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Shaokui Yi, Xiaoyun Zhou, Jie Li, Manman Zhang, Shuangshuang Luo
Reconstruction and annotation of transcripts, particularly for a species without reference genome, plays a critical role in gene discovery, investigation of genomic signatures, and genome annotation in the pre-genomic era. This study generated 33,330 full-length transcripts of diploid M. anguillicaudatus using PacBio SMRT Sequencing. A total of 6,918 gene families were identified with two or more isoforms, and 26,683 complete ORFs with an average length of 1,497 bp were detected. Totally, 1,208 high-confidence lncRNAs were identified, and most of these appeared to be precursor transcripts of miRNAs or snoRNAs...
August 3, 2018: Scientific Reports
Dominik K Kölmel, Richard P Loach, Thomas Knauber, Mark Flanagan
A new procedure for the photoredox-mediated conjugate addition of radicals that can be conveniently generated from a-amino acids, to DNA-tagged Michael acceptors and styrenes is presented. This C(sp3)-C(sp3) coupling tolerates a broad array of structurally diverse radical precursors, including all of the 20 proteinogenic amino acids. Importantly, this reaction proceeds under mild conditions and in DNA-compatible aqueous media. Furthermore, the presented reaction conditions are compatible with DNA, making this reaction platform well suited for the construction of DNA-encoded libraries...
July 31, 2018: ChemMedChem
Yuichi Kano, Jun Nakajima, Takeshi Yamasaki, Jyun-Ichi Kitamura, Ryoichi Tabata
Background: Loach is one of the major cypriniform fishes in freshwater habitats of Japan; 35 taxa/clades have, until now, been recognised. Parallel to genetic studies, morphological examinations are needed for further development of loach study, eventually ichthyology and fish biology. Digital archiving, concerning taxonomy, ecology, ethology etc., is one of the progressive challenges for the open science of biology. This paper aimed to online publish photo images, 3D models and CT scanned data of all the known clades of loaches inhabiting Japan (103 individuals in total with several type specimens), contributing to ichthyology and public interest of biodiversity/biology...
2018: Biodiversity Data Journal
S Shamsi, A Stoddart, L Smales, S Wassens
There is a paucity of information on the diversity and occurrence of freshwater fish parasites in Australia. This study investigates the distribution and occurrence of a parasitic nematode of the genus Contracaecum in freshwater fish from south-eastern Australia. Fish (n = 508) belonging to nine species and eight families were collected from eight wetlands associated with the Murrumbidgee River floodplain in the southern Murray-Darling Basin and subjected to laboratory examination. Third-stage nematode larvae were found in eight of the nine fish species...
July 18, 2018: Journal of Helminthology
Han Qu, Ruixue Ma, Bin Wang, Yizhe Zhang, Lina Yin, Gang Yu, Shubo Deng, Jun Huang, Yujue Wang
In this study, we investigated the enantioselective environmental behaviors of the chiral antidepressant venlafaxine (VFX) in lab-scale aquatic ecosystems in the presence of microplastics (MPs). To determine the bioaccumulation, distribution, and metabolism as well as the effects of MPs on aquatic ecosystems, water-sediment, water-Lemna.minor (L.minor), water-Misgurnus.anguillicaudatus (M.anguillicaudatus), and water-sediment-L.minor-M.anguillicaudatus ecosystems were set up and exposed to venlafaxine and two levels of microplastics over a 90-day period...
July 8, 2018: Journal of Hazardous Materials
Masamichi Kuroda, Takafumi Fujimoto, Masaru Murakami, Etsuro Yamaha, Katsutoshi Arai
Wild-type dojo loach (Misgurnus anguillicaudatus) commonly reproduces bisexually as a gonochoristic diploid (2n = 50), but gynogenetically reproducing clonal diploid lines (2n = 50) exist in certain districts in Japan. Clones have been considered to develop from past hybridization event(s) between two genetically diverse groups, A and B, within the species. Fluorescence in situ hybridization analyses using the repetitive sequence "ManDra" as a probe clearly distinguished 25 chromosomes derived from group B out of a total of 50 diploid chromosomes of the clone, providing strong molecular cytogenetic evidence of its hybrid origin...
June 7, 2018: Chromosome Research
He Zhou, Qi-Zheng Xu, Rui Zhang, Zi-Xin Zhuang, Yin-Qiang Ma, Wei Wang, Tian-Yu Ma, Yi Sui, Yang Liu, Xiaojuan Cao
Hybrid triploid loaches (Misgurnus anguillicaudatus) were generated from natural tetraploid and diploid loaches. We studied the gonads of parents and offspring from direct and reciprocal crosses through histological and transcriptome analyses. The triploid offspring had inferior ability to form sperm and egg cells compared with diploid forms. After sequencing the transcriptomes, 655,109,158 clean reads were obtained, and 62,821 unigenes and 178,962 transcripts were assembled. Of these unigenes, 23,189 were annotated in the GO database, 18,525 in the KEGG database and 24,661 in the KOG database...
