Microsatellite diversity in four cultivated species of Actinidiaceae and Rutaceae.

Microsatellites or Simple Sequence Repeats (SSRs) are short iterations of 1-6 bp in the genomes of almost all living organisms. Our study aimed to explore the microsatellite diversity in four cultivated species, namely Actinidia chinensis, Actinidia eriantha, Citrus maxima, and Citrus sinensis of the Actinidiaceae and Rutaceae families. We present a comprehensive analysis of microsatellite abundance, distribution, and motif composition in the genomes of these species. The association of microsatellite abundance with genomic features such as genome size, GC content, number of microsatellites, relative abundance, and relative density was also examined. The results revealed significant variations in the frequency and distribution of microsatellites across the genomes of these four species. Notably, a positive correlation was observed between genome size and microsatellite number as well as with GC content, indicating that larger genomes provide more opportunities for the accumulation of microsatellites. Furthermore, a negative correlation of genome size with relative microsatellite abundance and relative density was observed. These findings provide new insights into the microsatellite landscape of Actinidiaceae and Rutaceae, which could be explored for the development of microsatellite markers for diverse applications in the characterization of genetic diversity, molecular plant breeding, and phylogenetic analysis.

Varying protein architectures in 3-dimensions for scaffolding and modulating properties of catalytic gold nanoparticles.

Fabrication and development of nanoscale materials with tunable structural and functional properties require a dynamic arrangement of nanoparticles on architectural templates. The function of nanoparticles not only depends on the property of the nanoparticles but also on their spatial orientations. Proteins with self-assembling properties which can be genetically engineered to varying architectural designs for scaffolds can be used to develop different orientations of nanoparticles in three dimensions. Here, we report the use of naturally self-assembling bacterial micro-compartment shell protein (PduA) assemblies in 2D and its single-point mutant variant (PduA[K26A]) in 3D architectures for the reduction and fabrication of gold nanoparticles. Interestingly, the different spatial organization of gold nanoparticles resulted in a smaller size in the 3D architect scaffold. Here, we observed a two-fold increase in catalytic activity and six-fold higher affinity toward TMB (3,3',5,5'-tetramethylbenzidine) substrate as a measure of higher peroxidase activity (nanozymatic) in the case of PduA[K26A] 3D scaffold. This approach demonstrates that the hierarchical organization of scaffold enables the fine-tuning of nanoparticle properties, thus paving the way toward the design of new nanoscale materials.

The Nrf2 pathway in psychiatric disorders: pathophysiological role and potential targeting.

Introduction: All psychiatric disorders exhibit excitotoxicity, mitochondrial dysfunction, inflammation, oxidative stress, and neural damage as their common characteristic. The endogenous nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway is implicated in the defense mechanism against oxidative stress and has a significant role in psychiatric disorders.Areas covered: We explore the role of Nrf2 pathway and its modulators in psychiatric disorders. The literature was searched utilizing various databases such as Embase, Medline, Web of Science, Pub-Med, and Google Scholar from 2010 to 2020. The search included research articles, clinical reports, systematic reviews, and meta-analyses.Expert opinion: Environmental factors and genetic predisposition can be a trigger for the development of psychiatric disorders. Nrf2 downregulates certain inflammatory pathways and upregulates various antioxidant enzymes to maintain a balance. However, its intricate balance with NF-Kß (Nuclear factor kappa light chain enhancer of activated B cells) and its crosstalk with the transcription factor Nrf2 is critical in severe oxidative stress. Several Nrf2 modulators are now in clinical trials and can help reduce oxidative stress and neuroinflammation. There are immense potential opportunities for these modulators to become a novel therapeutic option.

Probe into a multi-protein prokaryotic organelle using thermal scanning assay reveals distinct properties of the core and the shell.

BACKGROUND: Bacterial microcompartments represent the only reported category of prokaryotic organelles that are capable of functioning as independent bioreactors. In this organelle, a biochemical pathway with all the enzyme machinery is encapsulated within an all protein shell. The shell proteins and the enzymes have distinct structural features. It is hypothesized that flat shell proteins align sideways to form extended sheets and, the globular enzymes fill up the central core of the organelle. METHODS: Using differential scanning fluorimetry, we explored the structure and functional alteration of Pdu BMC, involving tertiary or quaternary structures. RESULTS: Our findings exhibit that these intact BMCs as a whole behave similar to a globular protein with a rich hydrophobic core, which is exposed upon thermal insult. The encapsulated enzymes itself have a strong hydrophobic core, which is in line with the hydrophobic-collapse model of protein folding. The shell proteins, on the other hand, do not have a strong hydrophobic core and show a significant portion of exposed hydrophobic patches. CONCLUSION: We show for the first time the thermal unfolding profile of the BMC domain proteins and the unique exposure of hydrophobic patches in them might be required for anchoring the enzymes leading to better packaging of the micro-compartments. GENERAL SIGNIFICANCE: These observations indicate that the genesis of these unique bacterial organelles is driven by the hydrophobic interactions between the shell and the enzymes. Insights from this work will aid in the genetic and biochemical engineering of thermostable efficient enzymatic biomaterials.

