New method to predict conserved RNA structures

RNA secondary structure prediction is one of the classic problems of bioinformatics. The most efficient approaches to solving this problem are based on comparative analysis. As a rule, multiple RNA sequence alignment and subsequent determination of a common secondary structure are used. A new algorithm was developed to obviate the need for preliminary multiple sequence alignment. The algorithm is based on a multilevel MEME-like iterative search for a generalized profile. The search for common blocks in RNA sequences is carried out at the first level. Then the algorithm refines the chains consisting of these blocks. Finally, the search for sets of common helices, matched with alignment blocks, is carried out. The algorithm was tested with a tRNA set containing additional junk sequences and with RFN riboswitches. The algorithm is available at http://bioinf.fbb.msu.ru/RNAAlign.     

Gene Network and Database for Genes of Wheat’s Resistance to Pathogenic Fungi

An overview describing a gene network that controls the formation of plant responses to diseases caused by pathogenic fungi (http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet//viewer/Plant%20fungus%20pathogen.html) is presented. The gene network represents the coordinated interactions of genes, proteins, and regulatory molecules, including integrated defense mechanisms that prevent the development of infection, localize the lesion, and minimize damage. The gene network was reconstructed on the basis of literature data, and the elements of the gene network were associated with the records of the PGR database (Pathogenesis-Related Genes, http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+top+-newId), where information on plant genes resistant to pathogenic fungi is accumulated. Reconstruction of the gene network allows us to formalize, visualize, and systematize possible mechanisms for the response of plant cells to fungal infection, which may be useful for the planning of experiments and interpretation of experimental data in this field of science.     

Larval host records of butterflies in Japan

Using Japanese literature, we created a consolidated list of host records of butterflies in Japan. The list used the host records described in eight major illustrated reference books, two checklists, and 14 other pieces of literature. The presence of larvae on plants, the observation of larvae eating plants or insects in the field were considered as host records. We collected all species recorded in Japan. Scientific, family, and Japanese names of butterflies were consolidated using the BINRAN database (http://binran.lepimages.jp/). Scientific and Japanese names of host plants were based on the YList database (http://ylist.info/). If scientific names of host plants were not found in YList, we used scientific names based on The Plant List (http://www.theplantlist.org/). Family names of host plants were based on the Catalogue of Life database (http://www.catalogueoflife.org/). Scientific, family, and Japanese names of host insects were based on the MOKUROKU database (http://konchudb.agr.agr.kyushu-u.ac.jp/mokuroku/) for Hymenoptera and the catalogue of the Paraneoptera of Japan published by the Entomological Society of Japan for Hemiptera. We also provided the references of each host record and the original names described in the referred literature. Two datasets, HostDB and ReferenceDB, were created to include 3600 records of butterfly larval hosts in Japan, along with scientific and Japanese names of each species and a literature list. These datasets will be useful for basic and applied biological studies of butterflies. Data files are stored in the Ecological Research Data Archives (http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/) and available from http://hostbj.lepumus.net/. These datasets are published under the Creative Commons License Attribution-ShareAlike 4.0 (CC BY-SA, https://creativecommons.org/licenses/by-sa/4.0/).     

Paternal care behaviors of Japanese giant salamander <Emphasis Type="Italic">Andrias japonicus</Emphasis> in natural populations

Parental care among salamanders is typically provided by females. A rare case of parental care by male salamanders appears to occur in Cryptobranchidae. Yet, paternal behaviors have rarely been reported from natural populations of any Cryptobranchid salamanders, and their adaptive significance is poorly understood. The present study aimed to examine paternal care behaviors in a fully aquatic Japanese giant salamander (Andrias japonicus) in situ. At the beginning of the summer breeding season, large males, called den-masters, occupy burrows along stream banks for breeding and nesting. We videotaped post-breeding behaviors of two den-masters that stayed with the eggs, one in a natural and the other in an artificial nest in natural streams. We identified three behaviors, tail fanning, agitating and egg eating, to be parental care. Tail fanning provides oxygenated water for the eggs. We found that the den-master in the artificial nest, where dissolved oxygen level was lower, displayed tail fanning more frequently. Agitating the eggs with its head and body likely prevents yolk adhesions. The den-masters selectively ate whiter eggs that appeared to be dead or infected with water mold. This behavior, which we termed hygienic filial cannibalism, likely prevents water mold from spreading over healthy eggs. Digital video images relating to this article are available at http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj01a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj02a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj03a and http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj04a.     

