Suppression of SlDREB3 increases leaf ABA responses and promotes drought tolerance in transgenic tomato plants.

Drought susceptibility is a major yield limiting factor in agricultural crops especially in hybrids/varieties that have been bred for high yields. We show that manipulation of the SlDREB3 gene in tomato alters ABA responses and thereby sensitivity of stomatal closure to ABA. SlDREB3 suppression lines show ABA hypersensitivity and rapid stomatal closure in response to ABA while over-expression lines show reduced sensitivity to ABA and open stomata even at high ABA levels with rapid water loss after 10 days of water stress. This is accompanied with high ROS levels and increased membrane damage due to senescence of leaves and drastically reduced survival in drought. The relative water content (RWC) of OEx lines is much reduced even when grown under well-watered conditions. In contrast, suppression lines show greater tolerance to water stress and almost complete survival to 10-day water stress. They show much reduced ROS levels, reduced membrane damage, higher RWC and reduced leaf water loss. These changes are associated with higher expression of ABA signalling pathway genes in suppression lines while these are highly reduced in OEx lines. The studies suggest that control of ABA signalling by SlDREB3 can help in withstanding severe drought.

Comparison of 2-Octyl Cyanoacrylate with Prolene (4-0) Sutures in Extra Oral Wound Closure.

Aim: To compare the healing following various maxillofacial incisions using 2-octyl cyanoacrylate (2-OCA) and prolene (4-0) sutures. Objective: To evaluate the complications and aesthetic outcome of the incision wounds after closure using 2-OCA and prolene (4-0) sutures. Materials and Methods: The patient undergoing an extraoral incision was evaluated for pain, inflammation, infection, dehiscence, scar, and surface texture. In Group I, 15 patient incisions were closed with 2-OCA and in Group II, 15 patient incisions were closed with prolene (4-0) suture. Result: A few patients experienced pain with Group I and then Group II, but infection, inflammation, and dehiscence were more in Group I than in Group II. Conclusion: A cosmetic outcome was higher in the cyanoacrylate group, and the surface texture was satisfying in the same group.

Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations.

Despite seminal advances towards understanding the infection mechanism of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), it continues to cause significant morbidity and mortality worldwide. Though mass immunization programmes have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study the role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2-infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April 2020 to October 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this period. We also highlight the presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.

Serum Levels of Activin A: Predictor of Insulin Resistance and Atherosclerosis in Prediabetics.

BACKGROUND: Pathological effects of dysglycemia and insulin resistance on atherosclerosis and cardiac remodeling starts as early as in the prediabetic state before the onset of overt diabetes. Activin A is a molecule with multiple functions, including an important part in glucose homeostatic mechanisms as well as inflammatory processes and is therefore being researched as a useful novel biomarker for prompt recognition of the risk of cardiovascular disease (CVD) in prediabetic individuals, thereby helping in disease prognostication and early institution of therapeutic measuresObjective: The study aimed to measure serum levels of activin A in prediabetic patients and evaluate them in comparison to normoglycemic controls. The association of activin A with carotid intima media thickness (CIMT), left ventricular diastolic dysfunction (LVDD), and homeostatic assessment of insulin resistance (HOMA-IR) was also studiedMaterials and methods: A total of 60 prediabetic cases and 60 normoglycemic control subjects [matched as per age, gender, and body mass index (BMI)] were recruited. Measurement of serum glucose levels (fasting and postprandial) and fasting insulin levels and glycated hemoglobin (HbA1c) levels were done in all the subjects. The values of HOMA-IR were computed using established formulae. Enzyme-linked immunosorbent assay (ELISA) kits were used for the evaluation of serum levels of activin A in both groups. Parameters for the two groups were compared. In the cases, CIMT (using B-mode ultrasound) and LVDD (using two-dimensional (2D) echocardiography) were measured and correlated with activin A levelsResults: Serum fasting insulin (mIU/L) was considerably higher in cases than in the controls (p < 0.001). HOMA-IR median [interquartile range (IQR)] was 4 (3.25-4.93) in some cases, and that in the control group was 1.2 (0.88-1.5) (p < 0.001). Serum activin A levels in the cases group had a median (IQR) of 263.55 (227.1-279.5) ng/mL, which was substantially greater as compared to the control group 159.9 (150.7-178.7) ng/mL (p < 0.001). A significant positive association of serum activin A levels with HOMA-IR (ρ = 0.75, p < 0.001) and CIMT (ρ = 0.50, p < 0.001) was found. In LVDD grade I and II groups, the serum levels of activin A were 257.86 (219.3-271.2) ng/mL and 269 (244.19-291.5) ng/mL, respectively (p = 0.12)Conclusion: A substantial proportion of morbidity and mortality related to dysglycemic states can be attributed to cardiovascular complications. Elevated levels of activin A in prediabetes can act as an indicator of subclinical CVD leading to early diagnosis and intervention.

