Efficient mapping of RNA-binding residues in RNA-binding proteins using local sequence features of binding site residues in protein-RNA complexes.

Protein-RNA interactions play vital roles in plethora of biological processes such as regulation of gene expression, protein synthesis, mRNA processing and biogenesis. Identification of RNA-binding residues (RBRs) in proteins is essential to understand RNA-mediated protein functioning, to perform site-directed mutagenesis and to develop novel targeted drug therapies. Moreover, the extensive gap between sequence and structural data restricts the identification of binding sites in unsolved structures. However, efficient use of computational methods demanding only sequence to identify binding residues can bridge this huge sequence-structure gap. In this study, we have extensively studied protein-RNA interface in known RNA-binding proteins (RBPs). We find that the interface is highly enriched in basic and polar residues with Gly being the most common interface neighbor. We investigated several amino acid features and developed a method to predict putative RBRs from amino acid sequence. We have implemented balanced random forest (BRF) classifier with local residue features of protein sequences for prediction. With 5-fold cross-validations, the sequence pattern derived dipeptide composition based BRF model (DCP-BRF) resulted in an accuracy of 87.9%, specificity of 88.8%, sensitivity of 82.2%, Mathew's correlation coefficient of 0.60 and AUC of 0.93, performing better than few existing methods. We further validated our prediction model on known human RBPs through RBR prediction and could map ~54% of them. Further, knowledge of binding site preferences obtained from computational predictions combined with experimental validations of potential RNA binding sites can enhance our understanding of protein-RNA interactions. This may serve to accelerate investigations on functional roles of many novel RBPs.

Post-Transition State Direct Dynamics Simulations on the Ozonolysis of Catechol in an N2 Bath and Comparison with Gas-Phase Results.

Chemical dynamics simulations on the post-transition state dynamics of ozonolysis of catechol are performed in this article using a newly developed QM + MM simulation model. The reaction is performed in a bath of N2 molecules equilibrated at 300 K. Two bath densities, namely, 20 and 324 kg/m3, are considered for the simulation. The excitation temperatures of a catechol-O3 moiety are taken as 800, 1000, and 1500 K for each density. At these new excitation temperatures, the gas-phase results are also computed to compare the results and quantify the effect of surrounding molecules on this reaction. Like the previous findings, five reaction channels are observed in the present investigation, producing CO2, CO, O2, small carboxylic acid (SCA), and H2O. The probabilities of these products are discussed with the role of bath densities. Results from the gas-phase simulation and density of 20 kg/m3 are very similar, whereas results differ significantly at a higher bath density of 324 kg/m3. The rate constants for the unimolecular channel at each temperature and density are also calculated and reported. The QM + MM setup used here can also be used for other chemical reactions, where the solvent effect is important.

In COVID-19 acute hypoxemia, awake prone positioning vs. usual care did not reduce intubation at 30 d.

SOURCE CITATION: Alhazzani W, Parhar KK, Weatherald J, et al. Effect of awake prone positioning on endotracheal intubation in patients with COVID-19 and acute respiratory failure: a randomized clinical trial. JAMA. 2022;327:2104-13. 35569448.

The expanding arms of Zika virus: An updated review with recent Indian outbreaks.

Zika virus (ZIKV) outbreaks and their adverse clinical consequences have raised concerns throughout the world. ZIKV was little known during the initial outbreaks in Yap islands and French Polynesia, but it came to attention after the series of Brazil outbreaks in which severe complications like microcephaly in newborn babies was detected. During 2018, outbreaks of ZIKV occurred in two states of India which, being a tropical country, has congenial climatic conditions, abundance of highly competent mosquito vectors such as Aedes aegypti and Aedes albopictus, and an immunologically naïve population. In this review, we will briefly discuss the history, epidemiology, evolution, transmission (vector-borne and non-vector borne), pathogenesis, clinical signs and unusual presentations, laboratory diagnosis, treatment, prevention and control of ZIKV. Finally, we suggest priorities for urgent research required to address unanswered questions about Zika infections and help bring this virus under control.

Post-Transition-State Direct Dynamics Simulations on the Ozonolysis of Catechol.

