Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome

Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and informatic study, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in Drosophila melanogaster, offering significant improvements to the existing community reference assembly. Our work successfully recovers previously elusive segments, including complete reconstructions of the histone locus and the pericentric heterochromatin of the X chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative of crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.

Evidence of a Hardening in the Cosmic Ray Proton Spectrum at around 166 TeV Observed by the GRAPES-3 Experiment

We present the measurement of the cosmic ray proton spectrum from 50 TeV to 1.3 PeV using 7.81×10^{6} extensive air shower events recorded by the ground-based GRAPES-3 experiment between 1 January 2014 and 26 October 2015 with a live time of 460 day. Our measurements provide an overlap with direct observations by satellite and balloon-based experiments. The electromagnetic and muon components in the shower were measured by a dense array of plastic scintillator detectors and a tracking muon telescope, respectively. The relative composition of the proton primary from the air shower data containing all primary particles was extracted using the multiplicity distribution of muons which is a sensitive observable for mass composition. The observed proton spectrum suggests a spectral hardening at ∼166  TeV and disfavors a single power law description of the spectrum up to the Knee energy (∼3  PeV).

Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies

The acquisition of novel sexually dimorphic traits poses an evolutionary puzzle: How do new traits arise and become sex-limited? Recently acquired color vision, sexually dimorphic in animals like primates and butterflies, presents a compelling model for understanding how traits become sex-biased. For example, some Heliconius butterflies uniquely possess UV (ultraviolet) color vision, which correlates with the expression of two differentially tuned UV-sensitive rhodopsins, UVRh1 and UVRh2. To discover how such traits become sexually dimorphic, we studied Heliconius charithonia, which exhibits female-specific UVRh1 expression. We demonstrate that females, but not males, discriminate different UV wavelengths. Through whole-genome shotgun sequencing and assembly of the H. charithonia genome, we discovered that UVRh1 is present on the W chromosome, making it obligately female-specific. By knocking out UVRh1, we show that UVRh1 protein expression is absent in mutant female eye tissue, as in wild-type male eyes. A PCR survey of UVRh1 sex-linkage across the genus shows that species with female-specific UVRh1 expression lack UVRh1 gDNA in males. Thus, acquisition of sex linkage is sufficient to achieve female-specific expression of UVRh1, though this does not preclude other mechanisms, like cis-regulatory evolution from also contributing. Moreover, both this event, and mutations leading to differential UV opsin sensitivity, occurred early in the history of Heliconius. These results suggest a path for acquiring sexual dimorphism distinct from existing mechanistic models. We propose a model where gene traffic to heterosomes (the W or the Y) genetically partitions a trait by sex before a phenotype shifts (spectral tuning of UV sensitivity).

Design and operation of a hybrid LED/LD-pumped phosphor-converted white-light lamp

Illumination sources based on phosphors, pumped by laser diodes (LDs), have seen rapid developments over the past decade. Here, we present a new, to the best of our knowledge, design that features both spectral richness and the capability for high brightness. Complete design details and operational characterization have been described. This basic design can be extended in various ways to customize such lamps for different operational requirements. A hybrid arrangement of both LEDs and an LD is used to excite a mixture of two phosphors. The LEDs, in addition, provide a blue fill-in to enrich output radiation and to tune the chromaticity point inside the white region. The LD power, on the other hand, can be scaled up to generate very high brightness levels that are not achievable with pumping from LEDs alone. This capability is gained using a special transparent ceramic disk that carries the remote phosphor film. We also show that the radiation from our lamp is free from speckle-producing coherence.

O-031 Activation of NLRP3 inflammasome enhances neutrophil extracellular traps in women with stage III/IV endometriosis: convergence of multiple signaling portray association between genetics and lesion type

Study question

Do NOD-like receptor pyrin-containing 3 (NLRP3) signaling affect neutrophil extracellular traps (NET)-osis in women with stage III/IV endometriosis?

Summary answer

Inflammasome activation whether due to pathogen (disease itself) or damage-associated molecular pattern (through NET) might be one mechanism involved in establishing perturbed endometrium in endometriosis.

