Opportunities and challenges for microbiomics in ecosystem restoration.

Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant-soil-microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.

Microbial carbon use efficiency promotes global soil carbon storage.

Soils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5-7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8-11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.

Morphoscanner2.0: A new python module for analysis of molecular dynamics simulations.

Molecular dynamics simulations, at different scales, have been exploited for investigating complex mechanisms ruling biologically inspired systems. Nonetheless, with recent advances and unprecedented achievements, the analysis of molecular dynamics simulations requires customized workflows. In 2018, we developed Morphoscanner to retrieve structural relations within self-assembling peptide systems. In particular, we conceived Morphoscanner for tracking the emergence of ß-structured domains in self-assembling peptide systems. Here, we introduce Morphoscanner2.0. Morphoscanner2.0 is an object-oriented library for structural and temporal analysis of atomistic and coarse-grained molecular dynamics (CG-MD) simulations written in Python. The library leverages MDAnalysis, PyTorch and NetworkX to perform the pattern recognition of secondary structure patterns, and interfaces with Pandas, Numpy and Matplotlib to make the results accessible to the user. We used Morphoscanner2.0 on both simulation trajectories and protein structures. Because of its dependencies on the MDAnalysis package, Morphoscanner2.0 can read several file formats generated by widely-used molecular simulation packages such as NAMD, Gromacs, OpenMM. Morphoscanner2.0 also includes a routine for tracking the alpha-helix domain formation.

In silico screening of phytochemical compounds and FDA drugs as potential inhibitors for NSP16/10 5' methyl transferase activity.

The recent global pandemic associated with the highly contagious novel coronavirus (SARS-CoV-2) has led to an unpredictable loss of life and economy worldwide, and the discovery of antiviral drugs is an urgent necessity. For the discovery of new drug leads and for the treatment of various diseases, natural products and purified photochemical from medicinal plants are used. The RNA cap was methylated by two S-adenosyl-L-methionine (SAM)-dependent methyltransferases of SARS coronavirus (SARS-CoV-2), catalyzed by NSP16 2'-O-Mtase. Natural substrate SAM, 128 Phytocompounds retrieved from the Phytocompounds database, and 11 standard FDA-approved HIV drugs reclaimed from the PubChem database are subjected to docking analysis. The docking study was done using AutoDock Vina. Further, admetSAR and DruLiTO servers are used to analyze the drug-likeness properties. The NSP16/10 structure and natural substrate SAM, Phytocompounds Withanolide (WTL), and HIV standard drug Dolutegravir (DLT) as hit compounds were identified by molecular dynamics using the Gromacs GPU-enabled package. To examine the effectiveness of the identified drugs versus COVID-19, further in vitro and in vivo studies are required. Communicated by Ramaswamy H. Sarma.

In silico studies disclose the underlying link between binding affinity and redox potential in laccase isoforms.

Laccases are copper-containing enzymes belonging to the family of multicopper oxidases (MCOs). All MCOs use molecular oxygen to oxidize a wide range of organic compounds by radical catalysis. One of the key fundamental properties of laccases is having high or low redox potentials depending on the active site organization. Several experimental studies have been done to rationalize the high and low redox potential laccases (LRPL), however, molecular understanding is still lacking. In this work, we explored the proteomic profile of laccases produced in the fungal cultures, specifically induced with lignocellulosic biomass such as rice straw. This study was undertaken to explain the differences in the high redox and low redox potential values of different laccases using in-silico approaches. Proteomic profiling and structural and sequence analysis revealed a low level of similarity among them. Docking analyses and molecular dynamics simulation analysis revealed that high redox potential laccases (HRPL) are having good binding affinity compared to low or medium redox potential laccases (MRPL). The stability of these complexes was further analyzed based on reactive distances, active site volume comparison and a number of tunnel formations that were observed to be significantly higher for HRPL. Our results indicate that the number of tunnel formations calculated from the simulation's trajectories and available water molecules at the T3 site directly correlates with the laccases' redox potentials. This study will be helpful and provide valuable inputs for the designing of new laccases to improve lignin degradation.Communicated by Ramaswamy H. Sarma.

Interfacial Water in the SARS Spike Protein: Investigating the Interaction with Human ACE2 Receptor and In Vitro Uptake in A549 Cells.

