Comparison of Real-time RT-PCR cycle threshold (Ct) values with clinical features and severity of COVID-19 disease among hospitalized patients in the first and second waves of COVID-19 pandemic in Chennai, India.

Introduction: Real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) of nasopharyngeal/ oropharyngeal swab has been the gold standard test for detection of SARS-CoV-2 infection The relationship between cycle threshold (Ct) values of rRT-PCR and severity of disease remain disputable and not clearly defined in COVID-19. Methodology: This is a single-centered retrospective observational study conducted at Government Corona Hospital (GCH), Guindy, Chennai. In the present study, we compared the Ct value of rRT-PCR from nasopharyngeal swab specimens with a diverse range of symptoms and disease severity among 240 individuals who were hospitalized with COVID-19, viz., mild cases (MC; n = 160), moderately severe cases (MSC; n = 46) and severe cases (SC; n = 34) in the first and second waves of COVID-19 pandemic. Results: The study included 240 hospitalized COVID-19 patients with a median age of 52 years (range 21 to 90 years). MC, MSC, and SC all had median Ct values of 25.0 (interquartile range - IQR 20.0 to 30.5), 29.5 (IQR 23.0 to 34.0), and 29.0 (IQR 24 to 37.5) for the ORF1ab gene. The Ct value differed significantly between mild vs moderate, and mild vs severe cases. The Ct value of SC group with co-morbidity of type 2 diabetes have a significant difference compared to non-diabetes group (p value <0.05). There was a significant difference in the median Ct value of ORF1ab gene among the MSC group and MC but not in the SC group in the first and second waves of the pandemic (p<0.05). Conclusion: We conclude that SARS-CoV-2 Ct values of rRT-PCR alone does not have a role in aiding severity stratification among patients with COVID-19 since the viral dynamics and Ct value may vary due to the emerging variants that occur in different waves of the pandemic.

Targeting radiation-resistant hypoxic tumour cells through ATR inhibition.

BACKGROUND: Most solid tumours contain regions of sub-optimal oxygen concentration (hypoxia). Hypoxic cancer cells are more resistant to radiotherapy and represent the most aggressive fraction of a tumour. It is therefore essential that strategies continue to be developed to target hypoxic cancer cells. Inhibition of the DNA damage response (DDR) might be an effective way of sensitising hypoxic tumour cells to radiotherapy. METHODS: Here, we describe the cellular effects of pharmacological inhibition of the apical DDR kinase ATR (Ataxia Telangiectasia and Rad 3 related) with a highly selective inhibitor, VE-821, in hypoxic conditions and its potential as a radiosensitiser. RESULTS: VE-821 was shown to inhibit ATR-mediated signalling in response to replication arrest induced by severe hypoxia. In these same conditions, VE-821 induced DNA damage and consequently increased Ataxia Telangiectasia Mutated-mediated phosphorylation of H2AX and KAP1. Consistently, ATR inhibition sensitised tumour cell lines to a range of oxygen tensions. Most importantly, VE-821 increased radiation-induced loss of viability in hypoxic conditions. Using this inhibitor we have also demonstrated for the first time a link between ATR and the key regulator of the hypoxic response, HIF-1. HIF-1 stabilisation and transcriptional activity were both decreased in response to ATR inhibition. CONCLUSION: These findings suggest that ATR inhibition represents a novel strategy to target tumour cells in conditions relevant to pathophysiology and enhance the efficacy of radiotherapy.

Microplastic contamination in edible sea salt from the largest salt-producing states of India.

The presence of microplastics in all ecological and environmental conditions has been identified as a global problem. This article aimed to study edible salt-associated microplastics from the major salt-producing states of India. The crystal and powder salt from Tamil Nadu and Gujarat (five samples of powder salt and three samples of crystal salt from each state) were collected and analyzed for their microplastic content. The total microplastic content in the salts ranged from 46 to 115 particles per 200 g in Gujarat salt and 23 to 101 particles per 200 g in Tamil Nadu salt. The microplastics are dominated by red and blue color fibrous-shaped materials. The most common microplastics identified in the edible salts were polyethylene, polyester, and polyvinyl chloride derived from marine and salt-processing units.

Spatio-temporal dynamics of caddisflies in streams of southern Western Ghats.

