Insights into the differential proteome landscape of a newly isolated Paramecium multimicronucleatum in response to cadmium stress.

Employing microbial systems for the bioremediation of contaminated waters represent a potential option, however, limited understanding of the underlying mechanisms hampers the implication of microbial-mediated bioremediation. The omics tools offer a promising approach to explore the molecular basis of the bioremediation process. Here, a mass spectrometry-based quantitative proteome profiling approach was conducted to explore the differential protein levels in cadmium-treated Paramecium multimicronucleatum. The Proteome Discoverer software was used to identify and quantify differentially abundant proteins. The proteome profiling generated 7,416 peptide spectral matches, yielding 2824 total peptides, corresponding to 989 proteins. The analysis revealed that 29 proteins exhibited significant (p ≤ 0.05) differential levels, including a higher abundance of 6 proteins and reduced levels of 23 proteins in Cd2+ treated samples. These differentially abundant proteins were associated with stress response, energy metabolism, protein degradation, cell growth, and hormone processing. Briefly, a comprehensive proteome profile in response to cadmium stress of a newly isolated Paramecium has been established that will be useful in future studies identifying critical proteins involved in the bioremediation of metals in ciliates. SIGNIFICANCE: Ciliates are considered a good biological indicator of chemical pollution and relatively sensitive to heavy metal contamination. A prominent ciliate, Paramecium is a promising candidate for the bioremediation of polluted water. The proteins related to metal resistance in Paramecium species are still largely unknown and need further exploration. In order to identify and reveal the proteins related to metal resistance in Paramecia, we have reported differential protein abundance in Paramecium multimicronucleatum in response to cadmium stress. The proteins found in our study play essential roles during stress response, hormone processing, protein degradation, energy metabolism, and cell growth. It seems likely that Paramecia are not a simple sponge for metals but they could also transform them into less toxic derivatives or by detoxification by protein binding. This data will be helpful in future studies to identify critical proteins along with their detailed mechanisms involved in the bioremediation and detoxification of metal ions in Paramecium species.

Exploring the medicinal potential of Dark Chemical Matters (DCM) to design promising inhibitors for PLpro of SARS-CoV-2 using molecular screening and simulation approaches.

The growing concerns and cases of COVID-19 with the appearance of novel variants i.e., BA.2.75. BA.5 and XBB have prompted demand for more effective treatment options that could overcome the risk of immune evasion. For this purpose, discovering novel small molecules to inhibit druggable proteins such as PLpro required for viral pathogenesis, replication, survival, and spread is the best choice. Compounds from the Dark chemical matter (DCM) database is consistently active in various screening tests and offer intriguing possibilities for finding drugs that are extremely selective or active against uncommon targets. Considering the essential role of PLpro, the current study uses DCMdatabase for the identification of potential hits using in silico virtual molecular screening and simulation approaches to inhibit the current and emerging variants of SARS-CoV-2. Our results revealed the 10 best compounds with docking scores between -7.99 to -7.03 kcal/mol better than the control drug (GRL0617) among which DC 5977-0726, DC 6623-2024, DC C879-0379 and DC D135-0154 were observed as the best hits. Structural-dynamics properties such as dynamic stability, protein packing, and residue flexibility demonstrated the pharmacologically favorable properties of these top hits in contrast to GRL0617. The hydrogen bonding half-life revealed that Asp164, Arg166, Tyr264, and Tyr268 have major contributions to the hydrogen bonding during the simulation. However, some of the important hydrogen bonds were missing in the control drug (GRL0617). Finally, the total binding free energy was reported to be -34.41 kcal/mol for GRL0617 (control), -41.03 kcal/mol for the DC5977-0726-PLpro, for the DC6623-2024-Plpro complex the TBE was -48.87 kcal/mol, for the for DCC879-0379-Plpro complex the TBE was -45.66 kcal/mol while for the DCD135-0154-PLpro complex the TBE was calculated to be -40.09 kcal/mol respectively, which shows the stronger potency of these compounds against PLpro and further in in vivo and in vitro test are required for the possible usage as potential drug against SARS-CoV-2.

A sub-chronic feeding study of dual toxin insect-resistant transgenic maize (CEMB-413) on Wistar rats.

Genetically modified (GM) crops expressing insecticidal crystal proteins are widely accepted worldwide, but their commercial utilization demands comprehensive risk assessment studies. A 90-day risk assessment study was conducted on Wistar rats fed with GM maize (CEMB-413) expressing binary insect-resistant genes (cry1Ac and cry2Ab) at low (30%) and high (50%) dose along with a control diet group. The study used fifty Wistar rats randomly distributed in five treatment groups. Our study revealed that compared to controls, GM diet had no adverse effects on animal's health, including body weight, food consumption, clinical pathological parameters, serum hormone levels and histological parameters of testes and ovaries of rats. Differences were observed in transcripts levels of fertility related genes, but these were independent of treatment with GM diet.

