Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa.

Homozygosity mapping is an effective tool for detecting genomic regions responsible for a given trait when the phenotype is controlled by a limited number of dominant or co-dominant loci. Freezing tolerance is a major attribute in agricultural crops such as camelina. Previous studies indicated that freezing tolerance differences between a tolerant (Joelle) and susceptible (CO46) variety of camelina were controlled by a small number of dominant or co-dominant genes. We performed whole genome homozygosity mapping to identify markers and candidate genes responsible for freezing tolerance difference between these two genotypes. A total of 28 F3 RILs were sequenced to ∼30× coverage, and parental lines were sequenced to >30-40× coverage with Pacific Biosciences high fidelity technology and 60× coverage using Illumina whole genome sequencing. Overall, about 126k homozygous single nucleotide polymorphism markers were identified that differentiate both parents. Moreover, 617 markers were also homozygous in F3 families fixed for freezing tolerance/susceptibility. All these markers mapped to two contigs forming a contiguous stretch of chromosome 11. The homozygosity mapping detected 9 homozygous blocks among the selected markers and 22 candidate genes with strong similarity to regions in or near the homozygous blocks. Two such genes were differentially expressed during cold acclimation in camelina. The largest block contained a cold-regulated plant thionin and a putative rotamase cyclophilin 2 gene previously associated with freezing resistance in arabidopsis (Arabidopsis thaliana). The second largest block contains several cysteine-rich RLK genes and a cold-regulated receptor serine/threonine kinase gene. We hypothesize that one or more of these genes may be primarily responsible for freezing tolerance differences in camelina varieties.

Sleeve gastrectomy versus Roux-en-Y Gastric Bypass for remission of type 2 diabetes mellitus at 1, 3 and 5 years: a systematic review and meta-analysis.

BACKGROUND: Sleeve gastrectomy (SG) and Roux-en-Y Gastric Bypass (RYGB) are the two procedures used in the management of patient with obesity and type 2 diabetes mellitus (T2DM); however, it is still unclear which of the two is more efficient in the remission of type-2 diabetes mellitus. METHODS: The aim of this study was to analyze the efficiency of RYGB and SG in the remission of type-2 diabetes mellitus after 1, 3 and 5 years of surgery. Three databases (i.e., PubMed, Scopus, Central and Web of Science) were searched. All randomized control trial studies with at least 12-year follow-up were selected with type-2 diabetes mellitus in patients undergoing Roux-en-Y Gastric Bypass or sleeve gastrectomy. The broad and the narrow criteria were lined with individual patients reported, being analyzed and pooled using the random-effects model. RESULTS: The 15 selected articles, including 707 obese type 2 diabetes patients, met the eligibility criteria for this meta-analysis. RYGB when compared with SG shows increased broad remissions (RR=1.43, 95% CI: 1.13-1.80; P=0.003) and narrow remissions (RR=1.32, 95% CI: 1.15-1.58; P=0.003) after one year of surgery, and broad remissions 5 years after surgery (RR=1.58, 95% CI: 0.97-2.56; P=0.06). No significant difference was identified between the two groups in broad and narrow remissions 3 years after surgery and narrow remissions 5 years after surgery. CONCLUSIONS: Our results suggest that RYGB was more effective in the remission of type-2 diabetes mellitus at 1 year and 5 years considering the broad and narrow criteria, while there was no difference found 3 years after surgery.

Genome-wide association mapping and genomic prediction for adult stage sclerotinia stem rot resistance in Brassica napus (L) under field environments.

Sclerotinia stem rot (SSR) is a fungal disease of rapeseed/canola that causes significant seed yield losses and reduces its oil content and quality. In the present study, the reaction of 187 diverse canola genotypes to SSR was characterized at full flowering stage using the agar plug to stem inoculation method in four environments. Genome-wide association study (GWAS) using three different algorithms identified 133 significant SNPs corresponding with 123 loci for disease traits like stem lesion length (LL), lesion width (LW), and plant mortality at 14 (PM_14D) and 21 (PM_21D) days. The explained phenotypic variation of these SNPs ranged from 3.6 to 12.1%. Nineteen significant SNPs were detected in two or more environments, disease traits with at least two GWAS algorithms. The strong correlations observed between LL and other three disease traits evaluated, suggest they could be used as proxies for SSR resistance phenotyping. Sixty-nine candidate genes associated with disease resistance mechanisms were identified. Genomic prediction (GP) analysis with all the four traits employing genome-wide markers resulted in 0.41-0.64 predictive ability depending on the model specifications. The highest predictive ability for PM_21D with three models was about 0.64. From our study, the identified resistant genotypes and stable significant SNP markers will serve as a valuable resource for future SSR resistance breeding. Our study also suggests that genomic selection holds promise for accelerating canola breeding progress by enabling breeders to select SSR resistance genotypes at the early stage by reducing the need to phenotype large numbers of genotypes.

