Anomalous Posterior Branching of the Internal Jugular Vein: A Report of Two Patients

The internal jugular vein (IJV) is an important vein encountered during most routine major head and neck surgeries. The IJV is known to infrequently present with anatomical variations, commonly duplication and fenestration. This report presents two cases that highlight an unusual anatomical variation of the IJV, namely the posterior tributary, which was encountered during neck dissection for papillary carcinoma of the thyroid and metastatic cervical lymph nodes. The first case was a 50-year-old woman with papillary carcinoma of the thyroid and regional metastasis, who underwent extensive neck dissection. During dissection, an anomalous posterior tributary of the IJV was discovered, originating around 3 cm above the omohyoid tendon-IJV junction. In case 2, a 40-year-old woman with a history of thyroidectomy exhibited a similar anomaly during neck dissection. In both cases, the posterior tributary was observed branching into two divisions. These cases emphasize the significance of recognizing anatomical variations to avoid inadvertent damage during surgical procedures. Anomalies like the posterior IJV tributary could have implications for surgical planning, emphasizing the importance of thorough exploration and understanding of individual variations. Awareness of such variations will help facilitate surgeons in safely performing neck dissections.

Genetic mapping of quantitative trait loci associated with drought tolerance in chickpea (Cicer arietinum L.)

Elucidation of the genetic basis of drought tolerance is vital for genomics-assisted breeding of drought tolerant crop varieties. Here, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) derived from a cross between a drought tolerant chickpea variety, Pusa 362 and a drought sensitive variety, SBD 377. The GBS identified a total of 35,502 SNPs and subsequent filtering of these resulted in 3237 high-quality SNPs included in the eight linkage groups. Fifty-one percent of these SNPs were located in the genic regions distributed throughout the genome. The high density linkage map has total map length of 1069 cm with an average marker interval of 0.33 cm. The linkage map was used to identify 9 robust and consistent QTLs for four drought related traits viz. membrane stability index, relative water content, seed weight and yield under drought, with percent variance explained within the range of 6.29%-90.68% and LOD scores of 2.64 to 6.38, which were located on five of the eight linkage groups. A genomic region on LG 7 harbors quantitative trait loci (QTLs) explaining > 90% phenotypic variance for membrane stability index, and > 10% PVE for yield. This study also provides the first report of major QTLs for physiological traits such as membrane stability index and relative water content for drought stress in chickpea. A total of 369 putative candidate genes were identified in the 6.6 Mb genomic region spanning these QTLs. In-silico expression profiling based on the available transcriptome data revealed that 326 of these genes were differentially expressed under drought stress. KEGG analysis resulted in reduction of candidate genes from 369 to 99, revealing enrichment in various signaling pathways. Haplotype analysis confirmed 5 QTLs among the initially identified 9 QTLs. Two QTLs, qRWC1.1 and qYLD7.1, were chosen based on high SNP density. Candidate gene-based analysis revealed distinct haplotypes in qYLD7.1 associated with significant phenotypic differences, potentially linked to pathways for secondary metabolite biosynthesis. These identified candidate genes bolster defenses through flavonoids and phenylalanine-derived compounds, aiding UV protection, pathogen resistance, and plant structure.The study provides novel genomic regions and candidate genes which can be utilized in genomics-assisted breeding of superior drought tolerant chickpea cultivars.

The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes

Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.

LDL cholesterol an unmet target in diabetic, hypertensive population pan India exposing susceptive cardiovascular disorder risk

Funding Acknowledgements

Type of funding sources: None.

Background

Management and pathophysiology of diabetes and hypertension has always been the centre of research, with new insights being found consistently. CVD is the major cause of mortality in patients with type 2 diabetes and affects approximately 32.2% of people with type 2 diabetes. Southeast Asia stands out with a higher prevalence of CAD (29.4%) compared with other regions.

Purpose

The purpose of this EHR based real world study was to identify the proportion of patients with LDL-C out of control in people living with diabetes and hypertension who were under regular care of physicians. Specialized clinical care by super-specialists ensures management of specific disorders, yet risk factors for overall cardiovascular health continue to be expressed uncontrolled.

Methods

Patients reporting for routine care in 14 centers across the country were eligible to participate in the study. Patient recruitment at each site required informed consent signature, history of at least 6 months of diabetes mellitus type 2, was sequential and independent of other sites. An EMR (Medeva) integrated research proforma was created only for this study which collected data on medical history, comorbidities, diabetic complications, medications and laboratory values of relevance to the study. The recruitment started in March 2022 and ended in August 2022 (6 months).

Results

Average age of these patients was 54.36 years, and 1238 were male and 964 were female patients. Out of this sample, 1388 patients were only diabetic and 814 patients had diabetes as well as hypertension. 256 patients 44.8% patients had LDL-C within acceptable limits and the remaining 51.2% had hyperdyslipidemia. Average LDL-C value for all patients was 107.07, average LDL-C levels in only diabetic patients was 116.51, and LDL in patients with diabetes and hypertension is 90.97. In diabetes only patients, 37% patients had LDL-C under control whereas in diabetes and hypertension group 58% patients had LDL-C under control.

Conclusion

Although diabetic patients are under regular clinical care, their LDL-C values were higher in 55.2% of the patients. This is an alarming signal that calls all the stakeholders - diabetologists, researchers, educators, dieticians, policymakers, government agencies and people with diabetes must contribute towards the management of lipid profile for prevention of cardiovascular events. Also, the proportion of patients with LDL-C under control is lesser in patients who are only diabetic as compared to patients who are both diabetic and hypertensive. This finding suggests that there is either lesser focus or inadequate on lipid profile of patients who are only diabetic; more holistic management is an unprecedented requirement. More research is needed in this direction to recognize the loopholes, manage them and prevent them adequately.

Indian Psychiatric Society multicentre study: Diagnostic patterns, comorbidity and prescription practices for patients with Dementia

BACKGROUND

There are more than 5 million people with dementia in India. Multicentre studies looking at details of treatment for people with dementia In India are lacking. Clinical audit is a quality improvement process which aims to systematically assess, evaluate, and improve patient care. Evaluating current practice is the key to a clinical audit cycle.

AIM

This study aimed to assess the diagnostic patterns and prescribing practices of psychiatrists for patients with dementia in India.