Proteomics-based vaccine targets annotation and design of subunit and mRNA-based vaccines for Monkeypox virus (MPXV) against the recent outbreak.

Monkeypox Virus (MPXV) is a growing public health threat with increasing cases and fatalities globally. To date, no specific vaccine or small molecule therapeutic choices are available for the treatment of MPXV disease. In this work, we employed proteomics and structural vaccinology approaches to design mRNA and multi-epitopes-based vaccines (MVC) against MPXV. We first identified ten proteins from the whole proteome of MPXV as potential vaccine targets. We then employed structural vaccinology approaches to map potential epitopes of these proteins for B cell, cytotoxic T lymphocytes (CTL), and Helper T lymphocytes (HTL). Finally, 9 CTL, 6 B cell, and 5 HTL epitopes were joined together through suitable linkers to construct MVC (multi-epitope vaccine) and mRNA-based vaccines. Molecular docking, binding free energy calculation, and in silico cloning revealed robust interaction of the designed MVC with toll-like receptor 2 (TLR2) and efficient expression in E. Coli K12 strain. The immune simulation results revealed that the antigen titer after the injection reached to the maximum level on the 5th day and an abrupt decline in the antigen titer was observed upon the production of IgM, IgG and IgM + IgG, dendritic cells, IFN-gamma, and IL (interleukins), which suggested the potential of our designed vaccine candidate for inducing an immune response against MPXV.

Transcription elongation factor AtSPT4-2 positively modulates salt tolerance in Arabidopsis thaliana.

BACKGROUND: Salt stress significantly influences plant growth and reduces crop yield. It is highly anticipated to develop salt-tolerant crops with salt tolerance genes and transgenic technology. Hence, it is critical to identify salt tolerance genes that can be used to improve crop salt tolerance. RESULTS: We report that the transcription elongation factor suppressor of Ty 4-2 (SPT4-2) is a positive modulator of salt tolerance in Arabidopsis thaliana. AtSPT4-2 expression is induced by salt stress. Knockout mutants of AtSPT4-2 display a salt-sensitive phenotype, whereas AtSPT4-2 overexpression lines exhibit enhanced salt tolerance. Comparative transcriptomic analyses revealed that AtSPT4-2 may orchestrate the expression of genes associated with salt tolerance, including stress-responsive markers, protein kinases and phosphatases, salt-responsive transcription factors and those maintaining ion homeostasis, suggesting that AtSPT4-2 improves salt tolerance mainly by maintaining ion homeostasis and enhancing stress tolerance. CONCLUSIONS: AtSPT4-2 positively modulates salt tolerance by maintaining ion homeostasis and regulating stress-responsive genes and serves as a candidate for the improvement of crop salt tolerance.

Lack of CpG islands in human unitary pseudogenes and its implication.

CpG islands (CGIs) are aggregation of CpG dinucleotides in the promoters of mammalian genes. These CGIs are present in almost all the housekeeping genes and some tissue-specific genes in the mammalian genome. Extensive research has been done on the prevalence and role of CGIs in protein-coding genes. However, little is known about CGIs in pseudogenes. In the current research project, we focused on CGIs in three main classes of pseudogenes e.g., duplicated pseudogenes (DPGs), processed pseudogenes (PPGs), and unitary pseudogenes (UPGs). We discovered a predominant absence of CGIs in the promoters of all three pseudogenes. We also compared the CGI profile of these pseudogenes with their parent genes and found that unitary pseudogenes (UPGs) differ from the DPGs and PPGs in the sense that in the latter, lack of CGIs is a consequential event while in UPGs, this lack of CGIs in their promoters is not a result of pseudogenization process. We also discussed the implication of the results obtained from this comparison. To our knowledge, this is the first-ever study highlighting this aspect of UPGs throwing new insights into the evolution of genome in general and especially in the context of pseudogenes.

A Rare Case Report of Crigler Najjar Syndrome Type II.

Crigler-Najjar syndrome is an inborn error of metabolism caused by a point mutation in one of the five exons of UGT1A1 gene, the product of which is responsible for elimination of bilirubin via bile. A number of hyperbilirubinemia disorders similar to Crigler-Najjar syndrome are reported, but they differ in their level of unconjugated bilirubin and responses to the treatment. Here we report a 14-year-old male patient admitted to hospital with the complaint of vomiting and frequent tonsillitis. Further examination revealed that he was jaundiced since birth and had a family history of similar disorder. This report is about an extremely rare case of Crigler-Najjar syndrome type II and also management of the condition to provide the patient with a healthy lifestyle.

