Lung cancer is the leading cause of cancer related mortality worldwide, with non-small cell lung cancer (NSCLC) as the most prevalent form. Despite advances in treatment options including minimally invasive surgery, CT-guided radiation, novel chemotherapeutic regimens, and targeted therapeutics, prognosis remains dismal. Therefore, further molecular analysis of NSCLC is necessary to identify novel molecular targets that impact prognosis and the design of new-targeted therapies. In recent years, tumor “activated/reprogrammed” stromal cells that promote carcinogenesis have emerged as potential therapeutic targets. However, the contribution of stromal cells to NSCLC is poorly understood. Here, we show increased numbers of bone marrow (BM)-derived hematopoietic cells in the tumor parenchyma of NSCLC patients compared with matched adjacent non-neoplastic lung tissue. By sorting specific cellular fractions from lung cancer patients, we compared the transcriptomes of intratumoral myeloid compartments within the tumor bed with their counterparts within adjacent non-neoplastic tissue from NSCLC patients. The RNA sequencing of specific myeloid compartments (immature monocytic myeloid cells and polymorphonuclear neutrophils) identified differentially regulated genes and mRNA isoforms, which were inconspicuous in whole tumor analysis. Genes encoding secreted factors, including osteopontin (OPN), chemokine (C-C motif) ligand 7 (CCL7) and thrombospondin 1 (TSP1) were identified, which enhanced tumorigenic properties of lung cancer cells indicative of their potential as targets for therapy. This study demonstrates that analysis of homogeneous stromal populations isolated directly from fresh clinical specimens can detect important stromal genes of therapeutic value.
The relative impact of 23 mutations on biofilm formation was evaluated in the USA300, methicillin-resistant strain LAC. Mutation of sarA, atl, codY, rsbU, and sigB limited biofilm formation in comparison to the parent strain, but the limitation imposed by mutation of sarA was greater than that imposed by mutation of any of these other genes. The reduced biofilm formation of all mutants other than the atl mutant was correlated with increased levels of extracellular proteases. Mutation of fur- and mgrA-enhanced biofilm formation but in LAC had no impact on protease activity, nuclease activity, or accumulation of the polysaccharide intercellular adhesin (PIA). The increased capacity of these mutants to form a biofilm was reversed by mutation of sarA, and this was correlated with increased protease production. Mutation of sarA, mgrA, and sigB had the same phenotypic effect in the methicillin-sensitive strain UAMS-1, but mutation of codY increased rather than decreased biofilm formation. As with the UAMS-1 mgrA mutant, this was correlated with increased production of PIA. Examination of four additional clinical isolates suggests that the differential impact of codY on biofilm formation may be a conserved characteristic of methicillin-resistant versus methicillin-sensitive strains.
Biofilm; protease; regulation; sarA; Staphylococcus aureus
A case of 22 year old male gymnast, who suffered from suprascapular neuropathy due to compression of suprascapular nerve by paralabral cysts around suprascapular notch, leading to marked atrophy of supraspinatus and infraspinatus muscles. After arthroscopic decompression of paralabral cysts, weakness and atrophy of the supraspinatus and infraspinatus muscles improved.
Suprascapular neuropathy; Paralabral cyst; Arthroscopic decompression
Sleep-related bruxism may present with headache. However, in clinical practice it may be difficult to differentiate from other causes of headache, especially in subjects with substance abuse. We are presenting a case of sleep-related bruxism that presented with headache and sleep-related symptoms in the presence of substance abuse. Polysomnography was used to ascertain cause of headache. How the other possible causes of headache ruled out is also discussed in report. In short, Sleep-related bruxism can cause headache that is worse in the morning. It is associated with poor quality sleep.
Headache; I sleep initiation and maintenance disorders; sleep bruxism
We report the surgical outcome in 52 patients with acetabular otherwise considered as poor surgical choices.
43 male and 9 female patients were operated at a mean age of 43 years and followed up for a mean duration of 60.3 months. There were 22 elementary fractures and 31 associated ones according to Letournal and Judet classification. Osteosynthesis was attempted in 48 patients whereas a primary total hip arthroplasty was performed in 4 patients. Outcome was assessed radiologically and functionally employing Harris Hip Score (HHS).
