Drought-tolerant transgenic wheat HB4®: a hope for the future

Drought-tolerant transgenic [genetically modified (GM)] HB4® wheat carrying the drought-responsive sunflower gene Hahb4 was first developed in Argentina in 2019 and has already been approved for marketing and consumption as food/feed in at least ten countries. It has also been approved in Argentina and Brazil for commercial cultivation.

Comparative analysis of VMT genes/proteins in selected plant species with emphasis on bread wheat (Triticum aestivum L.)

BACKGROUND

In recent years, the study of molecular basis of uptake, transport and utilization of grain Fe/Zn (GFe/GZn) in wheat has been an active area of research. As a result, it has been shown that a number of transporters are involved in uptake and transport of Fe. In a recent study, knockout of a transporter gene OsVMT (VACUOLAR MUGINEIC ACID TRANSPORTER) in rice was shown to be involved in Fe homoeostasis.

OBJECTIVE

In this study, we analysed VMT genes among six monocots and three dicots with major emphasis on wheat VMT genes (TaVMTs), taking OsVMT gene as a reference.

METHODS AND RESULTS

Using OsVMT gene as a reference, VMT genes were identified and sequence similarities were examined among six monocots and three dicots. Each VMT protein carried one functional domain and 7 to 10 distinct motifs (including 9 novel motifs). The qRT-PCR analysis showed differential expression by all the six TaVMT genes in pairs of contrasting wheat genotypes with high (FAR4 and WB02) and low (K8027 and HD3226) GFe/GZn at two different grain filling stages (14 DAA and 28 DAA). TaVMT1 genes showed up-regulation in high GFe/Zn genotypes relative to low GFe/Zn genotypes, whereas the TaVMT2 genes showed down-regulation or nonsignificant up-regulation in a few cases.

CONCLUSIONS

At 14 DAA, each of the six TaVMT genes exhibited higher expression in wheat genotypes with high GFe and GZn relative to those with low GFe and GZn, suggesting major role of VMT genes in improvement of grain Fe/Zn homoeostasis, thus making TaVMT genes useful for improvement in Fe/Zn in wheat grains.

Intra-femoral tunnel graft lengths less than 20 mm do not predispose to early graft failure, inferior outcomes or poor function. A prospective clinico-radiological comparative study

PURPOSE

Increasing demands on skills with mounting pressures from expectations from arthroscopic anterior cruciate ligament (ACL) reconstructions requires precise knowledge of technical details by surgeons. One such element is the minimum length of graft in femoral tunnel to allow for adequate tendon-to-bone healing and early return to activities and sports. This has, however, remained an unanswered question.

PURPOSE

To study and compare clinico-radiological outcomes of ACL reconstructions in patients with < 20 mm of intra-femoral tunnel graft length with those measuring ≥ 20 mm.

METHODS

All eligible patients undergoing arthroscopic ACL reconstruction were sequentially divided into two groups based on the intra-femoral tunnel graft lengths (A: < 20 mm, n = 27; and B: ≥ 20 mm, n = 25). Exclusions were made for those > 45 years of age, with chondral and/or multi-ligamentous injuries and with systemic pathologies. All patients were postoperatively evaluated in clinics by physical examination and functional scoring (Lysholm and modified Cincinnati scores) at 3, 6 and 12-month intervals. Graft vascularity was assessed by signal-to-noise quotient ratio (SNQR) using magnetic resonance imaging (MRI) at 3 and 12 months.

RESULTS

No significant differences were noted in mean Lysholm and modified Cincinnati scores between the two groups at the end of 1 year. There were also no significant differences in graft maturation over time and SNQR at 3 and 12 months in the region of interest (ROI).

CONCLUSIONS

Intra-femoral tunnel graft length of less than 20 mm does not compromise early clinical and functional outcomes of ACL reconstructions.

Leaf rust responsive miRNA and their target genes in wheat

Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.

Meta-QTLs for multiple disease resistance involving three rusts in common wheat (Triticum aestivum L.)

In wheat, multiple disease resistance meta-QTLs (MDR-MQTLs) and underlying candidate genes for the three rusts were identified which may prove useful for development of resistant cultivars. Rust diseases in wheat are a major threat to global food security. Therefore, development of multiple disease-resistant cultivars (resistant to all three rusts) is a major goal in all wheat breeding programs worldwide. In the present study, meta-QTLs and candidate genes for multiple disease resistance (MDR) involving all three rusts were identified using 152 individual QTL mapping studies for resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR). From these 152 studies, a total of 1,146 QTLs for resistance to three rusts were retrieved, which included 368 QTLs for LR, 291 QTLs for SR, and 487 QTLs for YR. Of these 1,146 QTLs, only 718 QTLs could be projected onto the consensus map saturated with 2, 34,619 markers. Meta-analysis of the projected QTLs resulted in the identification of 86 MQTLs, which included 71 MDR-MQTLs. Ten of these MDR-MQTLs were referred to as the 'Breeders' MQTLs'. Seventy-eight of the 86 MQTLs could also be anchored to the physical map of the wheat genome, and 54 MQTLs were validated by marker-trait associations identified during earlier genome-wide association studies. Twenty MQTLs (including 17 MDR-MQTLs) identified in the present study were co-localized with 44 known R genes. In silico expression analysis allowed identification of several differentially expressed candidate genes (DECGs) encoding proteins carrying different domains including the following: NBS-LRR, WRKY domains, F-box domains, sugar transporters, transferases, etc. The introgression of these MDR loci into high-yielding cultivars should prove useful for developing high yielding cultivars with resistance to all the three rusts.

Pyramiding of genes for grain protein content, grain quality, and rust resistance in eleven Indian bread wheat cultivars: a multi-institutional effort

Improvement of grain protein content (GPC), loaf volume, and resistance to rusts was achieved in 11 Indian wheat cultivars that are widely grown in four different agro-climatic zones of India. This involved use of marker-assisted backcross breeding (MABB) for introgression and pyramiding of the following genes: (i) the high GPC gene Gpc-B1; (ii) HMW glutenin subunits 5 + 10 at Glu-D1 loci, and (iii) rust resistance genes, Yr36, Yr15, Lr24, and Sr24. GPC increased by 0.8 to 3.3%, although high GPC was generally associated with yield penalty. Further selection among high GPC lines allowed identification of progenies with higher GPC associated with improvement in 1000-grain weight and grain yield in the backgrounds of the following four cultivars: NI5439, UP2338, UP2382, and HUW468. The high GPC progenies (derived from NI5439) were also improved for grain quality using HMW glutenin subunits 5 + 10 at Glu-D1 loci. Similarly, progenies combining high GPC and rust resistance were obtained in the backgrounds of following five cultivars: Lok1, HD2967, PBW550, PBW621, and DBW1. The improved pre-bred lines developed following multi-institutional effort should prove a valuable source for the development of cultivars with improved nutritional quality and rust resistance in the ongoing wheat breeding programmes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01277-w.

Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.)

In wheat, 2852 major QTLs of 8998 QTLs available for yield and related traits were used for meta-analysis; 141 meta-QTLs were identified, which included 13 breeder's MQTLs and 24 ortho-MQTLs; 1202 candidate genes and 50 homologues of genes for yield from other cereals were also identified. Meta-QTL analysis was conducted using 2852 of the 8998 known QTLs, retrieved from 230 reports published during 1999-2020 (including 19 studies on tetraploid wheat) for grain yield (GY) and the following ten component traits: (i) grain weight (GWei), (ii) grain morphology-related traits (GMRTs), (iii) grain number (GN), (iv) spikes-related traits (SRTs), (v) plant height (PH), (vi) tiller number (TN), (vii) harvest index (HI), (viii) biomass yield (BY), (ix) days to heading/flowering and maturity (DTH/F/M), and (x) grain filling duration (GFD). The study resulted in the identification of 141 meta-QTLs (MQTLs), with an average confidence interval (CI) of 1.4 cM as against a CI of > 12.1 cM (8.8 fold reduction) in the QTLs that were used. The corresponding physical length of CI ranged from 0.01 Mb to 661.9 Mb (mean, 31.5 Mb). Seventy-seven (77) of these 141 MQTLs overlapped marker-trait associations (MTAs) reported in genome-wide association studies. Also, 63 MQTLs (each based on at least 10 QTLs) were considered stable and robust, with 13 MQTLs described as breeder's MQTLs (selected based on small CI, large LOD, and high level of phenotypic variation explained). Thirty-five yield-related genes from rice, barley, and maize were also utilized to identify 50 wheat homologues in MQTLs. Further, the use of synteny and collinearity allowed the identification of 24 ortho-MQTLs which were common among the wheat, barley, rice, and maize. The results of the present study should prove useful for wheat breeding and future basic research in cereals including wheat, barley, rice, and maize.

Multi-Locus GWAS for Grain Weight-Related Traits Under Rain-Fed Conditions in Common Wheat (Triticum aestivum L.)

In wheat, a multi-locus genome-wide association study (ML-GWAS) was conducted for the four grain weight-related traits (days to anthesis, grain filling duration, grain number per ear, and grain weight per ear) using data recorded under irrigated (IR) and rain-fed (RF) conditions. Seven stress-related indices were estimated for these four traits: (i) drought resistance index (DI), (ii) geometric mean productivity (GMP), (iii) mean productivity index (MPI), (iv) relative drought index (RDI), (v) stress tolerance index (STI), (vi) yield index, and (vii) yield stability index (YSI). The association panel consisted of a core collection of 320 spring wheat accessions representing 28 countries. The panel was genotyped using 9,627 single nucleotide polymorphisms (SNPs). The genome-wide association (GWA) analysis provided 30 significant marker-trait associations (MTAs), distributed as follows: (i) IR (15 MTAs), (ii) RF (14 MTAs), and (iii) IR+RF (1 MTA). In addition, 153 MTAs were available for the seven stress-related indices. Five MTAs co-localized with previously reported QTLs/MTAs. Candidate genes (CGs) associated with different MTAs were also worked out. Gene ontology (GO) analysis and expression analysis together allowed the selection of the two CGs, which may be involved in response to drought stress. These two CGs included: TraesCS1A02G331000 encoding RNA helicase and TraesCS4B02G051200 encoding microtubule-associated protein 65. The results supplemented the current knowledge on genetics for drought tolerance in wheat. The results may also be used for future wheat breeding programs to develop drought-tolerant wheat cultivars.

GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers

The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.

SWEET genes and TAL effectors for disease resistance in plants: Present status and future prospects

SWEET genes encode sugar transporter proteins and often function as susceptibility (S) genes. Consequently, the recessive alleles of these SWEET genes provide resistance. This review summarizes the available literature on the molecular basis of the role of SWEET genes (as S genes) in the host and corresponding transcription activator-like effectors (TALEs) secreted by the pathogen. The review has four major sections, which follow a brief introduction: The first part gives some details about the occurrence and evolution of SWEET genes in approximately 30 plant species; the second part gives some details about systems where (a) SWEET genes with and without TALEs and (b) TALEs without SWEET genes cause different diseases; the third part summarizes the available information about TALEs along with interfering/truncated TALEs secreted by the pathogens; this section also summarizes the available information on effector-binding elements (EBEs) available in the promoters of either the SWEET genes or the Executor R genes; the code that is used for binding of TALEs to EBEs is also described in this section; the fourth part gives some details about the available approaches that are being used or can be used in the future for exploiting SWEET genes for developing disease-resistant cultivars. The review concludes with a section giving conclusions and future possibilities of using SWEET genes for developing disease-resistant cultivars using different approaches, including conventional breeding and genome editing.

A novel bicistronic DNA vaccine with enhanced protective immune response against Bacillus anthracis through DNA prime-protein boost vaccination approach

Anthrax, by Bacillus anthracis, remains a dreadful fatal hazard worldwide. The currently used anthrax vaccines are plagued by numerous issues that limit their widespread use. As an immunization approach targeting both extracellular antigens and toxins of B. anthracis may achieve better sterile immunity, the present investigation designed a bicistronic secretory anti-anthrax DNA vaccine targeting immune response against toxin and cells. The efficacy of the vaccine was compared with monocistronic DNA vaccines and the currently used anthrax vaccine. For this, mice were immunized with the developed vaccine containing pag (encoding protective antigen to block toxin) and eag genes (encoding EA1 to target cells) of B. anthracis through DNA-prime/Protein-boost (D/P) and DNA prime/DNA-boost (D/D) approaches. There was a >2 and > 5 fold increase in specific antibody level by D/D and D/P approaches respectively, on 42nd days post-immunization (dpi). Serum cytokine profiling showed that both Th1 and Th2 immune responses were elicited, with more Th2 responses in D/P strategy. More importantly, challenge with 100 times LD₅₀ of B. anthracis at 42nd dpi exhibited maximum cumulative survival (83.33 %) by bicistronic D/P approach. Remarkably, immunization with EA1 delayed mortality onset in infection. The study forms the first report on complement-dependent bactericidal activity of antiEA1 antibodies. In short, co-immunization of PA and EA1 through the developed bicistronic DNA vaccine would be an effective immunization approach in anthrax vaccination. Further, D/P strategy could enhance vaccine-induced immunity against B. anthracis. Altogether, the study generates certain critical insights having direct applications in next-generation vaccine development against anthrax.