What is known already

Endometriosis is characterized by number of processes like vascularization, hypernociception, and fibrosis, cardinal cause being inflammation. Recently, expression of inflammasome components, including NLRP3 and apoptosis signal-regulating kinase has been demonstrated in human endometrium cueing involvement in uterine innate immunity. Moreover, a novel extracellular killing mechanism, NET, is documented to reflect an inflammatory status in deep infiltrating endometriosis. Since, endometriosis demonstrates similarities with chronic inflammatory and autoimmune disorders; we postulated inflammatory responses in endometriosis may become modulated through a feed-forward loop of NET-induced specific cytokine production thus providing insights against potentiality of endometriotic cells to limit progression of the disease.

Study design, size, duration

Twenty-two consented women (24-39 years) with endometriosis (Group A) (Stages III–IV) (based on ASRM-2018 guidelines) and age-matched counterpart/s of male sub-fertility (Group B; control), free of uterine abnormalities (n = 18) were recruited between January to December 2021 from Institute of Reproductive Medicine, Kolkata. Eutopic endometrium, were collected from women undergoing diagnostic laparoscopy (Group A) or by curettage from women undergoing endometrial ablation (Group B). Serum was collected during window-of-implantation (LH + 7) for both the group/s.

Participants/materials, setting, methods

Pro-(IFN-g, TNF-a, IL-6, TGF-b) and anti-inflammatory (IL-10, IL-13, IL-4, IL-5) cytokines was evaluated by western blot. Expression level of inflammasome-related proteins (NLRP3, ASC, CASPASE1, PYCARD, IL-1-b) and mRNA expression was estimated by western-blot and quantitative-real-time PCR (qRT-PCR) respectively from tissue biopsies in Group A and B. SYTOX® green assay by flow-cytometry and neutrophil-elastase activity by immunofluorescence was done to quantify and characterize NET production in blood monocytes. P < 0.05 was considered statistically significant.

Main results and the role of chance

The mean (±SD) age of study population was 31.6±5.2 years. Hyperestrogenic milieu possibly stimulated (p < 0.001) pro-inflammatory molecules (IFN-g, TNF-a, IL-6, TGF-b) in endometriosis as observed by western-blot and qRT-PCR. A significant up-regulation (p < 0.001) was observed in relative mRNA expression of NLRP3 and PYCARD gene in Group A. However, caspase 1 expression documented non-significant variation in biopsies from endometriosis patients. Western blot corroborated the finding/s. The outcome of NLRP3 activation was supported by increased (p < 0.002) mRNA expression of IL-1b. NETs were detected significantly higher (p < 0.01) in 54.54% (12/22) patients in group A compared to control (16.66%; (3/18)). Moreover, quantification of NETs showed a significantly higher amount in endometriosis compared to group B (0.097 vs. 0.02, p < 0.03).

Spermann-rank correlation by SPSS version22 revealed positive correlation between IL-1b with NLRP3 (r = 0.56, p< 0.001), PYCARD (r = 0.11, p< 0.01); and caspase1 (r = 0.16, p< 0.01) and IL-1b (r = 0.47, p< 0.01) with NET-positive cell/s in endometriosis. Moreover, posterior cul-de-sac lesions correlated positively with NET-positive cell/s (r = 0.29; p < 0.01) cueing to possible prognostic marker/s. In summary, a coordinated-fashioned action of components of NLRP3 inflammasome machinery may regulate production of NET/s forming a complex network allowing communication between cell-types in order to maintain viability and development of endometrial lesion/s.

Limitations, reasons for caution

Our findings need to be replicated in larger study cohort/s, especially stratified by severity of endometriosis sub-groups and in women of different ethnicities. Another limitation is the missing information about NETs in normal functioning human endometrium throughout the menstrual cycle.

Wider implications of the findings

The proposed study aims to understand potential role of NLRP3 inflammasome complex as a “double-edged sword” in the development and pathophysiology of endometriosis. Therapeutic alternatives that aim to re-balance the pro- to anti-inflammatory milieu in the endometrium should consider the inflammasome as part of the equation.

