http://www.hindawi.com The latest articles from Hindawi Publishing Corporation © 2013 , Hindawi Publishing Corporation . All rights reserved. Thu, 16 May 2013 11:30:17 +0000 http://www.hindawi.com/dpis/biology/2013/976758/ Peptides have a dominant role in biology; yet the study of their physical properties is at best sporadic. Peptide quantitative structure-activity relationship (QSAR) lags far behind the QSAR analysis of drug-like organic small molecules. Traditionally, QSAR has focussed on experimentally determined partition coefficients as the main descriptor of hydrophobicity. A partition coefficient () is the ratio between the concentrations of an uncharged chemical substance in two immiscible phases: most typically water and an organic solvent, usually 1-octanol. A distribution coefficient () is the equivalent ratio for charged molecules. We report here a compilation of partition and distribution coefficients for linear peptides compiled from literature reports, suitable for the development and benchmarking of peptide and prediction algorithms. Matthew N. Davies and Darren R. Flower Copyright © 2013 Matthew N. Davies and Darren R. Flower. All rights reserved. Wed, 20 Feb 2013 15:31:22 +0000 http://www.hindawi.com/dpis/biology/2013/706465/ Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available. Maurice H. T. Ling, Roel C. Rabara, Prateek Tripathi, Paul J. Rushton, and Xijin Ge Copyright © 2013 Maurice H. T. Ling et al. All rights reserved. Sun, 17 Feb 2013 11:58:13 +0000 http://www.hindawi.com/dpis/biology/2013/364725/ The Y-chromosome short tandem repeat (Y-STR) data are mainly collected for a performance benchmarking result in clustering methods. There are six Y-STR dataset items, divided into two categories: Y-STR surname and Y-haplogroup data presented here. The Y-STR data are categorical, unique, and different from the other categorical data. They are composed of a lot of similar and almost similar objects. This characteristic of the Y-STR data has caused certain problems of the existing clustering algorithms in clustering them. Ali Seman, Zainab Abu Bakar, and Mohamed Nizam Isa Copyright © 2013 Ali Seman et al. All rights reserved. Wed, 06 Feb 2013 16:19:26 +0000 http://www.hindawi.com/dpis/biology/2013/854869/ The gene encoding SSU-rRNA sequences is the tool of choice for phylogenetic analyses and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota. In Eukaryota, gene sequences may often be interrupted by long or several introns. Searching in GenBank release 188, we found descriptions of 3638 such sequences. Using a database of 180 000 SSU-rRNA sequences well annotated for taxonomy and a C++ program written for that purpose, we computed the presence of 18 691 introns (among which the 3638 described introns). Filtering on length and sequence quality, 3646 sequences were retained. These introns were clustered; clusters were analyzed for the presence of single or multiple clades at various levels of taxonomic depth, allowing future analyses of horizontal transfers. Various analyses of the results are provided as tabulated files as well as FASTA files of described or computed introns. Each sequence is annotated for cellular location (nuclear, chloroplast, and mitochondria), positions at which they were found in the SSU-rRNA sequences and taxonomy as provided by GenBank. Dipankar Bachar, Laure Guillou, and Richard Christen Copyright © 2013 Dipankar Bachar et al. All rights reserved. Wed, 24 Oct 2012 11:05:39 +0000 http://www.hindawi.com/dpis/biology/2013/362683/ We studied the fauna of leech and leech-like species inhabiting main water streams of Eastern Siberia and its tributaries, which are attributed to Lake Baikal basin and Lena River basin. Here we present their list for the first time. This study was mainly aimed for free-living parasitic and carnivorous leeches whereas piscine parasites were not included specially. In total, the potamic leech fauna of Eastern Siberia includes 12 described species belonging to 10 genera. Representatives of three unidentified species of two genera Erpobdella and Barbronia have been also recorded. Irina