Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses.
ABSTRACT: Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.
Project description:The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.
Project description:Polysomnographic investigation of sleep architecture in children presenting with pediatric acute-onset neuropsychiatric syndrome (PANS).Fifteen consecutive subjects meeting criteria for PANS (mean age = 7.2 y; range 3-10 y) underwent single-night full polysomnography (PSG) read by a pediatric neurologist.Thirteen of 15 subjects (87%) had abnormalities detected with PSG. Twelve of 15 had evidence of rapid eye movement (REM) sleep motor disinhibition, as characterized by excessive movement, laughing, hand stereotypies, moaning, or the continuation of periodic limb movements during sleep (PLMS) into REM sleep.This study shows various forms of REM sleep motor disinhibition present in a population of children with PANS.
Project description:Sudden onset clinically significant eating restrictions are a defining feature of the clinical presentation of some of the cases of pediatric acute-onset neuropsychiatric syndrome (PANS). Restrictions in food intake are typically fueled by contamination fears; fears of choking, vomiting, or swallowing; and/or sensory issues, such as texture, taste, or olfactory concerns. However, body image distortions may also be present. We investigate the clinical presentation of PANS disordered eating and compare it with that of other eating disorders.We describe 29 patients who met diagnostic criteria for PANS. Most also exhibited evidence that the symptoms might be sequelae of infections with Group A streptococcal bacteria (the pediatric autoimmune neuropsychiatric disorder associated with streptococcal infections [PANDAS] subgroup of PANS).The clinical presentations are remarkable for a male predominance (2:1?M:F), young age of the affected children (mean=9 years; range 5-12 years), acuity of symptom onset, and comorbid neuropsychiatric symptoms.The food refusal associated with PANS is compared with symptoms listed for the new Diagnostic and Statistical Manual of Mental Disorders, 5th ed. (DSM-V) diagnosis of avoidant/restrictive food intake disorder (ARFID). Treatment implications are discussed, as well as directions for further research.
Project description:Soda lakes and pans represent saline ecosystems with unique chemical composition, occurring on all continents. The purpose of this study was to identify and characterise the main environmental gradients and trophic state that prevail in the soda pans (n=84) of the Carpathian Basin in Central Europe. Underwater light conditions, dissolved organic matter, phosphorus and chlorophyll a were investigated in 84 pans during 2009-2010. Besides, water temperature was measured hourly with an automatic sensor throughout one year in a selected pan. The pans were very shallow (median depth: 15 cm), and their extremely high turbidity (Secchi depth median: 3 cm, min: 0.5 cm) was caused by high concentrations of inorganic suspended solids (median: 0.4 g L-1, max: 16 g L-1), which was the dominant (>50%) contributing factor to the vertical attenuation coefficient in 67 pans (80%). All pans were polyhumic (median DOC: 47 mg L-1), and total phosphorus concentration was also extremely high (median: 2 mg L-1, max: 32 mg L-1). The daily water temperature maximum (44 °C) and fluctuation maximum (28 °C) were extremely high during summertime. The combination of environmental boundaries: shallowness, daily water temperature fluctuation, intermittent hydroperiod, high turbidity, polyhumic organic carbon concentration, high alkalinity and hypertrophy represent a unique extreme aquatic ecosystem.
Project description:Objectives:To establish the psychometric properties of the Caregiver Burden Inventory (CBI) in patients with Pediatric Acute-onset Neuropsychiatric Syndrome (PANS), which is characterized by the abrupt onset of obsessive-compulsive disorder and/or restricted eating and at least two additional psychiatric symptoms. Parents of patients with PANS have reported high caregiver burden. However, no validated instrument of burden exists for this population. Methods:Study took place at a community-based PANS clinic where the CBI is administered as part of routine clinical care. The first CBI available during an active disease flare was analyzed (N?=104). Construct validity was evaluated within a confirmatory factor analytic framework. Associations between the CBI and patient/family characteristics were explored, and preliminary normative data for this population are presented. Results:Item-factor loadings were strong, and the overall fit of the model was good (root mean square error of approximation?=?.061). Strict/metric measurement invariance was demonstrated across age. The mean Total Score in this sample was 36.72?±?19.84 (interquartile range 19-53). Total Scores on the CBI were significantly elevated for parents of children who switched schools because of their illness (Cohen's d?=?0.75, 95% confidence interval [CI] 0.28-1.22) and for those who had reduced work hours to accommodate the child's illness (Cohen's d?=?0.65, 95% CI 0.10-1.20). However, in this relatively high-status sample, socioeconomic variables did not predict Total Scores. Conclusions:Parents of patients with PANS experience high caregiver burden. The CBI may be confidently used to assess caregiver burden in this population.