Application of Deep Learning on Student Engagement in e-learning environments

The drastic impact of COVID-19 pandemic is visible in all aspects of our lives including education. With a distinctive rise in e-learning, teaching methods are being undertaken remotely on digital platforms due to COVID-19. To reduce the effect of this pandemic on the education sector, most of the educational institutions are already conducting online classes. However, to make these digital learning sessions interactive and comparable to the traditional offline classrooms, it is essential to ensure that students are properly engaged during online classes. In this paper, we have presented novel deep learning based algorithms that monitor the student's emotions in real-time such as anger, disgust, fear, happiness, sadness, and surprise. This is done by the proposed novel state-of-the-art algorithms which compute the Mean Engagement Score (MES) by analyzing the obtained results from facial landmark detection, emotional recognition and the weights from a survey conducted on students over an hour-long class. The proposed automated approach will certainly help educational institutions in achieving an improved and innovative digital learning method.

Quantitative genetics: pan-genomes, SVs, and k-mers for GWAS

For identification of marker-trait associations (MTAs) for complex traits in animals and plants, thousands of genome-wide association studies (GWAS) were conducted during the past two decades. This involved regular improvement in methodology. Initially, a reference genome and SNPs were used; more recently pan-genomes and the markers structural variations (SVs)/k-mers are also being used.

Correction to: QTL analysis and fine mapping of a QTL for yield‑related traits in wheat grown in dry and hot environments

A correction to this paper has been published: https://doi.org/10.1007/s00122-021-03792-4

Biofortification and bioavailability of Zn, Fe and Se in wheat: present status and future prospects

Knowledge of genetic variation, genetics, physiology/molecular basis and breeding (including biotechnological approaches) for biofortification and bioavailability for Zn, Fe and Se will help in developing nutritionally improved wheat. Biofortification of wheat cultivars for micronutrients is a priority research area for wheat geneticists and breeders. It is known that during breeding of wheat cultivars for productivity and quality, a loss of grain micronutrient contents occurred, leading to decline in nutritional quality of wheat grain. Keeping this in view, major efforts have been made during the last two decades for achieving biofortification and bioavailability of wheat grain for micronutrients including Zn, Fe and Se. The studies conducted so far included evaluation of gene pools for contents of not only grain micronutrients as above, but also for phytic acid (PA) or phytate and phytase, so that, while breeding for the micronutrients, bioavailability is also improved. For this purpose, QTL interval mapping and GWAS were carried out to identify QTLs/genes and associated markers that were subsequently used for marker-assisted selection (MAS) during breeding for biofortification. Studies have also been conducted to understand the physiology and molecular basis of biofortification, which also allowed identification of genes for uptake, transport and storage of micronutrients. Transgenics using transgenes have also been produced. The breeding efforts led to the development of at least a dozen cultivars with improved contents of grain micronutrients, although land area occupied by these biofortified cultivars is still marginal. In this review, the available information on different aspects of biofortification and bioavailability of micronutrients including Zn, Fe and Se in wheat has been reviewed for the benefit of those, who plan to start work or already conducting research in this area.

Preparation of alpha cellulose from sugarcane bagasse and its cationization: Synthesis, characterization, validation and application as wet-end additive

Paper industry uses cationic polymers for imparting strong bonds with pulp furnish to enhance strength properties. Due to environmental reasons, emphasis is on utilization of biobased polymers in place of synthetic. Sugarcane bagasse, an agro-industrial waste, was processed for extraction of alpha cellulose and preparation of cationic derivative. Reaction conditions were optimized to achieve highly substituted cationic derivative with insertion of 2-hydroxy-3-(trimethylammonium) propyl group. Artificial neural network (ANN) was applied to analyze the experimental data for cationization modeling. Maximum degree of substitution 0.66, was achieved at 5.0 M NaOH/anhydro glucose unit (AGU), 20 °C alkalization temperature, 8 min alkalization time, 3.5 M/AGU etherification agent concentration, 45 min time and 60 °C etherification reaction temperature. The experimental results showed that mean square error values for input parameters were significantly low. The ANN based regression values of the output, and computed values of target were close to unity. ANN based fitting indicates better performance level to predict the degree of substitution. The synthesized cationic cellulose was characterized through FTIR, XRD, NMR, FESEM and TGA. The activity of cationized cellulose as wet-end additive was tested for bagasse, wheat straw and recycled pulps due to their shorten fiber and feeble pulp characters than wood pulp.

Development of a visible loop mediated isothermal amplification assay for rapid detection of Bacillus anthracis

Distressing effects on animal and human health with lethal progression, being used as bioweapon and shared features with non-pathogenic bacteria demands sensitive, specific, safe, cost effective and rapid detection methods for anthrax causing organisms. Conventional microbiology based diagnostics for anthrax are time consuming and need sophisticated equipment, while molecular diagnostics require less time and labor. The Loop mediated isothermal amplification assay (LAMP) is rapid, sensitive and specific assay and requires no specialized equipment. In the present study, we developed a LAMP assay for rapid as well as specific detection of Bacillus anthracis. The optimized assay produced positive results with the Sterne strain and one field isolate of B. anthracis and, negative results with other bacteria of the same and different genera within 2 h. Sensitivity was 500 fg of total DNA of B. anthracis, which was 100 times more sensitive than conventional PCR. The present study also demonstrated that the simple method of total DNA extraction by repeated boiling and freezing will not adversely affect the LAMP results. In conclusion, the optimized LAMP assay is a promising tool for the specific, sensitive, less time-consuming diagnosis for anthrax causing bacteria and also, for detecting the virulence of suspected B. anthracis cultures.

PSII-5 Chemical composition, in vitro dry matter digestibility, gas production and methane emission of maintenance, growth and production diets/rations of buffaloes

Ten types of diets were prepared to meet the nutrient requirements of buffaloes for maintenance (MD1 to MD10), growth (GD1 to GD10) and production/lactation (PD1 to PD10). A total of 30 diets were evaluated for chemical composition, in vitro gas and methane production, and dry matter (DM) disappearance using buffalo rumen liquor. The CNCPS was used to estimate the carbohydrate and protein fractions. Protein fractions PB1 and PB2 of maintenance diets were lower (P &lt; 0.05) than growth and production diets, while protein fractions (PB3) and Pc were (P &lt; 0.05) higher in maintenance than in growth and production diets. Mean values of PA was (P &lt; 0.05) higher in growth diets (136.9) than production (114.8) and maintenance diets (105.6 g/kg DM). Maintenance diets had (P &lt; 0.05) higher structural carbohydrate contents (586.2 g/kg DM) than production diets (513.0 g/kg DM). Carbohydrate fraction (CB1) was highest (P &lt; 0.05) in production diets (187.2 g/kg DM) followed by growth (129.5 g/kg DM) and maintenance diets (96.1 g/kg DM). In vitro gas production at different time periods (12, 24 and 48 h) was similar for maintenance (63.04, 51.98 and 48.15 ml/g DM), growth (63.83, 52.73 and 48.250) and production diets (63.51, 52.54 and 47.21 ml/g DM). Cumulative methane production was numerically lower for maintenance (28.40 ml/g DM) than growth (29.58 ml/g DM) and production diets (33.13 ml/g DM). In vitro methane production as a proportion of degraded DM (ml/g DDM and g/kg DDM) was similar for maintenance (14.21 and 29.53), growth (42.19 and 30.25) and production diets (41.26 and 29.58). Dietary chemical constituents such as EE, lignin, NDIN, ADIN and PB3 and Cc were (P &lt; 0.05) negatively associated with methane production, while OM, NPN, SP, PA and PB1, TCHO and CB2 were positively (P &lt; 0.05) correlated with methane production.