Role of Intra-articular Piroxicam in the Temporomandibular Joint After Arthrocentesis for Anterior Disc Displacement Without Reduction.

STUDY DESIGN: This is comparative experimental research to evaluate the role of piroxicam in the temporomandibular joint (TMJ) after arthrocentesis. OBJECTIVE: To evaluate the role of intra-articular piroxicam in the temporomandibular joint after arthrocentesis for anterior disc displacement without reduction. MATERIAL AND METHODS: Twenty-two individuals (twenty-two TMJs) were evaluated clinically and radiographically for the study, and then they were randomly assigned to one of two groups. As for group I, they were given arthrocentesis using Ringer's solution (100 ml). Group II received an intra-articular injection of 20 mg/mL of piroxicam (in 1 mL of Ringer's solution) after arthrocentesis (100 mL). The same individuals were assessed both before and after surgery to determine the degree to which their symptoms had improved. Patients were seen in the clinic once a week for the first month after surgery, then once a month for the next three months. RESULT:  Group II patients presented with better results when compared with Group I. CONCLUSION: It can be concluded that installing a 1 ml intra-articular injection of piroxicam at a concentration of 20 mg/ml after arthrocentesis improves the relief of symptoms, both qualitatively and quantitatively. Relief of TMJ symptoms reduced the anxiety in the patients as evaluated by the BAIS (Beck's Anxiety Inventory Scale) score.

SlDREB3, a negative regulator of ABA responses, controls seed germination, fruit size and the onset of ripening in tomato.

SlDREB3 was identified as a ripening up-regulated gene of the AP2/ERF-domain family of transcription factors. Its manipulation affects processes primarily governed by ABA. It negatively regulates ABA responses in tomato by altering ABA levels/signaling and is, in turn, negatively regulated by ABA. SlDREB3 over-expression lines show higher transcript levels of the ABA metabolism genes CYP707A3 and UGT75C1 and an 85% reduction in ABA levels leading to early seed germination. In contrast, suppression lines show decreased CYP707A3/UGT75C1 expression, 3-fold higher ABA levels and delayed germination. The expression of other ABA signaling and response genes is also affected. Suppression of SlDREB3 accelerates the onset of ripening by 4-5 days while its over-expression delays it and also reduces final fruit size. SlDREB3 manipulation effects large scale changes in the fruit transcriptome with suppression lines showing early increase in ABA levels and activation of most ripening pathway genes that govern ethylene, carotenoids and softening. Strikingly, key transcription factors like CNR, NOR, RIN, FUL1, governing ethylene-dependent and ethylene-independent aspects of ripening, are activated early upon SlDREB3 suppression suggesting their control by ABA. The studies identify SlDREB3 as a negative regulator of ABA responses across tissues and a key ripening regulator controlling ethylene-dependent and ethylene-independent aspects.

Serum levels of Activin A: Marker of insulin resistance and cardiovascular risk in prediabetics.