Testicular pain as an atypical presentation of sarcoidosis.

Sarcoidosis is a systemic granulomatous disease, with genitourinary tract involvement being very rare (0.2% of all sarcoidosis cases). Genitourinary sarcoidosis may present with a scrotal mass with or without testicular pain, often mimicking epididymo-orchitis or malignancy. Only 8 cases of genitourinary sarcoidosis have been reported in the literature in the last 14 years. We describe the case of a 25-year-old man who was referred with testicular pain. Scrotal ultrasonography demonstrated multiple bilateral hypoechoic testicular lesions that were of similar size and distributed unusually throughout the testicular parenchyma. Computed tomography detected a nodule in the middle lobe of the right lung, multiple small volume nodes in the retrocaval and left para-aortic regions, and enlarged bilateral external iliac and inguinal nodes, similar to those found in metastatic testicular cancer. Following ultrasound guided excision of one of the lesions, histopathological examination confirmed granulomatous inflammation consistent with sarcoidosis.

Purification and characterization of alkaline soda-bleach stable protease from Bacillus sp. APP-07 isolated from Laundromat soil.

The detergent-compatible alkaline protease was produced from the bacterial strain Bacillus sp. APP-07 isolated from Laundromat soil of Solapur, Maharashtra, India. The culture was grown in 1000 ml capacity baffled flask with a working volume of 100 ml and incubated at 55 °C for 33 h on a rotary shaker. After incubation, alkaline protease was partially purified by the sequential method of acetone precipitation followed by nominal molecular weight limit (NMWL) cut-off ultrafiltration using 50 K and 10 K filters. Finally, Sephadex G-100 gel filtration chromatographic purification was performed to obtain 3.12 fold purified alkaline protease enzyme with a 66.67% final yield. The purified enzyme showed 31907.269 units (U) of enzyme activity containing 8741.718 U/mg of specific enzyme activity. The molecular weight of the enzyme was confirmed about 33.0 kDa (kDa) by the SDS-PAGE analysis. The purified enzyme was stable at higher pH and temperature range, with an optimum pH 10.5 and temperature 55 °C. The enzyme showed excellent stability and compatibility in various detergents, surfactants, bleach, and oxidizing agents. The enzyme activity enhanced in the presence of Ca2+, Cu2+, and surfactants, whereas; the phenylmethylsulphonyl fluoride (PMSF) and Diisopropyl fluorophosphate (DFP) completely inhibit the enzymatic activity, which pointed out that the enzyme affiliated to serine-centered metalloproteases family. In conclusion, the remarkable tolerance and stability of the enzyme explored the promising candidature for the several potential applications in the laundry detergents. The sustainability of the enzyme might serve several possible applications in the laundry detergents, leather industries, and other harsh industrial processes.

Is it necessary to perform week three dosimetric analysis in low-dose-rate brachytherapy for prostate cancer when day 0 dosimetry is done? A quality assurance assessment.

PURPOSE: To determine whether computed tomography/magnetic resonance imaging-based day 0 (d0) dosimetry is a meaningful predictor of day 21 (d21) dosimetry in low-dose-rate brachytherapy for localized prostate cancer. METHODS AND MATERIALS: The study population consisted of 277 men with localized (T1-2 N0 M0), low-/intermediate-risk prostate cancer treated with low-dose-rate brachytherapy. Computed tomography/magnetic resonance imaging fusion was used for postimplant dosimetry at d0 and d21. Logistic regression was used to construct receiver operating characteristic curves for achieving each constraint at d21, based on d0 D90 and V100, and Youden's index was used to evaluate cutpoints. Freedom from biochemical failure (FBCF) was estimated with the Kaplan-Meier method. RESULTS: The median d0 D90 increased from 133 to 150 Gy at d21, and median d0 V100 increased from 87% to 91%. For achieving the D90 constraint at d21, the optimal cut-point for d0 D90 was 135 Gy, with 84% of these patients maintaining a d21 D90 > 145 Gy. For achieving the D90 constraint at d21, the optimal cut-point for d0 V100 was 87%, with 83% of these patients maintained a d21 V100 > 90%. There was no improvement in FBCF in patients with a d0 D90 > 135 Gy or D90 > 145 Gy. Similarly, there was no improvement in FBCF in patients with a d0 V100 > 87% or V100 > 90%. CONCLUSIONS: Meeting dosimetric constraints on d0 does not obviate d21 dosimetric analysis. Constraints used for dose prescriptions on d0 are not the ideal predictors of d21 dosimetry.

