Exploring the association between long-term MODIS aerosol and air pollutants data across the Northern Great Plains through machine learning analysis

Aerosol optical depth (AOD) and Ångström exponent (AE) are the major environmental indicators to perceive air quality and the impact of aerosol on climate change and health as well as the global atmospheric conditions. In the present study, an average of AOD and AE data from Tera and Aqua satellites of MODIS sensors has been investigated over 7 years i.e., from 2016 to 2022, at four locations over Northern Great Plains. Both temporal and seasonal variations over the study periods have been investigated to understand the behavior of AOD and AE. Over the years, the highest AOD and AE were observed in winter season, varying from 0.75 to 1.17 and 1.30 to 1.63, respectively. During pre-monsoon season, increasing trend of AOD varying from 0.65 to 0.95 was observed from upper (New Delhi) to lower (Kolkata) Gangetic plain, however, during monsoon and post-monsoon a reverse trend varying from 0.85 to 0.65 has been observed. Seasonal and temporal aerosol characteristics have also been analyzed and it has been assessed that biomass burning was found to be the major contributor, followed by desert dust at all the locations except in Lucknow, where the second largest contributor was dust instead of desert dust. During season-wise analysis, biomass burning was also found to be as the major contributor at all the places in all the seasons except New Delhi and Lucknow, where dust was the major contributor during pre-monsoon. A boosting regression algorithm was done using machine learning to explore the relative influence of different atmospheric parameters and pollutants with PM2.5. Water vapor was assessed to have the maximum relative influence i.e., 51.66 % followed by CO (21.81 %). This study aims to help policy makers and decision makers better understand the correlation between different atmospheric components and pollutants and the contribution of different types of aerosols.

Statistical estimation of noise induced hearing loss among the drivers in one of the most polluted cities of India

In the present study, an attempt has been made to assess the impact of vehicular noise upon the 3-wheeler tempo drivers and to know whether there is any relationship between hearing loss and cumulative noise exposure. For this purpose, 3-wheeler tempo drivers (Exposed group) and non-commercial light motor vehicle car drivers (Unexposed group) were chosen as study subjects. Three traffic routes were selected to assess the noise level during waiting and running time in the exposed and unexposed groups. Among all three routes, the highest mean noise level (Leq) was observed on the Chowk to Dubagga route for waiting and en-route noise measurement. It was measured as 84.13 dB(A) and 86.36 dB(A) for waiting and en-route periods of 7.68 ± 3.46 and 31.05 ± 6.6 min, respectively. Cumulative noise exposure was found to be significantly different (p < 0.001) in all age groups of exposed and unexposed drivers. Audiometric tests have been performed over both exposed and unexposed groups. The regression analysis has been done keeping hearing loss among tempo drivers as the dependent variable and age (years) and Energy (Pa2 Hrs) as the independent variable using three different criteria of hearing loss definitions, i.e., World Health Organization, National Institute for Occupational Safety and Health (NIOSH), Occupational Safety and Health Administration criteria. Among these three criteria, the NIOSH criterion of hearing loss best explained the independent variables. It could explain the total variation in dependent variable by independent variable quite well, i.e., 68.1%. The finding showed a linear relationship between cumulative noise exposures (Pa2 Hrs) and the exposed group's hearing loss (dB), i.e., hearing loss increases with increasing noise dose. Based on the findings, two model equations were developed to identify the safe and unsafe noise levels with exposure time.

Development, performance evaluation, and kinetic studies of microbial fuel cell based auto dripping bioelectrochemical reactor (AutoDriBER) for urine treatment

A bioelectrochemical reactor is an assembly, which facilitates energy generation and resource recovery using electrochemically active microorganisms. To maximise energy production from wastewater in this bioreactor system special design is required. Therefore, in the present study, continuous flow auto dripping bioelectrochemical reactors (AutoDriBERs) were developed as a single and multi-electrode assembly for urine treatment. Further, their performance was assessed by connecting reactors in series and parallel arrangements. AutoDriBER configured in series connection showed the highest 93.64 ± 1.57% chemical oxygen demand removal rate with the 1.38 ± 0.64 V voltage and 2.54 W m-3 polarisation power density. The optimum flow rate for maximum voltage production was tested with various models i.e. the linear, exponential, Sweibull-1, and Sweibull-2 models to confirm voltage prediction and its validity. The Linear and exponential models were found best fitted for voltage production with R2 value of 0.999. These findings infer a novel approach toward optimisation of the complex, inexpensive and self-sufficient design for electricity generation from energy-rich urine wastewater in rural areas.