METHOD

A retrospective case file study was conducted across several centers in India.

RESULTS

Information from the case records of 586 patients with dementia was obtained. Mean age of the patients was 71.14 years (standard deviation = 9.42). Three hundred twenty one (54.8%) were men. Alzheimer's disease (349; 59.6%) was the most frequent diagnosis followed by vascular dementia (117; 20%). Three hundred fifty five (60.6%) patients had medical disorders and 47.4% patients were taking medications for their medical conditions. Eighty one (69.2%) patients with vascular dementia had cardiovascular problems. Majority of the patients (524; 89.4%) were on medications for dementia. Most frequently prescribed treatment was Donepezil (230; 39.2%) followed by Donepezil-Memantine combination (225; 38.4%). Overall, 380 (64.8%) patients were on antipsychotics. Quetiapine (213, 36.3%) was the most frequently used antipsychotic. Overall, 113 (19.3%) patients were on antidepressants, 80 (13.7%) patients were on sedatives/hypnotics, and 16 (2.7%) patients were on mood stabilizers. Three hundred nineteen (55.4%) patients and caregivers of 374 (65%) patients were receiving psychosocial interventions.

CONCLUSIONS

Diagnostic and prescription patterns in dementia which emerged from this study are comparable to other studies both nationally and internationally. Comparing current practices at individual and national levels against accepted guidelines, obtaining feedback, identifying gaps and instituting remedial measures help to improve the standard of care provided.

Molecular mapping of QTLs for grain dimension traits in Basmati rice

Basmati rice is known for its extra-long slender grains, exceptional kernel dimensions after cooking, high volume expansion, and strong aroma. Developing high yielding Basmati rice varieties with good cooking quality is a gigantic task. Therefore, identifying the genomic regions governing the grain and cooked kernel dimension traits is of utmost importance for its use in marker-assisted breeding. Although several QTLs governing grain dimension traits have been reported, limited attempts have been made to map QTLs for grain and cooked kernel dimension traits of Basmati rice. In the current study, a population of recombinant inbred lines (RIL) was generated from a cross of Sonasal and Pusa Basmati 1121 (PB1121). In the RIL population, there was a significant positive correlation among the length (RRL: rough rice length, MRL: milled rice length, CKL: cooked kernel length) and breadth (RRB: rough rice breadth, MRB: milled rice breadth and CKB: cooked kernel breadth) of the related traits, while there was significant negative correlation between them. QTL mapping has led to the identification of four major genomic regions governing MRL and CKL. Two QTLs co-localize with the earlier reported major gene GS3 and a QTL qGRL7.1, while the remaining two QTLs viz., qCKL3.2 (qMRL3.2) and qCKL4.1 (qMRL4.1) were novel. The QTL qCKL3.2 has been bracketed to a genomic region of 0.78 Mb between the markers RM15247 and RM15281. Annotation of this region identified 18 gene models, of which the genes predicted to encode pentatricopeptides and brassinosteroid insensitive 1-associated receptor kinase 1 precursor may be the putative candidate genes. Furthermore, we identified a novel QTL qKER2.1 governing kernel elongation ratio (KER) in Basmati rice.

Fabrication of α-Fe2O3 Nanostructures: Synthesis, Characterization, and Their Promising Application in the Treatment of Carcinoma A549 Lung Cancer Cells

In the present work, iron nanoparticles were synthesized in the α-Fe₂O₃ phase with the reduction of potassium hexachloroferrate(III) by using l-ascorbic acid as a reducing agent in the presence of an amphiphilic non-ionic polyethylene glycol surfactant in an aqueous solution. The synthesized α-Fe₂O₃ NPs were characterized by powder X-ray diffraction, field emission scanning electron microscopy, transmission electron microscopy, atomic force microscopy, dynamic light scattering, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, and ultraviolet-visible spectrophotometry. The powder X-ray diffraction analysis result confirmed the formation of α-Fe₂O₃ NPs, and the average crystallite size was found to be 45 nm. The other morphological studies suggested that α-Fe₂O₃ NPs were predominantly spherical in shape with a diameter ranges from 40 to 60 nm. The dynamic light scattering analysis revealed the zeta potential of α-Fe₂O₃ NPs as -28 ± 18 mV at maximum stability. The ultraviolet-visible spectrophotometry analysis shows an absorption peak at 394 nm, which is attributed to their surface plasmon vibration. The cytotoxicity test of synthesized α-Fe₂O₃ NPs was investigated against human carcinoma A549 lung cancer cells, and the biological adaptability exhibited by α-Fe₂O₃ NPs has opened a pathway to biomedical applications in the drug delivery system. Our investigation confirmed that l-ascorbic acid-coated α-Fe₂O₃ NPs with calculated IC₅₀ ≤ 30 μg/mL are the best suited as an anticancer agent, showing the promising application in the treatment of carcinoma A549 lung cancer cells.

Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

Clay minerals identification in rock varnish by XRD: A one-step reduction approach

Rock varnishes are known to be fine, dark, glossy submicron films found in deserts bare rock surfaces. The oxides and hydroxides of manganese and iron bind together the clay minerals present in the varnish layer. The processes of oxide-hydroxide accumulation at varnish sites are due to iron and manganese oxidizing bacteria which may require clay minerals for additional nutrition. Quantification and identification of clay minerals in this biofilm is needed to understand its formation. Past attempts to analyze the mineralogical composition of rock varnish have led to inconclusive results as varnish is a submicron thin layer composed of a complex mineral matrix. The elimination of non-crystalline cementing groups comprising of free iron oxides is a key step in the identification of many types of clay minerals, particularly in soil/sediment mineral studies.•

The Fe-Mn oxide-hydroxide coatings, acting as cementing materials, can be easily removed using a one-step reduction method employing Na₂S₂O₄ at 70 °C, leading to separation of clay minerals.

•

We have taken the lead from earlier reported Jackson (1958) method, wherein a combination of reagents was used such as sodium acetate, sodium citrate, hydrogen peroxide, sodium bicarbonate, and sodium dithionite for removing carbonate, organic carbon and Fe-Mn oxy-hydroxide coatings respectively from sediment grains to segregate individual grains from each other.

•

Our modification helps in the unveiling of clay minerals from a solid substrate and reports the X-ray diffraction peaks, which are elsewise hard to detect and therefore earlier studies are inconclusive.

