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Heejung Kim, Dugin Kaown, Bernhard Mayer, Jin-Yong Lee, Kang-Kun Lee
Hyporheic zones are considered hot spots for numerically vast and phylogenetically diverse microbial communities. However, biogeochemical effects of hyporheic zones have rarely been investigated in detail because of the difficulty in accurately measuring denitrification in these zones. To date, little is known about the hydroecology of hyporheic zones. The effect of changes in hydraulic conditions on the community variations of indigenous microorganisms and water quality was examined based on the depth of the hyporheic zone...
March 12, 2018: Science of the Total Environment
Marian L Miller, Aleksey Porollo, Susan Wert
Alveolar type II cells from seven mammalian species were examined for a protein in the rough endoplasmic reticulum (RER), which showed a multi-layered, repeating motif. Each motif, 100nm in width, comprised two parallel outer dense layers, a less dense central layer, and often 1-3 faint layers on either side of the latter. Outer layers showed periodicities at 3-4 densities/100nm of width, while layers on either side of the central layer showed 5-7 densities/100nm of width. RER membranes were ribosome-free when parallel to these layers, but showed 4 ribosomes per motif at the growing ends: one ribosome at each outer dense layer, and one on either side of the less dense central layer...
March 15, 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
Nikita Woodhead, Kelly M Hare, Alison Cree
The existence of sex differences in digit-length ratio (especially between the second and fourth digits, 2D:4D) is well established for humans from fetal life onwards, and has been linked with later performance. In rodents, the ratio is affected prenatally by exposure to androgens and estrogens, with some research suggesting an influence from sex of the neighbouring intrauterine fetus. However, the ubiquity and ontogenetic development of sexual dimorphism in digit ratios is not well established among wild amniotes...
March 15, 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
Michelle M Leger, Laura Eme, Courtney W Stairs, Andrew J Roger
In a recent BioEssays paper [W. F. Martin, BioEssays 2017, 39, 1700115], William Martin sharply criticizes evolutionary interpretations that involve lateral gene transfer (LGT) into eukaryotic genomes. Most published examples of LGTs in eukaryotes, he suggests, are in fact contaminants, ancestral genes that have been lost from other extant lineages, or the result of artefactual phylogenetic inferences. Martin argues that, except for transfers that occurred from endosymbiotic organelles, eukaryote LGT is insignificant...
March 15, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
Yan Li, Zhirong Zhang, Junbo Yang, Guanghui Lv
Fritillaria spp. constitute important traditional Chinese medicinal plants. Xinjiang is one of two diversity hotspots in China in which eight Fritillaria species occur, two of which are endemic to the region. Furthermore, the phylogenetic relationships of Xinjiang Fritillaria species (including F. yuminensis) within the genus are unclear. In the present study, we sequenced the chloroplast (cp) genomes of seven Fritillaria species in Xinjiang using the Illumina HiSeq platform, with the aim of assessing the global structural patterns of the seven cp genomes and identifying highly variable cp DNA sequences...
2018: PloS One
ChengLin Zhong, SiChen Li, JingJing Li, FengPeng Li, MingXia Ran, LingYun Qiu, DiYan Li, Qing Zhu, Yan Wang, HuaDong Yin, Gang Shu, Chaowu Yang, XiaoLing Zhao
Peroxisome proliferator activated receptor-alpha (PPARα) and Egl nine homolog 3 (EGLN3) play critical roles in facilitating the adaptation to a hypoxic environment. However, the relationship between EGLN3 and PPARα variants and hypoxic adaptation remains poorly understood in Tibetan chickens. To better understand the effects of genetic variation, we sequenced exons of PPARα and EGLN3 in 138 Lowland chickens (LC) from 7 breeds that were located in Emei, Miyi, Shimian, Wanyuan, Pengxian, and Muchuan in the Sichuan province, and Wenchang in the Hainan province (altitudes for these locations are below 1800 meters)...
2018: PloS One
Maroua Ben Amira, Robin Mom, David Lopez, Hatem Chaar, Ali Khouaja, Valérie Pujade-Renaud, Boris Fumanal, Aurélie Gousset-Dupont, Gisèle Bronner, Philippe Label, Jean-Louis Julien, Mohamed Ali Triki, Daniel Auguin, Jean-Stéphane Venisse
Major intrinsic proteins (MIP) are characterized by a transmembrane pore-type architecture that facilitates transport across biomembranes of water and a variety of low molecular weight solutes. They are found in all parts of life, with remarkable protein diversity. Very little is known about MIP from fungi. And yet, it can legitimately be stated that MIP are pivotal molecular components in the privileged relationships fungi enjoy with plants or soil fauna in various environments. To date, MIP have never been studied in a mycoparasitism situation...
