Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation.

Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, nonsoil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring (Zodletone Spring) in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of 13 distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g., FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine learning approaches based on a set of 634 genes informative of social lifestyle predicted a nonsocial behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities but carried genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 million years ago (Mya) in response to the rise of soil as a distinct habitat on Earth. IMPORTANCE The phylum Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcota are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota have been encountered in a wide range of nonsoil, predominantly anaerobic habitats, and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remain unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA, that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity was confirmed through detailed comparative genomic analysis of 13 pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition. Our results highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcota has occurred in response to soil formation as a distinct habitat on Earth.

Endophytic strains of Trichoderma increase plants' photosynthetic capability.

The world faces two enormous challenges that can be met, at least in part and at low cost, by making certain changes in agricultural practices. There is need to produce enough food and fibre for a growing population in the face of adverse climatic trends, and to remove greenhouse gases to avert the worst consequences of global climate change. Improving photosynthetic efficiency of crop plants can help meet both challenges. Fortuitously, when crop plants' roots are colonized by certain root endophytic fungi in the genus Trichoderma, this induces up-regulation of genes and pigments that improve the plants' photosynthesis. Plants under physiological or environmental stress suffer losses in their photosynthetic capability through damage to photosystems and other cellular processes caused by reactive oxygen species (ROS). But certain Trichoderma strains activate biochemical pathways that reduce ROS to less harmful molecules. This and other mechanisms described here make plants more resistant to biotic and abiotic stresses. The net effect of these fungi's residence in plants is to induce greater shoot and root growth, increasing crop yields, which will raise future food production. Furthermore, if photosynthesis rates are increased, more CO2 will be extracted from the atmosphere, and enhanced plant root growth means that more sequestered C will be transferred to roots and stored in the soil. Reductions in global greenhouse gas levels can be accelerated by giving incentives for climate-friendly carbon farming and carbon cap-and-trade programmes that reward practices transferring carbon from the atmosphere into the soil, also enhancing soil fertility and agricultural production.

Establishing PCR Testing in Nepal for Covid-19: Challenges and Opportunities.

Polymerase chain reaction (PCR) invented by Kary Mullis (1983), has become the centrepiece of molecular detection of various infectious diseases including coronavirus disease 2019 (COVID-19). Many developing countries like Nepal faces various challenges and grab many future opportunities during and after establishment of molecular PCR laboratories throughout the country. This viewpoint describes the involvement of laboratory employees, development and adoption of new protocols or framework, deliberate partnership with national and international community is very efficient for the establishment of PCR laboratories. Beside this, continued alliance and nation leadership is crucial to generate a unified and sustainable PCR laboratory network in the country like Nepal. In future the established PCR laboratories can be utilized for the diagnosis of others pandemic diseases and can be used for multipurpose like in verification of infectious diseases; Oncology; Blood test; Genetic testing.

A Study of F Wave Latencies, Chronodispersion and Persistence in Healthy Medical Undergraduates at BPKIHS.

Background The F wave is a CMAP (compound muscle action potential) evoked by a supramaximal stimulation of a motor nerve. F waves are particularly useful for the diagnoses of polyneuropathies at a very early stage and proximal nerve lesions. F waves have a very high diagnostic role in neurophysiology; we would like to study different F wave parameters and effect of anthropometric variables on F wave parameters in normal healthy individuals. Objective To study the effect of anthropometric variables on F wave latencies, chronodispersion and persistence Method Healthy males (n=64) and females (n=26) medical students of BPKIHS with age 21.64±1.19 years were enrolled in the study. Anthropometric parameters and maximum and minimum F wave latencies, F persistence and chronodispersion of bilateral median, ulnar and tibial nerves were recorded in Neurophysiology Lab II of BPKIHS. Descriptive analysis was done for anthropometric and F wave parameters. Unpaired t test was applied for comparing anthropometric and F wave variables between males and females. Pearson correlation was applied between anthropometric variables and F wave parameters. Result Age, height and weight of the subjects were 21.64±1.19 years, 165.61±5.4 cms and 64.07±5.5 kg respectively. Minimum F wave latencies (ms) of right median, ulnar and tibial nerves were 24.09±1.95, 24.02±1.76 and 44.34±3.02 while on the left side were 23.92±1.96, 24.11±1.92 and 44.07±2.83 respectively. Anthropometric variables of male and females were statistically significant. Also, F wave latencies between groups were different which were statistically significant. F persistence was above 80% for all tested peripheral nerves. Height and weight showed a significant effect on F wave latencies (p<0.001). However, age did not show any significant effect on F wave parameters. Conclusion Males have prolonged latencies as compared to females. Height and weight showed a significant relationship with the F wave latencies of the tested peripheral nerves.

Surgical removal of traumatic herniation of buccal fat pad in young children.

Intraoral herniation of the buccal fat pad is traumatic lesion of oral cavity occurring in young children. It frequently presents as an expanding pedunculated mass of soft tissue emanating from the buccal mucosa following a minor trauma to the buccal soft tissues. This article aims to report an interesting and rare lesion, wherein a tiny traumatic perforation of the buccal mucosa and buccinator muscle forced a large portion of the buccal fat pad to extrude into the oral cavity in a young boy. Such a situation can alarm any clinician and reinforces the importance of careful history taking and thorough examination, before treating patients.

Measuring management training needs of hospital managers in Nepal.

