Capturing chromosome conformation in Crenarchaea.

While there is a considerable body of knowledge regarding the molecular and structural biology and biochemistry of archaeal information processing machineries, far less is known about the nature of the substrate for these machineries-the archaeal nucleoid. In this article, we will describe recent advances in our understanding of the three-dimensional organization of the chromosomes of model organisms in the crenarchaeal phylum.

Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India.

The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis and quantification of infectious pathogens within a population before clinical cases emerge. In the present study, we aimed to assess the trend and dynamics of SARS-CoV-2 variants using a longitudinal approach. Our objective included early detection and monitoring of these variants to enhance our understanding of their prevalence and potential impact. To achieve our goals, we conducted real-time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing on 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) in Pune city, India, spanning from November 2021 to April 2022. Our comprehensive analysis identified 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2. Notably, fragments of Omicron variant were detected in WW samples prior to its first clinical detection in Botswana. Furthermore, we observed highly contagious sub-lineages of the Omicron variant, including BA.1 (~28%), BA.1.X (1.0-72%), BA.2 (1.0-18%), BA.2.X (1.0-97.4%) BA.2.12 (0.8-0.25%), BA.2.38 (0.8-1.0%), BA.2.75 (0.01-0.02%), BA.3 (0.09-6.3%), BA.4 (0.24-0.29%), and XBB (0.01-21.83%), with varying prevalence rates. Overall, the present study demonstrated the practicality of WBE in the early detection of SARS-CoV-2 variants, which could help track future outbreaks of SARS-CoV-2. Such approaches could be implicated in monitoring infectious agents before they appear in clinical cases.

Improving Documentation of Pain Reassessment after Pain Management Interventions in the NICU.

Background: Neonates exposed to painful procedures require pain assessment and reassessment using nonverbal scales. Nurses perform initial assessments routinely, but reassessment is variable. The goal was to increase pain reassessments in neonates with a previous score of 4 or higher within 60 minutes from 50% to 75% within 12 months. Methods: After identifying key drivers, we tested several interventions using the IHI's Model for Improvement. The outcome measure was the rate of reassessments within 1 hour after scoring ≥4 on the Neonatal Pain Agitation and Sedation Scale (N-PASS). Duration of time between scoring and intervention was documented. Interventions included electronic health record (EHR) changes, direct communication with bedside nurses through text messages and emails, in-person education, and a yearly competency module. The process measure was the number of messages/emails to staff. Sedation scores were the balancing measure. Results: Baseline compliance was 50% with significant variability. A centerline shift occurred after the first intervention. After the first four interventions in the following 3 months, a 29% total increase occurred. Overall time-lapse between reassessments decreased from 102 to 90 minutes. Overall sedation scores decreased from -2.5 during the baseline to -1.7 during the sustain period. The goal of 75% pain reassessments was achieved and sustained for two years. Conclusions: Automated tools such as the trigger report provided data that increased noncompliance visibility. Real-time and personalized reminders and education improved awareness and set the tone for culture change. Electronic health record reminders for reassessments and standardized annual education helped in sustaining change.

Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India.

Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.

Chromosome organization affects genome evolution in Sulfolobus archaea.

In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.

Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential.

Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected ~ 41% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97%), followed by archaea (1.67%), Eukaryota (0.63%), and viruses (0.7%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03190-7.

COVID-19 associated mucormycosis: evolving technologies for early and rapid diagnosis.

The post-coronavirus disease (COVID-19) mucormycosis is a deadly addition to the pandemic spectrum. Although it's a rare, aggressive, and opportunistic disease, the associated morbidity and mortality are significant. The complex interplay of factors aggravating CAM is uncontrolled diabetes, irrational and excessive use of antibiotics, steroids, and an impaired immune system. Recently, India has been witnessing a rapid surge in the cases of coronavirus disease-associated mucormycosis (CAM), since the second wave of COVID-19. The devastating and lethal implications of CAM had now become a matter of global attention. A delayed diagnosis is often associated with a poor prognosis. Therefore, the rapid and early diagnosis of infection would be life-saving. Prevention and effective management of mucormycosis depend upon its early and accurate diagnosis followed by a multimodal therapeutic approach. The current review summarizes an array of detection methods and highlights certain evolving technologies for early and rapid diagnosis of CAM. Furthermore, several potential management strategies have also been discussed, which would aid in tackling the neglected yet fatal crisis of mucormycosis associated with COVID-19.