Average HHS in osteosynthesis group was 82.56 ± 12.4 with excellent to good results in 59.6% of the cases. Symptomatic osteoarthritis occurred in 13.5% of cases, avascular necrosis and severe heterotopic ossification in 7.7% each, infection and nerve palsy in 11.5% each.
Although the complication rates in this series is marginally more than that reported in literature, we recommend that the indications of surgical fixation in acetabular fractures need to be extended to those which were considered poor surgical choices.
Acetabulum; Fractures; Neglected; Osteoporosis
The study was conducted to find out the association of various naso-oro-pharyngeal structures with sleep macro-architecture in suspected obstructive sleep apnea subjects. Study included 51 subjects with suspected obstructive sleep apnea. Subjects with possible central apnea and those consuming any substance that can affect sleep architecture were excluded. Level I polysomnography was performed after thorough physical examination. Overnight study was scored in 30 s epochs to find out the polysomnographic variables. Surgical treatment was offered wherever indicated. Subjects with moderate to severe obstructive sleep apnea were manually titrated on CPAP with the polysomnogram. SPSS v 17.0 was used for statistical analysis. We did not find any difference in the sleep architecture between genders. Sleep Efficiency was better in subjects with dental overjet, dental attrition, high tongue base, macroglossia, lesser oral cavity volume, edematous uvula, increased submental fat, hypertrophied facial muscles and Mallampatti grade III–IV. Shorter Sleep Latency was seen in subjects with tender TMJ and Mallampatti Gr III–IV. REM latency was shorter in subjects with high tongue base, macroglossia and hypertrophied muscles of mastication. Increased REM was observed in subjects with high tongue base, edematous uvula and tender TMJ. Enlarged tonsils had reversed effect with poor sleep efficiency, increased REM latency and decreased REM. CPAP therapy (N = 20) lessened awake time, decreased N2 and increased REM. Oro-pharyngeal structures affect the sleep architecture in suspected OSA subjects. Nasal structures do not affect the sleep architecture in these subjects and enlarged tonsils have opposite effect. Sleep architecture changes on the titration night with CPAP.
Sleep-architecture; Sleep-apnea; Oro-naso-pharyngeal anatomy
low-abundance proteins; high-abundance proteins; two-dimensional gel electrophoresis; RuBisCO; post-translational modifications
Plant seeds lose their viability when they are exposed to long term storage or controlled deterioration treatments, by a process known as seed aging. Based on previous studies, artificially aging treatments have been developed to accelerate the process of seed aging in order to understand its underlying mechanisms. In this study, we used Brassica napus seeds to investigate the mechanisms of aging initiation. B. napus seeds were exposed to artificially aging treatment (40°C and 90% relative humidity) and their physio-biochemical characteristics were analyzed. Although the treatment delayed germination, it did not increase the concentration of cellular reactive oxygen species (ROS). Comparative proteomic analysis was conducted among the control and treated seeds at different stages of germination. The proteins responded to the treatment were mainly involved in metabolism, protein modification and destination, stress response, development, and miscellaneous enzymes. Except for peroxiredoxin, no changes were observed in the accumulation of other antioxidant enzymes in the artificially aged seeds. Increased content of abscisic acid (ABA) was observed in the artificially treated seeds which might be involved in the inhibition of germination. Taken together, our results highlight the involvement of ABA in the initiation of seed aging in addition to the ROS which was previously reported to mediate the seed aging process.
Brassica napus; seed aging; controlled deterioration treatments; proteomics
The extracellular space between cell wall and plasma membrane acts as the first battle field between plants and pathogens. Bacteria, fungi, and oomycetes that colonize the living plant tissues are encased in this narrow region in the initial step of infection. Therefore, the apoplastic region is believed to be an interface which mediates the first crosstalk between host and pathogen. The secreted proteins and other metabolites, derived from both host and pathogen, interact in this apoplastic region and govern the final relationship between them. Hence, investigation of protein secretion and apoplastic interaction could provide a better understanding of plant-microbe interaction. Here, we are briefly discussing the methods available for the isolation and normalization of the apoplastic proteins, as well as the current state of secretome studies focused on the in-planta interaction between the host and the pathogen.
apoplast; apoplastic proteins; pattern-triggered immunity; effector-triggered immunity; secretome; protein secretion; plant-pathogen interaction
Background. Staphylococcus aureus produces numerous virulence factors but little is known about their in vivo regulation during an infection.
