Comprehensive analysis of non-synonymous missense SNPs of human galactose mutarotase (GALM) gene: an integrated computational approach

Missense Non-synonymous single nucleotide polymorphisms (nsSNPs) of Galactose Mutarotase (GALM) are associated with the Novel type of Galactosemia (Galactosemia type 4) together with symptoms such as high blood galactose levels and eye cataracts. The objective of the present study was to identify deleterious nsSNPs of GALM recorded on the dbSNP database through comprehensive insilico analysis. Among the 319 missense nsSNPs reported, various insilco tools predicted R78S, R82G, A163E, P210S, Y281C, E307G and F339C as the most deleterious mutations. Structural analysis, PTM analysis and molecular dynamics simulations (MDS) were carried out to understand the effect of these mutations on the structural and physicochemical properties of the GALM protein. The residues R82G and E307G were found to be part of the binding site that resulted in decreased surface accessibility. Replacing the charged wild-type residue with a neutral mutant type affected its substrate binding. All 7 mutations were found to increase the rigidity of the protein structure, which is unfavorable during ligand binding. The mutation F339E made the protein structure more rigid than all the other mutations. Y281 is a phosphorylated site, and therefore, less significant structural changes were observed when compared to other mutations; however, it may have significant differences in the usual functioning of the protein. In summary, the structural and functional analysis of missense SNPs of GALM is important to reduce the number of potential mutations to be evaluated in vitro to understand the association with some genetic diseases.Communicated by Ramaswamy H. Sarma.

Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2

Many countries around the world are facing severe challenges due to the recently emerging variants of SARS-CoV-2. Over the last few months, scientists have been developing treatments, drugs, and vaccines to subdue the virus and prevent its transmission. In this context, a peptide-based vaccine construct containing pathogenic proteins of the virus known to elicit an immune response was constructed. An analysis of the spike protein-based epitopes allowed us to design an "epitope-based subunit vaccine" against coronavirus using the approaches of "reverse vaccinology" and "immunoinformatics." Computational experimentation and a systematic, comprehensive protocol were followed with an aim to develop and design a multi-epitope-based peptide (MEBP) vaccine candidate. Our study attempted to predict an MEBP vaccine by introducing mutations of SARS-CoV-2 (Delta, Lambda, Iota, Omicron, and Kappa) in Spike glycoprotein and predicting dual-purpose epitopes (B-cell and T-cell). This was followed by screening the selected epitopes based on antigenicity, allergenicity, and population coverage and constructing them into a vaccine by using linkers and adjuvants. The vaccine construct was analyzed for its physicochemical properties and secondary structure prediction, and a 3D structure was built, refined, and validated. Furthermore, the peptide-protein interaction of the vaccine construct with Toll-like receptor (TLR) molecules was performed. Immune profiling was performed to check the immune response. Codon optimization of the vaccine construct was performed to obtain the GC content before cloning it into the E. coli genome, facilitating its progression it into a vector. Finally, an in-silico simulation of the vaccine-protein complex was performed to comprehend its stability and conformational behavior.

Molecular Modelling and Insilico Engineering of PapMV-CP Towards Display and Development of Capripox Viral Like Particles Based on Immunogenic P32 Envelop Protein is the Homologous of the Vaccinia-Viral H3L Gene: An Insilico Approach

Viral-like particles are assembled from capsid protein structural subunits of different viruses and have ability to establish research in biomedicals, like construction of novel safety vaccines, gene therapy vectors by delivering systems for nucleic acids, small biomolecules and diagnostics. Papaya Mosaic Viral nanoparticals can provide as a vaccine candidate helps to increase the immunity by fusing the epitope based peptide antigen. Capripox viruses are the genus comprises Lymphy skin-disease, Sheep and Goat pox Viruses are notified by The World Animal Health Organization (OIE) based on their economic impotence act as a transboundary animal diseases viruses of sheep, goat, and cattle’s respectively. Plant viral based innovative vaccines have been emerged ineffective vaccine development. This research describes the engineering and development of a new vaccine candidate by display immunogenic peptide using the carrier capsid protein of Papaya Mosaic Virus. The Capripox virus P32 immunogenic protein is homologous of the vaccinia virus H3L gene displayed PapMV CP. The antigenicity of P32 protein epitope lowest score among epitopes C-terminally docked epitopes are EP6 > EP3 > EP8 as well the lowest score among epitopes N-terminally docked epitopes are EP8 > EP3 > EP6 presented on the N-terminus of PMV CP region which are found to be suitable for epitope display. And these modelled immunogenic peptide could be used to develop a viral like particles. Epitope based Antibody developed against immunogenic epitopic regions can contribute to a novel and robust protection from infection. As well might be used for developing cost effective detection kits for Transboundary animal disease viruses.

