Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing.

BACKGROUND: Moth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach. RESULTS: A total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo. CONCLUSION: Our study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties.

Complement drives glucosylceramide accumulation and tissue inflammation in Gaucher disease.

Gaucher disease is caused by mutations in GBA1, which encodes the lysosomal enzyme glucocerebrosidase (GCase). GBA1 mutations drive extensive accumulation of glucosylceramide (GC) in multiple innate and adaptive immune cells in the spleen, liver, lung and bone marrow, often leading to chronic inflammation. The mechanisms that connect excess GC to tissue inflammation remain unknown. Here we show that activation of complement C5a and C5a receptor 1 (C5aR1) controls GC accumulation and the inflammatory response in experimental and clinical Gaucher disease. Marked local and systemic complement activation occurred in GCase-deficient mice or after pharmacological inhibition of GCase and was associated with GC storage, tissue inflammation and proinflammatory cytokine production. Whereas all GCase-inhibited mice died within 4-5 weeks, mice deficient in both GCase and C5aR1, and wild-type mice in which GCase and C5aR were pharmacologically inhibited, were protected from these adverse effects and consequently survived. In mice and humans, GCase deficiency was associated with strong formation of complement-activating GC-specific IgG autoantibodies, leading to complement activation and C5a generation. Subsequent C5aR1 activation controlled UDP-glucose ceramide glucosyltransferase production, thereby tipping the balance between GC formation and degradation. Thus, extensive GC storage induces complement-activating IgG autoantibodies that drive a pathway of C5a generation and C5aR1 activation that fuels a cycle of cellular GC accumulation, innate and adaptive immune cell recruitment and activation in Gaucher disease. As enzyme replacement and substrate reduction therapies are expensive and still associated with inflammation, increased risk of cancer and Parkinson disease, targeting C5aR1 may serve as a treatment option for patients with Gaucher disease and, possibly, other lysosomal storage diseases.

Targeting the Complement-Sphingolipid System in COVID-19 and Gaucher Diseases: Evidence for a New Treatment Strategy.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)-induced disease (COVID-19) and Gaucher disease (GD) exhibit upregulation of complement 5a (C5a) and its C5aR1 receptor, and excess synthesis of glycosphingolipids that lead to increased infiltration and activation of innate and adaptive immune cells, resulting in massive generation of pro-inflammatory cytokines, chemokines and growth factors. This C5a-C5aR1-glycosphingolipid pathway- induced pro-inflammatory environment causes the tissue damage in COVID-19 and GD. Strikingly, pharmaceutically targeting the C5a-C5aR1 axis or the glycosphingolipid synthesis pathway led to a reduction in glycosphingolipid synthesis and innate and adaptive immune inflammation, and protection from the tissue destruction in both COVID-19 and GD. These results reveal a common involvement of the complement and glycosphingolipid systems driving immune inflammation and tissue damage in COVID-19 and GD, respectively. It is therefore expected that combined targeting of the complement and sphingolipid pathways could ameliorate the tissue destruction, organ failure, and death in patients at high-risk of developing severe cases of COVID-19.

C-X-C Motif Chemokine Ligand 9 and Its CXCR3 Receptor Are the Salt and Pepper for T Cells Trafficking in a Mouse Model of Gaucher Disease.