Growth Kinetic Study of Tannic Acid Mediated Monodispersed Silver Nanoparticles Synthesized by Chemical Reduction Method and Its Characterization

The complex process of nanoparticle formation in an aqueous solution is governed by kinetics and thermodynamic factors. This paper describes a room-temperature growth kinetic study and evaluation of thermodynamic activation parameters of monodispersed silver nanoparticles (AgNPs) synthesized in alkaline medium by chemical reduction method using AgNO₃ as a source of Ag⁺ ions and tannic acid (TA) as a reductant (reducing agent) as well as a capping or stabilizing agent in the absence of any other external stabilizer. A simple and conveniently handled reaction process was monitored spectrophotometrically to study the growth kinetics in an aqueous solution as a function of the concentration of silver ion, hydroxide ion, and TA, respectively. The neutral nucleophilic group donates the electron density via a lone pair of electrons to Ag⁺ ions for the reduction process, i.e., for the nucleation of AgNPs colloid. Also, a few silver ions form a silver oxide, which also facilitates the nucleation center to enhance the growth of AgNPs colloid. The decrease and increase in rate constant on varying the TA concentration showed its adsorption onto the surface of metallic AgNPs and stabilized by polygalloyl units of TA and were the main elements to control the growth kinetics. Consequently, stabilized TA-mediated AgNPs are formed using the electron donated by quinone form of TA followed by a pseudo-first-order reaction. Apart from this, nanoparticles formed were characterized using UV-visible spectrophotometry, Fourier transform infrared spectroscopy, field emission scanning electron microscopy, energy-dispersive X-ray spectroscopy, transmission electron microscopy, and powder X-ray diffraction techniques to confirm its formation during the present kinetic study.

Comparative transcriptome analyses revealed different heat stress responses in pigeonpea (Cajanus cajan) and its crop wild relatives

Comparative transcriptome analyses accompanied by biochemical assays revealed high variability in heat stress response in Cajanus species. Among the studied species, C. scarabaeoides was the most thermotolerant followed by C. cajanifolius, C. cajan, and C. acutifolius. Pigeonpea is one of the climate-resilient grain legumes. Though the optimum temperature for cultivated pigeonpea is ~ 25-35 °C, its wild relatives grow in temperatures ranging between 18 and 45 °C. To gain insight into molecular mechanisms responsible for the heat stress tolerance in pigeonpea, we conducted time-series transcriptome analysis of one pigeonpea cultivar (Cajanus cajan) and two wild relatives, Cajanus acutifolius, and Cajanus scarabaeoides subjected to heat stress at 42 ± 2 ºC for 30 min and 3 h. A total of 9521, 12,447, and 5282 identified transcripts were differentially expressed in C. cajan, C. acutifolius, and C. scarabaeoides, respectively. In this study, we observed that a significant number of genes undergo alternative splicing in a species-specific pattern during heat stress. Gene expression profiling analysis, histochemical assay, chlorophyll content, and electrolyte leakage assay showed that C. scarabaeoides has adaptive features for heat stress tolerance. The gene set enrichment analyses of differentially expressed genes in these Cajanus species during heat stress revealed that oxidoreductase activity, transcription factor activity, oxygen-evolving complex, photosystem-II, thylakoid, phenylpropanoid biosynthetic process, secondary metabolic process, and flavonoid biosynthetic process were highly affected. The histochemical assay showed more lipid peroxidation in C. acutifolius compared to other Cajanus species inferring the presence of higher quantities of polyunsaturated fatty acids in the plasma membrane which might have led to severe damage of membrane-bound organelles like chloroplast, and high electrolyte leakage during heat stress. This study paves the way for the identification of candidate genes, which can be useful for the development of thermo-tolerant pigeonpea cultivars.

Structural insight of two 4-Coumarate CoA ligase (4CL) isoforms in Leucaena suggests targeted genetic manipulations could lead to better lignin extractability from the pulp

4-Coumarate: coenzyme A ligase (4CL) is a key enzyme involved in the early steps of the monolignol biosynthetic pathway. It is hypothesized to modulate S and G monolignol content in the plant. Lignin removal is imperative to the paper industry and higher S/G ratio governs better extractability of lignin and economics of the pulping process. This background prompted us to predict 3D structure of two isoforms of 4CL in Leucaena leucocephala and evaluate their substrate preferences. The 3D structure of Ll4CL1 and Ll4CL2 protein were created by homology modeling and further refined by loop refinement. Molecular docking studies suggested differential substrate preferences of both the isoforms. Ll4CL1 preferred sinapic acid (- 4.91 kcal/mole), ferulic acid (- 4.84 kcal/mole), hydroxyferulic acid (- 4.72 kcal/mole), and caffeic acid (- 4.71 kcal/mole), in their decreasing order. Similarly, Ll4CL2 preferred caffeic acid (- 6.56 kcal/mole, 4 H bonds), hydroxyferulic acid (- 6.56 kcal/mole, 3 H bonds), and ferulic acid (- 6.32 kcal/mole) and sinapic acid (- 5.00 kcal/mole) in their decreasing order. Further, active site residues were identified in both the isoforms and in silico mutation and docking analysis was performed. Our analysis suggested that ASP228, TYR262, and PRO326 for Ll4CL1 and SER165, LYS247 and PRO315 for Ll4CL2 were important for their functional activity. Based on differential substrate preferences of the two isoforms, as a first step towards genetically modified Leuaena having the desired phenotype, it can be proposed that over-expression of Ll4CL1 gene and/or down-regulation of Ll4CL2 gene could yield higher S/G ratio leading to better extractability of lignin.

