Lung microbiome in lung cancer: A new horizon in cancer study.

Lung cancer (LC) is the second most prevalent cancer worldwide and a leading cause of cancer-related deaths. Recent technological advancements have revealed that the lung microbiome, previously thought to be sterile, is host to various microorganisms. The association between the lung microbiome and LC initiation, progression, and metastasis is complex and contradictory. However, disruption in the homeostasis of microbiome compositions correlated with the increased risk of LC. This review summarises current knowledge on the most recent developments and trends in lung cancer-related microbiota or microbial components. This manuscript aims to provide information on this rapidly evolving field while giving context to the general role of the lung microbiome in LC. In addition, this review briefly discussed the causative association of lung microbiome with LC. We will review the mechanisms of how lung microbiota influences carcinogenesis, focusing on microbiota dysbiosis. Moreover, we will also discuss the host-microbiome interaction as host-microbiota plays a crucial role in stimulating and regulating the immune response. Finally, we provide information on the diagnostic role of the microbiome in LC. It aims to offer an overview of the lung microbiome as a predictive and diagnostic biomarker in LC.

SpatialPrompt: spatially aware scalable and accurate tool for spot deconvolution and domain identification in spatial transcriptomics.

Efficiently mapping of cell types in situ remains a major challenge in spatial transcriptomics. Most spot deconvolution tools ignore spatial coordinate information and perform extremely slow on large datasets. Here, we introduce SpatialPrompt, a spatially aware and scalable tool for spot deconvolution and domain identification. SpatialPrompt integrates gene expression, spatial location, and single-cell RNA sequencing (scRNA-seq) dataset as reference to accurately infer cell-type proportions of spatial spots. SpatialPrompt uses non-negative ridge regression and graph neural network to efficiently capture local microenvironment information. Our extensive benchmarking analysis on Visium, Slide-seq, and MERFISH datasets demonstrated superior performance of SpatialPrompt over 15 existing tools. On mouse hippocampus dataset, SpatialPrompt achieves spot deconvolution and domain identification within 2 minutes for 50,000 spots. Overall, domain identification using SpatialPrompt was 44 to 150 times faster than existing methods. We build a database housing 40 plus curated scRNA-seq datasets for seamless integration with SpatialPrompt for spot deconvolution.

Molecularly Engineered Multifunctional Bridging Layer Derived from Dithiafulavene Capped Spiroxanthene for Stable and Efficient Perovskite Solar Cells.

This study introduces a novel approach centered around the design and synthesis of an interfacial passivating layer in perovskite solar cells (PSCs). This architectural innovation is realized through the development of a specialized material, termed dithiafulvene end-capped Spiro[fluorene-9,9'-xanthene], denoted by the acronym AF32. In this design architecture, dithiafulvene is thoughtfully attached to the spiroxanthene fluorene core with phenothiazine as the spacer unit, possessing multiple alkyl chains. AF32 passivates interfacial defects by coordinating the sulfur constituents of the phenothiazine and dithiafulvene frameworks to the uncoordinated Pb2+ cations on the surface of the perovskite film, and the alkyl chains construct a hydrophobic environment, preventing moisture from entering the hydrophilic perovskite layer and improving the long-term stability of PSCs. Furthermore, this conductive interlayer facilitates hole transport in PSCs due to its well-aligned molecular orbital levels. Such improvements translated into an enhanced power conversion efficiency (PCE) of 22.6% for the device employing 1.5 mg/mL AF32, and it maintained 85% of its initial PCE after more than 1800 h under ambient conditions [illumination and 45 ± 5% relative humidity (RH)]. This study not only marks progress in photovoltaic technology but also expands our understanding of manipulating interfacial properties for optimized device performance and stability.

Peribacillus frigoritolerans T7-IITJ, a potential biofertilizer, induces plant growth-promoting genes of Arabidopsis thaliana.