Gaucher disease is a lysosomal storage disease, which happens due to mutations in GBA1/Gba1 that encodes the enzyme termed as lysosomal acid ß-glucosidase. The major function of this enzyme is to catalyze glucosylceramide (GC) into glucose and ceramide. The deficiency of this enzyme and resultant abnormal accumulation of GC cause altered function of several of the innate and adaptive immune cells. For example, augmented infiltration of T cells contributes to the increased production of pro-inflammatory cytokines, (e.g., IFNγ, TNFα, IL6, IL12p40, IL12p70, IL23, and IL17A/F). This leads to tissue damage in a genetic mouse model (Gba19V/-) of Gaucher disease. The cellular mechanism(s) by which increased tissue infiltration of T cells occurs in this disease is not fully understood. Here, we delineate role of the CXCR3 receptor and its exogenous C-X-C motif chemokine ligand 9 (CXCL9) in induction of increased tissue recruitment of CD4+ T and CD8+ T cells in Gaucher disease. Intracellular FACS staining of macrophages (Mϕs) and dendritic cells (DCs) from Gba19V/- mice showed elevated production of CXCL9. Purified CD4+ T cells and the CD8+ T cells from Gba19V/- mice showed increased expression of CXCR3. Ex vivo and in vivo chemotaxis experiments showed CXCL9 involvement in the recruitment of Gba19V/- T cells. Furthermore, antibody blockade of the CXCL9 receptor (CXCR3) on T cells caused marked reduction in CXCL9- mediated chemotaxis of T cells in Gba19V/- mice. These data implicate abnormalities of the CXCL9-CXCR3 axis leading to enhanced tissue recruitment of T cells in Gaucher disease. Such results provide a rationale for blockade of the CXCL9/CXCR3 axis as potential new therapeutic targets for the treatment of inflammation in Gaucher disease.

A validation study of early warning system in high-risk pregnant women.

High-risk obstetric patients have chances of deterioration which can be detected by any early warning score. This study was aimed to assess the suitability of the Obstetrics National Early Warning System (ONEWS) for the pregnant women. This prospective study was conducted on 500 high-risk pregnant women attending a tertiary care teaching hospital. The ONEWS charts were plotted for each of them. The primary outcome measure was composite adverse maternal outcome (CAMO) in the form of one or more among mortality, severe maternal morbidity and intensive care unit admissions. Of the 500 women who participated, 200 (40%) had a score ≥3 (triggered an intervention). The CAMO among the triggered group [59.5% (n=119)] was significantly higher compared to that in the non-triggered group [13.3% (n=40) (P=0.001)]. The area under the receiver operating characteristic curve was 0.800 (95% confidence interval 0.752-0.847). The sensitivity of the ONEWS in predicting CAMO was 74.8 per cent, specificity 76.2 per cent, positive predictive value 59.5 per cent and negative predictive value 86.7 per cent at a cut-off score of 3. ONEWS appears to be a useful tool for predicting adverse maternal outcomes in high-risk pregnant women.

Maternal and neonatal vitamin-D status in twin versus singleton pregnancies.

AIM: There is a paucity of information on vitamin D status of women with twin pregnancy and their newborns. This case-control study compared maternal and neonatal vitamin-D status in twin versus singleton pregnancies. METHODS: Subjects included 50 women with twin pregnancy delivering at >28 weeks and 50 gestational-age-matched women with singleton pregnancy delivering during the same period. Maternal and neonatal serum 25-hydroxy vitamin D [25(OH)D] was compared between the two groups using the independent Student's t-test on log values. Serum albumin-adjusted calcium, inorganic phosphate, and intact parathormone levels were also compared. RESULTS: Maternal vitamin-D deficiency (VDD; serum 25(OH)D < 30 nmol/L) was present in 90% of twin and 88% of singleton pregnancies. The prevalence of neonatal VDD was 89% in twin and 74% in singleton pregnancies (P = 0.03). Maternal serum 25(OH)D was lower in the twin group as compared to the singleton group (14.3 ± 10.47 vs 18.5 ± 12.36 nmol/L; P = 0.02). Mean serum calcium, intact parathormone, and inorganic phosphate were comparable between the women in the two groups. Maternal and neonatal 25(OH)D showed positive correlation in the two groups (P < 0.001). Mean cord blood 25(OH)D was significantly lower in the twins than in singleton newborns (14.8 ± 12.63 vs 22.6 ± 16.68 nmol/L; P = 0.002). The difference persisted even after adjustment for birthweights and maternal serum 25(OH)D. Mean serum calcium was significantly lower in the twins. CONCLUSION: Twin newborns and their mothers have higher VDD as compared to singleton newborns and their mothers in the VDD population.

The FA pathway counteracts oxidative stress through selective protection of antioxidant defense gene promoters.