2018: PloS One
J J Kim, Y K Nam, I C Bang, S P Gong
  BACKGROUND: Miho spine loach (Cobitis choii) is an endangered Korean endemic fish. Whole testis cryopreservation is a good way for species preservation, but needs to the sacrifice of a large number of fish to optimize the freezing condition. Considering this limitation, a surrogate fish species was used for the protocol development. OBJECTIVE: This study was to establish the effective condition for Miho spine loach whole testis cryopreservation by optimizing the conditions for whole testis cryopreservation in an allied species, mud loach (Misgurnus mizolepis)...
January 2018: Cryo Letters
Jingwen Chen, Yun Cui, Jie Yan, Jimin Jiang, Xiaojuan Cao, Jian Gao
Elongase of very long-chain fatty acids 6 (ELOVL6) is a rate-limiting enzyme catalyzing elongation of saturated and monounsaturated long-chain fatty acid. Although functional characteristics of Elovl6 have been demonstrated in mammal, the role of elovl6 in fish remains unclear. In this study, we firstly cloned three isoforms of elovl6 (elovl6a, elovl6b and elovl6-like) from loach (Misgurnus anguillicaudatus). Molecular characterizations of the three elovl6 isoforms in loach and their expressions of early life stages and different tissues were then determined...
August 5, 2018: Gene
Mehrnaz Moghimi, Nasrollah Mahboobi-Soofiani, Pedram Malekpouri
Beyond the role of anthropogenic activities, natural sources of metal contaminations are still controversial, together counting, however, as a major threat to inland and coastal waters, becoming an even more prominent stressor for aquatic life. To address the effects of metals on the physiological response of fish, standard metabolic rate (SMR), maximum metabolic rate (MMR), aerobic scope (AS) and factorial aerobic scope (FAS) as well as specific rate of ammonia excretion (Jamm ) of Turcinoemacheilus bahaii were determined following different water-borne Cu2+ and Pb2+ treatments...
June 2018: Environmental Toxicology and Pharmacology
Han Qu, Ruixue Ma, Bin Wang, Jian Yang, Lei Duan, Gang Yu
In present study, we investigated the enantioselective behaviors of the chiral antidepressant venlafaxine and its metabolite O-desmethylvenlafaxine in loach Misgurnus anguillicaudatus (M. anguillicaudatus), as well as effects of microplastic on toxicity, distribution and metabolism through a 40-day co-exposure. The contents of SOD and MDA in loach liver elevated when the loach was exposed to venlafaxine and O-desmethylvenlafaxine. Moreover, co-exposure with microplastic might lead to more adverse effect against loach...
April 22, 2018: Journal of Hazardous Materials
C E Aalseth, N Abgrall, E Aguayo, S I Alvis, M Amman, I J Arnquist, F T Avignone, H O Back, A S Barabash, P S Barbeau, C J Barton, P J Barton, F E Bertrand, T Bode, B Bos, M Boswell, A W Bradley, R L Brodzinski, V Brudanin, M Busch, M Buuck, A S Caldwell, T S Caldwell, Y-D Chan, C D Christofferson, P-H Chu, J I Collar, D C Combs, R J Cooper, C Cuesta, J A Detwiler, P J Doe, J A Dunmore, Yu Efremenko, H Ejiri, S R Elliott, J E Fast, P Finnerty, F M Fraenkle, Z Fu, B K Fujikawa, E Fuller, A Galindo-Uribarri, V M Gehman, T Gilliss, G K Giovanetti, J Goett, M P Green, J Gruszko, I S Guinn, V E Guiseppe, A L Hallin, C R Haufe, L Hehn, R Henning, E W Hoppe, T W Hossbach, M A Howe, B R Jasinski, R A Johnson, K J Keeter, J D Kephart, M F Kidd, A Knecht, S I Konovalov, R T Kouzes, B D LaFerriere, J Leon, K T Lesko, L E Leviner, J C Loach, A M Lopez, P N Luke, J MacMullin, S MacMullin, M G Marino, R D Martin, R Massarczyk, A B McDonald, D-M Mei, S J Meijer, J H Merriman, S Mertens, H S Miley, M L Miller, J Myslik, J L Orrell, C O'Shaughnessy, G Othman, N R Overman, G Perumpilly, W Pettus, D G Phillips, A W P Poon, K Pushkin, D C Radford, J Rager, J H Reeves, A L Reine, K Rielage, R G H Robertson, M C Ronquest, N W Ruof, A G Schubert, B Shanks, M Shirchenko, K J Snavely, N Snyder, D Steele, A M Suriano, D Tedeschi, W Tornow, J E Trimble, R L Varner, S Vasilyev, K Vetter, K Vorren, B R White, J F Wilkerson, C Wiseman, W Xu, E Yakushev, H Yaver, A R Young, C-H Yu, V Yumatov, I Zhitnikov, B X Zhu, S Zimmermann
The Majorana Collaboration is operating an array of high purity Ge detectors to search for neutrinoless double-β decay in ^{76}Ge. The Majorana Demonstrator comprises 44.1 kg of Ge detectors (29.7 kg enriched in ^{76}Ge) split between two modules contained in a low background shield at the Sanford Underground Research Facility in Lead, South Dakota. Here we present results from data taken during construction, commissioning, and the start of full operations. We achieve unprecedented energy resolution of 2...