A deep learning and grad-CAM based color visualization approach for fast detection of COVID-19 cases using chest X-ray and CT-Scan images

The world is suffering from an existential global health crisis known as the COVID-19 pandemic. Countries like India, Bangladesh, and other developing countries are still having a slow pace in the detection of COVID-19 cases. Therefore, there is an urgent need for fast detection with clear visualization of infection is required using which a suspected patient of COVID-19 could be saved. In the recent technological advancements, the fusion of deep learning classifiers and medical images provides more promising results corresponding to traditional RT-PCR testing while making detection and predictions about COVID-19 cases with increased accuracy. In this paper, we have proposed a deep transfer learning algorithm that accelerates the detection of COVID-19 cases by using X-ray and CT-Scan images of the chest. It is because, in COVID-19, initial screening of chest X-ray (CXR) may provide significant information in the detection of suspected COVID-19 cases. We have considered three datasets known as 1) COVID-chest X-ray, 2) SARS-COV-2 CT-scan, and 3) Chest X-Ray Images (Pneumonia). In the obtained results, the proposed deep learning model can detect the COVID-19 positive cases in  ≤  2 seconds which is faster than RT-PCR tests currently being used for detection of COVID-19 cases. We have also established a relationship between COVID-19 patients along with the Pneumonia patients which explores the pattern between Pneumonia and COVID-19 radiology images. In all the experiments, we have used the Grad-CAM based color visualization approach in order to clearly interpretate the detection of radiology images and taking further course of action.

SWEET Genes for Disease Resistance in Plants

Sugar transporters called SWEETs are utilized by plants for a variety of functions. Invading pathogens utilize them for the supply of nutrition, thus rendering the host susceptible, as shown in several plant species. Therefore, naturally occurring and genetically manipulated SWEET gene variants are being deployed for the development of resistant crop cultivars.

Application of deep learning for fast detection of COVID-19 in X-Rays using nCOVnet

Presently, COVID-19 has posed a serious threat to researchers, scientists, health professionals, and administrations around the globe from its detection to its treatment. The whole world is witnessing a lockdown like situation because of COVID-19 pandemic. Persistent efforts are being made by the researchers to obtain the possible solutions to control this pandemic in their respective areas. One of the most common and effective methods applied by the researchers is the use of CT-Scans and X-rays to analyze the images of lungs for COVID-19. However, it requires several radiology specialists and time to manually inspect each report which is one of the challenging tasks in a pandemic. In this paper, we have proposed a deep learning neural network-based method nCOVnet, an alternative fast screening method that can be used for detecting the COVID-19 by analyzing the X-rays of patients which will look for visual indicators found in the chest radiography imaging of COVID-19 patients.

Genome-wide analysis of H3K4me3 and H3K27me3 modifications due to Lr28 for leaf rust resistance in bread wheat (Triticum aestivum)

Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.

The progress of leaf rust research in wheat

Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.

QTL analysis and fine mapping of a QTL for yield-related traits in wheat grown in dry and hot environments

Genetic control of grain yield and phenology was examined in the Excalibur/Kukri doubled haploid mapping population grown in 32 field experiments across the climatic zones of southern Australia, India and north-western Mexico where the wheat crop experiences drought and heat stress. A total of 128 QTL were identified for four traits: grain yield, thousand grain weight (TGW), days to heading and grain filling duration. These QTL included 24 QTL for yield and 27 for TGW, showing significant interactions with the environment (Q * E). We also identified 14 QTL with a significant, small main effects on yield across environments. The study focussed on a region of chromosome 1B where two main effect QTL were found for yield and TGW without the confounding effect of phenology. Excalibur was the source of favourable alleles: QYld.aww-1B.2 with a peak at 149.5-150.1 cM and QTgw.aww-1B at 168.5-171.4 cM. We developed near isogenic lines (NIL) for the interval including QYld.aww-1B.2 and QTgw.aww-1B and evaluated them under semi-controlled conditions. Significant differences in four pairs of NIL were observed for grain yield but not for TGW, confirming a positive effect of the Excalibur allele for QYld.aww-1B.2. The interval containing QYld.aww-1B.2 was narrowed down to 2.9 cM which corresponded to a 2.2 Mbp genomic region on the chromosome 1B genomic reference sequence of cv. Chinese Spring and contained 39 predicted genes.

Multi-Locus Genome Wide Association Mapping for Yield and Its Contributing Traits in Hexaploid Wheat under Different Water Regimes

Multi-locus genome wide association study was undertaken using a set of 320 diverse spring wheat accessions, which were each genotyped for 9,626 SNPs. The association panel was grown in replicated trials in four environments [two each in irrigated (IR) and rainfed (RF) environments], and phenotypic data were recorded for five traits including days to heading, days to maturity, plant height, thousand grain weight and grain yield. Forty-six significant marker-trait associations (MTAs) were identified for five traits. These included 20 MTAs in IR and 19 MTAs in RF environments; seven additional MTAs were common to both the environments. Five of these MTAs were co-localized with previously known QTL/MTAs and the remaining MTAs were novel and add to the existing knowledge. Three desirable haplotypes for agronomic traits, one for improvement in RF environment and two for improvement in IR environment were identified. Eighteen (18) promising candidate genes (CGs) involved in seven different biological activities were also identified. The expression profiles of four (Trehalose-6-Phosphate, APETALA2/Ethylene-responsive factor, DNA-binding One Zinc Finger and Gibberellin-dioxygenases) of the 18 genes showed that they were induced by drought stress in the wheat seedlings. The MTAs, haplotypes and CG-based markers may be used in marker-assisted breeding for drought tolerance in wheat.

A case report of carcinoma of uterine cervix throwing heterochronous metastasis to the skin, spleen, and pancreas: the role of multimodality treatment approach

BACKGROUND

Cancer of cervix often fails locally and/or within the pelvis. One to two percent of cervical squamous cell carcinoma patients have lung metastases at presentation, and 5-35% develop pulmonary metastases later on. Common sites of metastases are the liver, bone, and bowel. We report a rare case presentation of cervical squamous cell cancer where heterochronous metastasis occurred in the skin, spleen, and pancreas without loco-regional recurrence and skipping of visceral organs such as the lung, liver, and brain.