2018: PloS One
Stephen S Curran, Eric E Pulis, Michael J Andres, Robin M Oversteet
Two cryptic species of haploporid digeneans belonging in Saccocoelioides are described from Costa Rica; one from a poeciliid fish Poecilia gillii and the other from a characid fish, Astyanx aeneus. Traditional morphological features are examined and found to be largely inefficient for differentiate among new species and 20 New World congeners. Comparison of ribosomal DNA sequences among the 2 new species, 2 North American, 4 Middle American, and 3 South American species of Saccocoelioides, including the type-species Saccocoelioides nanii from Argentina and Saccocoelioides sogandaresi from Texas, is effective for differentiating among these species...
March 16, 2018: Journal of Parasitology
T P Loch, M Faisal
Flavobacterial diseases are significant impediments to hatchery-based fishery conservation and aquaculture productivity worldwide. Recent studies revealed a multitude of novel flavobacteria within the reproductive fluids and unfertilized eggs of feral Chinook salmon Oncorhynchus tshawytscha broodstock, some of which were associated with systemic disease. Herein, embryonated eggs/fry from these broodstock were assayed for flavobacteria while in incubator stacks in three hatcheries over 2 years, as was the water entering hatchery incubators...
March 15, 2018: Journal of Fish Diseases
Peng He, Patamarerk Engsontia, Guang-Lei Chen, Qian Yin, Jun Wang, Xu Lu, Ya-Nan Zhang, Zhao-Qun Li, Ming He
BACKGROUND: The white-backed planthopper (WBPH) Sogatella furcifera Horváth, the brown planthopper (BPH) Nilaparvata lugens, and the small brown planthopper (SBPH) Laodelphax striatellus (Hemiptera: Delphacidae) are rice pests that damage rice plants by sap-sucking and by transmitting viruses. Host-seeking behavior involves chemosensory receptor genes, which include odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors (GRs). RESULTS: We used genome and transcriptome data to identify 141 ORs, 28 GRs and 25 IRs in BPH, 135 ORs, 18 GRs and 16 IRs in WBPH and 37 ORs, 14 GRs and 6 IRs in SBPH...
March 15, 2018: Pest Management Science
Karolina Pierzynowska, Lidia Gaffke, Zuzanna Cyske, Michał Puchalski, Estera Rintz, Michał Bartkowski, Marta Osiadły, Michał Pierzynowski, Jagoda Mantej, Ewa Piotrowska, Grzegorz Węgrzyn
Autophagy is a process of degradation of macromolecules in the cytoplasm, particularly proteins of a long half-life, as well as whole organelles, in eukaryotic cells. Lysosomes play crucial roles during this degradation. Autophagy is a phylogenetically old, and evolutionarily conserved phenomenon which occurs in all eukaryotic cells. It can be found in yeast Saccharomyces cerevisiae, insect Drosophila melanogaster, and mammals, including humans. Its high importance for cell physiology has been recognized, and in fact, dysfunctions causing impaired autophagy are associated with many severe disorders, including cancer and metabolic brain diseases...
March 14, 2018: Metabolic Brain Disease
Xiang Wu, Yongfeng Wu, Ya Tang, Bingcheng Gan
We isolated a Pseudomonas phage infecting Pseudomonas fluorescens SA1 separated from a soil sample collected in Sichuan Province, China. This phage, which we named PPSC2, has a genome that is composed of a 97,330-bp-long linear double-stranded DNA with 47.51% G+C content and 168 putative protein-coding genes. We identified 20 tRNA genes in the genome of PPSC2, and the tRNA GC content ranged from 44.2% to 58.4%. Phylogenetic and BLASTn analysis revealed that the Pseudomonas phage PPSC2 should be considered a new member of the family Myoviridae...
March 14, 2018: Archives of Virology
Xian Qi, Xiaofei An, Yongjun Jiao, Huiyan Yu, Ke Xu, Lunbiao Cui, Shenjiao Wang, Fei Deng, Xiang Huo, Haodi Huang, Qigang Dai, Changjun Bao
Five epidemic waves of human infection with influenza A (H7N9) virus have emerged in China since spring 2013. We previously described the epidemiological characterization of the fifth wave in Jiangsu province. In this study, 41 H7N9 viruses from patients and live-poultry markets were isolated and sequenced to further elucidate the genetic features of viruses of the fifth wave in Jiangsu province. Phylogenetic analysis revealed substantial genetic diversity in the internal genes, and 18 genotypes were identified from the 41 H7N9 virus strains...
