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Jail-based competency restoration largely emerged as a method to address the backlog at forensic hospitals around the United States, as the number of justice-involved persons in need of restoration outgrew available beds. Jail-based competency restoration units (JBCRUs) appear to be highly effective and cost-saving. However, after the COVID-19 outbreak, services at some JBCRUs were stalled, as providers were forced to either quickly initiate or ramp up technology use to maintain services. The present study describes the course of programming for a JBCRU in Fulton County, Georgia, prior to and after the onset of COVID-19, during which time all treatment shifted to telehealth. A matched comparison group of prepandemic defendants was used to compare in-person versus telehealth services and findings indicated that while defendants’ length of stay remained effectively the same, the restoration rate for telehealth increased remarkably over prepandemic levels (χ2 = 10.1, p = .001). Such findings suggest that telehealth services are an effective mode of delivery for competency restoration.

Within this review, the literature and outcomes from animal models of maternal marijuana use and cigarette smoking are summarized. The existing data demonstrate that prenatal marijuana and nicotine exposure both have multifaceted adverse effects on maternal, gestational, placental, and fetal outcomes. These include placental function and development, fetal growth and birth weight, and offspring neurodevelopment.

Practical relevance: The femur is the most commonly fractured bone in cats. Femoral fractures usually result from high-velocity trauma such as a road traffic accident or fall from a height and, as such, are associated with a wide variety of concurrent injuries. The initial focus of treatment should always be on assessment and stabilisation of the major body systems. Once any concurrent injuries have been addressed, all femoral fractures need surgical stabilisation, with the notable exception of greenstick fractures in very young cats, which can heal with cage rest alone. A number of different surgical options are available depending on the fracture type, location, equipment, surgeon experience and owner finances. Clinical challenges: Femoral fractures can vary hugely in complexity and the small size of feline bones can limit the choice of implants. Furthermore, cats can present unique challenges in the postoperative period due to their active nature and the limited means to control their exercise level. Audience: This review is aimed at general and feline-specific practitioners who have some experience of feline orthopaedics, as well as those simply wishing to expand their knowledge. Aims: The aim of this review is to help clinicians assess, plan and manage feline femoral fractures. It provides an overview of diagnostic imaging and a discussion of a range of suitable surgical options, including the principles of different types of fixation. It also highlights cat-specific issues, approaches and implants pertinent to the management of these cases. Evidence base: A number of original articles and textbook chapters covering many aspects of femoral fractures in cats and dogs have been published. Where possible, this review draws on information from key feline research and, where necessary, extrapolates from relevant canine literature. The authors also offer practical guidance based on their own clinical experience.

This study describes the surgical management of a traumatic scapular avulsion including complications and clinical outcome in a 3-year-old Maine Coon cat. Traumatic scapular avulsion was diagnosed clinically and confirmed on a computed tomography scan, alongside severe scapula displacement. The scapula was stabilized surgically by the placement of two circumcostal sutures, through paired bone tunnels drilled both cranial and caudal to the base of the scapular spine, and two sutures passing through bone tunnels in the dorsal border of the scapula bone secured to the serratus ventralis muscle. The cat was able to bear weight on the affected limb within 48 hours of surgery; however, limb function subsequently deteriorated at home. Revision surgery was required 14 days postoperatively to replace failed polydioxanone suture with ultra-high molecular weight polyethylene suture (Fiberwire). Following revision surgery, the cat had a very acceptable functional outcome, with scapular stability and only intermittent lameness/stiffness noted in the medium-term follow-up. The present case report demonstrates that the described modified surgical technique may be used successfully in the treatment of scapular avulsion in cats and restores acceptable function to the affected limb.

The objective of the current systematic review was to investigate the organisational factors that enable and motivate non-accidental violence towards athletes in the sport context. The authors identified and reviewed 43 qualitative studies investigating psychological, physical, and sexual abuse of athletes, and developed a framework of organisational factors (i.e., structural, social, and stress factors) related to non-accidental violence. Athletes were the key informants, yet some studies included athletes’ entourages. The authors independently coded the findings sections of the primary research, using the developed framework. Organisational tolerance for abuse and conformity to dominant values within sports were related to all three types of non-accidental violence. Power imbalance appeared as a relevant factor in both psychological and sexual abuse, while isolation was also relevant in sexual abuse. Believing that non-accidental violence had instrumental effects appeared related to both psychological and physical abuse, whereas a winner-take-all reward system was related to physical abuse. Based on this systematic review, the authors proposed an integrated perspective of the organisational factors driving non-accidental violence in sport and conclude by proposing a whole-of-system approach to the prevention and management of non-accidental violence.