Background: A substantial proportion of health burden in diabetic individuals can be attributed to cardiovascular complications. The increasing risk of cardiovascular complications along the spectrum of dysglycemia warrants the need to devise novel markers for early assessment and management. Activin A is a multifunctional cytokine with an important role in glucose homeostasis and vascular diseases. It can thus serve as a guide for early identification of cardiovascular disease (CVD) risk in prediabetes. Objective: The aim of the study was to measure serum levels of activin A in prediabetics, compare them with normoglycemic controls and find the correlation of activin A with markers of insulin resistance such as the homeostatic model assessment of insulin resistance (HOMA-IR). Methods: Sixty prediabetic patients and similar age-, sex-, blood pressure-, and BMI-matched controls were recruited in the study. In both groups, serum levels of fasting blood glucose and post prandial glucose, glycated hemoglobin (HbA1c) and fasting insulin were measured. HOMA-IR values were calculated. Serum activin A levels were measured in both groups using ELISA. The obtained values were compared between the two groups. Results: The median (IQR) of s. fasting insulin (mIU/L) in the case group was 15.3 (12.2-18.62) which was significantly higher than that in the control group, which was 6 (4.2-7.3). The median (IQR) of s. activin A (ng/mL) in the case group was 263.55 (227.18-279.56) which was significantly higher than that in the control group, which was 159.9 (150.73-178.75) (P < 0.001). There was a very strong positive correlation of s. activin A (ng/mL) with s. fasting insulin (mIU/L) and HOMA-IR (rho = 0.67 and 0.75, respectively, P < 0.001). Conclusion: Activin A, if combined with other atherosclerotic markers, might improve the assessment of insulin resistance and cardiovascular risk in prediabetics and lead to focus on lifestyle modifications and preventive medical therapy, thereby contributing to the prevention of CVD-related mortality and morbidity in these patients.

A comprehensive profile of genomic variations in the SARS-CoV-2 isolates from the state of Telangana, India.

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 has rapidly turned into a pandemic, infecting millions and causing 1 157 509 (as of 27 October 2020) deaths across the globe. In addition to studying the mode of transmission and evasion of host immune system, analysing the viral mutational landscape constitutes an area under active research. The latter is expected to impart knowledge on the emergence of different clades, subclades, viral protein functions and protein-protein and protein-RNA interactions during replication/transcription cycle of virus and response to host immune checkpoints. In this study, we have attempted to bring forth the viral genomic variants defining the major clade(s) as identified from samples collected from the state of Telangana, India. We further report a comprehensive draft of all genomic variations (including unique mutations) present in SARS-CoV-2 strain in the state of Telangana. Our results reveal the presence of two mutually exclusive subgroups defined by specific variants within the dominant clade present in the population. This work attempts to bridge the critical gap regarding the genomic landscape and associate mutations in SARS-CoV-2 from a highly infected southern region of India, which was lacking to date.

Serum Heart Type Fatty Acid Binding Protein Levels in Prediabetes-An Invaluable Cardiovascular Biomarker.

BACKGROUND: The pathophysiological effects of diabetes on the heart and the rest of the cardiovascular system begins much earlier in its precedent stage of prediabetes and one major underlying defect is insulin resistance. Heart-type fatty acid binding protein (H-FABP) is a recently studied molecule inherent to the cardiac myocytes found to rise in both coronary and non-coronary heart diseases. The utility of the molecule in prediabetes and its relationship with insulin resistance is being studied. OBJECTIVE: The aim of the study is to compare serum levels of H-FABP in prediabetics and controls and correlate them with Homeostatic model assessment - insulin resistance (HOMA-IR). METHODS: 50 prediabetic patients and 50 age, sex and BMI matched controls were employed in the case control study. Serum fasting and postprandial blood sugars, glycosylated hemoglobin (HbA1c), fasting insulin levels were measured in cases and controls. HOMA-IR index was calculated from fasting glucose and insulin values. Serum H-FABP was measured in both cases and controls using Immunoturbidimetric method with anti- H-FABP coated latex reagent kits. The values were compared between both the groups. RESULTS: The mean serum fasting insulin level among cases was 12.22mIU/ml and that of the control group was 5.37mIU/ml (p value <0.0001). HOMA- IR mean values were 3.31 ± 1.56 and 1.16 ± 0.44 in cases and controls respectively (p- <0.001). The mean serum levels of H-FABP among cases and controls were 6.38± 2.76ng/ml and 3.24 ± 2.47 ng/ml respectively (p <0.0001). The correlation between the two variables, HOMA-IR and H-FABP was also found to be strongly positive (r=0.675). Linear regression analysis showed that for 1 unit increase in HOMA-IR, H-FABP increased by 1.095 and for 1 unit increase in Fasting insulin, H-FABP increased by 0.038. CONCLUSION: Prediabetics have a higher risk of cardiovascular morbidity when compared to normoglycemics with insulin resistance being the single most important contributor. Serum H-FABP levels are elevated in prediabetes representing a marker of subclinical cardiovascular disease (CVD).

