Genetic analysis for detection of genes associated to drought tolerance in rice accessions belonging to north east India.

INTRODUCTION: The North East (NE) India is rich in biodiversity and also considered as the secondary centre for origin of rice. The NE rice accessions was characterized previously using genetic markers and morphological traits. Simultaneously, genome-wide association studies (GWAS) reveal significant marker-trait associations for the drought tolerance traits. METHODS AND RESULTS: The genetic diversity and population structure of 296 NE rice accessions were studied using 96,712 single nucleotide polymorphism (SNP) markers distributed across 12 chromosomes. The accessions were clustered into two major sub-groups (SG). A total of 91 accessions were assembled as SG1 and 114 accessions as SG2, while the remaining 91 were admixture genotypes. A total of 200 genotypes belonging to different groups were phenotyped for yield component traits under drought and control conditions. The GWAS was performed to identify significant marker-trait associations (MTAs). Consequently, 47 MTAs were detected under drought, exhibiting 0.02-9.95% of phenotypic variance (P.V.). Whereas 58 MTAs were discovered under control conditions, showing a 0.01-9.74% contribution to the phenotype. Through in-silico mining of QTLs, 2999 genes were identified. Among these; only 22 genes were directly associated with stress response. CONCLUSION: These QTLs/genes may be deployed for marker-assisted pyramiding to improve drought tolerance in popular drought susceptible rice varieties.

GWAS to spot candidate genes associated with grain quality traits in diverse rice accessions of North East India.

INTRODUCTION: North East (NE) India is the second centre for the origin of rice and is enriched with a diverse collection of traditional rice accessions. These genotypes possess unique traits of breeding interest and are rich in grain nutritional and cooking qualities. Therefore, quantitative trait loci (QTLs)/genes associated with the various quality traits may be identified through genome-wide association studies (GWAS) and used in crop improvement programmes. METHODS AND RESULTS: A pool of 526 unique rice accessions from Assam, North East (NE) India were characterized by using 9 grain-quality traits and grouped into 16 clusters. Among these, the highest number of 156 (29.65%) genotypes belongs to diverse phenotypic classes; Sali, Lahi, and Chokuwa were grouped into cluster 6. The first three principal components showed 54.76% of morphological variability with Eigenvalue >1. Genome-wide association studies (GWAS) was performed in 103 rice accessions using 42,446 SNP markers. A total of 11 significant marker-trait associations were detected for 5 grain-quality traits, explaining 0.22-8.86% of phenotypic variation (PV). In-silico mining of QTLs detected 'candidate genes' associated with the quality traits. CONCLUSIONS: The phenotypic diversity among the 526 rice accessions of NE India was studied using grain quality traits and grouped into 16 significantly different clusters. The QTLs, or candidate genes identified for various grain quality traits, may be used in breeding programmes for the development of improved rice varieties.

Identification and characterization of genes for drought tolerance in upland rice cultivar 'Banglami' of North East India.

INTRODUCTION: Rice is a major crop in Assam, North East (NE) India. The rice accessions belonging to NE India possess unique traits of breeder's interest, i.e., tolerant to biotic and abiotic stresses. In the present research programme, the stress responsive genes were identified within the QTLs associated with drought tolerance. The differential expression profiling of genes were performed under drought stress and control conditions. Thus, the 'candidate genes' associated with drought tolerance were recognised and may be deployed in a breeding programme. METHODS AND RESULTS: A drought-tolerant traditional rice cultivar, Banglami, was crossed with a high-yielding, drought-susceptible variety, Ranjit. The mapping population (F4) was raised through the single seed descent (SSD) method and used in QTL analysis. Under drought stress, a total of 4752 genes were identified through in-silico mining of QTLs. Among these, only 21 genes primarily associated with the stress response. The maximum of four stress-responsive genes were located within the QTLs, qNOG12.1 and qGY1.1. However, under control conditions, 2088 genes were identified, out of which, only 15 were categorised as the major stress responsive genes. The functional characterization of genes recognized 24 different types of proteins. Among these, peroxidase and heat shock proteins (Hsp) are the principal proteins encoded during stress. In addition to that, OsbZIP23, inorganic pyrophosphatase, universal stress protein, serine threonine kinase, NADPH oxidoreductase, and proteins belonging to the ABC1 family were also produced during stress condition. The differential expression profiling showed a profound expression pattern of three candidate genes under drought stress condition, i.e., OsI_32199 (Ascorbate peroxidase), OsI_37694 (Universal stress protein) and OsI_32167 (Heat shock protein 81 - 1). CONCLUSION: The novel candidate genes identified for drought tolerance, may be used in the breeding programme for the development of 'climate smart rice varieties'.

