Forecasting of monthly relative humidity in Delhi, India, using SARIMA and ANN models.

Relative humidity plays an important role in climate change and global warming, making it a research area of greater concern in recent decades. The present study attempted to implement seasonal autoregressive moving average (SARIMA) and artificial neural network (ANN) with multilayer perceptron (MLP) models to forecast the monthly relative humidity in Delhi, India during 2017-2025. The average monthly relative humidity data for the period 2000-2016 have been used to carry out the objectives of the proposed study. The forecast trend in relative humidity declines from 2017 to 2025. The accuracy of the models has been measured using root mean squared error (RMSE) and mean absolute error (MAE). The results showed that the SARIMA model provides the forecasted relative humidity with RMSE of 6.04 and MAE of 4.56. On the other hand, MLP model reported the forecasted relative humidity with RMSE of 4.65 and MAE of 3.42. This study concluded that the ANN model was more reliable for predicting relative humidity than SARIMA model. Supplementary Information: The online version contains supplementary material available at 10.1007/s40808-022-01385-8.

A nonlinear epidemiological model considering asymptotic and quarantine classes for SARS CoV-2 virus.

In this article, we develop a mathematical model considering susceptible, exposed, infected, asymptotic, quarantine/isolation and recovered classes as in case of COVID-19 disease. The facility of quarantine/isolation have been provided to both exposed and infected classes. Asymptotic individuals either recovered without undergo treatment or moved to infected class after some duration. We have formulated the reproduction number for the proposed model. Elasticity and sensitivity analysis indicates that model is more sensitive towards the transmission rate from exposed to infected classes rather than transmission rate from susceptible to exposed class. Analysis of global stability for the proposed model is studied through Lyapunov's function.

Novel mutations in the antifolate drug resistance marker genes among Plasmodium vivax isolates exhibiting severe manifestations.

Plasmodium vivax is the predominant species of the human malaria parasite present in the Indian subcontinent. There have been recent reports on Chloroquine (CQ) resistance and severe manifestations shown by P. vivax from different regions of the world including India. This study focuses on Bikaner, India where during the last few years there have been continuous reports of severe manifestations by both Plasmodium falciparum and P. vivax. This region has a widespread use of Chloroquine and Sulfadoxine-Pyrimethamine for the treatment of malaria, but the resistance profiles of these drugs are not available. We report here the profile of mutations in marker genes associated with Chloroquine and antifolate drug resistance among the P. vivax parasites obtained from patients with severe (n=30) and non-severe (n=48) manifestations from this region. Most isolates showed the wild type alleles for both the Chloroquine and antifolate resistance markers (P<0.0005). Except for one isolate showing Y976F mutation in the Pvmdr-1 gene, no reported mutation was observed in the Pvmdr-1 or Pvcrt gene. This is in accordance with the fact that till date no Chloroquine resistance has been reported from this region. However, the single isolate with a mutation in Pvmdr-1 may suggest the beginning of the trend towards decreased susceptibility to Chloroquine. The frequency of PvDHFR-PvDHPS two locus mutations was higher among the patients showing severe manifestations than the patient group with non-severe (uncomplicated) malaria (P<0.003). None of the parasites from patients with uncomplicated P. vivax malaria showed the mutant PvDHPS genotype. Novel mutations in PvDHFR (S117H) and PvDHPS (F365L, D459A and M601I) were observed only in the parasite population obtained from patients exhibiting severe complications. Preliminary homology modeling and molecular docking studies predicted that these mutations apparently do not have any effect on the binding of the drug molecule to the enzyme. However, the presence of novel mutations in the PvDHPS gene indicate a degree of polymorphism of this molecule which is in contrast to available published information.

Peroxynitrite-induced modification of H2A histone presents epitopes which are strongly bound by human anti-DNA autoantibodies: role of peroxynitrite-modified-H2A in SLE induction and progression.

