Database of Trypanosoma cruzi repeated genes: 20 000 additional gene variants

<p>Abstract</p> <p>Background</p> <p>Repeats are present in all genomes, and often have important functions. However, in large genome sequencing projects, many repetitive regions remain uncharacterized. The genome of the protozoan parasite <it>Trypanosoma cruzi </it>consists of more than 50% repeats. These repeats include surface molecule genes, and several other gene families. In the <it>T. cruzi </it>genome sequencing project, it was clear that not all copies of repetitive genes were present in the assembly, due to collapse of nearly identical repeats. However, at the time of publication of the <it>T. cruzi </it>genome, it was not clear to what extent this had occurred.</p> <p>Results</p> <p>We have developed a pipeline to estimate the genomic repeat content, where shotgun reads are aligned to the genomic sequence and the gene copy number is estimated using the average shotgun coverage. This method was applied to the genome of <it>T. cruzi </it>and copy numbers of all protein coding sequences and pseudogenes were estimated. The 22 640 results were stored in a database available online. 18% of all protein coding sequences and pseudogenes were estimated to exist in 14 or more copies in the <it>T. cruzi </it>CL Brener genome. The average coverage of the annotated protein coding sequences and pseudogenes indicate a total gene copy number, including allelic gene variants, of over 40 000.</p> <p>Conclusion</p> <p>Our results indicate that the number of protein coding sequences and pseudogenes in the <it>T. cruzi </it>genome may be twice the previous estimate. We have constructed a database of the <it>T. cruzi </it>gene repeat data that is available as a resource to the community. The main purpose of the database is to enable biologists interested in repeated, unfinished regions to closely examine and resolve these regions themselves using all available shotgun data, instead of having to rely on annotated consensus sequences that often are erroneous and possibly misleading. Five repetitive genes were studied in more detail, in order to illustrate how the database can be used to analyze and extract information about gene repeats with different characteristics in <it>Trypanosoma cruzi</it>.</p

Highlights from the 1st Student Symposium on Computational Biology and Life Sciences, organised by ISCB Regional Student Group, UK

Abstract This short report summarises the scientific content and activities of a student-led event, the 1st student symposium by the UK Regional Student Group of the International Society for Computational Biology. The event took place on October 2014

Study to assess the prevalence of human leukocyte antigen-A*3101 allele among Indian epileptic patients and its influence on safety and efficacy of antiepileptic therapy

Background: The objective was to study the prevalence of human leukocyte antigen (HLA)-A*3101 allele among epileptic patients and to assess the safety and efficacy of antiepileptic therapy.Methods: 295 subjects were selected and divided into two groups, Group I had 192 epileptic patients and Group II had 103 normal healthy controls. After written informed consent, 30 ml of mouthwash sample was collected from each subject and DNA was extracted by standard salting-out technique and used for HLA-A*3101 genotyping by two-step nested allele-specific polymerase chain reaction amplification and agarose gel electrophoresis.Results: In Group I, 12 (6.25%) of the 192 patients were tested positive for HLA-A*3101 allele and all were taking carbamazepine (CBZ). Among them, 56 (30%) subjects had developed less severe adverse effects such as headache and giddiness, skin rashes and memory disturbances, and HLA-A*3101 was present in 8 of them while 136 had no adverse effects in which 4 of them were tested positive for the allele. In Group II, 3 (2.9%) of the 103 healthy controls were tested positive for the allele. No difference was found in response to antiepileptic therapy between allele positive and negative patients.Conclusion: The present study had shown that HLA-A*3101 is prevalent in 6.25% of the Indian epileptic population under study. The presence of this allele has a significant association with the development of mild cutaneous reactions like skin rashes. However, no difference was observed in allele positive patients in response to antiepileptic therapy in comparison with allele negative patients

Enhancement of the fruit quality and postharvest life expectancy of mango fruit (Mangifera indica L.) applying ecofriendly bio-coatings