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.

Advances in bioelectrochemical systems for bio-products recovery

Bioelectrochemical systems (BES) have emerged as a sustainable and highly promising technology that has garnered significant attention from researchers worldwide. These systems provide an efficient platform for the removal and recovery of valuable products from wastewater, with minimal or no net energy loss. Among the various types of BES, microbial fuel cells (MFCs) are a notable example, utilizing microbial biocatalytic activities to generate electrical energy through the degradation of organic matter. Other BES variants include microbial desalination cells (MDCs), microbial electrolysis cells (MECs), microbial electrosynthesis cells (MXCs), microbial solar cells (MSCs), and more. BESs have demonstrated remarkable potential in the recovery of diverse products such as hydrogen, methane, volatile fatty acids, precious nutrients, and metals. Recent advancements in scaling up BESs have facilitated a more realistic assessment of their net energy recovery and resource yield in real-world applications. This comprehensive review focuses on the practical applications of BESs, from laboratory-scale developments to their potential for industrial commercialization. Specifically, it highlights successful examples of value-added product recovery achieved through various BES configurations. Additionally, this review critically evaluates the limitations of BESs and provides suggestions to enhance their performance at a larger scale, enabling effective implementation in real-world scenarios. By providing a thorough analysis of the current state of BES technology, this review aims to emphasize the tremendous potential of these systems for sustainable wastewater treatment and resource recovery. It underscores the significance of bridging the gap between laboratory-scale achievements and industrial implementation, paving the way for a more sustainable and resource-efficient future.

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.

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.

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.

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.

Spatio-temporal assessment of ambient air quality, their health effects and improvement during COVID-19 lockdown in one of the most polluted cities of India

The present work aims to investigate seasonal variations in air pollution levels in Lucknow and assess the ambient air quality of the city together with highlighting the health impacts of major pollutants like PM₁₀, PM_2.5, SO₂, NO₂, Pb, Ni and aerosols from 2010 to 2019. The maximum and minimum values of PM₁₀, PM_2.5, SO₂, NO₂, Pb and Ni were found to be 270.75 and 122.45 μg/m³, 124.95 and 95.52 μg/m³, 25.60 and 8.05 μg/m³, 75.65 and 23.85 μg/m³, 0.66 and 0.03 μg/m³ and 0.07 and 0.01 ng/m³, respectively. Health impact of particulate matter has also been assessed with AirQ+, and it was estimated that long-term exposure of PM₁₀ was attributed to between 37 and 48% for post-neonatal (age 1-12 months) mortality rate due to all causes, whereas long-term attributable proportions in mortality due to exposure of PM_2.5 were to about 19 to 28% from all causes. Further, an attempt has also been made to evaluate the impact of lockdown amid COVID-19 on the ambient air quality of Lucknow. During the lockdown, PM_2.5 levels reduced by 65% (at Gomti Nagar), 23% (at central school), 79% (at Lalbagh) and 35% (at Talkatora), due to which, air quality index of Gomti Nagar came down to 43, well below 50 which falls in the healthy range. NO₂ levels also came down. However, levels of SO₂ did not show significant reduction. Correlating the data between aerosol optical depth and Angstrom exponent by Pearson correlation analysis revealed a significant positive correlation (r = 0.65, P < 0.001).

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.

Near-field Communication (NFC)

Libraries are the central agencies for the dissemination of knowledge. Every library aspires to provide maximum opportunities to its users and ensure optimum utilization of available resources. Hence, libraries have been seeking technological aids to improve their services. Near-field communication (NFC) is a type of radio-frequency technology that allows electronics devices—such as computers, mobile phones, tags, and others—to exchange information wirelessly across a small distance. The aim of this paper is to explore NFC technology and its applications in modern era. The paper will discuss potential use of NFC in the advancement of traditional library management system.

