INFECTION OF GASTRO-INTESTINAL TRACT BY SARS-CoV-2 AND ITS POTENTIAL FOR FAECAL-ORAL TRANSMISSION: A LITERATURE REVIEW

Context: SARS-CoV-2, has already affected more than 180 countries. 3,175,207 confirmed cases and 224,173 deaths due to the disease were reported worldwide till 1st May 2020. WHO has declared it a Public Health Emergency of International Concern. Aims: To present information from worldwide literature on infection of gastro-intestinal tract by SARS-CoV-2 and its potential for faecal-oral transmission. Material and Methods: Literature search was carried out using Google Scholar and PubMed in 3rd week of April, 2020. Search terms used were “SARS-CoV-2” or “COVID-19” or “New Coronavirus” or “Coronavirus” in title and “Transmission” or “Faecal” or “Oral” anywhere in the article. Studies from the year 2019 to 2020 published in “English” language were included in the search. Results: 15 studies were found relevant and were included in the review. Studies reported that SARS-CoV-2 infects and replicates in gastro-intestinal tract and manifests enteric symptoms. Viral RNA is excreted in stool. Fecal samples were found to be positive for the viral RNA for many days even after respiratory samples become negative. Virus has been detected in anal swabs and live virus could be successfully isolated from stool specimen. The virus was also reported to be viable in the environment for many days. Conclusions: SARS-CoV-2 can potentially be transmitted by faecal-oral route. The transmission can occur even after respiratory symptoms subside and respiratory tract samples test negative for the virus. Appropriate policy response is needed for awareness, testing, discharge and quarantine of patients to prevent spread of the disease. Keywords--SARS-CoV-2, Coronavirus Outbreak, COVID-19, New Coronaviru

Spatial and temporal variation of hydraulic conductivity and vegetation growth in green infrastructures using infiltrometer and visual technique

Hydraulic conductivity of a vegetated soil (i.e., mixed grass cover) is an important parameter governing the hydrological performance of green infrastructure (GI). This paper focuses on GI with mixed grass cover in the presence of trees. Due to shading effects (interception of radiant energy) of tree canopy, mixed grass cover in the vicinity of trees may not receive direct photosynthetically active radiation (PAR). This can hinder the growth rates resulting in the low grass cover (i.e., in density). The hydraulic conductivity and the performance of GI can be further affected. Several field studies were conducted to investigate hydraulic conductivity in different types of vegetated covers. However, any variation in growth and hydraulic conductivity of mixed grass cover in the vicinity of trees was rarely investigated. The objective of this study is to quantify spatial and temporal variation of vegetation growth and hydraulic conductivity in a mixed grass cover in the vicinity of a tree. Field monitoring of a mixed grass cover in the vicinity of a tree in a GI was conducted for about six months. Hydraulic conductivity tests were carried out using mini disk infiltrometer (MDI) at 149 locations in a selected site once every month. Vegetation density was quantified using image analysis and the images were captured by a DJI Phantom drone. The growth of mixed grass cover around tree vicinity (within 5 m radial distance) was found to be more uniform during months characterized by high rainfall depth. Spatial heterogeneity in both vegetation density and hydraulic conductivity is found to be more significant during a dry period than wet period. Variation of hydraulic conductivity with respect to the change in vegetation density is found to be significant in a wet period than dry period. It is also found that hydraulic conductivity is higher at the portions where shredded leaves are present. The obtained dynamic spatio-temporal relationship of soil, vegetation and atmospheric parameters can support the design of green infrastructures and contribute to a better understanding of the maintenance practices

Comparing the spatio-temporal variability of remotely sensed oceanographic parameters between the Arabian Sea and Bay of Bengal throughout a decade

The spatio-temporal variability of sea-surface temperature (SST), photosynthetically active radiation (PAR), chlorophyll-a (Chl-a), particulate organic carbon (POC) and particulate inorganic carbon (PIC) was evaluated in the Arabian Sea (ABS) and Bay of Bengal (BoB), from July 2002 to November 2014 by means of remotely sensed monthly composite Aqua MODIS level-3 data having a spatial resolution of 4.63 km. Throughout the time period under consideration, the surface waters of ABS (27.76 ± 1.12°C) were slightly cooler than BoB (28.93 ± 0.76°C); this was observed during all the seasons. On the contrary, the availability of PAR was higher in ABS (45.76 ± 3.41 mol m-2 d-1) compared to BoB (41.75 ± 3.75 mol m-2 d-1), and its spatial dynamics in the two basins was mainly regulated by cloud cover and turbidity of the water column. The magnitude and variability of Chl-a concentration were substantially higher in ABS (0.487 ± 0.984 mg m-3), compared to BoB (0.187 ± 0.243 mg m-3), and spatially higher values were observed near the coastal waters. Both POC and PIC exhibited higher magnitudes in ABS compared to BoB; however, the difference was substantially high in case of POC. None of the parameters showed any significant temporal trend during the 12-year span, except PIC, which exhibited a significant decreasing trend in ABS

Post-Kala-azar Dermal Leishmaniasis in Nepal: A Retrospective Cohort Study (2000–2010)