On-the-fly dynamics simulations are performed for the reaction of catechol + O3. The post transition state (TS) dynamics is studied at temperatures of 400 and 500 K. The PM7 semiempirical method is employed for calculating the potential energy gradient needed for integrating Hamilton's equations of motion. This semiempirical method provides excellent agreement in terms of energy and geometry of the TSs as well as minimum energy states of the system with respect to B3LYP/6-311+G (2df, 2p) calculated results. In the dynamics, first, a peroxyacid is formed, which further dissociates to different fragments. Four major channels forming CO, CO2, H2O, and small carboxylic acid (SCA) fragments are seen in this reaction. Rates of each of the channels and the overall unimolecular reaction are calculated at both temperatures. Branching ratios of all these product channels are calculated and compared with experiment. The minimum energy profile of CO2, CO, and H2O channels are calculated. A qualitative estimate of activation energies for all the channels are obtained and compared with the explicit TS energies of three product channels, which ultimately correlate with the reaction probabilities.

Any Role of High-Dose Vitamin C for Septic Shock in 2021?

While the use of vitamin C as a therapeutic agent has been investigated since the 1950s, there has been substantial recent interest in the role of vitamin C supplementation in critical illness and particularly, sepsis and septic shock. Humans cannot synthesize vitamin C and rely on exogenous intake to maintain a plasma concentration of approximately 70 to 80 µmol/L. Vitamin C, in healthy humans, is involved with antioxidant function, wound healing, endothelial function, and catecholamine synthesis. Its function in the human body informs the theoretical basis for why vitamin C supplementation may be beneficial in sepsis/septic shock.Critically ill patients can be vitamin C deficient due to low dietary intake, increased metabolic demands, inefficient recycling of vitamin C metabolites, and loss due to renal replacement therapy. Intravenous supplementation is required to achieve supraphysiologic serum levels of vitamin C. While some clinical studies of intravenous vitamin C supplementation in sepsis have shown improvements in secondary outcome measures, none of the randomized clinical trials have shown differences between vitamin C supplementation and standard of care and/or placebo in the primary outcome measures of the trials. There are some ongoing studies of high-dose vitamin C administration in patients with sepsis and coronavirus disease 2019; the majority of evidence so far does not support the routine supplementation of vitamin C in patients with sepsis or septic shock.

Encephalopathy and Encephalitis Associated with Cerebrospinal Fluid Cytokine Alterations and Coronavirus Disease, Atlanta, Georgia, USA, 2020.

There are few detailed investigations of neurologic complications in severe acute respiratory syndrome coronavirus 2 infection. We describe 3 patients with laboratory-confirmed coronavirus disease who had encephalopathy and encephalitis develop. Neuroimaging showed nonenhancing unilateral, bilateral, and midline changes not readily attributable to vascular causes. All 3 patients had increased cerebrospinal fluid (CSF) levels of anti-S1 IgM. One patient who died also had increased levels of anti-envelope protein IgM. CSF analysis also showed markedly increased levels of interleukin (IL)-6, IL-8, and IL-10, but severe acute respiratory syndrome coronavirus 2 was not identified in any CSF sample. These changes provide evidence of CSF periinfectious/postinfectious inflammatory changes during coronavirus disease with neurologic complications.

Impact of transmission cycles and vector competence on global expansion and emergence of arboviruses.

Arboviruses are transmitted between arthropod vectors and vertebrate host. Arboviral infection in mosquitoes is initiated when a mosquito feeds on a viremic host. Following ingestion of a viremic blood meal by mosquitoes, virus enters midgut along with the blood, infects and replicates in midgut epithelial cells, and then escapes to the hemocoel, from where it disseminates to various secondary organs including salivary glands. Subsequently, when mosquito bites another host, a new transmission cycle is initiated. The midgut and salivary glands act as anatomical barriers to virus infection and escape. These complex interactions between the virus and vector dictate the vector competence. Thus, vector competence reflects the success in overcoming different barriers within the vector. Along with these, other intrinsic factors like midgut microbiota and immune responses, extrinsic factors like temperature and humidity, and genetic factors like vector genotype and viral genotype have been discussed in this review. Recent advancement on novel molecular tools to study vector competence is also included. Different modes of arboviral transmission like horizontal, vertical, and venereal and how these play role in sustenance and emergence of arboviruses in nature are also discussed. These factors can be exploited to reduce the susceptibility of vectors for the viruses, so as to control arboviral diseases to certain extent.

Emergence of influenza A (H1N1)pdm09 genogroup 6B and drug resistant virus, India, January to May 2015.

To investigate the aetiology of the 2015 A(H1N1)pdm09 influenza outbreak in India, 1,083 nasopharyngeal swabs from suspect patients were screened for influenza A(H1N1)pdm09 in the state of Madhya Pradesh. Of 412 positive specimens, six were further characterised by phylogenetic analysis of haemagglutinin (HA) sequences revealing that they belonged to genogroup 6B. A new mutation (E164G) was observed in HA2 of two sequences. Neuraminidase genes in two of 12 isolates from fatal cases on prior oseltamivir treatment harboured the H275Y mutation.