The severity of global pandemic due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has engaged the researchers and clinicians to find the key features triggering the viral infection to lung cells. By utilizing such crucial information, researchers and scientists try to combat the spread of the virus. Here, in this work, we performed in silico analysis of the protein-protein interactions between the receptor-binding domain (RBD) of the viral spike protein and the human angiotensin-converting enzyme 2 (hACE2) receptor to highlight the key alteration that happened from SARS-CoV to SARS-CoV-2. We analyzed and compared the molecular differences between spike proteins of the two viruses using various computational approaches such as binding affinity calculations, computational alanine, and molecular dynamics simulations. The binding affinity calculations showed that SARS-CoV-2 binds a little more firmly to the hACE2 receptor than SARS-CoV. The major finding obtained from molecular dynamics simulations was that the RBD-ACE2 interface is populated with water molecules and interacts strongly with both RBD and ACE2 interfacial residues during the simulation periods. The water-mediated hydrogen bond by the bridge water molecules is crucial for stabilizing the RBD and ACE2 domains. Near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) confirmed the presence of vapor and molecular water phases in the protein-protein interfacial domain, further validating the computationally predicted interfacial water molecules. In addition, we examined the role of interfacial water molecules in virus uptake by lung cell A549 by binding and maintaining the RBD/hACE2 complex at varying temperatures using nanourchins coated with spike proteins as pseudoviruses and fluorescence-activated cell sorting (FACS) as a quantitative approach. The structural and dynamical features presented here may serve as a guide for developing new drug molecules, vaccines, or antibodies to combat the COVID-19 pandemic.

Optimal management of perioperative analgesia regarding immediate and short-term outcomes after liver transplantation - A systematic review, meta-analysis and expert panel recommendations.

BACKGROUND: Adequate pain control is essential for patients undergoing liver transplantation (LT). Multiple analgesic strategies have been implemented during the perioperative period. There is no consensus on the optimal perioperative analgesia management. OBJECTIVES: To provide recommendations, on the optimal perioperative analgesia management for LT. DATA SOURCES: Ovid MEDLINE, Embase, Scopus, Google Scholar, and Cochrane Central. METHODS: A systematic review and meta-analysis following PRISMA guidelines and recommendations using GRADE. Studies describing outcomes, morbidity, mortality, pain scores, intensive care unit and hospital length of stay in patients that received different pain management techniques during and after LT were included (CRD42021243282). RESULTS: One thousand nine hundred ten articles were screened, but only two randomized controlled trials, one prospective and six retrospective studies were included. The opioid-avoidance protocols included, thoracic epidural analgesia (TEA), Transversus Abdominis Plane (TAP) block, as well as other non-opioid analgesics, resulted in improved short-term outcomes. Mortality was reduced in this group versus control cohorts (OR = 0.51; CI 0.14, 1.83; P = 0.350), Time to extubation, and intensive care unit LOS were shorter; pain scores after surgery were lower in opioid-avoidance group (percentage decrease, 35%, 12%, and 55%, respectively). However, hospital LOS was longer (percentage increase 8%). CONCLUSIONS: Opioid-avoidance analgesia management for LT results in improved short-term outcomes. (Quality of Evidence; Moderate to low | Grade of Recommendation; Weak). Medications such as acetaminophen(paracetamol), gabapentin, ketamine, tramadol and local anesthesia may be used instead of, or as adjuncts to opioids for postoperative analgesia. Overall evidence remains weak and more robust studies are required.

Knowledge hiding in organizational crisis: The moderating role of leadership.

The COVID-19 pandemic has caused organizational crises leading to shutdowns, mergers, downsizing or restructuring to minimize survival costs. In such organizational crises, employees tend to experience a loss or lack of resources, and they are more likely to engage in knowledge hiding to maintain their resources and competitive advantage. Knowledge hiding has often caused significant adverse consequences, and the research on knowledge hiding is limited. Drawing upon the Conservation of Resources and Transformational Leadership theories, a conceptual framework was developed to examine knowledge hiding behavior and its antecedents and consequences. We collected data from 281 Vietnamese employees working during the COVID-19 pandemic. Our results show that role conflict, job insecurity, and cynicism positively impact knowledge hiding behavior. Knowledge hiding behavior negatively affects job performance and mediates the antecedents of knowledge hiding on job performance. Transformational leadership moderated the impact of role conflict on knowledge hiding.

Towards a microbial process-based understanding of the resilience of peatland ecosystem service provisioning - A research agenda.

