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Chao Qu, Meng Yan, Suming Yang, Lingbo Wang, Qi Yin, Yuan Liu, Yeguang Chen, Jinsong Li
Haploid mammalian embryonic stem cells (haESCs) serve as a powerful tool for genetic analyses at both cellular and organismal levels. However, spontaneous diploidization of haESCs limits their use in these analyses. Addition of small molecules to culture medium to control the cell cycle can slow down diploidization, but cell-sorting methods such as FACS are still required to enrich haploid cells for long-term maintenance in vitro. Here, acting on our observation that haploid and diploidized cells differ in diameter, we developed a simplified filtration method to enrich haploid cells from cultured haESCs...
February 15, 2018: Journal of Biological Chemistry
Sarah Marburger, Markos A Alexandrou, John B Taggart, Simon Creer, Gary Carvalho, Claudio Oliveira, Martin I Taylor
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size-0...
February 14, 2018: Proceedings. Biological Sciences
Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger, Inanc Birol
Motivation: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation. Results: We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations...
February 15, 2018: Bioinformatics
Stephen R Wellard, Jessica Hopkins, Philip W Jordan
Meiotic progression in males is a process that requires the concerted action of a number of highly regulated cellular events. Errors occurring during meiosis can lead to infertility, pregnancy loss or genetic defects. Commencing at the onset of puberty and continuing throughout adulthood, continuous semi-synchronous waves of spermatocytes undergo spermatogenesis and ultimately form haploid sperm. The first wave of mouse spermatocytes undergoing meiotic initiation appear at day 10 post-partum (10 dpp) and are released into the lumen of seminiferous tubules as mature sperm at 35 dpp...
February 6, 2018: Journal of Visualized Experiments: JoVE
Irene Scharf, Lisa Bierbaumer, Heidemarie Huber, Philipp Wittmann, Christine Haider, Christine Pirker, Walter Berger, Wolfgang Mikulits
Genomic editing using the CRISPR/Cas9 technology allows selective interference with gene expression. With this method, a multitude of haploid and diploid cells from different organisms have been employed to successfully generate knockouts of genes coding for proteins or small RNAs. Yet, cancer cells exhibiting an aberrant ploidy are considered to be less accessible to CRISPR/Cas9-mediated genomic editing, as amplifications of the targeted gene locus could hamper its effectiveness. Here we examined the suitability of CRISPR/Cas9 to knockout the receptor tyrosine kinase Axl in the human hepatoma cell lines HLF and SNU449...
February 2018: Oncology Letters
Dominik Müller, Pascal Schopp, Albrecht E Melchinger
Genomic selection (GS) offers the possibility to estimate the effects of genome-wide molecular markers, which can be used to calculate genomic estimated breeding values (GEBVs) for individuals without phenotypes. GEBVs can serve as a selection criterion in recurrent GS, maximizing single-cycle but not necessarily long-term genetic gain. As simple genome-wide sums, GEBVs do not take into account other genomic information, such as the map positions of loci and linkage phases of alleles. Therefore, we herein propose a novel selection criterion called expected maximum haploid breeding value (EMBV)...
February 6, 2018: G3: Genes—Genomes—Genetics
Josephine J Peter, Tommaso L Watson, Michelle E Walker, Jennifer M Gardner, Tom A Lang, Anthony Borneman, Angus Forgan, Tina Tran, Vladimir Jiranek
A deficiency of nitrogenous nutrients in grape juice can cause stuck and sluggish alcoholic fermentation, which has long been a problem in winemaking. Nitrogen requirements vary between wine yeast strains, and the ability of yeast to assimilate nitrogen depends on the nature and concentration of nitrogen present in the medium. In this study a wine yeast gene deletion collection (1844 deletants in the haploid AWRI1631 background) was screened to identify genes whose deletion resulted in a reduction in the time taken to utilise all sugars when grown in a chemically defined grape juice medium supplemented with limited nitrogen (75 mg L-1 as a free amino acid mixture)...
February 7, 2018: FEMS Yeast Research
Amanda M Hulse-Kemp, Shamoni Maheshwari, Kevin Stoffel, Theresa A Hill, David Jaffe, Stephen R Williams, Neil Weisenfeld, Srividya Ramakrishnan, Vijay Kumar, Preyas Shah, Michael C Schatz, Deanna M Church, Allen Van Deynze
Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper (Capsicum annuum) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus...
