Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis.

The true benefits of large single-cell transcriptome and epigenome data sets can be realized only with the development of new approaches and search tools for annotating individual cells. Matching a single-cell epigenome profile to a large pool of reference cells remains a major challenge. Here, we present scEpiSearch, which enables searching, comparison, and independent classification of single-cell open-chromatin profiles against a large reference of single-cell expression and open-chromatin data sets. Across performance benchmarks, scEpiSearch outperformed multiple methods in accuracy of search and low-dimensional coembedding of single-cell profiles, irrespective of platforms and species. Here we also demonstrate the unconventional utilities of scEpiSearch by applying it on single-cell epigenome profiles of K562 cells and samples from patients with acute leukaemia to reveal different aspects of their heterogeneity, multipotent behavior, and dedifferentiated states. Applying scEpiSearch on our single-cell open-chromatin profiles from embryonic stem cells (ESCs), we identified ESC subpopulations with more activity and poising for endoplasmic reticulum stress and unfolded protein response. Thus, scEpiSearch solves the nontrivial problem of amalgamating information from a large pool of single cells to identify and study the regulatory states of cells using their single-cell epigenomes.

Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs.

Finding direct dependencies between genetic pathways and diseases has been the target of multiple studies as it has many applications. However, due to cellular heterogeneity and limitations of the number of samples for bulk expression profiles, such studies have faced hurdles in the past. Here, we propose a method to perform single-cell expression-based inference of association between pathway, disease and cell-type (sci-PDC), which can help to understand their cause and effect and guide precision therapy. Our approach highlighted reliable relationships between a few diseases and pathways. Using the example of diabetes, we have demonstrated how sci-PDC helps in tracking variation of association between pathways and diseases with changes in age and species. The variation in pathways-disease associations in mice and humans revealed critical facts about the suitability of the mouse model for a few pathways in the context of diabetes. The coherence between results from our method and previous reports, including information about the drug target pathways, highlights its reliability for multidimensional utility.

Insights into cellular crosstalk regulating cytoplasmic male sterility and fertility restoration.

Cytoplasmic male sterility has been a popular genetic tool in development of hybrids. The molecular mechanism behind maternal sterility varies from crop to crop. An understanding of underlying mechanism can help in development of new functional CMS gene in crops which lack effective and stable CMS systems. In crops where seed or fruit is the commercial product, fertility must be recovered in F1 hybrids so that higher yield gains can be realized. This necessitates the presence of fertility restorer gene (Rf) in nucleus of male parent to overcome the effect of sterile cytoplasm. Fertility restoring genes have been identified in crops like wheat, maize, sunflower, rice, pepper, sugar beet, pigeon pea etc. But in crops like eggplant, bell pepper, barley etc. unstable fertility restorers hamper the use of Cytoplasmic genic male sterility (CGMS) system. Stability of CGMS system is influenced by environment, genetic background or interaction of these factors. This review thus aims to understand the genetic mechanisms controlling mitochondrial-nuclear interactions required to design strong and stable restorers without any pleiotropic effects in F1 hybrids.

Self-Assembled Redox-Sensitive Polymeric Nanostructures Facilitate the Intracellular Delivery of Paclitaxel for Improved Breast Cancer Therapy.

A two-tier approach has been proposed for targeted and synergistic combination therapy against metastatic breast cancer. First, it comprises the development of a paclitaxel (PX)-loaded redox-sensitive self-assembled micellar system using betulinic acid-disulfide-d-α-tocopheryl poly(ethylene glycol) succinate (BA-Cys-T) through carbonyl diimidazole (CDI) coupling chemistry. Second, hyaluronic acid is anchored to TPGS (HA-Cys-T) chemically through a cystamine spacer to achieve CD44 receptor-mediated targeting. We have established that there is significant synergy between PX and BA with a combination index of 0.27 at a molar ratio of 1:5. An integrated system comprising both BA-Cys-T and HA-Cys-T (PX/BA-Cys-T-HA) exhibited significantly higher uptake than PX/BA-Cys-T, indicating preferential CD44-mediated uptake along with the rapid release of drugs in response to higher glutathione concentrations. Significantly higher apoptosis (42.89%) was observed with PX/BA-Cys-T-HA than those with BA-Cys-T (12.78%) and PX/BA-Cys-T (33.38%). In addition, PX/BA-Cys-T-HA showed remarkable enhancement in the cell cycle arrest, improved depolarization of the mitochondrial membrane potential, and induced excessive generation of ROS when tested in the MDA-MB-231 cell line. An in vivo administration of targeted micelles showed improved pharmacokinetic parameters and significant tumor growth inhibition in 4T1-induced tumor-bearing BALB/c mice. Overall, the study indicates a potential role of PX/BA-Cys-T-HA in achieving both temporal and spatial targeting against metastatic breast cancer.