Trial registration number

Not applicable

P-390 Serum homocysteine and uterine artery Doppler ultrasound in combination has better predictive accuracy in women with preeclampsia: useful tool for early screening in everyday practice

Study question

Is serum homocysteine combined with uterine-artery Doppler were effective in predicting preeclampsia (≥140mmHg/≥90mmHg blood pressure) in singleton pregnancy during 11–15 weeks of gestation?

Summary answer

Combination of serum homocysteine levels with uterine-artery Doppler is superior to individual presence of biochemical/ultrasound marker/s making the duo effective for early screening in preeclampsia.

What is known already

American College of Obstetricians and Gynecologists and National Institute for Care and Health Excellence recommend identifying patients who are at high risk of developing preeclampsia based on medical history. Recently, biochemical and ultrasound markers were investigated for prediction of preeclampsia, but none of them were predictably reliable, valid, and suitable for routine clinical use. Increased levels of homocysteine in 1st-trimester, seems to signal onset of preeclampsia later in pregnancy portraying severity of the disease as well. We aimed to identify predictive value of serum homocysteine combined with uterine-artery Doppler in singleton pregnancy during 11–15 weeks of gestation for preeclampsia.

Study design, size, duration

One hundred forty-two consented singleton pregnant women (28-45 years) at gestational age of 11–15 weeks, recruited between January to December 2021 from Institute of Reproductive Medicine, Kolkata were enrolled in the study. Women who used aspirin as a prophylaxis for preeclampsia or were diagnosed to have fetal, structural or chromosomal abnormalities were excluded from the study (n = 7). Maternal age, weight and height, mean arterial pressure, parity, and obstetric history were documented.

Participants/materials, setting, methods

Uterine-artery Doppler ultrasound and serum homocysteine levels were performed transabdominally and using ELISA respectively. Pregnancy outcomes were recorded. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) at optimal cut-off values were determined to predict preeclampsia. Optimal cut-off values for homocysteine levels were calculated using receiver operator characteristic curve (ROC). Chi-square test, Fisher’s exact test, unpaired t test, and Mann–Whitney U test were used when appropriate. P-value <0.05 was considered statistically significant.

Main results and the role of chance

16 cases had preeclampsia (11.26%) of whom 9 had early-onset preeclampsia (6.33%). Baseline characteristics including maternal-age (>35 or<), parity, body-mass- index, and gestational-age at measurement were not significantly different between two groups excepting higher (p < 0.001) mean arterial blood pressure (mmHg) at first trimester (97.2±6.4 vs. 81.1±7.2) in preeclampsia. Preeclamptic women had significantly higher (p < 0.001) serum homocysteine levels (μmol/l) (26.1±3.5 vs 10.2± 5.6) than normotensive pregnant women (n = 119). No difference in mean pulsatility (PI) of uterine-artery was observed (1.78±0.64 vs. 1.72±0.48) excluding significantly high (p > 0.02) in women with early-onset preeclampsia than control (2.11±0.81 vs. 1.39±0.92). However, lower (p < 0.01) gestational age (weeks) (35.4±2.1 vs. 37.6±1.4), and neonatal birth weight (gms) (2937.3±578.2 vs. 3227.6±421.5) with higher (p < 0.001) preterm delivery (25% vs 5.04%), low birth weight (25% vs 5.04%) and neonatal respiratory distress syndrome (12.5% vs. 0.84%) was documented in preeclampsia than control/s. The optimal cut-off value of serum homocysteine with PI levels, from ROC (AUC=0.735, p < 0.001) was superior to individual ROC (AUC=0.451; AUC=0.268). The sensitivity, specificity, PPV, and NPV were 67.7%, 70.5%, 1.7%, and 98.5%, respectively using a combination of abnormal serum homocysteine levels with abnormal uterine artery Doppler PI (above 95th percentile) and used as a predictive value for preeclampsia.

Limitations, reasons for caution

The limitation of this study was that there were small cases of early-onset preeclampsia. Additional studies with a larger sample size of early-onset preeclampsia and other models using serum homocysteine, combined with uterine artery Doppler, and maternal characteristic risk factors should be conducted.