Peroxynitrite is a potent oxidant and nitrating agent and has in vivo existence. It is a powerful proinflammatory substance and may increase vascular permeability in inflamed tissues. Systemic lupus erythematosus (SLE) is an autoimmune inflammatory disease of unknown etiology. Since its discovery, numerous self- and non-self, nuclear, and cytoplasmic antigens have been suggested as stimuli for SLE initiation, but the exact trigger is yet to be identified. In this study, an attempt has been made to investigate the binding characteristics of SLE anti-DNA autoantibodies to native DNA and native and peroxynitrite-modified H2A histone to explore the possible role of modified protein antigen(s) in SLE initiation and progression. The nuclear protein (H2A histone) was modified by peroxynitrite synthesized in our laboratory. The peroxynitrite-modified H2A revealed generation of nitrotyrosine, dityrosine, and carbonyls when subjected to investigation by physicochemical methods. Binding characteristics and specificity of SLE anti-DNA antibodies were analyzed by direct binding and inhibition enzyme-linked immunosorbent assay. The data show preferential binding of SLE autoantibodies to peroxynitrite-modified H2A histone in comparison with native H2A histone or native DNA. A band shift assay further substantiated the enhanced recognition of peroxynitirite-modified H2A histone by anti-DNA autoantibodies. The results suggest that peroxynitrite modification of self-antigen(s) can generate neoepitopes capable of inducing SLE characteristic autoantibodies. The preferential binding of peroxynitrite-modified H2A histone by SLE anti-DNA antibodies points out the likely role of oxidatively modified and nitrated H2A histone in the initiation/progression of SLE. Moreover, oxidatively modified and nitrated nuclear protein antigen, rather than nucleic acid antigens, appear to be more suitable as a trigger for SLE.

Physicochemical studies on peroxynitrite-modified H3 histone.

Histones are DNA protective proteins and may adopt different structures under nitrosative stress. Peroxynitrite is a powerful oxidant and nitrating agent and has in vivo existence. In this communication, we report effect of peroxynitrite-mediated oxidation and nitration on the structure of calf thymus H3 histone. Fine details of peroxynitrite-modified H3 histone were worked out by UV, fluorescence, circular dichroism and Fourier-transformed infrared spectroscopy and polyacrylamide gel. The results revealed that peroxynitrite-mediated nitration and oxidation in H3 histone produced partially folded structure in comparison to the intrinsically disordered structure of native H3 histone. It may be concluded that the H3 histone, constituent of core histones, is highly sensitive to peroxynitrite and can adopt different structures under nitrosative stress in order to protect the packaged DNA from the deleterious insult of peroxynitrite.

Molecular typing of methicillin-resistant Staphylococcus aureus strains by PCR-RFLP of SPA gene: a reference laboratory perspective.

PURPOSE: To characterize methicillin-resistant Staphylococcus aureus (MRSA) strains by molecular typing based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of spa gene and to assess the utility of spa genotyping over bacteriophage typing in the discrimination of the strains. MATERIALS AND METHODS: Studies were undertaken on 125 MRSA strains representing the most predominant phage types and the non phage typeable strains. Strains were typed by bacteriophage typing and PCR-RFLP of spa gene. DNA sequence analysis of the amplified spa gene fragment of the representative RFLP patterns was performed using standard protocols. RESULTS: All the strains resistant to oxacillin were found to contain mec A gene. Fifty-two per cent of these strains were typeable by the international basic set of 23 phages. Five different PCR-RFLP patterns were observed among 125 MRSA strains. Non phage typeable strains were differentiated into four PCR-RFLP patterns. Sequencing of the spa gene from the representative strains of each RFLP pattern confirmed the length of these restriction fragments due to variation in the 24 bp and the 174 bp tandem repeats. It also revealed the presence of three new spa repeat patterns. CONCLUSION: The study demonstrates the importance of spa genotyping in the discrimination of MRSA strains, which were otherwise indistinguishable by bacteriophage typing. spa genotyping allowed differentiation of strains within a particular phage type. Nucleotide sequencing of isolates of different PCR-RFLP patterns indicated a correlation between the RFLP patterns of a variable number of tandem repeats and the phage type. The study provides valuable information on the epidemiological characterization of MRSA strains.

Cellular immune responses to recombinant Plasmodium vivax tryptophan-rich antigen (PvTRAg) among individuals exposed to vivax malaria.