Identification and characterization of Dicer-like genes in leaf rust pathogen (Puccinia triticina) of wheat

Puccinia triticina (P. triticina) is one of the most devastating fungal pathogens of wheat which causes significant annual yield loss to the crop. Understanding the gene regulatory mechanism of the biotrophic pathogen is one of the important aspects of host-pathogen interaction studies. Dicer-like genes are considered as important mediators of RNAi-based gene regulation. In this study, we report the presence of three Dicer-like genes (Pt-DCL1, Pt-DCL2, Pt-DCL3) in P. triticina genome identified through computational and biological analyses. Quantitative real-time PCR studies revealed an increase in the expression of these genes in germinating spore stages. Heterologous expression combined with mass spectrometry analysis of Pt-DCL2 confirmed the presence of a canonical Dicer-like gene in P. triticina. Phylogenetic analysis of the Pt-DCLs with the Dicer-like proteins from other organisms showed a distinct cluster of rust pathogens from the order Pucciniales. The results indicated a species-specific duplication of Dicer-like genes within the wheat rust pathogens. This study, for the first time, reports the presence of Dicer-dependent RNAi pathway in P. triticina that may play a role in gene regulatory mechanism of the pathogen during its development. Our study serves as a vital source of information for further RNAi-based molecular studies for better understanding and management of the wheat leaf rust disease.

Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat

Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.

Expressivity of the key genes associated with seed and pod development is highly regulated via lncRNAs and miRNAs in Pigeonpea

Non-coding RNA’s like miRNA, lncRNA, have gained immense importance as a significant regulatory factor in different physiological and developmental processes in plants. In an effort to understand the molecular role of these regulatory agents, in the present study, 3019 lncRNAs and 227 miRNAs were identified from different seed and pod developmental stages in Pigeonpea, a major grain legume of Southeast Asia and Africa. Target analysis revealed that 3768 mRNAs, including 83 TFs were targeted by lncRNAs; whereas 3060 mRNA, including 154 TFs, were targeted by miRNAs. The targeted transcription factors majorly belong to WRKY, MYB, bHLH, etc. families; whereas the targeted genes were associated with the embryo, seed, and flower development. Total 302 lncRNAs interact with miRNAs and formed endogenous target mimics (eTMs) which leads to sequestering of the miRNAs present in the cell. Expression analysis showed that notably, Cc_lncRNA-2830 expression is up-regulated and sequestrates miR160h in pod leading to higher expression of the miR160h target gene, Auxin responsive factor-18. A similar pattern was observed for SPIKE, Auxin signaling F-box-2, Bidirectional sugar transporter, and Starch synthetase-2 eTMs. All the identified target mRNAs code for transcription factor and genes are involved in the processes like cell division, plant growth and development, starch synthesis, sugar transportation and accumulation of storage proteins which are essential for seed and pod development. On a combinatorial basis, our study provides a lncRNA and miRNA based regulatory insight into the genes governing seed and pod development in Pigeonpea.

Changes in middle ear transmission characteristics secondary to altered bone remodelling

Alteration in the process of bone remodelling results in conditions like osteopenia and osteoporosis in which the bones become susceptible to fracture. The functioning of middle ear bones in such individuals were assessed in this study and it was found that the middle ear bones are equally susceptible to micro-fractures and can cause reduction in the transmission of sound energy.

INTRODUCTION

Alteration in the process of bone remodelling or increase in the number of osteoclasts cells as it occurs in osteoporosis and osteopenia are likely to affect the middle ear bones in the same way it affects the skeletal bones. Whether these micro-structural changes occurring at the level of the middle ear secondary to altered bone remodelling cause any significant impairment in its functioning is not explored. Thus, the present study aimed at assessing the different aspects of middle ear functioning in individuals with reduced BMD.

METHODS

The study included 25 normal, 39 osteopenic and 40 osteoporotic participants. The participants underwent pure-tone audiometry, otoscopic examination, conventional immittance evaluation using a 226 Hz probe tone, multi-component and multi-frequency tympanometry and acoustic reflex threshold testing. None of the participants had any current or previous history of middle ear effusion.

RESULTS

A significantly higher proportion of participants in the clinical group had hearing loss compared to the normal group. The clinical group participants also had reduced middle ear resonance frequency, elevated static compliance values and elevated or absent acoustic reflexes compared to the normal participants. There was no difference among the three groups for the proportion of participants having conductive hearing loss.

CONCLUSIONS

There is a detrimental impact of reduction in bone mineral density on middle ear transmission characteristics which may go unnoticed initially. Treatment of osteoporosis may potentially mitigate hearing loss from middle ear fractures due to reduced bone mineral density. Absence of significant air-bone gap with the presence of reduced middle ear resonance frequency may be early signs of reduced BMD.

Analysis of genetic control and QTL mapping of essential wheat grain quality traits in a recombinant inbred population

Wheat cultivars are genetically crossed to improve end-use quality for traits as per demands of baking industry and broad consumer preferences. The processing and baking qualities of bread wheat are influenced by a variety of genetic make-ups, environmental factors and their interactions. Two wheat cultivars, WL711 and C306, derived recombinant inbred lines (RILs) with a population of 206, were used for phenotyping of quality-related traits. The genetic analysis of quality traits showed considerable variation for measurable quality traits, with normal distribution and transgressive segregation across the years. From the 206 RILs, few RILs were found to be superior to those of the parental cultivars for key quality traits, indicating their potential use for the improvement of end-use quality and suggesting the probability of finding new alleles and allelic combinations from the RIL population. Mapping analysis identified 38 putative QTLs for 13 quality-related traits, with QTLs explaining 7.9-16.8% phenotypic variation spanning over 14 chromosomes, i.e., 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4A, 4B, 4D, 5D, 6A, 7A and 7B. In-silico analysis based on homology to the annotated wheat genes present in database, identified six putative candidate genes within QTL for total grain protein content, qGPC.1B.1 region. Major QTL regions for other quality traits such as TKW have been identified on 1B, 2A, and 7A chromosomes in the studied RIL population. This study revealed the importance of the combination of stable QTLs with region-specific QTLs for better phenotyping, and the QTLs presented in our study will be useful for the improvement of wheat grain and bread-making quality.

Unravelling the epigenomic interactions between parental inbreds resulting in an altered hybrid methylome in pigeonpea

DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation. Identification of differentially methylated regions (DMRs) in the sterile and fertile parent revealed remarkable differences between their methylation patterns. Investigation of methylation status of parental DMRs in hybrid revealed non-additive methylation patterns resulting from trans-chromosomal methylation and trans-chromosomal demethylation events. Furthermore, we discovered several DMRs negatively associated with gene expression in the hybrid and fertile parent. Interestingly, many of those DMRs belonged to transposable elements and genes encoding pentatricopeptide repeats associated proteins, which may mediate a role in modulating the genes impacting pollen fertility. Overall, our findings provide an understanding of two parental epigenomes interacting to give rise to an altered methylome in pigeonpea hybrids, from genome-wide point of view.

