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Molecular Genetics and Genomics: MGG

Ines Teichert, Miriam Lutomski, Ramona Märker, Minou Nowrousian, Ulrich Kück
During the sexual life cycle of filamentous fungi, multicellular fruiting bodies are generated for the dispersal of spores. The filamentous ascomycete Sordaria macrospora has a long history as a model system for studying fruiting body formation, and two collections of sterile mutants have been generated. However, for most of these mutants, the underlying genetic defect remains unknown. Here, we investigated the mutant spadix (spd) that was generated by X-ray mutagenesis in the 1950s and terminates sexual development after the formation of pre-fruiting bodies (protoperithecia)...
October 21, 2016: Molecular Genetics and Genomics: MGG
Nicolás Federico Villamil Munévar, Luiz Gustavo de Almeida, Beny Spira
Phosphate homeostasis is tightly regulated in bacteria. Phosphate scarcity is overcome by inducing the expression of genes associated with the scavenging of phosphate and phosphate-containing molecules, while phosphate surplus is stored in the form of polyphosphate (polyP). Regulation of the genes involved in polyP metabolism was investigated. Knockout of the most distal gene of the pstSCAB-phoU operon that encodes a Pi-transport system results in large accumulation of polyphosphate (polyP). Here, we show that the phoU mutation differentially affects the transcription of ppk and ppx, that respectively, encode a polyP kinase and a polyP exopolyphosphatase, by increasing the former and reducing the latter, further contributing the accumulation of polyP...
October 15, 2016: Molecular Genetics and Genomics: MGG
Sonika Ahlawat, Sachinandan De, Priyanka Sharma, Rekha Sharma, Reena Arora, R S Kataria, T K Datta, R K Singh
Hybrid sterility or reproductive isolation in mammals has been attributed to allelic incompatibilities in a DNA-binding protein PRDM9. Not only is PRDM9 exceptional in being the only known 'speciation gene' in vertebrates, but it is also considered to be the fastest evolving gene in the genome. The terminal zinc finger (ZF) domain of PRDM9 specifies genome-wide meiotic recombination hotspot locations in mammals. Intriguingly, PRDM9 ZF domain is highly variable between as well as within species, possibly activating different recombination hotspots...
October 15, 2016: Molecular Genetics and Genomics: MGG
Xiaozhu Wang, Shikai Liu, Chen Jiang, Xin Geng, Tao Zhou, Ning Li, Lisui Bao, Yun Li, Jun Yao, Yujia Yang, Xiaoxiao Zhong, Yulin Jin, Rex Dunham, Zhanjiang Liu
The ability to survive hypoxic conditions is important for various organisms, especially for aquatic animals. Teleost fish, representing more than 50 % of vertebrate species, are extremely efficient in utilizing low levels of dissolved oxygen in water. However, huge variations exist among various taxa of fish in their ability to tolerate hypoxia. In aquaculture, hypoxia tolerance is among the most important traits because hypoxia can cause major economic losses. Genetic enhancement for hypoxia tolerance in catfish is of great interest, but little was done with analysis of the genetic architecture of hypoxia tolerance...
October 12, 2016: Molecular Genetics and Genomics: MGG
Uwe Hoßfeld, Hans-Jörg Jacobsen, Christoph Plass, Benedikt Brors, Wilfried Wackernagel
No abstract text is available yet for this article.
October 11, 2016: Molecular Genetics and Genomics: MGG
Longxin Wang, Bowen Wang, Qingzhang Du, Jinhui Chen, Jiaxing Tian, Xiaohui Yang, Deqiang Zhang
Photosynthesis is one of the most important reactions on earth. PsbW, a nuclear-encoded subunit of photosystem II (PSII), stabilizes PSII structure and plays an important role in photosynthesis. Here, we used candidate gene-based linkage disequilibrium (LD) mapping to detect significant associations between allelic variations of PtoPsbW and traits related to photosynthesis, growth, and wood properties in Populus tomentosa. PtoPsbW showed the highest expression in leaves and it increased during the development of these leaves, suggesting that PtoPsbW may play an important role in plant growth and development...
October 8, 2016: Molecular Genetics and Genomics: MGG
Elena Barghini, Flavia Mascagni, Lucia Natali, Tommaso Giordani, Andrea Cavallini
Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs...