Simple Summary Half of all cancer patients receive radiation therapy during their course of treatment. The destructive effects of radiation on normal tissue causes side effects that significantly affect the patient’s quality of life. Microplanar radiation therapy (MRT) is a novel, promising method that, in animal models, has shown fewer effects on normal tissue and better therapeutic efficacy. MRT does not expose the entire tissue to intense radiation, but has micron-scale “valleys” between the peaks of radiation. We have previously developed an accessible method to apply MRT. Using our approach, here, we show that MRT greatly enhanced the response of the immune system to the tumor by stimulating specific signaling molecules. Moreover, we show that combining MRT with immune checkpoint therapy was even more effective in reducing the treated tumors, possibly pointing towards using similar approaches in the clinic. Abstract Spatially fractionated radiotherapy has been shown to have effects on the immune system that differ from conventional radiotherapy (CRT). We compared several aspects of the immune response to CRT relative to a model of spatially fractionated radiotherapy (RT), termed microplanar radiotherapy (MRT). MRT delivers hundreds of grays of radiation in submillimeter beams (peak), separated by non-radiated volumes (valley). We have developed a preclinical method to apply MRT by a commercial small animal irradiator. Using a B16-F10 murine melanoma model, we first evaluated the in vitro and in vivo effect of MRT, which demonstrated significant treatment superiority relative to CRT. Interestingly, we observed insignificant treatment responses when MRT was applied to Rag−/− and CD8-depleted mice. An immuno-histological analysis showed that MRT recruited cytotoxic lymphocytes (CD8), while suppressing the number of regulatory T cells (Tregs). Using RT-qPCR, we observed that, compared to CRT, MRT, up to the dose that we applied, significantly increased and did not saturate CXCL9 expression, a cytokine that plays a crucial role in the attraction of activated T cells. Finally, MRT combined with anti-CTLA-4 ablated the tumor in half of the cases, and induced prolonged systemic antitumor immunity.

Objective The aim of this study was to categorize the presentation, management, complications and long-term outcome of canine acetabular fractures, and to determine the factors affecting outcome. Materials and Methods Case records and imaging for dogs with acetabular fractures were reviewed with long-term follow-up via canine brief pain inventory (CBPI) and owner questionnaires. Results The majority of fractures were in the mid-third (36/52) and caudal-third (13/52) with few in the cranial-third of the acetabulum (3/52). Concurrent injuries were diagnosed in 47/49 dogs; 10/34 dogs had neurological deficits on presentation. Forty-seven fractures received treatment: 25/47 had direct surgical repair (DSR), 10/47 had salvage surgery (SS) and 12/47 had conservative management (CM). Fracture location significantly affected treatment group (p = 0.001). New neurological deficits were documented after DSR in 5/24 dogs and SS in 2/10 dogs. Short-term complications occurred after DSR in 10/18 dogs (five minor, five major) and CM in 1/8 dogs (major). Long-term complications occurred after DSR in 2/15 dogs (major) and CM in 2/7 dogs (catastrophic). Conservative management dogs had worse average owner-reported CBPI scores than DSR or SS dogs. Clinical Significance Acetabular fractures predominate in the mid and caudal acetabulum, with high levels of concurrent injuries. Fracture location significantly influenced the treatment approach taken. Postoperative neurological deficits are common following SS and DSR.

TP53 deficiency in cancer is associated with poor patient outcomes and resistance to DNA damaging therapies. However, the mechanisms underlying treatment resistance in p53-deficient cells remain poorly characterized. Using live cell imaging of DNA double-strand breaks (DSBs) and cell cycle state transitions, we show that p53-deficient cells exhibit accelerated repair of radiomimetic-induced DSBs arising in S phase. Low-dose DNA-dependent protein kinase (DNA-PK) inhibition increases the S-phase DSB burden in p53-deficient cells, resulting in elevated rates of mitotic catastrophe. However, a subset of p53-deficient cells exhibits intrinsic resistance to radiomimetic-induced DSBs despite DNA-PK inhibition. We show that p53-deficient cells under DNA-PK inhibition utilize DNA polymerase theta (Pol θ)-mediated end joining repair to promote their viability in response to therapy-induced DSBs. Pol θ inhibition selectively increases S-phase DSB burden after radiomimetic therapy and promotes prolonged G2 arrest. Dual inhibition of DNA-PK and Pol θ restores radiation sensitivity in p53-deficient cells as well as in p53-mutant breast cancer cell lines. Thus, combination targeting of DNA-PK- and Pol θ-dependent end joining repair represents a promising strategy for overcoming resistance to DNA damaging therapies in p53-deficient cancers.

