MyxoPortal: a database of myxobacterial genomic features.

Myxobacteria are predatory bacteria with antimicrobial activity, utilizing complex mechanisms to kill their prey and assimilate their macromolecules. Having large genomes encoding hundreds of secondary metabolites, hydrolytic enzymes and antimicrobial peptides, these organisms are widely studied for their antibiotic potential. MyxoPortal is a comprehensive genomic database hosting 262 genomes of myxobacterial strains. Datasets included provide genome annotations with gene locations, functions, amino acids and nucleotide sequences, allowing analysis of evolutionary and taxonomical relationships between strains and genes. Biosynthetic gene clusters are identified by AntiSMASH, and dbAMP-generated antimicrobial peptide sequences are included as a resource for novel antimicrobial discoveries, while curated datasets of CRISPR/Cas genes, regulatory protein sequences, and phage associated genes give useful insights into each strain's biological properties. MyxoPortal is an intuitive open-source database that brings together application-oriented genomic features that can be used in taxonomy, evolution, predation and antimicrobial research. MyxoPortal can be accessed at http://dicsoft1.physics.iisc.ac.in/MyxoPortal/. Database URL:  http://dicsoft1.physics.iisc.ac.in/MyxoPortal/. Graphical Abstract.

Impact of monsoon season rainfall spells on the ecosystem carbon exchanges of Himalayan Chir-Pine and Banj-Oak-dominated forests: a comparative assessment.

The Chir-Pine (Pinus roxburghii) and Banj-Oak (Quercus leucotrichophora)-dominated ecosystems of central Himalaya provide significant green services. However, responses of these ecosystems, with respect to ecosystem carbon flux variability, to changing microclimate are not yet studied. Since quantification of ecosystem responses to fluctuation in the microclimate, particularly rainfall, is expected to be beneficial for management of these ecosystems, this study aims (i) to quantify and compare amplitude of rainfall-induced change in the carbon fluxes of Chir-Pine and Banj-Oak-dominated ecosystems using wavelet methods, and (ii) to quantify and compare dissimilarities in the ecosystem exchanges due to varying rainfall spell and amount. Eddy covariance-based continuous daily micrometeorological and flux data, during the 2016-2017 monsoon seasons (total 244 days, 122 days of June-September), from two sites in Uttarakhand, India, are used for this purpose. We find that both Chir-Pine and Banj-Oak-dominated ecosystems are the sinks of carbon, and Chir-Pine-dominated ecosystem sequesters around 1.8 times higher carbon than the Banj-Oak. A systematic enhancement in the carbon assimilation of the Chir-Pine-dominated ecosystem is noted with increasing rainfall spell following a statistically significant power-law relationship. We have also identified a rainfall amount threshold for Chir-Pine and Banj-Oak-dominated ecosystems (10 ± 0.7 and 17 ± 1.2 mm, respectively) that resulted in highest ecosystem carbon assimilation in monsoon. The general inference of this study accentuates that Banj-Oak-dominated ecosystem is more sensitive to maximum rain within a spell whereas the Chir-Pine-dominated ecosystem is more responsive to increasing rainfall spell duration.

Structure of the hypothetical protein TTHA1873 from Thermus thermophilus.

The crystal structure of an uncharacterized hypothetical protein, TTHA1873 from Thermus thermophilus, has been determined by X-ray crystallography to a resolution of 1.78 Šusing the single-wavelength anomalous dispersion method. The protein crystallized as a dimer in two space groups: P43212 and P6122. Structural analysis of the hypothetical protein revealed that the overall fold of TTHA1873 has a ß-sandwich jelly-roll topology with nine ß-strands. TTHA1873 is a dimeric metal-binding protein that binds to two Ca2+ ions per chain, with one on the surface and the other stabilizing the dimeric interface of the two chains. A structural homology search indicates that the protein has moderate structural similarity to one domain of cell-surface proteins or agglutinin receptor proteins. Red blood cells showed visible agglutination at high concentrations of the hypothetical protein.

Dayara bugyal restoration model in the alpine and subalpine region of the Central Himalaya: a step toward minimizing the impacts.