Probiotics in the prophylaxis of COVID-19: something is better than nothing.

The new viral pandemic of COVID-19 is caused by a novel coronavirus (SARS-CoV-2) that has brought the world at another unprecedented crisis in terms of health and economy. The lack of specific therapeutics necessitates other strategies to prevent the spread of infection caused by this previously unknown viral etiological agent. Recent pieces of evidence have shown an association between COVID-19 disease and intestinal dysbiosis. Probiotics comprise living microbes that upon oral administration benefit human health by reshaping the composition of gut microbiota. The close kinship of the gastrointestinal and respiratory tract suggests why the dysfunction of one may incite illness in others. The emerging studies suggest the capability of probiotics to regulate immune responses in the respiratory system. The efficacy of probiotics has been studied previously on several respiratory tract viral infections. Therefore, the purpose of this review is to comprehend existing information on the gut mediated-pulmonary immunity conferred by probiotic bacteria, in the course of respiratory virus infections and administration as a prophylactic measure in COVID-19 pandemic in managing intestinal dysbiosis as well.

Biosensors: frontiers in rapid detection of COVID-19.

The rapid community-spread of novel human coronavirus 2019 (nCOVID19 or SARS-Cov2) and morbidity statistics has put forth an unprecedented urge for rapid diagnostics for quick and sensitive detection followed by contact tracing and containment strategies, especially when no vaccine or therapeutics are known. Currently, quantitative real-time polymerase chain reaction (qRT-PCR) is being used widely to detect COVID-19 from various types of biological specimens, which is time-consuming, labor-intensive and may not be rapidly deployable in remote or resource-limited settings. This might lead to hindrance in acquiring realistic data of infectivity and community spread of SARS-CoV-2 in the population. This review summarizes the existing status of current diagnostic methods, their possible limitations, and the advantages of biosensor-based diagnostics over the conventional ones for the detection of SARS-Cov-2. Novel biosensors used to detect RNA-viruses include CRISPR-Cas9 based paper strip, nucleic-acid based, aptamer-based, antigen-Au/Ag nanoparticles-based electrochemical biosensor, optical biosensor, and Surface Plasmon Resonance. These could be effective tools for rapid, authentic, portable, and more promising diagnosis in the current pandemic that has affected the world economies and humanity. Present challenges and future perspectives of developing robust biosensors devices for rapid, scalable, and sensitive detection and management of COVID-19 are presented in light of the test-test-test theme of the World Health Organization (WHO).

Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities.

River confluences are interesting ecological niche with limited information in respect of the structure and the functions of diverse microbial communities. Fungi are gaining global attention as promising biological spectacles for defining the trophic status of riverine systems. We condense existing knowledge in confluence diversity in two Indian rivers (i.e. Ganges and Yamuna), by combining sediment metagenomics using long read aided MinION nanopore sequencing. A total of 63 OTU's were observed, of which top 20 OTU's were considered based on relative abundance of each OTU at a particular location. Fungal genera such as Aspergillus, Penicillium, Kluveromyces, Lodderomyces, and Nakaseomyces were deciphered as potential bio indicators of river pollution and eutrophication in the confluent zone. In silico functional gene analysis uncovered hits for neurodegenerative diseases and xenobiotic degradation potential, supporting bioindication of river pollution in wake of anthropogenic intervention.

Physical and Functional Compartmentalization of Archaeal Chromosomes.

The three-dimensional organization of chromosomes can have a profound impact on their replication and expression. The chromosomes of higher eukaryotes possess discrete compartments that are characterized by differing transcriptional activities. Contrastingly, most bacterial chromosomes have simpler organization with local domains, the boundaries of which are influenced by gene expression. Numerous studies have revealed that the higher-order architectures of bacterial and eukaryotic chromosomes are dependent on the actions of structural maintenance of chromosomes (SMC) superfamily protein complexes, in particular, the near-universal condensin complex. Intriguingly, however, many archaea, including members of the genus Sulfolobus do not encode canonical condensin. We describe chromosome conformation capture experiments on Sulfolobus species. These reveal the presence of distinct domains along Sulfolobus chromosomes that undergo discrete and specific higher-order interactions, thus defining two compartment types. We observe causal linkages between compartment identity, gene expression, and binding of a hitherto uncharacterized SMC superfamily protein that we term "coalescin."