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

Background

The Maximal Pairing Problem (MPP) is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ω _xy for the paths between any two pairs of leaves (x, y), what is the collection of edge-disjoint paths between pairs of leaves that maximizes the total weight? Special cases of the MPP for binary trees and equal weights have been described previously; algorithms to solve the general MPP are still missing, however.

Results

We describe a relatively simple dynamic programming algorithm for the special case of binary trees. We then show that the general case of multifurcating trees can be treated by interleaving solutions to certain auxiliary Maximum Weighted Matching problems with an extension of this dynamic programming approach, resulting in an overall polynomial-time solution of complexity Open image in new window (n⁴ log n) w.r.t. the number n of leaves. The source code of a C implementation can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/Targeting. For binary trees, we furthermore discuss several constrained variants of the MPP as well as a partition function approach to the probabilistic version of the MPP.

Conclusions

The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations.

     

The scent of your enemy is my friend? The acquisition of large carnivore scent by a smaller carnivore

Scent marking is critical to intraspecific communication in many mammal species, but little is known regarding its role in communication among different species. We used 4 years of motion-triggered video to document the use of scent marking areas—termed “community scrapes”—by pumas (Puma concolor) (http://www.momo-p.com/showdetail-e.php?movieid=momo160812pc01a) and other carnivore species. We found that gray foxes (Urocyon cinereoargenteus) routinely rubbed their cheeks on puma scrapes (http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc01a), and tested a series of hypotheses to determine its function. We found that gray foxes selected puma scrapes over other objects, and cheek rubbing by foxes was also correlated with how recently a puma had visited the scrape, suggesting that foxes were intent upon accumulating fresh puma scent. Cheek rubbing by foxes was not correlated with their breeding season or with how recently another fox had visited the site. Finally we found a cascading pattern in the occurrence of pumas, coyotes (Canis latrans) and gray foxes at community scrapes, suggesting that gray foxes may use puma scent to deter predation. This is the first published study to find evidence of a subordinate species using the scent of a dominant species to communicate with heterospecifics. The behavioral cascade we found in scent marking patterns also suggests that scent marking could be a mechanism that impacts the distribution and abundance of species. Additional videos pertaining to this article include http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc02a, and http://www.momo-p.com/showdetail-e.php?movieid=momo160812uc03a.     

Comet assay for assessment of DNA damage in greenhouse workers exposed to pesticides

Purpose: The main goal of the present study was to determine DNA damage in pesticide-exposed greenhouse workers and pesticides non-exposed controls.

Materials and methods: The DNA damage was measured by alkaline comet assay method (pH?>?13) in 41 greenhouse workers and 45 non-exposed individuals as the control. Pesticide exposure was assessed by duration of working in the greenhouse and pesticide application in the greenhouse time. DNA damage was estimated by arbitrary unit and damage frequency.

Results: Arbitrary unit and damage frequency were consistently significantly higher in greenhouse workers than those of the controls (p?=?0.001). In terms of gender in greenhouse, DNA damage of female workers was significantly higher than those in male workers (p?<?0.05). We found significant correlation between DNA damage and working hours spent. Multiple linear regression analysis showed that working hours in the greenhouse as an indication of pesticide exposure were significantly associated with the DNA damage, which can be attributed to the genotoxic potential of the pesticide mixture.

Conclusions: The comet assay is sensitive to detect the damage exposed to chronic effect of pesticides in greenhouse workers. Significant DNA damage was obtained for the exposed group, which was associated with the pesticide exposure.     

Interspecific responses of wild African carnivores to odour of 3-mercapto-3-methylbutanol,a component of wildcat and leopard urine

The scent of 3-mercapto-3-methylbutanol (3-M-3-MB), a volatile component of leopard (Panthera pardus) and domestic cat (Felis silvestris catus) urine, released at about 10 ng/s from slow-release dispensers, elicited scent-marking from African civet (Civettictis civetta), small-spotted genet (Genetta genetta) and slender mongoose (Galerella sanguinea), as well as African wildcat (F. s. cafra). A female leopard was apparently repelled by the scent. The scent-marking and scent-rubbing by species other than African wildcats and leopards were unexpected and have important implications for the design of studies to investigate chemical communication between wild mammals and the use of camera traps to estimate animal numbers. Videos showing the behaviours referred to in this article are available at; http://www.momo-p.com/showdetail-e.php?movieid=momo161223fs01a; http://www.momo-p.com/showdetail-e.php?movieid=momo161223gs01a; http://www.momo-p.com/showdetail-e.php?movieid=momo161223gg01a.     