Surface-Modified Lyotropic Crystalline Nanoconstructs Bearing Doxorubicin and Buparvaquone Target Sigma Receptors through pH-Sensitive Charge Conversion to Improve Breast Cancer Therapy.

In the current study, we aimed to develop lyotropic crystalline nanoconstructs (LCNs) based on poly(l-glutamic acid) (PLG) with a two-tier strategy. The first objective was to confer pH-responsive charge conversion properties to facilitate the delivery of both doxorubicin (DOX) and buparvaquone (BPQ) in combination (B + D@LCNs) to harness their synergistic effects. The second goal was to achieve targeted delivery to sigma receptors within the tumor tissues. To achieve this, we designed a pH-responsive charge conversion system using a polymer consisting of poly(ethylenimine), poly(l-lysine), and poly(l-glutamic acid) (PLG), which was then covalently coupled with methoxybenzamide (MBA) for potential sigma receptor targeting. The resulting B + D@LCNs were further modified by surface functionalization with PLG-MBA to confer both sigma receptor targeting and pH-responsive charge conversion properties. Our observations indicated that at physiological pH 7.4, P/B + D-MBA@LCNs exhibited a negative charge, while under acidic conditions (pH 5.5, characteristic of the tumor microenvironment), they acquired a positive charge. The particle size of P/B + D-MBA@LCNs was determined to be 168.23 ± 2.66 nm at pH 7.4 and 201.23 ± 1.46 nm at pH 5.5. The crystalline structure of the LCNs was confirmed through small-angle X-ray scattering (SAXS) diffraction patterns. Receptor-mediated endocytosis, facilitated by P/B + D-MBA@LCNs, was confirmed using confocal laser scanning microscopy and flow cytometry. The P/B + D-MBA@LCNs formulation demonstrated a higher rate of G2/M phase arrest (55.20%) compared to free B + D (37.50%) and induced mitochondrial depolarization (59.39%) to a greater extent than P/B + D@LCNs (45.66%). Pharmacokinetic analysis revealed significantly improved area under the curve (AUC) values for both DOX and BPQ when administered as P/B + D-MBA@LCNs, along with enhanced tumor localization. Tumor regression studies exhibited a substantial reduction in tumor size, with P/B + D-MBA@LCNs leading to 3.2- and 1.27-fold reductions compared to B + D and nontargeted P/B + D@LCNs groups, respectively. In summary, this two-tier strategy demonstrates substantial promise for the delivery of a drug combination through the prototype formulation. It offers a potential chemotherapeutic option by minimizing toxic effects on healthy cells while maximizing therapeutic efficacy.

Identification of a Major-Effect Quantitative Trait Loci Associated with Begomovirus Resistance in Cucurbita moschata.