Methods. The production of capsule and α-toxin, and the expression of their respective genes, cap5 and hla, were analyzed by comparing CYL11481 (derivative of Newman) and its isogenic regulatory mutants in vitro. The temporal expression of cap5 and hla and the regulatory genes in vivo was carried out using a rat infective endocarditis model.
Results. In vitro analyses showed that capsule was positively regulated by MgrA, Agr, Sae, ArlR, and ClpC, and negatively by CodY and SbcDC. The α-toxin was positively regulated by MgrA, Agr, Sae, ArlR, and SbcDC but negatively by ClpC and CodY. In vivo analyses showed that cap5 expression correlated best with mgrA expression, whereas hla expression correlated best with sae expression. Mutation in mgrA drastically reduced cap5 expression in vivo.
Conclusions. Our results suggest that, in vitro, Agr is the most important regulator for capsule and α-toxin production, as well as for cap5 transcription, but SaeR is the most critical for hla transcription. However, in vivo, MgrA is the major transcriptional regulator of capsule, but not α-toxin, whereas saeR expression correlates best with hla expression.
Staphylococcus aureus; virulence; infective endocarditis model; mgrA; capsule; α-toxin
Due to its side effects stavudine (D4T) has been replaced by zidovudine (AZT) and tenofovir (TDF) in most low- and middle-income countries (LMICs). In 2014 about 38% of adult first-line regimens contain AZT and 62% TDF . Whereas the unfavourable metabolic outcomes of D4T in comparison to TDF have been described extensively, studies from LMICs comparing metabolic profiles between patients on AZT and TDF are scarce. Given the high number of patients in LMICs still taking AZT, data on their metabolic profile are needed. We present rates of metabolic syndrome (MS) in adult patients taking either AZT- or TDF-containing first-line, non-nucleoside reverse transcriptase (NNRTI)-based regimens.
Materials and Methods
Data derived from a cross-sectional multi-disease screening conducted in ten facilities in two rural districts of Lesotho, Southern Africa . Patients were eligible if aged ≥25 years and on NNRTI-containing first-line ART ≥6 months. The MS definition for Africa of the International Diabetes Federation was applied . Assessed potential predictors for MS were age, time on ART, virologic suppression, body-mass index (BMI), alcohol consumption, wealth quintile, NNRTI (nevirapine (NVP) or Efavirenz (EFV)), history of previous D4T exposure and ART-backbone (AZT or TDF). Statistical analyses – stratified for sex – comprised univariate logistic regression for each predictor variable with subsequent construction of a multivariate model including all predictors with an association to MS at a significance level<0.1 in univariate analysis.
Out of 1026 patients, 660 (64.3%) were female. MS prevalence was 9.8% (95% CI 6.9–13.4) in men and 22.9% (19.7–26.3) in women. In women, aged ≥35 years, AZT-backbone, NVP-base, BMI ≥25kg/m2 and taking ART for ≥4.5 years were associated with MS in univariate analysis. In the multivariate model only AZT (adjusted odds-ratio: 2.2, 95% CI 1.4–3.6; p=0.001) and BMI ≥25kg/m2 (9.8; 2.8–34.1, p<0.001) were associated with MS. For men, age, higher wealth quintile, history of D4T exposure and BMI were associated with MS in univariate analysis. In the multivariate model only a BMI ≥25kg/m2 was associated with MS (8.9; 3.8–20.9, p<0.001).
In rural Lesotho, Southern Africa, the use of AZT instead of TDF among women who are on ART for ≥6 months predisposes to the development of metabolic syndrome. Given that, still 38% of first-line regimens in LMIC contain AZT, this finding needs to be verified in other settings in Sub-Saharan Africa.
Computed tomographic (CT) based navigation is a technique to improve the accuracy of pedicle screw placement. It is believed to enhance accuracy of pedicle screw placement, potentially avoiding complications arising due to pedicle wall breach. This study aims to assess the results of dorsolumbar fractures operated by this technique.