INTRODUCTION: This is a study of hospital managers in Nepal, measuring their reported capability to undertake management tasks and explore their views about management development. METHODS: A questionnaire was administered through hospitals. Respondents were asked to rate a series of management tasks on a scale according to how important it was, for their role and their capability to perform it. These tasks were grouped into different factors. The sample included government hospital of each district and major private or hospitals run bu non-government organizations. RESULTS: A total of 31 hospitals were visited in 18 districts. Information was obtained from 103 managers from different professions. In most hospitals visited, overall management was provided by the doctors. Few had undergone some training to take on management responsibilities. All types of managers, regardless of profession or type of hospital, reported a 'competence gap'for each factor defined as the difference between reported importance and capability. Non-government managers consistently rated themselves as beingmore capable than government managers, but the difference was only significant when it concerned managing People. The need for a separate cadre of managers was supported by 85% of respondents but a majority of doctors (57%) felt that the best people to manage hospitals were doctors. CONCLUSIONS: Consistent with other studies from low income countries, there is an urgent need to provide different modalities of management developmentenabling hospital managers to improve their capabilities. There is widespread need of management training to be made available in Nepal.

Low-cost struvite production using source-separated urine in Nepal.

This research investigated the possibility of transferring phosphorus from human urine into a concentrated form that can be used as fertilizer in agriculture. The community of Siddhipur in Nepal was chosen as a research site, because there is a strong presence and acceptance of the urine-diverting dry toilets needed to collect urine separately at the source. Furthermore, because the mainly agricultural country is landlocked and depends on expensive, imported fertilizers, the need for nutrient security is high. We found that struvite (MgNH(4)PO(4)·6H(2)O) precipitation from urine is an efficient and simple approach to produce a granulated phosphorus fertilizer. Bittern, a waste stream from salt production, is a practical magnesium source for struvite production, but it has to be imported from India. Calculations show that magnesium oxide produced from locally available magnesite would be a cheaper magnesium source. A reactor with an external filtration system was capable of removing over 90% of phosphorus with a low magnesium dosage (1.1 mol Mg mol P), with coarse nylon filters (pore width up to 160±50 µm) and with only one hour total treatment time. A second reactor setup based on sedimentation only achieved 50% phosphate removal, even when flocculants were added. Given the current fertilizer prices, high volumes of urine must be processed, if struvite recovery should be financially sustainable. Therefore, it is important to optimize the process. Our calculations showed that collecting the struvite and calcium phosphate precipitated spontaneously due to urea hydrolysis could increase the overall phosphate recovery by at least 40%. The magnesium dosage can be optimized by estimating the phosphate concentration by measuring electrical conductivity. An important source of additional revenue could be the effluent of the struvite reactor. Further research should be aimed at finding methods and technologies to recover the nutrients from the effluent.

Genetic changes that correlate with the pine-oil disinfectant-reduced susceptibility mechanism of Staphylococcus aureus.

AIMS: To identify factors associated with the Staphylococcus aureus pine-oil disinfectant-reduced-susceptibility (PD(RS)) mechanism and to describe one possible PD(RS) model. METHODS AND RESULTS: Comparative genomic sequencing (CGS) and microarray analysis were utilized to detect mutations and transcriptome alterations that occur in a S. aureus PD(RS) mutant. Mutant analysis, antimicrobial gradient plates, growth studies and 3-hydroxy-3-methylglutaryl coenzyme A synthase assays were then performed to confirm the biological consequences of the 'omics' alterations detected in a PD(RS) mutant. CGS uncovered three mutations in a PD(RS) mutant in a(n): alcohol dehydrogenase (adh), catabolite control protein A (ccpA) and an NADPH-flavin oxidoreductase (frp). These mutations lead to increased growth rates; increased transcription of an NAD-dependent D-lactate dehydrogenase gene (ddh); and increased flux through the mevalonate pathway. PD(RS) mutants demonstrated reduced susceptibility to bacitracin and farnesol, and one PD(RS) mutant displayed upregulation of bacA, a bacitracin-resistance gene. Collectively, this evidence demonstrates altered undecaprenol metabolism in PD(RS) mutants. CONCLUSIONS: The PD(RS) mechanism proposed results from increased catabolic capabilities and increased flux through the mevalonate pathway as well as altered bactoprenol physiology. SIGNIFICANCE AND IMPACT OF THE STUDY: A novel mechanism that bacteria utilize to overcome the killing effects of PD formulations is proposed that is unique from the PD(RS) mechanism of the enterobacteraciae.

Oral cleanliness of 12-13-year-old and 15-year-old school children of Sunsari District, Nepal.

The aim of the study was to evaluate the oral cleanliness of school children in the District of Sunsari, Nepal. A multi-stage random sampling oral epidemiological survey was conducted in private and government, urban, rural town and rural village schools in 15 illakas of Sunsari District, Eastern Nepal. A total of 600, 12-13-year-old and 600 15-year-old school children were examined by trained examiners using the simplified oral hygiene index (OHI-S). The average age-group, debris and calculus index scores were combined to obtain the simplified oral hygiene index (OHI-S). The mean OHI-S scores were compared and evaluated using the parametric t-test for two independent samples. The mean OHI-S for urban 12-13-year-old school children was 0.98 compared to 1.34 for school children of rural towns and 1.44 for school children of rural villages and these differences in mean OHI-S were statistically significant (P < 0.005). In the 15-year-old age group, urban school children had a mean OHI-S score of 1.00 compared to 1.37 for rural towns and 1.43 for rural villages. The variance in the mean OHI-S scores were statistically significant (P < 0.005). The overall level of cleanliness in the school children surveyed was good. Children of urban schools had the lowest scores followed by school children from rural towns and then rural villages. When the mean OHI-S scores were compared with the DMFT scores, there was an inverse relationship between oral cleanliness and dental caries. Frequency of sugar consumption and the availability and affordability of fluoridated toothpaste may be important factors in the development of dental caries than oral cleanliness.