Phylogenetic analysis of sclerospora graminicola using internal transcribed spaced region-2

The internal transcribed spacer region (ITS) from fourteen samples of Sclerospora graminicola was amplified using a nested PCR. These regions of the rDNA were amplified by a combination of conserved primers (ITS 1 and 6 and ITS 3 and 4). These products were cloned into a puc-4 vector and transformed into E.coli competent cells. The inserts from transformants were isolated, then sequenced by the Gene Technologies Lab, Texas A& M University. The sequences produced were and aligned with the ITS2 region of other known Oomycete fungi( Peronospora, Phytophthora and Pythium) using CLUSTALX. Phylogenetic relationship among sequences from Indian and African samples was examined using a consensus bootstrap parsimony tree. All the samples from India, Mali, Nigeria and Niger, with the exception of Niger 4, formed a monophyletic group with the Oomycetes ( Peronospora, Phytophthora and Pythium). The three samples Niger 4, BFaso 2 and BFaso 17 from Burkina Faso shared a close relationship with the outgroup Cladosporium herbareum

New anti-infective compounds against Staphylococcus aureus

Owing to the development of antibiotic resistance in microorganisms, new anti-microbial and anti-infective agents are of dire need to keep these pathogens at bay. These agents are mainly derived from the pathogen (bacteria or fungi) itself or from different plant extracts. In our previous work, it was observed that Lipoprotein like lipoprotein (Lpl) is an essential virulence factor in Staphylococcus aureus. Lpl is membrane bound and encoded in a genomic island called νSaα. Lpl causes the invasion of S. aureus into the HaCaT keratinocyte cells through its interaction with Hsp90α receptor. Lpl1 administration also surges the murine kidney abscess - bacterial burden. Our aim was to identify peptides that can block Hsp90 and reduce the S.aureus pathogenicity caused by Lpl. Here, we show 2 small peptides, named L15 and its derivative, L13, both part of Lpl1 have anti-infective action towards Staphylococcus aureus. Pretreatment with L15 and L13 reduced the invasion of S. aureus USA300 into HaCaT keratinocytes, N/TERT-1 primary keratinocytes and S. aureus phagocytosis in human monocytes. The peptides were water soluble, non-cytotoxic and non-hemolytic at the tested concentrations. Dot blot studies showed that there is direct interaction of the peptides with Hsp90α. L15 and L13 significantly decreased lethality of S. aureus bacteremia in Galleria mellonella insect larvae model, but did not affect growth or hemolytic activity of S. aureus in vitro. In a mouse bacteremia model L15 was found to significantly decrease weight loss and lethality. In effect the small peptides showed the opposite effect from their mother protein, in terms of the invasion of S. aureus into host cell and mice bacteremia model. Although the molecular bases behind the protective effect of L15 remain unclear, in vitro data indicate that treatment with L15 or L13 and simultaneous infection with S. aureus significantly increase IL-6 production in host immune cells. Our findings highlight Hsp90-interacting peptides as potential anti-infective agents In a separate work, non-peptide, anti-microbial phytochemicals- Rhodomyrtone (Rom) and Polycyclic polyprenylated acylphloroglucinols (PPAP), capable of inhibiting S.aureus in vitro are described. A single point mutation at farR makes S.aureus resistant to Rom. The antibacterial activity of Rom was targeted towards the cell membrane by interacting with its phospatidylglycerol (PG). RomR mutants were seen to excrete far more PGs, thereby neutralizing the Rom before it reaches the cell membrane. PPAP, though very much active in vitro, failed to rescue G. mellonella larvae from S.aureus infection. The reason was found to be the neutralization of PPAPs by the serum albumin proteins found in the larval coelomic fluid. In silico docking studies showed that PPAP is binding to the Heme binding pocket of bovine serum albumin. On the other hand, PPAP was observed to have a beneficial but not fully protective effect in S. aureus septic arthritis mouse model