Computational Identification of microRNA-17-3p in Breast Cancer Cells

BACKGROUND

MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules involved in the RNA silencing and post-transcriptional regulation of gene expression. miRNAs are well conserved in both plants and animals, and are thought to be a vital and evolutionarily ancient component of gene regulation and also act as oncogenes or tumor suppressors. It is known that Express Sequence Tags (EST) are a short sub-sequence of cDNA sequence, which contain information of condition or tissue specific transcripts (coding and non-coding) of an organism.

METHODS

In the present study, we have applied the bioinformatics tools to identify miRNA from breast cancer using EST resource. Through bioinformatics approach, the presence of an EST encoding hsa-miR-17- 3p of breast cancer was identified.

RESULTS

Further studies reveal that hsa-miR-17 is confirmed in the breast cancer specific EST sequence among the predicted miRNAs secondary structure. Moreover, miR-17-3p could be responsible for a tumor suppression, which plays a major role in human breast cancer.

CONCLUSION

Further studies are required to investigate the molecular mechanisms behind miR-17-3p involves in the suppression of breast cancer cells. Interestingly, our target analysis suggesting that all the targets involved in multiple signaling pathways in different cell regulations moreover, we need to have more number of in vitro and in vivo studies that prove miR-17-3p as candidate microRNA for breast cancer cells.

Molecular dynamics and molecular docking studies on E166A point mutant, R274N/R276N double mutant, and E166A/R274N/R276N triple mutant forms of class A β-lactamases

Bacterial resistance to β-lactams antibiotics is a serious threat to human health. The most common cause of resistance to the β-lactams is the production of β-lactamase that inactivates β-lactams. Specifically, class A extended-spectrum β-lactamase produced by antibiotic resistant bacteria is capable of hydrolyzing extended-spectrum Cephalosporins and Monobactams. Mutations in class A β-lactamases play a crucial role in substrate and inhibitor specificity. In this present study, the E166A point mutant, R274N/R276N double mutant, and E166A/R274N/R276N triple mutant class A β-lactamases are analyzed. Molecular dynamics (MD) simulations are done to understand the consequences of mutations in class A β-lactamases. Root mean square deviation, root mean square fluctuation, radius of gyration, solvent accessibility surface area, hydrogen bond, and essential dynamics analysis results indicate notable loss in stability for mutant class A β-lactamases. MD simulations of native and mutant structures clearly confirm that the substitution of alanine at the position of 166, Asparagine at 274 and 276 causes more flexibility in 3D space. Molecular docking results indicate the mutation in class A β-lactamases which decrease the binding affinity of Cefpirome and Ceftobiprole which are third and fifth generation Cephalosporins, respectively. MD simulation of Ceftobiprole-native and mutant type Class A β-lactamases complexes reveal that E166A/R274N/R276N mutations alter the structure and notable loss in the stability for Ceftobirole-mutant type Class A β-lactamases complexes. Ceftobiprole is currently prescribed for patients with serious bacterial infections; this phenomenon is the probable cause for the effectiveness of Ceftobiprole in controlling bacterial infections.

In silico study on Penicillin derivatives and Cephalosporins for upper respiratory tract bacterial pathogens

Upper respiratory tract infection (URTI) is an acute infection which involves the upper respiratory tract: nose, sinuses, tonsils and pharynx. URT infections are caused mainly by pathogenic bacteria like Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus. Conventionally, β-lactam antibiotics are used to treat URT infections. Penicillin binding proteins (PBPs) catalyze the cell wall synthesis in bacteria. β-Lactam antibiotics like Penicillin, Cephalosporins, Carbapenems and Monobactams inhibit bacterial cell wall synthesis by binding with PBPs. Pathogenic bacteria have efficiently evolved to resist these β-lactam antibiotics. New generation antibiotics are capable of inhibiting the action of PBP due to its new and peculiar structure. New generation antibiotics and Penicillin derivatives are selected in this study and virtually compared on the basis of interaction studies. 3-Dimensional (3D) interaction studies between Lactivicin, Cefuroxime, Cefadroxil, Ceftaroline, Ceftobiprole and Penicillin derivatives with PBPs of the above-mentioned bacteria are carried out. The aim of this study was to suggest a potent new generation molecule for further modification to increase the efficacy of the drug for the URTI.

Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis

Mutations in the gene encoding vesicle-associated membrane protein (VAPB) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. The VAPB gene is mapped to chromosome number 20 and can be found at cytogenetic location 20q13.33 of the chromosome. VAPB is seen to play a significant role in the unfolded protein response (UPR), which is a process that suppresses the accumulation of unfolded proteins in the endoplasmic reticulum. Earlier studies have reported two points; which we have analyzed in our study. Firstly, the mutation P56S in the VAPB is seen to increase the stability of the protein and secondly, the mutation P56S in VAPB is seen to interrupt the functioning of the gene and loses its ability to be involved in the activation of the IRE1/XBP1 pathway which leads to ALS. With correlation on the previous research studies on the stability of this protein, we carried out Molecular dynamics (MD) simulation. We analyzed the SNP results of 17 nsSNPs obtained from dbSNP using SIFT, polyphen, I-Mutant, SNP&GO, PhDSNP and Mutpred to predict the role of nsSNPs in VAPB. MD simulation is carried out and plots for RMSD, RMSF, Rg, SASA, H-bond and PCA are obtained to check and prove the stability of the wild type and the mutant protein structure. The protein is checked for its aggregation and the results obtained show changes in the protein structure that might result in the loss of function.

Detection of OXA-1 β-lactamase gene of Klebsiella pneumoniae from blood stream infections (BSI) by conventional PCR and in-silico analysis to understand the mechanism of OXA mediated resistance

Klebsiella pneumoniae strains producing extended-spectrum β-lactamases (ESBL) exhibit resistance to antibiotic classes. The production of ESBLs (TEM-1, TEM-2, SHV-1, OXA-1) results in resistance to ampicillin, ticarcillin, piperacillin and cephalosporins. High levels of β-lactamases leads to development of resistance to β-lactamase inhibitors. The present study deals with characterizing antimicrobial resistance pattern among septicemia causing K. pneumoniae and the prevalence of inhibitor resistant OXA-1 β-lactamase genes among them. Of 151 study isolates, 59 were resistant to piperacillin/tazobactam and these isolates were further selected for blaOXA-1 screening. Amplification of β-lactamases genes by conventional PCR showed the presence of blaOXA-1 genes among 12 K. pneumoniae (20.3%) isolates. OXA-1 β-lactamase producing strains were found to be resistant to piperacillin/tazobactam(100%), levofloxacin (91.6%), amikacin (75%), cefoxitin (50%), ertapenem (25%), imipenem (16.6%) and meropenem (16.6%); all were susceptible to tigecycline. 3D models of OXA-1 β-lactamase were generated and docking was performed with various β-lactam antibiotics. Molecular docking (MD) revealed the molecular basis of drug sensitivity. MD simulation results clearly confirmed the notable loss in stability for tigecycline-blaOXA-1 complex. Findings of the present study will provide useful insights for understanding the mechanism of resistance and help with strategies for the development of new antibiotics. The conventional PCR assay designed in this study can be routinely used in clinical microbiology laboratories to determine the blaOXA-1 genes.

Molecular docking and molecular dynamics studies on β-lactamases and penicillin binding proteins