Functional protein shells fabricated from the self-assembling protein sheets of prokaryotic organelles.

Fabricating protein compartments from protein units is challenging and limited by the use of external stimuli and crosslinkers. Here we explore the fabrication of all-protein compartments using self-assembled proteins of prokaryotic organelles. These proteins have intrinsic interacting domains which are ionic in nature, and spontaneously self-assemble into sheets when over-expressed. Using a one-step approach, we maneuvered the formation of the protein shells from the sheets without any external stimuli or crosslinker. The spontaneous self-assembly of the native protein sheets into protein shells not only preserves the native functional properties of the protein but also enhances their thermal stability compared to the sheets. We further demonstrate that these compartments can encapsulate macromolecular enzymes and, more interestingly, permit the free exchange of small molecules and substrates through their intrinsic conduit channels. The porous nature of the shell housing active enzymes and allowing movement of small molecules makes them suitable as active bioreactors. Furthermore, to extend the tunability of these protein-compartments with respect to stability, enzyme-encapsulation, and permeability, we fabricated three different compartments using three different sheet proteins, PduA/B/B' and compared their properties. Interestingly we find that all three protein shells show similar behaviour with respect to an encapsulated diol-dehydratase enzyme and vitamin B12, which are native to the Pdu BMC system. Furthermore, for the non-native enzyme CytC, the small molecule R6G dye, doxorubicin, NR and curcumin they behave diversely. Insights from this analysis will allow us to design and develop sheet protein based synthetic active bioreactors requiring meticulous, compartmentalization in process optimization.

Broken force dispersal network in tip-links by the mutations at the Ca2+-binding residues induces hearing-loss.

Tip-link as force-sensor in hearing conveys the mechanical force originating from sound to ion-channels while maintaining the integrity of the entire sensory assembly in the inner ear. This delicate balance between structure and function of tip-links is regulated by Ca2+-ions present in endolymph. Mutations at the Ca2+-binding sites of tip-links often lead to congenital deafness, sometimes syndromic defects impairing vision along with hearing. Although such mutations are already identified, it is still not clear how the mutants alter the structure-function properties of the force-sensors associated with diseases. With an aim to decipher the differences in force-conveying properties of the force-sensors in molecular details, we identified the conformational variability of mutant and wild-type tip-links at the single-molecule level using FRET at the endolymphatic Ca2+ concentrations and subsequently measured the force-responsive behavior using single-molecule force spectroscopy with an Atomic Force Microscope (AFM). AFM allowed us to mimic the high and wide range of force ramps (103-106 pN s-1) as experienced in the inner ear. We performed in silico network analysis to learn that alterations in the conformations of the mutants interrupt the natural force-propagation paths through the sensors and make the mutant tip-links vulnerable to input forces from sound stimuli. We also demonstrated that a Ca2+ rich environment can restore the force-response of the mutant tip-links which may eventually facilitate the designing of better therapeutic strategies to the hearing loss.

Novel mutations conferring resistance to kanamycin in Mycobacterium tuberculosis clinical isolates from Northern India.

Twenty-nine Kanamycin resistant clinical isolates of Mycobacterium tuberculosis from Northern India were screened to evaluate genetic mutations in rrs gene, eis gene with its promoter, and whiB7 gene along with its 5'UTR. 14 strains (~48.0%) collectively exhibited mutations in rrs, eis or whiB7 target regions. While the highest frequency of mutations was found in rrs gene, eis and whiB7 loci displayed novel mutations. The novel mutations displayed by eis and whiB7 loci were found to be associated specifically with the Kanamycin resistance as none of the twenty nine Kanamycin sensitive strains harbor them. The inclusion of novel mutations of eis and whiB7 loci will be useful in improving the specificity of future diagnostics.

Reactive oxygen species in periodontitis.

