Integration of miRNA dynamics and drought tolerant QTLs in rice reveals the role of miR2919 in drought stress response.

To combat drought stress in rice, a major threat to global food security, three major quantitative trait loci for 'yield under drought stress' (qDTYs) were successfully exploited in the last decade. However, their molecular basis still remains unknown. To understand the role of secondary regulation by miRNA in drought stress response and their relation, if any, with the three qDTYs, the miRNA dynamics under drought stress was studied at booting stage in two drought tolerant (Sahbaghi Dhan and Vandana) and one drought sensitive (IR 20) cultivars. In total, 53 known and 40 novel differentially expressed (DE) miRNAs were identified. The primary drought responsive miRNAs were Osa-MIR2919, Osa-MIR3979, Osa-MIR159f, Osa-MIR156k, Osa-MIR528, Osa-MIR530, Osa-MIR2091, Osa-MIR531a, Osa-MIR531b as well as three novel ones. Sixty-one target genes that corresponded to 11 known and 4 novel DE miRNAs were found to be co-localized with the three qDTYs, out of the 1746 target genes identified. We could validate miRNA-mRNA expression under drought for nine known and three novel miRNAs in eight different rice genotypes showing varying degree of tolerance. From our study, Osa-MIR2919, Osa-MIR3979, Osa-MIR528, Osa-MIR2091-5p and Chr01_11911S14Astr and their target genes LOC_Os01g72000, LOC_Os01g66890, LOC_Os01g57990, LOC_Os01g56780, LOC_Os01g72834, LOC_Os01g61880 and LOC_Os01g72780 were identified as the most promising candidates for drought tolerance at booting stage. Of these, Osa-MIR2919 with 19 target genes in the qDTYs is being reported for the first time. It acts as a negative regulator of drought stress tolerance by modulating the cytokinin and brassinosteroid signalling pathway.

Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis.

Climate change has become a major source of concern, particularly in agriculture, because it has a significant impact on the production of economically important crops such as wheat, rice, and maize. In the present study, an attempt has been made to identify differentially expressed heat stress-responsive long non-coding RNAs (lncRNAs) in the wheat genome using publicly available wheat transcriptome data (24 SRAs) representing two conditions, namely, control and heat-stressed. A total of 10,965 lncRNAs have been identified and, among them, 153, 143, and 211 differentially expressed transcripts have been found under 0 DAT, 1 DAT, and 4 DAT heat-stress conditions, respectively. Target prediction analysis revealed that 4098 lncRNAs were targeted by 119 different miRNA responses to a plethora of environmental stresses, including heat stress. A total of 171 hub genes had 204 SSRs (simple sequence repeats), and a set of target sequences had SNP potential as well. Furthermore, gene ontology analysis revealed that the majority of the discovered lncRNAs are engaged in a variety of cellular and biological processes related to heat stress responses. Furthermore, the modeled three-dimensional (3D) structures of hub genes encoding proteins, which had an appropriate range of similarity with solved structures, provided information on their structural roles. The current study reveals many elements of gene expression regulation in wheat under heat stress, paving the way for the development of improved climate-resilient wheat cultivars.

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.

Genomic Selection: A Tool for Accelerating the Efficiency of Molecular Breeding for Development of Climate-Resilient Crops.

Since the inception of the theory and conceptual framework of genomic selection (GS), extensive research has been done on evaluating its efficiency for utilization in crop improvement. Though, the marker-assisted selection has proven its potential for improvement of qualitative traits controlled by one to few genes with large effects. Its role in improving quantitative traits controlled by several genes with small effects is limited. In this regard, GS that utilizes genomic-estimated breeding values of individuals obtained from genome-wide markers to choose candidates for the next breeding cycle is a powerful approach to improve quantitative traits. In the last two decades, GS has been widely adopted in animal breeding programs globally because of its potential to improve selection accuracy, minimize phenotyping, reduce cycle time, and increase genetic gains. In addition, given the promising initial evaluation outcomes of GS for the improvement of yield, biotic and abiotic stress tolerance, and quality in cereal crops like wheat, maize, and rice, prospects of integrating it in breeding crops are also being explored. Improved statistical models that leverage the genomic information to increase the prediction accuracies are critical for the effectiveness of GS-enabled breeding programs. Study on genetic architecture under drought and heat stress helps in developing production markers that can significantly accelerate the development of stress-resilient crop varieties through GS. This review focuses on the transition from traditional selection methods to GS, underlying statistical methods and tools used for this purpose, current status of GS studies in crop plants, and perspectives for its successful implementation in the development of climate-resilient crops.

Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach.

Rice is an important staple food grain consumed by most of the population around the world. With climate and environmental changes, rice has undergone a tremendous stress state which has impacted crop production and productivity. Plant growth hormones are essential component that controls the overall outcome of the growth and development of the plant. Cytokinin is a hormone that plays an important role in plant immunity and defense systems. Trans-zeatin is an active form of cytokinin that can affect plant growth which is mediated by a multi-step two-component phosphorelay system that has different roles in various developmental stages. Systems biology is an approach for pathway analysis to trans-zeatin treated rice that could provide a deep understanding of different molecules associated with them. In this study, we have used a weighted gene co-expression network analysis method to identify the functional modules and hub genes involved in the cytokinin pathway. We have identified nine functional modules comprising of different hub genes which contribute to the cytokinin signaling route. The biological significance of these identified hub genes has been tested by applying well-proven statistical techniques to establish the association with the experimentally validated QTLs and annotated by the DAVID server. The establishment of key genes in different pathways has been confirmed. These results will be useful to design new stress-resistant cultivars which can provide sustainable yield in stress-specific conditions.

Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo.

Single Nucleotide Polymorphism (SNP) is one of the important molecular markers widely used in animal breeding program for improvement of any desirable genetic traits. Considering this, the present study was carried out to identify, annotate and analyze the SNPs related to four important traits of buffalo viz. milk volume, age at first calving, post-partum cyclicity and feed conversion efficiency. We identified 246,495, 168,202, 74,136 and 194,747 genome-wide SNPs related to mentioned traits, respectively using ddRAD sequencing technique based on 85 samples of Murrah Buffaloes. Distribution of these SNPs were highest (61.69%) and lowest (1.78%) in intron and exon regions, respectively. Under coding regions, the SNPs for the four traits were further classified as synonymous (4697) and non-synonymous (3827). Moreover, Gene Ontology (GO) terms of identified genes assigned to various traits. These characterized SNPs will enhance the knowledge of cellular mechanism for enhancing productivity of water buffalo through molecular breeding.

MicroRNA-related markers associated with corpus luteum tropism in buffalo (Bubalus bubalis).

The study was undertaken to decipher the microRNA (miRNA) related markers associated with corpus luteum (CL) tropism in buffalo. The data obtained from deep sequencing of CL tissue from different physiological stages was mined in silico for the identification of miRNA-related markers (SSR & SNP). From the present study, 5 annotated and 176 unannotated miRNA were deduced while comparing with Bos taurus genome. In addition, 4 SSRs and 9 SNPs were deduced from the miRNA sequences. These SSRs were on the genes viz. Eukaryotic translation initiation factor 1-like, myocyte enhancer factor 2A, beta casein, T cell receptor gamma cluster 1. The SNP positions on genes viz. PYGO1 (Pygopus family PHD finger 1), LOC100337244 (Multidrug resistance-associated protein 4), FTH1 (Ferritin heavy chain 1), LOC788634 (BOLA class I histocompatibility antigen), PLXND1 (Plexin D1) and UBC (Ubiquitin C) show that these genes play critical role in CL tropism during estrous cycle in buffalo.

RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes.

Nearly two decades of revolution in the area of genomics serves as the basis of present-day molecular breeding in major food crops such as rice. Here we report an open source database on two major biotic stresses of rice, named RiceMetaSysB, which provides detailed information about rice blast and bacterial blight (BB) responsive genes (RGs). Meta-analysis of microarray data from different blast- and BB-related experiments across 241 and 186 samples identified 15135 unique genes for blast and 7475 for BB. A total of 9365 and 5375 simple sequence repeats (SSRs) in blast and BB RGs were identified for marker development. Retrieval of candidate genes using different search options like genotypes, tissue, developmental stage of the host, strain, hours/days post-inoculation, physical position and SSR marker information is facilitated in the database. Search options like 'common genes among varieties' and 'strains' have been enabled to identify robust candidate genes. A 2D representation of the data can be used to compare expression profiles across genes, genotypes and strains. To demonstrate the utility of this database, we queried for blast-responsive WRKY genes (fold change ≥5) using their gene IDs. The structural variations in the 12 WRKY genes so identified and their promoter regions were explored in two rice genotypes contrasting for their reaction to blast infection. Expression analysis of these genes in panicle tissue infected with a virulent and an avirulent strain of Magnaporthe oryzae could identify WRKY7, WRKY58, WRKY62, WRKY64 and WRKY76 as potential candidate genes for resistance to panicle blast, as they showed higher expression only in the resistant genotype against the virulent strain. Thus, we demonstrated that RiceMetaSysB can play an important role in providing robust candidate genes for rice blast and BB.