March 14, 2018: Archives of Virology
Jie-Wei Luo, Cong-Huai Lin, Yao-Bin Zhu, Xing-Yu Zheng, Yong-Xi Wu, Wei-Wei Chen, Xiao Yang
Structural changes in symbiotic human microorganisms can affect host phenotype. Liver-fire hyperactivity syndrome (LFHS) presents as bitter taste, halitosis, xerostomia, odontalgia, and other oral symptoms. LFHS is associated with hypertension (EH). In this study, tongue flora was analyzed to further understand the intrinsic relationship between tongue flora and LFHS. Samples of tongue coating, from 16 patients with EH-LFHS, 16 with EH-non-LFHS, and 16 controls, were obtained; then, 16S rRNA variable (V3-V4) regions were amplified and sequenced by MiSeq PE300 Sequencing...
2018: Evidence-based Complementary and Alternative Medicine: ECAM
Genki Yoshikawa, Ahmed Askora, Romain Blanc-Mathieu, Takeru Kawasaki, Yanze Li, Miyako Nakano, Hiroyuki Ogata, Takashi Yamada
Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host...
March 14, 2018: Scientific Reports
Shuai Zhao, Jun-Jie Liu, Samiran Banerjee, Na Zhou, Zhen-Yong Zhao, Ke Zhang, Chang-Yan Tian
While saline soils account for 6.5% of the total land area globally, it comprises about 70% of the area in northwestern China. Microbiota in these saline soils are particularly important because they are critical to maintaining ecosystem services. However, little is known about the microbial diversity and community composition in saline soils. To investigate the distribution patterns and edaphic determinants of bacterial communities in saline soils, we collected soil samples across the hypersaline Ebinur Lake shoreline in northwestern China and assessed soil bacterial communities using bar-coded pyrosequencing...
March 14, 2018: Scientific Reports
Dilruba Sharmin, Yong Guo, Tomoyasu Nishizawa, Shoko Ohshima, Yoshinori Sato, Yusuke Takashima, Kazuhiko Narisawa, Hiroyuki Ohta
Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454T ) and Mycoavidus cysteinexigens (B1-EBT ), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a soil/litter sample in the USA. In the present study, we elucidated the complete genome sequence of B1-EBT and compared it with those of Mc-AG77 and HKI 454T ...
March 14, 2018: Microbes and Environments
Ella Z Lattenkamp, Samuel Kaiser, Rožle Kaučič, Martina Großmann, Klemen Koselj, Holger R Goerlitz
Sensory systems experience a trade-off between maximizing the detail and amount of sampled information. This trade-off is particularly pronounced in sensory systems that are highly specialized for a single task and thus experience limitations in other tasks. We hypothesised that combining sensory input from multiple streams of information may resolve this trade-off and improve detection and sensing reliability. Specifically, we predicted that perceptive limitations experienced by animals reliant on specialised active echolocation can be compensated for by the phylogenetically older and less specialised process of passive hearing...
March 14, 2018: Journal of Experimental Biology
Mingsheng Yang, Lu Song, Jianhang Mao, Yuxia Shi, Changjing Wu, Yunxia Zhang, Li Huang, Weifeng Peng, Xiaomeng Liu
Complete mitochondrial genome (mitogenome) of the Omiodes indicata was sequenced and characterized. The circular mitogenome is 15,367 bp long, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (81.6%). All 13 PCGs initiate with canonical start codon (ATN), except for cox1 that initiates with CGA. All tRNAs have a typical clover-leaf structure, except for trnS1 (AGN) in which the base pairs of the dihydrouridine (DHU) arm are reduced...
March 11, 2018: International Journal of Biological Macromolecules
Junting Jia, Pincang Zhao, Liqin Cheng, Guangxiao Yuan, Weiguang Yang, Shu Liu, Shuangyan Chen, Dongmei Qi, Gongshe Liu, Xiaoxia Li
BACKGROUND: MADS-box genes are categorized into A, B, C, D and E classes and are involved in floral organ identity and flowering. Sheepgrass (Leymus chinensis (Trin.) Tzvel) is an important perennial forage grass and adapts well to many adverse environments. However, there are few studies on the molecular mechanisms of flower development in sheepgrass, especially studies on MADS-domain proteins. RESULTS: In this study, we cloned 11 MADS-box genes from sheepgrass (Leymus chinensis (Trin...
March 14, 2018: BMC Plant Biology
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