Genome-wide association studies for agronomical traits in winter rice accessions of Assam.

The 297 winter rice accessions of Assam, North East India were genotyped by sequencing (GBS). The 50,985 high-quality SNPs were filtered and assigned to 12 rice chromosomes. The population structure analysis revealed three major subgroups SG1, SG2, and SG3 consisting of 30, 8, and 143 accessions respectively. The remaining 116 accessions were grouped as admixture population. Phenotypic data were recorded on13 agronomical traits for genome-wide association studies (GWAS). The 60 significant marker-trait associations (MTAs) were identified for 11 agronomical traits, which explained 0 to 15% of phenotypic variance (PV). A QTL 'hot spot' was detected near the centromeric region on chromosome 6. The identified QTLs may be validated and utilized in 'genomics assisted breeding' for improvement of existing rice cultivars of Assam and North East India.

Formulation and optimization of silymarin-encapsulated binary micelles for enhanced amyloid disaggregation activity.

Silymarin (SLY) is a natural hydrophobic polyphenol that possesses antioxidant and amyloid fibril (Aß1-42) inhibition activity, but its activity is hindered due to low aqueous solubility. In this study, SLY is encapsulated in binary micelle (SLY-BM) that has been utilized to enhance the Aß1-42 fibril disaggregation. To enhance the aqueous solubility, SLY payload in micelles were optimized using Box-Behnken Design (BBD) to increase the efficiency of Aß1-42 fibril disaggregation. BBD was used to investigate the effect of ratio of Solutol HS15:Poloxamer-188, amount of acetone and hydration volume on critical quality attributes, particle size, and entrapment efficiency for SLY-BM. Furthermore, SLY-BM was characterized for its physical and drug release properties. The Aß1-42 fibril disaggregation and antioxidant studies were monitored using spectroscopic and microscopic techniques. BBD optimized the particle size <50 nm with %EE > 80%, and solubility factor of SLY-BM was enhanced to 460 folds than free SLY. Inhibitory concentration 50% (IC50) value of SLY-BM was 19.67 µg/mL compared to free SLY (30.06 µg/mL) in diphenylpicrahydrazyl assay. SLY-BM increased the Aß1-42 disaggregation compared to free SLY observed via thioflavin-T assay, photon correlation spectroscopy, and circular dichorism. Further morphological evaluation of Aß1-42 disaggregation was monitored by microscopy which showed that SLY-BM disaggregated the fibrils in 48 h. According to our findings, we concluded that SLY-BM micelles are potential candidates for delivery of neuroprotective agents.

Recent Developments in Tyrosine Kinase Inhibitor-based Nanotherapeutics for EGFR-resistant Non-small Cell Lung Cancer.

The advent of drug resistance in response to epidermal growth factor receptor (EGFR)- tyrosine kinase inhibitor (TKI) targeted therapy represents a serious challenge in the management of non-small cell lung cancer (NSCLC). These acquired resistance mutations, attributed to several advanced EGFR mutations and, necessitated the development of new-generation TKIs. Nanomedicine approaches provide a plausible way to address these problems by providing targeted delivery and sustained release, which have demonstrated success in preclinical trials. This review article provides a summary of nano-formulations designed for EGFR-TKI-resistant NSCLC, highlighting their efficacy in both in vitro and in vivo models. These findings reveal insights into the design of nanoparticles and multifunctional nanosystems, offering a potential avenue for efficacious treatment of EGFR-TKIresistant NSCLC.