Oxidative stress has been implicated in the pathogenesis of many human diseases including Fanconi anemia (FA), a genetic disorder associated with BM failure and cancer. Here we show that major antioxidant defense genes are down-regulated in FA patients, and that gene down-regulation is selectively associated with increased oxidative DNA damage in the promoters of the antioxidant defense genes. Assessment of promoter activity and DNA damage repair kinetics shows that increased initial damage, rather than a reduced repair rate, contributes to the augmented oxidative DNA damage. Mechanistically, FA proteins act in concert with the chromatin-remodeling factor BRG1 to protect the promoters of antioxidant defense genes from oxidative damage. Specifically, BRG1 binds to the promoters of the antioxidant defense genes at steady state. On challenge with oxidative stress, FA proteins are recruited to promoter DNA, which correlates with significant increase in the binding of BRG1 within promoter regions. In addition, oxidative stress-induced FANCD2 ubiquitination is required for the formation of a FA-BRG1-promoter complex. Taken together, these data identify a role for the FA pathway in cellular antioxidant defense.

Trefoil factor 2 negatively regulates type 1 immunity against Toxoplasma gondii.

IL-12-mediated type 1 inflammation confers host protection against the parasitic protozoan Toxoplasma gondii. However, production of IFN-γ, another type 1 inflammatory cytokine, also drives lethality from excessive injury to the intestinal epithelium. As mechanisms that restore epithelial barrier function following infection remain poorly understood, this study investigated the role of trefoil factor 2 (TFF2), a well-established regulator of mucosal tissue repair. Paradoxically, TFF2 antagonized IL-12 release from dendritic cells (DCs) and macrophages, which protected TFF2-deficient (TFF2(-/-)) mice from T. gondii pathogenesis. Dysregulated intestinal homeostasis in naive TFF2(-/-) mice correlated with increased IL-12/23p40 levels and enhanced T cell recruitment at baseline. Infected TFF2(-/-) mice displayed low rates of parasite replication and reduced gut immunopathology, whereas wild-type (WT) mice experienced disseminated infection and lethal ileitis. p38 MAPK activation and IL-12p70 production was more robust from TFF2(-/-)CD8+ DC compared with WT CD8+ DC and treatment of WT DC with rTFF2 suppressed TLR-induced IL-12/23p40 production. Neutralization of IFN-γ and IL-12 in TFF2(-/-) animals abrogated resistance shown by enhanced parasite replication and infection-induced morbidity. Hence, TFF2 regulated intestinal barrier function and type 1 cytokine release from myeloid phagocytes, which dictated the outcome of oral T. gondii infection in mice.

Design, Synthesis, Nematicidal Evaluation, and Molecular Docking Study of Pyrano[3,2-c]pyridones against Meloidogyne incognita.

Root-knot nematodes pose a serious threat to crops by affecting production and quality. Over a period of time, substantial work has been done toward the development of effective and environmentally benign nematicidal compounds. However, due to the inefficiencies of previously reported synthetics in achieving the target of safe, selective, and effective treatment, it is necessary to develop new efficacious and safer nematicidal agents considering human health and environment on top priority. This work aims to highlight the efficient and convenient l-proline catalyzed synthesis of pyrano[3,2-c]pyridone and their use as potential nematicidal agents. In vitro results of larval mortality and egg hatching inhibition revealed maximum nematicidal activity against Meloidogyne incognita from compounds 15b, 15m, and 15w with LC50 values of 28.8, 46.8, and 49.18 µg/mL at 48 h, respectively. Under similar conditions, pyrano[3,2-c]pyridones derivatives 15b (LC50 = 28.8 µg/mL) was found at par with LC50 (26.92 µg/mL) of commercial nematicide carbofuran. The in vitro results were further validated with in silico studies with the most active compound 15b nematicidal within the binding to the pocket of acetylcholine esterase (AChE). In docking, binding free energy values for compound 15b were found to be -6.90 kcal/mol. Results indicated that pyrano[3,2-c]pyridone derivatives have the potential to control M. incognita.

IFN-γ-driven IDO production from macrophages protects IL-4Rα-deficient mice against lethality during Schistosoma mansoni infection.