Diabetes during Ramadan - PRE-approach model: presentation, risk stratification, education.

OBJECTIVE: Fasting (Sawm) during Ramadan is one of the five pillars of Islam and mandatory for all Muslim healthy adults. Most of the Muslim diabetic patients insist on fasting in Ramadan despite their exemption. Due to paucity of literature, diabetes during Ramadan is underestimated and the statistics are not reflecting the actual reality. The aim of this study is to highlight the demographics in diabetic Muslim population and emphasize its ramifications on Ramadan fasting. METHODS: In this study, we developed a 3 step PRE-approach model based on Presentation, Risk stratification, Education in diabetics who fast during Ramadan. For the establishment of this model we identified 40 published studies in database searches including ISI-web of science and pub-med. We searched the related literature by using the key words including diabetes mellitus, Ramadan fasting. All studies in which diabetes and fasting in Ramadan was investigated were included. There was no limitation on publication status, design or language. Finally, we included 35 publications and remaining 5 were excluded from the study. RESULTS: The diabetic patients who fast are at risk of severe hypoglycemia, hyperglycemia, diabetic ketoacidosis, dehydration, thrombosis, strokes and retinal artery occlusion. Lack of education, poor healthcare and no structured guidance cause adeverse health consequences. CONCLUSIONS: It is vital to empower the healthcare workers and the patients in the frontlines with appropriate information. To preempt and minimize the problems faced by the diabetic patients who fast, available resources should be mobilized to efficiently and effectively reach out these patients. Diabetic patient educational guidelines about Ramadan fasting should be disseminated and translated into major regional languages to minimize the complications. Diabetic patients who are stable, free of deteriorating complications and able to manage can be allowed to fast.

Use of a virtual reality simulator to improve percutaneous renal access skills: a prospective study in urology trainees.

OBJECTIVES: This study aims to assess the impact of a virtual reality trainer in improving percutaneous renal access skills of urological trainees. METHODS: A total of 36 urology trainees participated in this prospective study. Initially, they were taken through the exercise of gaining access to the lower pole calyceal system and introducing a guidewire down the ureter. Trainees' performance was then assessed by virtual reality-derived parameters of the simulator at baseline and after 2 h of training. RESULTS: Participants who underwent training with the simulator demonstrated significant improvement in several parameters compared to their baseline performance. There was a statistically significant correlation between total time to perform the procedure and time of radiation exposure, radiation dose and correct calyx puncture (p < 0.01). Trainees needed a mean of 15.8 min from skin puncture to correct guidewire placement into the pelvicalyceal system before and 6.49 min following training. CONCLUSIONS: We found percutaneous renal access skills of trainees improve significantly on a number of parameters as a result of training on the PERC Mentor TM VR simulator. Such simulated training has the potential to decrease the risks and complications associated with the early stages of the learning curve when training for percutaneous renal access in patients.

Rare structural variation of synapse and neurotransmission genes in autism.

Autism spectrum disorders (ASDs) comprise a constellation of highly heritable neuropsychiatric disorders. Genome-wide studies of autistic individuals have implicated numerous minor risk alleles but few common variants, suggesting a complex genetic model with many contributing loci. To assess commonality of biological function among rare risk alleles, we compared functional knowledge of genes overlapping inherited structural variants in idiopathic ASD subjects relative to healthy controls. In this study we show that biological processes associated with synapse function and neurotransmission are significantly enriched, with replication, in ASD subjects versus controls. Analysis of phenotypes observed for mouse models of copy-variant genes established significant and replicated enrichment of observable phenotypes consistent with ASD behaviors. Most functional terms retained significance after excluding previously reported ASD loci. These results implicate several new variants that involve synaptic function and glutamatergic signaling processes as important contributors of ASD pathophysiology and suggest a sizable pool of additional potential ASD risk loci.

Laparoscopic sleeve gastrectomy in partial situs inversus.

Laparoscopic surgery in a patient with Partial Situs Inversus may pose interesting challenges to the surgeon. Here we report a case of a morbidly obese young female with partial situs inversus who underwent Laparoscopic Vertical Sleeve Gastrectomy (LSG). The peri-operative challenges very many and these have been enumerated. The mirror image approach is recommended in such cases for a successful surgery which was not employed in this case. Postoperative barium swallow was normal and the patient has been on regular follow up.

Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes.

Attention-deficit/hyperactivity disorder (ADHD) is a common and highly heritable disorder, but specific genetic factors underlying risk remain elusive. To assess the role of structural variation in ADHD, we identified 222 inherited copy number variations (CNVs) within 335 ADHD patients and their parents that were not detected in 2026 unrelated healthy individuals. Although no excess CNVs, either deletions or duplications, were found in the ADHD cohort relative to controls, the inherited rare CNV-associated gene set was significantly enriched for genes reported as candidates in studies of autism, schizophrenia and Tourette syndrome, including A2BP1, AUTS2, CNTNAP2 and IMMP2L. The ADHD CNV gene set was also significantly enriched for genes known to be important for psychological and neurological functions, including learning, behavior, synaptic transmission and central nervous system development. Four independent deletions were located within the protein tyrosine phosphatase gene, PTPRD, recently implicated as a candidate gene for restless legs syndrome, which frequently presents with ADHD. A deletion within the glutamate receptor gene, GRM5, was found in an affected parent and all three affected offspring whose ADHD phenotypes closely resembled those of the GRM5 null mouse. Together, these results suggest that rare inherited structural variations play an important role in ADHD development and indicate a set of putative candidate genes for further study in the etiology of ADHD.

Detailed analysis of 22q11.2 with a high density MLPA probe set.

The presence of chromosome-specific low-copy repeats (LCRs) predisposes chromosome 22 to deletions and duplications. The current diagnostic procedure for detecting aberrations at 22q11.2 is chromosomal analysis coupled with fluorescence in situ hybridization (FISH) or PCR-based multiplex ligation dependent probe amplification (MLPA). However, there are copy number variations (CNVs) in 22q11.2 that are only detected by high-resolution platforms such as array comparative genomic hybridization (aCGH). We report on development of a high-definition MLPA (MLPA-HD) 22q11 kit that detects copy number changes at 37 loci on the long arm of chromosome 22. These include the 3-Mb region commonly deleted in DiGeorge/velocardiofacial syndrome (DGS/VCFS), the cat eye syndrome (CES) region, and more distal regions in 22q11 that have recently been shown to be deleted. We have used this MLPA-HD probe set to analyze 363 previously well-characterized samples with a variety of different rearrangements at 22q11 and demonstrate that it can detect copy number alterations with high sensitivity and specificity. In addition to detection of the common recurrent deletions associated with DGS/VCFS, variant and novel chromosome 22 aberrations have been detected. These include duplications within as well as deletions distal to this region. Further, the MLPA-HD detects deletion endpoint differences between patients with the common 3-Mb deletion. The MLPA-HD kit is proposed as a cost effective alternative to the currently available detection methods for individuals with features of the 22q11 aberrations. In patients with the relevant phenotypic characteristics, this MLPA-HD probe set could replace FISH for the clinical diagnosis of 22q11.2 deletions and duplications.

Fast 3D motif search of EM density maps using a locally normalized cross-correlation function.

Three-dimensional motif search is becoming increasingly important both in the search for molecular signatures within a tomographic reconstruction, at low resolution, and in the search for atomic structures within high-resolution cryo-EM maps of macromolecular complexes. The present work describes the implementation of a fast local correlation algorithm suitable for template matching in the SPIDER environment. Two examples are given, one in each of the areas of application: (i). within a 7.8A single-particle reconstruction of the Escherichia coli ribosome, four proteins and one RNA structure were located with high accuracy; (ii). within a cryo-tomogram of sarcoplasmic reticulum vesicles, ryanodine receptors were located in positions that agreed with expert knowledge.

Antithrombin and anti-Xa agents in the control of thrombogenesis.

Recent developments as well as future trends in the area of thrombin inhibitors and anti-Xa agents are reviewed.

Segmental duplications: an 'expanding' role in genomic instability and disease.

The knowledge that specific genetic diseases are caused by recurrent chromosomal aberrations has indicated that genomic instability might be directly related to the structure of the regions involved. The sequencing of the human genome has directed significant attention towards understanding the molecular basis of such recombination 'hot spots'. Segmental duplications have emerged as a significant factor in the aetiology of disorders that are caused by abnormal gene dosage. These observations bring us closer to understanding the mechanisms and consequences of genomic rearrangement.

Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: an update and literature review.