A retrospective analysis on seroprevalence of acute viral hepatitis observed among dengue patients attending a tertiary care centre in central India.

PURPOSE: The present study was conducted retrospectively to assess the frequency of acute viral hepatitis among the clinically suspected dengue cases presented at our tertiary care centre during 2021. METHODS: To determine the presence of acute viral hepatitis; Hepatitis A virus (HAV) and Hepatitis E virus (HEV) infections, 104 specimens were selected from the dengue-suspected clinical specimens received during 2021 on the basis of acute viral hepatitis symptoms. Following this, serological diagnosis was performed on those samples using anti-HAV IgM and anti-HEV IgM ELISA kits. RESULTS: Based on sero-positivity for IgM antibodies, 3 (5.3%) dengue virus (DENV) seropositive samples were positive for both HAV and HEV, while among DENV seronegative cases, 11 (22.91%) samples were positive for HEV and 1 (2.08%) sample was positive for HAV, pointing towards misdiagnosis due to overlapping symptoms. Additionally, co-infection of HAV & HEV in 1 sample was also observed in this study. CONCLUSIONS: This study revealed the presence of acute hepatitis infections among the dengue cases during monsoon and post-monsoon season. Overlapping of the clinical manifestations of these diseases can create misdiagnosis incidences raising risk for underreporting of the true cases of acute viral hepatitis infection. Dengue-suspected patients with selected symptoms during the monsoon and post-monsoon season should additionally be screened for acute hepatitis infections, as suggested in this study.

Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2.

Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001-2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a unique clade in South Asia.

Molecular and virological investigation of a focal chikungunya outbreak in northern India.

Chikungunya (CHIK) fever is one of the most important arboviral infections of medical significance. The objective of the present study is to identify and characterize the etiology of a focal febrile arthritis outbreak from Gwalior, northern India, during October-November 2010. A detailed virological (isolation) and molecular (end-point RT-PCR, quantitative RT-PCR, and nucleotide sequencing) investigation of this outbreak was carried out by collecting and studying 52 clinical samples and 15 mosquito pools from the affected region. The investigation revealed the presence of CHIK viral RNA in 29% of clinical samples and 13% mosquito pool by RT-PCR. The quantification of CHIK viral RNA in samples varied from 10(2.50) to 10(6.67) copies/mL, as demonstrated through quantitative RT-PCR. In addition, six CHIK viruses were isolated from RT-PCR positive samples. The nucleotide sequences of partial E1 gene of five representative CHIK viruses were deciphered, which revealed that all the viral strains from this outbreak belong to the recently emerging ECS African genotype. Identification of Chikungunya virus ECSA African genotype as the etiology of the present outbreak confirms the continued circulation of the novel genotype, since 2006, in India. The identification of CHIK virus in Aedes aegypti also confirmed it as the major vector in northern India.

Modular architecture and functional annotation of human RNA-binding proteins containing RNA recognition motif.

RNA-binding proteins (RBPs) are structurally and functionally diverse macromolecules with significant involvement in several post-transcriptional gene regulatory processes and human diseases. RNA recognition motif (RRM) is one of the most abundant RNA-binding domains in human RBPs. The unique modular architecture of each RBP containing RRM is crucial for its diverse target recognition and function. Genome-wide study of these structurally conserved and functionally diverse domains can enhance our understanding of their functional implications. In this study, modular architecture of RRM containing RBPs in human proteome is identified and systematically analysed. We observe that 30% of human RBPs with RNA-binding function contain RRM in single or multiple repeats or with other domains with maximum of six repeats. Zinc-fingers are the most frequently co-occurring domain partner of RRMs. Human RRM containing RBPs mostly belong to RNA metabolism class of proteins and are significantly enriched in two functional pathways including spliceosome and mRNA surveillance. Various human diseases are associated with 18% of the RRM containing RBPs. Single RRM containing RBPs are highly enriched in disorder regions. Gene ontology (GO) molecular functions including poly(A), poly(U) and miRNA binding are highly depleted in RBPs with single RRM, indicating the significance of modular nature of RRMs in specific function. The current study reports all the possible domain architectures of RRM containing human RBPs and their functional enrichment. The idea of domain architecture, and how they confer specificity and new functionalities to RBPs, can help in re-designing of modular RRM containing RBPs with re-engineered function.