Biopython: Comparing the DNA Polymerase I (polA) Gene of Thermophilic, Mesophilic, and Psychrophilic Bacteria

Biopython is a specialized Python tool for computational molecular biology. Various computational molecular analysis that can be performed using Biopython, such as reconstructing phylogenetic trees, multiple sequence analysis, generating complementary sequences, counting amino acids, etc. This technical notes paper describes in detail the procedures computational DNA sequence analysis using Biopython. The DNA polymerase I (polA) gene sequences of bacteria were used in this study to compare the differences between Thermophilic, Mesophilic, and Psychrophilic bacteria

Identification of Cis-regulatory Elements of Butyrophilin Gene of the Mammary Gland

Butyrophilin subfamily 1 member A1 is a highly expressed gene in  mammary gland of all mammals during lactation. It is found to be the major integral protein in the milk fat globule membrane. Its interactions with other membrane elements and soluble proteins of the mammary  epithelial cells regulate the secretion of milk fat. In order to reveal any shared cis-acting elements, the human butyrophilin subfamily 1member A1 5’-flanking genomic sequence was analyzed and compared with four mammals comprising of a rodent and three primates, viz., Mus musculus, and Pan troglodytes, Pongo obelli, and Macaca mulata, and three other mammary specific human milk genes using publicly available  bioinformatics tools. Prior to a multiple sequence analysis, low complexityDNA sequences were masked using CENSOR. The multiple sequence  analysis revealed nine highly conserved regions of similarities in the 5’- flanking region of butyrophilin genes across species. Consensus putative transcription factor binding sites were identified using MatInspector and compared with SiteGA results. They were subsequently examined for the expression in the mammary gland as well as for their occurrence in the previously identified region of homology. Finally, CCCTCbinding factor (CTCF) and nuclear receptor subfamily 2 - factor (NR2F) were identifiedat a similar distance from the transcription start site in the 5’- flanking region of butyrophilin gene across the species. However, the exact  interaction of these transcription factors with the butyrophilin gene is not known, which needs further investigation

PHYLOGENETIC ANALYSIS OF COLD SHOCK PROTEINS IN PSEUDOMONAS SPECIES

Objective: The present study focuses on the determination of the relativity of the different types of cold shock proteins.Methods: Our study was to determine the relationship among the types of CSPs. Three different strains of pseudomonas genus, Pseudomonas fluorescens, Pseudomonas aeruginosa and Pseudomonas putida were chosen and molecular profiling was performed. The sequences thus obtained were subjected to multiple sequence analysis in ClustalW database. The molecular evolution and phylogenetic study have been carried out using phylodraw.Results: The phylogenetic analysis has clearly revealed the evolutionary pattern of cold shock proteins in pseudomonas species and the current stress of mutation among the strains.Conclusion: Phylogenetic analysis of cold shock proteins has clearly shown that important conserved sequences can be very useful to study the phylogeny of bacteria

In vitro Quinolones Susceptibility Analysis of Chinese Mycoplasma bovis Isolates and their Phylogenetic Scenarios based upon QRDRs of DNA Topoisomerases Revealing a Unique Transition in ParC

Mycoplasma bovis can cause different systemic problems in cattle, and recently has been resulted in huge economic losses in China. In vitro susceptibilities of 26 twice sub-cultured Chinese M. bovis field isolates were determined at physiological pH including PG45 through broth micro-dilution method. Except Huanggang isolate, all isolates and PG45 were in the sensitive range for levofloxacin, lomefloxacin and ciprofloxacin, whereas, for norfloxacin and nalidixic acid, they had shown intermediate resistant and complete resistant patterns, respectively. The multiple sequence analysis revealed point mutations in QRDRs of gyrA and parC genes of Huanggang isolate resulting in amino acid substitutions at positions 83 (S-F) in GyrA (E. coli numbering) and 80 (S-I) in ParC proteins, the latter is reported for first time in M. bovis. Conclusively, fluoroquinolones are the potential veterinary therapeutic agents for mycoplasmosis in China and resistance to these agents comes through point mutations in QRDRs of gyrA and parC genes with ParC and GyrA mutation orientation

Highly heterogeneous Ty3/Gypsy-like retrotransposon sequences in the genome of cassava (Manihot esculenta Crantz)

The use of PCR has enabled the survey of transposable elements in many plants; thereby making the study of their diversity and applications possible in species where the full genome sequence data are not yet available. In the present study, we used PCR primers anchored on the conserved domain of reverse transcriptase and endonuclease to amplify the Ty3/Gypsy-like polyprotein fragment from the genome of cassava (Manihot esculenta Crantz). The PCR product was cloned and sequenced. Sequence analysis of individual clones clearly identified the conserved domain of the polyprotein enzymes and showed the cassava Ty3/Gypsy-like retrotransposon, Megyp (for Manihot esculenta gypsy-like), sequences to be highly heterogeneous. Some Megyps clustered with other plants’ Ty3/Gypsy-like retrotransposons, while some clustered with Gypsy of Drosophila melanogaster and Ty3-2 of Saccharomyces cerevisiae in the comparative multiple sequence analysis. This suggests that the later belong to the retrovirus lineage of this group of elements. Southern analysis showed that, the Megyps and analogues were highly repeated within the genomes of cassava cultivars.Key words: Cassava, transposable-elements, retrotransposons, retroviruses, Manihot esculenta, Ty3/Gypsy

