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January 2019

Table of Contents - PeerJ (Biology Articles)

Descriptive anatomy of the largest known specimen of Protoichthyosaurus prostaxalis

Three-dimensional skull of BMT 1955.G35.1, Protoichthyosaurus prostaxalis.

January 8, 2019

Descriptive anatomy of the largest known specimen of Protoichthyosaurus prostaxalis

Representing one of the first times that medical imaging and three-dimensional reconstruction methods have been applied to a large skull of a marine reptile, researchers describe the partial skeleton of a large ichthyosaur from the Lower Jurassic of Warwickshire, England. The unusual three-dimensional preservation of the specimen permitted computed tomography (CT) scanning of individual braincase elements as well as the entire reassembled skull.

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January 31, 2019

Genome-wide identification and expression analysis of new cytokinin metabolic genes in bread wheat (Triticum aestivum L.)

Muhammad Shoaib, Wenlong Yang, Qiangqiang Shan, Muhammad Sajjad, Aimin Zhang

https://doi.org/10.7717/peerj.6300 PubMed 30723619

January 31, 2019

Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish

Violaine Colson, Morgane Cousture, Danielle Damasceno, Claudiane Valotaire, Thaovi Nguyen, Aurélie Le Cam, Julien Bobe

https://doi.org/10.7717/peerj.6338 PubMed 30723624

January 30, 2019

Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets

Paul Greenfield, Nai Tran-Dinh, David Midgley

https://doi.org/10.7717/peerj.6174 PubMed 30723610

January 28, 2019

Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus

Yujie Zhou, Won Kyong Cho, Hee-Seong Byun, Vivek Chavan, Eui-Joon Kil, Sukchan Lee, Seung-Woo Hong

https://doi.org/10.7717/peerj.6286 PubMed 30713817

January 25, 2019

The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

Zhen Yang, Guixi Wang, Qinghua Ma, Wenxu Ma, Lisong Liang, Tiantian Zhao

https://doi.org/10.7717/peerj.6320 PubMed 30701138

January 24, 2019

Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China

Jiaqi Wang, Feimeng An, Yuju Cao, Hongyan Gao, Mingqi Sun, Chao Ma, Hao Wu, Baoxin Zhang, Wanlin Liu, Jianzhong Wang

https://doi.org/10.7717/peerj.6270 PubMed 30697482

January 24, 2019

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

Gabriel A. Vieira, Francisco Prosdocimi

https://doi.org/10.7717/peerj.6271 PubMed 30697483

January 24, 2019

Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma

Jie Chen, Chaofeng Xing, Li Yan, Yabing Wang, Haosen Wang, Zongmeng Zhang, Daolun Yu, Jie Li, Honglin Li, Jun Li, Yafei Cai

https://doi.org/10.7717/peerj.6352 PubMed 30697495

January 24, 2019

Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube

Ji Qing, Wang Dawei, Zhou Jun, Xu Yulan, Shen Bingqi, Zhou Fan

https://doi.org/10.7717/peerj.6353 PubMed 30697496

January 23, 2019

GenoDup Pipeline: a tool to detect genome duplication using the dS-based method

Yafei Mao

https://doi.org/10.7717/peerj.6303 PubMed 30697488

January 14, 2019

Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments

Hugo R. Barajas, Miguel F. Romero, Shamayim Martínez-Sánchez, Luis D. Alcaraz

https://doi.org/10.7717/peerj.6233 PubMed 30656069

January 14, 2019

Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics

Deric R. Learman, Zahra Ahmad, Allison Brookshier, Michael W. Henson, Victoria Hewitt, Amanda Lis, Cody Morrison, Autumn Robinson, Emily Todaro, Ethan Wologo, Sydney Wynne, Elizabeth W. Alm, Peter S. Kourtev

https://doi.org/10.7717/peerj.6258 PubMed 30671291

January 11, 2019

A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

Clicia Grativol, Flavia Thiebaut, Sara Sangi, Patricia Montessoro, Walaci da Silva Santos, Adriana S. Hemerly, Paulo C.G. Ferreira

https://doi.org/10.7717/peerj.6080 PubMed 30648010

January 11, 2019

Detection and variability analyses of CRISPR-like loci in the H. pylori genome

Jerson Alexander García-Zea, Roberto de la Herrán, Francisca Robles Rodríguez, Rafael Navajas-Pérez, Carmelo Ruiz Rejón

https://doi.org/10.7717/peerj.6221 PubMed 30648020

January 11, 2019

Assigning confidence scores to homoeologs using fuzzy logic

Natasha M. Glover, Adrian Altenhoff, Christophe Dessimoz

https://doi.org/10.7717/peerj.6231 PubMed 30648004

January 11, 2019

Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)

Kebin Yang, Ying Li, Sining Wang, Xiurong Xu, Huayu Sun, Hansheng Zhao, Xueping Li, Zhimin Gao

https://doi.org/10.7717/peerj.6242 PubMed 30648007

January 9, 2019

Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay

Guangxi Wu, Wayne M. Jurick II, Franz J. Lichtner, Hui Peng, Guohua Yin, Verneta L. Gaskins, Yanbin Yin, Sui-Sheng Hua, Kari A. Peter, Joan W. Bennett

https://doi.org/10.7717/peerj.6170 PubMed 30643697

January 8, 2019

Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance

Tatyana I. Odintsova, Marina P. Slezina, Ekaterina A. Istomina, Tatyana V. Korostyleva, Artem S. Kasianov, Alexey S. Kovtun, Vsevolod J. Makeev, Larisa A. Shcherbakova, Alexander M. Kudryavtsev

https://doi.org/10.7717/peerj.6125 PubMed 30643692

January 8, 2019

Direct and indirect parental exposure to endocrine disruptors and elevated temperature influences gene expression across generations in a euryhaline model fish

Bethany M. DeCourten, Richard E. Connon, Susanne M. Brander

https://doi.org/10.7717/peerj.6156 PubMed 30643694

January 3, 2019

Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides

Liang-Yu Chen, Hao-Tian Cui, Chun Su, Feng-Wu Bai, Xin-Qing Zhao

https://doi.org/10.7717/peerj.6122 PubMed 30627488