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.

Association of hepcidin and anemia in early chronic kidney disease

Hepcidin is being extensively studied for anemia and inflammation in chronic kidney disease (CKD) patients. Hepcidin is thought to regulate iron metabolism by iron blockade through various mechanisms. Patients with CKD have early cardiac mortality due to anemia and subclinical inflammation; hence, we studied hepcidin as a biomarker in patients with early stage of CKD in relation to anemia and inflammation. In our cross-sectional study, a total of 80 patients were enrolled of whom, there were 25, 26, and 29 patients in CKD stages 1, 2, and 3, respectively. Patients were divided into normal iron level (39), functional iron deficiency (FID) (18), and absolute iron deficiency (AID) (23) based on transferrin saturation and ferritin. We found significantly high level of hepcidin (P <0.05) and high-sensitivity C-reactive protein (hsCRP) (P <0.05) in FID as compared to AID as well as normal iron level. We also found other inflammatory markers such as albumin, transferrin, and ferritin to be significantly associated with FID. In univariate analysis, hemoglobin (Hb) varied significantly with serum total iron-binding capacity (r = 0.40, P <0.001), log hsCRP (r = -0.32, P <0.01), and log ferritin (r = -0.23, P <0.05); however, Hb was not affected significantly with log hepcidin (r = -0.07, P >0.05). The study indicates that among early CKD patients with FID, there was high level of hepcidin along with other inflammatory parameters, which may be associated with poor cardiovascular disease outcome due to increased inflammation.

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.

Computational Models Accurately Predict Multi-Cell Biomarker Profiles in Inflammation and Cancer

Individual computational models of single myeloid, lymphoid, epithelial, and cancer cells were created and combined into multi-cell computational models and used to predict the collective chemokine, cytokine, and cellular biomarker profiles often seen in inflamed or cancerous tissues. Predicted chemokine and cytokine output profiles from multi-cell computational models of gingival epithelial keratinocytes (GE KER), dendritic cells (DC), and helper T lymphocytes (HTL) exposed to lipopolysaccharide (LPS) or synthetic triacylated lipopeptide (Pam3CSK4) as well as multi-cell computational models of multiple myeloma (MM) and DC were validated using the observed chemokine and cytokine responses from the same cell type combinations grown in laboratory multi-cell cultures with accuracy. Predicted and observed chemokine and cytokine responses of GE KER + DC + HTL exposed to LPS and Pam3CSK4 matched 75% (15/20, p = 0.02069) and 80% (16/20, P = 0.005909), respectively. Multi-cell computational models became ‘personalized’ when cell line-specific genomic data were included into simulations, again validated with the same cell lines grown in laboratory multi-cell cultures. Here, predicted and observed chemokine and cytokine responses of MM cells lines MM.1S and U266B1 matched 75% (3/4) and MM.1S and U266B1 inhibition of DC marker expression in co-culture matched 100% (6/6). Multi-cell computational models have the potential to identify approaches altering the predicted disease-associated output profiles, particularly as high throughput screening tools for anti-inflammatory or immuno-oncology treatments of inflamed multi-cellular tissues and the tumor microenvironment.

Panhypopituitarism- An unusual presenation of tuberculous meningitis

Pituitary gland involvement is a very rare entity of central nervous system tuberculosis. Tubercular meningitis (TBM) is a chronic meningitis on hypothalamic-pituitary axis which causes high morbidity and mortality hence it is the most dreaded form of extra pulmonary tuberculosis. Here we report a case of 24 year old female presenting with three months history of fever and headache along with altered sensorium since four days. There was also complain of secondary amenorrhea and generalised apathy. Neuroimaging revealed subependymal tuberculomas with meningitis and obstructive hydrocephalus. Cerebrospinal fluid (CSF) examination was also suggestive of tubercular meningitis. Endocrinological investigations showed multiple hormonal deficiencies manifesting as pituitary hypothyroidism, hypocortisolism, hypogonadotropic hypogonadism, and hypoprolactinemia. Anti-tuberculosis treatment was started, and it led to significant improvement in the general condition of the patient.