Are Consanguineous Marriages to Blame for Usher Syndrome Type 1, a Rare Disease in Pakistan?

Usher syndrome type I is a rare genetic autosomal recessive disease caused by mutations in specific genes that provide instructions for making proteins involved in normal hearing, vision, and balance. It is characterized by hearing impairment due to the inability of auditory nerves to send sensory input to the brain leading to hearing loss along with retinitis pigmentosa (RP), which is a progressive, bilateral, symmetrical retinal degeneration involving photoreceptor cells. We report a 32-year-old male patient who presented to us with complaints of night blindness and progressive vision loss for the past 20 years. He had bilateral hearing loss leading to deaf-mutism. In addition, his developmental milestones were delayed. His fundoscopic findings were consistent with RP and his electroretinography confirmed reduced retinal activity. Pure tone audiometry confirmed bilateral sensory neural hearing. His mother was a known case of Usher syndrome type 1. His family history was remarkable for multiple consanguineous marriages in both his parental and maternal families and a confirmed diagnosis of Usher syndrome in paternal uncle. The patient was tried on hearing aids and vitamin A medication but with minimal improvement in his overall condition. A multidisciplinary approach, involving an audiologist, speech, and language therapist was adapted to help the patient. Early genetic testing can help diagnose such cases in its early stages and genetic counseling regarding the detrimental effects of consanguineous marriages can play a very positive role in genetic diseases, especially those with autosomal recessive inheritance patterns.

Green and Cost-Effective Synthesis of Metallic Nanoparticles by Algae: Safe Methods for Translational Medicine.

Metal nanoparticles (NPs) have received much attention for potential applications in medicine (mainly in oncology, radiology and infectiology), due to their intriguing chemical, electronical, catalytical, and optical properties such as surface plasmon resonance (SPR) effect. They also offer ease in controlled synthesis and surface modification (e.g., tailored properties conferred by capping/protecting agents including N-, P-, COOH-, SH-containing molecules and polymers such as thiol, disulfide, ammonium, amine, and multidentate carboxylate), which allows (i) tuning their size and shape (e.g., star-shaped and/or branched) (ii) improving their stability, monodispersity, chemical miscibility, and activity, (iii) avoiding their aggregation and oxidation over time, (iv) increasing their yield and purity. The bottom-up approach, where the metal ions are reduced in the NPs grown in the presence of capping ligands, has been widely used compared to the top-down approach. Besides the physical and chemical synthesis methods, the biological method is gaining much consideration. Indeed, several drawbacks have been reported for the synthesis of NPs via physical (e.g., irradiation, ultrasonication) and chemical (e.g., electrochemisty, reduction by chemicals such as trisodium citrate or ascorbic acid) methods (e.g., cost, and/ortoxicity due to use of hazardous solvents, low production rate, use of huge amount of energy). However, (organic or inorganic) eco-friendly NPs synthesis exhibits a sustainable, safe, and economical solution. Thereby, a relatively new trend for fast and valuable NPs synthesis from (live or dead) algae (i.e., microalgae, macroalgae and cyanobacteria) has been observed, especially because of its massive presence on the Earth's crust and their unique properties (e.g., capacity to accumulate and reduce metallic ions, fast propagation). This article discusses the algal-mediated synthesis methods (either intracellularly or extracellularly) of inorganic NPs with special emphasis on the noblest metals, i.e., silver (Ag)- and gold (Au)-derived NPs. The key factors (e.g., pH, temperature, reaction time) that affect their biosynthesis process, stability, size, and shape are highlighted. Eventually, underlying molecular mechanisms, nanotoxicity and examples of major biomedical applications of these algal-derived NPs are presented.

A 90-day subchronic toxicity study of transgenic cotton expressing Cry1Ac, Cry2A and CP4-EPSPS proteins in Sprague-Dawley rats.

Genetically engineered crops expressing insecticidal and herbicide-tolerant traits offer a new strategy for crop protection and enhanced production; however, at the same time present a challenge in terms of toxicology and safety. The current experiment presents the findings of a 90-day feeding study in Sprague-Dawley rats with transgenic cottonseed which is expressing insecticidal Cry proteins (Cry1Ac and Cry2A), and tolerant to the herbicide glyphosate. There were 100 rats in this experiment divided into 5 groups of 10 rats/sex/group. Cottonseed from transgenic and control (near-isogenic) lines was formulated into standard diets at levels of 10% and 30% (w/w). All formulated diets were nutritionally balanced. Overall appearance, feed consumption, body weight, organ weight, haematology, serum chemistry and urinalysis were comparable between control and treatment groups. In addition, there was no treatment-related difference in findings of microscopic histopathology and gross appearance of tissues. In conclusion, following the 13-week of feeding transgenic cottonseed, no treatment-related adverse effects were observed in any of the parameters measured in this experiment. Thus, this study demonstrated that transgenic cottonseeds do not cause toxicity and are nutritionally equivalent to its conventional counterpart.