CASE PRESENTATION

A 55-year-old, postmenopausal lady presented with a complaint of bleeding of the vagina for 2 months duration. Cervical biopsy revealed squamous cell carcinoma of the cervix, and she was staged as a case of FIGO stage IIIB. She received external beam-beam radiotherapy of 50 Gy in 25 fractions along with concurrent weekly cisplatin at 35 mg/m² followed by 3 fractions of intracavitary brachytherapy of 6 Gy each. After 30 months of follow-up, she presented with a skin lesion of 6 × 5 cm² in the infrascapular region for 2 months duration. Biopsy revealed metastatic squamous cell carcinoma. Her metastatic work-up revealed no other lesions. Palliative radiotherapy to local site of 8 Gy in single fraction was delivered. The lesion disappeared within 4 weeks. She was given 6 cycles of cisplatin and paclitaxel salvage chemotherapy. After 30 months of follow-up, she presented with a skin lesion of 6 × 5 cm² in the infrascapular region. Biopsy revealed metastatic squamous cell carcinoma. Her metastatic work-up revealed no other lesions. Palliative radiotherapy to the local site was planned, and a dose of 8 Gy in a single fraction was delivered. The lesion disappeared within 4 weeks. She was given 6 cycles of cisplatin and paclitaxel salvage chemotherapy. Six months after the completion of salvage therapy, she reported with the complaints of recurrent bouts of hematemesis and melena. Her CECT scan revealed 2 × 1.5 cm² growth in the body of the pancreas and a subcentric splenic hilum node. She underwent open splenectomy with distal pancreatectomy. Histopathology report showed metastatic infiltration in pancreatic tissue by squamous cell carcinoma and one metastatic node in the splenic hilum. Post-treatment, 6 months, the patient was asymptomatic with no recurrence.

CONCLUSIONS

This is a rare heterochronous metastatic presentation of cervical cancer without loco-regional recurrence and visceral organs such as the lung, liver, and brain. The optimal treatment remains undefined for these patients. Multimodality treatment is necessary to manage the patients.

Further studies on sugar transporter (SWEET) genes in wheat (Triticum aestivum L.)

SWEET proteins represent one of the largest sugar transporter family in the plant kingdom and play crucial roles in plant development and stress responses. In the present study, a total of 108 TaSWEET genes distributed on all the 21 wheat chromosomes were identified using the latest whole genome sequence (as against 59 genes reported in an earlier report). These 108 genes included 14 of the 17 types reported in Arabidopsis and also included three novel types. Tandem duplications (22) and segmental duplications (5) played a significant role in the expansion of TaSWEET family. A number of cis-elements were also identified in the promoter regions of TaSWEET genes, indicating response of TaSWEET genes during development and also during biotic/abiotic stresses. The TaSWEET proteins carried 4-7 trans-membrane helices (TMHs) showing diversity in structure. Phylogenetic analysis using SWEET proteins of wheat and 8 other species gave four well-known clusters. Expression analysis involving both in silico and in planta indicated relatively higher expression of TaSWEET genes in water/heat sensitive and leaf rust resistant genotypes. The results provided insights into the functional role of TaSWEETs in biotic and abiotic stresses, which may further help in planning strategies to develop high yielding wheat varieties tolerant to environmental stresses.

H3K4/K9 acetylation and Lr28-mediated expression of six leaf rust responsive genes in wheat (Triticum aestivum)

Development of leaf rust-resistant cultivars is a priority during wheat breeding, since leaf rust causes major losses in yield. Resistance against leaf rust due to Lr genes is partly controlled by epigenetic modifications including histone acetylation that is known to respond to biotic/abiotic stresses. In the present study, enrichment of H3K4ac and H3K9ac in promoters of six defense responsive genes (N-acetyltransferase, WRKY 40, WRKY 70, ASR1, Peroxidase 12 and Sarcosine oxidase) was compared with their expression in a pair of near-isogenic lines (NILs) for the gene Lr28 following inoculation with leaf rust pathotype '77-5'; ChIP-qPCR was used for this purpose. The proximal and distal promoters of these genes contained a number of motifs that are known to respond to biotic stresses. The enrichment of two acetylation marks changed with passage of time; changes in expression of two of the six genes (N-acetyltransferase and peroxidase12), largely matched with changes in H3K4/H3K9 acetylation patterns of the two promoter regions. For example, enrichment of both the marks matched with higher expression of N-acetyltransferase gene in susceptible NIL and the deacetylation (H3K4ac) largely matched with reduced gene expression in resistant NIL. In peroxidase12, enrichment of H3K4ac and H3K9ac largely matched with higher expression in both the NILs. In the remaining four genes, changes in H3 acetylation did not always match with gene expression levels. This indicated complexity in the regulation of the expression of these remaining four genes, which may be controlled by other epigenetic/genetic regulatory mechanisms that need further analysis.

A study of transcriptome in leaf rust infected bread wheat involving seedling resistance gene Lr28

Leaf rust disease causes severe yield losses in wheat throughout the world. During the present study, high-throughput RNA-Seq analysis was used to gain insights into the role of Lr28 gene in imparting seedling leaf rust resistance in wheat. Differential expression analysis was conducted using a pair of near-isogenic lines (NILs) (HD 2329 and HD 2329+Lr28) at early (0h before inoculation (hbi), 24 and 48h after inoculation (hai)) and late stages (72, 96 and 168 hai) after inoculation with a virulent pathotype of pathogen Puccinia triticina. Expression of a large number of genes was found to be affected due to the presence/absence of Lr28. Gene ontology analysis of the differentially expressed transcripts suggested enrichment of transcripts involved in carbohydrate and amino acid metabolism, oxidative stress and hormone metabolism, in resistant and/or susceptible NILs. Genes encoding receptor like kinases (RLKs) (including ATP binding; serine threonine kinases) and other kinases were the most abundant class of genes, whose expression was affected. Genes involved in reactive oxygen species (ROS) homeostasis and several genes encoding transcription factors (TFs) (most abundant being WRKY TFs) were also identified along with some ncRNAs and histone variants. Quantitative real-time PCR was also used for validation of 39 representative selected genes. In the long term, the present study should prove useful in developing leaf rust resistant wheat cultivars through molecular breeding.

A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants

Cereals are key contributors to global food security. Genes involved in the uptake (transport), assimilation and utilization of macro- and micronutrients are responsible for the presence of these nutrients in grain and straw. Although many genomic databases for cereals are available, there is currently no cohesive web resource of manually curated nutrient use efficiency (NtUE)-related genes and quantitative trait loci (QTLs). In this study, we present a web-resource containing information on NtUE-related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops (wheat ( Triticum aestivum), rice ( Oryza sativa), maize ( Zea mays), barley ( Hordeum vulgare)), two alien species related to wheat ( Triticum urartu and Aegilops tauschii), and two model species ( Brachypodium distachyon and Arabidopsis thaliana). Gene annotations integrated in the current web resource were manually curated from the existing databases and the available literature. The primary goal of developing this web resource is to provide descriptions of the NtUE-related genes and their functional annotation. MicroRNAs targeting some of the NtUE related genes and the QTLs for NtUE-related traits are also included. The genomic information embedded in the web resource should help users to search for the desired information.