New anti-infective compounds against Staphylococcus aureus

This publication is an edited version of my submitted dissertation “New anti-infective compounds against Staphylococcus aureus” that was accepted by the faculty on 14.12.2022 and published on TOBIAS-lib on 17.01.2023. Owing to the development of antibiotic resistance in microorganisms, new anti-microbial and anti-infective agents are of dire need to keep these pathogens at bay. These agents are mainly derived from the pathogen (bacteria or fungi) itself or from different plant extracts. In our previous work, it was observed that Lipoprotein like lipoprotein (Lpl) is an essential virulence factor in Staphylococcus aureus. Lpl is membrane bound and encoded in a genomic island called νSaα. Lpl causes the invasion of S. aureus into the HaCaT keratinocyte cells through its interaction with Hsp90α receptor. Lpl1 administration also surges the murine kidney abscess - bacterial burden. Our aim was to identify peptides that can block Hsp90 and reduce the S.aureus pathogenicity caused by Lpl. Here, we show 2 small peptides, named L15 and its derivative, L13, both part of Lpl1 have anti-infective action towards Staphylococcus aureus. Pretreatment with L15 and L13 reduced the invasion of S. aureus USA300 into HaCaT keratinocytes, N/TERT-1 primary keratinocytes and S. aureus phagocytosis in human monocytes. The peptides were water soluble, non-cytotoxic and non-hemolytic at the tested concentrations. Dot blot studies showed that there is direct interaction of the peptides with Hsp90α. L15 and L13 significantly decreased lethality of S. aureus bacteremia in Galleria mellonella insect larvae model, but did not affect growth or hemolytic activity of S. aureus in vitro. In a mouse bacteremia model L15 was found to significantly decrease weight loss and lethality. In effect the small peptides showed the opposite effect from their mother protein, in terms of the invasion of S. aureus into host cell and mice bacteremia model. Although the molecular bases behind the protective effect of L15 remain unclear, in vitro data indicate that treatment with L15 or L13 and simultaneous infection with S. aureus significantly increase IL-6 production in host immune cells. Our findings highlight Hsp90-interacting peptides as potential anti-infective agents In a separate work, non-peptide, anti-microbial phytochemicals- Rhodomyrtone (Rom) and Polycyclic polyprenylated acylphloroglucinols (PPAP), capable of inhibiting S.aureus in vitro are described. A single point mutation at farR makes S.aureus resistant to Rom. The antibacterial activity of Rom was targeted towards the cell membrane by interacting with its phospatidylglycerol (PG). RomR mutants were seen to excrete far more PGs, thereby neutralizing the Rom before it reaches the cell membrane. PPAP, though very much active in vitro, failed to rescue G. mellonella larvae from S.aureus infection. The reason was found to be the neutralization of PPAPs by the serum albumin proteins found in the larval coelomic fluid. In silico docking studies showed that PPAP is binding to the Heme binding pocket of bovine serum albumin. On the other hand, PPAP was observed to have a beneficial but not fully protective effect in S. aureus septic arthritis mouse model

Genomic sequence derived simple sequence repeats markers: A case study with Medicago spp.

Simple sequence repeats (SSR) or micro-satellites are becoming standard DNA markers for plant genome analysis and are being used as markers in marker assisted breeding. De novo generation of micro-satellite markers through laboratory-based screening of SSR-enriched genomic libraries is highly time consuming and expensive. An alternative is to screen the public databases of related model species where abundant sequence data is already available. All the genomic sequences of Medicago from the public domain database were searched and analysed of di, tri, and tetra nucleotide repeats. Of the total of about 156,000 sequences which were searched, 7325 sequences were found to contain repeat motif and may yield SSR which will yield product sizes of around 200 bp. Of these the most abundantly found repeats were the tri-nucleotide (5210) group. Except for a very small proportion (436), these link to the gene annotation database at TIGR (http://www.tigr.org). To facilitate further exploration of this resource, a dynamic database with options to search and link to other resources is available at (http://www.icrisat.org/text/research/grep/homepage/genomics/medssrs1.asp) and on CDs from [email protected]

The prevalence of antimicrobial-producing Gram-positive bacteria in human gut: a preliminary study

Background: Human gut microbiome is an excellent source for searching novel antimicrobials which is currently in need due to the raise of drug resistance bacteria. Many Gram-positive bacteria isolated from human gut have been reported to produce antimicrobial compounds but still only few studies investigating the prevalence of these bacteria in human gut.Methods: We took stool samples from 19 adult participants (age: 20–70 years; ethnicity: European and Asian). Stool samples obtained from 7 females and 12 males. We screened for Gram-positive antimicrobial-producing bacteria from the stool samples and identified the positive ones using 16s rRNA sequencing.Results: Here, we reported that antimicrobial-producing Gram-positive bacteria can be found in the stool samples of 6 out of 19 participants. By screening against Staphylococcus aureus USA300 and Pseudomonas aeruginosa PAO1, some isolates exhibited a different inhibition activity compared to the previously reported antimicrobial compounds.Conclusion: Our findings showed that some strains isolated from human gut exhibits a novel antimicrobial activity which implies that there could still be novel antimicrobial compounds in human gut produced by Gram-positive bacteria