AIMS: This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the nutrient-poor rhizosphere soil of Thar desert plants and unravel their molecular mechanisms of plant growth promotion. METHODS AND RESULTS: Among our rhizobacterial isolates, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth (4-5-fold) in Arabidopsis thaliana under PEG-induced drought stress. Whole genome sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of phosphate (40-73 µg/ml), iron (24 ± 0.58 mm halo on chrome azurol S media), and nitrate (1.58 ± 0.01 µg/ml nitrite), along with production of exopolysaccharides (125 ± 20 µg/ml) and auxin-like compounds (42.6 ± 0.05 µg/ml). Transcriptome analysis of A. thaliana inoculated with T7-IITJ and exposure to drought revealed the induction of 445 plant genes (log2fold-change > 1, FDR < 0.05) for photosynthesis, auxin and jasmonate signalling, nutrient uptake, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction, but repression of 503 genes (log2fold-change < -1) including many stress-responsive genes. T7-IITJ enhanced proline 2.5-fold, chlorophyll 2.5-2.8-fold, iron 2-fold, phosphate 1.6-fold, and nitrogen 4-fold, and reduced reactive oxygen species 2-4.7-fold in plant tissues under drought. T7-IITJ also improved the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought and inhibited the growth of two plant pathogenic fungi, Fusarium oxysporum, and Rhizoctonia solani. CONCLUSIONS: P. frigoritolerans T7-IITJ is a potent biofertilizer that regulates plant genes to promote growth and drought tolerance.

The colibactin-producing Escherichia coli alters the tumor microenvironment to immunosuppressive lipid overload facilitating colorectal cancer progression and chemoresistance.

Intratumoral bacteria flexibly contribute to cellular and molecular tumor heterogeneity for supporting cancer recurrence through poorly understood mechanisms. Using spatial metabolomic profiling technologies and 16SrRNA sequencing, we herein report that right-sided colorectal tumors are predominantly populated with Colibactin-producing Escherichia coli (CoPEC) that are locally establishing a high-glycerophospholipid microenvironment with lowered immunogenicity. It coincided with a reduced infiltration of CD8+ T lymphocytes that produce the cytotoxic cytokines IFN-γ where invading bacteria have been geolocated. Mechanistically, the accumulation of lipid droplets in infected cancer cells relied on the production of colibactin as a measure to limit genotoxic stress to some extent. Such heightened phosphatidylcholine remodeling by the enzyme of the Land's cycle supplied CoPEC-infected cancer cells with sufficient energy for sustaining cell survival in response to chemotherapies. This accords with the lowered overall survival of colorectal patients at stage III-IV who were colonized by CoPEC when compared to patients at stage I-II. Accordingly, the sensitivity of CoPEC-infected cancer cells to chemotherapies was restored upon treatment with an acyl-CoA synthetase inhibitor. By contrast, such metabolic dysregulation leading to chemoresistance was not observed in human colon cancer cells that were infected with the mutant strain that did not produce colibactin (11G5∆ClbQ). This work revealed that CoPEC locally supports an energy trade-off lipid overload within tumors for lowering tumor immunogenicity. This may pave the way for improving chemoresistance and subsequently outcome of CRC patients who are colonized by CoPEC.

A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas.

The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.

Stem Rot of Pearl Millet Prevalence, Symptomatology, Disease Cycle, Disease Rating Scale and Pathogen Characterization in Pearl Millet-Klebsiella Pathosystem.

The oldest and most extensively cultivated form of millet, known as pearl millet (Pennisetum glaucum (L.) R. Br. Syn. Pennisetum americanum (L.) Leeke), is raised over 312.00 lakh hectares in Asian and African countries. India is regarded as the significant hotspot for pearl millet diversity. In the Indian state of Haryana, where pearl millet is grown, a new and catastrophic bacterial disease known as stem rot of pearl millet spurred by the bacterium Klebsiella aerogenes (formerly Enterobacter) was first observed during fall 2018. The disease appears in form of small to long streaks on leaves, lesions on stem, and slimy rot appearance of stem. The associated bacterium showed close resemblance to Klebsiella aerogenes that was confirmed by a molecular evaluation based on 16S rDNA and gyrA gene nucleotide sequences. The isolates were also identified to be Klebsiella aerogenes based on biochemical assays, where Klebsiella isolates differed in D-trehalose and succinate alkalisation tests. During fall 2021-2023, the disease has spread all the pearl millet-growing districts of the state, extending up to 70% disease incidence in the affected fields. The disease is causing considering grain as well as fodder losses. The proposed scale, consisting of six levels (0-5), is developed where scores 0, 1, 2, 3, 4, and 5 have been categorized as highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible disease reaction, respectively. The disease cycle, survival of pathogen, and possible losses have also been studied to understand other features of the disease.