Begomoviruses, viz. squash leaf curl China virus and tomato leaf curl New Delhi virus causative diseases are major concerns of quantitative and qualitative losses in pumpkin (Cucurbita moschata) worldwide. Punjab Agricultural University (PAU) in India has identified a resistant source (PVR-1343) against mixed infection (MI-Sq/To) of these begomoviruses. Introgression of resistance in diverse genetic backgrounds requires the identification of quantitative trait loci (QTLs) associated with MI-Sq/To resistance. Phenotyping of 229 F2:3 progenies derived from the PVR-1343 × P-135 cross revealed digenic recessive inheritance against MI-Sq/To resistance in PVR-1343. To identify the genomic region, resistant and susceptible bulks were subjected to whole-genome resequencing along with their parents. The whole-genome resequence analysis of parents and bulks using QTLseq/QTLseqr approaches identified an overlapping 1.52 Mb region on chromosome 7 (qMI-Sq/To7.1), while chromosomal region spanning 0.87 Mb on chromosome17 (qMI-Sq/To17.1) was additionally identified by QTLseqr. However, the highest peak value on chromosome 7 with three algorithms {G', ∆(SNP-index) and -log10 (P value)} highlighted the major contribution of qMI-Sq/To7.1 in MI-Sq/To resistance. Nine polymorphic SNPs identified within the highly significant qMI-Sq/To7.1 region were converted into KASP markers. KASP genotyping of F2 individuals narrowed down the qMI-Sq/To7.1 interval to 103 kb region flanked by two markers, Cmo3914729 and Cmo4018182, which contained 16 annotated genes and accounted for 59.84% of phenotypic variation. The Cmo4018182 KASP marker accurately predicted disease reaction in 91% of diverse Cucurbita genotypes and showed nonsynonym substitutions in the coding region of putative candidate SYNTAXIN-121 gene. These findings pave the way for marker-assisted breeding and elucidating the underlying mechanism of begomovirus resistance in C. moschata.

[Assessment of prescribing practices in overactive bladder pharmacotherapy across different specialties of India: a prescription trend analysis].

PURPOSE: To assess the prescribing practices for overactive bladder (OAB) pharmacotherapy based on the prescription trend analysis across different specialties of India. METHOD: s: IQVIA (Quintiles and IMS Health) secondary sales audit (SSA), as well as a prescription audit for antimuscarinics and beta-3 adrenoceptor agonists (mirabegron) from 2014 to 2021, were analyzed. The data includes SSA data of various antimuscarinics like solifenacin, oxybutynin, tolterodine, darifenacin, trospium and mirabegron change in the prescription trend of antimuscarinics and mirabegron across different specialties; prescribers overlap analysis for solifenacin and mirabegron among Indian urologists were also analyzed. RESULTS: Urologists prescription rates of OAB drugs were 65% in 2016 and 54% in 2021. The rate of OAB medication prescription by non-urologist was highest from the surgeon (11%), followed by gynecologists (9%) and consultant physicians (8%) in 2021. In addition, among OAB medication prescription rates for antimuscarinics were 100% in 2016 and 58% in 2021 whereas for mirabegron, it was 0% in 2016 and 42% in 2021. Solifenacin was most frequently prescribed anticholinergics, followed by oxybutynin, tolterodine, darifenacin, and trospium. The proportion of prescribers of OAB medication among urologists was 38% in 2016 and 33% in 2021. Exclusive prescribers of solifenacin were 748 in 2018 and 739 in 2021 at the urologist, whereas for mirabegron, it was 961 in 2018 and 934 in 2021. The compound annual growth rate for prescription of the last 6 years (from 2016-2021) for solifenacin and mirabegron was -3% and 8% respectively. CONCLUSIONS: Urology remained a top prescribing specialty for OAB drugs, although prescription share increased at surgeon and consultant physician. OAB medicines prescriptions by urologists are shifting from leading antimuscarinic solifenacin to beta-agonist mirabegron. Data from this study will ultimately lead to the OAB medication preference by the specialist that could lead to more advanced OAB management.

Amalgamated Microneedle Array Bearing Ribociclib-Loaded Transfersomes Eradicates Breast Cancer via CD44 Targeting.

HR+/HER2- metastatic breast cancer (MBC) is one of the most common and life-threatening conditions diagnosed in women. The endocrine therapy using an orally active CDK4/6 inhibitor, ribociclib (RB), is the most intriguing approach for treating HR+/HER2- MBC. However, the repeated three to six cycles of multiple dosing and non-targeted distribution of RB led to severe neutropenia; hepatobiliary, gastrointestinal, and renal toxicities, and QT interval prolongation. Here, a novel organic solvent-free HA-PVA-PVP (hyaluronic acid-polyvinyl alcohol-polyvinyl pyrrolidone) composed of a microneedle (MN) array is formulated to deliver RB, integrated with amphiphilic conjugated polymer (HA-GMS)-anchored ultradeformable transfersomes. This unique MN array efficiently crafts microchannels in the skin, allowing HA-RB-Ts to internalize into the tumor cells through lymphatic and systemic absorption and interact with CD44 both spatially and temporally with an amplification of drug release time up to 6-folds. The pharmacokinetic and tissue distribution studies portray drug concentrations within the therapeutic window as long as 48 h, facilitating thrice-a-week frequency with the lower dose, and rule out severe toxicities, with a significant reduction in 8.3-fold RB concentration in vital organs that ultimately enhances the survival rate. Thus, the novel MN system pursues a unique embeddable feature and offers an effective, self-administrable, biodegradable, and chronic treatment option for patients requiring long-term cancer treatments.