October 6, 2016: Molecular Genetics and Genomics: MGG
Feng Pan, Jinwei You, Yuan Liu, Xuefeng Qiu, Wen Yu, Jiehua Ma, Lianjun Pan, Aixia Zhang, Qipeng Zhang
To better understand the molecular aetiology of type 2 diabetes mellitus-associated erectile dysfunction (T2DMED) and to provide candidates for further study of its diagnosis and treatment, this study was designed to investigate differentially expressed microRNAs (miRNAs) in the corpus cavernosum (CC) of mice with T2DMED using GeneChip array techniques (Affymetrix miRNA 4.0 Array) and to predict target genes and signalling pathways regulated by these miRNAs based on bioinformatic analysis using TargetScan, the DAIAN web platform and DAVID...
September 28, 2016: Molecular Genetics and Genomics: MGG
Wei Gao, Lu Long, Xinquan Tian, Jingjing Jin, Huili Liu, Hui Zhang, Fuchun Xu, Chunpeng Song
Stress-associated proteins (SAPs) containing the A20/AN1 zinc-finger domain play important roles in response to both biotic and abiotic stresses in plants. Nevertheless, few studies have focused on the SAP gene family in cotton. To explore the distributions and expression patterns of these genes, we performed genome-wide identification and characterization of SAPs in tetraploid Gossypium hirsutum L. TM-1 (AD1). A total of 37 genes encoding SAPs were identified, 36 of which were duplicated in the A and D sub-genomes...
September 28, 2016: Molecular Genetics and Genomics: MGG
Yan Qiao, Jinjin Zhang, Jinwen Zhang, Zhiwei Wang, An Ran, Haixia Guo, Di Wang, Junlian Zhang
Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus...
September 27, 2016: Molecular Genetics and Genomics: MGG
Qi Qi, Lunguang Yao, Zhisheng Liang, Donghua Yan, Zhuo Li, Yadong Huang, Jingchen Sun
Human type II collagen is a macromolecular protein found throughout the human body. The baculovirus expression vector system is one of the most ideal systems for the routine production and display of recombinant eukaryotic proteins in insect, larvae, and mammalian cells. We use this system to express a full-length gene, human type II collagen cDNA (4257 bp), in cultured Spodoptera frugiperda 9 cells (Sf9), Bombyx mori cells, and silkworm larvae. In this study, the expression of human type II collagen gene in both insect cells and silkworm larvae was purified by nickel column chromatography, leading to 300-kDa bands in SDS-PAGE and western blotting indicative of collagen α-chains organized in a triple-helical structure...
September 26, 2016: Molecular Genetics and Genomics: MGG
Ge Zhao, Yun Song, Caixiang Wang, Hamama Islam Butt, Qianhua Wang, Chaojun Zhang, Zuoren Yang, Zhao Liu, Eryong Chen, Xueyan Zhang, Fuguang Li
Jasmonates control many aspects of plant biological processes. They are important for regulating plant responses to various biotic and abiotic stresses, including drought, which is one of the most serious threats to sustainable agricultural production. However, little is known regarding how jasmonate ZIM-domain (JAZ) proteins mediate jasmonic acid signals to improve stress tolerance in cotton. This represents the first comprehensive comparative study of TIFY transcription factors in both diploid A, D and tetraploid AD cotton species...
September 17, 2016: Molecular Genetics and Genomics: MGG
Victoria Wosika, Eric Durandau, Clémence Varidel, Delphine Aymoz, Marta Schmitt, Serge Pelet
The tractability of the budding yeast genome has provided many insights into the fundamental mechanisms regulating cellular life. With the advent of synthetic biology and single-cell measurements, novel tools are required to manipulate the yeast genome in a more controlled manner. We present, here, a new family of yeast shuttle vectors called single integration vectors (pSIV). Upon transformation in yeast, these plasmids replace the entire deficient auxotrophy marker locus by a cassette containing an exogenous marker...
September 16, 2016: Molecular Genetics and Genomics: MGG
Wei Li, Tingcai Cheng, Wenbo Hu, Zhangchuan Peng, Chun Liu, Qingyou Xia
Juvenile hormone (JH) regulates the insect growth and development. JH appears in the hemolymph bound by a specific glycoprotein, juvenile hormone-binding protein (JHBP), which serves as a carrier to release the hormone to target tissues and cells. However, JHBP family candidates, expression patterns, and functional implications are still unclear. In this study, we identified 41 genes-containing conserved JHBP domains distributed across eight chromosomes of the silkworm Bombyx mori. A phylogenetic tree showed that the silkworm JHBP (BmJHBP) genes could be classified into two major branches and four subfamilies...