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.

Abstract 4285: Genomics-driven clustering of disease-related biomarkers identifies therapeutic options in myelodysplastic syndromes (MDS)

Hypomethylating agents (HMA) and lenalidomide (LEN) are approved and used in the treatment of patients (pts) with MDS, though these drugs fail in most pts. No method exists to predict drug response beyond associating single actionable mutations with a single drug's response. We hypothesized that MDS pts can be clustered by similarities in genomic/molecular profiles, & that each cluster may be assigned combos of FDA-approved drugs to target their unique biomarker profile. Bone marrow cells from 88 MDS pts & the MDS-L cell line were analyzed by cytogenetics & for mutations in 14 myeloid genes using NGS. 31 pts had sufficient data for analysis. 20 profiles had similar aberrations & were grouped. Genomic data from pts and MDS-L were entered into a computational biology modeling (CBM) software, which generates a disease-specific protein network map using PubMed to create digital models and identify characteristic biomarkers unique to each pt. An algorithm was created to cluster the models based on overlapping disease-specific biomarkers. Digital drug simulations (DDS) were conducted both on MDS-L & pt simulation models by quantitatively measuring drug effect on a cell growth score (CGS), a composite of cell proliferation, viability & apoptosis. DDS identified drugs by assessing their impact on disease-specific biomarkers and calculated CGSs. Predictions were validated using MTT. 14/31 MDS pt profiles, including the MDS-L cell line, clustered into 4 groups based on biomarker characteristics.MDS-L cells harbor NRAS (G12A) mutation,-7,-12,+1,+8,+19,+20 and +21. Genes associated with increased copy number (CN) include AURKA, IGFR, PAR5, MTOR, IL6, JAK3, MDM4, MYC, MCL1, COX2, PDE4A, and RCE1; genes associated with decreased CN include DUSP1, RASA1, NR3C1, IRF1, ETV6, and SHH. CBM identified active biomarkers in MDS-L cells (90RSK, MAPK7, AKT and BTK), validated by western blot. DDS predicted nelfinavir+celecoxib to be effective in MDS-L. MDS-L cells were treated with nelfinavir, celecoxib, and nelfinavir+celecoxib with increasing doses. Nelfinavir & celecoxib reduced MDS-L viability in a dose-dependent manner, while nelfinavir+celecoxib showed additive reduction of MDS-L viability. DDS was performed on each pt to predict response to HMA and LEN. Two of the clusters (n=2/cluster) were predicted to be non-responders to any SOC therapy. A third cluster (n=3) was predicted to respond to HMA, but not LEN, and the fourth cluster (n=6) showed varying or no response to either HMA/LEN. These results use a novel concept of using genomics & CBM to cluster profiles with overlapping disease-relevant biomarkers & similar drug response predictions. CBM can identify pt populations who may benefit from certain therapeutic regimens, improving response rates, & give insights into the mechanisms by which each drug impacts the MDS-specific biomarkers

Citation Format: Leylah M. Drusbosky, Kimberly E. Hawkins, Amy Meacham, Elizabeth Wise, Neeraj Kumar Singh, Chandan Kumar, Sumanth M. Vasista, Rakhi P. Suseela, Taher Abbasi, Shireen Vali, Kaoru Tohyama, Maher Albitar, Peter P. Sayeski, Christopher R. Cogle. Genomics-driven clustering of disease-related biomarkers identifies therapeutic options in myelodysplastic syndromes (MDS) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4285.

Agenesis of dorsal pancreas in a young adult: a rare cause of diabetes mellitus

Dorsal pancreatic agenesis is an extremely rare entity characterised by absence of body and tail of pancreas, while there are so many other developmental anomalies of the pancreas that have been reported. Here we report a 25-year-old young man who presented with pain in the abdomen, recurrent loose stools and hyperglycaemia. On radiological imaging study, there was complete agenesis of the dorsal pancreas except for thin stripe of tissue at the level of the uncinate process. Both exocrinedysfunction and endocrine dysfunction were present in this patient. Patient was supplemented with pancreatic enzyme preparation and insulin.