Materials and Methods:
Thirty consecutive skeletally mature patients of fractures of dorsolumbar spine (T9–L5) were subjected to an optoelectronic navigation system. All patients were thoroughly examined for neurological deficit. The criterion for instability were either a tricolumnar injury or presence of neurological deficit or both. Patients with multilevel fractures and distorted spine were excluded from study. Time taken for insertion of each pedicle screw was recorded and placement assessed with a postoperative CT scan using Laine's grading system.
Only one screw out of a total of 118 screws was misplaced with a Laine's Grade 5 placement, showing a misplacement rate of 0.847%. Average time for matching was 7.8 min (range 5-12 min). Average time taken for insertion of a single screw was 4.19 min (range 2-8 min) and total time for all screws after exposure was 34.23 min (range 24-45 min) for a four screw construct. No neurovascular complications were seen in any of the patients postoperatively and in subsequent followup of 1-year duration.
CT-based navigation is effective in improving accuracy of pedicle screw placement in traumatic injuries of dorsolumbar spine (T9-L5), however additional cost of procuring CT scan to the patient and cost of equipment is of significant concern in developing countries. Reduced radiation exposure and lowered ergonomic constraints around the operation table are its additional benefits.
Dorso lumbar spine; Laine's grading; navigation; paired point matching; Spine; spinal fractures; bone screws; neuronavigation; tomography
No single study has established the superiority of one treatment of Kienböck’s disease over the other. Pooled outcome data is presently considered the best way to add to the knowledge and understanding of Kienböck’s disease.
A total of 12 patients (9 male and 3 female) with Kienböck’s disease were included in the present case series. The mean age of the 12 patients was 28 years. One patient presented in Lichtman stage I, five in Lichtman stage II, five in Lichtman stage IIIa, and one in Lichtman stage IV. Univariate and multivariate analyses of the obtained data were performed to identify any correlations.
The mean follow-up time was 62 months, and the mean modified Mayo wrist score improved from the preoperative value of 29.5 to the final value of 89.6. Lichtman stage at presentation showed moderate positive correlation with the duration of symptoms (r = 0.56), and a strong negative correlation with the preoperative and final modified Mayo scores (r = –0.89 and r = –0.77, respectively). The final modified Mayo score showed moderate negative correlation with the duration of the symptoms (r = –0.55). There was a significant difference in the preoperative modified Mayo scores of patients who presented in stage II and those of patients who presented in stage IIIa (p = 0.03). However, the difference in the final modified Mayo scores of the patients in these stages was not significant (p = 0.14).
Lichtman’s stage is moderately related to the duration of symptoms, suggesting natural progression of the disease. The final outcomes of stages II and IIIa were the same irrespective of the surgical treatment (radial shortening and/or vascularised bone grafting).
Kienböck’s disease; lunate; wrist
Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications.
Electronic supplementary material
The online version of this article (doi:10.1007/s12298-013-0198-y) contains supplementary material, which is available to authorized users.
Proteomics; Plants; Agriculture; Food security; Abiotic stress; Biotic stress
Head banging is a sleep-related rhythmic movement disorder of unknown etiology. It is common during infancy; however, available literature suggests that prevalence decreases dramatically after childhood. We report the case of a 16-year-old male who presented with head banging. The symptoms were interfering with his functioning and he had been injured because of the same in the past. We are presenting the video-polysomnographic data of the case. Possible differential diagnoses, etiology, and treatment modalities are discussed. The boy was prescribed clonazepam and followed up for 3 months. Parents did not report any episode afterward.
Head banging; parasomnia; sleep-related rhythmic movement disorder
This study was carried out to assess different counteracting strategies used by patients with idiopathic Willis-Ekbom disease (RLS/WED). Whether these strategies were influenced by gender or disease severity was also assessed.
Materials and Methods:
A total of 173 patients of idiopathic RLS/WED were included in this study. Their demographic data was recorded. Details regarding the RLS/WED and strategies that they used to counteract the symptoms were asked. The severity of RLS/WED was measured with the help of the Hindi version of international restless legs syndrome severity rating scale. They were asked to provide the details regarding the relief obtained from all the strategies they used on three-point scale: no relief, some relief, and complete relief.