The dynamics of physico-chemical factors and their effects on caddisfly communities were examined in 29 streams of southern Western Ghats. Monthly samples were collected from the Thadaganachiamman stream of Sirumalai Hills, Tamil Nadu from May 2006 to April 2007. Southwest and northeast monsoons favored the existence of caddisfly population in streams. A total of 20 caddisfly taxa were collected from 29 streams of southern Western Ghats. Hydropsyche (Trichoptera: Hydropsychidae) were more widely distributed throughout sampling sites than were the other taxa. Canonical correspondence analysis showed that elevation was a major variable and pH, stream order, and stream substrates were minor variables affecting taxa richness. These results suggested that habitat heterogeneity and seasonal changes were stronger predictors of caddisfly assemblages than large-scale patterns in landscape diversity.

A baseline study on elemental concentration and potential ecological risk status of the surface sediments of Ashtamudi Lake, south west coast of India.

Element concentration (Fe, Mn, Pb, Zn, Cu, Cr, Ni and Co) in the surface sediments of Ashtamudi estuary, Southwest coast of India, has been analyzed to understand the spatial variation and potential ecological risk status. The sediment pollution index and Potential Ecological Risk index suggest that the northeastern part of the estuary exhibits low to moderate polluted sediments with moderate ecological risk. The results of correlation analysis indicate that the natural weathering process and river input play an important role in the distribution of the elements in the surface sediments of the estuary. The extracted factor results indicate that the fine sediment fractions supporting for accumulation of the trace elements, whereas the enriched level of Fe and Mn is chiefly controlled by the riverine process, and other elements are contributed by anthropogenic influences.

Bioavailable trace metals and their ecological risks in the tourist beaches of the Southeast coast of India.

The concentration of Acid Leachable Trace Metals (ALTMs) was assessed in urbanized tourist beaches (96 samples from Marina beach, 34 samples from Edward Elliot's beach, and 28 samples from Silver beach) of southeast coast of India. The concentration of metals accumulated in the beach sediment was less than the Upper Continental Crust (UCC) background reference values. The mean enrichment of ALTMs in the studied urban tourist beaches showed the following descending order: Marina beach - Cr > Pb > Ni > Zn > Cu > Mn > Co; Edward Elliot's beach - Cr > Pb > Ni > Mn > Co > Zn > Cu; Silver beach - Cr > Pb > Ni > Co > Mn > Cu > Zn. The ALTMs such as Fe, Mn, Co, Cu, and Zn were probably derived from natural weathering and mild anthropogenic influences whereas other metals were derived from anthropogenic induced factors.

Macroinvertebrate colonization and breakdown of leaves in an astatic pond in south India.

Macroinvertebrate colonization and breakdown of Pongamia pinnata and Morinda tinctoria leaves were studied in an astatic pond in Madura College, Madurai. Morinda tinctoria leaves broke down fasterthan the leaves of P. pinnata. Breakdown capacities of astatic pond cannot be attributed to colonization of macroinvertebrates. Instead, microbial processing, and abiotic fragmentation are suggested as factors controlling breakdown rates. Tanypus sp (midgelarva) was abundant in leaf bags during the experimental period. This midge-larva appeared to use litter accumulations as a microhabitat that provided shelter and a rich supply of food in the form of organic matter Their abundance and regular occurrence of two leaves suggest that midge larvae enhance leaf fragmentation and possibly mediate the incorporation of organic matter in pond sediments once the plant tissue is sufficiently macerated.

Anthropogenic impacts on aquatic insects in six streams of South Western ghats.

Diversity patterns of aquatic insects among sampling sites lying with!ç the unprotected and protected areas of Western Ghats were studied. This study primarily emphasizes whether anthropogenic influence is the prime cause for the presence of aquatic insects especially of pollution-sensitive organisms belonging to the orders Ephemeroptera, Plecoptera and Trichoptera, or to factors such as the physico-chemical features of the water, or sampling methods. Six streams were sampled quantitatively, of which three streams (Abbifalls, Monkey falls and Silver Cascade) were within protected areas and the remaining three streams (Kumbakarai, Shenbagadevi and Manimutharu falls) were in unprotected areas. A total of 3,209 individual aquatic insects belonging to 25 genera, 18 families and 7 orders were collected. The highest species richness and abundance was observed in Monkey falls followed by Kumbakkarai falls. Large numbers of more habitat-sensitive organisms such as Ecdyonurus sp., Epeorus sp., Thalerosphyrus sp., Euthraulus sp., and Nathanella sp., were found in Monkey falls. Though the species assemblage was somewhat different, pollution-sensitive taxa were also observed in Kumbakkarai falls. Shenbagadevi and Manimutharu falls had a lower diversity of aquatic insects. The likely causes of these differences are discussed.

Effect of vitamin D3 on chemokine levels and regulatory T-cells in pulmonary tuberculosis.