2018: Horticulture Research
Yi Zhou, Gaofeng Zhou, Sue Broughton, Sharon Westcott, Xiaoqi Zhang, Yanhao Xu, Le Xu, Chengdao Li, Wenying Zhang
Tiller angle, an important agronomic trait, contributes to crop production and plays a vital role in breeding for plant architecture. A barley line V-V-HD, which has prostrate tillers during vegetative growth and erect tillers after booting, is considered the ideal type for repressing weed growth and increasing leaf area during early growth. Genetic analysis identified that the prostrate trait in V-V-HD is controlled by a single gene. A double haploid population with 208 lines from V-V-HD × Buloke was used to map the prostrate growth gene...
2018: PloS One
Masanobu Itoh, Ryutaro Kajihara, Yasuko Kato, Toshiyuki Takano-Shimizu, Yutaka Inoue
In order to investigate genetic impact of a large amount of radionuclides released by the Fukushima Dai-ichi Nuclear Power Plant accident in 2011, we surveyed 2,304 haploid genomes of Drosophila melanogaster collected in three localities in Fukushima in 2012 and 2013 for chromosomal inversions. No unique inversion was found in 298 genomes in 2012 and only two in 2,006 genomes in 2013. The observed frequencies were even lower than the long-term average frequency of unique inversions in Japan. The common cosmopolitan inversions were also examined in Fukushima, Kyoto, and Iriomote (Okinawa) in 2012...
2018: PloS One
Marie-Chantal Grégoire, Frédéric Leduc, Martin H Morin, Tiphanie Cavé, Mélina Arguin, Martin Richter, Pierre-Étienne Jacques, Guylain Boissonneault
De novo germline mutations arise preferentially in male owing to fundamental differences between spermatogenesis and oogenesis. Post-meiotic chromatin remodeling in spermatids results in the elimination of most of the nucleosomal supercoiling and is characterized by transient DNA fragmentation. Using three alternative methods, DNA from sorted populations of mouse spermatids was used to confirm that double-strand breaks (DSB) are created in elongating spermatids and repaired at later steps. Specific capture of DSB was used for whole-genome mapping of DSB hotspots (breakome) for each population of differentiating spermatids...
February 7, 2018: Cellular and Molecular Life Sciences: CMLS
Brian Burke
Meiosis is a key processes of sexual reproduction in eukaryotes. By combining two cell division cycles with a single round of DNA replication meiosis provides a mechanism to generate haploid gametes. Coincidentally, processes involved in ensuring appropriate segregation of homologous chromosomes also result in genetic recombination and shuffling of genes between each generation. During the first meiotic prophase, rapid telomere-led chromosome movements facilitate alignment and pairing of homologous chromosomes...
January 29, 2018: Current Opinion in Cell Biology
Misato Okamoto Miyakawa, Koji Tsuchida, Hitoshi Miyakawa
A female diploid, male haploid sex determination system (haplodiploidy) is found in hymenopteran taxa, such as ants, wasps, bees and sawflies. In this system, a single, complementary sex-determination (sl-CSD) locus functions as the primary sex-determination signal. In the taxa that has evolved this system, females and males are heterozygous and hemi/homozygous at the CSD locus, respectively. While the sl-CSD system enables females to alter sex ratios in the nest, it carries a high cost in terms of inbreeding, as individuals that are homozygous at the CSD locus become sterile diploid males...
February 2, 2018: Insect Biochemistry and Molecular Biology
Yuncheng Zhao, Shicheng Ye, Dongli Liang, Pengxiang Wang, Jing Fu, Qing Ma, Ruijiao Kong, Linghong Shi, Xueping Gong, Wei Chen, Wubin Ding, Wenjing Yang, Zijue Zhu, Huixing Chen, Xiaoxi Sun, Jun Zhu, Zheng Li, Yuan Wang
Due to differences across species, the mechanisms of cell fate decisions determined in mice cannot be readily extrapolated to humans. In this study, we developed a feeder- and xeno-free culture protocol that efficiently induced human pluripotent stem cells (iPSCs) into PLZF+/GPR125+/CD90+ spermatogonium-like cells (SLCs). These SLCs were enriched with key genes in germ cell development such as MVH, DAZL, GFRα1, NANOS3, and DMRT1. In addition, a small fraction of SLCs went through meiosis in vitro to develop into haploid cells...