Molecular analysis of anthocyanin biosynthesis pathway genes and their differential expression in mango peel

Mango fruit is cherished by masses for its taste and nutrition, contributed by color, flavor, and aroma. Among these, peel color is an important trait contributing to fruit quality and market value. We attempted to elucidate the role of key genes of the anthocyanin biosynthesis pathway related to fruit peel color from the leaf transcriptome of mango cultivar Amrapali. A total of 108 mined transcript sequences were assigned to the phenylpropanoid-flavonoid pathway from which 15 contigs representing anthocyanin biosynthesis genes were annotated. Alternate splice variants were identified by mapping against genes of Citrus clementina and Vitis vinifera (closest relatives) and protein subcellular localization was determined. Phylogenetic analysis of these pathway genes clustered them into distinct groups aligning with homologous genes of Magnifera indica, C. clementina, and V. vinifera. Expression profiling revealed higher relative fold expressions in mature fruit peel of red-colored varieties (Arunika, Ambika, and Tommy Atkins) in comparison with the green-peeled Amrapali. MiCHS, MiCHI, and MiF3H alternate splice variants revealed differential gene expression. Functionally divergent variants indicate availability of an allelic pool programmed to play critical roles in peel color. This study provides insight into the molecular genetic basis of peel color and offers scope for development of biomarkers in varietal improvement programs.

Designing and construction of simulated constructed wetland for treatment of sewage containing metals

A simulated horizontal flow constructed wetland (CW) has been designed with gravel medium and aquatic plants Typha latifolia and Polygonum hydropiper to assess its performance efficiency for sewage treatment. Monitoring of fully developed CW revealed a high removal of nutrients and metals from sewage after treatment at varying retention times. The percent (%) removal of biological oxygen demand, total dissolved solids, total suspended solids, PO₄-P and total nitrogen in CW planted with T. latifolia were 88.20, 61.9, 72.12, 74.23 and 66.78%; however, with P. hydropiper, reductions were 79.47, 53.47, 55.46, 60.40 and 52.87%, respectively, at 8 d retention time. In addition, T. latifolia and P. hydropiper accumulated substantial amount of metals in their tissues particularly in roots. T. latifolia root accumulated maximum amount of Zn (40.44 µg/g dw) followed by Cu (39.24 µg/g dw), Pb (37.78 µg/g dw) and Cr (19.95 µg/g dw) as compared to P. hydropiper, which was 17.85, 33.43, 36.19 and 9.67 µg/g dw, respectively. Further, plant-specific high translocation factor (>1) of metals were observed at different retention times. Results suggest that simulated CW may be applied as an ecofriendly and low-cost tool to treat sewage before discharge into a fresh water body.

Differential characterization of myogenic satellite cells with linolenic and retinoic acid in the presence of thiazolidinediones from prepubertal Korean black goats

Objective

Myogenic satellite cells were isolated from semitendinosus muscle of prepubertal Korean black goat to observe the differential effect of linolenic and retinoic acid in thepresence of thiazolidinediones (TZD) and also to observe the production insulin sensitive preadipocyte.

Methods

Cells were characterized for their stemness with cluster of differentiation 34 (CD34), CD13, CD106, CD44, Vimentin surface markers using flow cytometry. Cells characterized themselves as possessing significant (p<0.05) levels of CD13, CD34, CD106, Vimentin revealing their stemness potential. Goat myogenic satellite cells also exhibited CD44, indicating that they possessed a % of stemness factors of adipose lineage apart from their inherent stemness of paxillin factors 3/7.

Results

Cells during proliferation stayed absolutely and firmly within the myogenic fate without any external cues and continued to show a significant (p<0.05) fusion index % to express myogenic differentiation, myosin heavy chain, and smooth muscle actin in 2% horse serum. However, confluent myogenic satellite cells were the ones easily turning into adipogenic lineage. Intriguingly, upregulation in adipose specific genetic markers such as peroxisome proliferation-activated receptor γ, adiponectin, lipoprotein lipase, and CCAAT/enhancer binding protein α were observed and confirmed in all given treatments. However, the amount of adipogenesis was found to be statistically significant (p<0.01) with linolenic acid as compared to retinoic acid in combination with TZD’s.

Conclusion

Retinoic acid was found to produce smaller preadipocytes which have been assumed to have insulin sensitization and hence retinoic acid could be used as a potential agent to sensitize tissues to insulin in combination with TZD’s to treat diabetic conditions in humans and animals in future.

De novo Assembly and Characterization of Cajanus scarabaeoides (L.) Thouars Transcriptome by Paired-End Sequencing

Pigeonpea [Cajanus cajan (L.) Millsp.] is a heat and drought resilient legume crop grown mostly in Asia and Africa. Pigeonpea is affected by various biotic (diseases and insect pests) and abiotic stresses (salinity and water logging) which limit the yield potential of this crop. However, resistance to all these constraints is not readily available in the cultivated genotypes and some of the wild relatives have been found to withstand these resistances. Thus, the utilization of crop wild relatives (CWR) in pigeonpea breeding has been effective in conferring resistance, quality and breeding efficiency traits to this crop. Bud and leaf tissue of Cajanus scarabaeoides, a wild relative of pigeon pea were used for transcriptome profiling. Approximately 30 million clean reads filtered from raw reads by removal of adaptors, ambiguous reads and low-quality reads (3.02 gigabase pairs) were generated by Illumina paired-end RNA-seq technology. All of these clean reads were pooled and assembled de novo into 1,17,007 transcripts using the Trinity. Finally, a total of 98,664 unigenes were derived with mean length of 396 bp and N50 values of 1393. The assembly produced significant mapping results (73.68%) in BLASTN searches of the Glycine max CDS sequence database (Ensembl). Further, uniprot database of Viridiplantae was used for unigene annotation; 81,799 of 98,664 (82.90%) unigenes were finally annotated with gene descriptions or conserved protein domains. Further, a total of 23,475 SSRs were identified in 27,321 unigenes. This data will provide useful information for mining of functionally important genes and SSR markers for pigeonpea improvement.