Project description:Traditional salt farming in Goa, India has been practised for the past 1,500?years by a few communities. Goa's riverine estuaries, easy access to sea water and favourable climatic conditions makes salt production attractive during summer. Salt produced through this natural evaporation process also played an important role in the economy of Goa even during the Portuguese rule as salt was the chief export commodity. In the past there were 36 villages involved in salt production, which is now reduced to 9. Low income, lack of skilled labour, competition from industrially produced salt, losses incurred on the yearly damage of embankments are the major reasons responsible for the reduction in the number of salt pans.Salt pans (Mithagar or Mithache agor) form a part of the reclaimed waterlogged khazan lands, which are also utilised for aquaculture, pisciculture and agriculture. Salt pans in Goa experience three phases namely, the ceased phase during monsoon period of June to October, preparatory phase from December to January, and salt harvesting phase, from February to June. After the monsoons, the salt pans are prepared manually for salt production. During high tide, an influx of sea water occurs, which enters the reservoir pans through sluice gates. The sea water after 1-2?days on attaining a salinity of approximately 5ºBé, is released into the evaporator pans and kept till it attains a salinity of 23 - 25ºBé. The brine is then released to crystallizer pans, where the salt crystallises out 25 - 27ºBé and is then harvested.Salt pans form a unique ecosystem where succession of different organisms with varying environmental conditions occurs. Organisms ranging from bacteria, archaea to fungi, algae, etc., are known to colonise salt pans and may influence the quality of salt produced.The aim of this review is to describe salt farming in Goa's history, importance of salt production as a community activity, traditional method of salt production and the biota associated with salt pans.
Project description:STUDY OBJECTIVES:A major component of pediatric acute-onset neuropsychiatric syndrome (PANS) is disruption of sleep. These disturbances have been reported in the acute phase of diagnosis but it is unknown if these sleep disruptions persist, especially in patients with chronic static symptoms. This retrospective chart review sought to review polysomnography (PSG) tests of patients in whom PANS has been clinically diagnosed in order to assess sleep architecture, periodic limb movements, and presence of rapid eye movement (REM) sleep without atonia (RSWA) after a chronic static course of symptoms, which were refractory to immunomodulatory interventions. METHODS:Patients were retrospectively identified through the PANS clinic at our institution and had to have fully completed a PSG study and be younger than 18 years. PSG with video were reviewed and scored based on established criteria. RESULTS:We identified 9 patients who met inclusion criteria. The median time from presentation to PSG was 4 years. This study identified PSG-measured periodic limb movement index (PLMI) > 5 events/h in REM sleep in 7 of 9 patients. Two patients with elevated PLMI also demonstrated RSWA, although neither fit a clinical diagnosis of REM sleep behavior disorder. This cohort also demonstrated increased onset of REM sleep (median 134 minutes), insomnia (median total sleep time of 389 minutes), and decreased sleep efficiency (77%). CONCLUSIONS:This study identifies continued sleep disturbances in patients with refractory PANS symptoms several years after diagnosis and treatment. Continued sleep disturbances after presentation and treatment in patients with chronic static PANS may be a contributing factor in prolonged symptomatology of this disease process.
Project description:Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genus Diporeia and the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived from Diporeia were compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 106 genome copies organism-1). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, ?-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential infection.
Project description:The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein-protein or viral-host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles.
Project description:Astatic soda pans of the Pannonian Steppe are unique environments with respect to their multiple extreme physical and chemical characteristics (high daily water temperature fluctuation, high turbidity, alkaline pH, salinity, polyhumic organic carbon concentration, hypertrophic state and special ionic composition). However, little is known about the seasonal dynamics of the bacterial communities inhabiting these lakes and the role of environmental factors that have the main impact on their structure. Therefore, two soda pans were sampled monthly between April 2013 and July 2014 to reveal changes in the planktonic community. By late spring in both years, a sudden shift in the community structure was observed, the previous algae-associated bacterial communities had collapsed, resulting the highest ratio of Actinobacteria within the bacterioplankton (89%, with the dominance of acIII-A1 lineage) ever reported in the literature. Before these peaks, an extremely high abundance (>?10,000 individuum l-1) of microcrustaceans (Moina brachiata and Arctodiaptomus spinosus) was observed. OTU-based statistical approaches showed that in addition to algal blooms and water-level fluctuations, zooplankton densities had the strongest effect on the composition of bacterial communities. In these extreme environments, this implies a surprisingly strong, community-shaping top-down role of microcrustacean grazers.