Unique Pediatric Gallstones Composed of Calcium Oxalate Phosphate.

Calcium oxalate phosphate is extremely rare composition of gall stones, with only one case reported in pediatric population till date. We report a case of pediatric cholelithiasis with a unique composition of calcium oxalate phosphate, detected at eight years of age. Its etiology remains unknown. An 8-year girl presented in Emergency Room with complaints of acute pain in right upper quadrant and nausea without any complaints of jaundice or fever. She was admitted to the hospital with the provisional diagnosis of acute cholecystitis keeping in view her symptoms and obesity, which was later found to be true after an ultrasound report; but the uniqueness and rarity of this case was determined after cholecystectomy, when the specimen containing her gall bladder along with stones was sent for analysis of the composition, which showed the rarest composition i.e., calcium oxalate phosphate. We report our experience on the unique composition of gallstones in a young girl with no known risk factors except obesity. These rare pediatric gallstones have not been associated with obesity in any literature earliar. Key Words: Gallstones, Calcium oxalate phosphate, Pediatric.

Pharmacokinetics profile of serum and cellular Sofosbuvir along with its concentration effect analysis in HCV patients receiving Sofosbuvir and Ribavirin.

Sofosbuvir along with ribavirin is being widely used for treatment of HCV in Pakistan but it may show delayed response and reoccurrence of disease in some cases. The aim of the study was to investigate pharmacokinetics and concentration effect analysis of sofosbuvir. HCV patients (n=100) received 400 mg sofosbuvir along with low dose or weight based ribavirin (400 mg). Nonlinear mixed effects modeling (NONMEM) and unpaired t-test were used for the association of concentrations and treatment outcomes. Average day 10 sofosbuvir metabolite BM 331007 concentration was higher in patients having haemoglobin nadir value <10 g/dl compared to the patients having heamoglobin nadir value >10 g/dl (5.34 versus 4.87 pmol/106 cells; p=0.03). The average concentration trends of GS331007 at day 10 was towards being higher in the patients achieved sustained virologic response (SVR) as compare to the patients relapsed (5.19 versus 4.86 pmol/106 cells; p=0.05). Sofosbuvir (GS331007) thresholds concentration (suggested at day 10 through receiver operating characteristic curve) was 5.4 pmol/106 cells for SVR (p=0.05) and haemoglobin nadir cells was 6.3 pmol/106 with sensitivity and specificity of >60%. Dosing simulations shows that 400 mg sofosbuvir twice daily produce day 10 concentration range of 5.4 to 6.7 pmol/106 cells. The range of therapeutic values was identified for HCV patients receiving sofosbuvir in combination with ribavirin for 24 weeks, suggesting a potential pharmaceutical basis for individualized therapeutic dosing.

Crigler-Najjar Syndrome Type II Diagnosed in a Patient with Jaundice Since Birth.

Crigler-Najjar syndrome type II is caused by mutations in the UGT1A1 gene resulting in severely reduced hepatic activity of UDP-glucoronyltransferase - an enzyme required to convert bilirubin into a more soluble form that can then be removed from the body. Absence or severe deficiency of this enzyme can lead to bilirubin accumulation in the body resulting in yellow skin and eyes (jaundice). The earliest signs of this disease can be apparent in the neonatal period. Patients with Crigglar-Najjar syndrome type II respond to phenobarbital therapy which decreases their chances of getting bilirubinemia by 60-70% in 3 weeks. A 17 years old boy presented with the complaint of gastroenteritis. On examination, he was jaundiced and his parents reported that it has been present since birth. He was admitted in the hospital with the differential diagnosis of Gilbert syndrome, but later it was found that the unconjugated bilirubin levels were higher than those required for Gilbert's criteria. We report, herein, an extremely rare case of Crigler-Najjar syndrome type II and how the patient responded to phenobarbital therapy. Periods of fasting, stress and any kind of illness can worsen unconjugated hyperbilirubinemia leading to complications like kernicterus, so higher levels of unconjugated bilirubin should be addressed immediately and the patient along with his/her family should be educated about this disease.