140 research outputs found

    DNA profiles generated from a range of touched sample types

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    © 2018 Elsevier B.V. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 12 month embargo from date of publication (June 2018) in accordance with the publisher’s archiving policy.Direct PCR from touch DNA has a range of potential applications in the field of forensic investigation for exhibit examination that, under standard extraction methods, rarely produce informative DNA profiles. Previous studies from ‘touch DNA’ have focussed on fingermarks created under laboratory conditions. Here we report on successful STR DNA profiling from a range of touched items. Direct PCR, with no increase in cycle number, was performed after eight different sample types, typical of those submitted for forensic investigation, were handled by volunteers for a maximum of 15 s to deposit trace amounts of their DNA. Amplifications were performed using either GlobalFiler® or Identifiler® Plus following manufacturer’s instructions. These two kits were chosen deliberately as many laboratories worldwide have adopted and validated them in their workflow, thus allowing for direct PCR to be incorporated within their practises easily. It was found that informative STR profiles were obtained from all eight substrates using both STR kits. Identifiler® Plus out-performed GlobalFiler® in terms of the percentage of alleles amplified using the direct PCR approach. Both generated informative profiles from all items and all individuals, at different rates, with Identifiler® Plus being informative in a larger percentage of samples. GlobalFiler® produced profiles with an average of 60% ± 24% (36 ± 15 alleles) alleles present while Identifiler® Plus produced profiles with an average of 96% ± 4% (31 ± 1 alleles) alleles present. A comparison was made between the direct PCR approach and subjecting touched samples to a standard DNA extraction process, both using Identifiler®. An average of 4% of profiles were informative for samples that underwent extraction with 100% being informative from the same subset of samples amplified by direct PCR. Our findings further demonstrate the success of direct PCR to enhance the STR DNA profiles from touch DNA. Further, Identifiler® Plus was found to generate informative profiles more often than GlobalFiler®. Direct PCR is fast, simple, and non-destructive of evidence with the ability to generate informative genetic data where standard methods are likely to fail

    Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross

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    The oligoadenylate-synthetase (Oas) gene locus provides innate immune resistance to virus infection. In mouse models, variation in the Oas1b gene influences host susceptibility to flavivirus infection. However, the impact of Oas variation on overall innate immune programming and global gene expression among tissues and in different genetic backgrounds has not been defined. We examined how Oas1b acts in spleen and brain tissue to limit West Nile virus (WNV) susceptibility and disease across a range of genetic backgrounds. The laboratory founder strains of the mouse Collaborative Cross (CC) (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, and NZO/HlLtJ) all encode a truncated, defective Oas1b, whereas the three wild-derived inbred founder strains (CAST/EiJ, PWK/PhJ, and WSB/EiJ) encode a full-length OAS1B protein. We assessed disease profiles and transcriptional signatures of F1 hybrids derived from these founder strains. F1 hybrids included wild-type Oas1b (F/F), homozygous null Oas1b (N/N), and heterozygous offspring of both parental combinations (F/N and N/F). These mice were challenged with WNV, and brain and spleen samples were harvested for global gene expression analysis. We found that the Oas1b haplotype played a role in WNV susceptibility and disease metrics, but the presence of a functional Oas1b allele in heterozygous offspring did not absolutely predict protection against disease. Our results indicate that Oas1b status as wild-type or truncated, and overall Oas1b gene dosage, link with novel innate immune gene signatures that impact specific biological pathways for the control of flavivirus infection and immunity through both Oas1b-dependent and independent processes

    Documenting ---- in Bloomington-Normal: A Community Report on Intolerance, Segregation, Accessibility, Inclusion, and Progress, and Improvement

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    For the local chapter of Not In Our Town, we document intolerance, discrimination, segregation, disparities of access, and disparities in the criminal justice system in Bloomington-Normal, IL. Using archival material, secondary data, and primary data, we examine these issues from the mid-1990s to the present. We also assess the position of the organization in the community and provide strategies for future success. In sum, Bloomington-Normal was and is intolerant; discrimination did and does take place in this community; there are disparities of access and in the criminal justice system; we are segregated. The community is also less of these things than it used to be and is less of these things than other places. Fifteen undergraduate students in Sociology 300, twelve graduate students in Sociology 477, a teaching assistant, and an instructor conducted this study in spring 2017