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Global burden of 288 causes of death and life expectancy decomposition in 204 countries and territories and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BACKGROUND Regular, detailed reporting on population health by underlying cause of death is fundamental for public health decision making. Cause-specific estimates of mortality and the subsequent effects on life expectancy worldwide are valuable metrics to gauge progress in reducing mortality rates. These estimates are particularly important following large-scale mortality spikes, such as the COVID-19 pandemic. When systematically analysed, mortality rates and life expectancy allow comparisons of the consequences of causes of death globally and over time, providing a nuanced understanding of the effect of these causes on global populations. METHODS The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 cause-of-death analysis estimated mortality and years of life lost (YLLs) from 288 causes of death by age-sex-location-year in 204 countries and territories and 811 subnational locations for each year from 1990 until 2021. The analysis used 56 604 data sources, including data from vital registration and verbal autopsy as well as surveys, censuses, surveillance systems, and cancer registries, among others. As with previous GBD rounds, cause-specific death rates for most causes were estimated using the Cause of Death Ensemble model-a modelling tool developed for GBD to assess the out-of-sample predictive validity of different statistical models and covariate permutations and combine those results to produce cause-specific mortality estimates-with alternative strategies adapted to model causes with insufficient data, substantial changes in reporting over the study period, or unusual epidemiology. YLLs were computed as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2·5th and 97·5th percentiles from a 1000-draw distribution for each metric. We decomposed life expectancy by cause of death, location, and year to show cause-specific effects on life expectancy from 1990 to 2021. We also used the coefficient of variation and the fraction of population affected by 90% of deaths to highlight concentrations of mortality. Findings are reported in counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2021 include the expansion of under-5-years age group to include four new age groups, enhanced methods to account for stochastic variation of sparse data, and the inclusion of COVID-19 and other pandemic-related mortality-which includes excess mortality associated with the pandemic, excluding COVID-19, lower respiratory infections, measles, malaria, and pertussis. For this analysis, 199 new country-years of vital registration cause-of-death data, 5 country-years of surveillance data, 21 country-years of verbal autopsy data, and 94 country-years of other data types were added to those used in previous GBD rounds. FINDINGS The leading causes of age-standardised deaths globally were the same in 2019 as they were in 1990; in descending order, these were, ischaemic heart disease, stroke, chronic obstructive pulmonary disease, and lower respiratory infections. In 2021, however, COVID-19 replaced stroke as the second-leading age-standardised cause of death, with 94·0 deaths (95% UI 89·2-100·0) per 100 000 population. The COVID-19 pandemic shifted the rankings of the leading five causes, lowering stroke to the third-leading and chronic obstructive pulmonary disease to the fourth-leading position. In 2021, the highest age-standardised death rates from COVID-19 occurred in sub-Saharan Africa (271·0 deaths [250·1-290·7] per 100 000 population) and Latin America and the Caribbean (195·4 deaths [182·1-211·4] per 100 000 population). The lowest age-standardised death rates from COVID-19 were in the high-income super-region (48·1 deaths [47·4-48·8] per 100 000 population) and southeast Asia, east Asia, and Oceania (23·2 deaths [16·3-37·2] per 100 000 population). Globally, life expectancy steadily improved between 1990 and 2019 for 18 of the 22 investigated causes. Decomposition of global and regional life expectancy showed the positive effect that reductions in deaths from enteric infections, lower respiratory infections, stroke, and neonatal deaths, among others have contributed to improved survival over the study period. However, a net reduction of 1·6 years occurred in global life expectancy between 2019 and 2021, primarily due to increased death rates from COVID-19 and other pandemic-related mortality. Life expectancy was highly variable between super-regions over the study period, with southeast Asia, east Asia, and Oceania gaining 8·3 years (6·7-9·9) overall, while having the smallest reduction in life expectancy due to COVID-19 (0·4 years). The largest reduction in life expectancy due to COVID-19 occurred in Latin America and the Caribbean (3·6 years). Additionally, 53 of the 288 causes of death were highly concentrated in locations with less than 50% of the global population as of 2021, and these causes of death became progressively more concentrated since 1990, when only 44 causes showed this pattern. The concentration phenomenon is discussed heuristically with respect to enteric and lower respiratory infections, malaria, HIV/AIDS, neonatal disorders, tuberculosis, and measles. INTERPRETATION Long-standing gains in life expectancy and reductions in many of the leading causes of death have been disrupted by the COVID-19 pandemic, the adverse effects of which were spread unevenly among populations. Despite the pandemic, there has been continued progress in combatting several notable causes of death, leading to improved global life expectancy over the study period. Each of the seven GBD super-regions showed an overall improvement from 1990 and 2021, obscuring the negative effect in the years of the pandemic. Additionally, our findings regarding regional variation in causes of death driving increases in life expectancy hold clear policy utility. Analyses of shifting mortality trends reveal that several causes, once widespread globally, are now increasingly concentrated geographically. These changes in mortality concentration, alongside further investigation of changing risks, interventions, and relevant policy, present an important opportunity to deepen our understanding of mortality-reduction strategies. Examining patterns in mortality concentration might reveal areas where successful public health interventions have been implemented. Translating these successes to locations where certain causes of death remain entrenched can inform policies that work to improve life expectancy for people everywhere. FUNDING Bill & Melinda Gates Foundation