An efficient algorithm for protein structure comparison using elastic shape analysis.

BACKGROUND: Protein structure comparison play important role in in silico functional prediction of a new protein. It is also used for understanding the evolutionary relationships among proteins. A variety of methods have been proposed in literature for comparing protein structures but they have their own limitations in terms of accuracy and complexity with respect to computational time and space. There is a need to improve the computational complexity in comparison/alignment of proteins through incorporation of important biological and structural properties in the existing techniques. RESULTS: An efficient algorithm has been developed for comparing protein structures using elastic shape analysis in which the sequence of 3D coordinates atoms of protein structures supplemented by additional auxiliary information from side-chain properties are incorporated. The protein structure is represented by a special function called square-root velocity function. Furthermore, singular value decomposition and dynamic programming have been employed for optimal rotation and optimal matching of the proteins, respectively. Also, geodesic distance has been calculated and used as the dissimilarity score between two protein structures. The performance of the developed algorithm is tested and found to be more efficient, i.e., running time reduced by 80-90 % without compromising accuracy of comparison when compared with the existing methods. Source codes for different functions have been developed in R. Also, user friendly web-based application called ProtSComp has been developed using above algorithm for comparing protein 3D structures and is accessible free. CONCLUSIONS: The methodology and algorithm developed in this study is taking considerably less computational time without loss of accuracy (Table 2). The proposed algorithm is considering different criteria of representing protein structures using 3D coordinates of atoms and inclusion of residue wise molecular properties as auxiliary information.

Purification and dose-dependent toxicity study of abrin in swiss albino male mice.

Abrin, a phytotoxin obtained from the seeds of the Abrus precatorius plant, is highly toxic with an estimated human fatal dose of 0.1­1 µg/kg. In this study, abrin was purified and characterized through SDS PAGE and mass spectrometry analysis; further study on toxicity was carried out to investigate the alteration in biochemical, and hematological variables through histopathological observations in mice. The intraperitoneal LD50 value of purified abrin for mice was found to be 0.91µg/kg of body weight. Mice were exposed to 0.4 and 1.0 LD50 abrin doses intraperitoneally and observed on days 1, 3, and 7. Plasma GOT and GPT levels increased significantly at both doses. At 1.0 LD50 dose, alkaline phosphatase, bilirubin, urea, uric acid, and creatinine levels increased, whereas albumin, total protein, glucose and cholesterol levels decreased significantly. Abrin intoxication also altered the hemoglobin, WBC, and RBC counts significantly at 1.0 LD50 dose. Liver GSH levels decreased while lipid peroxidation increased significantly in a dose­dependent manner. Biochemical changes were supported by the histological investigation, which also showed the degenerative changes in organs. In conclusion, abrin intoxication caused toxic effects and severe damages on studied organs mediated through alteration in biochemical and hematological variables, lipid peroxidation, and degeneration.

Ovarian stromal luteoma in a patient with endometrial carcinoma.

A 65-year-old patient with endometrial adenocarcinoma underwent hysterectomy. Pathological examination of the right ovary revealed a coexisting stromal luteoma. The possible relationship between the two neoplasms as well as the intriguing pathogenesis and controversial nomenclature of ovarian steroid cell tumors are discussed. The incidental discovery of a stromal luteoma in a total hysterectomy specimen removed for endometrial carcinoma raises interesting questions about the perceived innocuous nature of these rare lipid cell tumors.

Thermal immobilization of Cr, Cu and Zn of galvanizing wastes in the presence of clay and fly ash.

In the present investigation thermal treatment of galvanizing waste with clay and fly ash has been carried out to immobilize Cr, Zn, Cu and other metals of the waste at temperature range 850 degrees C to 950 degrees C. Leaching of the metals from the waste and solidified product was analyzed using toxic characteristic leaching procedure (TCLP). Results indicated that the composition of waste and clay treatment temperature are the key factors in determining the stability of solidified product. After heating at 950 degrees C, the solidified specimens of 10% waste with clay have shown comparatively a high compressive strength and less water absorption. However, a decrease in compressive strength and increase in water absorption were noticed after addition of 15% of waste with clay. The leachability of all the metals present in the waste was found to reduce considerably with the increase of treatment temperature. In the case of Cr and Zn, their leachabilty was found at unacceptable levels from the treated product obtained after heating at 850 degrees C However, their leachability was reduced significantly within an acceptable level after treatment at 950 degrees C. The thermal treatment has shown an increase of re-oxidation trend of Cr (III) to Cr (VI) up to 900 degrees C of heating and this trend became almost zero after heating at 950 degrees C. Addition of fly ash did not show any improvement in strength, durability and leachability of metals from the thermally treated product. X-ray diffraction (XRD) analysis of the product confirmed the presence of mixed phases of oxides of toxic metals.