Eco-restoration initiative work in the high altitude Dayara pastureland (3501 m) from the Indian Himalayan Region has been considered to be one of the successful field demonstration against both natural and anthropogenic degradation. The present study therefore attempts to assess the implications of entire eco-restoration model as practiced by Department of Forest, Government of Uttarakhand in 2019. Its assessment was done by calculating restoration success index by way of considering three categories, viz., direct management measure (M), environmental desirability (E) and socio-economic feasibility (SE) considering 22 individual variables. 'M' comprised both biotic and abiotic pressures. Grazing and tourism were biotic, while abiotic pressure was considered mainly soil erosion in alpine area due to topographic fragility. Above ground vegetation profile and below ground soil nutrient profile (N, P, K, pH and water holding capacity) were analyzed in 'E' component. In the last but not least, 'SE' was analyzed to assess the social acceptability of the local communities and stakeholders who are supposed to be ultimate beneficiary of alike interventions. Direct management measure was found with the variable index score of 0.8 indicating the higher score as compared to environmental desirability (0.56). Under direct management measure, grazing and tourists' carrying capacity of the area was analyzed with high management needs to call the region sustainable in terms of availability of bio-resources. The ecosystem index score was evaluated for the reference (81.94), treated (64.5) and untreated zones (52.03), wherein increasing profile of these values were found. The outcomes like improved vegetation profile in terms of total herb density, soil nutrient profile of the restored area along with soil pH (4.96) and water holding capacity (49.85%) were found to be restored significantly along with controlling 169.64 tonne year-1 soil erosion from draining. The assessment of grazing pattern of 118 migratory Cow Unit (CU) (76 horse/mule and 18 sheep/goat, already controlled), 318 local CU (30 horse/mule and 187 sheep/goat) were calculated and recommended to be controlled. Tourists' carrying capacity of 274 tourists per day and manual removal of Rumex nepalensis at the shepherd camping site were found to be worth to apply in the area. Use of biodegradable but locally sourced material and engaging local villagers in this endeavor were also found to be in harmony with SDG Goal 1 (no poverty). Therefore, the restoration and its evaluation model could have its future prospects to prove as a successful restoration practice. This restoration practice could not only be worth in high altitude degraded alpine pastures of the Indian Himalayan Region but also to other mountain alpine and sub-alpine ecosystems.

Unhealthy alcohol use independently associated with unfavorable TB treatment outcomes among Indian men.

BACKGROUND: Approximately 10% of incident TB cases worldwide are attributable to alcohol. However, evidence associating alcohol with unfavorable TB treatment outcomes is weak.METHODS: We prospectively evaluated men (≥18 years) with pulmonary TB in India for up to 24 months to investigate the association between alcohol use and treatment outcomes. Unhealthy alcohol use was defined as a score of ≥4 on the Alcohol Use Disorders Identification Test-Concise (AUDIT-C) scale at entry. Unfavorable TB treatment outcomes included failure, recurrence, and all-cause mortality, analyzed as composite and independent endpoints.RESULTS: Among 751 men, we identified unhealthy alcohol use in 302 (40%). Median age was 39 years (IQR 28-50); 415 (55%) were underweight (defined as a body mass index [BMI] <18.5 kg/m²); and 198 (26%) experienced an unfavorable outcome. Unhealthy alcohol use was an independent risk factor for the composite unfavorable outcome (adjusted incidence rate ratio [aIRR] 1.47, 95% CI 1.05-2.06; P = 0.03) and death (aIRR 1.90, 95% CI 1.08-3.34; P = 0.03), specifically. We found significant interaction between AUDIT-C and BMI; underweight men with unhealthy alcohol use had increased risk of unfavorable outcomes (aIRR 2.22, 95% CI 1.44-3.44; P < 0.001) compared to men with BMI ≥18.5 kg/m² and AUDIT-C <4.CONCLUSION: Unhealthy alcohol use was independently associated with unfavorable TB treatment outcomes, highlighting the need for integrating effective alcohol interventions into TB care.

Disassociation of ß1-α1-ß2 from the α2-α3 domain of prion protein (PrP) is a prerequisite for the conformational conversion of PrPC into PrPSc: Driven by the free energy landscape.