Plasmodium vivax, the most widespread species of human malaria parasite responsible for 70-80 million cases each year requires a vaccine. In recent years, many potential vaccine candidate antigens have been identified from P. vivax including PvTRAg. We describe here cellular immune response to recombinant PvTRAg expressed in Escherichia coli. The in vitro stimulation of PBMCs derived from P. vivax-exposed individuals (n = 16) showed strong proliferative response (SI > 2.2) to PvTRAg as compared to PBMCs from normal healthy controls (n = 8). Although both Th1 (IFN-gamma, TNF-alpha and IL-12) and Th2 (IL-4 and IL-10) cytokines were secreted by the PBMCs of the P. vivax-exposed individuals in response to PvTRAg, the overall response was more inclined towards Th2. In conclusion, recombinant PvTRAg was found to elicit strong cellular immune response among the P. vivax-exposed individuals.

Histone as future drug target for malaria.

Malaria continues to be a major cause of mortality and morbidity in tropical countries and affecting around 100 countries of the world. As per WHO estimates, 300-500 million are being infected and 1-3 million deaths annually due to malaria. With the emerging knowledge about genome sequence of all the three counterparts involved in the disease of malaria, the parasite Plasmodium, vector Anopheles and host Homo sapien have helped the scientists to understand interactions between them. Simultaneous advancement in technology further improves the prospects to discover new targets for vaccines and drugs. Though the malaria vaccine is still far away in this situation there is need to develop a potent and affordable drug(s). Histones are the key protein of chromatin and play an important role in DNA packaging, replication and gene expression. They also show frequent post-translation modifications. The specific combinations of these posttranslational modifications are thought to alter chromatin structure by forming epigenetic bar codes that specify either transient or heritable patterns of genome function. Chromatin regulators and upstream pathways are therefore seen as promising targets for development of therapeutic drugs.

Genetic alteration in drug resistance markers of Plasmodium falciparum.

Plasmodium falciparum shows plasticity in its genome. For its survival it can delete certain genes (or portions) if not needed for its growth and has the capability to regulate its genes under various stages of its life cycle as well as under unfavourable environmental conditions. Parasite shows enormous amount of antigenic variation under immune pressure leading to the emergence of vaccine resistant strains. Similarly, under drug pressure it allows mutations to settle in the target genes. It is becoming more and more clear that with the continuous exposure to a drug, the parasite accumulates more and more number of mutations in these genes. By measuring the number of these point mutations among field isolates one can predict the efficacy of a particular drug. Therefore, these markers are useful tools at epidemiological level. This molecular surveillance can also help in slowing down the drug resistance if supported by a careful drug usage policy. Further studies are required to develop molecular markers for rest of the antimalarial drugs as well as the improvement on the existing molecular tools for accurate and rapid detection of drug resistant malaria.

Prevalence of the K76T mutation in the pfcrt gene of Plasmodium falciparum among chloroquine responders in India.

Chloroquine-resistant Plasmodium falciparum needs to be monitored in the field for effective malaria control strategies. A point mutation K76T in the P. falciparum chloroquine resistance transporter (Pfcrt) protein has recently been proposed as a molecular marker for the faster detection of chloroquine-resistant falciparum malaria in field. We describe here the evaluation of this marker in Indian P. falciparum isolates. A total of 274 Indian P. falciparum isolates were analyzed for the K76T mutation. This mutation was detected in all the clinical isolates obtained from the in vivo chloroquine non-responders. But majority of the clinical isolates from chloroquine responders (71 of 74 patients, i.e. 96%) also harbored this mutation. The K76T mutation was indeed highly prevalent (91%) among 213 clinical isolates. There was a significant association between K76T mutation and the in vitro chloroquine response (P<0.05) but six isolates showed discordant results. In conclusion, the K76T mutation fails to differentiate majority of the chloroquine responders from that of the non-responders and thus will be of limited use in the field in India.

Malaria genome project and its impact on the disease.

Malaria remains uncontrolled to-date due to lack of effective parasite and vector control strategies. With the completion of the host, parasite and vector genome projects more suitable and effective disease control measures can be achieved. Here we have reviewed the Plasmodium falciparum genome project and its impact on malaria research in future. The parasite genome project has revealed certain metabolic pathways which can be targeted to develop antimalarial drugs. It has also identified large number of potential antigens for the future potential vaccines. Now the researchers in the malaria field can plan to take up the studies, which can yield more fruitful results within the limited financial resources using bioinformatics, proteomics, structural, functional and comparative genomics, etc.