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.

The minimum test battery to screen for binocular vision anomalies: report 3 of the BAND study

PURPOSE

This study aims to report the minimum test battery needed to screen non-strabismic binocular vision anomalies (NSBVAs) in a community set-up. When large numbers are to be screened we aim to identify the most useful test battery when there is no opportunity for a more comprehensive and time-consuming clinical examination.

METHODS

The prevalence estimates and normative data for binocular vision parameters were estimated from the Binocular Vision Anomalies and Normative Data (BAND) study, following which cut-off estimates and receiver operating characteristic curves to identify the minimum test battery have been plotted. In the receiver operating characteristic phase of the study, children between nine and 17 years of age were screened in two schools in the rural arm using the minimum test battery, and the prevalence estimates with the minimum test battery were found.

RESULTS

Receiver operating characteristic analyses revealed that near point of convergence with penlight and red filter (> 7.5 cm), monocular accommodative facility (< 10 cycles per minute), and the difference between near and distance phoria (> 1.25 prism dioptres) were significant factors with cut-off values for best sensitivity and specificity. This minimum test battery was applied to a cohort of 305 children. The mean (standard deviation) age of the subjects was 12.7 (two) years with 121 males and 184 females. Using the minimum battery of tests obtained through the receiver operating characteristic analyses, the prevalence of NSBVAs was found to be 26 per cent. Near point of convergence with penlight and red filter > 10 cm was found to have the highest sensitivity (80 per cent) and specificity (73 per cent) for the diagnosis of convergence insufficiency. For the diagnosis of accommodative infacility, monocular accommodative facility with a cut-off of less than seven cycles per minute was the best predictor for screening (92 per cent sensitivity and 90 per cent specificity).

CONCLUSION

The minimum test battery of near point of convergence with penlight and red filter, difference between distance and near phoria, and monocular accommodative facility yield good sensitivity and specificity for diagnosis of NSBVAs in a community set-up.

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.

Scientometric Analysis of the Research Output of Physics and Astronomy of Guru Nanak Dev University during 2006-15

<div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p><span>The study attempts to analyse research contributions of the Guru Nanak Dev University, Amritsar in physics and astronomy during the period 2006-15. The data for this study was extracted from Scopus. The study analyses the </span><span>year-wise research productivity, national and international collaborations, top collaborating institutions, most prolific </span><span>authors, journals used for communication, most preferred journals for publication, number of citations received by the University during the period under study. This paper analyses that the university has published 652 papers in physics and astronomy. The University had registered the average citation impact per paper of 7.01 per cent and 6 publications received 51 to 100 citations. Among the Indian universities, University stood at 23</span><span>rd </span><span>rank in term of publications output (652) and h-index (29), 16</span><span>th </span><span>rank in average citation per paper (7.01 per cent) and 18</span><span>th </span><span>rank in share of high cited papers (1 per cent) and 19</span><span>th </span><span>rank in terms of international collaborative papers (27.45 per cent) during 2006-15. Around 68.71 per cent publications of the University in physics and astronomy were in national collaboration between GNDU and several other Indian organisations. The study clearly indicates that journals are the most preferred form of publication to communicate research works by the researchers. </span></p></div></div></div>

Scientometric Analysis of the Research Output of Physics and Astronomy of Guru Nanak Dev University during 2006-15

<div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p><span>The study attempts to analyse research contributions of the Guru Nanak Dev University, Amritsar in physics and astronomy during the period 2006-15. The data for this study was extracted from Scopus. The study analyses the </span><span>year-wise research productivity, national and international collaborations, top collaborating institutions, most prolific </span><span>authors, journals used for communication, most preferred journals for publication, number of citations received by the University during the period under study. This paper analyses that the university has published 652 papers in physics and astronomy. The University had registered the average citation impact per paper of 7.01 per cent and 6 publications received 51 to 100 citations. Among the Indian universities, University stood at 23</span><span>rd </span><span>rank in term of publications output (652) and h-index (29), 16</span><span>th </span><span>rank in average citation per paper (7.01 per cent) and 18</span><span>th </span><span>rank in share of high cited papers (1 per cent) and 19</span><span>th </span><span>rank in terms of international collaborative papers (27.45 per cent) during 2006-15. Around 68.71 per cent publications of the University in physics and astronomy were in national collaboration between GNDU and several other Indian organisations. The study clearly indicates that journals are the most preferred form of publication to communicate research works by the researchers. </span></p></div></div></div>

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.