The balance between alternatively activated macrophages (AAMs)/M2 cells and classically activated macrophages (M1 cells) is largely dependent on the effects of IL-4 and interferon (IFN)-γ, respectively. Although AAM/M2 cells can suppress inflammation and repair damaged tissue, M1 cells produce an array of pro-inflammatory molecules. Macrophage effector functions are critical for host protection against many infectious diseases, but it remains unknown whether lethal immunopathological characteristics, caused by Schistosoma mansoni infection in IL-4 receptor α-deficient mice (IL-4Rα(-/-)), results from the absence of M2 cells or increased numbers of M1 cells. In this study, we generated mice that completely lack IL-4Rα signaling in the context of a macrophage-specific loss of IFN-γ responsiveness (MIIG × IL-4Rα(-/-)). Contrary to what we expected, acute schistosomiasis resulted in greater liver injury and mortality in MIIG × IL-4Rα(-/-) mice compared with IL-4Rα(-/-) mice. Greater tissue injury in MIIG × IL-4Rα(-/-) mice was likely because of a lack of indoleamine 2,3 dioxygenase (IDO), a critical regulator of immunosuppression. Indeed, MIIG × IL-4Rα(-/-) failed to up-regulate IDO expression, and IL-4Rα(-/-) mice treated with an IDO antagonist underwent greater liver damage and mortality compared with mock-treated IL-4Rα(-/-) mice. Thus, we propose that, in the absence of AAM/M2 cells, IFN-γ-induced M1 cells suppress tissue-damaging inflammation during acute schistosomiasis through an IDO-dependent mechanism.

TGF-ß-responsive myeloid cells suppress type 2 immunity and emphysematous pathology after hookworm infection.

Transforming growth factor ß (TGF-ß) regulates inflammation, immunosuppression, and wound-healing cascades, but it remains unclear whether any of these functions involve regulation of myeloid cell function. The present study demonstrates that selective deletion of TGF-ßRII expression in myeloid phagocytes i) impairs macrophage-mediated suppressor activity, ii) increases baseline mRNA expression of proinflammatory chemokines/cytokines in the lung, and iii) enhances type 2 immunity against the hookworm parasite Nippostrongylus brasiliensis. Strikingly, TGF-ß-responsive myeloid cells promote repair of hookworm-damaged lung tissue, because LysM(Cre)TGF-ßRII(flox/flox) mice develop emphysema more rapidly than wild-type littermate controls. Emphysematous pathology in LysM(Cre)TGF-ßRII(flox/flox) mice is characterized by excessive matrix metalloprotease (MMP) activity, reduced lung elasticity, increased total lung capacity, and dysregulated respiration. Thus, TGF-ß effects on myeloid cells suppress helminth immunity as a consequence of restoring lung function after infection.

Molecular dynamics simulation of RAC1 protein and its de novo variants related to developmental disorders.

Neurodevelopmental disorders (NDDs) are conceptualized as childhood disability, but it has increasingly been recognized as lifelong neurological conditions that could notably impact adult functioning and quality of life. About 1%-3% of the general population suffers from NDDs including ADHD, ASD, IDD, communication disorders, motor disorders, etc. Studies suggest that Rho GTPases are key in neuronal development, highlighting the importance of altered GTPase signaling in NDDs. RAC1, a member of the Rho GTPase family, plays a critical role in neurogenesis, migration, synapse formation, axon growth, and regulation of actin cytoskeleton dynamics. We performed 6µs all-atom molecular dynamics simulation of native RAC1 (PDB: 3TH5) and three-point mutations (C18Y, N39S, and Y64D) related to developmental disorders to understand the impact of mutations on protein stability and functional dynamics. Our analysis, which included root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent accessible surface area (SASA), radius of gyration (Rg), free energy landscape (FEL), and principal component analysis (PCA), revealed that the N39S and Y64D mutations induced significant structural changes in RAC1. These alterations primarily occurred in the functional region adjacent to switch II, a region crucial for complex conformational rearrangements during the GDP and GTP exchange cycle.Communicated by Ramaswamy H. Sarma.