A. Kaygorodova, Elena V. Dzyuba, and Natalya V. Sorokovikova Copyright © 2013 Irina A. Kaygorodova et al. All rights reserved. Sun, 23 Sep 2012 13:19:40 +0000 http://www.hindawi.com/dpis/biology/2013/839671/ The lancelet (amphioxus) performs metamorphosis and produces minute and ciliate pelagic larvae commonly found in other metamorphic marine invertebrates. During larval life and metamorphosis, however, the animal displays interesting combination of features not found in other animals such as long coexistence of ciliate and muscular locomotion and no change in feeding behavior. The uniqueness of lancelet metamorphosis can provide important data to understand the evolutionary history of this animal as well as the metamorphosis broadly appeared in metazoans. Although lancelet metamorphosis has been studied, all previous studies depended on cross-sectional observations. To get serial data on metamorphic events, we performed longitudinal observations on the Japanese lancelet under the culture condition and confirmed the following: (1) there were individual variations of the duration of metamorphosis from 15 to 27 days; (2) growth was arrested for a month and the maximum reduction of the body length (2.2%–3.2%) occurred when gill slits became paired; (3) during rather long duration of metamorphosis, the oral transformation and the division of the gill pores by tongue bar were completed within two to four days. Our observations suggest that the duration and mode of lancelet metamorphosis depend mainly on intrinsic requirements rather than on extrinsic selective pressures. Takao Kaji, Yoichi Hoshino, Yasuhisa Henmi, and Kinya Yasui Copyright © 2013 Takao Kaji et al. All rights reserved. Thu, 13 Sep 2012 14:29:44 +0000 http://www.hindawi.com/dpis/biology/2013/219095/ Escherichia coli (E. coli) is a nonhalophilic microbe and used to indicate faecal contamination. Salt (sodium chloride, NaCl) is a common food additive and is used in preservatives to encounter microbial growth. The effect of how E. coli interacts with the salt present in the human diet is unclear. Thus, it is important to investigate this relationship. In order to adapt and survive the changes in the environment, E. coli may undergo halophilization. In this study, we observed the genetic changes and growth kinetics of E. coli ATCC 8739 under 3%–11% NaCl over 80 passages. Our results suggest that E. coli adapted to 1% increase in NaCl every month with a successful adaptation to 11% NaCl. Gram staining and PCR/RFLP showed that the cultures are Gram negative and the DNA profiles of all 4 replicates to be similar, suggesting that the cultures had not been contaminated. Jian Ann How, Joshua Z. R. Lim, Desmond J. W. Goh, Wei Chuan Ng, Jack S. H. Oon, Kun Cheng Lee, Chin How Lee, and Maurice H. T. Ling Copyright © 2013 Jian Ann How et al. All rights reserved. Thu, 30 Aug 2012 11:53:54 +0000 http://www.hindawi.com/dpis/biology/2013/261521/ New data on Lake Baikal fauna of Hirudinida (Annelida, Clitellata) are presented. The species composition of Baikal leeches extends to 20 species belonging to two orders, four families, and 12 genera. An updated checklist includes information on five species recorded in Eastern Siberia for the first time. All specimens from author’s collection are provided with illustration. Irina Kaygorodova Copyright © 2013 Irina Kaygorodova. All rights reserved. Tue, 28 Aug 2012 11:14:12 +0000 http://www.hindawi.com/dpis/biology/2013/949637/ A set of 42 SSRs of wheat were evaluated for their cross-amplification on the DNA of Thinopyrum ponticum, Thinopyrum intermedium, Thinopyrum elongatum, Thinopyrum bessarabicum, Pseudoroegneria stipifolia, and Dasypyrum villosum. The number of the wheat SSR markers that amplified DNA fragments with determined size for Th. ponticum was 33 (78.6%); for Th. intermedium, 28 (66.7%); for Th. elongatum, 24 (57.1%); for Th. bessarabicum, 24 (57.1%); for P. stipifolia, 26 (69.1%); and for D. villosum, 29 (69.0%). Twenty-four primer pairs of wheat SSR markers were successfully amplified from all investigated species. The dataset can be used for phylogenetic studies of wild