Clinico-pathological profile of 22 cases of cystic renal dysplasia.

Renal dysplasia is one of the major renal developmental anomaly characterized by abnormal structural organization and development of metanephric elements. It is usually detected antenatally or in early childhood. The kidney may be multicystic, aplastic, hypoplastic or duplex. We studied 22 cases of cystic renal dysplasia diagnosed over a period often years to identify the spectrum of morphological changes in dysplastic kidney, with special emphasis on mesenchymal changes. Clinical, radiological and gross morphologicalfeatures were noted. Microscopic features were studied in detail, including the epithelial and mesenchymal changes. Twenty-one of the 22 cases studied were children. One case was a 21-year-old adult, which is a rare age at presentation. Male to female ratio was 1.1:1. One of our patients had contra-lateral ureteric stenosis, a rare anomaly reported with renal dysplasia. Ten patients, all autopsy cases, had multi-system congenital anomalies. As cystic renal dysplasia is not a hereditary disease, it must be differentiated from polycystic kidney disease. Other differential diagnoses are cystic nephroma and cystic partially differentiated nephroblastoma. Histopathological examination is the final diagnostic tool since radiological features alone may not be sufficient to exclude other cystic renal lesions. Cartilage may not be seen in all cases of renal dysplasia. Once diagnosed, other associated anomalies should also be looked for.

A retrospective review of the histopathology and clinicopathologic correlates of appendices removed from patients of acute appendicitis.

AIM: Appendicitis is the most common intra-abdominal condition requiring emergency surgery, with a life time risk of about 6%. Although considerable data are available in the literature regarding the histopathology of appendicectomy specimens, such information from the Indian subcontinent remains unreported. METHODS: A total of 348 consecutive appendices removed because of clinical suspicion of acute appendicitis were selected. Three sections from each specimen were submitted for histopathology. Histopathologic acute appendicitis if present was further classified into 3 subcategories. A retrospective analysis was performed on all these specimens. RESULTS: The male female ratio was 2.6:1 with highest number of cases in the age group 21-30 years; 282 specimens out of 348 showed features consistent with acute appendicitis with an overall higher occurrence in males. Statistically significant association was obtained between perforation and male sex, older age and acute suppurative appendicitis. CONCLUSIONS: Present study shows that acute appendicitis in India is a disease of young males. The negative appendicectomy rate is about 10.9%. On further subclassification of acute appendicitis, uncomplicated acute appendicitis seems to be the most common followed by acute suppurative appendicitis.

Thermal treatment of toxic metals of industrial hazardous wastes with fly ash and clay.

Waste generated from galvanizing and metal finishing processes is considered to be a hazardous due to the presence of toxic metals like Pb, Cu, Cr, Zn, etc. Thermal treatment of such types of wastes in the presence of clay and fly ash can immobilizes their toxic metals to a maximum level. After treatment solidified mass can be utilized in construction or disposed off through land fillings without susceptibility of re-mobilization of toxic metals. In the present investigation locally available clay and fly ash of particular thermal power plant were used as additives for thermal treatment of both of the wastes in their different proportions at 850, 900 and 950 degrees C. Observed results indicated that heating temperature to be a key factor in the immobilization of toxic metals of the waste. It was noticed that the leachability of metals of the waste reduces to a negligible level after heating at 950 degrees C. Thermally treated solidified specimen of 10% waste and remaining clay have shown comparatively a higher compressive strength than clay fired bricks used in building construction. Though, thermally heated specimens made of galvanizing waste have shown much better strength than specimen made of metal finishing waste. The lechability of toxic metals like Cr, Cu, Pb and Zn became far below from their regulatory threshold after heating at 950 degrees C. Addition of fly ash did not show any improvement either in engineering property or in leachability of metals from the solidified mass. X-ray diffraction (XRD) analysis of the solidified product confirmed the presence of mixed phases of oxides of metals.

Pyrexia of unknown origin with neutropenia, cervical lymphadenopathy, pneumonia and marrow hypoplasia.