Wider implications of the findings

Early screening of preeclampsia by using combination of serum homocysteine and uterine artery Doppler during first trimester (11–15 weeks) at the same visit may be more effective and allows the timing for using early low-dose aspirin prophylaxis in order to prevent preeclampsia.

Trial registration number

Not applicable

ADRENAL HISTOPLASMOSIS: AN EASTERN INDIAN PERSPECTIVE

CONTEXT

The clinical presentation of histoplasmosis is varied. Due to its propensity for adrenal involvement, histoplasmosis is an important differential diagnosis in any patient presenting with adrenal mass, bilateral in particular.

OBJECTIVE

Data on clinical presentation, pattern of adrenal involvement, radiological appearance and long-term follow-up of adrenal histoplasmosis are relatively sparse; hence we looked at it.

DESIGN

This record based single-centre retrospective study was conducted in one of the tertiary care hospitals, situated in eastern India catering the Gangetic delta.

SUBJECTS AND METHODS

Data on demographic characters, presenting manifestations, biochemical & hormonal parameters and radiological appearance of confirmed adrenal histoplasmosis cases (n=9), admitted between 2015-2019 have been retrieved. The treatment outcome and condition of patients after 1-4 years of follow-up has also been discussed.

RESULTS

Four out of the nine (44.4%) patients had predisposing immunocompromised conditions in the form of diabetes and/or chronic alcoholism while rest were immunocompetent. Seven out of nine patients (77.8 %) had signs and symptoms suggestive of adrenal insufficiency, while two (22.2%) presented with only pyrexia of unknown origin. All of them had bilateral adrenal mass, though the radiologically appearances were different. All patients received anti-fungal agents with/without hydrocortisone and/or fludrocortisone. One patient died (11.1%), while majority responded favourably to treatment. Adrenocortical function did not recover completely.

CONCLUSIONS

The possibility of adrenal histoplasmosis should always be considered in patients presenting with bilateral adrenal mass, irrespective of adrenal morphology. Treatment is effective, but many of them require supplemental hydrocortisone for quite a long period, if not lifelong. Mineralocorticoid deficiency, however, is not permanent.

Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii

Studying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework combining behavioral, gene expression, and genomic analyses to understand the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii. First, we used egg-laying behavioral assays to understand the evolution of ripe fruit oviposition preference in D. suzukii compared with closely related species D. subpulchrella and D. biarmipes as well as D. melanogaster. We show that D. subpulchrella and D. biarmipes lay eggs on both ripe and rotten fruits, suggesting that the transition to ripe fruit preference was gradual. Second, using two-choice oviposition assays, we studied how D. suzukii, D. subpulchrella, D. biarmipes, and D. melanogaster differentially process key sensory cues distinguishing ripe from rotten fruit during egg-laying. We found that D. suzukii's preference for ripe fruit is in part mediated through a species-specific preference for stiff substrates. Last, we sequenced and annotated a high-quality genome for D. subpulchrella. Using comparative genomic approaches, we identified candidate genes involved in D. suzukii's ability to seek out and target ripe fruits. Our results provide detail to the stepwise evolution of pest activity in D. suzukii, indicating important cues used by this species when finding a host, and the molecular mechanisms potentially underlying their adaptation to a new ecological niche.

Evolution of genome structure in the Drosophila simulans species complex

The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly

BACKGROUND

The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vector's genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution.

RESULTS

To access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element (TE) families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y chromosome in any mosquito. By tracking full-length mRNA for > 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively throughout male development and adulthood, suggesting an important role.

CONCLUSION

Collectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate the development of genetic control strategies of malaria transmission.