relatives of wheat, for the estimation of their diversity, and for the introgression of agronomically valuable genes into wheat genome. Pavel Yu. Kroupin, Mikhail G. Divashuk, Igor A. Fesenko, and Gennady I. Karlov Copyright © 2013 Pavel Yu. Kroupin et al. All rights reserved. Thu, 09 Aug 2012 11:12:34 +0000 http://www.hindawi.com/dpis/biology/2013/451461/ This dataset gives details on a study which was conducted in seventeen forests in western Uganda (Albertine region) between 1993 and 1995. Different methods were used to sample butterflies from these forests. A total of 630 butterfly species were collected in 5 main families. Key characteristics of the forests were recorded, and these were found to influence the butterfly species richness of the forests. Patrice Kasangaki, Anne M. Akol, and Gilbert Isabirye Basuta Copyright © 2013 Patrice Kasangaki et al. All rights reserved. Thu, 09 Aug 2012 08:12:19 +0000 http://www.hindawi.com/dpis/biology/2013/670926/ We performed RNA sequencing of fruit from three normal and three mantled (somaclonal variant affecting flower development) oil palm plants using a 454 pyrosequencer. The three normal fruit samples were combined and sequenced, generating 237 748 reads. The three mantled fruit samples were combined and sequenced giving 231 438 reads. The reads were assembled into 13 984 sequences that were clustered into 10 218 genes or gene families. This paper describes the generation of this transcriptome database and includes annotation of these genes from Blast2GO and blast results against the Arabidopsis protein database as well as identification of putative transcription factors. In addition to this, the expression values for each gene sequence of the normal samples are presented. This dataset will be of use to anyone working in oil palm genetics. Jeremy R. Shearman, Chatchawan Jantasuriyarat, Duangjai Sangsrakru, Thippawan Yoocha, Apichart Vannavichit, Sithichoke Tangphatsornruang, and Somvong Tragoonrung Copyright © 2013 Jeremy R. Shearman et al. All rights reserved. Thu, 09 Aug 2012 08:11:44 +0000 http://www.hindawi.com/dpis/biology/2013/370103/ The object of the paper is to show the heterogeneity of 300 cord samples processed in the current research. The differences in effectiveness of mesenchymal stem cell (MSC) isolation are shown. Moreover, the recommendations for choosing the method of MSC isolation depending on the value of stromal-vascular rate are given. The data can be useful for selecting the optimal conditions to obtain MSC and for further cryopreservation of umbilical cord tissue. O. O. Maslova, N. S. Shuvalova, O. M. Sukhorada, S. M. Zhukova, O. G. Deryabina, M. V. Makarenko, D. O. Govseiev, and V. A. Kordium Copyright © 2013 O. O. Maslova et al. All rights reserved. Wed, 01 Aug 2012 14:43:28 +0000 http://www.hindawi.com/dpis/biology/2013/607541/ To study the reproductive dynamics of the mandi-beiçudo, Iheringichthys labrosus, in the Capivara Reservoir, Paranapanema River, Parana, Brazil, specimens were captured trimonthly from March 2001 to July 2004 at four sampling sites. The sex ratio showed a predominance of females in most of months sampled and the larger length classes. The majority of the individuals captured showed a standard length between 16 and 22 cm, with a maximal length of 27.5 cm. The size at first maturity was estimated to be 18.1 and 19.7 cm for females and males, respectively. Analysis of the temporal variation of the gonadosomatic index (GSI) and frequency of occurrence of gonadal maturation stages of males and females for the months sampled showed that I. labrosus reproduces during the whole year, with peak reproduction in November and December. There was a positive correlation between the mean values of GSI and variation in rainfall values, suggesting that this abiotic factor can influence the reproduction of this species. The mean absolute fecundity was 67274.5 ± 16562.5 oocytes, and the mean relative fecundity was 350.6 ± 186.3 oocytes per gram of total weight. Fábio Mineo Suzuki, Diego Azevedo Zoccal Garcia, and Mário Luís Orsi Copyright © 2013 Fábio Mineo Suzuki et al. All rights reserved.