A 56 years adult male presented with fever for 3 weeks with neutropenia and cervical lymphadenopathy with left sided pneumonitis. Histopathology of lymphnode was consistent with Kikuchi's Necrotizing Lymphadenitis. Kikuchi's disease is usually a self- limiting illness characterized by pyrexia, neutropenia and cervical lymphadenopathy in young women of Asian decent. This often leads to the misdiagnosis of lymphoma or tuberculosis. The notable feature here is an older male presented with severe neutropenia and pneumonia with hypoplastic marrow.

Adenomatoid odontogenic tumor - a rare cause of jaw swelling

O tumor odontogênico adenomatóide (TOA) é um tumor incomum de origem odontogênica, caracterizado histologicamente pela formação de estruturas tubulares com depósitos do tipo amilóide. A histogênese do TOA ainda é indeterminada e este tumor é frequentemente considerado mais como uma lesão hamartomatosa do que propriamente um neoplasma. O TOA tem comportamento benigno, sendo suficiente a enucleação cirúrgica conservadora ou curetagem. Neste artigo, é descrito um caso de TOA em paciente de 15 anos do sexo feminino, que exibia um edema no lado esquerdo da mandíbula com reabsorção dental. A histopatologia revelou uma variante folicular intra-óssea do tumor odontogênico adenomatóide. Uma breve revisão da literatura é também apresentada.

Diagnosis of nail psoriasis: importance of biopsy and histopathology.

BACKGROUND: Involvement of the nail is quite common in psoriasis and at times may be the sole diagnostic clue. However, the histopathology of nail psoriasis has not been adequately evaluated. A confirmation of the diagnosis is required in cases suspected to have nail psoriasis in order to plan long-term therapy. OBJECTIVES: To assess the diagnostic significance and safety profile of nail biopsy in cases with nail psoriasis. METHODS: Clinical and mycological features were studied in 42 patients with nail psoriasis. Of these, 22 patients gave consent for nail biopsies to be taken and the histopathological changes were assessed. RESULTS: Males were affected more commonly (57%) with a peak incidence in the age group of 10-20 years (29%). Distal onycholysis, discoloration of nail plate, subungual hyperkeratosis and fine nail pitting were the predominant clinical features. In the 22 biopsies done, hyperkeratosis with parakeratosis (91%) was found to be the most common and hypergranulosis was the least common histological finding (36%). Clinicohistological correlation was possible only in 55% cases. Periodic acid-Schiff (PAS) staining was done for all biopsies. CONCLUSIONS: Histopathological examination of nails is a valuable diagnostic aid, especially in the absence of skin lesions. Examination of the PAS-stained sections is necessary before making a histological diagnosis of nail psoriasis because onychomycosis and psoriasis may show similar histology.

Thermal stabilization of metal finishing waste with clay.

Thermal treatment of metal finishing waste with locally available clay, in their varying ratios, was carried out at 850 degrees C and above temperatures. In the presence of 1:1 ratio of waste and clay a solidified product was obtained at 950 degrees C. Measurement of an appreciably high compressive strength, approximately 500 kg cm(-2) and a very small (0.4%) water absorption from the solidified product indicated its stable nature. Toxicity Characteristic Leaching Procedure (TCLP) test of the waste showed nearly 85 to 90% decrease of leaching of Fe, Cu, Ni, Zn, Mn and Cr after thermal treatment compared to their leaching without treatment. No hexavalent chromium (Cr(VI)) was observed from the leachate of the solidified product. This indicates the absence of re-oxidation phenomena of chromium during thermal treatment up to 950 degrees C. X - ray diffraction (XRD) of solidified product indicated the presence of hematite, and aluminum silicate as main phases of the solidified product. Involvement of the above waste metals with these phases during thermal treatment could be the reason for their immobilization.

Granulocytic sarcoma of the female genital tract: report of a case with an unusual presentation.

Granulocytic sarcoma of the female genital tract is a rare occurrence. A case of a perimenopausal female is presented who reported with a history of menorrhagia with a lump in the abdomen. A diagnosis of fibroid uterus was made but laparotomy findings were suggestive of inoperable ovarian malignancy with metastases. Postoperatively the patient suddenly became very anemic. Hematological investigations and histopathological reports from ovaries, myometrium, endometrium and intraperitoneal deposits all revealed acute myeloid leukemia. The patient received two cycles of chemotherapy but later succumbed to her disease. Extrauterine causes of menorrhagia should be considered before instituting definitive treatment. Preoperative induction chemotherapy may be more successful in cases of granulocytic sarcoma who tend to have a poor prognosis.