A Cross-cohort Description of Young People’s Housing Experience in Britain over 30 Years: An Application of Sequence Analysis

Methods. Sequence Analysis supported by Event History Analysis. Key Findings. Despite only 12 years separating both cohorts, the younger 1970 cohort exhibited very different patterns of housing including a slower progression out of the parental home and into stable tenure, and an increased reliance on privately rented housing. Returns to the parental home occurred across the twenties and into the thirties in both cohorts, although occurred more frequently and were more concentrated among certain groups in the 1970 cohort compared to the 1958 cohort. Although fewer cohort members in the 1970 cohort experienced social housing, and did so at a later age, social housing was also associated with greater tenure immobility in this younger cohort. Conclusions. The housing experiences of the younger cohort became associated with more unstable tenure (privately rented housing) for the majority. Leaving the parental home was observed to be a process, as opposed to a one-off event, and several returns to the parental home were documented, more so for the 1970 cohort. These findings are not unrelated, and in the current environment of rising house prices, collapses in the (youth) labour market and rising costs of higher education, are likely to increase in prevalence across subsequent cohorts

Comparison of articulate brachiopod nuclear and mitochondrial gene trees leads to a clade-based redefinition of protostomes (Protostomozoa) and deuterostomes (Deuterostomozoa)

Nuclear and mtDNA sequences from selected short-looped terebratuloid (terebratulacean) articulate brachiopods yield congruent and genetically independent phylogenetic reconstructions by parsimony, neighbor-joining and maximum likelihood methods, suggesting that both sources of data are reliable guides to brachiopod species phylogeny. The present-day genealogical relationships and geographical distributions of the tested terebratuloid brachiopods are consistent with a tethyan dispersal and subsequent radiation. Concordance of nuclear and mitochondrial gene phylogenies reinforces previous indications that articulate brachiopods, inarticulate brachiopods, phoronids and ectoprocts cluster with other organisms generally regarded as protostomes. Since ontogeny and morphology in brachiopods, ectoprocts and phoronids depart in important respects from those features supposedly diagnostic of protostomes, this demonstrates that the operational definition of protostomy by the usual ontological characters must be misleading or unreliable. New, molecular, operational definitions are proposed to replace the traditional criteria for the recognition of protostomes and deuterostomes, and the clade-based terms 'Protostomozoa' and 'Deuterostomozoa' are proposed to replace the existing terms 'Protostomia' and 'Deuterostomia'

In silico Characterization of Industrial Important Cellulases using Computational Tools

Cellulases refer to a class of enzymes produced majorly by fungi, bacteria and protozoans that catalyze cellulolysis. Cellulase enzyme is used extensively in various industries, especially in textile, food and in the bioconversion of lignocellulosic wastes to alcohol. The extensive use of cellulase in industries depends on the cost of the enzyme and hence considerable research is being carried out to isolate better microbial strains and also to develop new fermentation processes with the aim to reduce the product cost. Cellulases from different strains of Pseudomonas species were analyzed using computational tools. The physicochemical properties of the selected cellulases were analyzed by using ExPASy’s ProtParam tool and it was found that the molecular weight (M.Wt) ranges between 40927.4-100058.7 Da. Isoelectric Points (pI) of all the organisms were found to be acidic in nature. The aliphatic index infers that all the cellulases are stable. The negative value of GRAVY indicates that there will be better interaction with water. The secondary structure prediction was done by SOPMA which showed that random coils dominated all the other conformations. Multiple sequence analysis and evolutionary analysis of cellulases were carried out by CLC workbench. The Phylogenetic analysis was done using Neighbour joining method. The 3D structures of cellualses were obtained by ESyPred 3D server. Keywords: Cellulases, Enzymes, ProtParam, SOPMA, ESyPred 3D

A cross-cohort description of young people's housing experience in Britain over 30 years: An application of Sequence Analysis

Methods. Sequence Analysis supported by Event History Analysis. Key Findings. Despite only 12 years separating both cohorts, the younger 1970 cohort exhibited very different patterns of housing including a slower progression out of the parental home and into stable tenure, and an increased reliance on privately rented housing. Returns to the parental home occurred across the twenties and into the thirties in both cohorts, although occurred more frequently and were more concentrated among certain groups in the 1970 cohort compared to the 1958 cohort. Although fewer cohort members in the 1970 cohort experienced social housing, and did so at a later age, social housing was also associated with greater tenure immobility in this younger cohort. Conclusions. The housing experiences of the younger cohort became associated with more unstable tenure (privately rented housing) for the majority. Leaving the parental home was observed to be a process, as opposed to a one-off event, and several returns to the parental home were documented, more so for the 1970 cohort. These findings are not unrelated, and in the current environment of rising house prices, collapses in the (youth) labour market and rising costs of higher education, are likely to increase in prevalence across subsequent cohorts.Housing, Young People, Sequence Analysis, Housing Tenure