Differential Hepatotoxic Effects of Sodium Valproate at Different Doses in Albino Rats

Background Liver plays an essential role for transforming and clearing chemicals that may cause harmful effects to it. Sodium Valproate, renowned to be a potent antiepileptic drug, when taken in overdose may cause toxic effects to liver and other organs as well. Liver damage can be assessed with histological changes and measurement of enzymes produced by it. Objective To investigate the histological changes induced by different doses of Sodium Valproate ranging from 100-500 mg/kg/day and observe its correlation with liver enzymes level in serum. Method Three-months old albino rats were divided into six groups, five in each. Control group was treated with normal saline and rest five groups with Sodium Valproate in different doses 100, 200, 300, 400 and 500 mg/kg/day respectively. Then, liver of those experimented rats were examined histologically under the light microscope. Furthermore, Liver enzymes; Alanine Transaminase and Aspartate transaminase were measured to assess the micro-anatomical changes in liver. Result Distorted hepatic lobular architecture with aggregations of nuclei at certain interval was observed in the groups of higher doses; 300 mg/kg/day and above. However, accumulation of adipocytes was observed in all the Sodium Valproate treated rats unlike the control group. When compared the enzyme levels among the groups, it was found to be significantly increased in dose dependent manner. Besides, it also showed skin lesions in all rats treated with the dose 400 mg/kg/day and above. Conclusion Higher doses of Sodium Valproate; 300 mg/kg/day and above induces hepatotoxicity and skin lesions in adult albino rats.

Noninvasive assessment of cutaneous alterations in mice exposed to whole body gamma irradiation using optical imaging techniques

We report the results of a study carried out to investigate the potential of optical techniques such as optical coherence tomography, Mueller matrix spectroscopy, and cross-polarization imaging for noninvasive monitoring of the ionizing radiation exposure-induced alterations in cutaneous tissue of mice. Radiation dose-dependent changes were observed in tissue microvasculature and tissue optical parameters like retardance and depolarization as early as 1 h post radiation exposure. Results suggest that these optical techniques may allow early detection of radiation dose-dependent alterations which could help in screening of population exposed to radiation.

Fabrication of Pliable Biodegradable Polymer foams to Engineer Soft Tissues

We have fabricated pliable, porous, biodegradable scaffolds with poly(lactic-co-glycolic acid) (PLGA) and poly(ethylene glycol) (PEG) blends using a solvent-casting and particulate-leaching technique. Our study investigated the effects of four different processing parameters on pliability and pore morphology of the biodegradable scaffolds. The parameters investigated were the PLGA copolymer ratio, the PLGA/PEG blend ratio, the initial salt weight fraction, and the salt particle size. A wide range of shear moduli (0.59 to 9.55 MPa), porosities (0.798 to 0.942), and median pore diameters (71 to 154 μm) was able to be achieved by varying the combination of these parameters. Our study indicates that initial salt weight fraction and PLGA/PEG blend ratio have the most significant effects on the physico-mechanical properties of the scaffolds. Enhanced pliability of the three dimensional foams made with blends of PLGA and PEG is evidenced by the ability to roll them into a tube without macroscopic damage to the scaffold. Pliable polymer substrates hold great promise for regeneration of soft tissues such as skin, or those requiring a tubular conformation such as intestine or vascular grafts.

Effect of Yb doping on the refractive index and thermo-optic coefficient of YVO4 single crystals

Single crystals of YVO₄ with different doping concentrations of Yb (1.5, 3.0, 8.0, and 15.0 at. %) and with good crystalline quality (FWHM ∼43-55 arc sec of rocking curve) were grown by the optical floating zone technique. Refractive index measurements were carried out at four wavelengths as a function of temperature. The measurements show that as the doping concentration of Yb is increased, the refractive index varies marginally for n_e whereas there is a significant change in the value of n_o. The thermo-optic coefficient (dn/dT) was found to be positive with a value ∼10^-5/°C, which is 1 order higher than that for the undoped YVO₄ crystal. The thermo-optic coefficient is higher for n_e compared to that of n_o. Also, a set of relations describing the wavelength dependence of the thermo-optic coefficient were established that are useful for calculating the thermo-optic coefficient at any temperature in the range 30°C-150°C and at any wavelength in the range 532-1551 nm.

A comparative study on the effect of Curcumin and Chlorin-p6 on the transport of the LDS cation across a negatively charged POPG bilayer: Effect of pH

We report the use of interface selective Second Harmonic generation technique to investigate the transport of the LDS cation across POPG liposomes in the pH range of 4.0 to 8.0 in the presence and absence of two amphiphilic drugs, Curcumin and Chlorin-p₆ (Cp₆). Our results show that bilayer permeability of liposomes is significantly affected by the presence of the drugs and pH of the medium as evidenced by significant changes in the transport kinetics of the LDS. Studies carried out in the pH range 4.0-8.0 show that while Cp₆ significantly enhanced the transport of LDS at pH4.0, the transport of the cation was seen to increase with increasing pH, with maximum effect at pH7.4 for Curcumin. The pH dependent bilayer localization of both the drugs was investigated by conducting steady state FRET studies using DPH labeled lipids as donors. The FRET results and the relative population of the various ionic/nonionic species of the drugs at different pH suggest that distance dependent interaction between the various ionic species of the drugs and polar head groups of the lipid is responsible for the observed pH dependence enhancement of the drug induced membrane permeability. Another interesting observation was that the stability of Curcumin in presence of POPG liposomes was observed to degrade significantly near physiological pH (7.4 and 8.0). Although this degradation did not affect the liposome integrity, interestingly this was observed to enhance the transport of the LDS cation across the bilayer. That the degradation products of Curcumin are equally effective as the drug itself in enhancing the membrane permeability lends additional support to the current opinion that the bioactive degradation products of the drug may have a significant contribution to its observed pharmacological effects.

Comparative Analysis of AGPase Genes and Encoded Proteins in Eight Monocots and Three Dicots with Emphasis on Wheat

ADP-glucose pyrophosphorylase (AGPase) is a heterotetrameric enzyme with two large subunits (LS) and two small subunits (SS). It plays a critical role in starch biosynthesis. We are reporting here detailed structure, function and evolution of the genes encoding the LS and the SS among monocots and dicots. "True" orthologs of maize Sh2 (AGPase LS) and Bt2 (AGPase SS) were identified in seven other monocots and three dicots; structure of the enzyme at protein level was also studied. Novel findings of the current study include the following: (i) at the DNA level, the genes controlling the SS are more conserved than those controlling the LS; the variation in both is mainly due to intron number, intron length and intron phase distribution; (ii) at protein level, the SS genes are more conserved relative to those for LS; (iii) "QTCL" motif present in SS showed evolutionary differences in AGPase belonging to wheat 7BS, T. urartu, rice and sorghum, while "LGGG" motif in LS was present in all species except T. urartu and chickpea; SS provides thermostability to AGPase, while LS is involved in regulation of AGPase activity; (iv) heterotetrameric structure of AGPase was predicted and analyzed in real time environment through molecular dynamics simulation for all the species; (v) several cis-acting regulatory elements were identified in the AGPase promoters with their possible role in regulating spatial and temporal expression (endosperm and leaf tissue) and also the expression, in response to abiotic stresses; and (vi) expression analysis revealed downregulation of both subunits under conditions of heat and drought stress. The results of the present study have allowed better understanding of structure and evolution of the genes and the encoded proteins and provided clues for exploitation of variability in these genes for engineering thermostable AGPase.