Susceptibility of clinical isolates of novel pathogen Stenotrophomonas sepilia to novel benzoquinolizine fluoroquinolone levonadifloxacin.

Background: Stenotrophomonas sepilia, identified in 2021, is part of the Stenotrophomonas maltophilia complex (Smc) and shares high genomic identity with S. maltophilia. Resistance to levofloxacin, the recommended fluoroquinolone for S. maltophilia, is being increasingly reported. Recent studies indicate that levonadifloxacin, a novel benzoquinolizine, may be more effective. This study evaluates the antimicrobial efficacy of levofloxacin and levonadifloxacin against clinical isolates of S. sepilia. Objectives: To assess the antibacterial effectiveness of levofloxacin and levonadifloxacin against novel pathogen S. sepilia. Methods: A total of 116 S. maltophilia isolates, identified by MALDI-TOF MS, were collected from five centres across India. S. sepilia was confirmed by PCR using primers targeting a unique genomic sequence (NCBI accession number LXXZ00000000.1). Minimum inhibitory concentrations (MICs) of levonadifloxacin and levofloxacin were determined by using the microbroth-dilution method and Etest as per CLSI guidelines. The levofloxacin breakpoint was used to interpret MICs of levonadifloxacin. Results: Among a total of 116 circulating S. maltophilia isolates collected, 46 were identified as S. sepilia, representing a prevalence rate of (∼40%), thus highlighting its significance as an important pathogen within the Smc. Both levofloxacin and levonadifloxacin demonstrated a 98% inhibition rate against the 46 S. sepilia tested. Only one S. sepilia isolate resistant to levofloxacin showed intermediate susceptibility to levonadifloxacin, which consistently had lower MICs. Conclusions: Levofloxacin and levonadifloxacin show similar susceptibility rates against S. sepilia, with levonadifloxacin exhibiting lower MICs. Further studies are required to establish clinical utility of levonadifloxacin in managing these infections.

Harnessing personalized tailored medicines to digital-based data-enriched edible pharmaceuticals.

Tailoring drug products to personalized medicines poses challenges for conventional dosage forms. The prominent reason is the restricted availability of flexible dosage strengths in the market. Inappropriate dosage strengths lead to adverse drug reactions or compromised therapeutic effects. The situation worsens when the drug has a narrow therapeutic window. To overcome these challenges, data-enriched edible pharmaceuticals (DEEP) are novel concepts for designing solid oral products. DEEP have individualized doses and information embedded in quick response (QR) code form. When data are presented in a QR code, the information is printed with edible ink that contains the drug in tailored doses required for the patients.

Inhalable microparticles containing nitric oxide donors: saying NO to intracellular Mycobacterium tuberculosis.

Although nitric oxide (NO) is a bactericidal component of the macrophage's innate response to intracellular infections such as tuberculosis (TB), prolonged inhalation of NO gas has little benefit in chemotherapy of TB. The impact of controlled release of NO through intracellular delivery of NO donors to macrophages infected in vitro with Mycobacterium tuberculosis (Mtb) was investigated. Inhalable microparticles (MP) were prepared by spray-drying. Isosorbide mononitrate (ISMN), sodium nitroprusside (SNP), and diethylenetriamine nitric oxide adduct (DETA/NO) were incorporated in poly(lactic-co-glycolic acid) (PLGA) with encapsulation efficiencies of >90% to obtain MP yields of ∼70%. The mass median aerodynamic diameter (MMAD) of the MP was 2.2-2.4 µm within geometric standard deviations (GSD) of ≤0.1 µm. MP were phagocytosed by THP-1 derived macrophages in culture and significantly (P < 0.05) sustained NO secretion into culture supernatant from 6 to 72 h in comparison to equivalent amounts of drugs in solution. Significantly (P < 0.05) higher dose-dependent killing of intracellular Mtb by MP compared to equivalent amounts of drugs in solution was observed on estimation of colony forming units (CFU) surviving 24 h after exposure to drugs or MP. The cytotoxicity of MP toward macrophages was lower than that of dissolved drugs. It was concluded that inhalable MP can target NO donors to the macrophage, control NO release in the macrophage cytosol, and reduce Mtb CFU by up to 3-log in 24 h, at doses that are much lower than those required for cardiovascular effects.