Changes in stimulus and response AC/A ratio with vision therapy in Convergence Insufficiency

PURPOSE

To evaluate the changes in the stimulus and response Accommodative Convergence to Accommodation (AC/A) ratio following vision therapy (VT) in Convergence Insufficiency (CI).

METHODS

Stimulus and response AC/A ratio were measured on twenty five CI participants, pre and post 10 sessions of VT. Stimulus AC/A ratio was measured using the gradient method and response AC/A ratio was calculated using modified Thorington technique with accommodative responses measured using WAM-5500 open-field autorefractor. The gradient stimulus and response AC/A cross-link ratios were compared with thirty age matched controls.

RESULTS

Mean age of the CI and control participants were 23.3±5.2 years and 22.7±4.2 years, respectively. The mean stimulus and response AC/A ratio for CI pre therapy was 2.2±0.72 and 6.3±2.0 PD/D that changed to 4.2±0.9 and 8.28±3.31 PD/D respectively post vision therapy and these changes were statistically significant (paired t-test; p<0.001). The mean stimulus and response AC/A ratio for controls was 3.1±0.81 and 8.95±2.5 PD/D respectively.

CONCLUSIONS

Stimulus and response AC/A ratio increased following VT, accompanied by clinically significant changes in vergence and accommodation parameters in subjects with convergence insufficiency. This represents the plasticity of the AC/A crosslink ratios that could be achieved with vision therapy in CI.

Abstract CT085: iCare 1: A prospective clinical trial to predict treatment response based on mutanome-informed computational biology in patients with AML and MDS

Hypomethylating agents (HMAs) (azacitidine (aza), decitabine (dec)) and lenalidomide (len) are approved agents and used to treat patients with myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML). Despite their widespread use, HMAs fail in the majority of these patients, and len fails in 75% of non-del(5q) MDS. Currently, no method exists to predict disease response, thus the management of MDS and AML patients is challenging.

Methods: Patients with AML or MDS were recruited to a clinical trial (NCT02435550) designed to assess predictive values by comparing computer predictions of drug response to actual clinical response. Genomic profiling was conducted by cytogenetics, whole exome sequencing, and array CGH. Genomic results were inputted into a computational software (Cellworks), which generates disease-specific protein network maps using PubMed and other resources. Digital drug simulations were conducted by quantitatively measuring drug effect on a cell growth score (proliferation + viability + apoptosis). Each patient-specific protein network was screened for the extent by which aza, dec or len reduced disease growth in a dose-respondent manner. Treatment was physician’s choice of SOC. Clinical outcomes were prospectively recorded. IWG criteria were used to define response. Western blot assays were performed to validate the predicted protein network perturbations. Fisher’s exact test was used to compare prediction values of the genomics-informed computer method versus empiric drug administration.

Results: 88 patients have had all molecular tests and computational modeling performed. Lab validation of computer-predicted, activated protein networks in 19 samples from 13 different patients showed correct prediction of 5 activated networks (Akt2, Akt3, PIK3CA, p38, Erk1/2) in 17 samples, with 89% accuracy. At the time of this report, 26/88 patients were eligible for efficacy evaluation. 8/26 patients showed clinical response to SOC therapy, 18/26 did not. 24/26 outcome predictions were correctly matched to their clinical outcomes, and 2/20 were incorrectly matched, resulting in 92% prediction accuracy, 80% PPV, 100% NPV, 100% sensitivity, and 89% specificity. The accuracy of the genomics-informed computer method was significantly greater than empiric drug administration (p=1.664e-05). New genomic signature rules were discovered to correlate with clinical response after aza, dec or len.