In silico characterization of five novel disease-resistance proteins in Oryza sativa sp. japonica against bacterial leaf blight and rice blast diseases.

In the current study, gene network analysis revealed five novel disease-resistance proteins against bacterial leaf blight (BB) and rice blast (RB) diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (M. oryzae), respectively. In silico modeling, refinement, and model quality assessment were performed to predict the best structures of these five proteins and submitted to ModelArchive for future use. An in-silico annotation indicated that the five proteins functioned in signal transduction pathways as kinases, phospholipases, transcription factors, and DNA-modifying enzymes. The proteins were localized in the nucleus and plasma membrane. Phylogenetic analysis showed the evolutionary relation of the five proteins with disease-resistance proteins (XA21, OsTRX1, PLD, and HKD-motif-containing proteins). This indicates similar disease-resistant properties between five unknown proteins and their evolutionary-related proteins. Furthermore, gene expression profiling of these proteins using public microarray data showed their differential expression under Xoo and M. oryzae infection. This study provides an insight into developing disease-resistant rice varieties by predicting novel candidate resistance proteins, which will assist rice breeders in improving crop yield to address future food security through molecular breeding and biotechnology. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03893-5.

A comprehensive review on therapeutic potentials of photobiomodulation for neurodegenerative disorders.

A series of experimental trials over the past two centuries has put forth Photobiomodulation (PBM) as a treatment modality that utilizes colored lights for various conditions. While in its cradle, PBM was used for treating simple conditions such as burns and wounds, advancements in recent years have extended the use of PBM for treating complex neurodegenerative diseases (NDDs). PBM has exhibited the potential to curb several symptoms and signs associated with NDDs. While several of the currently used therapeutics cause adverse side effects alongside being highly invasive, PBM on the contrary, seems to be broad-acting, less toxic, and non-invasive. Despite being projected as an ideal therapeutic for NDDs, PBM still isn't considered a mainstream treatment modality due to some of the challenges and knowledge gaps associated with it. Here, we review the advantages of PBM summarized above with an emphasis on the common mechanisms that underlie major NDDs and how PBM helps tackle them. We also discuss important questions such as whether PBM should be considered a mainstay treatment modality for these conditions and if PBM's properties can be harnessed to develop prophylactic therapies for high-risk individuals and also highlight important animal studies that underscore the importance of PBM and the challenges associated with it. Overall, this review is intended to bring the major advances made in the field to the spotlight alongside addressing the practicalities and caveats to develop PBM as a major therapeutic for NDDs.

Gestational intermittent hypoxia induces endothelial dysfunction and hypertension in pregnant rats: role of endothelin type B receptor†.

Obstructive sleep apnea is a recognized risk factor for gestational hypertension, yet the exact mechanism behind this association remains unclear. Here, we tested the hypothesis that intermittent hypoxia, a hallmark of obstructive sleep apnea, induces gestational hypertension through perturbed endothelin-1 signaling. Pregnant Sprague-Dawley rats were subjected to normoxia (control), mild intermittent hypoxia (10.5% O2), or severe intermittent hypoxia (6.5% O2) from gestational days 10-21. Blood pressure was monitored. Plasma was collected and mesenteric arteries were isolated for myograph and protein analyses. The mild and severe intermittent hypoxia groups demonstrated elevated blood pressure, reduced plasma nitrate/nitrite, and unchanged endothelin-1 levels compared to the control group. Western blot analysis revealed decreased expression of endothelin type B receptor and phosphorylated endothelial nitric oxide synthase, while the levels of endothelin type A receptor and total endothelial nitric oxide synthase remained unchanged following intermittent hypoxia exposure. The contractile responses to potassium chloride, phenylephrine, and endothelin-1 were unaffected in endothelium-denuded arteries from mild and severe intermittent hypoxia rats. However, mild and severe intermittent hypoxia rats exhibited impaired endothelium-dependent vasorelaxation responses to endothelin type B receptor agonist IRL-1620 and acetylcholine compared to controls. Endothelium denudation abolished IRL-1620-induced vasorelaxation, supporting the involvement of endothelium in endothelin type B receptor-mediated relaxation. Treatment with IRL-1620 during intermittent hypoxia exposure significantly attenuated intermittent hypoxia-induced hypertension in pregnant rats. This was associated with elevated circulating nitrate/nitrite levels, enhanced endothelin type B receptor expression, increased endothelial nitric oxide synthase activation, and improved vasodilation responses. Our data suggested that intermittent hypoxia exposure during gestation increases blood pressure in pregnant rats by suppressing endothelin type B receptor-mediated signaling, providing a molecular mechanism linking intermittent hypoxia and gestational hypertension.