Bacterial resistance to β-lactam antibiotics poses a serious threat to human health. Penicillin binding proteins (PBPs) and β-lactamases are involved in both antibacterial activity and mediation of β-lactam antibiotic resistance. The two major reasons for resistance to β-lactams include: (i) pathogenic bacteria expressing drug insensitive PBPs rendering β-lactam antibiotics ineffective and (ii) production of β-lactamases along with alteration of their specificities. Thus, there is an urgent need to develop newer β-lactams to overcome the challenge of bacterial resistance. Therefore the present study aims to identify the binding affinity of β-lactam antibiotics with different types of PBPs and β-lactamases. In this study, cephalosporins and carbapenems are docked into PBP2a of Staphylococcus aureus, PBP2b and PBP2x of Streptococcus pneumoniae and SHV-1 β-lactamase of Escherichia coli. The results reveal that Ceftobiprole can efficiently bind to PBP2a, PBP2b and PBP2x and not strongly to SHV-1 β-lactamase. Furthermore, molecular dynamics (MD) simulations are performed to refine the binding mode of the docked complex structure and to observe the differences in the stability of free PBP2x and Ceftobiprole bound PBP2x. MD simulation supports the greater stability of the Ceftobiprole-PBP2x complex compared to free PBP2x. This work demonstrates that potential β-lactam antibiotics can efficiently bind to different types of PBPs for circumventing β-lactam resistance and opens avenues for the development of newer antibiotics that can target bacterial pathogens.

Rupture of the pectoralis major muscle: surgical treatment in athletes

Pectoralis major tendon rupture is a relatively rare injury, resulting from violent, eccentric contraction of the muscle. Over 50% of these injuries occur in athletes, classically in weight-lifters during the 'bench press' manoeuvre. We present 13 cases of distal rupture of the pectoralis major muscle in athletes. All patients underwent open surgical repair. Magnetic resonance imaging was used to confirm the diagnosis in all patients. The results were analysed using (1) the visual analogue pain score, (2) functional shoulder evaluation and (3) isokinetic strength measurements. At the final follow-up of 23.6 months (14-34 months), the results were excellent in six patients, good in six and one had a poor result. Eleven patients were able to return to their pre-injury level of sports. The mean time for a return to sports was 8.5 months. The intraoperative findings correlated perfectly with the reported MRI scans in 11 patients and with minor differences in 2 patients. We wish to emphasise the importance of accurate clinical diagnosis, appropriate investigations, early surgical repair and an accelerated rehabilitation protocol for the distal rupture of the pectoralis major muscle as this allows complete functional recovery and restoration of full strength of the muscle, which is essential for the active athlete.

Allgrove syndrome--a syndrome of primary adrenocortical insufficiency with achalasia of the cardia and deficient tear production

Primary adrenal insufficiency is an uncommon disease which has worldwide distribution. The commonest cause in underdeveloped countries is tuberculosis followed by autoimmune destruction of the adrenal gland. We report a case of a 15 years boy who had congenital adrenal insufficiency associated with achalasia of the cardia and deficient tear secretion.

Adrenal tumor presenting as precocious puberty

We present a case report of a two and a half-year-old boy who presented with precocious puberty. A clinical diagnosis of congenital adrenal hyperplasia was made. Patient was investigated and found to have an adrenocortical tumor. The tumor was about 7 cms in diameter. The tumor was secreting androgens, 17OHP and cortisol. This is an unusual array of hormones to be secreted by an adrenal tumor.

Behavioural intervention in the management of compliance in young type-I diabetics

OBJECTIVES

a) To examine the efficacy of a behavioural intervention programme in the management of compliance in young Type I diabetics, b) To examine the efficacy of a behavioural management programme in enhancing metabolic control in young Type I diabetics, c) To examine the effect of behavioural intervention on level of diabetes knowledge and quality of life in young Type I diabetics.

METHODS

A total of 40 patients (Experimental group n = 20, Control group n = 20) was selected from local hospitals' pediatric, endocrinology and diabetology units. The experimental group received 15 individual sessions of behavioural intervention, consisting of behavioural counseling for family and significant others, relaxation, diabetes education and specific behavioural and cognitive strategies such as reinforcement, target-setting and cognitive restructuring. Assessment was carried out on various psychological measures as well as the glycosylated hemoglobin test (HbA1), at pre and post treatment periods.

RESULTS

The scores of the two groups were compared at post treatment point. Results indicate that there was significant improvement in the experimental group in compliance and metabolic control. There were also significant changes noted in the level of diabetes knowledge as well as the reported quality of life. These changes in compliance and metabolic control were maintained at a three month follow-up period.

CONCLUSIONS

Behavioural intervention can be included as an effective adjunct to routine medical care in the management of young Type I diabetics, especially in the management of compliance and metabolic control, enhancement of knowledge and quality of life.