Misfolding of the cellular prion protein (PrPC) into ß-sheet-rich scrapie form (PrPSc) is associated with transmissible spongiform encephalopathies. A point mutation F198S is responsible for the development of a rare inherited Gerstmann-Straussler-Scheinker disease caused by the aggregation of PrPC. Thus, identification and the structural characterization of aggregation-prone regions are essential to delineate the conversion of PrPC to the disease-associated PrPSc upon F198S mutation. In the present study, molecular dynamics simulations on the wild-type PrP (WT-PrP) and its mutant were performed to explore the structural basis responsible for aggregation driven by the mutation. Secondary structure analysis revealed that the mutant exhibited a partial unfolding on α2 and the complete distortion in the 310-helix of the ß2-α2 loop. Remarkably, the ß2-α2 loop is in proximity to α3 attributed by the long-range hydrophobic interactions and such structural intimacy is not observed in the WT-PrP. Owing to this, the ß1-α1-ß2 regions have separated from α2-α3 domain resulting in the impairment on the hydrogen bond between α1 and α3. Thus, the present study provides a detailed structural description of the F198S mutant in line with previous experimental results and delivers insights into the structural basis responsible for the conversion of PrPC to the disease-associated PrPSc.

RepEx: A web server to extract sequence repeats from protein and DNA sequences.

Evolution builds up new genetic material from existing ones, not in random, but in highly ordered and eloquent patterns. Most of these sequence repeats are revelatory of valuable information contributing to areas of disease research and function of macromolecules, to name a few. In the age of next generation genome sequencing, rapid and efficient extraction of all unbiased sequence repeats from macromolecules is the need of the hour. In view of this reckoning, an online web-based computing server, RepEx, has been developed to extract and display all possible repeats for DNA and protein sequences. Apart from exact or identical repeats, the server has been designed adeptly to identify and extract degenerate, inverted, everted and mirror repeats from both DNA and protein sequences. The server has striking output displays, featuring interactive graphs and comprehensive output files. In addition, RepEx has been accoutered with an easy-to-use interface and search filters to facilitate a user-defined query or search and is freely available and accessible via the World Wide Web at http://bioserver2.physics.iisc.ac.in/RepEx/.

Glaucoma Pred: Glaucoma prediction based on Myocilin genotype and phenotype information.

Glaucoma is the second leading cause of blindness after cataract and is heterogeneous in nature. Employing a genetic approach for the detection of the diseased condition provides an advantage that the gene responsible for the disease can be identified by genetic test. The availability of predictive tests based on the published literature would provide a mechanism for early detection and treatment. The genotype and phenotype information could be a valuable source for predicting the risk of the disease. To this end, a web server has been developed, based on the genotype and phenotype of myocilin mutation, which were identified by familial linkage analysis and case studies. The proposed web server provides clinical data and severity index for a given mutation. The server has several useful options to help clinicians and researchers to identify individuals at a risk of developing the disease. Glaucoma Pred server is available at http://bioserver1.physics.iisc.ac.in/myocilin.

Predictive Analysis on Behavioural Risk Factor Surveillance System through Ensemble Classifiers and Clusters.

INTRODUCTION: The World Health Organization (WHO) has been asserting the importance of health care in today's world. The objective of this research is to find out the type of medication that needs to be provided to the people at early stages to prevent behavioural risk factors. The health department of United States has a great vision to improve the immune system of the people and has taken measures to do the same through a Behavioural Risk Factor Surveillance System (BRFSS). This research aims to prevent behavioural risk factors by predictive analysis using the above mentioned dataset from the Centres for Disease Control and Prevention (CDC). METHODOLOGY: The methods of ensemble classification and clustering is applied on the dataset, pre and post weighted classification, thereby classifying and prescribing the type of healthcare required for people exhibiting behaviours such as obesity, nutrition and physical activity. RESULTS AND DISCUSSION: This analyses help improve the quality of health of the citizens. In an extensive study, it was observed that the result obtained was 92.87% accurate.

Molecular docking and molecular dynamics simulations of fumarate hydratase and its mutant H235N complexed with pyromellitic acid and citrate.

