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Abstract A highly efficient approach for synthesizing a supramolecular metallogel of Co(II) ions, denoted as CoA-TA, has been established under room temperature and atmospheric pressure conditions. This method employs the metal-coordinating organic ligand benzene-1,3,5-tricarboxylic acid as a low molecular weight gelator (LMWG) in DMF solvent. A comprehensive analysis of the mechanical properties of the resulting supramolecular Co(II)-metallogel was conducted through rheological investigation, considering angular frequency and thixotropic study. The hierarchical rocky network structure of the supramolecular Co(II)-metallogel was unveiled using field emission scanning electron microscopy (FESEM). Transmission electron microscopic (TEM) analysis showed rod-shaped structures via low-magnification high angle annular dark field (HAADF) bright field scanning transmission electron microscopic (STEM) imaging, while energy dispersive X-ray (EDX) elemental mapping confirmed its primary chemical constituents. The formation mechanism of the metallogel was examined via fourier transform infrared spectroscopy (FTIR) spectroscopy. The nature of the synthesized CoA-TA metallogel was affirmed through powder X-ray diffraction (PXRD) analysis. Furthermore, this study involved fabrication of Schottky diode structures in a metal-semiconductor-metal geometry based on cobalt(II) metallogel (CoA-TA), enabling observation of charge transport behavior. Remarkably, a resistive random access memory (RRAM) device utilizing cobalt(II) metallohydrogel (CoA-TA) demonstrated bipolar resistive switching at room temperature and under ambient conditions. The switching mechanism was investigated, revealing the formation and rupture of conductive filaments between metal electrodes that govern the resistive switching behavior. This RRAM device exhibited an impressive ON/OFF ratio (~ 414) and exceptional endurance over 5000 switching cycles. These structures offer great potential for diverse applications such as non-volatile memory design, neuromorphic computing, flexible electronics and optoelectronics. Their advantages lie in their fabrication process, reliable resistive switching behavior and overall performance stability.

Abstract Thermal Power Plant generates FGD gypsum as by-product during coal combustion. This study evaluates the characterization (spectroscopic and elemental), potentially toxic elements (PTEs) distribution, and environmental risk assessment of FGD gypsum for safe and sustainable use in agriculture. The XRD and SEM analysis confirmed the dominance of crystalline CaSO4·2H2O in FGD gypsum. The order of concentrations of PTEs in FGD gypsum was Fe > Al > Mn > Zn > Ni > Co. The residual fraction was the dominant pool, sharing 80–90% of the total PTEs. The heavy metals (HMs) were below the toxic range in the leachates. The Co, Ni, Al, Fe Mn, Zn had low (

Abstract Phyllanthus emblica (Aonla, Indian Gooseberry) is known to have various medicinal properties, but studies to understand its genetic structure are limited. Among the various secondary metabolites, ascorbic acid, flavonoids, terpenoids, phenols and tannins possess great potential for its pharmacological applications. Keeping this consideration, we assembled the transcriptome using the Illumina RNASeq500 platform, generating 39,933,248 high-quality paired-end reads assembled into 1,26,606 transcripts. A total of 87,771 unigenes were recovered after isoforms and unambiguous sequences deletion. Functional annotation of 43,377 coding sequences against the NCBI non-redundant (Nr) database search using BlastX yielded 38,692 sequences containing blast hits and found 4685 coding sequences to be unique. The transcript showed maximum similarity to Hevea brasilensis (16%), followed by to Jatropha curcas (12%). Considering key genes involved in the biosynthesis of flavonoids and various classes of terpenoid compounds, thirty EST-SSR primer sequences were designed based on transcriptomic data. Of which, 12 were found to be highly polymorphic with an average of 86.38%. The average value for marker index (MI), effective multiplicity ratio (EMR), resolution power (Rp) and polymorphic information content (PIC) was 7.20, 8.34, 8.64 and 0.80, respectively. Thus, from this study, we developed newly EST-SSRs linked to important genes involved in the secondary metabolites biosynthesis that will be serving as an invaluable genetic resource for crop improvement including the selection of elite genotypes in P. emblica and its closely related Phyllanthaceae species.