The higher losses of fruits and vegetables during post-harvest handling are a serious matter for any country whose economy is based on agriculture. The products of this plant are a significant source of horticultural produce storage used for the control of different post-harvest losses, which include diseases as well as microorganisms. Bio-coatings may be used as a better alternative to the synthetic chemicals. The impact of edible coating on the quality and storage life of mango (cv. ‘Anwar Rataul’) fruit was investigated by harvesting the fruits at a firm green stage of physiological maturity and coating them with corn oil, peanut oil, sunflower oil, soya bean oil, and animal fat. The uncoated and coated fruits were stored at 25 °C and the relative humidity (RH) was 75%. The fruits were analyzed for physicochemical quality attributes during storage at 0 (harvest time), 5, 10, 15, 20, and 25 days. The data showed that most of the parameters were affected significantly by the materials of coating and storage intervals (P ≤ 0.05). The fruits coated with animal fat had significantly superior fruit color, taste, aroma, firmness, total sugar content, and acidity of fruit juice, total soluble solids, and ascorbic acid content, as well as delayed ripening. Animal fat-coated fruits retained titratable acidity, ascorbic acid content (mg.100g-1) and fruit firmness (kg.cm-2) with minimal disease incidence, and weight loss (%), whereas uncoated fruits did not retain all quality attributes and deteriorated after 20 days of storage. In conclusion, mango fruits could be coated with animal fat and stored for up to 25 days without deterioration in quality

Phenotypic characterization, genetic analysis and antibiotic sensitivity of Aeromonas hydrophila isolates causing dropsy in cultured Labeo rohita from Punjab, Pakistan

Motile Aeromonas septicemia (MAS) is a common freshwater fish disease and major threat to the aquaculture in Pakistan. The present study was carried out on suspected fish samples to isolate and characterize local strains of Aeromonas hydrophila, a key pathogen responsible for the said disease in aquacultured fishes. A total of ninety suspected fish specimens were collected from fish farms in Kasur, Okara and Gujranwala districts of Punjab, Pakistan from June 2018 to April 2019. The specimens were processed and A. hydrophila strains were isolated. The primary identification of sixty seven isolates were verified by colony morphology, microscopy and phenotypic characterization with ten biochemical reactions. The A. hydrophila strains of test samples were molecularly characterized by polymerase chain reaction (PCR) using 16S rRNA at desired size of 356bp. The PCR amplified product was subjected to DNA sequencing and phylogenetic analysis showed homology with related strains of Aeromonas spp. By antibiotic sensitivity test, the isolates were checked for nine antibiotics in which the pathogen was sensitive to four and resistant to five drugs. Results of genetic analysis confirmed strains as A. hydrophila which are useful to take preventive measures against the said disease

Lack of association of methylenetetrahydrofolate reductase 677C\u3eT mutation with coronary artery disease in a Pakistani population

Pakistanis belong to the South Asian population which has the highest known rate of coronary artery disease. Folic acid deficiency also appears to be highly prevalent in this population. Methylenetetrahydrofolate reductase (MTHFR) 677C\u3eT polymorphism decreases the activity of this enzyme and can be associated with mild to moderate hyperhomocysteinemia in homozygotes, particularly when there is folic acid deficiency, as well as with coronary artery disease. To assess the value of genotyping the MTHFR 677C\u3eT dimorphism, we carried out a case-control study of dimorphism 677C\u3eT for putative association with myocardial infarction (MI) among Pakistani nationals. We investigated a sample population of 622 Pakistanis consisting of 225 controls and 397 patients with clinical diagnosis of acute MI (AMI). MTHFR C677T alleles were determined by assays based on polymerase chain reaction and restriction endonuclease analysis. Frequencies of C alleles were 0.87 among controls and 0.86 among AMI patients. The MTHFR 677C\u3eT dimorphism showed no association with MI (chi(2) = 0.25, 1df, P=0.62), serum levels of folate and vitamin B12 and plasma level of vitamin B6. A significant association, however, was found between homozygous 677T genotype and plasma levels of homocysteine. Multivariate analysis of the data showed that in case of log homocysteine, age and MTHFR genotypes were significantly different (PT polymorphism, though associated with homocysteine levels, confers no significant risk of coronary artery disease in the Pakistani population investigated here. We suggest that the higher incidence of AMI in South Asia occurs through mechanisms other than the MTHFR related pathways

How does the belt and road initiative affect the carbon emissions of China’s cities?