Fumarase catalyzes the reversible, stereospecific hydration/dehydration of fumarate to L-malate during the Kreb's cycle. In the crystal structure of the tetrameric fumarase, it was found that some of the active site residues S145, T147, N188 G364 and H235 had water-mediated hydrogen bonding interactions with pyromellitic acid and citrate which help to the protonation state for the conversion of fumarate to malate. When His 235 is mutated with Asn (H235N), water-mediated interactions were lost due to the shifting of active site water molecule by 0.7 Å away. Molecular dynamics (MD) simulations were also carried out by NAMD and analyzed using Assisted Model Building with Energy Refinement (AMBER) program to better understand the conformational stability and other aspects during the binding of pyromellitic acid and citrate with native and mutant FH. The role of hydrogen bonds and hydrophobic interactions was also analyzed. The present study confirms that the H235N mutation has a major effect on the catalytic activity of fumarase which is evident from the biochemical studies.

New biochemical insight of conserved water molecules at catalytic and structural Zn2+ ions in human matrix metalloproteinase-I: a study by MD-simulation.

Human matrix metalloproteinase (MMP)-1 or collagenase-1 plays a significant role in embryonic development, tissue remodeling, and is also involved in several diseases like arthritis, metastasis, etc. Molecular dynamics simulation studies on hMMP-1 X-ray structures (PDB Id. 1CGE, 1CGF, 1CGL, 1HFC, and 2TCL) suggest that the three conserved water molecules (WH/1, WI, WS) are coordinated with catalytic zinc (ZnC), and one water molecule (W) is associated at structural zinc ion (ZnS). Transition of the coordination geometry around ZnC from tetrahedral to octahedral and tetrahedral to trigonal bipyramidal at ZnS are also observed during the dynamics. Recognition of two zinc ions through water mediated bridges (ZnC - WH (W1)…W2….H183 - ZnS) and stabilization of secondary coordination zone around the metal ions indicates the possibility of ZnC…ZnS coupled catalytic mechanism in hMMP-I. This study not only reveals a functionally important role of conserved water molecules in hMMP-I but also highlights the involvement of other non catalytic residues, such as S172 and D170 in the catalytic mechanism. The results obtained in this study could be relevant for importance of conserved water mediated recognition site of the sequence residue id. 202(RWTNNFREY)210, interaction of W(tryptophan)203 to zinc bound histidine, their influence on the water molecules that are involved in bridging between ZnC and ZnS, and structure-based design of specific hMMP inhibitors. Graphical abstract Water mediated recognition of structural and catalytic zinc ions of hMMP-1 structure (MD simulatated conformation).

Catecholamine-resistant hypotension and myocardial performance following patent ductus arteriosus ligation.

OBJECTIVE: We performed a multicenter study of preterm infants, who were about to undergo patent ductus arteriosus ligation, to determine whether echocardiographic indices of impaired myocardial performance were associated with subsequent development of catecholamine-resistant hypotension following ligation. STUDY DESIGN: A standardized treatment approach for hypotension was followed at each center. Infants were considered to have catecholamine-resistant hypotension if their dopamine infusion was > 15 µg kg(-1)min(-1). Echocardiograms and cortisol measurements were obtained between 6 and 14 h after the ligation (prior to the presence of catecholamine-resistant hypotension). RESULT: Forty-five infants were enrolled, 10 received catecholamines (6 were catecholamine-responsive and 4 developed catecholamine-resistant hypotension). Catecholamine-resistant hypotension was not associated with decreased preload, shortening fraction or ventricular output. Infants with catecholamine-resistant hypotension had significantly lower levels of systemic vascular resistance and postoperative cortisol concentration. CONCLUSION: We speculate that low cortisol levels and impaired vascular tone may have a more important role than impaired cardiac performance in post-ligation catecholamine-resistant hypotension.

Conserved water-mediated recognition and dynamics of NAD+ (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor.

Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in GMP biosynthesis pathway. Type I hIMPDH is expressed at lower levels in all cells, whereas type II is especially observed in acute myelogenous leukemia, chronic myelogenous leukemia cancer cells, and 10 ns simulation of the IMP-NAD(+) complex structures (PDB ID. 1B3O and 1JCN) have revealed the presence of a few conserved hydrophilic centers near carboxamide group of NAD(+). Three conserved water molecules (W1, W, and W1') in di-nucleotide binding pocket of enzyme have played a significant role in the recognition of carboxamide group (of NAD(+)) to D274 and H93 residues. Based on H-bonding interaction of conserved hydrophilic (water molecular) centers within IMP-NAD(+)-enzyme complexes and their recognition to NAD(+), some covalent modification at carboxamide group of di-nucleotide (NAD(+)) has been made by substituting the -CONH2group by -CONHNH2 (carboxyl hydrazide group) using water mimic inhibitor design protocol. The modeled structure of modified ligand may, though, be useful for the development of antileukemic agent or it could be act as better inhibitor for hIMPDH-II.