Investigations into an alternate approach to target mannose receptors on macrophages using 4-sulfated N-acetyl galactosamine more efficiently in comparison with mannose-decorated liposomes: an application in drug delivery.

In this study the potential of 2 different ligands, i.e., palmitoyl mannose (Man-Lip) and 4-SO(4)GalNAc (Sulf-Lip) to target resident macrophages was investigated after surface decoration of Amphotericin B (AmB) loaded liposomes. In the case of Sulf-Lip, the 4-SO(4)GalNAc was adsorbed through electrostatic interaction on cationic liposomes, which was confirmed by change in zeta potential from +48.2 ± 3.7 mV for Lip to +12.2 ± 1.3 mV for Sulf-Lip. The mean particle size of Sulf-Lip and Man-Lip was found to be 139.4 ± 7.4 nm and 147.4 ± 8.6 nm, respectively. Flow cytometric data reveal enhanced uptake of Sulf-Lip in both J774 and RAW cell lines in comparison with the uptake of Man-Lip. Intracellular localization studies indicate that the fluorescence intensity of Sulf-Lip was much higher in comparison with that of Man-Lip and Lip formulations. Sulf-Lip and Man-Lip showed significantly higher localization of AmB at all time points in comparison with Lip (P < 0.05) after intravenous (IV) administration. The studies provide evidence that 4-SO(4)GalNAc possesses a promising feature for targeting resident macrophages and its application in the conditions of leishmaniasis is in the offing. FROM THE CLINICAL EDITOR: This in vivo study compares two different ligands to deliver Amphotericin B l(AmB) loaded liposomes to resident macrophages. Targeted approaches showed significantly higher localization of AmB at all time points in comparison to non-targeted liposomes, and future applications in leishmaniasis are already under preparation.

Nucleotide-based genetic networks: Methods and applications.

Genomic variations have been acclaimed as among the key players in understanding the biological mechanisms behind migration, evolution, and adaptation to extreme conditions. Due to stochastic evolutionary forces, the frequency of polymorphisms is affected by changes in the frequency of nearby polymorphisms in the same DNA sample, making them connected in terms of evolution. This article presents all the ingredients to understand the cumulative effects and complex behaviors of genetic variations in the human mitochondrial genome by analyzing co-occurrence networks of nucleotides, and shows key results obtained from such analyses. The article emphasizes recent investigations of these co-occurrence networks, describing the role of interactions between nucleotides in fundamental processes of human migration and viral evolution. The corresponding co-mutation-based genetic networks revealed genetic signatures of human adaptation in extreme environments. This article provides the methods of constructing such networks in detail, along with their graph-theoretical properties, and applications of the genomic networks in understanding the role of nucleotide co-evolution in evolution of the whole genome.

Role of mitochondrial genetic interactions in determining adaptation to high altitude human population.

Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a near-by polymorphism on the same DNA sample making them connected in terms of evolution. Here, first, we provide a method to model these mitochondrial polymorphisms as "co-mutation networks" for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions of CYB and CO3 genes in Tibetan and Andean populations, while NADH dehydrogenase genes in the Ethiopian population playing a significant role in high altitude adaptation. These co-mutation based genetic networks provide insights into the role of different set of genes in high-altitude adaptation in human sub-populations.

Formulation development of tocopherol polyethylene glycol nanoengineered polyamidoamine dendrimer for neuroprotection and treatment of Alzheimer disease.