Quantitative Data Visualization in Compartmented Force-Directed Graphs using Calibrated Columns

Networks are commonly used to represent data and relationships. However, when mapping nodes to quantitative data, it is often difficult to accurately identify both the values of individual nodes and the overall relationships among nodes. Simultaneous group detection and precise quantitative data reading are necessary for scientists interpreting critical data. Here, we hypothesize that the calibrated columns method for encoding large-range quantitative values will provide a more accurate reading of data values than the common approach of variable-area circles. We also hypothesize that the addition of subtle halos around nodes will support accurate grouping of spatially distributed nodes in a network. We have conducted a pilot study with seven critical tasks in order to understand quantitative data reading and group inferencing in networks having up to three-levels of complexity. Our results show that (1) network size has a significant effect on confidence levels in grouping tasks; (2) the grouping encodings do not have a significant effect on confidence levels, but do significantly affect accuracy in the overall task; (3) the quantitative data encodings do not have a significant effect on confidence levels, but do significantly affect accuracy when determining exact node values; and (4) the colored halos and calibrated columns encodings are particularly useful in tasks involving both precise and global perception of the network. This work has contributed to understanding effective construction of quantitative networks and their groupings and our results suggest design guidelines broadly applicable to inform visualization design in domains such as biology and the social sciences

New anti-infective compounds against Staphylococcus aureus

Owing to the development of antibiotic resistance in microorganisms, new anti-microbial and anti-infective agents are of dire need to keep these pathogens at bay. These agents are mainly derived from the pathogen (bacteria or fungi) itself or from different plant extracts. In our previous work, it was observed that Lipoprotein like lipoprotein (Lpl) is an essential virulence factor in Staphylococcus aureus. Lpl is membrane bound and encoded in a genomic island called νSaα. Lpl causes the invasion of S. aureus into the HaCaT keratinocyte cells through its interaction with Hsp90α receptor. Lpl1 administration also surges the murine kidney abscess - bacterial burden. Our aim was to identify peptides that can block Hsp90 and reduce the S.aureus pathogenicity caused by Lpl. Here, we show 2 small peptides, named L15 and its derivative, L13, both part of Lpl1 have anti-infective action towards Staphylococcus aureus. Pretreatment with L15 and L13 reduced the invasion of S. aureus USA300 into HaCaT keratinocytes, N/TERT-1 primary keratinocytes and S. aureus phagocytosis in human monocytes. The peptides were water soluble, non-cytotoxic and non-hemolytic at the tested concentrations. Dot blot studies showed that there is direct interaction of the peptides with Hsp90α. L15 and L13 significantly decreased lethality of S. aureus bacteremia in Galleria mellonella insect larvae model, but did not affect growth or hemolytic activity of S. aureus in vitro. In a mouse bacteremia model L15 was found to significantly decrease weight loss and lethality. In effect the small peptides showed the opposite effect from their mother protein, in terms of the invasion of S. aureus into host cell and mice bacteremia model. Although the molecular bases behind the protective effect of L15 remain unclear, in vitro data indicate that treatment with L15 or L13 and simultaneous infection with S. aureus significantly increase IL-6 production in host immune cells. Our findings highlight Hsp90-interacting peptides as potential anti-infective agents In a separate work, non-peptide, anti-microbial phytochemicals- Rhodomyrtone (Rom) and Polycyclic polyprenylated acylphloroglucinols (PPAP), capable of inhibiting S.aureus in vitro are described. A single point mutation at farR makes S.aureus resistant to Rom. The antibacterial activity of Rom was targeted towards the cell membrane by interacting with its phospatidylglycerol (PG). RomR mutants were seen to excrete far more PGs, thereby neutralizing the Rom before it reaches the cell membrane. PPAP, though very much active in vitro, failed to rescue G. mellonella larvae from S.aureus infection. The reason was found to be the neutralization of PPAPs by the serum albumin proteins found in the larval coelomic fluid. In silico docking studies showed that PPAP is binding to the Heme binding pocket of bovine serum albumin. On the other hand, PPAP was observed to have a beneficial but not fully protective effect in S. aureus septic arthritis mouse model