Introduction Contamination occurs when participants allocated to trial control arms receive elements of the active intervention. Randomisation at cluster level, rather than individual level, may reduce or eliminate contamination, avoiding the dilution of intervention effectiveness that it may cause. However, cluster randomisation can result in selection bias and may not be feasible to deliver. We explored the extent of contamination in a qualitative study nested within a feasibility study of HENRY (Health, Exercise and Nutrition for the Really Young); a UK community-based child obesity prevention programme. We aimed to determine the nature and impact of contamination to inform a larger planned trial and other trials in community based public health settings. Method We invited participants to take part in the nested qualitative study who were already involved in the HENRY feasibility study. Semi-structured interviews/focus groups were conducted with children’s centre managers (n=7), children’s centre staff (n=15), and parents (n=29). Data were transcribed and analysed using an integrative approach. First, deductively organised using a framework guided by the topic guide and then organised using inductive thematic analysis. Results Potential for contamination between treatment arms was recognised by all stakeholder groups. Staff within the intervention centres presented the greatest risk of contamination, predominantly because they were often asked to work in other children centre’s (including control group centres). ‘Sharing of best practice’ by staff was reported to be a common and desirable phenomenon within community based settings. Parental sharing of HENRY messages was reported inconsistently; though some parents indicated a high degree of knowledge transfer within their immediate circles. Conclusions The extent of contamination identified has influenced the design of a future effectiveness trial of HENRY which will be clustered at the centre level (with geographically distinct clusters). The common practice of knowledge sharing amongst community teams means that this clustering approach is also likely to be most suitable for other trials based within these settings. We provide recommendations (e.g. cluster randomisation, training intervention facilitators on implications of contamination) to help reduce the impact of contamination in public health intervention trials with or without clustering, whilst enabling transfer of knowledge where appropriate. Trial registration ClinicalTrials.gov Identifier NCT03333733 registered 6th November 2017

TP53 mutations in cancer are associated with poor patient outcomes and resistance to DNA damaging therapies1–3. However, the mechanisms underlying treatment resistance in p53-deficient cells remain poorly characterized. Here, we show that p53-deficient cells exhibit hyperactive repair of therapy-induced DNA double strand breaks (DSBs), which is suppressed by inhibition of DNA-dependent protein kinase (DNA-PK). Single-cell analyses of DSB repair kinetics and cell cycle state transitions reveal an essential role for DNA-PK in suppressing S phase DNA damage and mitotic catastrophe in p53-deficient cells. Yet, a subset of p53-deficient cells exhibit intrinsic resistance to therapeutic DSBs due to a repair pathway that is not sensitive to DNA-PK inhibition. We show that p53 deficiency induces overexpression of DNA Polymerase Theta (Pol θ), which mediates an alternative end-joining repair pathway that becomes hyperactivated by DNA-PK inhibition4. Combined inhibition of DNA-PK and Pol θ restores therapeutic DNA damage sensitivity in p53-deficient cells. Thus, our study identifies two targetable DSB end joining pathways that can be suppressed as a strategy to overcome resistance to DNA-damaging therapies in p53-deficient cancers.

Protein-protein interactions are essential for biological function, but structures of protein-protein complexes are difficult to obtain experimentally. To derive the protein complex of the DNA-repair enzyme human uracil-DNA-glycosylase (hUNG) with its protein inhibitor (UGI), we combined rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). Computational docking of the unbound protein structures provides a list of possible three-dimensional models of the complex; DXMS identifies solvent-protected protein residues. DXMS showed that unbound hUNG is compactly folded, but unbound UGI is loosely packed. An increased level of solvent protection of hUNG in the complex was localized to four regions on the same face. The decrease in the number of incorporated deuterons was quantitatively interpreted as the minimum number of main-chain hUNG amides buried in the protein-protein interface. The level of deuteration of complexed UGI decreased throughout the protein chain, indicating both tighter packing and direct solvent protection by hUNG. Three UGI regions showing the greatest decreases were best interpreted leniently, requiring just one main-chain amide from each in the interface. Applying the DXMS constraints as filters to a list of docked complexes gave the correct complex as the largest favorable energy cluster. Thus, identification of approximate protein interfaces was sufficient to distinguish the protein complex. Surprisingly, incorporating the DXMS data as added favorable potentials in the docking calculation was less effective in finding the correct complex. The filtering method has greater flexibility, with the capability to test each constraint and enforce simultaneous contact by multiple regions, but with the caveat that the list from the unbiased docking must include correct complexes.

