Use of SNPs to determine the breakpoints of complex deficiencies, facilitating gene mapping in Caenorhabditis elegans

BACKGROUND: Genetic deletions or deficiencies have been used for gene mapping and discovery in various organisms, ranging from the nematode Caenorhabditis elegans all the way to humans. One problem with large deletions is the determination of the location of their breakpoints. This is exacerbated in the case of complex deficiencies that delete a region of the genome, while retaining some of the intervening sequence. Previous methods, using genetic complementation or cytology were hampered by low marker density and were consequently not very precise at positioning the breakpoints of complex deficiencies. The identification of increasing numbers of Single Nucleotide Polymorphisms (SNPs) has resulted in the use of these as genetic markers, and consequently in their utilization for defining the breakpoints of deletions using molecular biology methods. RESULTS: Here, we show that SNPs can be used to help position the breakpoints of a complex deficiency in C. elegans. The technique uses a combination of genetic crosses and molecular biology to generate robust and highly reproducible results with strong internal controls when trying to determine the breakpoints of deficiencies. The combined use of this technique and standard genetic mapping allowed us to rapidly narrow down the region of interest in our attempts to clone a gene. CONCLUSION: Unlike previous methods used to locate deficiency breakpoints, our technique has the advantage of not being limited by the amount of starting material. It also incorporates internal controls to eliminate false positives and negatives. The technique can also easily be adapted for use in other organisms in which both genetic deficiencies and SNPs are available, thereby aiding gene discovery in these other models

Chromatin status and transcription factor binding to gonadotropin promoters in gonadotrope cell lines.

BackgroundProper expression of key reproductive hormones from gonadotrope cells of the pituitary is required for pubertal onset and reproduction. To further our understanding of the molecular events taking place during embryonic development, leading to expression of the glycoproteins luteinizing hormone (LH) and follicle-stimulating hormone (FSH), we characterized chromatin structure changes, imparted mainly by histone modifications, in model gonadotrope cell lines.MethodsWe evaluated chromatin status and gene expression profiles by chromatin immunoprecipitation assays, DNase sensitivity assay, and RNA sequencing in three developmentally staged gonadotrope cell lines, αT1-1 (progenitor, expressing Cga), αT3-1 (immature, expressing Cga and Gnrhr), and LβT2 (mature, expressing Cga, Gnrhr, Lhb, and Fshb), to assess changes in chromatin status and transcription factor access of gonadotrope-specific genes.ResultsWe found the common mRNA α-subunit of LH and FSH, called Cga, to have an open chromatin conformation in all three cell lines. In contrast, chromatin status of Gnrhr is open only in αT3-1 and LβT2 cells. Lhb begins to open in LβT2 cells and was further opened by activin treatment. Histone H3 modifications associated with active chromatin were high on Gnrhr in αT3-1 and LβT2, and Lhb in LβT2 cells, while H3 modifications associated with repressed chromatin were low on Gnrhr, Lhb, and Fshb in LβT2 cells. Finally, chromatin status correlates with the progressive access of LHX3 to Cga and Gnrhr, followed by PITX1 binding to the Lhb promoter.ConclusionOur data show the gonadotrope-specific genes Cga, Gnrhr, Lhb, and Fshb are not only controlled by developmental transcription factors, but also by epigenetic mechanisms that include the modulation of chromatin structure, and histone modifications

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

INTRODUCTION: Invertebrate communities are central to many environmental monitoring programs. In freshwater ecosystems, aquatic macroinvertebrates are collected, identified and then used to infer ecosystem condition. Yet the key step of species identification is often not taken, as it requires a high level of taxonomic expertise, which is lacking in most organizations, or species cannot be identified as they are morphologically cryptic or represent little known groups. Identifying species using DNA sequences can overcome many of these issues; with the power of next generation sequencing (NGS), using DNA sequences for routine monitoring becomes feasible. RESULTS: In this study, we test if NGS can be used to identify species from field-collected samples in an important bioindicator group, the Chironomidae. We show that Cytochrome oxidase I (COI) and Cytochrome B (CytB) sequences provide accurate DNA barcodes for chironomid species. We then develop a NGS analysis pipeline to identifying species using megablast searches of high quality sequences generated using 454 pyrosequencing against comprehensive reference libraries of Sanger-sequenced voucher specimens. We find that 454 generated COI sequences successfully identified up to 96% of species in samples, but this increased up to 99% when combined with CytB sequences. Accurate identification depends on having at least five sequences for a species; below this level species not expected in samples were detected. Incorrect incorporation of some multiplex identifiers (MID’s) used to tag samples was a likely cause, and most errors could be detected when using MID tags on forward and reverse primers. We also found a strong quantitative relationship between the number of 454 sequences and individuals showing that it may be possible to estimate the abundance of species from 454 pyrosequencing data. CONCLUSIONS: Next generation sequencing using two genes was successful for identifying chironomid species. However, when detecting species from 454 pyrosequencing data sets it was critical to include known individuals for quality control and to establish thresholds for detecting species. The NGS approach developed here can lead to routine species-level diagnostic monitoring of aquatic ecosystems