Peatlands are wetland ecosystems with great significance as natural habitats and as major global carbon stores. They have been subject to widespread exploitation and degradation with resulting losses in characteristic biota and ecosystem functions such as climate regulation. More recently, large-scale programmes have been established to restore peatland ecosystems and the various services they provide to society. Despite significant progress in peatland science and restoration practice, we lack a process-based understanding of how soil microbiota influence peatland functioning and mediate the resilience and recovery of ecosystem services, to perturbations associated with land use and climate change. We argue that there is a need to: in the short-term, characterise peatland microbial communities across a range of spatial and temporal scales and develop an improved understanding of the links between peatland habitat, ecological functions and microbial processes; in the medium term, define what a successfully restored 'target' peatland microbiome looks like for key carbon cycle related ecosystem services and develop microbial-based monitoring tools for assessing restoration needs; and in the longer term, to use this knowledge to influence restoration practices and assess progress on the trajectory towards 'intact' peatland status. Rapid advances in genetic characterisation of the structure and functions of microbial communities offer the potential for transformative progress in these areas, but the scale and speed of methodological and conceptual advances in studying ecosystem functions is a challenge for peatland scientists. Advances in this area require multidisciplinary collaborations between peatland scientists, data scientists and microbiologists and ultimately, collaboration with the modelling community. Developing a process-based understanding of the resilience and recovery of peatlands to perturbations, such as climate extremes, fires, and drainage, will be key to meeting climate targets and delivering ecosystem services cost effectively.

A Comparison of Reproductive Hormones and Biochemical Parameters in Hypothyroid and Euthyroid Postmenopausal Women.

BACKGROUND: Menopause and hypothyroidism, both individually, affect the reproductive hormone profile as well as body metabolism which is reflected in the form of a deranged biochemical profile. It will be interesting to observe the effects on both these profiles, when menopause is associated with hypothyroidism. METHODS: This study was conducted on 30 postmenopausal women with newly diagnosed primary hypothyroidism and 30 euthyroid menopausal females as controls. Serum samples of all the subjects were analyzed for complete thyroid profile including total T3 (TT3), total T4 (TT4), free T3 (FT3), free T4 (FT4), thyroid stimulating hormone (TSH), estradiol, progesterone, fasting glucose, renal function tests, liver function tests, and lipid profile. Data of both the groups was compared using Student's t-test. RESULTS: There was no statistically significant difference observed between the fasting glucose levels and renal and liver function tests in both the groups (p > 0.05). Serum triglycerides, total cholesterol, low density lipoprotein cholesterol (LDL-C) and very low density lipoprotein cholesterol (VLDL-C) were found to be significantly increased (p < 0.05) while high density lipoprotein cholesterol (HDL-C), estradiol, and progesterone were found to be significantly decreased (p < 0.05) in menopausal hypothyroid women as compared to their euthyroid counterparts. CONCLUSIONS: Thus, an association of both menopause and hypothyroidism may lead to accentuation of effect of each on biochemical and reproductive hormone profile.

Drought and plant litter chemistry alter microbial gene expression and metabolite production.

Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic and metabolomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems. We hypothesised that drought causes greater microbial allocation to stress tolerance relative to growth pathways. In grass litter, communities from the decade-long ambient and reduced precipitation treatments had distinct taxonomic and functional profiles. The most discernable physiological signatures of drought were production or uptake of compatible solutes to maintain cellular osmotic balance, and synthesis of capsular and extracellular polymeric substances as a mechanism to retain water. The results show a clear functional response to drought in grass litter communities with greater allocation to survival relative to growth that could affect decomposition under drought. In contrast, communities on chemically more diverse and complex shrub litter had smaller physiological differences in response to long-term drought but higher investment in resource acquisition traits across precipitation treatments, suggesting that the functional response to drought is constrained by substrate quality. Our findings suggest, for the first time in a field setting, a trade off between microbial drought stress tolerance, resource acquisition and growth traits in plant litter microbial communities.

Liver transplantation and COVID-19 (Coronavirus) infection: guidelines of the liver transplant Society of India (LTSI).

The Liver Transplant Society of India (LTSI) has come up with guidelines for transplant centres across the country to deal with liver transplantation during this evolving pandemic of COVID-19 infection. The guidelines are applicable to both deceased donor as well as living donor liver transplants. In view of the rapidly changing situation of COVID-19 infection in India and worldwide, these guidelines will need to be updated according to the emerging data.

Bio-sensing of organophosphorus pesticides: A review.