A novel Sphingobacterium sp. RB, a rhizosphere isolate degrading para-nitrophenol with substrate specificity towards nitrotoluenes and nitroanilines.

Sphingobacterium sp. RB, a novel bacterial strain isolated from a soil sample, was able to utilize para-nitrophenol (PNP) as sole source of carbon and energy at high concentrations (1.0-5.0 mM). The culture completely degraded 3.0 mM PNP within 36 h with proportionate increase in biomass. With 5.0 mM PNP (700 ppm), 70% degradation was observed within 72 h of incubation. Scanning electron microscope images of the isolate in the presence and absence of PNP showed no significant morphological variations. Liquid chromatography-mass spectrometry analysis indicated that the biodegradation of PNP in this bacterium proceeded via the formation of 1,2,4-benzenetriol. Cells previously exposed to PNP (induced) were 30% more effective in degrading PNP. With catechol and phenol, such induction was not observed. Uninduced cells of Sphingobacterium sp. RB were capable of degrading a variety of other nitroaromatic compounds, including 2-nitroaniline, 2,4-dinitroaniline, 2-nitrotoluene, 3-nitrotoluene and 2,4-dinitrophenol, within 72 h, thus proving its candidacy as a potent bioremediation agent. To the best of our knowledge, this is the first report on a Sphingobacterium species degrading PNP via formation of 1,2,4-benzenetriol.

Analysis of the Archaeal ESCRT Apparatus.

Members of the archaeal domain of life that lack homologs of actin and tubulin divide by binary fission in a process that is dependent upon orthologs of eukaryotic ESCRT components. Many of these archaeal organisms are hyperthermophilic acidophiles with unique cell wall structures, which create technical challenges for performing traditional cell biological techniques. Here, we describe the "baby machine" method for synchronizing microorganisms at high temperatures in order to study cell cycle-related processes. We also provide details for fixing, permeabilizing, and staining archaeal cells and ESCRT assemblies for observation by light microscopy.

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges.

River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy river of India with great mythological history and religious significance. The Yamuna River meets Ganges at the Prayagraj (formerly known as Allahabad), India to form a unique confluence. The influence of Yamuna River on taxonomic and functional aspects of microbiome at this confluence and its downstream, remains unexplored. To unveil this dearth, whole metagenome sequencing of the microbial (bacterial and archaeal) community from the sediment samples of December 2017 sampling expedition was executed using high throughput MinION technology. Results revealed differences in the relative abundance of bacterial and archaeal communities across the confluence. Grouped by the confluence, a higher abundance of Proteobacteria and lower abundance of Bacteroidetes and Firmicutes was observed for Yamuna River (G15Y) and at immediate downstream of confluence of Ganges (G15DS), as compared to the upstream, confluence, and farther downstream of confluence. A similar trend was observed for archaeal communities with a higher abundance of Euryarchaeota in G15Y and G15DS, indicating Yamuna River's influence. Functional gene(s) analysis revealed the influence of Yamuna River on xenobiotic degradation, resistance to toxic compounds, and antibiotic resistance interceded by the autochthonous microbes at the confluence and succeeding downstream locations. Overall, similar taxonomic and functional profiles of microbial communities before confluence (upstream of Ganges) and farther downstream of confluence, suggested a transient influence of Yamuna River. Our study is significant since it may be foundational basis to understand impact of Yamuna River and also rare event of mass bathing on the microbiome of River Ganges. Further investigation would be required to understand, the underlying cause behind the restoration of microbial profiles post-confluence farther zone, to unravel the rejuvenation aspects of this unique ecosystem.

Emergence of ß-Band Oscillations in the Aged Rat Amygdala during Discrimination Learning and Decision Making Tasks.