The impact of recent vincristine on human hematopoietic progenitor cell collection in pediatric patients with central nervous system tumors

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108370/1/trf12574.pd

On the mesoscopic origins of high viscosities in some polyelectrolyte-surfactant mixtures

This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 143, 074902 (2015) and may be found at https://doi.org/10.1063/1.4928583.Oppositely charged polyelectrolyte (PE) surfactant mixtures allow the control of rheological parameters of a solution even at fairly low concentrations. For example, addition of 0.3 wt. % of anionic surfactant to a 1 wt. % solution of the polycation JR 400 increases the viscosity by 4 orders of magnitude. Recently, we could show that this increase is related to the formation of mixed, rod-like PE/surfactant aggregates which interconnect several polyelectrolyte chains [Hoffmann et al., Europhys. Lett. 104, 28001 (2013)]. In this paper, we refine our structural model of the aggregates to obtain a more consistent picture of their internal structure for different anionic surfactants. Combining small angle neutron scattering (SANS) and neutron spin-echo (NSE) allows us to determine the size of the aggregates. By comparing different contrasts, the internal structure of the aggregates can be elucidated and it is seen that the PE in the aggregates retains a relatively high freedom of movement. We proceeded to investigate the influence of the surfactant concentration and the surfactant type on structure and dynamics of the mixed aggregates. It is seen that the structural parameters of the aggregates depend very little on the surfactant concentration and headgroup. However, it is crucial to incorporate a sufficient amount of PE in the aggregates to increase the viscosity of the aggregates. By comparing viscous samples at 1 wt. % PE concentration with samples at a PE concentration of 0.3 wt. %, where no significant increase in viscosity is observed, we find that similar aggregates are formed already at this lower PE concentrations. However, the amount of PE incorporated in them is insufficient to interconnect several PE chains and therefore, they do not increase viscosity. So, our detailed investigation combining contrast variation SANS and NSE does not only allow to explain the viscosity behavior but also to deduced detailed information regarding the structures and the dynamics especially of the polyelectrolyte within the complexes.BMBF, 05K13KT1, Probenumgebung und paralle Charakterisierung bei hochpräzisen Neutronen Spin-Echo (NSE) Messungen an komplexen Systemen der weichen Materi

A 52-Week Study of Olanzapine with a Randomized Behavioral Weight Counseling Intervention in Adolescents with Schizophrenia or Bipolar I Disorder

Objectives: To evaluate the 52-week safety/tolerability of oral olanzapine for adolescents with schizophrenia or bipolar mania and compare effectiveness of a standard versus intense behavioral weight intervention in mitigating risk of weight gain. Methods: Patients 13?17 years old with schizophrenia (Brief Psychiatric Rating Scale for Children [BPRS-C] total score >30; item score ≥3 for hallucinations, delusions, or peculiar fantasies) or bipolar I disorder (manic or mixed episode; Young Mania Rating Scale [YMRS] total score ≥15) received open-label olanzapine (2.5?20?mg/day) and were randomized to standard (n?=?102; a single weight counseling session) or intense (n?=?101; weight counseling at each study visit) weight intervention. The primary outcome measure was mean change in body mass index (BMI) from baseline to 52 weeks using mixed-model repeated measures. Symptomatology was also assessed. Results: No statistically significant differences between groups were observed in mean baseline-to-52-week change in BMI (standard: +3.6?kg/m2; intense: +2.8?kg/m2; p?=?0.150) or weight (standard: +12.1?kg; intense: +9.6?kg; p?=?0.148). Percentage of patients at endpoint who had gained ≥15% of their baseline weight was 40% for the standard group and 31% for the intense group (p?=?0.187). Safety/tolerability results were generally consistent with those of previous olanzapine studies in adolescents, with the most notable exception being the finding of a mean decrease in prolactin. On symptomatology measures, patients with schizophrenia had a mean baseline-to-52-week change in BPRS-C of ?32.5 (standard deviation [SD]?=?10.8), and patients with bipolar disorder had a mean change in YMRS of ?16.7 (SD?=?8.9), with clinically and statistically significant improvement starting at 3?4 days for each. Conclusions: Long-term weight gain was high in both groups, with no statistically significant differences between the standard or intense behavioral weight interventions in BMI or weight. Safety, tolerability, and effectiveness findings were generally consistent with the known profile of olanzapine in adolescents.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140324/1/cap.2016.0010.pd