March 30, 2018: Physical Review Letters
Tie-Jun Wu, Mu-Lan Wei, Jia-Hu Lan, Li-Na Du
A new cave-dwelling fish, Triplophysa anshuiensis , is described here based on specimens collected from a karst cave in Guangxi Zhuang Autonomous Region, China, interconnected with the Hongshui River system, a tributary of the Xijiang River in the Pearl River (Zhu Jiang) Drainage. The species can be distinguished from its congeners by a combination of morphological characters. A key to the cave-dwelling species of Triplophysa in the Xijiang River is provided.
2018: ZooKeys
Bing Feng, Soojin V Yi, Manman Zhang, Xiaoyun Zhou
The co-existence of several ploidy types in natural populations makes the cyprinid loach Misgurnus anguillicaudatus an exciting model system to study the genetic and phenotypic consequences of ploidy variations. A first step in such effort is to identify the specific ploidy of an individual. Currently popular methods of karyotyping via cytological preparation or flow cytometry require a large amount of tissue (such as blood) samples, which can be damaging or fatal to the fishes. Here, we developed novel microsatellite markers (SSR markers) from M...
2018: PloS One
Jun-Ichi Miyazaki, Toshio Tamura, Seiya Hida, Takehiko Sakai
The evolutionary history of eight-barbel loaches of the genus Lefua was investigated to resolve the faunal formation and evolutionary history of Japanese and East Asian freshwater fishes. In the present study, we found that seven Lefua specimens obtained from western Japan could not be assigned genetically to any population recognized so far, although they were morphologically and ecologically indistinguishable from Lefua sp 1. We tentatively designated the specimens as the Nihonkai population. Sequencing of the mitochondrial D-loop region showed that five specimens of the Nihonkai population were allied with the Kinki and Tokai populations of L...
April 2018: Zoological Science
Alexandr Sember, Jörg Bohlen, Vendula Šlechtová, Marie Altmanová, Šárka Pelikánová, Petr Ráb
Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei-an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness...
2018: PloS One
Xiaohua Xia, Weiran Huo, Ruyan Wan, Peijin Wang, Linxia Zhang, Zhongjie Chang
A number of studies have established that in vertebrates, Sox3 is involved in a wide range of developmental processes, including sex differentiation and neurogenesis. However, the exact functions of the Sox3 gene have not been documented so far in teleosts. Here, we cloned the full length cDNA of Sox3 from the teleost fish, Paramisgurnus dabryanus, which we designated PdSox3. Sequence analysis revealed that PdSox3 encodes a hydrophilic protein, and shares high homology with Sox3 in other species, ranging from mammals to fishes...
May 2018: Evolution & Development
Shengdong Pan, Xiaohong Chen, Qian He, Xiaohai Li, Li Wang, Jian Zhou, Micong Jin
A method for the characterization of the metabolite pentachlorophenol hydrogen sulfate (PCP-SO3 H) of pentachlorophenol (PCP) in loaches was developed based on ultra-performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS). The loach samples exposed in low concentration of PCP solution were firstly crushed, then extracted by acetonitrile-water solution (70:30, v/v) containing 8% (v/v) triethylamine and purified by mixed anion exchange solid-phase extraction (SPE) cartridges. The chromatographic separation was carried out on a Waters ACQUITY BEH C18 column (100 mm×2...
December 8, 2017: Se Pu, Chinese Journal of Chromatography
Jie Yan, Xiao Liang, Yun Cui, Xiaojuan Cao, Jian Gao
In this study, full-length cDNA sequences of elovl4a and elovl4b from loach Misgurnus anguillicaudatus were cloned. The full-length cDNAs of loach elovl4a and elovl4b were 2423 and 2054bp, encoding 315 and 300 amino acids, respectively. The deduced amino acid sequences of elovl4a and elovl4b in loach both shared the highest identity with those of Danio rerio, whereas lower identity score between loach elovl4a and elovl4b was present. Temporal expression and tissue expression of loach elovl4a and elovl4b were studied by reverse transcriptase PCR...
January 22, 2018: Biochemical and Biophysical Research Communications
Yongyao Yu, Yangzhou Liu, Huili Li, Shuai Dong, Qingchao Wang, Zhenyu Huang, Weiguang Kong, Xiaoting Zhang, Yongshen Xu, Xiaoyao Chen, Zhen Xu
The polymeric immunoglobulin receptor (pIgR) is an essential component of the mucosal immune system in jawed vertebrates including teleost fish, which mediate transepithelial transport of secretory immunoglobulins (sIgs) to protect organisms against environmental pathogens. In this study, we firstly cloned and identified the pIgR from dojo loach (Misgurnus anguillicaudatus). The full-length cDNA of Ma-pIgR was of 1145 bp, containing an open reading frame (ORF) of 1101 bp encoded a predicted protein of 336 amino acids...
February 2018: Fish & Shellfish Immunology
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