Gene expression profiling and protein-protein network analysis revealed prognostic hub biomarkers linking cancer risk in type 2 diabetic patients.

Type 2 diabetes mellitus (T2DM) and cancer are highly prevalent diseases imposing major health burden globally. Several epidemiological studies indicate increased susceptibility to cancer in T2DM patients. However, genetic factors linking T2DM with cancer have been poorly studied. In this study, we followed computational approaches using the raw gene expression data of peripheral blood mononuclear cells of T2DM and cancer patients available in the gene expression omnibus (GEO) database. Our analysis identified shared differentially expressed genes (DEGs) in T2DM and three common cancer types, namely, pancreatic cancer (PC), liver cancer (LC), and breast cancer (BC). The functional and pathway enrichment analysis of identified common DEGs highlighted the involvement of critical biological pathways, including cell cycle events, immune system processes, cell morphogenesis, gene expression, and metabolism. We retrieved the protein-protein interaction network for the top DEGs to deduce molecular-level interactions. The network analysis found 7, 6, and 5 common hub genes in T2DM vs. PC, T2DM vs. LC, and T2DM vs. BC comparisons, respectively. Overall, our analysis identified important genetic markers potentially able to predict the chances of PC, LC, and BC onset in T2DM patients.

Improved Efficiency and Stability in 1,5-Diaminonaphthalene Iodide-Passivated 2D/3D Perovskite Solar Cells.

Engineering multidimensional two-dimensional/three-dimensional (2D/3D) perovskite interfaces as light harvesters has recently emerged as a potential strategy to obtain a higher photovoltaic performance in perovskite solar cells (PSCs) with enhanced environmental stability. In this study, we utilized the 1,5-diammonium naphthalene iodide (NDAI) bulky organic spacer for interface modification in 3D perovskites for passivating the anionic iodide/uncoordinated Pb2+ vacancies as well as facilitating charge carrier transfer by improving the energy band alignment at the perovskite/HTL interface. Consequently, the NDAI-treated 2D/3D PSCs showed an enhanced open-circuit voltage and fill factor with a remarkable power conversion efficiency (PCE) of 21.48%. In addition, 2D/3D perovskite devices without encapsulation exhibit a 77% retention of their initial output after 1000 h of aging under 50 ± 5% relative humidity. Furthermore, even after 200 h of storage in 85 °C thermal stress, the devices maintain 60% of their initial PCE. The defect passivation and interface modification mechanism were studied in detail by UV vis absorption, photoluminescence spectroscopy, atomic force microscopy (AFM), scanning electron microscopy (SEM), Fourier transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), solid-state NMR, space-charge-limited current (SCLC) mobility measurement, and impedance spectroscopy. This study provides a promising path for perovskite surface modification in slowing their degradation against external stimuli, providing a future direction for increasing the perovskite device efficiency and durability.

PFOS Impairs Mitochondrial Biogenesis and Dynamics and Reduces Oxygen Consumption in Human Trophoblasts.