Abstract In pregnant animals, communication between the mother and conceptus occurs via extracellular vesicles (EVs) that carry several biomolecules such as nucleic acids (miRNAs, mRNAs), proteins, and lipids. At the time of implantation, the endometrium undergoes several morphological and physiological changes, such as angiogenesis, apoptosis, and cell proliferation regulation at the implantation site, to attain a receptive state. This study was conducted to detect pregnancy-specific miRNAs derived from extracellular vesicles in the systemic circulation of Bubalus bubalis (water buffalo) and to assess their functional significance in the modulation of endometrial primary cells. The extracellular vesicles were isolated from the blood plasma using a precipitation-based method and further characterized by various methods such as Differential light scattering, Nanoparticle tracking assay, Western blot, and transmission electron microscopy. The relative expression of the selected extracellular vesicles associated miRNAs (EV-miRNA) at different intervals (days 15, 19, 25, and 30) post artificial insemination (AI) was analyzed using RT-qPCR, and expression of miR-195-5p was found to be significantly higher (P

Abstract Synbiotics are employed as feed additives in animal production as an alternate to antibiotics for sustaining the gut microbiota and providing protection against infections. Dairy calves require a healthy diet and management to ensure a better future for the herd of dairy animals. Therefore, the present study was carried out to investigate the effect of synbiotics formulation on growth performance, nutrient digestibility, fecal bacterial count, metabolites, immunoglobulins, blood parameters, antioxidant enzymes and immune response of pre-ruminant Murrah buffalo calves. Twenty-four apparently healthy calves (5 days old) were allotted into four groups of six calves each. Group I (control) calves were fed a basal diet of milk, calf starter and berseem with no supplements. Group II (SYN1) calves were fed with 3 g fructooligosaccharide (FOS) + Lactobacillus plantarum CRD-7 (150 ml). Group III (SYN2) calves were fed with 6 g FOS + L. plantarum CRD-7 (100 ml), whereas calves in group IV (SYN3) received 9 g FOS + L. plantarum CRD-7 (50 ml). The results showed that SYN2 had the highest (P

Abstract A home point-of care FCP test (IBDoc) and a self-reported clinical disease activity program (IBD Dashboard) may improve routine monitoring of IBD activity during pregnancy. We aimed to evaluate the feasibility of tight control management using remote monitoring in pregnant patients with IBD. Pregnant patients (

Abstract A detailed understanding of the different mechanisms being responsible for terahertz (THz) emission in ferromagnetic (FM) materials will aid in designing efficient THz emitters. In this report, we present direct evidence of THz emission from single layer Co $$_{0.4}$$ 0.4 Fe $$_{0.4}$$ 0.4 B $$_{0.2}$$ 0.2 (CoFeB) FM thin films. The dominant mechanism being responsible for the THz emission is the anomalous Hall effect (AHE), which is an effect of a net backflow current in the FM layer created by the spin polarized current reflected at the interfaces of the FM layer. The THz emission from the AHE-based CoFeB emitter is optimized by varying its thickness, orientation, and pump fluence of the laser beam. Results from electrical transport measurements show that skew scattering of charge carriers is responsible for the THz emission in the CoFeB AHE-based THz emitter.

Abstract Early detection of cancer will improve survival rates. The blood biomarker 5-hydroxymethylcytosine has been shown to discriminate cancer. In a large covariate-controlled study of over two thousand individual blood samples, we created, tested and explored the properties of a 5-hydroxymethylcytosine-based classifier to detect colorectal cancer (CRC). In an independent validation sample set, the classifier discriminated CRC samples from controls with an area under the receiver operating characteristic curve (AUC) of 90% (95% CI [87, 93]). Sensitivity was 55% at 95% specificity. Performance was similar for early stage 1 (AUC 89%; 95% CI [83, 94]) and late stage 4 CRC (AUC 94%; 95% CI [89, 98]). The classifier could detect CRC even when the proportion of tumor DNA in blood was undetectable by other methods. Expanding the classifier to include information about cell-free DNA fragment size and abundance across the genome led to gains in sensitivity (63% at 95% specificity), with similar overall performance (AUC 91%; 95% CI [89, 94]). We confirm that 5-hydroxymethylcytosine can be used to detect CRC, even in early-stage disease. Therefore, the inclusion of 5-hydroxymethylcytosine in multianalyte testing could improve sensitivity for the detection of early-stage cancer.