Effect of Bilayer Partitioning of Curcumin on the Adsorption and Transport of a Cationic Dye Across POPG Liposomes Probed by Second-Harmonic Spectroscopy

The effect of Curcumin partitioning into the bilayer during the adsorption and transport of a cationic dye, LDS, across a negatively charged POPG bilayer was investigated by the interface-selective second-harmonic (SH) spectroscopic technique. The intensity of SH electric field (E_2ω) arising due to LDS adsorbed on the outer bilayer of the POPG liposome was observed to increase instantaneously (<1 s) following the addition of Curcumin. The fractional increase in the SH electric field (E^f_2ω) and the bilayer transport rates (k_T) of LDS were studied with respect to the pH of the solution and also with the Curcumin content in the lipid bilayer. Results obtained indicate that compared with the anionic form of the drug, its neutral form is more conducive of increasing the E^f_2ω of LDS. With increasing Curcumin content in the lipid bilayer, two distinct regimes could be observed in terms of E^f_2ω and k_T values of LDS. For Curcumin:Lipid (C/L) ratio ≤0.02, the E^f_2ω of LDS increases rapidly, while k_T remains unchanged; and for C/L ratio ≥0.02, the E^f_2ω values remains more or less constant, while there is a significant (∼40 times) increase followed by a modest increase in the k_T values of LDS. The observed results support an earlier two-state binding model of Curcumin with the POPG bilayer. In addition, it is further proposed that at low C/L ratio Curcumin binds to the surface of the bilayer replacing the counterions (Na⁺) bound to the lipid head groups, which changes the bilayer surface charge density, thereby causing more LDS cations to adsorb on the bilayer surface. At high C/L ratio, Curcumin intercalates within the hydrophobic domain of the bilayer, altering its hydrophobicity and inducing enhanced transport of the LDS cation. Results presented in this work provide further insights into how Curcumin alters bilayer properties when it partitions from the aqueous to the bilayer phase.

Synthesis and characterization of carboxymethyl cellulose from office waste paper: a greener approach towards waste management

In the present study, functionalization of mixed office waste (MOW) paper has been carried out to synthesize carboxymethyl cellulose, a most widely used product for various applications. MOW was pulped and deinked prior to carboxymethylation. The deinked pulp yield was 80.62 ± 2.0% with 72.30 ± 1.50% deinkability factor. The deinked pulp was converted to CMC by alkalization followed by etherification using NaOH and ClCH2COONa respectively, in an alcoholic medium. Maximum degree of substitution (DS) (1.07) of prepared CMC was achieved at 50 °C with 0.094 M and 0.108 M concentrations of NaOH and ClCH2COONa respectively for 3h reaction time. The rheological characteristics of 1-3% aqueous solution of optimized CMC product showed the non-Newtonian pseudoplastic behavior. Fourier transform infra red (FTIR), nuclear magnetic resonance (NMR) and scanning electron microscope (SEM) study were used to characterize the CMC product.

Trends in antimicrobial susceptibility of Salmonella Typhi from North India (2001-2012)

PURPOSE

Enteric fever is endemic in India with Salmonella Typhi being the major causative agent. Antibiotic therapy constitutes the mainstay of management. The present study was undertaken to find the susceptibility profile of Salmonella enterica var Typhi (S. Typhi) blood isolates in a tertiary care hospital between January 2001 and December 2012.

MATERIALS AND METHODS

A retrospective analysis of laboratory records was carried out. Conventional blood culture method was used until 2009; from January 2010 onwards BACTEC 9240 system has been in use. Salmonella were confirmed by serotyping using group and type specific antisera. Antibiotic susceptibility was performed using the disk diffusion method. In addition 116 isolates were subjected to minimum inhibitory concentration testing for chloramphenicol, ciprofloxacin, amoxicillin and nalidixic acid (NA) using agar dilution and for ceftriaxone and azithromycin using E-strips (Biomerieux).

RESULT

A total of 1016 typhoidal salmonellae were obtained. The predominant serotype obtained was S. Typhi (852, 83.8%) followed by Salmonella enterica var Paratyphi A (164, 16.2%). We observed a re-emergence of susceptibility to first line antibiotics and a notable decline in multidrug resistant (MDR) strains. We also found all recent isolates resistant to NA and susceptible to third generation cephalosporins and 84.5% of isolates having decreasing ciprofloxacin susceptibility using revised criteria as per Clinical and Laboratory Standards Institute 2012 guidelines.

CONCLUSION

There has been re-emergence of susceptibility to first line antibiotics and a notable decline in MDR strains of S. Typhi. We have a very high resistance to NA and decreasing susceptibility to ciprofloxacin. Third generation cephalosporins and azithromycin seem to be effective therapeutic options. Judicious use of these antibiotics is mandatory to prevent emergence of resistant strains.

Acute inhalation toxicity of smoke of fentanyl and its 1-substituted analogs in Swiss albino mice

Fentanyl (N-(1-phenethyl-4-piperidinyl)propionanilide) is a synthetic, potent narcotic analgesic agent. However, it is known to have several side effects, which led to synthesis and evaluation of its new analogs for the management of pain. We have earlier reported the comparative bioassay of fentanyl and its eight 1-substituted analogs (1-8) in mice. Three compounds, viz., N-(1-(2-phenoxyethyl)-4-piperidinyl)propionanilide (2), N-isopropyl-3-(4-(N-phenylpropionamido)piperidin-1-yl)propanamide (5), and N-t-butyl-3-(4-(N-phenylpropionamido)piperidin-1-yl)propanamide (6) were found to be more effective and less toxic compared to fentanyl. The present study reports the comparative acute inhalation toxicity of smoke of fentanyl and its three analogs, viz., 2, 5, and 6 in mice. Animals were exposed to different concentrations of smoke generated by heating the compounds. Exposure was performed in a head only all glass static exposure assembly for 15 min to determine the median lethal concentration (LC50). The breathing pattern and various respiratory parameters of the animals were also monitored online using a polygraph. Out of three compounds tested, analog 5 was found to be most toxic (LC50 = 2820 mg/m3) while 2 was least toxic (LC50 = >8000 mg/m3). All the compounds caused long lasting respiratory depression in a dose-dependent manner, which did not completely resolve even after discontinuation of exposure. Aerodynamic median diameter and geometric standard deviation of smoke particles was determined employing eight-stage Andersen sampler. The particles were found to be within the respirable range. The study, however, concludes that due to possible decomposition of the compounds by heating or its poor absorption by the alveolar surface, the present inhalation technique cannot be employed to generate smoke of fentanyl and its analogs for any medical or surreptitious use.