Allelic variation in the cg2 gene does not correlate with chloroquine resistance among Indian Plasmodium falciparum isolates.

The cg2 gene of Plasmodium falciparum has been proposed to be associated with chloroquine resistance. Here we describe PCR amplification and sequencing of all the four repeat regions (kappa (kappa), gamma (gamma), psi (psi) and omega (omega)) of this gene, from Indian isolates. There were variant forms for each of these repeat regions (two for kappa and gamma, and three for psi and omega) among the 123 Indian isolates of P. falciparum. Among these isolates certain forms of psi and omega repeats were uniquely present while some of the reported forms of the kappa and omega repeats were absent. The pattern of combination of all four repeat regions of cg2 gene (genotype) was analysed from 52 isolates. A total of 11 different genotypes were observed among these cases, of which 10 were unique to Indian isolates. Certain genotypes were more common than others. The nucleotide sequencing of all the four repeat regions revealed that Indian isolates have some unique repeating units within the gamma and omega domains. Altogether, the PCR and sequencing results showed that there was an unrelatedness between cg2 repeats and chloroquine resistance.

Computer modeling of small heat-shock metalloprotease of the human malaria parasite Plasmodium vivax.

We present here computer generated model of N-terminal fragment, amino acids (aa) 36-245, of a Plasmodium vivax heat shock metalloprotease called PVHSP28, whose gene was cloned and characterised earlier. The fragment showed homology with HSPs from many organisms, including Escherichia coli and Haemophilus influenzae. PVHSP28 had the signature sequence 'HEXXH' and 'EXXXD' of Zinc metalloproteases. Being the first malarial HSP possessing metalloprotease activity, PVHSP28 is an ideal target for the design of new anti-malarial drugs. However, except for a small region (aa 62-132) which had 24.6% sequence similarity with 1TAQ (a DNA polymerase), it did not show sequence similarity with any published structures in protein data bank. Hence it could not be modelled using any automated modeling programs. We modelled 36-245 aa of PVHSP28 using predicted secondary structure as well as experimentally determined and predicted properties of the protein on the basis of its amino acid sequence, using various Internet tools and in-house package MODEL. The model was energy minimised using Sander's module of AMBER 5.0, working on a Silicon Graphics machine, with all atom force field.

Complete nucleotide sequence of the 6 kb element and conserved cytochrome b gene sequences among Indian isolates of Plasmodium falciparum.

The malaria parasite contains a nuclear genome with 14 chromosomes and two extrachromosomal DNA molecules of 6 kb and 35 kb in size. The smallest genome, known as the 6 kb element or mitochondrial DNA, has been sequenced from several Plasmodium falciparum isolates because this is a potential drug target. Here we describe the complete nucleotide sequence of this element from an Indian isolate of P. falciparum. It is 5967 bp in size and shows 99.6% homology with the 6 kb element of other isolates. The element contains three open reading frames for mitochondrial proteins-cytochrome oxidase subunit I (CoI), subunit III (CoIII) and cytochrome b (Cyb) which were found to be expressed during blood stages of the parasite. We have also sequenced the entire cyb gene from several Indian isolates of P. falciparum. The rate of mutation in this gene was very low since 12 of 14 isolates showed the identical sequence. Only one isolate showed a maximum change in five amino acids whereas the other isolate showed only one amino acid change. However, none of the Indian isolates showed any change in those amino acids of cyb which are associated with resistance to various drugs as these drugs are not yet commonly used in India.

Antibodies detected against Plasmodium falciparum haemozoin with inhibitory properties to cytokine production.

Haemozoin, the malaria pigment, regulates the synthesis of several host cytokines and has been found to be associated with the disease severity. Here we describe that malarial patients produce a significant amount of anti-haemozoin IgM antibodies. Levels of these antibodies were higher among the complicated Plasmodium falciparum cases compared to the non-complicated P. falciparum group and Plasmodium vivax patients. The P. falciparum haemozoin also induced the synthesis of tumour necrosis factor-alpha (TNF-alpha) and interleukin-1beta (IL-1beta) by the monocytes of the healthy individuals, but the production of these cytokines by the monocytes was inhibited in the presence of the anti-haemozoin IgM antibodies. Therefore, it seems that the host produces these antibodies (mainly IgM types) during malarial infection that can influence the progression of the disease by inhibiting the production of cytokines.