    Site-Selective Solid-Phase Synthesis of a CCR5 Sulfopeptide Library To Interrogate HIV Binding and Entry

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    Tyrosine (Tyr) sulfation is a common post-translational modification that is implicated in a variety of important biological processes, including the fusion and entry of human immunodeficiency virus type-1 (HIV-1). A number of sulfated Tyr (sTyr) residues on the N-terminus of the CCR5 chemokine receptor are involved in a crucial binding interaction with the gp120 HIV-1 envelope glycoprotein. Despite the established importance of these sTyr residues, the exact structural and functional role of this post-translational modification in HIV-1 infection is not fully understood. Detailed biological studies are hindered in part by the difficulty in accessing homogeneous sulfopeptides and sulfoproteins through biological expression and established synthetic techniques. Herein we describe an efficient approach to the synthesis of sulfopeptides bearing discrete sulfation patterns through the divergent, site-selective incorporation of sTyr residues on solid support. By employing three orthogonally protected Tyr building blocks and a solid-phase sulfation protocol, we demonstrate the synthesis of a library of target N-terminal CCR5(2-22) sulfoforms bearing discrete and differential sulfation at Tyr10, Tyr14, and Tyr15, from a single resin-bound intermediate. We demonstrate the importance of distinct sites of Tyr sulfation in binding gp120 through a competitive binding assay between the synthetic CCR5 sulfopeptides and an anti-gp120 monoclonal antibody. These studies revealed a critical role of sulfation at Tyr14 for binding and a possible additional role for sulfation at Tyr10. N-terminal CCR5 variants bearing a sTyr residue at position 14 were also found to complement viral entry into cells expressing an N-terminally truncated CCR5 receptor

    Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B [Letter]

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    Members of the killer cell immunoglobulin-like receptor (KIR) family, a large group of polymorphic receptors expressed on natural killer (NK) cells, recognize particular peptide-laden human leukocyte antigen (pHLA) class I molecules and have a pivotal role in innate immune responses1. Allelic variation and extensive polymorphism within the three-domain KIR family (KIR3D, domains D0–D1–D2) affects pHLA binding specificity and is linked to the control of viral replication and the treatment outcome of certain haematological malignancies1, 2, 3. Here we describe the structure of a human KIR3DL1 receptor bound to HLA-B*5701 complexed with a self-peptide. KIR3DL1 clamped around the carboxy-terminal end of the HLA-B*5701 antigen-binding cleft, resulting in two discontinuous footprints on the pHLA. First, the D0 domain, a distinguishing feature of the KIR3D family, extended towards β2-microglobulin and abutted a region of the HLA molecule with limited polymorphism, thereby acting as an ‘innate HLA sensor’ domain. Second, whereas the D2–HLA-B*5701 interface exhibited a high degree of complementarity, the D1–pHLA-B*5701 contacts were suboptimal and accommodated a degree of sequence variation both within the peptide and the polymorphic region of the HLA molecule. Although the two-domain KIR (KIR2D) and KIR3DL1 docked similarly onto HLA-C4, 5 and HLA-B respectively, the corresponding D1-mediated interactions differed markedly, thereby providing insight into the specificity of KIR3DL1 for discrete HLA-A and HLA-B allotypes. Collectively, in association with extensive mutagenesis studies at the KIR3DL1–pHLA-B*5701 interface, we provide a framework for understanding the intricate interplay between peptide variability, KIR3D and HLA polymorphism in determining the specificity requirements of this essential innate interaction that is conserved across primate species

    Association between neighborhood safety and overweight status among urban adolescents