This study reports on restoration outcomes of a sample of pretrial defendants (

Films from the cephalopod protein reflectin demonstrate multifaceted functionality as infrared camouflage coatings, proton transport media, and substrates for growth of neural stem cells. A detailed study of the in vitro formation, structural characteristics, and stimulus response of such films is presented. The reported observations hold implications for the design and development of advanced cephalopod-inspired functional materials.

A recent judgement from a landmark employment case against British Cycling and UK Sport found that Jess Varnish, a former professional British cyclist, was neither an employee nor a worker of either organisation within the meaning of the Employment Rights Act 1996 or the Equality Act 2010. The relationship between the cyclist and British Cycling was judged to be more akin to a relationship between a student and a University (eg, service provider), and that funding provided to the cyclist by UK Sport was analogous to a grant.1 Jess Varnish brought her claims of unfair dismissal (ie, termination of her Athlete Performance Award, which is a means-tested financial contribution towards an athlete’s living expenses), direct sex discrimination, victimisation and unlawful detriment for having made protected disclosures (ie, whistle-blowing) to the Employment Tribunal.1 She sought protections offered to employees or workers but not offered to professional athletes. The case highlights a problem: athletes are not considered to be employees nor workers and therefore are not entitled to employee nor worker protection, but no other equivalent form of protection for athletes exists. Why …

Like other counties across the nation, Fulton County, GA, has seen a significant increase in the number of arrests of people with serious mental illness. While Fulton County has accountability courts, some defendants with mental illness are not able to take advantage of these options due to their mental illness rendering them incompetent to understand the expectations required by these courts. The WISE (Women's Initiative for Success with Early Intervention) pilot project created a pathway for incompetent women to be diverted out of jail and into mental health treatment that was faster than the traditional evaluation for competency to stand trial pathway. A total of 16 female misdemeanants with non-violent charges were referred to the program. All women in WISE received intensive case management services. Some women were sent to a psychiatric hospital for involuntary hospitalization, some were released back to the community, and some were sent to a state forensic hospital for competency restoration services. Compared with a similar group of female misdemeanants prior to inception of the pilot project, women in the WISE group spent significantly fewer days in jail (mean of 64.9 days versus 163.46 days). Thus, preliminary findings from the pilot project indicate that referral to the WISE program significantly reduced the burden of excess time in jail associated with having an untreated mental illness.

International audience; Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialized topics. At IFPA meeting 2016 there were twelve themed workshops, four of which are summarized in this report. These workshops addressed challenges, strengths and limitations of techniques and model systems for studying the placenta, as well as future directions for the following areas of placental research: 1) placental imaging; 2) sexual dimorphism; 3) placenta and development of other organs; 4) trophoblast cell lines.

Workplace abuse, broadly defined as interpersonal mistreatment against employees in the workplace that might harm or injure them and contribute to a hostile work environment, is one of the most pervasive and harmful problems faced by organizations worldwide. In the current symposium, we focus attention on the macro-level drivers of workplace abuse that occur within organizations and in society more generally. At the societal level, we will have one paper about important global trends affecting today’s organizations. The paper investigates how, why, and for whom these macro forces have implications when it comes to workplace harassment. At the organizational level, we will have three papers, one dedicated to unpacking the multiple dimensions of organizational tolerance for abuse. Two more papers will focus on structural organizational features, namely the mechanisms of communication, and structural pay inequality that can impact perceptions of interpersonal abuse at work. We argue that a stronger focus on studying the “barrel” and “orchard”, rather than “apples” and “cases”, can enhance our understanding of social and structural factors that underpin everyday workplace interactions and help us identify new avenues of theorizing and practice to prevent interpersonal workplace abuse.

The present research examines elites’ moral voice in a situation where a fellow member of the elite faces accusations of misconduct. Based on theories of bystander intervention, we hypothesize that...