Valorization of agricultural waste for biogas based circular economy in India: A research outlook.

Environmental deterioration and the need for energy security are intrinsic problems linked with the linear economy based on fossil fuels. Recently, a transformation to a sustainable circular bio-economy is being experienced where biomass waste is being valorized for energy production as well as minimization of waste and greenhouse gas emissions. The agricultural waste, generated in vast quantities in India is a prospective feedstock for biogas production. Agri-waste to biogas based circular economy requires an integration of agri-waste management, biogas production and utilization and policy support. This paper comprehensively discusses the potential of biogas production from agricultural waste, its upgradation and utilization along with the government initiatives, policy regulations. In addition, barriers that impede the development of an efficient agri-waste to biogas based circular economy, and the future research opportunities to meet the growing needs for agri-waste management, energy production and climate change mitigation are discussed.

RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.

RNA structures are widely distributed across all life forms. The global conformation of these structures is defined by a variety of constituent structural units such as helices, hairpin loops, kissing-loop motifs and pseudoknots, which often behave in a modular way. Their ubiquitous distribution is associated with a variety of functions in biological processes. The location of these structures in the genomes of RNA viruses is often coordinated with specific processes in the viral life cycle, where the presence of the structure acts as a checkpoint for deciding the eventual fate of the process. These structures have been found to adopt complex conformations and exert their effects by interacting with ribosomes, multiple host translation factors and small RNA molecules like miRNA. A number of such RNA structures have also been shown to regulate translation in viruses at the level of initiation, elongation or termination. The role of various computational studies in the preliminary identification of such sequences and/or structures and subsequent functional analysis has not been fully appreciated. This review aims to summarize the processes in which viral RNA structures have been found to play an active role in translational regulation, their global conformational features and the bioinformatics/computational tools available for the identification and prediction of these structures.

Comparative analysis of canal-centering ratio, apical transportation, and remaining dentin thickness between single-file systems, i.e., OneShape and WaveOne reciprocation: An in vitro study.

AIM: This study aimed to compare the canal-centering ability, apical transportation, and remaining dentin thickness (RDT) of OneShape and WaveOne (WO) systems using cone-beam computed tomography. OBJECTIVE: The objective of this study was to evaluate the efficiency of two rotary systems in maintaining original root canal anatomy. MATERIALS AND METHODS: Forty extracted human single-rooted mandibular premolars were used in the present study. Preinstrumentation scans of all teeth were taken, canal curvatures were calculated, and the samples were randomly divided into two groups with twenty samples in each group: Group 1 - OneShape (OS) rotary system and Group 2 - WO reciprocation system. Postinstrumentation scans were performed using DICOM software and the two scans were compared to determine the canal-centering ability, canal transportation, and RDT at 1, 3, and 5 mm from the root apex. RESULTS: Using Student's unpaired t-test, results were as follows: for canal-centering ability and RDT, Group 1 showed nonstatistically significant difference at 1 and 5 mm, while statistically significant difference (P < 0.05) at 3 mm was obtained. For canal transportation, Group 1 showed statistically significant difference (P < 0.05) at 1 and 3 mm and nonsignificant difference was obtained at 5 mm, but for Group 2, nonstatistically significant difference (P > 0.05) was obtained at 1, 3, and 5 mm. When comparing the RDT between both the groups, the difference was not statistically significant (P > 0.05). CONCLUSION: WO single reciprocation file has better canal-centering ability, maintains original canal curvature, causes lesser canal transportation, and preserves more dentine as compared to OS.