Development of a simple method for the rapid identification of organisms causing anthrax by coagglutination test

A protective antigen (PA) based coagglutination test was optimized in the present study for the specific and sensitive identification of bacteria causing anthrax in a cost effective and less risky manner. The test showed 100% specificity and sensitivity up to 9 × 10(3) formalinized vegetative cells or 11 ng of PA. The optimized test also detected anthrax toxin directly from the serum as well as blood of anthrax infected animals indicating the potential application for direct diagnosis of anthrax under field conditions.

Immune responses and protective efficacy of recombinant outer membrane protein R (rOmpR)-based vaccine of Aeromonas hydrophila with a modified adjuvant formulation in rohu (Labeo rohita)

Despite the importance and success of developing a candidate vaccine against Aeromonas hydrophila infection in fish, little is known about the molecular mechanisms of the vaccine-induced immunoprotection in Indian major carp, Labeo rohita, primarily due to lack of information on most of the immune related genes of the species. In this study, a novel candidate antigen recombinant outer membrane protein R (rOmpR) of A. hydrophila was evaluated as a vaccine candidate along with a modified adjuvant formulation. Protective efficacy of the rOmpR immunization was assessed in terms of survival against A. hydrophila challenge as well as modulation of immune response in vaccinated fish after 1, 3, 6, 12, 24, 72 h and 10 days post-injection (using immune gene expression analysis) and 10, 28, 56 and 140 days post-injection (serum immune parameter analysis). The generated immune response was compared with a formalin-killed A. hydrophila antigen preparation using mineral oil only and modified adjuvant alone. We report a variable up-regulation of the immune-related genes viz., lysozyme G, complement factor 4, immunoglobulin M, β2-microglobulin, major histocompatibility complex I and II, and interleukin-1β in anterior kidney and spleen tissues at early time points post-immunization in all the groups, when compared to the control fish. The vaccinated fish also showed an increase in serum natural hemolysin titer, lysozyme and myeloperoxidase activities, and antibody titer irrespective of vaccine formulations as compared to control fish on days 10, 28 and 56. However, the increase in the serum parameters was more pronounced on day 140 in rOmpR-modified adjuvant injected group, indicating the modulatory role of this new vaccine formulation. Upon challenge with live A. hydrophila on days 56 and 140 post-immunization, significantly reduced percent mortality was noted in the group immunized with modified adjuvant based rOmpR vaccine formulation. Taken together, our results suggest that rOmpR along with modified adjuvant could potentially be used as a vaccine formulation to handle A. hydrophila infection on a long-term basis.

Hyper-Rayleigh scattering from gold nanoparticles: effect of size and shape

We report hyper-Rayleigh scattering (HRS) properties of gold nanoparticles (GNPs) of five different shapes, quasi-spherical (∼10 and ∼20 nm diameter), rod (aspect ratio ∼2), and branched shapes, tetrapod, flower and star with 800 nm, 150 fs laser excitation. Using ∼10 nm spherical GNPs as reference, the first hyperpolarizability (β) values were calculated for all other shapes. Star and flower shaped GNPs have the highest hyperpolarizability (∼130 and ∼52 times higher, respectively), while rod and tetrapod shaped GNPs only have modest enhancement (∼7 times), which is similar to ∼20 nm size quasi-spherical particles. These enhancements are attributed to reduced symmetry as well as the presence of sharp tips on GNP surface. When the β values are normalized with respect to the number of atoms per particle, the flower and star shaped GNPs still have the highest hyperpolarizability values. The polar plots of vertically polarized HRS signal as a function of the angle of polarization of the incoming incident light shows two lobes, indicating that excitation is predominantly dipolar in nature although the size of some GNPs are big enough to show a quadrupolar response. It is believed that the presence of sharp tips at the surface of these large sized GNPs is responsible for the observed dipolar response. This study shows that GNPs having sharp tips might be a better candidate when their nonlinear properties are used for sensing applications.

Association mapping in crop plants: opportunities and challenges

The research area of association mapping (AM) is currently receiving major attention for genetic studies of quantitative traits in all major crops. However, the level of success and utility of AM achieved for crop improvement is not comparable to that in the area of human health care for diagnosis of complex human diseases. These AM studies in plants, as in humans, became possible due to the availability of DNA-based molecular markers and a variety of sophisticated statistical tools that are evolving on a regular basis. In this chapter, we first briefly review the significance of a variety of populations that are used in AM studies, then briefly describe the molecular markers and high-throughput genotyping strategies, and finally describe the approaches used for AM studies. The major part of the chapter is, however, devoted to analysis of reasons why the results of AM have been underutilized in plant breeding. We also examine the opportunities available and challenges faced while using AM for crop improvement programs. This includes a detailed discussion of the issues that have plagued AM studies, and the solutions that have become available to deal with these issues, so that in future, the results of AM studies may prove increasingly fruitful for crop improvement programs.

DTI correlates of cognition in conventional MRI of normal-appearing brain in patients with clinical features of subacute combined degeneration and biochemically proven vitamin B(12) deficiency

BACKGROUND AND PURPOSE

Vitamin B12 deficiency may cause neural injury that results in cognitive deficits. The main purpose of our study was to evaluate morphometric and microstructural changes in the brain and relate them to cognition in subacute combined degeneration of the spinal cord and patients with biochemically deficient vitamin B12.

MATERIALS AND METHODS

Fifty-one patients were recruited and underwent nerve-conduction velocity tests and routine hematologic examinations. Serum vitamin B12 and homocystine levels were also measured. All patients and 46 age- and sex-matched controls underwent cervical spine and brain MR imaging along with cognition tests. MR imaging included conventional scans and DTI. Voxel-based morphometry was performed for determining the WM and GM volumes, based on T1-weighted images. DTI measures that included fractional anisotropy, ADC, radial diffusivity, and axial diffusivity were determined by using tract-based statistics.

RESULTS

None of the patients showed any abnormality on conventional MR imaging. No significant changes in GM and WM volumes were observed in patients compared with controls. Significant reductions in the fractional anisotropy and an increase in ADC and radial diffusivity values were observed in multiple brain regions in patients compared with controls. These changes were confirmed on the region-of-interest analysis. Neuropsychological scores were significantly different in patients compared with controls and showed significant correlation with fractional anisotropy and radial diffusivity in a few brain regions.

CONCLUSIONS

Microstructural changes are seen in WM regions on DTI in patients with vitamin B12 deficiency and correlate with cognition scores. DTI can be used for objective assessment of microstructural changes in the brain in vitamin B12 deficiency.