Metabolic syndrome is associated to high-sensitivity cardiac troponin T elevation

Introduction: Metabolic syndrome (MetS) and high-sensitivity cardiac troponin T (hs-TnT) are associated with higher risk for cardiovascular diseases (CVD). Our aim was to assess the relation between hs-TnT elevation and MetS in a general population sample.

Materials and methods: Individuals participating in an annual health survey program between 2010 and 2016 were included in the study. Blood samples including hs-TnT levels were collected. The study population was divided into three groups based on hs-TnT levels – undetectable (<5?ng/L), intermediate (5–14?ng/L) and elevated (>14?ng/L).

Results: A total of 5994 subjects were included in the study, the mean age was 48.5 and 4336 (72%) were males. Compared with subjects with undetectable hs-TnT the prevalence of MetS was higher in those with detectable and elevated levels – 392 (10%) vs. 270 (15%) and 51 (33%), respectively (p?<?0.001). In a multivariate model adjusted for age, gender and multiple co-morbidities, the number of MetS components and presence of MetS were significantly associated with an increased risk for detectable hs-TnT levels (OR?=?1.02 {for each component}; 95% CI [1.00–1.05], p?=?0.04) and (OR?=?1.13; 95% CI [1.07–1.2], p?<?0.001) respectively. Only the waist, glucose and hypertension components of the MetS were significantly associated with elevated troponin.

Conclusions: The MetS and its distinct components have a cumulative impact on hs-TnT levels in apparently healthy subjects.     

Novel structural tree of (α + β)-proteins containing abCd units

A database of 926 (α + β)-proteins and (α + β)-domains containing abCd units, including 401 non-homologous, was compiled from the Protein Data Bank (total of 2636 PDB entries). A novel structural tree of this structural class of proteins was constructed to include 286 possible polypeptide chain folds. A structural classification of (α + β)-proteins containing abCd unit was developed on the basis of the structural tree. The database and the structural tree are available at http://strees.protres.ru/.     

The Year of the Wisent

Delving into European prehistory, two recent studies analyze ancient DNA from bison species depicted by our ancestors on the walls of their caves. The DNA tells a story of migrations driven by climate change but leaves some mystery clouding the genetic descent and climate preference of the still-extant wisent, otherwise known as the European bison.See research articles: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0317-7 http://www.nature.com/articles/ncomms13158     

Advances in transgenic animal models and techniques

On May 11th and 12th 2017 was held in Nantes, France, the international meeting “Advances in transgenic animal models and techniques” (http://www.trm.univ-nantes.fr/). This biennial meeting is the fifth one of its kind to be organized by the Transgenic Rats ImmunoPhenomic (TRIP) Nantes facility (http://www.tgr.nantes.inserm.fr/). The meeting was supported by private companies (SONIDEL, Scionics computer innovation, New England Biolabs, MERCK, genOway, Journal Disease Models and Mechanisms) and by public institutions (International Society for Transgenic Technology, University of Nantes, INSERM UMR 1064, SFR François Bonamy, CNRS, Région Pays de la Loire, Biogenouest, TEFOR infrastructure, ITUN, IHU-CESTI and DHU-Oncogeffe and Labex IGO). Around 100 participants, from France but also from different European countries, Japan and USA, attended the meeting.     

Mating and aggressive behaviour of <Emphasis Type="Italic">Brachyrhaphis olomina</Emphasis> (Cyprinodontiformes: Poeciliidae)

Despite the increasing interest in the use of intromittent male genitalia and coercive mating behaviour in poeciliids, detailed studies of the mating behaviour of most species in this family are lacking. We describe here the mating and aggressive behaviours of Brachyrhaphis olomina, and correlate them with the condition of the female’s ovum and embryos (immature, mature and pregnant). B. olomina performed a wide range of aggressive (sidle spread, tail beating, coordinate) and mating behaviours (approximation, touch, lateral display, touch-lateral display). Some behaviours (e.g. tail beating) are shared with other poeciliids, but two sexual behaviours (touch and lateral display) and one aggressive (coordinate) behaviour may be unique to B. olomina and were not reported in a previous study. Differences in male behaviour when paired with a female with mature ovum (more mating displays, no agonistic movements) suggest that males detect the female’s reproductive condition from some distance. The distinctive nature of mating behaviour in B. olomina highlights the importance of studying different species to have a better understanding of the evolution of mating and aggressive behaviours in poeciliids. Digital video images related to the article are available at http://www.momo-p.com/showdetail-e.php?movieid=momo170720bo01a, http://www.momo-p.com/showdetail-e.php?movieid=momo170720bo02a and http://www.momo-p.com/showdetail-e.php?movieid=momo170720bo03a.     