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila

Topologically associating domains (TADs) were recently identified as fundamental units of three-dimensional eukaryotic genomic organization, although our knowledge of the influence of TADs on genome evolution remains preliminary. To study the molecular evolution of TADs in Drosophila species, we constructed a new reference-grade genome assembly and accompanying high-resolution TAD map for D. pseudoobscura Comparison of D. pseudoobscura and D. melanogaster, which are separated by ∼49 million years of divergence, showed that ∼30%-40% of their genomes retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower expression divergence than those located in nonconserved TADs. Furthermore, we found that a substantial proportion of long genes (>50 kbp) in D. melanogaster (42%) and D. pseudoobscura (26%) constitute their own TADs, implying transcript structure may be one of the deterministic factors for TAD formation. By using structural variants (SVs) identified from 14 D. melanogaster strains, its three closest sibling species from the D. simulans species complex, and two obscura clade species, we uncovered evidence of selection acting on SVs at TAD boundaries, but with the nature of selection differing between SV types. Deletions are depleted at TAD boundaries in both divergent and polymorphic SVs, suggesting purifying selection, whereas divergent tandem duplications are enriched at TAD boundaries relative to polymorphism, suggesting they are adaptive. Our findings highlight how important TADs are in shaping the acquisition and retention of structural mutations that fundamentally alter genome organization.

Two Synthetic 18-Way Outcrossed Populations of Diploid Budding Yeast with Utility for Complex Trait Dissection

Advanced-generation multiparent populations (MPPs) are a valuable tool for dissecting complex traits, having more power than genome-wide association studies to detect rare variants and higher resolution than F2 linkage mapping. To extend the advantages of MPPs in budding yeast, we describe the creation and characterization of two outbred MPPs derived from 18 genetically diverse founding strains. We carried out de novo assemblies of the genomes of the 18 founder strains, such that virtually all variation segregating between these strains is known, and represented those assemblies as Santa Cruz Genome Browser tracks. We discovered complex patterns of structural variation segregating among the founders, including a large deletion within the vacuolar ATPase VMA1, several different deletions within the osmosensor MSB2, a series of deletions and insertions at PRM7 and the adjacent BSC1, as well as copy number variation at the dehydrogenase ALD2 Resequenced haploid recombinant clones from the two MPPs have a median unrecombined block size of 66 kb, demonstrating that the population is highly recombined. We pool-sequenced the two MPPs to 3270× and 2226× coverage and demonstrated that we can accurately estimate local haplotype frequencies using pooled data. We further downsampled the pool-sequenced data to ∼20-40× and showed that local haplotype frequency estimates remained accurate, with median error rates 0.8 and 0.6% at 20× and 40×, respectively. Haplotypes frequencies are estimated much more accurately than SNP frequencies obtained directly from the same data. Deep sequencing of the two populations revealed that 10 or more founders are present at a detectable frequency for > 98% of the genome, validating the utility of this resource for the exploration of the role of standing variation in the architecture of complex traits.

Process improvement to effectively manage and reduce sharps injuries in a Tertiary Hospital in Northern India

INTRODUCTION AND OBJECTIVES

Needle stick injuries are associated with a 0.3-30% risk of transmission of Human Immunodeficiency virus, Hepatitis C virus, and Hepatitis B virus. Despite causing psychological trauma they also involve a huge financial burden. A robust process improvement (RPI) toolkit was introduced in order to effectively manage and reduce needle stick injuries, as well as an attempt to report prevalence, post-exposure management, and associated economic burden.

MATERIALS AND METHODS

Prospective Observational Study (2015-2018) has been design in a Corporate Tertiary Care Hospital. The participants included were needle stick injuries exposed staff. RPI toolkit was implemented (2015-2018) focusing on root cause analysis, availability of safety engineered devices, immunization and post-exposure management of needle stick injuries exposed staff. The main outcome measure was needle stick injuries incidence.

RESULTS

A total of 211 needle stick injuries were reported (mean - 52.72/year, needle stick injury incidence - 13.18/year/100 beds). Yearly trends showed a decrease of 21.3% in injuries from 2015 (61) to 2018 (48). Half (106, 50%) of the total injuries were reported among nurses. Use of hypodermic needles was involved in 116 (55%) injuries, with 114 (54%) occurring due to nonadherence to hospital policies. Overall, 204 staff had protective immunity, and 135 (64%) of these had completed their Hepatitis B immunizations. The source was known in 165 (78%) cases, and 113 of these cases had an injury from a source with negative viral markers. A 6-month follow-up was completed in 90 cases. No seroconversion was reported. Overall costs incurred in post-exposure prophylaxis was approximately €30,000 (mean cost €143.50/needle stick injury).