Comparative results of transluminal extraction coronary atherectomy in saphenous vein graft lesions with and without thrombus

AbstractObjectives. The purpose of this retrospective study was to compare the results of transluminal extraction coronary atherectomy in saphenous vein graft lesions with and without angiographic thrombus.Background. Percutaneous interventions in lesions with thrombus are associated with reduced procedural success and increased risk of complications. Use of the transluminal extraction catheter, which cuts and aspirates atheroma and thrombus, has been advocated as a potential revascularization strategy for lesions with thrombus.Methods. Baseline patient characteristics, lesion morphology, immediate angiographic results, in-hospital complications and follow-up were prospectively entered into an interventional cardiology data base. The results of transluminal extraction coronary atherectomy in saphenous vein bypass grafts with angiographic thrombus were compared with results in similar grafts without angiographic thrombus.Results. Transluminal extraction coronary atherectomy was performed in 175 patients with 183 vein graft lesions, including 59 lesions (32%) with thrombus (Group 1) and 124 (68%) without thrombus (Group 2). Compared with lesions in Group 2, lesions in Group 1 were associated with a higher incidence of baseline total occlusion, diffuse disease and abnormal Thrombolysis in Myocardial Infarction (TIMI) grade flow (p < 0.05); more severe diameter stenosis at baseline, after atherectomy and after final angiography (p < 0.05); a lower rate of clinical success (69% vs, 88%, p < 0.01); and more angiographic and clinical complications, including no reflow (p < 0.05), vascular repair (p < 0.05) and Q wave myocardial infarction (p = 0.09).Conclusions. In transluminal extraction coronary atherectomy of saphenous vein bypass grafts, the presence of thrombus is associated with more baseline lesion complexity, reduced clinical success and increased risk of no reflow, Q wave myocardial infarction and vascular repair

Systematic Study of Decryption and Re-Encryption Leakage: the Case of Kyber

The side-channel cryptanalysis of Post-Quantum (PQ) key encapsulation schemes has been a topic of intense activity over the last years. Many attacks have been put forward: Simple Power Analysis (SPAs) against the re-encryption of schemes using the Fujisaki-Okamoto (FO) transform are known to be very powerful; Differential Power Analysis (DPAs) against the decryption are also possible. Yet, to the best of our knowledge, a systematic and quantitative investigation of their impact for designers is still missing. In this paper, we propose to capture these attacks with shortcut formulas in order to compare their respective strength in function of the noise level. Taking the case of Kyber for illustration, we then evaluate the (high) cost of preventing them with masking and the extent to which different parts of an implementation could benefit from varying security levels. We finally discuss tweaks to improve the situation and enable a better leveling of the countermeasures. Our conclusions confirm that current solutions for side-channel secure PQ key encapsulation schemes like Kyber are unlikely to be efficient in low-noise settings without (design or countermeasures) improvements

Proposal for the delineation of neoadjuvant target volumes in oesophageal cancer

PURPOSE: To define instructions for delineation of target volumes in the neoadjuvant setting in oesophageal cancer. MATERIALS AND METHODS: Radiation oncologists of five European centres participated in the following consensus process: [1] revision of published (MEDLINE) and national/institutional delineation guidelines; [2] first delineation round of five cases (patient 1-5) according to national/institutional guidelines; [3] consensus meeting to discuss the results of step 1 and 2, followed by a target volume delineation proposal; [4] circulation of proposed instructions for target volume delineation and atlas for feedback; [5] second delineation round of five new cases (patient 6-10) to peer review and validate (two additional centres) the agreed delineation guidelines and atlas; [6] final consensus on the delineation guidelines depicted in an atlas. Target volumes of the delineation rounds were compared between centres by Dice similarity coefficient (DSC) and maximum/mean undirected Hausdorff distances (Hmax/Hmean). RESULTS: In the first delineation round, the consistency between centres was moderate (CTVtotal: DSC = 0.59-0.88; Hmean = 0.2-0.4 cm). Delineations in the second round were much more consistent. Lowest variability was obtained between centres participating in the consensus meeting (CTVtotal: DSC: p < 0.050 between rounds for patients 6/7/8/10; Hmean: p < 0.050 for patients 7/8/10), compared to validation centres (CTVtotal: DSC: p < 0.050 between validation and consensus meeting centres for patients 6/7/8; Hmean: p < 0.050 for patients 7/10). A proposal for delineation of target volumes and an atlas were generated. CONCLUSION: We proposed instructions for target volume delineation and an atlas for the neoadjuvant radiation treatment in oesophageal cancer. These will enable a more uniform delineation of patients in clinical practice and clinical trials