Post-kala-azar dermal leishmaniasis (PKDL) is a skin disorder seen in patients treated for Leishmania donovani visceral leishmaniasis (VL), a neglected tropical disease that is fatal if left untreated. In the Indian subcontinent, PKDL is seen in 5–10% of all past VL cases and is also reported in some without history of VL. As persons with PKDL do not feel sick, the disease has only cosmetic significance for the individual and treatment is rarely sought. However, PKDL lesions harbour parasites and therefore could represent a source of transmission, through the bite of female sand flies. Our study shows that the occurrence of PKDL in patients with past treated VL is low in Nepal compared to neighboring countries. Treatment of the original VL episode with SSG (sodium stibogluconate), inadequate treatment and treatment on ambulatory basis were significantly associated with PKDL. Though SSG has since been replaced by other drugs, counseling and supervision of adherence to the prescribed VL treatment is of vital importance to reduce risk of treatment failure and relapse as well as later development of PKDL. Policy makers should include surveillance and case management of PKDL in the VL elimination program

First documented cure of a suggestive exogenous reinfection in polymyositis with same but multidrug resistant M. tuberculosis

BACKGROUND: MDR Mycobacterium tuberculosis is the major cause of treatment failure in tuberculosis patients, especially in immunosuppressed. We described a young polymyositis patient on immunosuppressive therapy who was started with antituberculosis therapy as a susceptible strain of M. tuberculosis was isolated from a single cutaneous abscess in his neck and from regional lymph nodes. CASE PRESENTATION: He had non-reactive miliary tuberculosis and multiple cutaneous abscesses 6 months later with the same strain, which was resistant this time to 9 antituberculosis drugs. We described clinical presentation, radiological and laboratory work-up, treatment and follow-up as the patient was cured after 1.5 years with 6 antituberculosis drugs. CONCLUSION: To our knowledge, this is the first reported case where an immunosuppressed patient with suggestive exogenous reinfection within 6 months with the same but MDR strain of M. tuberculosis was cured. Intense management and regular follow up were important since the patient was a potent source of MDR M. tuberculosis infection and there was limited choice for therapy

A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling

<p>Abstract</p> <p>Background</p> <p>High-throughput DNA methylation arrays are likely to accelerate the pace of methylation biomarker discovery for a wide variety of diseases. A potential problem with a standard set of probes measuring the methylation status of CpG sites across the whole genome is that many sites may not show inter-individual methylation variation among the biosamples for the disease outcome being studied. Inclusion of these so-called "non-variable sites" will increase the risk of false discoveries and reduce statistical power to detect biologically relevant methylation markers.</p> <p>Results</p> <p>We propose a method to estimate the proportion of non-variable CpG sites and eliminate those sites from further analyses. Our method is illustrated using data obtained by hybridizing DNA extracted from the peripheral blood mononuclear cells of 311 samples to an array assaying 1505 CpG sites. Results showed that a large proportion of the CpG sites did not show inter-individual variation in methylation.</p> <p>Conclusions</p> <p>Our method resulted in a substantial improvement in association signals between methylation sites and outcome variables while controlling the false discovery rate at the same level.</p

Unraveling the Design Principle for Motif Organization in Signaling Networks

Cellular signaling networks display complex architecture. Defining the design principle of this architecture is crucial for our understanding of various biological processes. Using a mathematical model for three-node feed-forward loops, we identify that the organization of motifs in specific manner within the network serves as an important regulator of signal processing. Further, incorporating a systemic stochastic perturbation to the model we could propose a possible design principle, for higher-order organization of motifs into larger networks in order to achieve specific biological output. The design principle was then verified in a large, complex human cancer signaling network. Further analysis permitted us to classify signaling nodes of the network into robust and vulnerable nodes as a result of higher order motif organization. We show that distribution of these nodes within the network at strategic locations then provides for the range of features displayed by the signaling network

Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere

Background and aims: To form nitrogen-fixing nodules on pea roots, Rhizobium leguminosarum biovar viciae must be competitive in the rhizosphere. Our aim was to identify genes important for rhizosphere fitness. Methods: Signature-tagged mutants were screened using microarrays to identify mutants reduced for growth in pea rhizospheres. Candidate mutants were assessed relative to controls for growth in minimal medium, growth in pea rhizospheres and for infection of peas in mixed inoculants. Mutated genes were identified by DNA sequencing and confirmed by transduction. Results: Of 5508 signature-tagged mutants, microarrays implicated 50 as having decreased rhizosphere fitness. Growth tests identified six mutants with rhizosphere-specific phenotypes. The mutation in one of the genes (araE) was in an arabinose catabolism operon and blocked growth on arabinose. The mutation in another gene (pcaM), encoding a predicted solute binding protein for protocatechuate and hydroxybenzoate uptake, decreased growth on protocatechuate. Both mutants were decreased for nodule infection competitiveness with mixed inoculants, but nodulated peas normally when inoculated alone. Other mutants with similar phenotypes had mutations predicted to affect secondary metabolism. Conclusions: Catabolism of arabinose and protocatechuate in the pea rhizosphere is important for competitiveness of R.l. viciae. Other genes predicted to be involved in secondary metabolism are also important