Molecular prevalence of Babesia bigemina in Rhipicephalus microplus ticks infesting cross-bred cattle of Punjab, India

Babesiosis is an economically important tick-borne apicomplexan protozoan disease of cattle in tropical and subtropical regions. In the present study, Rhipicephalus microplus engorged female ticks were collected from 135 apparently healthy cattle from different agro-climatic zones of Punjab, India, to investigate the carrier status of Babesia bigemina infection in vector tick by using microscopy and PCR based assays. PCR when applied on DNA extracted from the egg masses harvested from ticks showed 1.48% (2/135) samples as positive, whereas 4.44% (6/135) samples were positive when product of primary PCR was used as template in nPCR. Further, among the DNA samples isolated from the unfed larval stages that emerged from egg masses laid by ticks, only 1.48% (2/135) samples were detected as positive for B. bigemina in PCR, while 7.41% (10/135) samples were detected positive in nPCR assay. Statistically, non-significant (p > 0.05) difference in prevalence rates was observed across different agro-climatic zones and between different age groups of cattle from which engorged ticks were collected. It can, thus, be concluded that prevalence of B. bigemina in the vector tick, R. microplus in Punjab state of India indicates an endemic status of the organism and a further study is needed for the management and control of the bovine babesiosis.

A Young Boy with L-asparaginase-Induced Seizure

L-Asparaginase is a critical component in the treatment of acute lymphoblastic leukemia in children. It is known to cause coagulation abnormalities, thrombosis and hemorrhage in the central nervous system in addition to vasculitis and hypersensitivity reactions. This syndrome generally occurs after a few weeks of therapy and may occur after L-asparaginase therapy is completed. Seizures are uncommon symptoms. We report a case of seizure associated with L-asparaginase therapy but no evidence of hemorrhagic or thrombotic cerebrovascular events, completed in the department of Hematology of Bangabandhu Sheikh Mujib Medical University during March & April 2016.

Detection of amitraz and malathion resistance in field populations of Rhipicephalus (Boophilus) microplus (Acari: Ixodidae) in Jammu region of India

Detection of resistance levels against amitraz and malathion in Rhipicephalus (Boophilus) microplus collected from four districts of Jammu region (India) was carried out using the adult immersion test. The regression graphs of probit mortality of ticks plotted against log values of concentration of drugs were utilised for the determination of slope of mortality, lethal concentration for 50% (LC₅₀), 95% (LC₉₅) and resistance factor (RF). On the basis of the data generated on variables (mortality, egg mass weight, reproductive index and percentage inhibition of oviposition) the resistance level was categorised as I, II, III and IV. Out of these four districts, resistance to amitraz was detected at level I in Udhampur (RF = 2.81), Jammu (RF = 2.53) and Samba isolates (RF = 2.24) whereas Rajouri isolate was found susceptible (RF = 1.0). Resistance to malathion was detected at level I in Udhampur (RF = 4.01) and Jammu isolates (RF = 1.76) whereas Rajouri (RF = 0.472) and Samba (RF = 0.199) isolates were found susceptible. The data generated on amitraz and malathion resistance status will help in formulating a tick control strategy in the region.

Augmentation of arsenic enhances lipid yield and defense responses in alga Nannochloropsis sp

The present study was conducted with microalga Nannochloropsis sp. to evaluate its tolerance responses and biofuel perspectives under different arsenic regime (0-1000μM As(III)). Results showed that optimal biomass (61.00±3.72mg/L/d) and lipid productivity (20.27mg/L/d) were obtained in culture treated with 100μM As(III) in comparison to other treatments. In addition, fatty acid profile of alga was in accordance with European biodiesel standards (EN 14214), which reflects good oxidative stability of oil. High antioxidants viz., ascorbic acid, GSH and cysteine tolerance responses as well as lipid yield at 100μM As(III), opens a new insight in the field of algal biology. Thus, microalgae Nannochloropsis sp. may be employ in remediation as well as biodiesel production.

Hemin, a heme oxygenase-1 inducer, restores the attenuated cardioprotective effect of ischemic preconditioning in isolated diabetic rat heart

BACKGROUND

Attenuated cardioprotective effect of ischemic preconditioning (IPC) by reduced nitric oxide (NO) is a hallmark during diabetes mellitus (DM). Recently, we reported that the formation of caveolin-endothelial nitric oxide synthase (eNOS) complex decreases the release of NO, which is responsible for attenuation of IPC-induced cardioprotection in DM rat heart. Heme oxygenase-1 (HO-1) facilitates release of NO by disrupting caveolin-eNOS complex. The activity of HO-1 is decreased during DM. This study was designed to investigate the role of hemin (HO-1 inducer) in attenuated cardioprotective effect of IPC in isolated diabetic rat heart.

METHODS

DM was induced in male Wistar rat by single dose of streptozotocin. Cardioprotective effect was assessed in terms of myocardial infarct size and release of lactate dehydrogenase and creatine kinase in coronary effluent. The release of NO was estimated indirectly by measuring the release of nitrite in coronary effluent. Perfusion of sodium nitrite, a precursor of NO, was used as a positive control.

RESULT

IPC-induced cardioprotection and increased release of nitrite were significantly attenuated in a diabetic rat as compared to a normal rat. Pretreatment with hemin and daidzein, a caveolin inhibitor, alone or in combination significantly restored the attenuated cardioprotection and increased the release of nitrite in diabetic rat heart. Zinc protoporphyrin, a HO-1 inhibitor, significantly abolished the observed cardioprotection and decreased the release of nitrite in hemin pretreated DM rat heart.

CONCLUSION

Thus, it is suggested that hemin restores the attenuated cardioprotective effect in diabetic rat heart by increasing the activity of HO-1 and subsequently release of NO.

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22

BACKGROUND

Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought.

RESULTS

We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network.

CONCLUSIONS

From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.

Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22

BACKGROUND

Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought.

RESULTS

We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network.

CONCLUSIONS

From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.

Genetic diversity trend in Indian rice varieties: an analysis using SSR markers

Background

The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940–2013), conserved in the National Gene Bank of India using SSR markers.

Result

A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend.

Conclusion

Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which resulted in loss of gene diversity during 2006 to 2013. The present study indicates the need for broadening the genetic base of Indian rice varieties through the use of diverse parents in the current breeding program.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0437-7) contains supplementary material, which is available to authorized users.