1,25-Dihydroxyvitamin D3 [1,25(OH)2D3] the active form of vitamin D3 acts as an immunomodulator in various immune cells. The present study is aimed to study the effect of 1,25(OH)2D3 on chemokine levels and regulatory T-cells in 51 healthy controls (HCs) and 50 pulmonary tuberculosis (PTB) patients. Peripheral blood mononuclear cells were cultured with culture filtrate antigen (CFA) of Mycobacterium tuberculosis in the presence or absence of 1,25(OH)2D3 at 10(-7) M concentration for 72 h and the percentage positive regulatory T-cell subsets were studied using flow cytometry. The chemokine levels were estimated in the culture supernatants by ELISA. 1,25(OH)2D3 significantly upregulated the frequency of regulatory T-cell subsets while suppressed the production of chemokine levels in CFA stimulated cultures of HCs and PTB patients (p<0.05). Correlation analysis revealed a significant negative correlation between CD4+Foxp3+ regulatory T-cells and MCP-1, MIP-1ß and IP-10 in CFA stimulated with 1,25(OH)2D3 treated cells (p<0.05). The results suggested that 1,25(OH)2D3 upregulated regulatory T-cells and act as anti-inflammatory by downregulating chemokine levels which could be beneficial to protect the host from inflammation and tissue damage during infection.

Spatio-temporal dynamics of mosquitoes in stream pools of a biosphere reserve of Southern Western Ghats, India.

The spatial and temporal dynamics of mosquitoes in stream pools were examined in a biosphere reserve of the Southern Western Ghats, India. The immature mosquitoes in stream pools were collected from stream substrates of bedrock pool, boulder cavity and sand puddle. The collected larvae and pupae were reared and identified. In total, 16 species from four genera of mosquitoes were collected. The mosquito species from Culex and Anopheles were predominantly occurred. The bedrock pool had the highest diversity and abundance of mosquitoes. The statistical analyses showed that the substrate specificity and the seasons were positively related to the distribution of mosquitoes rather than spatial pattern. This study described the spatial and temporal pattern of mosquitoes in stream pools of the Southern Western Ghats. This information would be helpful to National Vector borne disease control program for surveillance and control.

Simulium (Gomphostilbia) (Diptera: Simuliidae) from Southern Western Ghats, India: two new species and DNA barcoding.

Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) are described on the basis of reared adult, pupal and larval specimens collected from Southern Western Ghats India. The morphological data of two new species S. (Gomphostilbia) panagudiense sp. n. and S. (Gomphostilbia) kottoorense sp. n. are assigned to the batoense species group in the subgenus Gomphostilbia. S. (Gomphostilbia) panagudiense sp.n. is characterized in the female by having the scutum without longitudinal vitta and arms of the genital fork wide basally and in the pupa by the stalk of ventral pair medium-long. S. (Gomphostilbia) kottoorense sp.n. is characterized by the arm of genital fork tapered near apex in the female and style in medial view 0.63 times as long as coxite in the male. Phylogeny of members in the genus Simulium was reconstructed based on DNA barcoding gene (cytochrome oxidase c subunit I). Tree analysis using new technology and maximum likelihood analyses are congruent with evidence of two new species in the subgenus Gomphostilbia and separated from other species.

Automatic leukocyte classification using cytochemically stained smears.

A leukocyte classification algorithm suitable for automated differential counting has been developed for blood smears stained with a new three-component cytochemical stain which has relatively narrow absorption bands centered at 460, 540 and 640 nm, respectively. The classification procedure is the result of a pattern recognition experiment using a sample of 223 leukocytes distributed evenly over the five normal cell types. The basic data for each cell were three digital microscopic images obtained with narrow band illumination at the above central wavelengths using a TV-digitizer system interfaced to a PDP-15 computer. The classification algorithm involves a sequential decision procedure utilizing five pattern features computed from the intensity histograms of the green and blue digital images. Thus the number of arithmetic operations and the number of computer memory words necessary to perform the classification into one of the five normal white blood cell types are both proportional to n where n is the number of gray levels into which the intensity scale is divided. In this experiment, n equals 256. Comparison of our results with work of others on smears prepared with Romanowski-type stains indicates that such narrow-band, spectrally well separated cytochemical multiple stains can permit the use of algorithms which are approximately ten times faster.

Infectivity analysis of two variable DNA B components of Mungbean yellow mosaic virus-Vigna in Vigna mungo and Vigna radiata.