Amyloid-beta (Aß) aggregates deposition at extra neuronal sites induces neurotoxicity and major hallmarks of Alzheimer's disease (AD). To reduce the Aß fibril toxicity, multi-functional polyamidoamine (PAMAM) dendrimer was conjugated with tocopheryl polyethylene glycol succinate-1000 (TPGS) which acts as a carrier matrix for the delivery of neuroprotective molecule piperine (PIP). This PIP-TPGS-PAMAM dendrimer was fabricated to mitigate the Aß1-42 fibril toxicity on SHSY5Y cells. TPGS-PAMAM was fabricated through carbodiimide coupling reaction, and PIP was encapsulated in dendrimer through solvent injection method to prepare PIP-TPGS-PAMAM. Antioxidant assay of PIP-TPGS-PAMAM showed 90.18% inhibition of 1, 1-diphenyl-2-picrylhydrazyl (DPPH) free radicals compared to free PIP, which was 28.27%. The SHSY5Y cells showed 37.25% for negative control group and 82.55% cell viability for PIP-TPGS-PAMAM treated group against Aß1-42 toxicity. PIP-TPGS-PAMAM reduced the ROS activity to 15.21% and 48.5% for free PIP treated in cell group. Similarly, extent of Aß1-42-induced apoptosis also reduced significantly from 38.2% to 12.36% in PIP-TPGS-PAMAM treated group. In addition, PIP-TPGS-PAMAM also disaggregated the Aß1-42 fibril in SHSY5Y cells. Our findings suggested that PIP-TPGS-PAMAM showed mitigation of Aß1-42-induced toxicity in neuronal cells, which can offer excellent prospect of neuroprotection and AD therapy.

Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes.

Networks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mtDNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects of variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clustering revealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral 'RSRS50' variant 10,398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.

Inhalable particles containing isoniazid and rifabutin as adjunct therapy for safe, efficacious and relapse-free cure of experimental animal tuberculosis in one month.

We investigated the preclinical efficacy and safety/tolerability of biodegradable polymeric particles containing isoniazid (INH) and rifabutin (RFB) dry powder for inhalation (DPI) as an adjunct to oral first-line therapy. Mice and guinea pigs infected with Mycobacterium tuberculosis H37Rv (Mtb) were treated with ∼80 and ∼300 µg of the DPI, respectively, for 3-4 weeks starting 3, 10, and 30 days post-infection. Adjunct combination therapy eliminated culturable Mtb from the lungs and spleens of all but one of 52 animals that received the DPI. Relapse-free cure was not achieved in one mouse that received DPI + oral, human-equivalent doses (HED) of four drugs used in the Directly Observed Treatment, Short Course (DOTS), starting 30 days post-infection. Oral doses (20 mg/Kg/day, each) of INH + RFB reduced Mtb burden from ∼106 to ∼103 colony-forming units. Combining half the oral dose with DPI prevented relapse of infection four weeks after stopping the treatment. The DPI was safe in rodents, guinea pigs, and monkeys at 1, 10, and 100 µg/day doses over 90 days. In conclusion, we show the efficacy and safety/tolerability of the DPI as an adjunct to oral chemotherapy in three different animal models of TB.

Silymarin encapsulated nanoliquid crystals for improved activity against beta amyloid induced cytotoxicity.

Silymarin (SLY) a natural Aß aggregation inhibitor, antioxidant and act as neuroprotectant. In the present study, we have prepared nano liquid crystals (NLCs) of negatively charged glycerylmonooleate (GMO) loaded with SLY for enhancing activity against Aß1-42 induced toxicity. SLY-NLCs are characterized for physicochemical parameters such as particle size, zeta potential, and drug-loading. The average particle size, zeta potential and % DL were found ≤200 nm, -22 mV, and 8.73% respectively. The amorphous form and entrapment of SLY in NLC were confirmed using DSC and FTIR analysis. The cubosomal SLY-NLCs shape was characterized by SEM and TEM. The cumulative drug release of SLY was ~76% at pH 7.4 (cerebrospinal fluid) from lyophilized SLY-NLC in 48 h. In order to understand the Aß1-42 aggregation inhibition due to SLY-NLC ThT (Thioflavin T) kinetic binding assay was also performed. The cell viability assessment of SLY-NLC was performed on SHSY5Y cell line that showed the highest viability in comparison to free SLY treated groups. ROS and apoptosis activity study SLY-NLCs reduced the Aß1-42 induced free radical with cell death. Cellular uptake study proved enhanced intracellular internalization of FITC tagged NLCs in 24 h. SLY-NLCs can offer great prospects in the field of drug delivery for neuroprotection.