Adsorption-desorption dynamics of synthetic and naturally weathered microfibers with toxic heavy metals and their ecological risk in an estuarine ecosystem.

Microfibers (MFs) in aquatic and marine ecosystems adsorb toxic heavy metals and then transfer the heavy metals enriched MFs to living organisms. In this research paper, the adsorption-desorption dynamics of heavy metals onto MFs was studied by using theoretical models and experimental investigations. The adsorption of metals onto MFs was well correlated for the Freundlich model and the adsorption kinetics follows pseudo-second order rate equation. The adsorption capacity of naturally weathered MFs was 30.8 mg g-1 which is about 35% higher than the synthetic fiber of similar range of size of MFs. The leaching of heavy metals from MFs was found that 90-95% of adsorbed metals were leached within 24 h. The leaching of Ti(II) and Al(III) were slower than the other metal ions. The salinity has shown decrease in adsorption capacity of MFs for heavy metals. Based on the Nemerov pollution index (PN), the naturally weathered MFs enriched with heavy metals in sediments became heavily polluted with PN values between 2.98 and 3.49. The risk index value of 396 represents that the bottom dwellers and other marine organisms in the Narmada estuary high risk from MFs and MFs enriched with metals. This study indicates that MFs play dominant role in fate and distribution of heavy metals in the estuarine ecosystems.

Ambulatory Blood Pressure Patterns in Children, Adolescents, and Young Adults With Childhood-Onset Systemic Lupus Erythematosus and Normal Office Blood Pressure.

OBJECTIVE: Cardiovascular disease is a major cause of morbidity and mortality in systemic lupus erythematosus (SLE). Hypertension (HTN) and nondipping are modifiable risk factors for cardiovascular disease. Limited studies are available for childhood-onset SLE (cSLE). We aimed to assess ambulatory blood pressure monitoring (ABPM) pattern in cSLE patients with normal office blood pressure. METHODS: This cross-sectional single-center study enrolled 25 patients with cSLE, normal office blood pressure and normal renal function. We performed 24-hour ABPM and echocardiography to assess end-organ damage. Descriptive statistics were obtained, and comparison of variables using Fisher exact test, t test, and Mann-Whitney U test was performed to identify potential risk factors for nondipping. RESULTS: Of the 25 patients, 22 were women; the median age was 18 years (interquartile range, 16-20 years). Median SLE duration was 4.2 years (interquartile range, 2.9-8.1 years); 18 patients had a history of lupus nephritis (LN). Four patients, 3 of whom had LN, had masked HTN. Fourteen patients (56%) were nondipping. The majority of patients without LN (71%) had a nondipping profile. Echocardiography was done for 15 patients. Left ventricular mass index, relative wall thickness, and ejection fraction were normal in all patients. Ambulatory blood pressure monitoring results led to changes in therapy in 5 patients. CONCLUSION: Our data provide evidence of high prevalence of nondipping and masked HTN in patients with cSLE, even in patients without LN. Identifying ABPM abnormalities in these patients could potentially improve outcomes.

Diagnostic and Prognostic Role of Neutrophil-to-Lymphocyte Ratio in Early and Late Phase of Sepsis.

OBJECTIVE: Early diagnosis of sepsis is necessary to decrease morbidity and mortality. This study aims to evaluate neutrophil-to-lymphocyte ratio (NLR) as diagnostic and prognostic of early and late phase of sepsis. METHODS: It was a prospective, observational study, conducted in Intensive Care and High Dependency Unit (Daycare) of the Department of Pulmonary and Critical Care Medicine (tertiary care center), Rohtak, from January 2017 to December 2017. A total of 56 cases of newly diagnosed cases of sepsis were included in the study and 20 healthy adults were taken as controls. Daily NLR was calculated in cases till the primary outcome. RESULTS: The results suggested that NLR seems to have promising role as diagnostic and prognostic marker (with P = 0.001 and P = 0.045, respectively) in sepsis. CONCLUSION: The study suggests that NLR can be a useful diagnostic and prognostic marker in sepsis.