Organophosphorus (OP) pesticides have been used widely as agricultural and household pest control agents for almost five decades and persist in our water resources, fruits, vegetables and processed food as health and environmental hazardous compounds. Thus, detection of these harmful OP pesticides at an ease with high sensitivity and selectivity is the need of hour. Bio-sensing technology meet these requirements and has been employed at a large scale for detection. The present review is aimed mainly to provide the overview of the past and recent advances occurred in the field of biosensor technology employed for the detection of these OP compounds. The review describes the principle and strategy of various OP biosensors including electrochemical (amperometric, potentiometric), thermal, piezoelectric, optical (fluorescence, Surface Plasmon Resonance (SPR)), microbial and DNA biosensors in detail. The electrochemical biosensors are generally, based on inhibition of enzyme, acetyl cholinesterase (AChE), butyryl cholinesterase (BChE), tyrosinase and alkaline phosphatase or enzyme (organophosphorus hydrolase, OPH)) catalyzed reaction. The detection limits and linearity range of various OP biosensors have also been compared. AChE inhibition based amperometric OP biosensors exhibited the lowest detection limit of 1 × 10-11 µM with a linearity range of 1.0 × 10-11 - 1.0 × 10-2 µM.

Land use driven change in soil pH affects microbial carbon cycling processes.

Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates.

Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics.

Environmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where "low-pH" is ~pH 4.3 and "high-pH" is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category). Low-pH soils, also exhibiting higher organic matter and moisture, consistently had lower taxonomic alpha and gamma diversity, but this was not apparent in assessments of functional alpha and gamma diversity. However, coherent changes in the relative abundances of annotated genes between low- and high-pH soils were identified; with strong multivariate clustering of samples according to pH independent of geography. Assessment of indicator genes revealed that the acidic organic-rich soils possessed a greater abundance of cation efflux pumps, C and N direct fixation systems, and fermentation pathways, indicating adaptations to both acidity and anaerobiosis. Conversely, high-pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings highlight the distinctive physiological adaptations required for bacteria to survive in soils of various nutrient availability and edaphic conditions and more generally indicate that bacterial functional versatility with respect to functional gene annotations may not be constrained by taxonomy.IMPORTANCE Over a set of soil samples spanning Britain, the widely reported reductions in bacterial taxonomic richness at low pH were found not to be accompanied by significant reductions in the richness of functional genes. However, consistent changes in the abundance of related functional genes were observed, characteristic of differential ecological and nutrient acquisition strategies between high-pH mineral soils and low-pH organic anaerobic soils. Our assessment at opposing ends of a soil gradient encapsulates the limits of functional diversity in temperate climates and identifies key pathways that may serve as indicators for soil element cycling and C storage processes in other soil systems. To this end, we make available a data set identifying functional indicators of the different soils; as well as raw sequences, which given the geographic scale of our sampling should be of value in future studies assessing novel genetic diversity of a wide range of soil functional attributes.

Balancing cognitive diversity and mutual understanding in multidisciplinary teams.

BACKGROUND: Interprofessional health care teams are increasingly utilized in health care organizations. Although there is support for their capacity to solve complex problems, there is also evidence that such teams are not always successful. In an effort to understand the capacity of interprofessional teams to innovate successfully, we investigate the role of cognitive diversity to establish whether and how knowledge differences lead to innovation. PURPOSES: The aim of this study was to construct and investigate a model of team innovation predicted by cognitive diversity. In addition to investigating the direct impact of cognitive diversity in interprofessional health care teams, we develop a model incorporating mediated and moderated effects. In this study, we explore the role of debate as a mediating factor capable of explaining the impact of cognitive diversity on innovation. We further propose that the link between cognitive diversity and innovation through debate is contingent upon trans-specialist knowledge, knowledge shared by health care professionals, spanning specialist divides and enabling mutual understanding. METHODOLOGY: The hypotheses were investigated using a cross-sectional, correlational design. Survey data received from 75 interprofessional teams employed in an acute care setting, representing a 36% response rate, were used to investigate our model. FINDINGS: Analysis supports a significant relationship between cognitive diversity and debate, which is stronger when teams rate highly for trans-specialist knowledge. Results also support a positive relationship between debate and innovation and our full moderated mediated pathway. PRACTICE IMPLICATIONS: A range of strategies are indicated by our results to increase innovation in interprofessional teams. In particular, interventions such as interprofessional education and training, which have been shown to facilitate the development of shared language and meaning, are recommended by our findings.