Perfluorooctane sulfonate (PFOS), a synthetic chemical used in various commercial applications and industrial settings, has led to contamination of drinking water and has been detected in the bloodstream of pregnant women with gestational complications. Recent investigations have indicated that PFOS disrupts placental function; however, the mechanism remains elusive. Given the significant abundance of mitochondria in the placenta, which play a pivotal role in fulfilling the heightened energy requirements of pregnancy, our research aimed to examine the repercussions of PFOS exposure on mitochondrial dynamics within placental trophoblasts. Specifically, human trophoblasts (HTR-8/SVneo) were exposed to environmentally relevant concentrations of PFOS ranging from 0.1 to 50 µM for 48 hours. Findings revealed that PFOS exposure elicited a concentration-dependent decrease in basal, maximal, and ATP-linked respiration. PFOS inhibited the activity of electron transport complexes I, II, and III, resulting in diminished ATP production. Furthermore, PFOS reduced mitochondrial DNA copy number, indicating less mitochondrial content. Concurrently, there was a downregulation in the expression of mitochondrial biogenesis-related genes, including PGC-1α, NRF1, and NRF2. Notably, PFOS perturbed mitochondrial dynamics by suppressing the expression of fission-related genes (FIS1 and DRP1) and fusion-related genes (MFN1 and MFN2). In summary, our findings suggest that PFOS exposure leads to a decline in mitochondrial content and compromises the bioenergetic capacity of trophoblasts by impairing cellular respiration. This reduction in mitochondrial biogenesis and alterations in fission/fusion dynamics induced by PFOS may contribute to mitochondrial dysfunction in trophoblasts. Consequently, strategies that preserve mitochondrial function in trophoblasts may mitigate PFOS-induced impairment of placental energy metabolism.

Restoring Angiotensin Type 2 Receptor Function Reverses PFOS-Induced Vascular Hyper-Reactivity and Hypertension in Pregnancy.

Perfluorooctane sulfonic acid (PFOS) exposure during pregnancy induces hypertension with decreased vasodilatory angiotensin type-2 receptor (AT2R) expression and impaired vascular reactivity and fetal weights. We hypothesized that AT2R activation restores the AT1R/AT2R balance and reverses gestational hypertension by improving vascular mechanisms. Pregnant Sprague-Dawley rats were exposed to PFOS through drinking water (50 µg/mL) from gestation day (GD) 4-20. Controls received drinking water with no detectable PFOS. Control and PFOS-exposed rats were treated with AT2R agonist Compound 21 (C21; 0.3 mg/kg/day, SC) from GD 15-20. In PFOS dams, blood pressure was higher, blood flow in the uterine artery was reduced, and C21 reversed these to control levels. C21 mitigated the heightened contraction response to Ang II and enhanced endothelium-dependent vasorelaxation in uterine arteries of PFOS dams. The observed vascular effects of C21 were correlated with reduced AT1R levels and increased AT2R and eNOS protein levels. C21 also increased plasma bradykinin production in PFOS dams and attenuated the fetoplacental growth restriction. These data suggest that C21 improves the PFOS-induced maternal vascular dysfunction and blood flow to the fetoplacental unit, providing preclinical evidence to support that AT2R activation may be an important target for preventing or treating PFOS-induced adverse maternal and fetal outcomes.

Green Synthesis of Pristine and Ag-Doped TiO2 and Investigation of Their Performance as Photoanodes in Dye-Sensitized Solar Cells.

Dye-sensitized solar cells (DSSCs) have emerged as a potential candidate for third-generation thin film solar energy conversion systems because of their outstanding optoelectronic properties, cost-effectiveness, environmental friendliness, and easy manufacturing process. The electron transport layer is one of the most essential components in DSSCs since it plays a crucial role in the device's greatest performance. Silver ions as a dopant have drawn attention in DSSC device applications because of their stability under ambient conditions, decreased charge recombination, increased efficient charge transfer, and optical, structural, and electrochemical properties. Because of these concepts, herein, we report the synthesis of pristine TiO2 using a novel green modified solvothermal simplistic method. Additionally, the prepared semiconductor nanomaterials, Ag-doped TiO2 with percentages of 1, 2, 3, and 4%, were used as photoanodes to enhance the device's performance. The obtained nanomaterials were characterized using XRD, FTIR, FE-SEM, EDS, and UV-vis techniques. The average crystallite size for pristine TiO2 and Ag-doped TiO2 with percentages of 1, 2, 3, and 4% was found to be 13 nm by using the highest intensity peaks in the XRD spectra. The Ag-doped TiO2 nanomaterials exhibited excellent photovoltaic activity as compared to pristine TiO2. The incorporation of Ag could assist in successful charge transport and minimize the charge recombination process. The DSSCs showed a Jsc of 8.336 mA/cm2, a Voc of 698 mV, and an FF of 0.422 with a power conversion efficiency (PCE) of 2.45% at a Ag concentration of 4% under illumination of 100 mW/cm2 power with N719 dye, indicating an important improvement when compared to 2% Ag-doped (PCE of 0.97%) and pristine TiO2 (PCE of 0.62%).