Arsenic and other heavy metal accumulation in plants and algae growing naturally in contaminated area of West Bengal, India

The present study was conducted to quantify the arsenic (As) and other heavy metal concentrations in the plants and algae growing naturally in As contaminated blocks of North-24-Pargana and Nandia district, West Bengal, India to assess their bioaccumulation potential. The plant species included five macrophytes and five algae were collected from the nine selected sites for estimation of As and other heavy metals accumulated therein by using Inductively Coupled Plasma Mass Spectrophotometer (ICP-MS). Results revealed that maximum As concentration (117mgkg(-1)) was recorded in the agricultural soil at the Barasat followed by Beliaghat (111mgkg(-1)) sites of North-24-Pargana. Similarly, concentration of selenium (Si, 249mgkg(-1)), lead (Pb, 79.4mgkg(-1)), chromium (Cr, 138mgkg(-1)) was also found maximum in the soil at Barasat and cadmium (Cd, 163mgkg(-1)) nickel (Ni, 36.5mgkg(-1)) at Vijaynagar site. Among the macrophytes, Eichhornia crassipes found more dominating species in As contaminated area and accumulate As (597mgkg(-1)) in the shoot at kanchrapara site. The Lemna minor found to accumulate maximum As (735mgkg(-1)) in the leaves at Sonadanga and Pistia stratiotes accumulated minimum As (24.5mgkg(-1)) in the fronds from Ranaghat site. In case of diatoms, maximum As (760mgkg(-1)) was accumulated at Kanchrapara site followed by Hydrodictiyon reticulatum (403mgkg(-1)) at the Ranaghat site. High concentration of As and other heavy metal in soil indicates long term effects of irrigation with contaminated ground water, however, high concentration of heavy metals in naturally growing plants and algae revealed their mobilization through leaching and possible food chain contamination. Therefore, efficient heavy metal accumulator macrophytes Eichhornia crassipes, Lemna minor, Spirodela polyrhiza may be exploited in removing metals from contaminated water by developing a plant based treatment system. However, As accumulator algal species may be used as a bioresource for understanding algae mediated As detoxification and bioindication studies.

Genotyping-by-Sequencing Analysis for Determining Population Structure of Finger Millet Germplasm of Diverse Origins

Finger millet [ (L.) Gaertn.] is grown mainly by subsistence farmers in arid and semiarid regions of the world. To broaden its genetic base and to boost its production, it is of paramount importance to characterize and genotype the diverse gene pool of this important food and nutritional security crop. However, as a result of nonavailability of the genome sequence of finger millet, the progress could not be made in realizing the molecular basis of unique qualities of the crop. In the present investigation, attempts have been made to characterize the genetically diverse collection of 113 finger millet accessions through whole-genome genotyping-by-sequencing (GBS), which resulted in a genome-wide set of 23,000 single-nucleotide polymorphisms (SNPs) segregating across the entire collection and several thousand SNPs segregating within every accession. A model-based population structure analysis reveals the presence of three subpopulations among the finger millet accessions, which are in parallel with the results of phylogenetic analysis. The observed population structure is consistent with the hypothesis that finger millet was domesticated first in Africa, and from there it was introduced to India some 3000 yr ago. A total of 1128 gene ontology (GO) terms were assigned to SNP-carrying genes for three main categories: biological process, cellular component, and molecular function. Facilitated access to high-throughput genotyping and sequencing technologies are likely to improve the breeding process in developing countries, and as such, this data will be very useful to breeders who are working for the genetic improvement of finger millet.

Identification and gene-silencing of a putative odorant receptor transcription factor in Varroa destructor: possible role in olfaction

The ectoparasitic mite Varroa destructor is one of the major threats to apiculture. Using a behavioural choice bioassay, we determined that phoretic mites were more successful in reaching a bee than reproductive mites, suggesting an energy trade-off between reproduction and host selection. We used both chemo-ecological and molecular strategies to identify the regulation of the olfactory machinery of Varroa and its association with reproduction. We focused on transcription regulation. Using primers designed to the conserved DNA binding region of transcription factors, we identified a gene transcript in V. destructor homologous to the pheromone receptor transcription factor (PRTF) gene of Pediculus humanus corporis. Quantitative PCR (qPCR) revealed that this PRTF-like gene transcript is expressed in the forelegs at higher levels than in the body devoid of forelegs. Subsequent comparative qPCR analysis showed that transcript expression was significantly higher in the phoretic as compared to the reproductive stage. Electrophysiological and behavioural studies revealed a reduction in the sensitivity of PRTF RNA interference-silenced mites to bee headspace, consistent with a reduction in the mites' ability to reach a host. In addition, vitellogenin expression was stimulated in PRTF-silenced mites to similar levels as found in reproductive mites. These data shed light upon the regulatory mechanism of host chemosensing in V. destructor.

Amelioration of arsenic toxicity in rice: Comparative effect of inoculation of Chlorella vulgaris and Nannochloropsis sp. on growth, biochemical changes and arsenic uptake

The present study was conducted to assess the responses of rice (Oryza sativa L. var. Triguna) by inoculating alga; Chlorella vulgaris and Nannochlropsis sp. supplemented with As(III) (50µM) under hydroponics condition. Results showed that reduced growth variables and protein content in rice plant caused by As toxicity were restored in the algae inoculated plants after 7d of treatment. The rice plant inoculated with Nannochloropsis sp. exhibited a better response in terms of increased root, shoot length and biomass than C. vulgaris under As(III) treatment. A significant reduction in cellular toxicity (thiobarbituric acid reactive substances) and antioxidant enzyme (SOD, APX and GR) activities were observed in algae inoculated rice plant under As(III) treatment in comparison to uninoculated rice. In addition, rice treated with As(III), accumulated 35.05mgkg(-1)dw arsenic in the root and 29.96mgkg(-1)dw in the shoot. However, lower accumulation was observed in As(III) treated rice inoculated with C. vulgaris (24.09mg kg(-1)dw) and Nannochloropsis sp. (20.66mgkg(-1)dw) in the roots, while in shoot, it was 20.10mgkg(-1)dw and 11.67mgkg(-1)dw, respectively. Results demonstrated that application of these algal inoculum ameliorates toxicity and improved tolerance in rice through reduced As uptake and modulating antioxidant enzymes. Thus, application of algae could provide a low-cost and eco-friendly mitigation approach to reduce accumulation of arsenic in edible part of rice as well as higher yield in the As contaminated agricultural field.