Abstract Celiac disease (CeD) is a common small bowel enteropathy characterized by an altered adaptive immune system and increased mucosal antigen presenting cells. This study aims to establish if quantification of corneal Langerhans cells (LCs) using corneal confocal microscopy (CCM) could act as a surrogate marker for antigen presenting cell status and hence disease activity in children with CeD. Twenty children with stable CeD and 20 age-matched controls underwent CCM and quantification of central corneal total, mature and immature LC density. There was no difference in age (11.78 ± 1.7 vs. 12.83 ± 1.91; P = 0.077) or height (1.38 ± 0.14 vs. 1.44 ± 0.13; P = 0.125). BMI (18.81 ± 3.90 vs. 22.26 ± 5.47; P = 0.031) and 25 OHD levels (43.50 ± 13.36 vs. 59.77 ± 22.45; P = 0.014) were significantly lower in children with CeD compared to controls. The total (33.33(16.67–59.37) vs. 51.56(30.21–85.42); P = 0.343), immature (33.33(16.67–52.08) vs. 44.79(29.17–82.29); P = 0.752) and mature (1.56(0–5) vs. 1.56(1.04–8.33); P = 0.752) LC density did not differ between the CeD and control groups. However, immature (r = 0.535, P = 0.015), mature (r = 0.464, P = 0.039), and total (r = 0.548, P = 0.012) LC density correlated with age. Immature (r = 0.602, P = 0.038) and total (r = 0.637, P = 0.026) LC density also correlated with tissue transglutaminase antibody (Anti-TtG) levels assessed in 12/20 subjects with CeD. There was no difference in corneal LC density between children with CeD and controls. However, the correlation between corneal LC density and anti-TtG levels suggests a relationship with disease activity in CeD and requires further study.

Abstract CoViD19 is a novel disease which has created panic worldwide by infecting millions of people around the world. The last significant variant of this virus, called as omicron, contributed to majority of cases in the third wave across globe. Though lesser in severity as compared to its predecessor, the delta variant, this mutation has shown higher communicable rate. This novel virus with symptoms of pneumonia is dangerous as it is communicable and hence, has engulfed entire world in a very short span of time. With the help of machine learning techniques, entire process of detection can be automated so that direct contacts can be avoided. Therefore, in this paper, experimentation is performed on CoViD19 chest X-ray images using higher order statistics with iterative and non-iterative models. Higher order statistics provide a way of analyzing the disturbances in the chest X-ray images. The results obtained are quite good with 96.64% accuracy using a non-iterative model. For fast testing of the patients, non-iterative model is preferred because it has advantage over iterative model in terms of speed. Comparison with some of the available state-of-the-art methods and some iterative methods proves efficacy of the work.

Abstract Long axial length is one of the ocular protective factors in development of diabetic retinopathy (DR). In this study we examined the effect of axial length (AL) on aqueous humor vascular endothelial growth factor (VEGF) levels in patients with diabetes mellitus with or without DR. Forty-eight eyes of 48 participants were divided into three groups of 16 each. Group A consisted of non-diabetic patients, Group B had diabetic patients without DR, and Group C had diabetic patients with treatment-naive non-proliferative DR (NPDR). The groups were further subdivided based on axial lengths i.e., AL ≤ 23.30 mm (A1, B1, C1) and AL > 23.30 mm (A2, B2, C2). Undiluted aqueous humor was obtained during cataract surgery to measure the VEGF levels. We observed significant decrease in VEGF concentration in patients with AL ≥ 23.30 mm as compared with AL ≤ 23.30 mm in non-diabetic as well as diabetic patients. As the eye elongates, there is less secretion of VEGF in non-diabetics as well in diabetics with or without DR. Our findings strengthened the concept that an increase in AL leads to less VEGF in diabetic eyes, thus leading to less severe DR changes.

Abstract Wheat, one of the major cereal crops worldwide, get adversely affected by rising global temperature. We have identified the diploid B genome progenitor of wheat, Aegilops speltoides (SS), as a potential donor for heat stress tolerance. Therefore, the present work was planned to study the total transcriptome profile of heat stress-tolerant Ae. speltoides accession pau3809 (AS3809) and compare with that of tetraploid and hexaploid wheat cultivars PDW274 and PBW725, respectively. The comparative transcriptome was utilized to identify and validate heat stress transcription factors (HSFs), the key genes involved in imparting heat stress tolerance. Transcriptome analysis led to the identification of a total of 74 K, 68 K, and 76 K genes in AS3809, PDW274, and PBW725, respectively. There was a high uniformity of GO profiles under the biological, molecular, and cellular functions across the three wheat transcriptomes, suggesting the conservation of gene function. Twelve HSFs having the highest FPKM value were identified in the AS3809 transcriptome data, while six of these HSFs namely HSFA3, HSFA5, HSFA9, HSFB2a, HSFB2b, and HSFC1b, were validated with qRT PCR. These six HSFs were identified as an important component of thermotolerance in AS3809 as evident from their comparative higher expression under heat stress.

Abstract This study explores the comparative effect of conventional and organic treatments on the rhizosphere microbiome of Mangifera indica cv. Dashehari. The long-term exposures (about 20 years) were monitored under a subtropical ecosystem. Based on plant growth properties and acetylene reduction assay, 12 bacterial isolates (7 from G1-organic and 5 from G2-conventional systems) were identified as Pseudomonas and Bacillus spp. In the conventional system, dehydrogenase activity significantly decreased (0.053 µg TPF formed g−1 of soil h−1) and adversely affected the bacterial diversity composition. In comparison, organic treatments had a good impact on dehydrogenase activity (0.784 µg TPF formed g−1 of soil h−1), alkaline phosphatase (139.25 µg PNP g−1 soil h−1), and bacterial community composition. The Metagenomics approach targeted the V3 and V4 regions to see the impact in the phylum, order, family, genus, and species for both the treatments. Results showed that phylum Acidobacteria (13.6%), Firmicutes (4.84%), and Chloroflexi (2.56%) were dominating in the G2 system whereas phylum Bacteroides (14.55%), Actinobacteria (7.45%), and Proteobacteria (10.82%) were abundantly dominated in the G1 system. Metagenome sequences are at the NCBI-GenBank sequence read archive with SRX8289747 (G1) and SRX8289748 (G2) in the study PRJNA631113. Results indicated that conventional and organic conditions affect rhizosphere microbiome and their environment.

Abstract Pre-eclampsia (PE) is a pregnancy-specific disorder, characterized by hypertension and proteinuria. In PE, trophoblasts mediated inadequate remodeling of uterine spiral arteries seem to interrupt uteroplacental blood flow, one of the hallmarks in the early onset of PE (EO-PE). This, in turn, results in placental ischemia–reperfusion injury during hypoxia and reoxygenation episodes, leading to the generation of reactive oxygen species (ROS) and oxidative stress (OS). But still it is debatable if OS is a cause or consequence of PE. In this present study, we have investigated the effects of OS on PE placentae and trophoblast cell functions using BeWo and HTR8/SVneo cell lines. PE placental tissues showed abnormal ultrastructure, high level of reactive oxygen species (ROS) with altered unfolded protein responses (UPR) in compare with term placental tissues. Similar to PE placentae, during OS induction, the trophoblast cells showed altered invasion and migration properties with significantly variable expression of differentiation and invasion markers, e.g., syncytin and MMPs. The effect was rescued by antioxidant, N-acetyl cysteine, thereby implying a ROS-specific effect and in the trophoblast cells, OS triggers UPR pathway through IRE1α-XBP1 axis. Taken together, these findings highlight the harmful effect of unfolded protein response, which was induced due to OS on trophoblast cells and deformed invasion and differentiation programme and can be extended further to clinical settings to identify clinically approved antioxidants during pregnancy as a therapeutic measure to reduce the onset of PE.

Abstract In this study, the extraction conditions extracted maximize amounts of phenolic and bioactive compounds from the fruit extract of Ficus auriculata by using optimized response surface methodology. The antioxidant capacity was evaluated through the assay of radical scavenging ability on DPPH and ABTS as well as reducing power assays on total phenolic content (TPC). For the extraction purpose, the ultrasonic assisted extraction technique was employed. A second-order polynomial model satisfactorily fitted to the experimental findings concerning antioxidant activity (R2 = 0.968, P

Abstract New Onset Diabetes After Transplantation (NODAT) is a serious metabolic complication. While β-cell dysfunction is considered the main contributing factor in the development of NODAT, the precise pathogenesis is not well understood. Cytokines are thought to be involved in the inflammation of islet β-cells in diabetes; however, few studies have investigated this hypothesis in NODAT. A total of 309 kidney transplant recipients (KTRs) were included in this study. An association between kidney transplants, and the development of diabetes after transplant (NODAT) was investigated. Comparison was made between KTRs who develop diabetes (NODAT cases) or did not develop diabetes (control), using key cytokines, IL-6 G (− 174)C, macrophage mediator; IL-4 C (− 490)T, T helper (Th)-2 cytokine profile initiator; Th-1 cytokine profile initiator interferon-γ T (+ 874) A gene and TGF β1 C (+ 869) T gene polymorphisms were investigated. The genes were amplified using well-established polymerase chain reaction (PCR) techniques in our laboratory. Compared to the AA and AT genotypes of interferon gamma (IFNG), there was a strong association between the TT genotype of IFNG and NODAT kidney transplant recipients (KTRs) versus non-NODAT KTRs (p = 0.005). The AA genotype of IFNG was found to be predominant in the control group (p = 0.004). Also, significant variations of IL6 G (− 174) C, IL-4 C (− 590) T, interferon-γ T (+ 874) A gene and transforming growth factor β1 C (+ 869) T may contribute to NODAT. Our data is consistent with theTh-1/T-reg pathway of immunity. Further larger pan Arab studies are required to confirm our findings.

Abstract Dandruff is a recurrent chronic scalp disorder, affecting majority of the population worldwide. Recently a metagenomic study of the Indian scalp microbiome described an imperative role of bacterial commensals in providing essential vitamins and amino acids to the scalp. Coconut oil and its formulations are commonly applied on the scalp in several parts of the world to maintain scalp health. Thus, in this study we examined the effect of topical application of coconut oil on the scalp microbiome (bacterial and fungal) at the taxonomic and functional levels and their correlation with scalp physiological parameters. A 16-weeks-long time-course study was performed including 12-weeks of treatment and 4-weeks of relapse phase on a cohort of 140 (70 healthy and 70 dandruff) Indian women, resulting in ~ 900 metagenomic samples. After the treatment phase, an increase in the abundance of Cutibacterium acnes and Malassezia globosa in dandruff scalp was observed, which were negatively correlated to dandruff parameters. At the functional level, an enrichment of healthy scalp-related bacterial pathways, such as biotin metabolism and decrease in the fungal pathogenesis pathways was observed. The study provides novel insights on the effect of coconut oil in maintaining a healthy scalp and in modulating the scalp microbiome.

Abstract Biosensors based on liquid-gated carbon nanotubes field-effect transistors (LG-CNTFETs) have attracted considerable attention, as they offer high sensitivity and selectivity; quick response and label-free detection. However, their practical applications are limited due to the numerous fabrication challenges including resist-based lithography, in which after the lithography process, the resist leaves trace level contaminations over the CNTs that affect the performance of the fabricated biosensors. Here, we report the realization of LG-CNTFET devices using silicon shadow mask-based chemical-free lithography process on a 3-in. silicon wafer, yielding 21 sensor chips. Each sensor chip consists of 3 × 3 array of LG-CNTFET devices. Field emission scanning electron microscope (FESEM) and Raman mapping confirm the isolation of devices within the array chip having 9 individual devices. A reference electrode (Ag/AgCl) is used to demonstrate the uniformity of sensing performances among the fabricated LG-CNTFET devices in an array using different KCl molar solutions. The average threshold voltage (Vth) for all 9 devices varies from 0.46 to 0.19 V for 0.1 mM to 1 M KCl concentration range. This developed chemical-free process of LG-CNTFET array fabrication is simple, inexpensive, rapid having a commercial scope and thus opens a new realm of scalable realization of various biosensors.

Abstract Due to the limited utility of Bacillus Calmette–Guérin (BCG), the only approved vaccine available for tuberculosis, there is a need to develop a more effective and safe vaccine. We evaluated the safety and efficacy of a dry powder aerosol (DPA) formulation of BCG encapsulated alginate particle (BEAP) and the conventional intradermal BCG immunization in infant rhesus macaques (Macaca mulatta). The infant macaques were immunized intratracheally with DPA of BEAP into the lungs. Animals were monitored for their growth, behaviour, any adverse and allergic response. The protective efficacy of BEAP was estimated by the ex-vivo H37Rv infection method. Post-immunization with BEAP, granulocytes count, weight gain, chest radiography, levels of liver secreted enzymes, cytokines associated with inflammation like TNF and IL-6 established that BEAP is non-toxic and it does not elicit an allergic response. The T cells isolated from BEAP immunized animals’ blood, upon stimulation with M.tb antigen, secreted high levels of IFN-γ, TNF, IL-6 and IL-2. The activated T cells from BEAP group, when co-cultured with M.tb infected macrophages, eliminated largest number of infected macrophages compared to the BCG and control group. This study suggests the safety and efficacy of BEAP in Non-human primate model.

Abstract Judicious application of saline water except for critical growth stages, could be the only practical solution to meet the crop water demand in arid and semi-arid regions, due to limited access to freshwater, especially during dry winter months. A field experiment was conducted to study the effect of tillage [conventional (CT), reduced (RT), and zero (ZT)], rice straw mulch and deficit saline-water irrigation in wheat (100, 80 and 60% of wheat water requirement, CWR) followed by rainfed sorghum on soil properties and the yields of the cropping system. Yields of both the crops were comparable between RT and CT, but the wheat yield was reduced in ZT. The RT, mulching and deficit saline irrigation in wheat season (60% CWR) increased the sorghum fodder yield. Olsen’s P (8.7–20.6%) and NH4OAc-K (2.5–7.5%) increased in RT and ZT, respectively, over CT under both the crops. Deficit irrigation reduced soil salinity (ECe) by 0.73–1.19 dS m−1 after each crop cycle, while soil microbial biomass C (MBC) and N (MBN), dehydrogenase, urease and alkaline phosphatase reduced with an increase in ECe. The α-glucosidase, MBC, ECe, KMnO4oxidizable N, and urease were identified as major contributors in developing the soil health index. Deficit irrigation (60% CWR) and rice straw mulching under ZT and RT showed higher values of soil health index. Overall, deficit saline-water irrigation under reduced tillage and straw mulching had the greatest potential in maintaining soil health, saving fresh irrigation water without affecting the productivity of the sorghum-wheat system in the semi-arid regions of India. Results also demonstrated that salt affected areas of arid and semiarid countries can replicate the protocol for indexing and screening of soil health indicators to assess the sustainability of a cropping system. This integrated management based on the nature of the available resources also provided a practical approach to achieve the target of land degradation neutrality and land restoration.

Abstract Vitamin D deficiency affects approximately 80% of individuals in some countries and has been linked with gut dysbiosis and inflammation. While the benefits of vitamin D supplementation on the gut microbiota have been studied in patients with chronic diseases, its effects on the microbiota of otherwise healthy individuals is unclear. Moreover, whether effects on the microbiota can explain some of the marked inter-individual variation in responsiveness to vitamin D supplementation is unknown. Here, we administered vitamin D to 80 otherwise healthy vitamin D-deficient women, measuring serum 25(OH) D levels in blood and characterizing their gut microbiota pre- and post- supplementation using 16S rRNA gene sequencing. Vitamin D supplementation significantly increased gut microbial diversity. Specifically, the Bacteroidetes to Firmicutes ratio increased, along with the abundance of the health-promoting probiotic taxa Akkermansia and Bifidobacterium. Significant variations in the two-dominant genera, Bacteroides and Prevotella, indicated a variation in enterotypes following supplementation. Comparing supplementation responders and non-responders we found more pronounced changes in abundance of major phyla in responders, and a significant decrease in Bacteroides acidifaciens in non-responders. Altogether, our study highlights the positive impact of vitamin D supplementation on the gut microbiota and the potential for the microbial gut signature to affect vitamin D response.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Abstract Nitrate is the main source of inorganic nitrogen for plants, which also act as signaling molecule. Present study was aimed to understand nitrate regulatory mechanism in Brassica juncea cultivars, with contrasting nitrogen-use-efficiency (NUE) viz. Pusa Bold (PB, high-NUE) and Pusa Jai Kisan (PJK, low-NUE), employing RNA-seq approach. A total of 4031, 3874 and 3667 genes in PB and 2982, 2481 and 2843 genes in PJK were differentially expressed in response to early, low (0.25 mM KNO3), medium (2 mM KNO3) and high (4 mM KNO3) nitrate treatments, respectively, as compared to control (0 mM KNO3). Genes of N-uptake (NRT1.1, NRT1.8, and NRT2.1), assimilation (NR1, NR2, NiR, GS1.3, and Fd-GOGAT) and remobilization (GDH2, ASN2–3 and ALaT) were highly-upregulated in PB than in PJK in response to early nitrate treatments. We have also identified transcription factors and protein kinases that were rapidly induced in response to nitrate, suggesting their involvement in nitrate-mediated signaling. Co-expression network analysis revealed four nitrate specific modules in PB, enriched with GO terms like, “Phenylpropanoid pathway”, “Nitrogen compound metabolic process” and “Carbohydrate metabolism”. The network analysis also identified HUB transcription factors like mTERF, FHA, Orphan, bZip and FAR1, which may be the key regulators of nitrate-mediated response in B. juncea.

Abstract Azadirachta indica A. Juss, commonly known as Neem, is the reservoir of triterpenoids of economic importance. Metabolite analysis of different developmental stages of leaf and fruit suggests tissue-specific accumulation of the major triterpenoids in this important tree. Though biosynthesis of these complex molecules requires substrate flux from the isoprenoid pathway, enzymes involved in late biosynthetic steps remain uncharacterized. We established and analyzed transcriptome datasets from leaf and fruit and identified members of gene families involved in intermediate steps of terpenoid backbone biosynthesis and those related to secondary transformation leading to the tissue-specific triterpenoid biosynthesis. Expression analysis suggests differential expression of number of genes between leaf and fruit and probable participation in the biosynthesis of fruit-specific triterpenoids. Genome-wide analysis also identified members of gene families putatively involved in secondary modifications in late biosynthetic steps leading to the synthesis of highly oxygenated triterpenoids. Expression and molecular docking analyses suggest involvement of specific members of CYP450 family in secondary modifications for the biosynthesis of bioactive triterpenoids. This study generated rich genomic resource and identified genes involved in biosynthesis of important molecules, which will aid in the advancement of tools for functional genomics and elucidation of the biosynthesis of triterpenoid from this important tree.

Early detection of cancer will improve survival rates. The blood biomarker 5-hydroxymethylcytosine has been shown to discriminate cancer. In a large covariate-controlled study of over two thousand individual blood samples, we created, tested and explored the properties of a 5-hydroxymethylcytosine-based classifier to detect colorectal cancer (CRC). In an independent validation sample set, the classifier discriminated CRC samples from controls with an area under the receiver operating characteristic curve (AUC) of 90% (95% CI [87, 93]). Sensitivity was 55% at 95% specificity. Performance was similar for early stage 1 (AUC 89%; 95% CI [83, 94]) and late stage 4 CRC (AUC 94%; 95% CI [89, 98]). The classifier could detect CRC even when the proportion of tumor DNA in blood was undetectable by other methods. Expanding the classifier to include information about cell-free DNA fragment size and abundance across the genome led to gains in sensitivity (63% at 95% specificity), with similar overall performance (AUC 91%; 95% CI [89, 94]). We confirm that 5-hydroxymethylcytosine can be used to detect CRC, even in early-stage disease. Therefore, the inclusion of 5-hydroxymethylcytosine in multianalyte testing could improve sensitivity for the detection of early-stage cancer.