Elevated Maternal Testosterone Levels Alter PFOA Elimination and Tissue Distribution in Pregnant Rats.

Perfluorooctanoic acid (PFOA) is an enduring synthetic chemical that harms human health. Recent studies indicate heightened bioaccumulation of PFOA, particularly in pregnant women experiencing preeclampsia. Since plasma testosterone levels are elevated in pregnant women with preeclampsia, we hypothesized that hyperandrogenic conditions during pregnancy may hinder PFOA elimination and contribute to their higher body burden. Pregnant Sprague-Dawley rats were s/c injected with vehicle or testosterone propionate from gestational day (GD) 15 to 20 to increase plasma testosterone levels by 2-fold, similar to levels in preeclampsia. On GD 16, [14C]-PFOA (9.4 pmol/kg) was given intravenously, and subsequently, 14C radioactivity was measured in maternal blood, urine, feces, and tissues. PFOA was primarily eliminated through urine; however, less PFOA was excreted in urine of pregnant rats with elevated testosterone levels than controls. Fecal excretion of PFOA was minimal and did not significantly differ between groups. The total elimination of PFOA (urine plus feces) was significantly reduced by 12% in pregnant rats with elevated testosterone levels. In controls, PFOA distribution was highest in placenta, followed by the kidneys, liver, brain, heart, lungs, and spleen. Pregnant rats with elevated testosterone levels displayed 12% higher concentrations of PFOA in these tissues than controls. Furthermore, the renal expression of Oat2 and Oat3 was significantly decreased, while Oatp1 and Oat-k expression was significantly increased in pregnant rats with elevated testosterone levels than controls. In conclusion, elevated maternal testosterone levels decrease urinary elimination of PFOA, possibly through altered expression of renal transporters leading to increased tissue concentrations of PFOA in pregnant rats.

Genome-wide association study as a powerful tool for dissecting competitive traits in legumes.

Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.

Red emitting carbon dots: surface modifications and bioapplications.

Quantum dots (QDs), and carbon quantum dots (CDs) in particular, have received significant attention for their special characteristics. These particles, on the scale of several nanometers, are often produced using simple and green methods, with naturally occurring organic precursors. In addition to facile production methods, CDs present advantageous applications in the field of medicine, primarily for bioimaging, antibacterial and therapeutics. Also, CDs present great potential for surface modification through methods like doping or material mixing during synthesis. However, the bulk of current literature focuses on CDs emitting in the blue wavelengths which are not very suitable for biological applications. Red emitting CDs are therefore of additional interest due to their brightness, photostability, novelty and deeper tissue penetration. In this review article, red CDs, their methods of production, and their biological applications for translational research are explored in depth, with emphasis on the effects of surface modifications and doping.

Single-cell transcriptome analysis identifies novel biomarkers involved in major liver cancer subtypes.

Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are the two aggressive subtypes of liver cancer (LC). Immense cellular heterogeneity and cross-talk between cancer and healthy cells make it challenging to treat these cancer subtypes. To address these challenges, the study aims to systematically characterize the tumor heterogeneity of LC subtypes using single-cell RNA sequencing (scRNA-seq) datasets. The study combined 51,927 single cells from HCC, ICC, and healthy scRNA-seq datasets. After integrating the datasets, cell groups with similar gene expression patterns are clustered and cluster annotation has been performed based on gene markers. Cell-cell communication analysis (CCA) was implemented to understand the cross-talk between various cell types. Further, differential gene expression analysis and enrichment analysis were carried out to identify unique molecular drivers associated with HCC and ICC. Our analysis identified T cells, hepatocytes, epithelial cells, and monocyte as the major cell types present in the tumor microenvironment. Among them, abundance of natural killer (NK) cells in HCC, epithelial cells, and hepatocytes in ICC was detected. CCA revealed key interaction between T cells to NK cells in HCC and smooth muscle cells to epithelial cells in the ICC. Additionally, SOX4 and DTHD1 are the top differentially expressed genes (DEGs) in HCC, while keratin and CCL4 are in ICC. Enrichment analysis of DEGs reveals major upregulated genes in HCC affect protein folding mechanism and in ICC alter pathways involved in cell adhesion. The findings suggest potential targets for the development of novel therapeutic strategies for the treatment of these two aggressive subtypes of LC.