Performance of fenugreek bioinoculated with Rhizobium meliloti strains under semi-arid condition

Rhizobium meliloti strains were isolated from the fields of S.D. Agricultural University (Gujarat, India) and were maintained in the Congo Red Yeast Extract Mannitol Agar medium. These strains were tested for their effectiveness for fenugreek crop grown under semi-arid condition. Among the six Rhizobium strains, FRS-7 strain showed best plant growth parameters like shoot length, shoot dry weight, shoot total nitrogen, root length, root dry weight, root total nitrogen, seed yield, 1000 grain weight, number of root nodules, and nodules fresh and dry weight. The performance of this strain was better as compared to 20 kgN ha(-1) treatment through urea and was even far better over control plot. Seed yields obtained with FRS-7 during two years were 10.14 and 9.66 q ha(-1); which was about 36.8% and 45.9% high over control. This strain resulted in saving of about 20 kgN ha(-1) accompanied with better crop yield and soil health. Results of the present experiments can be utilized in integrated nutrient management for cultivation of fenugreek in semi-arid areas to provide sustainability to agricultural productivity in such regions.

From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network

Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, "From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance" was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into seven popular locally adapted rice varieties, namely, ADT 45, CR 1009, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. Genotypic background selection is being done after BC2F2 stage using an in-house designed 50K SNP chip on a set of twenty lines for each combination, identified with phenotypic similarity in the field to the recipient parent. Near-isogenic lines with more than 90% similarity to the recipient parent are now in advanced generation field trials. These climate smart varieties are expected to improve rice productivity in the adverse ecologies and contribute to the farmer's livelihood.

Molecular detection of Babesia bigemina infection in apparently healthy cattle of central plain zone of Punjab

Bovine babesiosis is an important tick-borne disease caused by the parasites belonging to the genus Babesia, distributed worldwide and infecting a wide range of domesticated and wild cattle, occasionally man. The present study was conducted to determine the prevalence of B. bigemina infection in apparently healthy cattle from central plain zone of Punjab, India. Examination of Giemsa-stained peripheral thin blood smears revealed 2.45 % (5/204) animals to be positive for piroplasms of B. bigemina. However, genomic DNA isolated from these blood samples when subjected to primary PCR revealed a positivity of 7.35 % (15/204) as detected by the amplification of a 278-bp product in the agarose gel. PCR products obtained from the primary PCR of B. bigemina, when employed as template in nested PCR produced the amplicons of desired size (170 bp) was detected in 30.39 % (62/204) of the samples. It can thus be concluded that B. bigemina infection is prevalent in apparently healthy cattle population of this region and PCR assays can serve as a valuable tool for epidemiological studies in endemic areas.

Syndrome of remitting seronegative symmetrical synovitis with pitting edema: a case series

Remitting Seronegative Symmetrical Synovitis with Pitting Edema (RS3PE) is a rare clinical entity that is easily missed due to lack of knowledge. It was formerly considered as a subset of rheumatoid arthritis (RA), but is now regarded as a distinct disease/syndrome. The diagnosis of RS3PE is not easy, as it is always hindered by the lack of definite diagnostic criteria and presence of other much common rheumatological disorders that mimic it. We report a series of seven cases that attended our clinic in the last year, which highlight the salient features of the disease. The disease was found to have a heterogeneous presentation. Immunogenetic, clinical, laboratory, radiological, and possible etiological factors and associations with the neoplasm are described, as also other peculiar presentations. Finally, a comparison with other common rheumatological disorders is made to alert the clinician about this rare, but easily treatable disease.

Deltamethrin resistance in field populations of Rhipicephalus (Boophilus) microplus (Acari: Ixodidae) in Jammu and Kashmir, India

Detection of resistance levels against deltamethrin in Rhipicephalus (Boophilus) microplus collected from six districts of Jammu and Kashmir (India) was carried out using the adult immersion test. The regression graphs of probit mortality of ticks plotted against log values of concentration of drug were utilised for the determination of slope of mortality, lethal concentration for 50% (LC50), 95% (LC95) and resistance factor (RF). On the basis of the data generated on mortality, egg mass weight, reproductive index and percentage inhibition of oviposition, the resistance level was categorised as I, II, III and IV. Out of these six districts, resistance to deltamethrin at level I was detected in one district (RF = 1.9), at level II in two districts (RF = 7.08-10.07) and at level IV in three districts (RF = 96.08-288.72). The data generated on deltamethrin resistance status will help in formulating tick control strategy in the region.

In vitro acaricidal activity of ethanolic and aqueous floral extracts of Calendula officinalis against synthetic pyrethroid resistant Rhipicephalus (Boophilus) microplus

Detection of resistance levels against deltamethrin and cypermethrin in Rhipicephalus (Boophilus) microplus collected from Jammu (India) was carried out using larval packet test (LPT). The results showed the presence of resistance level II and I against deltamethrin and cypermethrin, respectively. Adult immersion test (AIT) and LPT were used to evaluate the in vitro efficacy of ethanolic and aqueous floral extracts of Calendula officinalis against synthetic pyrethroid resistant adults and larvae of R. (B.) microplus. Four concentrations (1.25, 2.5, 5 and 10 %) of each extract with four replications for each concentration were used in both the bioassays. A concentration dependent mortality was observed and it was more marked with ethanolic extract. In AIT, the LC50 values for ethanolic and aqueous extracts were calculated as 9.9 and 12.9 %, respectively. The egg weight of the live ticks treated with different concentrations of the ethanolic and aqueous extracts was significantly lower than that of control ticks; consequently, the reproductive index and the percent inhibition of oviposition values of the treated ticks were reduced. The complete inhibition of hatching was recorded at 10 % of ethanolic extract. The 10 % extracts caused 100 % mortality of larvae after 24 h. In LPT, the LC50 values for ethanolic and aqueous extracts were determined to be 2.6 and 3.2 %, respectively. It can be concluded that the ethanolic extract of C. officinalis had better acaricidal properties against adults and larvae of R. (B.) microplus than the aqueous extract.