September 8, 2016: Molecular Genetics and Genomics: MGG
Taofeng Lu, Yujiao Sun, Qin Ma, Minghao Zhu, Dan Liu, Jianzhang Ma, Yuehui Ma, Hongyan Chen, Weijun Guan
The Siberian tiger, Panthera tigris altaica, is an endangered species, and much more work is needed to protect this species, which is still vulnerable to extinction. Conservation efforts may be supported by the genetic assessment of wild populations, for which highly specific microsatellite markers are required. However, only a limited amount of genetic sequence data is available for this species. To identify the genes involved in the lung transcriptome and to develop additional simple sequence repeat (SSR) markers for the Siberian tiger, we used high-throughput RNA-Seq to characterize the Siberian tiger transcriptome in lung tissue (designated 'PTA-lung') and a pooled tissue sample (designated 'PTA')...
September 8, 2016: Molecular Genetics and Genomics: MGG
Wei Huang, Guang-Long Wang, Hui Li, Feng Wang, Zhi-Sheng Xu, Ai-Sheng Xiong
Ascorbic acid (AsA) is an important nutrient in the human body and performs various healthy functions. With considerable medicinal properties, celery (Apium graveolens L.) could be a good source of AsA for human health. However, the biosynthetic, recycling, and degradation pathways of AsA in celery have yet to be characterized. To study the metabolic pathways involved in AsA, the genes involved in AsA biosynthesis, recycling, and degradation were isolated from celery, and their expression profiles and AsA levels were analyzed in the leaf blades and petioles of two celery varieties at three different growth stages...
September 7, 2016: Molecular Genetics and Genomics: MGG
Juan Pablo Isaza, Juan Fernando Alzate
The Apicomplexa phylum groups include unicellular and obligate intracellular protozoan parasites with an apical complex used for attachment and invasion to host cells. In this study, we analyze single sequence repeats (SSRs) in the whole genome of 20 apicomplexan organisms that represent four different lineages within the phylum. Only perfect SSRs with at least 12 nucleotides and composed of 2-6 mers were included. To better understand the association of SSR types with the genomic regions, the SSRs were classified accordingly with the genomic location into exon, intron and intergenic categories...
September 2, 2016: Molecular Genetics and Genomics: MGG
Wei Chen, Pengmian Feng, Hui Ding, Hao Lin
N (6)-Methyladenosine (m(6)A) plays important roles in many biological processes. The knowledge of the distribution of m(6)A is helpful for understanding its regulatory roles. Although the experimental methods have been proposed to detect m(6)A, the resolutions of these methods are still unsatisfying especially for Arabidopsis thaliana. Benefitting from the experimental data, in the current work, a support vector machine-based method was proposed to identify m(6)A sites in A. thaliana transcriptome. The proposed method was validated on a benchmark dataset using jackknife test and was also validated by identifying strain-specific m(6)A sites in A...
September 2, 2016: Molecular Genetics and Genomics: MGG
Yue Hao, Yuejin Feng, Peige Yang, Yanjun Cui, Jiru Liu, Chunhe Yang, Xianhong Gu
Exposure to high ambient temperatures is detrimental to pig rearing and porcine meat quality. Deep molecular sequencing allows for genomic characterization of porcine skeletal muscles and helps understand how the genomic landscape may impact meat quality. To this end, we performed mRNA-seq to molecularly dissect the impact of heat stress on porcine skeletal muscles, longissimus dorsi. Sixteen castrated, male DLY pigs [which are crossbreeds between Duroc (D) boars and Landrace (L) × Yorkshire (Y) sows, 79...
August 25, 2016: Molecular Genetics and Genomics: MGG
D R Gimhani, Glenn B Gregorio, N S Kottearachchi, W L G Samarasinghe
Breeding for salt tolerance is the most promising approach to enhance the productivity of saline prone areas. However, polygenic inheritance of salt tolerance in rice acts as a bottleneck in conventional breeding for salt tolerance. Hence, we set our goals to construct a single nucleotide polymorphism (SNP)-based molecular map employing high-throughput SNP marker technology and to investigate salinity tolerant QTLs with closest flanking markers using an elite rice background. Seedling stage salinity responses were assessed in a population of 281 recombinant inbred lines (RILs) derived from the cross between At354 (salt tolerant) and Bg352 (salt susceptible), by 11 morpho-physiological indices under a hydroponic system...
August 17, 2016: Molecular Genetics and Genomics: MGG
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