Comparative Evaluation of Chlorhexidine Polymer Scaffold, 3Mixtatin, and Formocresol for Vital Primary Pulp Therapy: A Randomized 6-month Clinical Study.

Introduction: The study was performed to evaluate and compare the clinical and radiographic efficacy of chlorhexidine (CHX) polymer scaffold, 3Mixtatin, and formocresol for vital primary pulp therapy-a randomized clinical study. Materials and methods: A total of 120 primary molars were included from children aged between 6 and 8 years in this randomized clinical study based on inclusion and exclusion criteria and were randomly allocated into three groups (group I-CHX polymer scaffold, group II-3Mixtatin, and group III-formocresol. Pulpotomy was performed in a vital cariously exposed primary tooth with healthy periodontium where their retention is more beneficial than extraction. Subjects were followed up at 1, 3, and 6 months for clinical and radiographic evaluations. Results: At 6 months of follow-up, the overall success rate of pulpotomy in groups I, II, and III was 56.41, 71.05, and 60.52% in each group, respectively. Nonsignificant difference (p > 0.05) was seen during intergroup comparison. Conclusion: However, among the three materials used in this study, 3mixtatin comparatively had better results. How to cite this article: Goel N. Comparative Evaluation of Chlorhexidine Polymer Scaffold, 3Mixtatin, and Formocresol for Vital Primary Pulp Therapy: A Randomized 6-month Clinical Study. Int J Clin Pediatr Dent 2023;16(3):478-482.

Comparative Evaluation of Effectiveness of TheraCal LC, MTA, and Calcium Hydroxide in Direct Pulp Capping in Primary Molars: Randomized Clinical Study.

Introduction: This study was performed to evaluate the clinical and radiographic effectiveness of TheraCal light cured (LC) comparison to mineral trioxide aggregate (MTA) and calcium hydroxide in direct pulp capping of primary molars over a period of 9 months. Materials and methods: A total of 90 primary molars from children aged between 5 and 8 years were included in this randomized clinical study based on inclusion and exclusion criteria and were randomly divided into three groups-group I, TheraCal LC; group II, MTA; and group III, calcium hydroxide. Direct pulp capping (DPC) was performed in noncontaminated pulpal exposure with hemostasis achieved within 2-3 minutes followed by restoring the tooth using glass ionomer cement (GIC). Subjects were followed up at 3, 6, and 9 months for clinical and radiographic evaluations. Results: At 9 months of follow-up, the overall success rate of direct pulp capping in groups I, II, and III were 60%, 72.41%, and 48.14%, respectively. Intergroup comparison showed nonsignificant differences (p >0.05). Conclusion: The outcomes of this study suggest the limited success of direct pulp capping in primary molars. However, among the three materials used in this study, MTA comparatively had better results. How to cite this article: Jha S, Namdev R, Singhal R, et al. Comparative Evaluation of Effectiveness of TheraCal LC, MTA, and Calcium Hydroxide in Direct Pulp Capping in Primary Molars: Randomized Clinical Study. Int J Clin Pediatr Dent 2023;16(S-2):S213-S219.

Knowledge, Attitude, and Perception of Undergraduate Dental Students on Information and Communication Technology and Computer-assisted Learning.

Introduction: The use of information and communication technology (ICT) in education and clinical purposes is growing immensely. The usage skill, attitude of dental students, and difficulties faced by students are important concerns to be addressed. Objective: The study was designed to investigate the knowledge, attitude, and skills of ICT of undergraduate dental students via assessing the ease of computer and internet use among students, the level of computer skills and training of the students, and usage pattern of computer activities. Materials and methods: A cross-sectional survey was conducted among students of three dental colleges in Haryana using a self-designed questionnaire having sections related to demographics, devices, softwares and search engine usage, ICT skills, ICT attitude, and educational and social use. Results: The response rate was 81.96%. A total of 99.1% of the individuals responded affirmatively to the usage of mobile phones, 48.4 and 13.1% for laptops and tablets, respectively. The average duration of use of smartphones per day was 4.2121 ± 2.834 hours. Google was opted as the most popular search engine used and PubMed the least popular. Only 12.9% of participants showed a negative attitude toward the use of ICT in studies. More social use than academic use was observed. Attitude scores showed a significant correlation with the educational use of ICT (r = 0.89, p = 0.003). Conclusion: Most of the participants were well acquainted with the usage and had a positive attitude toward ICT for educational purposes. Sensitization and training in scientific literature search and basics of ICT and their practical utilization in dental education, research, and practice should be included in the curriculum. How to cite this article: Sikka N, Arya L, Bala S, et al. Knowledge, Attitude, and Perception of Undergraduate Dental Students on Information and Communication Technology and Computer-assisted Learning. Int J Clin Pediatr Dent 2023;16(5):711-715.

Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits.

Soybean (Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of oil and protein. Owing to the rising demand for soybean products, there is an increasing need for improved varieties for more productive farming. However, complex correlation patterns among quantitative traits along with genetic interactions pose a challenge for soybean breeding. Association studies play an important role in the identification of accession with useful alleles by locating genomic sites associated with the phenotype in germplasm collections. In the present study, a genome-wide association study was carried out for seven agronomic and yield-related traits. A field experiment was conducted in 2015/2016 at two locations that include 155 diverse soybean germplasm. These germplasms were genotyped using SoySNP50K Illumina Infinium Bead-Chip. A total of 51 markers were identified for node number, plant height, pods per plant, seeds per plant, seed weight per plant, hundred-grain weight, and total yield using a multi-locus linear mixed model (MLMM) in FarmCPU. Among these significant SNPs, 18 were putative novel QTNs, while 33 co-localized with previously reported QTLs. A total of 2,356 genes were found in 250 kb upstream and downstream of significant SNPs, of which 17 genes were functional and the rest were hypothetical proteins. These 17 candidate genes were located in the region of 14 QTNs, of which ss715580365, ss715608427, ss715632502, and ss715620131 are novel QTNs for PH, PPP, SDPP, and TY respectively. Four candidate genes, Glyma.01g199200, Glyma.10g065700, Glyma.18g297900, and Glyma.14g009900, were identified in the vicinity of these novel QTNs, which encode lsd one like 1, Ergosterol biosynthesis ERG4/ERG24 family, HEAT repeat-containing protein, and RbcX2, respectively. Although further experimental validation of these candidate genes is required, several appear to be involved in growth and developmental processes related to the respective agronomic traits when compared with their homologs in Arabidopsis thaliana. This study supports the usefulness of association studies and provides valuable data for functional markers and investigating candidate genes within a diverse germplasm collection in future breeding programs.

Genetic diversity and population structure analysis in cultivated soybean (Glycine max [L.] Merr.) using SSR and EST-SSR markers.

Soybean (Glycine max) is an important legume that is used to fulfill the need of protein and oil of large number of population across the world. There are large numbers of soybean germplasm present in the USDA germplasm resources. Finding and understanding genetically diverse germplasm is a top priority for crop improvement programs. The current study used 20 functional EST-SSR and 80 SSR markers to characterize 96 soybean accessions from diverse geographic backgrounds. Ninety-six of the 100 markers were polymorphic, with 262 alleles (average 2.79 per locus). The molecular markers had an average polymorphic information content (PIC) value of 0.44, with 28 markers ≥ 0.50. The average major allele frequency was 0.57. The observed heterozygosity of the population ranged from 0-0.184 (average 0.02), while the expected heterozygosity ranged from 0.20-0.73 (average 0.51). The lower value for observed heterozygosity than expected heterozygosity suggests the likelihood of a population structure among the germplasm. The phylogenetic analysis and principal coordinate analysis (PCoA) divided the total population into two major groups (G1 and G2), with G1 comprising most of the USA lines and the Australian and Brazilian lines. Furthermore, the phylogenetic analysis and PCoA divided the USA lines into three major clusters without any specific differentiation, supported by the model-based STRUCTURE analysis. Analysis of molecular variance (AMOVA) showed 94% variation among individuals in the total population, with 2% among the populations. For the USA lines, 93% of the variation occurred among individuals, with only 2% among lines from different US states. Pairwise population distance indicated more similarity between the lines from continental America and Australia (189.371) than Asia (199.518). Overall, the 96 soybean lines had a high degree of genetic diversity.