Several constitutional rearrangements, including deletions, duplications, and translocations, are associated with 22q11.2. These rearrangements give rise to a variety of genomic disorders, including DiGeorge, velocardiofacial, and conotruncal anomaly face syndromes (DGS/VCFS/CAFS), cat eye syndrome (CES), and the supernumerary der(22)t(11;22) syndrome associated with the recurrent t(11;22). Chromosome 22-specific duplications or low copy repeats (LCRs) have been directly implicated in the chromosomal rearrangements associated with 22q11.2. Extensive sequence analysis of the different copies of 22q11 LCRs suggests a complex organization. Examination of their evolutionary origin suggests that the duplications in 22q11.2 may predate the divergence of New World monkeys 40 million years ago. Based on the current data, a number of models are proposed to explain the LCR-mediated constitutional rearrangements of 22q11.2.

Cis-acting influences on Alu RNA levels.

The human short interspersed repeated element (SINE), Alu, amplifies through a poorly understood RNA-mediated mechanism, termed retroposition. There are over one million copies of Alu per haploid human genome. The copies show some internal variations in sequence and are very heterogeneous in chromosomal environment. However, very few Alu elements actively amplify. The amplification rate has decreased greatly in the last 40 million years. Factors influencing Alu transcription would directly affect an element's retroposition capability. Therefore, we evaluated several features that might influence expression from individual Alu elements. The influence of various internal sequence variations and 3' unique flanks on full-length Alu RNA steady-state levels was determined. Alu subfamily diagnostic mutations do not significantly alter the amount of Alu RNA observed. However, sequences containing random mutations throughout the right half of selected genomic Alu elements altered Alu RNA steady-state levels in cultured cells. In addition, sequence variations at the 3' unique end of the transcript also significantly altered the Alu RNA levels. In general, sequence mutations and 3' end sequences contribute to Alu RNA levels, suggesting that the master Alu element(s) have a multitude of individual differences that collectively gives them a selective advantage over other Alu elements.

Alu-mediated PCR artifacts and the constitutional t(11;22) breakpoint.

The breakpoints of the recurrent t(11;22)(q23;q11) have recently been cloned. We identified palindromic AT-rich repeats (PATRRs) on 11q23 and 22q11 as the mechanism responsible for the rearrangement. Contradictory to our results, A.S. Hill et al. (Hum. Mol. Genet., 9, 1525-1532) suggested that Alu-mediated recombination is responsible. To clarify this discrepancy, the cloned 4.5 kb der(11) junction fragment has been completely sequenced. This sequence has been compared with that of an inverse PCR-generated der(11) junction fragment obtained by Hill et al. This reveals that the inverse PCR product has sustained a deletion between two Alu elements, such that the true breakpoint region is deleted from the PCR product. Utilizing PCR primers designed by Hill et al. to amplify across the der(11) breakpoint, we obtained a deleted PCR product even when our cloned der(11) junction fragment was used as template. Further, we find that the PCR primers that they utilized for amplification of the der(22) junction fragment are not located on the der(22). They are oriented in opposite directions within the region deleted from the der(11) PCR product, generating an artifact derived from the der(11) chromosome. Analysis of the truncated PCR products indicates a mixture of sequences from two distinct Alu elements, suggesting that the putative junction fragment described by Hill et al. is an Alu-mediated PCR artifact. These data suggest that caution should be exercised when analyzing PCR-based data, particularly when amplification is carried out in a region containing repeat structures with specific, difficult-to-amplify sequences.

Tightly clustered 11q23 and 22q11 breakpoints permit PCR-based detection of the recurrent constitutional t(11;22).

Palindromic AT-rich repeats (PATRRs) on chromosomes 11q23 and 22q11 at the constitutional t(11;22) breakpoint are predicted to induce genomic instability, which mediates the translocation. A PCR-based translocation-detection system for the t(11;22) has been developed with PCR primers flanking the PATRRs of both chromosomes, to examine the involvement of the PATRRs in the recurrent rearrangement. Forty unrelated carriers of the t(11;22) balanced translocation, plus two additional, independent cases with the supernumerary-der(22) syndrome, were analyzed to compare their translocation breakpoints. Similar translocation-specific junction fragments were obtained from both derivative chromosomes in all 40 carriers of the t(11;22) balanced translocation and from the der(22) in both of the offspring with unbalanced supernumerary-der(22) syndrome, suggesting that the breakpoints in all cases localize within these PATRRs and that the translocation is generated by a similar mechanism. This PCR strategy provides a convenient technique for rapid diagnosis of the translocation, indicating its utility for prenatal and preimplantation diagnosis in families including carriers of the balanced translocation.