There is growing concern about carbon emissions as the economy grows, which is of great importance to the implementation of the green Belt and Road Initiative (BRI) development strategy. Using panel data of 282 prefecture-level cities in China from 2006–2020 and the difference-in-differences method, this paper empirically examines the effects of the BRI on carbon emissions. Both theoretical and empirical analyses indicate that the BRI can significantly reduce the carbon emission level of cities along the routes, but the impact varies in different regions and cities. The mechanism analysis shows that the BRI reduces the carbon emission level of the Belt and Road cities through the economic agglomeration effect and industrial structure effect. Therefore, China should vigorously promote green Belt and Road construction, implement a regional integration strategy, and promote the transformation and upgrading of the industrial structure. These findings have a certain reference value for the follow-up implementation of the BRI

Molecular characterisation and genetic analysis of aerolysin and haemolysin in Aeromonas hydrophila isolated from diseased Labeo rohita by polymerase chain reaction

The present study investigates pathogenicity of local Aeromonas hydrophila strains by molecular characterisation of two virulence factor genes: aerolysin (aerA) and haemolysin (Ahh1) using polymerase chain reaction (PCR) technique. Phenotypically identified presumptive Aeromonas isolates recovered from diseased Labeo rohita were genetically analysed using type-specific primers by amplifying 309 bp and 130 bp conserved regions of aerolysin and haemolysin genes respectively. The partial nucleotide sequences of aerA and Ahh1 were determined from representative strains in which aerA was confirmed in 75% isolates, whereas Ahh1 was confirmed in 50% isolates. The nucleotide blast results of the representative strains revealed close homology of 95% (aerolysin) and 97% (haemolysin) with published sequences

Antimicrobial activity analysis of extracts of Acacia modesta, Artimisia absinthium, Nigella sativa and Saussurea lappa against Gram positive and Gram negative microorganisms

Antimicrobial activity of extracts of certain herbs including Acacia modesta (leaf and stem), Artimisia absinthium (leaf and stem), Nigella sativa (seeds) and i (root) was evaluated against three Gram positive and two Gram negative microorganisms. The Gram positive organisms included Bacillus subtalis (ATCC 6633), Entereococcus faecalis (ATCC 14506) and Staphylococcus aureus (ATCC 6538) and the Gram negative organisms included Pseudomonas aeruginosa (ATCC 27853) and Salmonella typhi (ATCC 14028). Methanolic, hot water and cold water extracts of these plants were taken for antibacterial assay through Discs agar diffusion technique using commercial filter paper discs applied on inoculated Muellar Hinton agar plates. The objective of this study was to explore the curative powers of these herbs that exist in nature as a tool to counter disease causing agents. The maximum zone of inhibition of 18 mm of methanolic extract of N. sativa was observed against B. subtalis and S. aureus. Similarly, the maximum zone of inhibition of 18 mm of cold water extract of N. sativa against S. aureus and methanolic extract of Saussurea lappa against S. aureus and Pseudomonas aeruginosa was also observed. The antibacterial action was compared with the effect of ceftriaxone, ceftriaxone sodium, cefuroxine, ciprofloxacin, gentamycine, levofloxacin, metronidazole and tranexamic acid that were used as standered drugs. Based on the results obtained in this study, it may be concluded that plant extracts of A. modesta, A. absinthium, N. sativa and Saussurea lappa have a stronger and broader spectrum of antimicrobial activity against a number of food borne bacteria.Key words: Herbs, methanolic extract, Acacia modesta, Bacillus subtalis, gentamycine, gram negative, gram positive