4-Nonylphenol induced DNA damage and repair in fish, Channa punctatus after subchronic exposure.

The detection of a possible DNA damaging effect of 4-nonylphenol (NP) after subchronic exposure and repair after cessation of exposure to Channa punctatus is the aim of the present study. Channa punctatus was exposed to different concentrations (0.15 mg/l, 0.10 mg/l, and 0.07 mg/l) of NP along with positive control (ethanol) and negative control (water) for 90 d and after that allowed to recover for 30 d. Comet assay and micronucleus assay were used for the determination of DNA damage and repair by using blood cells. The effect was seen after 30, 60, and 90 d of exposure. Time- and dose-dependent increase in DNA damage was found as revealed by both the end points studied. Evident recovery was observed after 30 d of cessation of exposure. Blood cells were successfully appeared to achieve the restoration of DNA integrity. Hence, the study aimed to improve the knowledge of the genetic hazard to fish associated with NP exposure and provide a wide scope to discover the efficiency of DNA repair system in C. punctatus.

Biotechnological approaches to the production of shikonins: a critical review with recent updates.

Shikonins are commercially important secondary compounds, known for array of biological activities such as antimicrobial, insecticidal, antitumor, antioxidants, etc. These compounds are usually colored and therefore have application in food, textiles and cosmetics. Shikonin and its derivatives, which are commercially most important of the naphthoquinone pigments, are distributed among members of the family Boraginaceae. These include different species of Lithospermum, Arnebia, Alkanna, Anchusa, Echium and Onosma. The growing demand for plant-based natural products has made this group of compounds one of the enthralling targets for their in vitro production. The aim of this review is to highlight the recent progress in production of shikonins by various biotechnological means. Different methods of increasing the levels of shikonins in plant cells such as selection of cell lines, optimization of culture conditions, elicitation, in situ product removal, genetic transformation and metabolic engineering are discussed. The experience of different researchers working worldwide on this aspect is also considered. Further, to meet market demand, the needs for continuous and reliable production systems, as well as future prospects, are included.

Study on DNA damaging effects of 4-nonylphenol using erythrocytes from peripheral circulation, gill and kidney of fish Channapunctatus.

The present study aimed to evaluate the genotoxic effect of 4-nonylphenol (NP) on blood cells of fish Channapunctatus. Fish were exposed to three sublethal concentrations (0.15 mg l⁻¹; 0.31 mg l⁻¹ and 0.63 mg l⁻¹) of 4-NP for 24, 48, 72 and 96 hrs. Blood cells from kidney, gills and peripheral circulation were analyzed for the presence of micronuclei and other changes in the erythrocytes. Significant changes were observed in all the experimental groups tested when compared with control. Highest genotoxicity was observed in blood cells obtained from gills (MN-2.92%, aberrant cell- 70.64%), followed by kidney (MN-1.34%, aberrant cells-64.94%), were least effect was observed in blood cells obtained from peripheral circulation (MN-0.88%, aberrant cells-46.27%).Therefore, micronucleus test performed on blood cells obtained from different sources showed that gills were more sensitive as compared to peripheral blood and kidney revealing genotoxic effect of 4-NP on fish C. punctatus.

The DrrAB efflux system of Streptomyces peucetius is a multidrug transporter of broad substrate specificity.

The soil bacterium Streptomyces peucetius produces two widely used anticancer antibiotics, doxorubicin and daunorubicin. Present within the biosynthesis gene cluster in S. peucetius is the drrAB operon, which codes for a dedicated ABC (ATP binding cassette)-type transporter for the export of these two closely related antibiotics. Because of its dedicated nature, the DrrAB system is believed to belong to the category of single-drug transporters. However, whether it also contains specificity for other known substrates of multidrug transporters has never been tested. In this study we demonstrate under both in vivo and in vitro conditions that the DrrAB system can transport not only doxorubicin but is also able to export two most commonly studied MDR substrates, Hoechst 33342 and ethidium bromide. Moreover, we demonstrate that many other substrates (including verapamil, vinblastine, and rifampicin) of the well studied multidrug transporters inhibit DrrAB-mediated Dox transport with high efficiency, indicating that they are also substrates of the DrrAB pump. Kinetic studies show that inhibition of doxorubicin transport by Hoechst 33342 and rifampicin occurs by a competitive mechanism, whereas verapamil inhibits transport by a non-competitive mechanism, thus suggesting the possibility of more than one drug binding site in the DrrAB system. This is the first in-depth study of a drug resistance system from a producer organism, and it shows that a dedicated efflux system like DrrAB contains specificity for multiple drugs. The significance of these findings in evolution of poly-specificity in drug resistance systems is discussed.