Recent epidemiological studies reveal that more than two-third of the world's population suffers from one of the chronic forms of periodontal disease. The primary etiological agent of this inflammatory disease is a polymicrobial complex, predominantly Gram negative anaerobic or facultative bacteria within the sub-gingival biofilm. These bacterial species initiate the production of various cytokines such as interleukin-8 and TNF-α, further causing an increase in number and activity of polymorphonucleocytes (PMN) along with these cytokines, PMNs also produce reactive oxygen species (ROS) superoxide via the respiratory burst mechanism as the part of the defence response to infection. ROS just like the interleukins have deleterious effects on tissue cells when produced in excess. To counter the harmful effects of ROS, human body has its own defence mechanisms to eliminate them as soon as they are formed. The aim of this review is to focus on the role of different free radicals, ROS, and antioxidants in the pathophysiology of periodontal tissue destruction.

Ellis-van Creveld syndrome: A rare clinical entity.

Ellis-van Creveld (EVC) syndrome is a genetic disorder with autosomal recessive transmission, which may clinically present as small stature, short limbs, fine sparse hair, hypoplastic fingernails, multiple musculofibrous frenula, conical teeth, hypoplasia of the enamel, hypodontia, and malocclusion. Heart defects, especially abnormalities of atrial septation, have been found in about 60% of cases. The mutation in EVC and EVC2 gene is responsible for this syndrome. The presence of multiple orodental findings makes this syndrome important for dentists. The aim of this article is to present a rare case of EVC syndrome in a 10-year-old girl along with the review of literature.

Preliminary analysis of polycyclic aromatic hydrocarbons in air particles (PM10) in Amritsar, India: sources, apportionment, and possible risk implications to humans.

Preliminary analysis was performed to assess human health risks of exposure to 16 polycyclic aromatic hydrocarbons (PAHs) by way of inhalation by children and adults living in urban area of Amritsar, Punjab, India. In particular, the United States Environmental Protection Agency's (USEPA's) 16 priority PAH compounds were analyzed in air particulate matter (PM10) from different geographical locations by high-volume air sampler. Sum concentrations of PAHs (37-274 ng m(-3)) were comparable with those of other cities in India as well many cities on a global scale. Pyrene, naphthalene, acenaphthene, acenaphthylene, fluoranthene, fluorene, and dibenzo(a,h)anthracene accounted for >80% of ∑16PAH concentrations. Furthermore, the contribution of seven carcinogenic PAHs accounted for 12% of ∑16PAHs. The estimated carcinogenicity of PAHs in terms of benzo(a)pyrene toxic equivalency (BaPTEQ) was assessed and confirmed that dibenzo(a,h)anthracene was the dominant PAH contributor (88.7%) followed by benzo(a)pyrene (6.67%). Homolog pattern and diagnostic ratios of PAHs suggested that mixed pyrogenic sources--including biomass burning, coal combustion, and petrogenic sources, such as vehicular emissions--are dominant PAH sources in Amritsar. Health risk of adults and children by way of PAHs was assessed by estimating the lifetime average daily dose (LADD) and corresponding incremental lifetime cancer risk (ILCR) using USEPA guidelines. The assessed cancer risk (ILCR) was found to be within the acceptable range (10(-6)-10(-4)).

The Role of a Single Dose of Sublingual Nifedipine in Managing Hypertensive Emergencies in the Patients who Undergo Haemodialysis.

INTRODUCTION: The hypertensive emergencies in haemodialysis require immediate therapy, usually by parenteral drug administration; however, sublingual medications may have a potential in this special condition. METHODS: A prospective, non randomized, case control study was carried out to know the effectiveness and the safety of a single dose of 5mg Nifedipine (sublingual) in this subset of patients. About 100 patients were studied, who were on maintained haemodialysis and were having high Blood Pressure (BP) during the haemodialysis. The patients were monitored for about 5 hours. RESULTS: The patients who had chronic renal failure, who were maintained on regular haemodialysis, who had high systolic and diastolic blood pressure of >220 (systolic) and >125 (diastolic) respectively, were subjected to the study. These patients were of the 20-70 years age group, who visited our hospital between January 2010 to January 2011. Out of the 100 patients 30% were females and the rest (70%) were males. A single dose of nifedipine (5 mg by the sublingual route) was prescribed to determine its effectiveness and safety in the treatment of hypertensive emergencies during haemodialysis. The side effects of the drug were closely monitored. The blood pressure and the heart rate were measured continuously up to 280 min post-dose. The response rates were 90 % for nifedipine. The significant hypotensive effects of sublingual nifedipine occurred at 10 min, and a maximum reduction occurred after 30 mins and it continued up to 120 min. CONCLUSIONS: We concluded that sublingual nifedipine was effective and that it seemed to have less side effects. It may be an excellent drug in the urgent treatment of hypertensive emergencies in haemodialysis.