Of the patients, 72% were females. Mean age of the subjects in this study was 39.6 ± 12.6 years, and male subjects were older than females. Four common strategies were reported by the patients to counter the sensations of RLS/WED: moving legs while in bed (85.5%), asking somebody to massage their legs or massaging legs themselves (76.9%), walking (53.2%), and tying a cloth/rope tightly on the legs (39.3%). Of all the patients who moved their legs, 6.7% did not experience any relief, 64.2% reported some relief, and 28.4% reported complete relief. Similarly, of all the patients who used “walking” to counteract symptoms, 50% reported complete relief, 44.5% reported some relief, and the rest did not experience any relief. Many of these patients reported that massage and tying a cloth/rope on legs brought greater relief than any of these strategies. Tying cloth on the leg was more common among females as compared to males (45.9% females vs. 23.5% males; χ2 = 7.54; P = 0.006), while patients with moderately severe to severe RLS/WED reported “moving legs in bed” (79.3% in mild to moderate RLS/WED; 91.8% in severe to very severe RLS; χ2 = 5.36; P = 0.02).
Patients with RLS/WED use a variety of strategies to counteract symptoms. These strategies may be influenced by gender, disease severity, and cultural practices.
Counter-acting strategies; gender; severity; Willis-Ekbom disease (RLS/WED)
To determine incidence of various types of sport injuries and other associated factors, among competitive sports playing school children of Chandigarh.
This study is a survey based study, and spanned for a period of one year. School going students in age group 11–18 years of Chandigarh (Union Territory) India, who were in competitive sports, were included for this survey after taking informed consent from concerned school authorities. 33 schools consisting of 36.165 students were analysed in the study, 7230 students were found to participate in 40 different categories of sports.
Total of 246 filled questionnaires were analyzed making it an injury frequency of 3.40% among 7230 participating young athletes in 12 months study duration. Estimated incidence rate, considering hours of exposure in practice, came out to be 48.07 injuries per 1000 h of exposure in practice among 246 injured cases.
40.2% of the injured children (99/246) attributed their injury to poor ground condition while other 30.5% (75/246) to faulty techniques. Rest attributed their injuries to poor fitness levels, improper use of equipment and other reasons. Of the 33 schools surveyed, 27.3% (9/33) had a doctor as health professional, 9.1% (2/33) had a physiotherapist while 66.6% of the schools (22/33) had no health care professional.
The incidence of sports injuries in the region is high as compared to the global data. The findings has highlighted the need for a nationwide surveillance system and then taking appropriate measures for future injury prevention and appropriate management.
Sports injuries; School children; Indian; Epidemiology
Emergence and spread of carbapenemases in Enterobacteriaceae is a cause of concern worldwide, the latest threat being New Delhi metallo-β-lactamase (NDM-1). This report is of an orthopedic case with fracture femur managed with internal fixation and bone grafting, who subsequently developed secondary infection with Klebsiella pneumoniae harboring blaNDM-1 gene. Minimum inhibitory concentration (MIC) of imipenem was ≥8 μg/ml by E-test, suggestive of carbapenemase production. Phenotypic and further genotypic detection confirmed the presence of blaNDM-1 gene. The isolate remained susceptible only to tigecycline, colistin, and polymyxin B.
Carbapenemase; Klebsiella pneumoniae; New Delhi metallo-β-lactamase; Klebsiella; orthopedic surgery; betalactamase
Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.
No study has ever evaluated the causes and effect of neglect on the outcome of post burns contractures of hand in children.
66 hands in 61 children (mean age 12.22 years) with a mean neglect of 11.6 years (range 5–17 years) were assessed for the causes of neglect and the outcome of surgery. Average follow up was 6.6 years. The results were assessed in two groups of 5–10 years neglect as group I and >10 years neglect as group II.
In a total number of 134 contracted rays in 66 hands, the surgical procedures included local Z/V-Y flap (51 rays), cross finger flap (48 rays), full thickness graft (35 rays). Additional external fixator with a distracter was used in 3 patients treated at a delay of 14, 16 and 17 years.
50 (81.96%) patients belonged to rural and slum areas. The reasons for delayed treatment included poverty – 33 patients, lack of awareness of surgical treatment – 16 patients; and indifference of parents – 12 patients. 44 (72.13%) children were illiterates. With treatment the average DASH score improved from 65.10 to 36.90 (p < .000) and from 68.14 to 45.93 (p < .000) in group I and II respectively. The results were significantly superior in group I (p < .000).
