic maps are a reliable tool for genetic dissection of complex plant traits. Mapping resolution is often hampered by the variable crossover and non-crossover events occurring across the genome, with pericentromeric regions (pCENR) showing highly suppressed recombination rates. The efficiency of linkage mapping can further be improved by characterizing and understanding the distribution of recombinational activity along individual chromosomes. In order to evaluate the genome wide recombination rate in common beans (Phaseolus vulgaris L.) we developed a SNP-based linkage map using the genotype-by-sequencing approach with a 188 recombinant inbred line family generated from an inter gene pool cross (Andean x Mesoamerican). We identified 1,112 SNPs that were subsequently used to construct a robust linkage map with 11 groups, comprising 513 recombinationally unique marker loci spanning 943 cM (LOD 3.0). Comparative analysis showed that the linkage map spanned >95% of the physical map, indicating that the map is almost saturated. Evaluation of genome-wide recombination rate indicated that at least 45% of the genome is highly recombinationally suppressed, and allowed us to estimate locations of pCENRs. We observed an average recombination rate of 0.25 cM/Mb in pCENRs as compared to the rest of genome that showed 3.72 cM/Mb. However, several hot spots of recombination were also detected with recombination rates reaching as high as 34 cM/Mb. Hotspots were mostly found towards the end of chromosomes, which also happened to be gene-rich regions. Analyzing relationships between linkage and physical map indicated a punctuated distribution of recombinational hot spots across the genome. 相似文献
62.
Identification and characterization of novel factors that act in the nonsense‐mediated mRNA decay pathway in nematodes,flies and mammals
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Angela Casadio Dasa Longman Nele Hug Laurent Delavaine Raúl Vallejos Baier Claudio R Alonso Javier F Cáceres 《EMBO reports》2015,16(1):71-78
Nonsense‐mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNAs harboring premature termination codons (PTCs). We have conducted a genome‐wide RNAi screen in Caenorhabditis elegans that resulted in the identification of five novel NMD genes that are conserved throughout evolution. Two of their human homologs, GNL2 (ngp‐1) and SEC13 (npp‐20), are also required for NMD in human cells. We also show that the C. elegans gene noah‐2, which is present in Drosophila melanogaster but absent in humans, is an NMD factor in fruit flies. Altogether, these data identify novel NMD factors that are conserved throughout evolution, highlighting the complexity of the NMD pathway and suggesting that yet uncovered novel factors may act to regulate this process. 相似文献
63.
Salazar Jonathan Arley Ocampo Marisol Castañeda-Ramirez Jeimmy Johana Samacá Jhoan Patarroyo Manuel Alfonso Patarroyo Manuel Elkin 《International journal of peptide research and therapeutics》2021,27(4):2823-2830
International Journal of Peptide Research and Therapeutics - This study was aimed at characterising Mycobacterium tuberculosis (Mtb) H37Rv Rv0292 protein peptides. As this protein forms a... 相似文献
64.
Brandon M. Hurr Donald J. HuberC. Eduardo Vallejos Eunkyung LeeSteven A. Sargent 《Journal of plant physiology》2013
Watersoaking is an ethylene-induced disorder observed in some members of the Cucurbitaceae including cucumber (Cucumis sativus L.), watermelon (Citrullus lanatus Thunb. Matsum and Nakai), and tropical pumpkin (Cucurbita moschata Duch.). Previous studies have found that immature beit-alpha cucumber (cv. Manar) exhibit watersoaking after 6 d of continuous exposure to 10 μL L−1 ethylene in air (21 kPa O2). The present study was designed to investigate the early dynamics of ethylene responses in immature cucumber fruit in order to provide insight into the watersoaking triggering mechanism. Changes in respiration, epidermal color, firmness, reactive oxygen species (ROS) production and electrolyte leakage were evaluated as a function of time under different ethylene concentrations and exposure duration. Ethylene concentrations exceeding 10 μL L−1 did not accelerate changes in any of the evaluated responses. The first detectable change was a significant rise in respiration on day 2, followed by a significant rise in ROS on day 4, and significant degreening, mesocap softening, and increased electrolyte leakage on day 6; the latter responses coincident with incipient watersoaking. Varying the duration of exposure to ethylene indicated that the critical exposure time is between 2 and 4 d. Notably, all deleterious responses to ethylene were suppressed under a hypoxic atmosphere. A model is proposed in which ethylene induces a sharp increase in respiration with a concomitant sharp rise in ROS, which the immature fruit is incapable of quenching. The resulting production of excess ROS leads to discoloration and membrane deterioration, leading to the release of cytoplasmic content, rapid softening, and the visual symptom of watersoaking. 相似文献
65.