On a new species of Euchondrus Boettger, 1883 from Syria (Pulmonata: Enidae)

A new species of Euchondrus, Euchondrus adwani n. sp., is described from Syria. It is morphologically similar to E. desertorum Rochanaburananda in Forcart, 1981 Forcart, L. (1981): Neubeschreibungen von Landschnecken aus Palästina. Basteria, 45, 97–108. [Google Scholar], which is endemic to the Negev desert.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:C030F4D1-D722-4186-BA7B-EACCF9BFA563     

First record of the genus Gynecaptera Skorikov, 1935 (Hymenoptera: Bradynobaenidae: Apterogyninae) from Saudi Arabia,with description of a new species

In the present study, the genus Gynecaptera Skorikov, 1935 Skorikov, A. S. (1935): Zur Mutilliden-Fauna Zentralasiens. Trudy tadzhikskoi basy Akademii Nauk. SSSR, 5, 257–349 + 7 plates. [Google Scholar] is recorded from the Arabian Peninsula for the first time, with a nocturnal new species, G. arabica Soliman &; Gadallah, which has been collected from the Riyadh region in Saudi Arabia and which is described and illustrated.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:F7ACB779-3750-4DC6-B29B-B7F290E7C7B4     

A new species of Paratheuma (Araneae: Dictynidae) from Southwestern Asia and transfer of the genus

The marine spider genus Paratheuma Bryant, 1940 Bryant, E. B. (1940): Cuban spiders in the Museum of Comparative Zoology. Bulletin of the Museum of Comparative Zoology, 86, 247–532. [Google Scholar] is recorded in southwestern Asia for the first time, and a new species, P. enigmatica sp. n. is described from southern and southeastern Iran on the basis of both sexes. Based on morphological and molecular evidence, the genus is transferred from Desidae to Litisedinae, Dictynidae.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:BC5B70CB-E6C9-4624-8BE8-22FF14AF6DC7     

Assessment of Effects of Human Development on the Environment by Using System Dynamic Modeling Technique (SD): A Case Study of the Mkomazi Watershed (Pangani Basin) in Northeastern Tanzania

This study analyzes land use changes due to human development in the Mkomazi Valley, Tanzania, and its impacts on nature using the SD–Modeling (System Dynamic modeling) technique. Ultimately this method relates environment and economy of society with regard to a seasonal rainfall–based agriculture practice and their harmonization with irrigation agriculture for development sustainability. VENSIM PLE (VENTANA SIMULATION ENVIRONMENT, PERSONAL LEARNING EDITION 2002 VENSIM PLE (VENTANA SIMULATION ENVIRONMENT PERSONAL LEARNING EDITION), 2002, Vensim Product Center,Ventana Systems Inc URL:http://www.vensim.com, E-mail: plesupport@vensim.com  [Google Scholar]) software, which simplified the assessment, was used to build a SD–model that accommodated changes in Population, Deforestation, Gross Domestic Product (GDP), and Basin Storage. Model results indicate groundwater behavior, deforestation, public opinion and decreased health of the farmers all relate to changes in land use (i.e., introduction of a rice development project) with its associated environment degradation, deforestation, and poverty due to deforestation. Moreover, these changes might be the cause of animal flight from the Mkomazi game reserve and an increase in human disease and deaths. Finally, it is concluded that uncontrolled human activities and behavior are the main causes of environmental degradation and therefore a brief summary is presented on challenges and opportunities for decision–makers on the sustainable development of the Mkomazi Valley.     

Prediction of contact numbers of amino acid residues using a neural network regression algorithm

The profile of contact numbers of amino acid residues in proteins contains important information about the protein structure and is connected with the accessibility of residues to solvent. Here we propose a method for predicting the profile of contact numbers of residues in protein from its amino acid sequence. The method is based on regression using a neural network algorithm. The algorithm predicts two types of profiles, namely, the total number of contacts and the number of close contacts with the neighbors in the chain. The Pearson coefficient of correlation between the actual and predicted values of total contact numbers amounted to 0.526–0.703. As for the number of close contacts, this coefficient was higher (0.662–0.743) for all the considered threshold contact distances (6, 8, 10, and 12 Å). The program for prediction of contact numbers CONNP is available at http://wwwmgs2.bionet.nsc.ru/reloaded.