The Lactamase Engineering Database: a critical survey of TEM sequences in public databases

<p>Abstract</p> <p>Background</p> <p>TEM β-lactamases are the main cause for resistance against β-lactam antibiotics. Sequence information about TEM β-lactamases is mainly found in the NCBI peptide database and TEM mutation table at <url>http://www.lahey.org/Studies/temtable.asp</url>. While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM β-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship.</p> <p>Description</p> <p>The LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM β-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM β-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM β-lactamase were common to both data sets. The 180 TEM β-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at <url>http://www.LacED.uni-stuttgart.de</url> and contains multisequence alignments, structure information and reconciled annotation of TEM β-lactamases. The LacED is weekly updated and supplies all data for download.</p> <p>Conclusion</p> <p>The Lactamase Engineering Database enables a systematic analysis of TEM β-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM β-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur.</p

Evaluation of genetic diversity of Vietnamese dogs based on mitochondrial DNA hypervariable-1 region

Haplogroup E were detected with high frequency in the population of Phu Quoc ridgeback dogs suggesting that this Vietnamese valuable dog breed originated from domestic dogs harbouring haplogroup E from Vietnam’s mainland or from East Asia where the presence of haplogroup E was reported. Evaluation of the genetic diversity of the Vietnam’s mainland dogs and haplogroup Escreening would support us in tracking out the origin of Phu Quoc ridgeback dog

Examining the effects of lead on the life of larval zebrafish (1-7 days old)

Lead (Pb) is a toxic metal and and can cause variety of disorders and effect on neu-ronal function and neurodevelopment. Using zebrafish as a model, the aim of this study was to evaluate the effects of concentrations of Pb2+ on the life of zebrafish larvae (from 1 to 7 days old)yesBelgorod State Universit

Effect of time and temperature on the survival rate of mouse sperm (Mus musculus var. Albino) in short-term preservation without cryoprotectant agents

In this study, we studied the use of physiological saline solution (NaCl 0,9%) or dulbecco’s phosphatebuffered saline (D-PBS) for mature sperms short-term preservation. After being collected from epididymides, sperms were adjusted to desired concentration (2x106 sperms/ml) with NaCl 0.9% solution or D-PBS solution (the dishes containing sperms were covered by mineral oil) and stored at 4oC, iooC and room temperature (RT/26oC

Evaluation of genetic diversity of Vietnamese dogs based on mitochondrial DNA hypervariable-1 region

Haplogroup E were detected with high frequency in the population of Phu Quoc ridgeback dogs suggesting that this Vietnamese valuable dog breed originated from domestic dogs harbouring haplogroup E from Vietnam’s mainland or from East Asia where the presence of haplogroup E was reported. Evaluation of the genetic diversity of the Vietnam’s mainland dogs and haplogroup Escreening would support us in tracking out the origin of Phu Quoc ridgeback dog

Complete Range of the Universal mtDNA Gene Pool and High Genetic Diversity in the Thai Dog Population

The dog population of Southern East Asia is unique in harboring virtually the full range of the universal mtDNA gene pool, and consequently, it has the highest genetic diversity worldwide. Despite this, limited research has been performed on dog genetics within this region. Here we present the first comprehensive study of a sub-region within Southern East Asia, analyzing 528 bp of mtDNA for 265 dogs from Thailand, in the context of dogs from across the Old World. We found that Thailand was the only region in the world that has the full range of the universal mtDNA gene pool, that is, all 10 sub-haplogroups. Consequently, the statistics for diversity are among the highest, especially in North Thailand, which had high values for haplotype diversity and the number of haplotypes, and the lowest proportion of individuals with a universal type-derived haplotype (UTd) among all regions. As previously observed, genetic diversity is distinctly lower outside Southern East Asia and it decreases following a cline to the lowest values in western Eurasia. Thus, the limited geographical region of Thailand harbors a distinctly higher genetic diversity than much larger regions in western Eurasia, for example, Southwest Asia and Europe which have only five and four of the 10 sub-haplogroups, respectively. Within Thailand, diversity statistics for all four sub-regions follow the general pattern of Southern East Asia, but North Thailand stands out with its high diversity compared to the other regions. These results show that a small part of Southern East Asia harbors the full range of the mtDNA gene pool, and they emphasize the exceptional genetic status of Southern East Asia. This indicates that today&rsquo;s dogs can trace a major part of their ancestry to Southern East Asia or closely situated regions, highlighting Thailand as a region of special interest. Considering the large genetic diversity found in Thailand and that many neighboring regions, e.g., Myanmar and Laos, have not been studied for dog genetics, it is possible that large parts of the dog gene pool remain undiscovered. It will be an important task for future studies to fill in these blanks on the phylogeographic map

Effect of time and temperature on the survival rate of mouse sperm (Mus musculus var. Albino) in short-term preservation without cryoprotectant agents

yesIn this study, we studied the use of physiological saline solution (NaCl 0,9%) or dulbecco’s phosphatebuffered saline (D-PBS) for mature sperms short-term preservation. After being collected from epididymides, sperms were adjusted to desired concentration (2x106 sperms/ml) with NaCl 0.9% solution or D-PBS solution (the dishes containing sperms were covered by mineral oil) and stored at 4oC, iooC and room temperature (RT/26oC)Belgorod State Universit

Examining the effects of lead on the life of larval zebrafish (1-7 days old)

yesLead (Pb) is a toxic metal and and can cause variety of disorders and effect on neu-ronal function and neurodevelopment. Using zebrafish as a model, the aim of this study was to evaluate the effects of concentrations of Pb2+ on the life of zebrafish larvae (from 1 to 7 days old)Belgorod State Universit