Mungbean yellow mosaic virus-Vigna (MYMV-Vig), a Begomovirus that causes yellow mosaic disease, was cloned from field-infected blackgram (Vigna mungo). One DNA A clone (KA30) and five different DNA B clones (KA21, KA22, KA27, KA28 and KA34) were obtained. The sequence identity in the 150-nt common region (CR) between DNA A and DNA B was highest (95%) for KA22 DNA B and lowest (85.6%) for KA27 DNA B. The Rep-binding domain had three complete 11-nt (5'-TGTATCGGTGT-3') iterons in KA22 DNA B (and KA21, KA28 and KA34), while the first iteron in KA27 DNA B (5'-ATCGGTGT-3') had a 3-nt deletion. KA27 DNA B, which exhibited 93.9% CR sequence identity to the mungbean-infecting MYMV, also shared the 3-nt deletion in the first iteron besides having an 18-nt insertion between the third iteron and the conserved nonanucleotide. MYMV was found to be closely related to KA27 DNA B in amino acid sequence identity of BV1 (94.1%) and BC1 (97.6%) proteins and in the organization of nuclear localization signal (NLS), nuclear export signal (NES) and phosphorylation sites. Agroinoculation of blackgram (V. mungo) and mungbean (V. radiata) with partial dimers of KA27 and KA22 DNA Bs along with DNA A caused distinctly different symptoms. KA22 DNA B caused more intense yellow mosaic symptoms with high viral DNA titre in blackgram. In contrast, KA27 DNA B caused more intense yellow mosaic symptoms with high viral DNA titre in mungbean. Thus, DNA B of MYMVVig is an important determinant of host-range between V. mungo and V. radiata.

Sequence analysis of infectious bursal disease virus isolates from India: phylogenetic relationships.

Prevalence of infectious bursal disease (IBD) among chickens in different parts of Tamil Nadu, India, has been studied by collection of bursal samples from suspected flocks and by performing reverse transcription-polymerase chain reaction (RT-PCR) for amplification of a specific product of 474 bp from the variable region of the VP2 gene. Among 53 bursal samples examined by RT-PCR, 40 showed a positive reaction. The amplified products were subjected to nucleotide sequencing and the obtained sequences were compared with those of IBD virus (IBDV) vaccine strain Georgia, the classical virulent strain 52/70 and the very virulent Japanese OKYM strain. Nucleotide homology data indicated that all the Tamil Nadu isolates showed homology ranging from 91 to 99.6% among themselves. When compared with the very virulent Japanese OKYM strain, four isolates grouped with that strain. Majority of the isolates clustered with the very the virulent OKYM strain as evident from phylogenetic analysis performed using the MEGA program. Comparison of the deduced amino acid sequences of IBDV isolates with those of the vaccine strain Georgia, the classical virulent strain 52/70 and the very virulent strain OKYM also revealed the presence of conserved serine-rich heptapeptide sequence in most of the isolates. Results of this study indicate that majority of the IBDV isolates are very virulent, which is evident from heavy mortality that has been reported in few flocks of poultry in spite of regular vaccination.

Mitogen-activated protein kinases mediate Mycobacterium tuberculosis-induced CD44 surface expression in monocytes.

CD44, an adhesion molecule, has been reported to be a binding site for Mycobacterium tuberculosis (M. tuberculosis) in macrophages and it also mediates mycobacterial phagocytosis, macrophage recruitment and protective immunity against pulmonary tuberculosis in vivo. However, the signalling pathways that are involved in M. tuberculosis-induced CD44 surface expression in monocytic cells are currently unknown. Exposure of THP-1 human monocytes to M. tuberculosis H37Rv and H37Ra induced distinct, time-dependent, phosphorylation of mitogen-activated protein kinase kinase-1, extracellular signal regulated kinase 1/2, mitogen-activated protein kinase kinase 3/6, p38 mitogen-activated protein kinase and c-jun N-terminal kinases. The strains also differed in their usage of CD14 and human leukocyte antigen-DR (HLA-DR) receptors in mediating mitogen-activated protein kinase activation. M. tuberculosis H37Rv strain induced lower CD44 surface expression and tumour necrosis factor-alpha levels, whereas H37Ra the reverse. Using highly specific inhibitors of mitogen-activated protein kinase kinase-1, p38 mitogen-activated protein kinase and c-jun N-terminal kinase, we report that inhibition of extracellular signal regulated kinase 1/2 and c-jun N-terminal kinases increases, but that inhibition of p38 mitogen-activated protein kinase decreases M. tuberculosis-induced CD44 surface expression in THP-1 human monocytes.