CONCLUSION

Nurses are most at risk of needle stick injury in healthcare settings. Implementation of RPI toolkit led to a 21.3% reduction in sharps injury incidences. These injuries incur huge financial burden on the hospital. Appropriate immunization strategies saved about €1360 expenditure on post-exposure prophylaxis.

Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish

Adopting a new diet is a significant evolutionary change, and can profoundly affect an animal's physiology, biochemistry, ecology and genome. To study this evolutionary transition, we investigated the physiology and genomics of digestion of a derived herbivorous fish, Cebidichthys violaceus. We sequenced and assembled its genome (N50 = 6.7 Mb) and digestive transcriptome, and revealed the molecular changes related to digestive enzymes (carbohydrases, proteases and lipases), finding abundant evidence of molecular adaptation. Specifically, two gene families experienced expansion in copy number and adaptive amino acid substitutions: amylase and carboxyl ester lipase (cel), which are involved in the digestion of carbohydrates and lipids, respectively. Both show elevated levels of gene expression and increased enzyme activity. Because carbohydrates are abundant in the prickleback's diet and lipids are rare, these findings suggest that such dietary specialization involves both exploiting abundant resources and scavenging rare ones, especially essential nutrients, like essential fatty acids.

Impact of water deficit stress in maize: Phenology and yield components

Fifteen million farmers in India engaged in Maize cultivation. India would require 45 MMT of Maize by 2022. But, only 15% of cultivated area of maize is under irrigation and water shortage has been a challenge for sustainability of maize production. Water deficit stress (WDS) during pre-flowering and grain filling stages massively affects the plant performance due to imprecise traits function. Thus, the effect of WDS on non-drought tolerant (NDT) and drought tolerant (DT) maize lines were investigated. WDS increased the flowering days, days to maturity, anthesis silk interval, decreased the leaf number, abnormal expression of secondary stress responsive traits, loss of normal root architecture which overall lead to a reduction in GY/ha. WDS at flowering and grain filling stage leads to significant yield penalty especially in NDT lines than DT lines. The yield penalty was ranged from 34.28 to 66.15% in NDT and 38.48 to 55.95% in DT lines due to WDS. Using multiple statistics, traits which improve WDS tolerance in maize were identified viz; number of leaves, number of stomata on lower surface of leaf, leaf angle at ear forming node internodal length between 3^rd and 4^th leaf from top, flag leaf length, flag leaf width, ear per plants, leaf senescence, pollen stainability, root fresh weight and root length. These traits would help in trait specific breeding in maize for WDS tolerance.

Antimicrobial effects of different extracts of medicinally used green leafy vegetables collected from local market of Dhaka, Bangladesh

The present study was carried out to determine the antimicrobial efficacy of green leafy vegetable samples which are traditionally used as medicinal herbs. Therefore, three samples each of Neem (Azadirachta indica, leaves), Ivy Gourd (Coccinia grandis, leaves), Water Spinach (Ipomoea aquatica, leaves) and Skunkvine (Paederia foetida, leaves) were collected and subjected to microbiological analysis, and agar well diffusion and microdilution assays to check antimicrobial activity. The samples contained total viable bacteria and fungi up to 107 and 105 CFU/g, respectively. Staphylococcus spp., Klebsiella spp. and Pseudomonas spp. were recovered in all the samples. All the samples showed potential antibacterial activity against most of the tested bacteria, especially their ethanolic and methanolic extracts. Although, crude and hot water extracts almost had no effect on the bacterial growth. The MIC value of the samples was found in a range of 3 mg/mL to 12 mg/mL and the average MIC value was recorded to be 6 mg/mL. Overall, the findings of the present study justified the therapeutic potential of the tested green leafy vegetable samples.

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).

Microsatellite Instability in Chronic Myeloid Leukemia using D17S261 and D3S643 markers: A Pilot Study in Gujarat Population

CONTEXT

Tumor progresses through a series of genetic alterations that involve proto-oncogenes and tumor suppressor genes - the gatekeeper, caretakers, and landscaper genes. Microsatellites are short tandem repeat sequences, present over the span of human genome and are known to be variable at multiple loci due to errors in DNA Mismatch Repair machinery.