The main factors for neglect in treatment of post burns contracture include poverty, lack of awareness and illiteracy. All the patients showed significant improvement in function after the surgery. Contractures with higher neglect had significantly inferior outcome.
Neglected; Post burn; Hand contractures; Surgical outcome; Pediatric
The mechanism of chloroquine (CQ) resistance in Plasmodium falciparum is not clearly understood. However, CQ resistance has been shown to be associated with point mutations in Pfcrt and Pfmdr1. These genes encode for digestive vacuole transmembrane proteins Pfcrt and Pgh1, respectively. The present study was carried out to analyze the association of Pfcrt-K76T and Pfmdr1-N86Y mutations with CQ resistance in Northeast Indian P. falciparum isolates. 115 P. falciparum isolates were subjected to in vitro CQ sensitivity testing and PCR-RFLP analysis for the Pfmdr1-N86Y and Pfcrt-K76T mutations. 100 isolates of P. falciparum were found to be resistant to CQ by the in vitro susceptibility test (geometric mean EC50 2.21 µM/L blood) while 15 were found to be CQ sensitive (geometric mean EC50 0.32 µM/L blood). All the CQ resistant isolates showed the presence of Pfmdr1 and Pfcrt mutations. CQ sensitive isolates were negative for these mutations. Strong linkage disequilibrium was observed between the alleles at these two loci (Pfmdr1-N86Y and Pfcrt-K76T). The results indicate that Pfmdr1-N86Y and Pfcrt-K76T mutations can be used as molecular markers to identify CQ resistance in P. falciparum. The result necessitates the evaluation of CQ in vivo therapeutic efficacy in endemic areas for more effective malaria control strategies.
Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. We have sequenced the genome and transcriptome of Amaranthus hypochondriacus, a diploid (2n = 32) belonging to the order Caryophyllales with an estimated genome size of 466 Mb. Of the 411 linkage single-nucleotide polymorphisms (SNPs) reported for grain amaranths, 355 SNPs (86%) are represented in the scaffolds and 74% of the 8.6 billion bases of the sequenced transcriptome map to the genomic scaffolds. The genome of A. hypochondriacus, codes for at least 24,829 proteins, shares the paleohexaploidy event with species under the superorders Rosids and Asterids, harbours 1 SNP in 1,000 bases, and contains 13.76% of repeat elements. Annotation of all the genes in the lysine biosynthetic pathway using comparative genomics and expression analysis offers insights into the high-lysine phenotype. As the first grain species under Caryophyllales and the first C4 dicot genome reported, the work presented here will be beneficial in improving crops and in expanding our understanding of angiosperm evolution.
Caryophyllales; grain amaranth; Amaranthus hypochondriacus; lysine biosynthesis; C4 photosynthesis
From an immunologist perspective, sharks are an important group of jawed cartilaginous fishes and survey of the public database revealed a great gap in availability of large-scale sequence data for the group of Chondrichthyans the elasmobranchs. In an attempt to bridge this deficit we generated the transcriptome from the spleen and kidney tissues (a total of 1,606,172 transcripts) of the shark, Chiloscyllium griseum using the Illumina HiSeq2000 platform. With a cut off of > = 300 bp and an expression value of >1RPKM we used 43,385 transcripts for BLASTX analysis which revealed 17,548 transcripts matching to the NCBI nr database with an E-value of < = 10−5 and similarity score of 40%. The longest transcript was 16,974 bases with matched to HECT domain containing E3 ubiqutin protein ligase. MEGAN4 annotation pipeline revealed immune and signalling pathways including cell adhesion molecules, cytokine-cytokine receptor interaction, T-cell receptor signalling pathway and chemokine signaling pathway to be highly expressed in spleen, while different metabolism pathways such as amino acid metabolism, carbohydrate metabolism, lipid metabolism and xenobiotic biodegradation were highly expressed in kidney. Few of the candidate genes were selected to analyze their expression levels in various tissues by real-time PCR and also localization of a receptor by in-situ PCR to validate the prediction. We also predicted the domains structures of some of the identified pattern recognition receptors, their phylogenetic relationship with lower and higher vertebrates and the complete downstream signaling mediators of classical dsRNA signaling pathway. The generated transcriptome will be a valuable resource to further genetic and genomic research in elasmobranchs.