Genome-Wide Identification and Analysis of the Hsp40/J-Protein Family Reveals Its Role in Soybean (Glycine max) Growth and Development.

The J-protein family comprises molecular chaperones involved in plant growth, development, and stress responses. Little is known about this gene family in soybean. Hence, we characterized J-protein genes in soybean, with the most highly expressed and responsive during flower and seed development. We also revealed their phylogeny, structure, motif analysis, chromosome location, and expression. Based on their evolutionary links, we divided the 111 potential soybean J-proteins into 12 main clades (I-XII). Gene-structure estimation revealed that each clade had an exon-intron structure resembling or comparable to others. Most soybean J-protein genes lacked introns in Clades I, III, and XII. Moreover, transcriptome data obtained from a publicly accessible soybean database and RT-qPCR were used to examine the differential expression of DnaJ genes in various soybean tissues and organs. The expression level of DnaJ genes indicated that, among 14 tissues, at least one tissue expressed the 91 soybean genes. The findings suggest that J-protein genes could be involved in the soybean growth period and offer a baseline for further functional research into J-proteins' role in soybean. One important application is the identification of J-proteins that are highly expressed and responsive during flower and seed development in soybean. These genes likely play crucial roles in these processes, and their identification can contribute to breeding programs to improve soybean yield and quality.

TGF-ß limits IL-33 production and promotes the resolution of colitis through regulation of macrophage function.

Mϕs promote tissue injury or repair depending on their activation status and the local cytokine milieu. It remains unclear whether the immunosuppressive effects of transforming growth factor ß (TGF-ß) serve a nonredundant role in Mϕ function in vivo. We generated Mϕ-specific transgenic mice that express a truncated TGF-ß receptor II under control of the CD68 promoter (CD68TGF-ßDNRII) and subjected these mice to the dextran sodium sulfate (DSS) model of colitis. CD68TGF-ßDNRII mice have an impaired ability to resolve colitic inflammation as demonstrated by increased lethality, granulocytic inflammation, and delayed goblet cell regeneration compared with transgene negative littermates. CD68TGF-ßDNRII mice produce significantly less IL-10, but have increased levels of IgE and numbers of IL-33+ Mϕs than controls. These data are consistent with associations between ulcerative colitis and increased IL-33 production in humans and suggest that TGF-ß may promote the suppression of intestinal inflammation, at least in part, through direct effects on Mϕ function.

Immunological cell type characterization and Th1-Th17 cytokine production in a mouse model of Gaucher disease.

Gaucher disease is a lysosomal storage disease resulting from insufficient acid ß-glucosidase (glucocerebrosidase, GCase, EC 4.2.1.25) activity and the resultant accumulation of glucosylceramide. Macrophage (Mϕ) lineage cells are thought to be the major disease effectors because of their secretion of numerous cytokines and chemokines that influence other poorly defined immunological cell populations. Increases in several such populations were identified in a Gba1 mouse model (D409V/null; 9V/null) of Gaucher disease including antigen presenting cells (APCs), i.e., Mϕ, dendritic cells (DCs), neutrophils (PMNs), and CD4(+) T cells. FACS analyses showed increases in these cell types in 9V/null liver, spleen lung, and bone marrow. T-cells or APCs enhanced activations were evident by positivity of CD40L, CD69, as well as CD40, CD80, CD86, and MHCII on the respective cells. Mϕ, and, unexpectedly, DCs, PMNs, and T cells, from 9V/null mice showed excess glucosylceramides as potential bases for activation of APCs and T cells to induce Th1 (IFNγ, IL12, TNFα,) and Th17 (IL17A/F) cytokine production. These data imply that excess glucosylceramides in these cells are pivotal for activation of APCs and T cell induction of Th1 and Th17 responses and PMN recruitment in multiple organs of this model of Gaucher disease.