Temporal transcriptome of tomato elucidates the signaling pathways of induced systemic resistance and systemic acquired resistance activated by Chaetomium globosum

C. globosum is an endophytic fungus, which is recorded effective against several fungal and bacterial diseases in plants. The exclusively induce defense as mechanism of biocontrol for C. globosum against phyto-pathogens is reported. Our pervious study states the effectiveness of induced defense by C. globosum (Cg), in tomato against Alternaria solani. In this study the temporal transcriptome analysis of tomato plants after treatment with C. globosum was performed for time points at 0 hpCi, 12 hpCi, 24 hpCi and 96 phCi. The temporal expression analysis of genes belonging to defense signaling pathways indicates the maximum expression of genes at 12 h post Cg inoculation. The sequential progression in JA signaling pathway is marked by upregulation of downstream genes (Solyc10g011660, Solyc01g005440) of JA signaling at 24 hpCi and continued to express at same level upto 96 hpCi. However, the NPR1 (Solyc07g040690), the key regulator of SA signaling is activated at 12 h and repressed in later stages. The sequential expression of phenylpropanoid pathway genes (Solyc09g007920, Solyc12g011330, Solyc05g047530) marks the activation of pathway with course of time after Cg treatment that results in lignin formation. The plant defense signaling progresses in sequential manner with time course after Cg treatment. The results revealed the involvement of signaling pathways of ISR and SAR in systemic resistance induced by Cg in tomato, but with temporal variation

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Pearl millet [Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) Morrone], is a staple food for over 90 million poor farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. We report the ~1.79 Gb genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. Resequencing analysis of 994 (963 inbreds of the highly cross-pollinated cultigen, and 31 wild accessions) provides insights into population structure, genetic diversity, evolution and domestication history. In addition we demonstrated the use of re-sequence data for establishing marker trait associations, genomic selection and prediction of hybrid performance and defining heterotic pools. The genome wide variations and abiotic stress proteome data are useful resources for pearl millet improvement through deploying modern breeding tools for accelerating genetic gains in pearl millet.publishersversionPeer reviewe

Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers

Pearl millet [Pennisetum glaucum (L.) R. Br; also Cenchrus americanus (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-sequencing (GBS) markers can be used to build high-density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines ‘Tift 99D2B1’ and ‘Tift 454’. DNA from 186 RILs, the parents, and the F1 was used for 96-plex ApeKI GBS library development, which was further used for sequencing. The sequencing results showed that the average number of good reads per individual was 2.2 million, the pass filter rate was 88%, and the CV was 43%. High-quality GBS markers were developed with stringent filtering on sequence data from 179 RILs. The reference genetic map developed using 150 RILs contained 16,650 single-nucleotide polymorphisms (SNPs) and 333,567 sequence tags spread across all seven chromosomes. The overall average density of SNP markers was 23.23 SNP/cM in the final map and 1.66 unique linkage bins per cM covering a total genetic distance of 716.7 cM. The linkage map was further validated for its utility by using it in mapping quantitative trait loci (QTLs) for flowering time and resistance to Pyricularia leaf spot [Pyricularia grisea (Cke.) Sacc.]. This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Molecular Docking and Molecular Dynamic studies of Phytocompounds with HIF-1 alpha, HIF-2 alpha, and SREBP1c to Explore its Inhibitory Effect on Metabolic disorders and in Cancer

Hypoxia-inducible factors (HIFs) are important components of the cellular oxygen-signaling pathway. In response to low oxygen tensions, HIFs facilitate both oxygen delivery and adaptation to oxygen deprivation by regulating the expression of genes that are involved in glucose uptake and metabolism, angiogenesis, erythropoiesis, cell proliferation, and apoptosis. Hence HIFs role in the regulation of different cancers is crucial. Moreover, these proteins also play a role in the hepatic lipid metabolism. SREBP1c is a transcriptional factor and as well as key regulator of lipid metabolism through different signaling pathways. Hence, our study focuses to study the association between different inhibitory ligands with these key proteins. In order to investigate the binding mechanism of five phytocompounds, Curcumin, Digoxin, Epigallocatechin gallate (EGCG), Epigallocatechin (EGC) and Gallocatechin gallate (GCG) with drug targeted receptors viz., HIF-1α (PDB ID:5LA9), SREBP1c (PDB ID:1AM9) and HIF-2α (PDB ID:2A24) molecular docking and molecular dynamics simulation were performed. The best score among above compounds, on the basis of hydrogen bonding while docking by FlexX software, curcumin showed best score among all phytocompounds to HIF-1α (-20.72) and HIF-2α (-11.76), also for SREBP1c protein though Curcumin showed good score (-12.23) but EGC had an superiority, because the complex had more hydrogen and aromatic hydrogen bond and it also has an interaction with cytosine (DC26) residue from DNA and has score -12.03. Three independent molecular dynamics simulations (20ns) runs indicated general stability of curcumin in binding pocket of HIF-1α, HIF-2 α and EGC in SREBP1c as well as the tendency to form hydrogen bonds with water molecules in HIF-1α and SREBP1c also EGC form hydrogen bond with cytosine in SREBP1c.These results enhance further in vitro and in vivo experimentation and can probably serve as an ideal molecule for cancer treatment and metabolic disorders

Renal allograft dysfunction secondary to recurrent perigraft lymphatic collection managed with percutaneous sclerotherapy with povidone iodine

Lymphatic leak and lymphocele are well-known complications after renal transplantation, occurring among one-fourth of the recipients. We present a case of 42 year old male who underwent renal transplantation and developed recurrent perigraft collection causing hydronephrosis and rise in serum creatinine. Biochemical analysis of the fluid confirmed lymphocele. Successful treatment was done by ultrasound guided percutaneous catheter placement and instillation of 0.5% povidone iodine for 15 days. Percutaneous drainage catheter placement and sclerotherapy with 0.5% povidone-iodine is safe and effective for treatment lymphoceles and lymphatic leaks in renal allograft recipient

A case of iatrogenic thyroid storm

Thyroid storm is a rare entity and can be fatal if not properly managed on time. A 75 year old lady reported to the emergency room with agitation, restlessness, breathlessness. On further evaluation she was found to have atrial fibrillation with a heart rate of 180 beats per minute. She was carrying a blood report indicative of thyrotoxicosis, which was confirmed subsequently. The patient was diagnosed as a case of thyroid storm and managed accordingly. On taking the detail history it was found that the patient had palpitation since last 2 years and had been taking levothyoxine 75 microgram/day after consulting a paramedical health worker in a hospital. The dose had been escalated to one and half tablet of 75mcg strength, in July 2021 as per the advice of the same health care worker after seeing the report. But the lab report of July 2021, the patient had, indicated thyrotoxicosis. Ideally the dose of levothyroxine should have been reduced or discontinued.&nbsp

A case of iatrogenic thyroid storm

Thyroid storm is a rare entity and can be fatal if not properly managed on time. A 75 year old lady reported to the emergency room with agitation, restlessness, breathlessness. On further evaluation she was found to have atrial fibrillation with a heart rate of 180 beats per minute. She was carrying a blood report indicative of thyrotoxicosis, which was confirmed subsequently. The patient was diagnosed as a case of thyroid storm and managed accordingly. On taking the detail history it was found that the patient had palpitation since last 2 years and had been taking levothyoxine 75 microgram/day after consulting a paramedical health worker in a hospital. The dose had been escalated to one and half tablet of 75mcg strength, in July 2021 as per the advice of the same health care worker after seeing the report. But the lab report of July 2021, the patient had, indicated thyrotoxicosis. Ideally the dose of levothyroxine should have been reduced or discontinued.&nbsp