AIM

The present study was aimed to evaluate the association between Microsatellite Instability (MSI) and evolution of Chronic Myeloid Leukemia (CML) - genetically a rare event but profound in this pilot study.

SETTINGS AND DESIGNS

We explore the possibility of MSI in primary CML patients confirmed by t(9;22) using capillary electrophoresis. Fifteen CML patients and healthy individual samples, respectively, were used to study the markers D17S261 and D3S643.

MATERIALS AND METHODS

The DNA was amplified using tagged and nontagged primers and further subjected to bioanalysis and fragment analysis.

RESULTS

While the results from bioanalyzer fluctuated, fragment analysis indicated the presence of microsatellite variability in 80% of the patients' samples as compared to no MSI in normal individuals for both the markers.

CONCLUSION

These findings suggest that MSI is a genetic event that may have a role in CML progression or evolution. Further studies are warranted to understand the plausible underlying causes.

Development and characterization of a helicon plasma source

The Helicon Plasma Source (HeliPS) designed and developed at the Centre of Plasma Physics-Institute for Plasma Research is a versatile helicon plasma device, which operates in a wide range of magnetic field configurations from 50 G to 500 G. This device is dedicated to perform a broad range of research activities. The main objective for development of the HeliPS is to carry out studies on ion-ion plasmas in electronegative gases. In the near future, ion-ion plasmas will be formed in electronegative gases in the downstream of the plasma production region. Although the system is primarily designed to carry out ion-ion plasma experiments, the same system can also be used for experimental studies on some basic helicon plasma properties such as wave propagation, wave coupling, and plasma instability. At present, argon plasma is produced with a RF power supply of 13.56 MHz frequency. External circuit parameters, such as antenna current, plasma resistance (R_p), and internal parameters, such as electron density and temperature, are measured. The details of the experimental setup development, device characteristic, as well as preliminary plasma production and characterization to confirm occurrence of the helicon plasma in the system are presented in this article.

Hidden genetic variation shapes the structure of functional elements in Drosophila

Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, although the fragmented nature of most contemporary assemblies obscures them. To discover such mutations, we assembled the first new reference-quality genome of Drosophila melanogaster since its initial sequencing. By comparing this new genome to the existing D. melanogaster assembly, we created a structural variant map of unprecedented resolution and identified extensive genetic variation that has remained hidden until now. Many of these variants constitute candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that amplifies the expression of detoxification-related genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high-quality reference genomes are to deciphering phenotypes.

A new approach of oral cancer detection using bilateral texture features in digital infrared thermal images

Oral cancer is one of the most prevalent form of cancer and its severity is aggrandized specially among the socio-economically backward population in developing countries. A major fraction of patient population is unable to avail diagnosis for oral cancer due to scarcity of state-of-the-art infrastructure and experienced oral and maxillofacial pathologist. Contemporary gold standard of oral cancer confirmation relies on biopsy report. But biopsy is invasive and thus patients are usually reluctant to undergo this test. Moreover, biopsy yields considerable false negatives if investigated tissue is not collected precisely from the carcinogenic location. Till date, there is dearth of computer aided pre-screening tool for detection of oral cancer. The paper presents Digital Infrared Thermal Imaging as a viable modality for early screening of oral cancer. This is the pioneering attempt to discriminate normal subjects from patients by leveraging discriminating texture features on oral thermograms. Statistically significant texture features were selected from a) both halves of frontal face and b) right and left profile faces. Due to disparity of distribution of facial temperature between normal subjects and patients, the corresponding texture features form discriminative class specific local clusters. Such local conglomeration was exploited using k-means and fuzzy k-means clustering. We adopt the concept of cluster prototype classifier which assigns label to each cluster according to majority class labels within that cluster. Highest classification accuracy of 86.12% is attained on fusion of features from left and right half of frontal face of precancerous subject followed by fuzzy k-means guided cluster prototype classification. The proposed work outperforms our previously developed pre-screening framework by upto 6.5%. Such promising results boosts the viability of our approach.