Heparin-Encapsulated Metered-Dose Topical "Nano-Spray Gel" Liposomal Formulation Ensures Rapid On-Site Management of Frostbite Injury by Inflammatory Cytokines Scavenging.

The critical time window between the incidence of frostbite injury and the initiation of treatment in remote snowbound areas is a determining factor for an effective therapeutic response. It is an emergency condition and challenging to treat due to the poor vascularity of affected body parts, and it requires immediate action. In addition to cold trauma-induced tissue damage, the inflammatory mediators majorly contribute to pathologic aggravations. We have designed and evaluated a topical "nano-spray gel (NSG)" formulation, which is based on a combination of liposomal heparin sodium (Hp) and ibuprofen (Ibu) for rapid relief of frostbite injury in extremely low temperatures. The scientific literature suggests that heparin is associated with rapid endothelial cell repair, normalizing blood circulation in capillaries, and has a potential role in wound healing. Hp-containing liposomes were prepared by the extruder method, which suitably formulated an ibuprofen-containing gel to obtain a nano-Spray formulation (HLp-Ibu-NSG) applicable for topical delivery. A single spray puff of the formulation delivers ∼154 mg of the gel, which corresponds to ∼205 U of heparin. In this study, heparin liposomes exhibited significant healing of wound in vitro (scratch assay, fibroblast cells) and in vivo (wound healing in Sprague Dawley rats) at a low dose. In the rat model of frostbite injury, the HLp-Ibu-NSG formulation demonstrated significant reduction in the wound area (up to ∼96%) and improvement of histopathology in 14 days as compared to the control groups. No edema and erythema were detected post-treatment of HLp-Ibu-NSG in the affected area. The underlying mechanism was delineated as a modulation of the inflammatory cytokine (IL-6, TNF-α, IL-10, IL-4) mediators at the wound site and blood circulation to foster frostbite healing. Future clinical studies on the nano-spray gel are required to evaluate its efficacy for the treatment of frostbite symptoms. The instant on-site application of this formulation might be helpful in saving extremities of soldiers, mountaineers, and pilgrims having frostbite.

Loading and release of amphotericin-B from biodegradable poly(lactic-co-glycolic acid) nanoparticles.

Amphotericin B (AmB)-loaded poly(lactic-co-glycolic acid, PLGA) nanoparticles (NP) were prepared by solvent displacement. NP of size 160.7 +/- 10.45 nm, with a polydispersity index of 0.093 +/- 0.012 and a zeta-potential of -15.5 +/- 7.2 mV had satisfactory drug entrapment efficiency (42.5 +/- 6.41%). Biphasic drug release characterized by an initial burst followed by subsequent sustained release was observed. Applicability against visceral leishmaniasis and cancer is under investigation.

Nanoparticles containing nitric oxide donor with antileishmanial agent for synergistic effect against visceral leishmaniasis.

Poly(lactide-co-glycolide) nanoparticles (NP) containing Doxorubicin (DOX) along with a nitric oxide (NO) donor Sodium Nitroprusside (SNP) were prepared by solvent displacement. NO is expected to synergise with antileishmanial activity of DOX. Preformulation studies showed no significant interaction between DOX and SNP. DOX and SNP loaded NP had an average size of 352 nm with 48% entrapment efficiency and a drug content of 10% w/w. Biphasic drug release was observed in vitro, with an initial burst of DOX and SNP (approximately 26% and 35% respectively) followed by sustained release for over 72 hrs.