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    <p>Abstract</p> <p>Background</p> <p>Neighborhood safety may be an important social environmental determinant of overweight. We examined the relationship between perceived neighborhood safety and overweight status, and assessed the validity of reported neighborhood safety among a representative community sample of urban adolescents (who were racially and ethnically diverse).</p> <p>Methods</p> <p>Data come from the 2006 Boston Youth Survey, a cross-sectional study in which public high school students in Boston, MA completed a pencil-and-paper survey. The study used a two-stage, stratified sampling design whereby schools and then 9<sup>th</sup>–12<sup>th </sup>grade classrooms within schools were selected (the analytic sample included 1,140 students). Students reported their perceptions of neighborhood safety and several associated dimensions. With self-reported height and weight data, we computed body mass index (BMI, kg/m<sup>2</sup>) for the adolescents based on CDC growth charts. Chi-square statistics and corresponding <it>p</it>-values were computed to compare perceived neighborhood safety by the several associated dimensions. Prevalence ratios (PRs) and 95% confidence intervals (CI) were calculated to examine the association between perceived neighborhood safety and the prevalence of overweight status controlling for relevant covariates and school site.</p> <p>Results</p> <p>More than one-third (35.6%) of students said they always felt safe in their neighborhood, 43.9% said they sometimes felt safe, 11.6% rarely felt safe, and 8.9% never felt safe. Those students who reported that they rarely or never feel safe in their neighborhoods were more likely than those who said they always or sometimes feel safe to believe that gang violence was a serious problem in their neighborhood or school (68.0% vs. 44.1%, <it>p </it>< 0.001), and to have seen someone in their neighborhood assaulted with a weapon (other than a firearm) in the past 12 months (17.8% vs. 11.3%, <it>p </it>= 0.025). In the fully adjusted model (including grade and school) stratified by race/ethnicity, we found a statistically significant association between feeling unsafe in one's own neighborhood and overweight status among those in the Other race/ethnicity group [(PR = 1.56, (95% CI: 1.02, 2.40)].</p> <p>Conclusion</p> <p>Data suggest that perception of neighborhood safety may be associated with overweight status among urban adolescents in certain racial/ethnic groups. Policies and programs to address neighborhood safety may also be preventive for adolescent overweight.</p

    PSR J1024-0719:A Millisecond Pulsar in an Unusual Long-Period Orbit

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    PSR J1024-0719 is a millisecond pulsar that was long thought to be isolated. However, puzzling results concerning its velocity, distance, and low rotational period derivative have led to a reexamination of its properties. We present updated radio timing observations along with new and archival optical data which show that PSR J1024-0719 is most likely in a long-period (2-20 kyr) binary system with a low-mass (approximate to 0.4 M-circle dot), low-metallicity (Z approximate to -0.9 dex) main-sequence star. Such a system can explain most of the anomalous properties of this pulsar. We suggest that this system formed through a dynamical exchange in a globular cluster that ejected it into a halo orbit, which is consistent with the low observed metallicity for the stellar companion. Further astrometric and radio timing observations such as measurement of the third period derivative could strongly constrain the range of orbital parameters

    Combined Forward-Backward Asymmetry Measurements in Top-Antitop Quark Production at the Tevatron

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    The CDF and D0 experiments at the Fermilab Tevatron have measured the asymmetry between yields of forward- and backward-produced top and antitop quarks based on their rapidity difference and the asymmetry between their decay leptons. These measurements use the full data sets collected in proton-antiproton collisions at a center-of-mass energy of s=1.96\sqrt s =1.96 TeV. We report the results of combinations of the inclusive asymmetries and their differential dependencies on relevant kinematic quantities. The combined inclusive asymmetry is AFBttˉ=0.128±0.025A_{\mathrm{FB}}^{t\bar{t}} = 0.128 \pm 0.025. The combined inclusive and differential asymmetries are consistent with recent standard model predictions

    Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

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    Background and aims: Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress and novel therapeutic response in PC to develop a biomarker driven therapeutic strategy targeting DDR and replication stress in PC. Methods: We interrogated the transcriptome, genome, proteome and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient derived xenografts and human PC organoids. Results: Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, co-segregates with response to platinum (P &lt; 0.001) and PARP inhibitor therapy (P &lt; 0.001) in vitro and in vivo. We generated a novel signature of replication stress with which predicts response to ATR (P &lt; 0.018) and WEE1 inhibitor (P &lt; 0.029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P &lt; 0.001) but not associated with DDR deficiency. Conclusions: Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR proficient PC, and post-platinum therapy
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