Older adults tend to use strategies that differ from those used by young adults to solve decision-making tasks. MRI experiments suggest that altered strategy use during aging can be accompanied by a change in extent of activation of a given brain region, inter-hemispheric bilateralization or added brain structures. It has been suggested that these changes reflect compensation for less effective networks to enable optimal performance. One way that communication can be influenced within and between brain networks is through oscillatory events that help structure and synchronize incoming and outgoing information. It is unknown how aging impacts local oscillatory activity within the basolateral complex of the amygdala (BLA). The present study recorded local field potentials (LFPs) and single units in old and young rats during the performance of tasks that involve discrimination learning and probabilistic decision making. We found task- and age-specific increases in power selectively within the ß range (15-30 Hz). The increased ß power occurred after lever presses, as old animals reached the goal location. Periods of high-power ß developed over training days in the aged rats, and was greatest in early trials of a session. ß Power was also greater after pressing for the large reward option. These data suggest that aging of BLA networks results in strengthened synchrony of ß oscillations when older animals are learning or deciding between rewards of different size. Whether this increased synchrony reflects the neural basis of a compensatory strategy change of old animals in reward-based decision-making tasks, remains to be verified.

A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans.

Based on serial sectioning, focused ion beam scanning electron microscopy (FIB/SEM), and electron tomography, we depict in detail the highly unusual anatomy of the marine hyperthermophilic crenarchaeon, Ignicoccus hospitalis. Our data support a complex and dynamic endomembrane system consisting of cytoplasmic protrusions, and with secretory function. Moreover, we reveal that the cytoplasm of the putative archaeal ectoparasite Nanoarchaeum equitans can get in direct contact with this endomembrane system, complementing and explaining recent proteomic, transcriptomic and metabolomic data on this inter-archaeal relationship. In addition, we identified a matrix of filamentous structures and/or tethers in the voluminous inter-membrane compartment (IMC) of I. hospitalis, which might be responsible for membrane dynamics. Overall, this unusual cellular compartmentalization, ultrastructure and dynamics in an archaeon that belongs to the recently proposed TACK superphylum prompts speculation that the eukaryotic endomembrane system might originate from Archaea.

The Structure, Function and Roles of the Archaeal ESCRT Apparatus.

Although morphologically resembling bacteria, archaea constitute a distinct domain of life with a closer affiliation to eukaryotes than to bacteria. This similarity is seen in the machineries for a number of essential cellular processes, including DNA replication and gene transcription. Perhaps surprisingly, given their prokaryotic morphology, some archaea also possess a core cell division apparatus that is related to that involved in the final stages of membrane abscission in vertebrate cells, the ESCRT machinery.

Mechanism of Archaeal MCM Helicase Recruitment to DNA Replication Origins.

Cellular DNA replication origins direct the recruitment of replicative helicases via the action of initiator proteins belonging to the AAA+ superfamily of ATPases. Archaea have a simplified subset of the eukaryotic DNA replication machinery proteins and possess initiators that appear ancestral to both eukaryotic Orc1 and Cdc6. We have reconstituted origin-dependent recruitment of the homohexameric archaeal MCM in vitro with purified recombinant proteins. Using this system, we reveal that archaeal Orc1-1 fulfills both Orc1 and Cdc6 functions by binding to a replication origin and directly recruiting MCM helicase. We identify the interaction interface between these proteins and reveal how ATP binding by Orc1-1 modulates recruitment of MCM. Additionally, we provide evidence that an open-ring form of the archaeal MCM homohexamer is loaded at origins.

Age differences in strategy selection and risk preference during risk-based decision making.

Studies of the effects of aging on decision making suggest that choices can be altered in a variety of ways depending on the situation, the nature of the outcome and risk, or certainty levels. To better characterize how aging impacts decision making in rodents, young and aged Fischer 344 rats underwent a series of probabilistic discounting tasks in which reward magnitude and probabilities were manipulated. Young rats tended to choose 1 of 2 different strategies: (a) to press for the large/uncertain reward, regardless of the reward probability; or (b) to continually adapt their behavior according to the odds of winning. The first strategy was adopted by about half of the younger rats, the second by the remaining young animals and the entire group of aged rats. Additionally, we found that when the odds of winning were varied from uncertain to certain during a session, aged rats chose most often the lever associated with the small/certain reward. This is consistent with an interpretation of increased risk aversion. When this behavior was further characterized using a lose-shift analysis, it appears that older rats exhibited an increased sensitivity to negative feedback. In contrast, sensitivity to wins was unaltered in aged rats compared with young, suggesting that aging selectively impacts rat's behavior following losses. In line with some human aging studies, it appears that aged rats are either more risk averse or have a greater certainty bias, which may result from age differences in emotion regulation.