Guido A. Herrera‐R Thierry Oberdorff Elizabeth P. Anderson Sbastien Brosse Fernando M. Carvajal‐Vallejos Renata G. Frederico Max Hidalgo Cline Jzquel Mabel Maldonado Javier A. Maldonado‐Ocampo Hernn Ortega Johannes Radinger Gislene Torrente‐Vilara Jansen Zuanon Pablo A. Tedesco 《Global Change Biology》2020,26(10):5509-5523
Upstream range shifts of freshwater fishes have been documented in recent years due to ongoing climate change. River fragmentation by dams, presenting physical barriers, can limit the climatically induced spatial redistribution of fishes. Andean freshwater ecosystems in the Neotropical region are expected to be highly affected by these future disturbances. However, proper evaluations are still missing. Combining species distribution models and functional traits of Andean Amazon fishes, coupled with dam locations and climatic projections (2070s), we (a) evaluated the potential impacts of future climate on species ranges, (b) investigated the combined impact of river fragmentation and climate change and (c) tested the relationships between these impacts and species functional traits. Results show that climate change will induce range contraction for most of the Andean Amazon fish species, particularly those inhabiting highlands. Dams are not predicted to greatly limit future range shifts for most species (i.e., the Barrier effect). However, some of these barriers should prevent upstream shifts for a considerable number of species, reducing future potential diversity in some basins. River fragmentation is predicted to act jointly with climate change in promoting a considerable decrease in the probability of species to persist in the long‐term because of splitting species ranges in smaller fragments (i.e., the Isolation effect). Benthic and fast‐flowing water adapted species with hydrodynamic bodies are significantly associated with severe range contractions from climate change. 相似文献
66.
Rgine Janel‐Bintz Lauriane Kuhn Philippe Frit Johana Chicher Jrme Wagner Lajos Haracska Philippe Hammann Agns M Cordonnier 《Proteomics》2020,20(3-4)
It is established that short inverted repeats trigger base substitution mutagenesis in human cells. However, how the replication machinery deals with structured DNA is unknown. It has been previously reported that in human cell‐free extracts, DNA primer extension using a structured single‐stranded template is transiently blocked at DNA hairpins. Here, the proteomic analysis of proteins bound to the DNA template is reported and evidence that the DNA‐PK complex (DNA‐PKcs and the Ku heterodimer) recognizes, and is activated by, structured single‐stranded DNA is provided. Hijacking the DNA‐PK complex by double‐stranded oligonucleotides results in a large removal of the pausing sites and an elevated DNA extension efficiency. Conversely, DNA‐PKcs inhibition results in its stabilization on the template, along with other proteins acting downstream in the Non‐Homologous End‐Joining (NHEJ) pathway, especially the XRCC4‐DNA ligase 4 complex and the cofactor PAXX. Retention of NHEJ factors to the DNA in the absence of DNA‐PKcs activity correlates with additional halts of primer extension, suggesting that these proteins hinder the progression of the DNA synthesis at these sites. Overall these results raise the possibility that, upon binding to hairpins formed onto ssDNA during fork progression, the DNA‐PK complex interferes with replication fork dynamics in vivo. 相似文献
67.
Zalocar Y Frutos SM Casco SL Forastier ME Vallejos SV 《Revista de biología tropical》2011,59(3):1295-1306
Colacium vesiculosum (Euglenophyceae) is an epibiont common on planktonic microcrustaceans of continental waters. The interaction between epibionts and substrate organisms is not very well known, particularly in subtropical environments of South America. In the present work, we analyzed the prevalence, density, biomass and attachment sites of C. vesiculosum on planktonic microcrustaceans from Paiva Lake, a subtropical lake of Argentina. With the aim to evaluate whether epibionts affect the filtering rates of Notodiaptomus spiniger, the dominant planktonic crustacean, we carried out bioassays using phytoplankton < 53 microm. Crustaceans were sampled using a PVC tube (1.2m long and 10cm in diameter), filtering 50L of water through a 53 microm-mesh. Microcrustaceans were counted in Bogorov chambers under a stereoscopic microscope. The infested organisms were separated and observed with a photonic microscope to determine density and biovolume of epibionts, by analyzing their distribution on the exoskeleton. The prevalence of C. vesiculosum was higher in adult crustaceans than in their larvae and juveniles. The most infested group was that of calanoid copepods, related to their high density. The attachment sites on the exoskeleton were found to be the portions of the body which have a higher probability of encounter with epibionts during locomotion and feeding, i.e., antennae and thoracic legs in copepods, and thoracic legs and postabdomen in cladocerans. The similar values found in the filtering rate of infested and uninfested individuals of N. spiniger and the constant prevalence (< 40%) of epibiont algae, suggest that C. vesiculosum does not condition the life of planktonic crustaceans of Paiva Lake. 相似文献
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70.
A. Lofa V. Velasco M. Gerding M.D. López D. Vallejos A.M. Bonilla C.M. Logue 《Journal of applied microbiology》2019,127(4):1048-1056