Summary: A computational method that models multiple genomic abnormalities simultaneously showed high predictive value of protein network aberrations and clinical outcomes after SOC treatments. The network method uncovered molecular reasons for drug failure and highlighted resistance pathways that could be targeted to recover chemosensitivity. This technology could also be used to establish eligibility criteria for precision enrollment in drug development trials

Citation Format: Leylah Drusbosky, Kimberly E. Hawkins, Shireen Vali, Taher Abbasi, Ansu Kumar, Neeraj Kumar Singh, Kabya Basu, Chandan Kumar, Amjad Husain, Caitlin Tucker, Randy A. Brown, Maxim Norkin, John Hiemenz, Jack Hsu, John Wingard, Christopher R. Cogle. iCare 1: A prospective clinical trial to predict treatment response based on mutanome-informed computational biology in patients with AML and MDS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr CT085. doi:10.1158/1538-7445.AM2017-CT085

Abstract 4545: A computational biology method to predict HMA or lenalidomide treatment response in non-Del(5q) MDS

60% of myelodysplastic syndromes (MDS) patients fail to achieve clinical improvement with hypomethylating agents (HMAs). 26% of patients with non-del5q MDS respond to lenalidomide (LEN), but the mechanism of response is unknown. Treatment of non-del5q patients who fail HMA is challenging and predicting response to LEN would address this unmet clinical need.

Methods: A retrospective analysis was performed on non-del5q MDS patient cytogenetics, gene mutations, treatments, and clinical response data. Using Cellworks Group software, genomic data was used to generate disease-specific protein network maps. Digital drug simulations were done by quantitatively measuring drug effect and calculating a MDS inhibition score. Each patient-specific map was digitally screened for the extent by which LEN and HMAs inhibited MDS in a dose-dependent manner and compared to the patient's clinical outcome.

Results: Patient 1 is a non-del5q patient with trisomy 8 (+8) and an ASXL1 frameshift mutation. Simulation modeling revealed overexpression (OE) of MYC leading to IRF4 and IKZF expression, key pathways for LEN sensitivity. MYC OE also leads to CCND1 expression, aiding proliferation of MDS cells. Simulated LEN treatment targets MYC-induced upregulation of IKZF1, STUB1, CRBN, and CSNK1A1 to reduce MDS cell survival. Upregulated TP53 inhibits MYC expression, augmenting the patient's response to LEN. To compare response to other SOC drugs, azacitidine (AZA), was screened. The ASXL1 mutation led to loss of PRC2-mediated DNMT1 function. +8 results in OE of GGH, reducing methylation of CpG regions. Given loss of DNMT1 function, patient 1 was predicted be a non-responder to AZA. Patient 2 is a non-del5q patient with +8, add(14q)(11.1-11.2), add(8)(p23.3-q24.3), and an ASXL1 mutation. Modeling revealed the same dysregulated pathways as patient 1, predicting sensitivity to LEN and resistance to AZA. Patient 3 is a non-del5q patient with complex karyotype and mutations in IDH2, TET2, and SRSF2. Modeling revealed OE of CARD11 yielding sensitivity to LEN. OE of CDH1 and AXIN1 decreased beta-catenin activity, a known resistance mechanism to LEN. OE of apoptotic TP53, BAX, and BBC3 sensitize this patient's MDS cells to LEN. Modeling revealed reduced EZH2 mRNA levels due to the SRSF2 mutation, directly impacting the PRC2 complex needed for DNMT1-mediated CpG methylation. EZH2 is further down regulated by L3MBTL2 OE. TET2 is functionally challenged from the lack of CpG methylation, diminishing IDH activity, resulting in AZA resistance.

Conclusions: Computer modeling of non-del5q MDS patient biology can deduce the abnormal protein networks and consequent drug effects. This method could be used to understand drug failure and highlight resistance pathways that can be targeted to recover chemosensitivity. This technology can also be used to predict MDS patient response prior to treatment, increasing drug effectiveness and reducing side effects and treatment costs.

Citation Format: Leylah Drusbosky, Neeraj Kumar Singh, Shireen Vali, Taher Abbasi, Christopher R. Cogle. A computational biology method to predict HMA or lenalidomide treatment response in non-Del(5q) MDS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4545. doi:10.1158/1538-7445.AM2017-4545

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.