Alterations in sperm characteristics of follicle-stimulating hormone (FSH)-immunized men are similar to those of FSH-deprived infertile male bonnet monkeys

The quality of sperm ejaculated by bonnet monkeys and normal, healthy proven fertile volunteer men, both actively immunized with ovine follicle-stimulating hormone (oFSH), was examined at different times of study for chromatin packaging and acrosomal glycoprotein concentration by flow cytometry. Susceptibility of sperm nuclear DNA to dithiothreitol (DTT)-induced decondensation, as measured by ethidium bromide binding, was markedly high compared with values at day 0 in men and monkeys during periods when FSH antibody titer was high. Sperm chromatin structure assay yields alphat values, which is another index of chromatin packaging. Higher alphat values, signifying poor packaging, occurred in both species following immunization with heterologous pituitary FSH. The binding of fluorosceinated pisum sativum agglutinin (PSA-FITC) to acrosome of sperm of monkeys and men was significantly low, compared with values at day 0 (control) during periods when cross-reactive FSH antibody titer was high and endogenous FSH was not detectable. Blockade of FSH function in monkeys by active immunization with a recombinant oFSH receptor protein corresponding to a naturally occurring messenger RNA (mRNA) also resulted in production of sperm with similar defects in chromatin packaging and reduced acrosomal glycoprotein concentration. Thus, it appears that in monkeys and men, lack of FSH signaling results in production of sperm that exhibit defective chromatin packaging and reduction in acrosomal glycoprotein content. These characteristics are similar to that exhibited by sperm of some class of infertile men. Interestingly, these alterations in sperm quality occur well ahead of decreased sperm counts in the ejaculate.

Laparoscopic hysterectomy with automatic stapling devices

PURPOSE

To evaluate outcomes including operating time, blood loss, length of stay (LOS), return to work and complications of laparoscopic hysterectomy performed with automatic stapling devices.

METHODS

Between 6/11/91 and 11/23/95, 127 laparoscopic hysterectomies were performed with automatic stapling devices. On an average, 6 firings with the stapler were done per case. Postoperative telephone survey and retrospective review of records were done.

RESULTS

Data averages for operating time, blood loss, LOS and return to work, respectively, were 90 minutes, 190 cc's, 1.1 day and 2 weeks. Significant complications included delayed postoperative bleeding in 4 patients, all of which occurred within the first 35 cases. One was controlled laparoscopically and 3 others required exploratory laparotomies. Since certain precautionary measures as described were taken, hemorrhagic complications were eliminated.

CONCLUSIONS

Laparoscopic hysterectomy can be performed safely and effectively with automatic stapling devices in properly selected patients. A potential hazard inherent with this technique includes intraoperative and postoperative bleeding from the staple lines, the incidence of which can be minimized by taking certain precautionary measures such as the use of white cartridges only and bipolar desiccation of staple lines when indicated.

Inhibition of cold insolubility of an IgA cryoglobulin by decanedicarboxylic acid and related compounds

Cold insolubility of a serum IgA cryoimmunoglobulin was found to be inhibited by the addition of 1.5 mM sodium decanedicarboxylate in vitro. The patient with the cryoglobulin had advanced multiple myeloma complicated by severe hyperviscosity that caused lethargy and episodic loss of consciousness. Decanedicarboxylic acid administered orally resulted in transient relief of symptoms and the loss of cryoprecipitability of the paraprotein. Further in vitro studies revealed that sodium salts of long-chain monocarboxylic acids with a minimum of eight carbons, and dicarboxylic acids with a minimum of 12 carbons inhibited cryoprecipitation. Salts of short-chain carboxylic acids, by contrast, enhanced cryoprecipitation. Sodium phenolate and sodium salts of benzoic acid, 2,4-DNP, phenylpropionic acid, and salicylic acid were also inhibitory. These latter compounds, which have a ring structure, did not cause precipitation at any concentration. It was demonstrated that the presence of a free carboxylic group was required for these activities; conversion of carboxylic acid to amide resulted in the loss of both the inhibitory and cryoprecipitation-enhancing effects. Normal plasma, or plasma from five other patients who had IgG, IgM, or mixed-type cryoglobulinemia, were not affected by any of these compounds. It is suggested that in selected cases of hyperviscosity syndrome associated with cryoglobulinemia, some of these compounds, especially monocarboxylic acids with appropriate chain lengths, or those with a ring structure, may have therapeutic applications.