February 13, 2018: Stem Cell Reports
Hualin Yi, Sa Xiao, Yan Zhang
Spermatogenesis in vitro has been demonstrated using spermatogonial stem cells (SSCs) in monolayer culture or testis tissue fragments in agarose-constructed three-dimensional (3-D) conditions. However, the low efficiency of gamete maturation and the lack of a novel induction platform have limited the progress of its use in further research and clinical applications. Here, we provide modified stage-specific induction approaches for spermatogenesis in in vitro culture with cells possessing a totipotent status...
February 2, 2018: In Vitro Cellular & Developmental Biology. Animal
Wenteng He, Xiaobai Zhang, Yalin Zhang, Weisheng Zheng, Zeyu Xiong, Xinjie Hu, Mingzhu Wang, Linfeng Zhang, Kun Zhao, Zhibin Qiao, Weiyi Lai, Cong Lv, Xiaochen Kou, Yanhong Zhao, Jiqing Yin, Wenqiang Liu, Yonghua Jiang, Mo Chen, Ruimin Xu, Rongrong Le, Chong Li, Hong Wang, Xiaoping Wan, Hailin Wang, Zhiming Han, Cizhong Jiang, Shaorong Gao, Jiayu Chen
Androgenetic haploid embryonic stem cells (AG-haESCs) hold great promise for exploring gene functions and generating gene-edited semi-cloned (SC) mice. However, the high incidence of self-diploidization and low efficiency of SC mouse production are major obstacles preventing widespread use of these cells. Moreover, although SC mice generation could be greatly improved by knocking out the differentially methylated regions of two imprinted genes, 50% of the SC mice did not survive into adulthood. Here, we found that the genome-wide DNA methylation level in AG-haESCs is extremely low...
February 13, 2018: Stem Cell Reports
Shohei Yamaoka, Ryuichi Nishihama, Yoshihiro Yoshitake, Sakiko Ishida, Keisuke Inoue, Misaki Saito, Keitaro Okahashi, Haonan Bao, Hiroyuki Nishida, Katsushi Yamaguchi, Shuji Shigenobu, Kimitsune Ishizaki, Katsuyuki T Yamato, Takayuki Kohchi
Land plants differentiate germ cells in the haploid gametophyte. In flowering plants, a generative cell is specified as a precursor that subsequently divides into two sperm cells in the developing male gametophyte, pollen. Generative cell specification requires cell-cycle control and microtubule-dependent nuclear relocation (reviewed in [1-3]). However, the generative cell fate determinant and its evolutionary origin are still unknown. In bryophytes, gametophytes produce eggs and sperm in multicellular reproductive organs called archegonia and antheridia, respectively, or collectively called gametangia...
January 17, 2018: Current Biology: CB
David V Phizicky, Luke E Berchowitz, Stephen P Bell
Meiotic cells undergo a single round of DNA replication followed by two rounds of chromosome segregation (the meiotic divisions) to produce haploid gametes. Both DNA replication and chromosome segregation are similarly regulated by CDK oscillations in mitotic cells. Yet how these two events are uncoupled between the meiotic divisions is unclear. Using Saccharomyces cerevisiae, we show that meiotic cells inhibit both helicase loading and helicase activation to prevent DNA replication between the meiotic divisions...
February 1, 2018: ELife
Tania Zaviezo, Romina Retamal, Teddy Urvois, Xavier Fauvergue, Aurélie Blin, Thibaut Malausa
Inbreeding and inbreeding depression are processes in small populations of particular interest for a range of human activities such as animal breeding, species conservation, or pest management. In particular, biological control programs should benefit from a thorough understanding of the causes and consequences of inbreeding because natural enemies experience repetitive bottlenecks during importation, laboratory rearing, and introduction. Predicting the effect of inbreeding in hymenopteran parasitoid wasps, frequently used in biological control programs, is nonetheless a difficult endeavor...
February 2018: Evolutionary Applications
Daniel S Jones, Xunliang Liu, Andrew C Willoughby, Benjamin E Smith, Ravishankar Palanivelu, Sharon A Kessler
In flowering plants, cell-cell communication plays a key role in reproductive success, as both pollination and fertilization require pathways that regulate interactions between many different cell types. Some of the most critical of these interactions are those between the pollen tube (PT) and the embryo sac, which ensure the delivery of the sperm cells required for double fertilization. Synergid cells function to attract the PT through the secretion of small peptides and in PT reception via membrane-bound proteins associated with the endomembrane system and the surface of the cell...
January 31, 2018: Plant Journal: for Cell and Molecular Biology
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