Reactivity of Cyclanols Towards Quinaldinium Fluorochromate Oxidation.

The kinetics of oxidation of cyclanols, viz., cyclohexanol, cyclopentanol, cycloheptanol and cyclooctanol by quinaldinium fluorochromate has been studied in aqueous acid medium at 313 K (±0.1 K). The cyclanols were converted to the corresponding cyclic ketones. The order of reaction was found to be one with respect to oxidant and fractional with respect to the substrate and hydrogen ion concentrations. Increase in the percentage of acetic acid increases the rate of reaction. The reaction mixture shows the absence of any free radicals in the reaction, which has ruled out the possibility of a one-electron transfer during the addition of acrylonitrile. The reaction has been studied at four different temperatures and the activation parameters were calculated. From the observed kinetic results a suitable mechanism was proposed. The relative reactivity order was found to be cyclohexanol < cyclopentanol < cycloheptanol < cyclooctanol. This was explained on the basis of I-strain theory.

RepEx: repeat extractor for biological sequences.

Genomic sequences are far from being random but are made up of systematically ordered and information rich patterns. These repeated sequence patterns have been vastly utilized for their fundamental importance in understanding the genome function and organization. To this end, a comprehensive toolkit, RepEx, has been developed which extracts repeat (inverted, everted and mirror) patterns from the given genome sequence(s) without any constraints. The toolkit can also be used to fetch the inverted repeats present in the protein sequence(s). Further, it is capable of extracting exact and degenerate repeats with a user defined spacer intervals. It is remarkably more precise and sensitive when compared to the existing tools. An example with comprehensive case studies and a performance evaluation of the proposed toolkit has been presented to authenticate its efficiency and accuracy.

Antibiofilm and quorum sensing inhibitory activity of Achyranthes aspera on cariogenic Streptococcus mutans: an in vitro and in silico study.

CONTEXT: Traditionally, many cultures use chewing sticks for oral hygiene maintenance. When properly used, these chewing sticks are found to be efficient due to the combined effect of mechanical cleaning, enhanced salivation and the antimicrobial action of leached out plant compounds. OBJECTIVE: Achyranthes aspera L. (Amaranthaceae), an ethanomedicinal herb was evaluated for its potential to inhibit growth and biofilm formation by cariogenic isolate Streptococcus mutans as an alternative means of caries management by quorum quenching (QQ). MATERIALS AND METHODS: Biofilm forming cariogenic isolates were isolated and their susceptibility to the petroleum ether, benzene, methanol, aqueous extracts of A. aspera was evaluated. Gas chromatography-mass spectrometry (GC-MS), phytochemical analyses and structure-based virtual screening for their quorum sensing (QS) inhibitory activities, drug-likeness and bioavailability were also carried out. RESULTS: The biofilm inhibition percentage obtained for methanol, benzene, petroleum ether and aqueous extracts (125 µg/mL) were ≤94%, ≤74%, ≤62% ≤42%, respectively. GC-MS analyses indicated 61 compounds, of which betulin recorded efficient interaction exhibiting comparable binding energy of -8.72 with S. mutans glycosyltransferase (GTF-SI) whereas 3,12-oleandione exhibited binding energy -5.92 with OmpR subfamily QS regulatory DNA-binding response regulator. Computer-assisted molecular descriptor and Lipinski's rule violation calculation uncovered the presence of more drug-like compounds. DISCUSSION AND CONCLUSION: Anticaries bioactive compounds of A. aspera with higher QS response regulator binding energy, low toxicity and optimal pharmacokinetic properties were revealed. These compounds with possible QQ ability hold the potential for use as anticaries drug leads and antibiofilm preventative medicine.

An algorithm to find all palindromic sequences in proteins.

A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.