Description of Pelistega indica sp. nov., isolated from human gut.

A Gram-stain-negative, motile, non-spore-forming, coccoid bacterium was isolated from a stool sample of a healthy human subject and formed cream colour colonies on tryptic soy agar. Almost full-length (1500 bp) small subunit rRNA (16S rRNA) gene sequences were generated and a similarity search was conducted by blast. The results of the similarity search indicated that the bacterium belongs to the class Betaproteobacteria, family Alcaligenaceae. It showed maximum sequence similarity (96.5 %) with Pelistega europaea CCUG 39967(T) followed by Advenella mimigardefordensis DSM 17166(T) (96.1 %) and Taylorella asinigenitalis LMG 19572(T) (95.3 %). The DNA G+C content of strain HM-7(T) was 42 mol%. Strain HM-7(T) contained C14 : 0, C16 : 0, C16 : 0 3-OH and C18 : 0 as the dominant fatty acids. Morphological, physiological and biochemical data also indicated that strain HM-7(T) represents a member of the genus Pelistega, but at the same time distinguished it from Pelistega europaea CCUG 39967(T), the only species of the genus with a validly published name. Based on polyphasic characterization we conclude that the bacterium represents a novel species of the genus Pelistega and propose the name Pelistega indica sp. nov., with strain HM-7(T) ( = MCC 2185(T) = DSM 27484(T)) as the type strain of the species.

Mass propagation of Cymbidium giganteum Wall. ex Lindl. using in vitro seedlings.

In vitro seedlings were used as explants for protocorm like bodies (PLBs) production which in turn were used for regeneration purpose. PLBs were induced from the base of seedlings (1.0-1.5 cm in size) in MS + BAP (8.88 microM). After 90 days of inoculation, PLBs production rate started declining and most of the PLBs turned into plantlets. Preculture of seedlings in 1.0 microM thidiazuron (TDZ) for 7 days and transfer to BAP supplemented medium resulted in production of 16 PLBs per seedling within 90 days of culture. Increase of TDZ concentration to 2.5 microM and preculture time 15 days, resulted in induction of highest number of PLBs (19 PLBs per seedling) in the basal medium. The results emphasized the importance of thidiazuron (TDZ) concentration and preculture time for PLBs proliferation from the base of seedlings. The PLBs thus produced were used for regeneration studies. Irrespective of single, segmented or clumps of PLBs, the regeneration response was 100% in 2,4-D (4.52 microM) and KN (4.64 microM) but when KN was replaced by BAP (8.88 microM), response was observed only in clumps of PLBs, whereas in single and segmented ones it was 99 and 97%, respectively. Regenerants developed stout root system in half strength M medium supplemented with 2.84 microM of IAA and transferred to greenhouse with 90% survival. The present study holds tremendous potential as the mother plant is not destroyed and PLBs are produced as a continuous system.

A simple technique for tracking individual spore and gametophyte development in Adiantum lunulatum Burm. f. using modified extra thin alginate film technique.

A new technique was developed for accurate calculation of percent germination and tracking of individual spores from germination to gametophyte development in Adiantum lunulatum. High percentage of ETAF immobilized spore germination (72.4%) was followed by development of gametophytic clumps. The ETAF immobilized clumps were cut into pieces and multiplied en masse. Apomictic sporophytes developed from the gametophytes. This indicated the potential of ETAF for mass propagation of A. lunulatum without the need to start from spores. Since individual spores can be tracked from germination to gametophyte development, the ETAF technique has the potential to be used for (i) harvesting uniformly developed plants of similar age for extensive experimentations and commercial utilization and (ii) detailed study on developmental and reproductive biology of different ferns and fern allies.