Epidemiologic investigations of a malaria outbreak in northern Delhi area.

Epidemiologic investigations revealed a 56.7 and 13.32% slide positivity rate in febrile and afebrile malaria cases, respectively. In both cases, Plasmodium falciparum was predominant. Anopheles culicifacies resistant to dichlorodiphenyltrichloroethane and benzene hexachloride (hexachlorocyclohexane) was found breeding profusely in pools and ponds created by excavation of earth around brick kiln in the region. Furthermore, children were not found to be producing significant levels of antibodies and a large percentage of patients harbored chloroquine-resistant parasites. Also, more than 1 P. falciparum strain was present in the population. We detected 2 strains, VI and VII, of which type VI was predominant.

Metalloprotease activity in a small heat shock protein of the human malaria parasite Plasmodium vivax.

The malaria parasite affects millions of people each year, lives and multiplies in two different hosts, and synthesizes a large number of proteases and heat shock proteins (HSPs) for its survival. We describe here the characterization of a metalloprotease activity which resides in the small HSP (PVHSP28) of the common but noncultivable human malaria parasite Plasmodium vivax. The protein is expressed by erythrocytic stages of the parasite. It is expressed as a approximately 55-kDa polypeptide which is then processed to the 28-kDa mature protein. The latter was found to be an active protease in gelatin zymography. This protease showed its optimal activity at 37 degrees C (pH 7.6). It also retained its proteolytic activity at higher temperatures of up to 55 degrees C. The enzyme belongs to the metalloprotease class, as its proteolytic activity was most effectively blocked by 1,10-phenanthroline and was restored to a maximal level by the addition of zinc metal ions. Inhibitors for the cysteine, serine, and aspartate classes of proteases were ineffective against this enzyme. A homology search indicates that PVHSP28 probably belongs to a new class of HSPs which possess the metalloprotease signature sequence.

Comparison of various calpain inhibitors in reduction of light scattering, protein precipitation and nuclear cataract in vitro.

PURPOSE: To compare effects of calpain inhibitors on in vitro light-scattering in rat lens soluble protein and calcium-ionophore (A23187)-induced cataract formation in cultured rat lenses. METHODS: Rat lens soluble protein was hydrolyzed for 24 hours by activation of endogenous lens calpain. Ten calpain inhibitors were tested in this model at 10 and 25 microM concentration. As an index of protein precipitation, light scattering was measured daily at 405 nm for 8 days. Lens proteins were analyzed by isoelectric-focussing. Subsequently, rat lenses were cultured for 5 days with 10 microM A23187. Calpain inhibitors (SJA6017, MDL28170, AK295 and PD150606), which inhibited light-scattering were tested at 100 microM concentration in this model. Cataract evaluation, isoelectric-focussing and calcium determinations were performed. RESULTS: At 25 microM concentration AK295, SJA6017, E-64, PD-150606 and MDL28170 produced greater than 25% inhibition of light-scattering. Isoelectric-focussing revealed that addition of Ca(2+) produced characteristic crystallin proteolysis and aggregation patterns. AK295, SJA6017, MDL28170 and E64c prevented these changes. Lenses cultured in A23187 exhibited nuclear cataract, elevated calcium and proteolysis and aggregation of crystallins. Co-culture with SJA6017, MDL28170 and E64c reduced A23187-induced nuclear opacities, proteolysis and aggregation of crystallins without affecting increased total calcium. CONCLUSIONS: Endogenous calpain-activation model and A23187-induced cataract model can be used sequentially to screen calpain inhibitors for potential anti-cataract activity. Proteolytic changes in lens cortex after exposure to A23187 are also due to calpain activation. AK295, SJA6017 and MDL28170 possess efficacy against calcium-induced models of rodent cataracts. Use of calpain inhibitors represents a promising approach to cataract therapy.