Ectopic expression of a tomato DREB gene affects several ABA processes and influences plant growth and root architecture in an age-dependent manner.

Regulation of whole plant growth and adaptive responses by abscisic acid is complex, requires multiple regulators and largely unknown in plants other than Arabidopsis. We show that over-expression of the tomato SlDREB3/SlERF.H12 (DEHYDRATION RESPONSE ELEMENT BINDING PROTEIN3/ETHYLENE RESPONSE FACTOR. H12) gene can negatively affect many ABA-governed processes across tissues. Its expression leads to early germination in presence of ABA and in response to mannitol, NaCl and glucose. Its expression delays ABA-mediated leaf senescence and natural senescence leading to an increase in plant life by about 20days. Transgenic SlDREB3 lines show reduced ABA-mediated inhibition of conductance and transpiration and a greater sensitivity to water stress. Reduction in sensitivity to ABA-mediated stomatal closure leads to higher photosynthetic rates in transgenic plants than controls. Consequently, transgenic SlDREB3 plants produce a larger number of capsules and greater number of seeds with the increase in yield ranging from 18 to 35% in different seasons under well-watered conditions. Root growth, but not shoot growth, also undergoes a profound increase of about 50% in transgenic SlDREB3 lines. The increase occurs in an age-dependent manner with the most prominent changes being observed between 1.5 and 2.5 months in several independent experiments in different years. SlDREB3 thus seems to govern several ABA-regulated processes across tissues, partly through control over ABA levels. It may encode a factor that is most likely a component of the central ABA response machinery.

Analysis and optimization of process parameters for production of polyhydroxyalkanoates along with wastewater treatment by Serratia sp. ISTVKR1.

A previously reported biodegrading bacterial strain Serratia sp. ISTVKR1 was studied for polyhydroxyalkanoate (PHA) production along with wastewater contaminant removal. Nile red fluorescence, GC-MS, FT-IR, NMR and TEM confirmed the accumulation of homopolymer poly-3-hydroxyvalerate (PHV) within the bacterial cells. Analysis of culture after 72h of bacterial treatment showed maximum COD removal (8.4-fold), non-detection of organic contaminants such as 1H-Cyclopropa [a] naphthalene (R.T.=10.12) using GC-MS and increased proportion of elements like Cr, Mn, Fe, Ni, Cu, Cd and Pb in the bacterial cell pellets by SEM-EDX analysis. Optimization of process parameters for enhanced PHA production along with wastewater treatment done using Response Surface Methodology (RSM) showed 5% and 0.74% increase in the PHA production (0.3368±0.13gL-1) and % COD reduction (88.93±2.41) of wastewater, respectively. The study, thus established the production of PHA along with wastewater contaminant removal by Serratia sp. ISTVKR1.

The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study.

Mechanical unfolding studies on Ribonucleic Acid (RNA) structures are a subject of tremendous interest as they shed light on the principles of higher order assembly of these structures. Pseudoknotting is one of the most elementary ways in which this higher order assembly is achieved as discrete secondary structural units in RNA are brought in close proximity to form a tertiary structure. Using steered molecular dynamics (SMD) simulations, we have studied the unfolding of five RNA pseudoknot structures that differ from each other either by base substitutions in helices or loops. Our SMD simulations reveal the manner in which a biologically functional RNA pseudoknot unfolds and the effect of changes in the primary structure on this unfolding pathway, providing necessary insights into the driving forces behind the functioning of these structures. We observed that an A → C mutation in the loop sequence makes the pseudoknot far more resistant against force induced disruption relative to its wild type structure. In contrast to this, a base-pair substitution GC → AU near the pseudoknot junction region renders it more vulnerable to this disruption. The quantitative estimation of differences in the unfolding paths was carried out using force extension curves, potential of mean force profiles, and the opening of different Watson-Crick and non-Watson-Crick interactions. The results provide a quantified view in which the unfolding paths of the small RNA structures can be used for investigating the programmability of RNA chains for designing RNA switches and aptamers as their biological folding and unfolding could be assessed and manipulated.

Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t.

Exportin-t (Xpot) transports mature 5'- and 3'-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes.

Study of optimization of wastewater contaminant removal along with extracellular polymeric substances (EPS) production by a thermotolerant Bacillus sp. ISTVK1 isolated from heat shocked sewage sludge.

The present work involved study of wastewater contaminant removal along with EPS production by a thermotolerant bacterium Bacillus sp. ISTVK1, isolated from heat shocked sewage sludge. EPS production in basal and mineral medium containing 50% filter sterilized wastewater and 0.5% sucrose was found to be 0.83±0.12gL(-1) and 0.31±0.10gL(-1) culture, respectively. GC-MS analysis of EPS revealed the presence of ß-d-glucose, α-d-galactose and ß-d-arabinose. FT-IR spectrum confirmed the presence carbohydrates. Box-Behnken design was used to optimize process parameters for enhanced EPS production along with % COD reduction of wastewater. The optimised conditions when used in a 1.5L bioreactor showed EPS production of 1.67±0.06gL(-1) culture and 93.0±0.21 % COD removal.

Carbon dioxide sequestration by chemolithotrophic oleaginous bacteria for production and optimization of polyhydroxyalkanoate.

The present work involved screening of a previously reported carbon concentrating oleaginous bacterial strain Serratia sp. ISTD04 for production of PHA and optimization of process parameters for enhanced PHA and biomass generation. The selected bacterial strain was screened for PHA production based on Nile red staining followed by visualization under fluorescence microscope. Spectrofluorometric measurement of Nile red fluorescence of the bacterial culture was also done. Confirmatory analysis of PHA accumulation by GC-MS revealed the presence of 3-hydroxyvalerate. Detection of characteristic peaks in the FT-IR spectrum further confirmed the production of PHA by the bacterium. Response Surface Methodology was used for optimization of pH and carbon sources' concentrations for higher PHA production. There was almost a 2 fold increase in the production of PHA following optimization as compared to un-optimized condition. The study thus establishes the production of PHA by Serratia sp. ISTD04.

Combined chemical and toxicological evaluation of leachate from municipal solid waste landfill sites of Delhi, India.

In the present study, landfill leachate of three landfill sites of Delhi, India, was toxico-chemically analyzed for human risk assessment. Raw leachate samples were collected from the municipal solid waste (MSW) landfills of Delhi lacking liner systems. Samples were characterized with relatively low concentrations of heavy metals while the organic component exceeded the upper permissible limit by up to 158 times. Qualitative analysis showed the presence of numerous xenobiotics belonging to the group of halogenated aliphatic and aromatic compounds, polycyclic aromatic hydrocarbons (PAHs), phthalate esters, and other emerging contaminants. Quantitative analysis of PAHs showed that the benzo(a)pyrene-toxic equivalence quotient (BaP-TEQ) ranged from 41.22 to 285.557 ng L(-1). The human risk assessment methodology employed to evaluate the potential adverse effects of PAHs showed that the cancer risk level was lower than the designated acceptable risk of 10(-6). However, significant cytotoxic and genotoxic effects of leachates on HepG2 cell line was observed with MTT EC50 value ranging from 11.58 to 20.44 % and statistically significant DNA damage. Thus, although the leachates contained low concentrations of PAHs with proven carcinogenic potential, but the mixture of contaminants present in leachates are toxic enough to cause synergistic or additive cytotoxicity and genotoxicity and affect human health.

Local structural and environmental factors define the efficiency of an RNA pseudoknot involved in programmed ribosomal frameshift process.

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry.