A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Regenerative failure of intrahepatic biliary cells in Alagille syndrome rescued by elevated Jagged/Notch/Sox9 signaling.

Despite the robust healing capacity of the liver, regenerative failure underlies numerous hepatic diseases, including the JAG1 haploinsufficient disorder, Alagille syndrome (ALGS). Cholestasis due to intrahepatic duct (IHD) paucity resolves in certain ALGS cases but fails in most with no clear mechanisms or therapeutic interventions. We find that modulating jag1b and jag2b allele dosage is sufficient to stratify these distinct outcomes, which can be either exacerbated or rescued with genetic manipulation of Notch signaling, demonstrating that perturbations of Jag/Notch signaling may be causal for the spectrum of ALGS liver severities. Although regenerating IHD cells proliferate, they remain clustered in mutants that fail to recover due to a blunted elevation of Notch signaling in the distal-most IHD cells. Increased Notch signaling is required for regenerating IHD cells to branch and segregate into the peripheral region of the growing liver, where biliary paucity is commonly observed in ALGS. Mosaic loss- and-gain-of-function analysis reveals Sox9b to be a key Notch transcriptional effector required cell autonomously to regulate these cellular dynamics during IHD regeneration. Treatment with a small-molecule putative Notch agonist stimulates Sox9 expression in ALGS patient fibroblasts and enhances hepatic sox9b expression, rescues IHD paucity and cholestasis, and increases survival in zebrafish mutants, thereby providing a proof-of-concept therapeutic avenue for this disorder.

Delineation of loci governing an extra-earliness trait in lentil (Lens culinaris Medik.) using the QTL-Seq approach.

Developing early maturing lentil has the potential to minimize yield losses, mainly during terminal drought. Whole-genome resequencing (WGRS) based QTL-seq identified the loci governing earliness in lentil. The genetic analysis for maturity duration provided a good fit to 3:1 segregation (F2), indicating earliness as a recessive trait. WGRS of Globe Mutant (late parent), late-flowering, and early-flowering bulks (from RILs) has generated 1124.57, 1052.24 million raw and clean reads, respectively. The QTL-Seq identified three QTLs (LcqDTF3.1, LcqDTF3.2, and LcqDTF3.3) on chromosome 3 having 246244 SNPs and 15577 insertions/deletions (InDels) and 13 flowering pathway genes. Of these, 11 exhibited sequence variations between bulks and validation (qPCR) revealed a significant difference in the expression of nine candidate genes (LcGA20oxG, LcFRI, LcLFY, LcSPL13a, Lcu.2RBY.3g060720, Lcu.2RBY.3g062540, Lcu.2RBY.3g062760, LcELF3a, and LcEMF1). Interestingly, the LcELF3a gene showed significantly higher expression in late-flowering genotype and exhibited substantial involvement in promoting lateness. Subsequently, an InDel marker (I-SP-383.9; LcELF3a gene) developed from LcqDTF3.2 QTL region showed 82.35% PVE (phenotypic variation explained) for earliness. The cloning, sequencing, and comparative analysis of the LcELF3a gene from both parents revealed 23 SNPs and InDels. Interestingly, a 52 bp deletion was recorded in the LcELF3a gene of L4775, predicted to cause premature termination of protein synthesis after 4 missense amino acids beyond the 351st amino acid due to the frameshift during translation. The identified InDel marker holds significant potential for breeding early maturing lentil varieties.

Understanding consumer preferences to develop dahi using pineapple pomace powder and monk-fruit extract.

Consumer preferences refer to the subjective assessments of products and services expressed by individuals. The objective of this investigation aims to examine the preferences of consumers regarding dahi, followed by the development of a corresponding product. The initial phase of the experimental design involves understanding the interests of consumers and the variables that influence their purchasing intentions through the administration of a questionnaire. The subsequent phase entails the development of dahi in accordance with consumer preferences, followed by an assessment of its nutritional value, sensory acceptability, and storage study. Subsequently, a significant proportion of consumers (91%) expressed an interest for the introduction of a pineapple-flavour (61.5%) spoon-able dahi (77%) containing natural sugar (65%) and packaged in a cup (71.5%) within the market. To adjust the sweetness intensity of monk fruit, a series of preliminary experiments were carried out to regulate the concentration to a level that can be considered sensory acceptable, specifically 05 g/100 ml. Afterwards, dahi was prepared by altering the concentration of FPP (freeze-dried pine-apple pomace powder) within the range of 0.5 to 2.5 g/100 ml. Prepared dahi were further subjected to sensory evaluation and storage study. Based on the obtained results and sensory analyst feedback, we conclude that the dahi formulation TPM2 exhibits considerable organoleptic acceptance and also has the potential for industrial-scale production to cater wider consumer demands. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-023-05919-5.

Elucidation of an Aggregate Excited State in the Electrochemiluminescence and Chemiluminescence of a Thermally Activated Delayed Fluorescence (TADF) Emitter.

The electrochemistry, electrochemiluminescence (ECL), and chemiluminescence (CL) properties of a thermally activated delayed fluorescence (TADF) emitter 4,4'-(1,2-dihydroacenaphthylene-5,6-diyl)bis(N,N-diphenylaniline) (TPA-ace-TRZ) and three of its analogues were investigated. TPA-ace-TRZ exhibits both (a) delayed onset of ECL and (b) long-persistent luminescence, which we have attributed to the formation of an aggregate excited state in excimer or exciplex form. The evidence of this aggregate excited state was consistent across ECL annihilation and coreactant pathways as well as in CL. The absolute ECL efficiency of TPA-ace-TRZ using benzoyl peroxide (BPO) as a coreactant was found to be 0.028%, which was 9-fold stronger than the [Ru(bpy)3]2+/BPO reference coereactant system. Furthermore, the absolute CL quantum efficiency of TPA-ace-TRZ was determined to be 0.92%. The performance and flexibility of the TADF emitter TPA-ace-TRZ under these various emissive pathways are highly desirable toward applications in sensing, imaging, and light-emitting devices.

Hesperidin: Enrichment, forced degradation, and structural elucidation of potential degradation products using spectral techniques.

RATIONALE: Hesperidin (HES) is a well-known citrus bioflavonoid phyto-nutraceutical agent with polypharmacological properties. After 2019, HES was widely used for prophylaxis and COVID-19 treatment. Moreover, it is commonly prescribed for treating varicose veins and other diseases in routine clinical practice. Pharmaceutical impurities and degradation products (DP) impact the drug's quality and safety and thus its effectiveness. Therefore, forced degradation studies help study drug stability, degradation mechanisms, and their DPs. This study was performed because stress stability studies using detailed structural characterization of hesperidin are currently unavailable in the literature. METHODS: In the HES enrichment method crude HES was converted to its pure form (98% purity) using column chromatography and then subjected to forced degradation under acid, base, and neutral hydrolyses followed by oxidative, reductive, photolytic, and thermal stress testing (International Conference on Harmonization guidelines). The stability-indicating analytical method (SIAM) was developed to determine DPs using reversed-phase high-performance liquid chromatography (C18 column with methanol and 0.1% v/v acetic acid in deionized water [70:30, v/v] at 284 nm). Further, structural characterization of DPs was performed using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) and nuclear magnetic resonance (NMR) spectroscopy. In addition, in silico toxicity predictions were performed using pKCSM and DataWarior freeware. RESULTS: HES was found to be susceptible to acidic and basic hydrolytic conditions and yielded three DPs in each, which were detected using designed SIAM. Of six DPs, three were pseudo-DPs (short lived), and the remaining were characterized using LC-MS/MS and NMR spectroscopy. The tentative mechanism of the formation of proposed DPs was explained. The proposed DPs were found inactive from in silico toxicity predictions. CONCLUSIONS: Hesperidin was labile under acidic and basic stress conditions. The potential DPs were characterized using LC-ESI-MS/MS and NMR spectral techniques. The proposed mechanism of formation was hypothesized. In addition, to identify and characterize the DPs, a SIAM, which has broad biomedical applications, was successfully developed.

Observation of Topological Flat Bands in the Kagome Semiconductor Nb3Cl8.

The destructive interference of wavefunctions in a kagome lattice can give rise to topological flat bands (TFBs) with a highly degenerate state of electrons. Recently, TFBs have been observed in several kagome metals, including Fe3Sn2, FeSn, CoSn, and YMn6Sn6. Nonetheless, kagome materials that are both exfoliable and semiconducting are lacking, which seriously hinders their device applications. Herein, we show that Nb3Cl8, which hosts a breathing kagome lattice, is gapped out because of the absence of inversion symmetry, while the TFBs survive because of the protection of the mirror reflection symmetry. By angle-resolved photoemission spectroscopy measurements and first-principles calculations, we directly observe the TFBs and a moderate band gap in Nb3Cl8. By mechanical exfoliation, we successfully obtain monolayer Nb3Cl8, which is stable under ambient conditions. In addition, our calculations show that monolayer Nb3Cl8 has a magnetic ground state, thus providing opportunities to study the interplay among geometry, topology, and magnetism.

Observation of One-Dimensional Dirac Fermions in Silicon Nanoribbons.

Dirac materials, which feature Dirac cones in the reciprocal space, have been one of the hottest topics in condensed matter physics in the past decade. To date, 2D and 3D Dirac Fermions have been extensively studied, while their 1D counterparts are rare. Recently, Si nanoribbons (SiNRs), which are composed of alternating pentagonal Si rings, have attracted intensive attention. However, the electronic structure and topological properties of SiNRs are still elusive. Here, by angle-resolved photoemission spectroscopy, scanning tunneling microscopy/spectroscopy measurements, first-principles calculations, and tight-binding model analysis, we demonstrate the existence of 1D Dirac Fermions in SiNRs. Our theoretical analysis shows that the Dirac cones derive from the armchairlike Si chain in the center of the nanoribbon and can be described by the Su-Schrieffer-Heeger model. These results establish SiNRs as a platform for studying the novel physical properties in 1D Dirac materials.

Insight into Unusual Supramolecular Self-Assemblies of Terthiophenes Directed by Weak Hydrogen Bonding.

A supramolecular self-assembly of semiconducting polymers and small molecules plays an important role in charge transportation, performance, and lifetime of an optoelectronic device. Tremendous efforts have been put into the strategies to self-organize these materials. In this regard, here, we present the self-organization of terthiophene and its methyl alcohol derivative with 4,4'-bipyridine (44BiPy). An unexpected 2D layered organization of 5,5″-dimethyl-2,2':5',2″-terthiophene (DM3T) and 44BiPy was obtained and analyzed. Single-crystal X-ray diffraction analysis revealed that DM3T and 44BiPy consist of stacked, almost independent, infinite 2D layers while held together by weak hydrogen bonds. In addition to this peculiar supramolecular arrangement of these compounds, the investigation of their photophysical properties showed strong fluorescence quenching of DM3T by 44BiPy in the solid state, suggesting an efficient charge transfer. On the other hand, the methyl alcohol derivative of terthiophene, DM3TMeOH, organized in a closed cyclic motif with 44BiPy via hydrogen bonds.

Exploring the role of microbes for the management of persistent organic pollutants.

Persistent organic pollutants (POPs) are chemicals which have been persisting in the environment for many years due to their longer half-lives. POPs have gained attention over the last few decades due to the unsustainable management of chemicals which led to their widespread and massive contamination of biota from different strata and environments. Due to the widespread distribution, bio-accumulation and toxic behavior, POPs have become a risk for organisms and environment. Therefore, a focus is required to eliminate these chemicals from the environment or transform into non-toxic forms. Among the available techniques for the removal of POPs, most of them are inefficient or incur high operational costs. As an alternative to this, microbial bioremediation of POPs such as pesticides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pharmaceuticals and personal care products is much more efficient and cost-effective. Additionally, bacteria play a vital role in the biotransformation and solubilization of POPs, which reduces their toxicity. This review specifies the Stockholm Convention that evaluates the risk profile for the management of existing as well as emerging POPs. The sources, types and persistence of POPs along with the comparison of conventional elimination and bioremediation methods of POPs are discussed comprehensively. This study demonstrates the existing bioremediation techniques of POPs and summaries the potential of microbes which serve as enhanced, cost-effective, and eco-friendly approach for POPs elimination.

'Omics' approaches in developing combined drought and heat tolerance in food crops.

Global climate change will significantly increase the intensity and frequency of hot, dry days. The simultaneous occurrence of drought and heat stress is also likely to increase, influencing various agronomic characteristics, such as biomass and other growth traits, phenology, and yield-contributing traits, of various crops. At the same time, vital physiological traits will be seriously disrupted, including leaf water content, canopy temperature depression, membrane stability, photosynthesis, and related attributes such as chlorophyll content, stomatal conductance, and chlorophyll fluorescence. Several metabolic processes contributing to general growth and development will be restricted, along with the production of reactive oxygen species (ROS) that negatively affect cellular homeostasis. Plants have adaptive defense strategies, such as ROS-scavenging mechanisms, osmolyte production, secondary metabolite modulation, and different phytohormones, which can help distinguish tolerant crop genotypes. Understanding plant responses to combined drought/heat stress at various organizational levels is vital for developing stress-resilient crops. Elucidating the genomic, proteomic, and metabolic responses of various crops, particularly tolerant genotypes, to identify tolerance mechanisms will markedly enhance the continuing efforts to introduce combined drought/heat stress tolerance. Besides agronomic management, genetic engineering and molecular breeding approaches have great potential in this direction.

Ventx Family and Its Functional Similarities with Nanog: Involvement in Embryonic Development and Cancer Progression.

The Ventx family is one of the subfamilies of the ANTP (antennapedia) superfamily and belongs to the NK-like (NKL) subclass. Ventx is a homeobox transcription factor and has a DNA-interacting domain that is evolutionarily conserved throughout vertebrates. It has been extensively studied in Xenopus, zebrafish, and humans. The Ventx family contains transcriptional repressors widely involved in embryonic development and tumorigenesis in vertebrates. Several studies have documented that the Ventx family inhibited dorsal mesodermal formation, neural induction, and head formation in Xenopus and zebrafish. Moreover, Ventx2.2 showed functional similarities to Nanog and Barx1, leading to pluripotency and neural-crest migration in vertebrates. Among them, Ventx protein is an orthologue of the Ventx family in humans. Studies have demonstrated that human Ventx was strongly associated with myeloid-cell differentiation and acute myeloid leukemia. The therapeutic potential of Ventx family inhibition in combating cancer progression in humans is discussed. Additionally, we briefly discuss genome evolution, gene duplication, pseudo-allotetraploidy, and the homeobox family in Xenopus.

Neurotoxin (N-Oxalyl-L-α,ß-Diamino Propionic Acid) Content in Different Plant Parts of Grass Pea (Lathyrus sativus L.) Spanning Seedling to Maturity Stage: Does It Increase over Time?

ODAP (N-oxalyl-L-2,3-diaminopropionic acid) is present in the seeds of grass pea. In this study, variation of total ODAP accumulation in leaves throughout the crop growth starting from 40 days after sowing to maturity, and the distribution pattern of ODAP in different plant parts including the seeds at the mature stage was analyzed. Five grass pea accessions were evaluated for two subsequent growing seasons in one location of ICARDA, Aleppo (Syria). The results found that the rate of accumulation of total ODAP varied during plant development. Increased rates of synthesis were noticed in young leaves of grass pea. The highest total ODAP content in leaves was noted in the early growth stage (40-50 days after sowing). Mean total ODAP content in leaves ranged from 0.17 to 0.96 percent during 2010-2011 and from 0.19 to 1.28 percent during 2011-2012. During maturity, the total ODAP content was lowest in the seeds than in leaves, stems, pod cover, seed coat, and cotyledons. The ranges of total ODAP content were 0.13 (seed)-0.34 (stem), 0.20 (seed)-1.01 (leaf), 0.22 (seed)-0.62 (leaf), 0.21 (seed)-0.66 (leaf), and 0.21 (seed)-0.78 (leaf) percent in B387, B222, B390, Bio-520, and B587 accessions, respectively, during maturity. The results indicated that the rate of accumulation and synthesis of total ODAP varied during the plant lifespan. The lowest total ODAP content of leaves was observed after 130 days of sowing. The lower total ODAP content after the early vegetative stage of grass pea plants makes them suitable as a feed.

In Silico Evaluation of Natural Flavonoids as a Potential Inhibitor of Coronavirus Disease.

The recent coronavirus disease (COVID-19) outbreak in Wuhan, China, has led to millions of infections and the death of approximately one million people. No targeted therapeutics are currently available, and only a few efficient treatment options are accessible. Many researchers are investigating active compounds from natural plant sources that may inhibit COVID-19 proliferation. Flavonoids are generally present in our diet, as well as traditional medicines and are effective against various diseases. Thus, here, we reviewed the potential of flavonoids against crucial proteins involved in the coronavirus infectious cycle. The fundamentals of coronaviruses, the structures of SARS-CoV-2, and the mechanism of its entry into the host's body have also been discussed. In silico studies have been successfully employed to study the interaction of flavonoids against COVID-19 Mpro, spike protein PLpro, and other interactive sites for its possible inhibition. Recent studies showed that many flavonoids such as hesperidin, amentoflavone, rutin, diosmin, apiin, and many other flavonoids have a higher affinity with Mpro and lower binding energy than currently used drugs such as hydroxylchloroquine, nelfinavir, ritonavir, and lopinavir. Thus, these compounds can be developed as specific therapeutic agents against COVID-19, but need further in vitro and in vivo studies to validate these compounds and pave the way for drug discovery.

Manufacturing and characterization of whey and stevia-based popsicles enriched with concentrated beetroot juice.

The beet-root (Beta vulgaris) and whey powder together, can potentially use as a multifunctional ingredient in the manufacturing of the "Popsicles", due to their biochemical composition that can enhance the concentration of bioactive compounds. In the present study, beet-root juice concentrates were prepared at different time/temperature treatments viz 45 °C, 55 °C, and 65 °C for 120, 80 and 45 min. The effect of different time/temperature treatments on physicochemical composition, colour, antioxidant activity (%), bioactive compounds, spectral data and sensory acceptance were evaluated. The physicochemical parameters of popsicles (PTI, PT2, PT3) including protein, total phenols, betalain, radical scavenging activity %, colour and melting values were significantly affected (p ≤ 0.05) by the different time/temperature treatments. The concentration of betalain and protein in all the popsicles ranged from 1134 to 1299 mg/L and 1.92 to 1.54 g/100 g respectively. The reduction of bioactive components viz betacyanins, betaxanthins, betanin, oxalic and syringic acid was also observed in popsicle (PTI) as compared to control. Furthermore, popsicle (PT1) was prepared with beet-root juice concentrated at 45 °C showed maximum sensory acceptance. The physicochemical and organoleptic attributes of processed popsicles encourage the commercial usage of whey powder and concentrated beetroot juice.

Smad2 and Smad3 differentially modulate chordin transcription via direct binding on the distal elements in gastrula Xenopus embryos.

Transforming growth factor (TGF)ß/activin superfamily regulates diverse biological processes including germ layer specification and axis patterning in vertebrates. TGFß/activin leads to phosphorylation of Smad2 and Smad3, followed by regulation of their target genes. Activin treatment also induces the essential organizer gene chordin (chrd). The involvement of Smad2/3 in chrd expression has been unclear as to whether Smad2/3 involvement is direct or indirect and whether any cis-acting response elements for Smad2/3 are present in the proximal or distal regions of its promoter. In the present study, we isolated the -2250 bps portion of the chrd promoter, showing that it contained Smad2/3 direct binding sites at its distal portion, separate from the proximal locations of other organizer genes, goosecoid and cerberus. The pattern of transcription activation for the promoter (-2250 bps) was indistinguishable from that of the endogenous chrd in gastrula Xenopus embryos. Reporter gene assays and site-directed mutagenesis analysis of the chrd promoter mapped two active activin/Smad response elements (ARE1 and ARE2) for Smad2 and Smad3. For a differential chrd induction, Smad2 acted on both ARE1 and ARE2, but Smad3 was only active for ARE2. Collectively, the results demonstrate that the distal region of chrd promoter contains the direct binding cis-acting elements for Smad2 and Smad3, which differentially modulate chrd transcription in gastrula Xenopus embryos.

Observation of Spin-Momentum-Layer Locking in a Centrosymmetric Crystal.

The spin polarization in nonmagnetic materials is conventionally attributed to the outcome of spin-orbit coupling when the global inversion symmetry is broken. The recently discovered hidden spin polarization indicates that a specific atomic site asymmetry could also induce measurable spin polarization, leading to a paradigm shift in research on centrosymmetric crystals for potential spintronic applications. Here, combining spin- and angle-resolved photoemission spectroscopy and theoretical calculations, we report distinct spin-momentum-layer locking phenomena in a centrosymmetric, layered material, BiOI. The measured spin is highly polarized along the Brillouin zone boundary, while the same effect almost vanishes around the zone center due to its nonsymmorphic crystal structure. Our work demonstrates the existence of momentum-dependent hidden spin polarization and uncovers the microscopic mechanism of spin, momentum, and layer locking to each other, thus shedding light on the design metrics for future spintronic materials.

An NHC-Stabilised Phosphinidene for Catalytic Formylation: A DFT-Guided Approach.

In recent years, the applications of low-valent main group compounds have gained momentum in the field of catalysis. Owing to the accessibility of two lone pairs of electrons, NHC-stabilised phosphinidenes have been found to be excellent Lewis bases; however, they cannot yet be used as catalysts. Herein, an NHC-stabilised phosphinidene, 1,3-dimethyl-2-(phenylphosphanylidene)-2,3-dihydro-1H imidazole (1), for the activation of CO2 is reported.A closer inspection of the CO2 activation process by DFT calculations along with intrinsic bond orbital analysis shows that phosphinidene is associated with phenylsilane through a noncovalent π-π interaction between two phenyl rings which activates the Si-H bond facilitating hydride transfer to the CO2 molecule. Detailed DFT studies along with spectroscopic experiments were combined to understand the mechanism of CO2 activation and its catalytic reductive functionalisation leading to the formylation of a range of chemically inert primary amides under mild reaction conditions.

Root-omics for drought tolerance in cool-season grain legumes.

Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.