Protein-DNA interactions are essential for many biological processes, X-ray crystallography can provide high-resolution structures, but protein-DNA complexes are difficult to crystallize and typically contain only small DNA fragments. Thus, there is a need for computational methods that can provide useful predictions to give insights into mechanisms and guide the design of new experiments. We used the program DOT, which performs an exhaustive, rigid-body search between two macromolecules, to investigate four diverse protein-DNA interactions. Here, we compare our computational results with subsequent experimental data on related systems. In all cases, the experimental data strongly supported our structural hypotheses from the docking calculations: a mechanism for weak, non-sequence-specific DNA binding by a transcription factor, a large DNA-binding footprint on the surface of the DNA-repair enzyme uracil-DNA-glycosylase, viral and host DNA-binding sites on the catalytic domain of HIV integrase, and a three-DNA-contact model of the linker histone bound to the nucleosome. In the case of uracil-DNA-glycosylase, the experimental design was based on the DNA-binding surface found by docking, rather than the much smaller surface observed in the crystallographic structure. These comparisons demonstrate that the DOT electrostatic energy gives a good representation of the distinctive electrostatic properties of DNA and DNA-binding proteins. The large, favorably-ranked clusters resulting from the dockings identify active sites, map out large DNA-binding sites, and reveal multiple DNA contacts with a protein. Thus, computational docking can not only help to identify protein-DNA interactions in the absence of a crystal structure, but also expand structural understanding beyond known crystallographic structures.

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome.

Previously, we identified 14-3-3 beta and zeta isoforms and proteolytic fragments of alpha-spectrin as proteins released from degenerating neurons that also rise markedly in cerebrospinal fluid (CSF) following experimental brain injury or ischemia in rodents, but these proteins have not been studied before as potential biomarkers for ischemic central nervous system injury in humans. Here we describe longitudinal analysis of these proteins along with the neuron-enriched hypophosphorylated neurofilament H (pNFH) and the deubiquitinating enzyme UCH-L1 in lumbar CSF samples from 19 surgical cases of aortic aneurysm repair, 7 involving cardiopulmonary bypass with deep hypothermic circulatory arrest (DHCA). CSF levels of the proteins were near the lower limit of detection by Western blot or enzyme-linked fluorescence immunoassay at the onset of surgical procedures, but increased substantially in a subset of cases, typically within 12-24 h. All cases involving DHCA were characterized by3-fold elevations in CSF levels of the two 14-3-3 isoforms, UCH-L1, and pNFH. Six of 7 also exhibited marked increases in alpha-spectrin fragments generated by calpain, a protease known to trigger necrotic neurodegeneration. Among cases involving aortic cross-clamping but not DHCA, the proteins rose in CSF preferentially in the subset experiencing acute neurological complications. Our results suggest the neuron-enriched 14-3-3beta, 14-3-3zeta, pNFH, UCH-L1, and calpain-cleaved alpha-spectrin may serve as a panel of biomarkers with clinical potential for the detection and management of ischemic central nervous system injury, including for mild damage associated with surgically-induced circulation arrest.

Preterm labour (PTL) is the most important cause of neonatal morbidity and mortality. While some causes have been identified, the mechanisms involved remain elusive. This study investigates whether term labour (TL) is an appropriate model for PTL by examining pro-labour gene expression, using quantitative rtPCR, and protein synthesis, using Western analysis, in preterm and term myometrial samples obtained from the upper and lower uterine segments before and after the onset of labour. In the lower segment, the levels of prostaglandin H synthase type-2 (PGHS-2), interleukin-1beta (IL-1beta), IL-6 and IL-8 mRNA expression were significantly higher in TL compared with PTL samples. Compared with non-labour controls, the expression of IL-1beta and IL-8 mRNA was increased in both PTL and TL samples and the expression of PGHS-2 and IL-6 mRNA was increased in TL samples only. In the upper segment, there were no differences between PTL and TL samples and the mRNA expression of PGHS-2 and IL-1beta was increased in TL compared with term no labour samples. No effect of PTL or TL was seen on either oxytocin receptor or connexin-43 mRNA expression or protein levels. The multiple regression analysis and studies in primary cultures of uterine myocytes suggest that the inflammatory cytokines, IL-1beta and tumour necrosis factor-alpha, are the most important regulators of PGHS-2 and IL-8. Our data show that preterm and term labouring myometrium are significantly different and that the most marked labour-induced changes in gene expression are in the lower segment. These changes may occur in response to the release of inflammatory cytokines by the labour-associated inflammatory infiltration.

HIV integrase (HIV-IN), one of three HIV enzymes, is a target for the treatment of AIDS, but the full biological assembly has been difficult to characterize, hampering inhibitor design. The recent crystallographic structures of integrase from prototype foamy virus (PFV-IN) with bound DNA were a breakthrough, revealing how viral DNA organizes two integrase dimers into a tetramer that has the two active sites appropriately spaced for insertion of the viral DNA into host DNA. The organization of domains within each PFV-IN protein chain, however, varies significantly from that found in HIV-IN structures. With the goal of identifying shared structural characteristics, the interactions among components of the PFV-IN and HIV-IN assemblies were investigated with the macromolecular docking program DOT. DOT performs an exhaustive, rigid-body search between two macromolecules. Computational docking reproduced the crystallographic interactions of the PFV-IN catalytic and N-terminal domains with viral DNA and found similar viral DNA interactions for HIV-IN. Computational docking did not reproduce the crystallographic interactions of the PFV-IN C-terminal domain (CTD). Instead, two symmetry-related positions were found for the PFV-IN CTD that indicate formation of a CTD dimer between the two active sites. Our predicted CTD dimer is consistent with cross-linking studies showing interactions of the CTD with viral DNA that appear to be blocked in the PFV-IN structures. The CTD dimer can insert two arginine-rich loops between the two bound vDNA molecules and the host DNA, a region that is unoccupied in the PFV-IN crystallographic structures. The positive potential from these two loops would alleviate the large negative potential created by the close proximity of two viral vDNA ends, helping to bring together the two active sites and assisting host DNA binding. This study demonstrates the ability of computational docking to evaluate complex crystallographic assemblies, identify interactions that are influenced by the crystal environment, and provide plausible alternatives.

Polychlorinated biphenyls (PCBs) are a family of 209 isomers (congeners) with a wide range of toxic effects. In structural terms, they are of two types: those with and those without chlorines at the ortho positions (2, 2′, 6 and 6′). Only 20 congeners have no ortho chlorines. Three of these are bound by the aryl hydrocarbon receptor and are one to four orders of magnitude more toxic than all others. A monoclonal antibody, S2B1, and its recombinant Fab have high selectivity and nanomolar binding affinities for two of the most toxic non-ortho-chlorinated PCBs, 3,4,3′,4′-tetrachlorobiphenyl and 3,4,3′,4′,5′-pentachlorobiphenyl. To investigate the basis for these properties, we built a three-dimensional structure model of the S2B1 variable fragment (Fv) based on the high-resolution crystallographic structures of antibodies 48G7 and N1G9. Two plausible conformations for the complementarity-determining region (CDR) H3 loop led to two putative PCB-binding pockets with very different shapes (models A and B). Docking studies using molecular mechanics and potentials of mean force (PMF) indicated that model B was most consistent with the selectivity observed for S2B1 in competition ELISAs. The binding site in model B had a deep, narrow pocket between VL and VH, with a slight constriction at the top that opened into a wider pocket between CDRs H1 and H3 on the antibody surface. This binding site resembles those of esterolytic antibodies that bind haptens with phenyl rings. One phenyl ring of the PCB fits into the deep pocket, and the other ring is bound in the shallower one. The bound PCB is surrounded by the side chains of TyrL91, TyrL96 and TrpH98, and it has a π-cation interaction with ArgL46. The tight fit of the binding pocket around the ortho positions of the bound PCBs indicates that steric hindrance of ortho chlorines in the binding site, rather than induced conformational change of the PCBs, is responsible for the selectivity of S2B1. Copyright © 2005 John Wiley & Sons, Ltd.

Determining protein–DNA interactions is important for understanding gene regulation, DNA repair and chromatin structure. Unfortunately, the structures of DNA-bound complexes are often difficult to obtain experimentally, so the development of computational methods that provide good models of these complexes would be valuable. Here, we present a rigid-body docking approach using the computer program DOT. DOT performs a complete, six-dimensional search of all orientations for two rigid molecules and calculates the interaction energy as the sum of electrostatic and van der Waals terms. DOT was applied to three winged-helix transcription factors that share similar DNA-binding structural motifs but bind DNA in different ways. Docking with linear B-form DNA models accomplished several objectives; it (1) distinguished the different ways the transcription factors bind DNA, (2) identified each protein's DNA-binding site and the DNA orientation at the site and (3) gave at least one solution among the three best-ranked that shows the protein side chain–DNA base interactions responsible for recognition. Furthermore, the ensemble of top-ranked, docked linear B-DNA fragments indicated the DNA bending induced upon protein binding. Docking linear B-DNA to structures of the transcription factor FadR suggests that the allosteric, conformational change induced upon effector binding results in loss of the ability to bend DNA as well as loss of sequence-specific interactions with DNA. The electrostatic energy term calculated by DOT is comparable to the electrostatic binding energy calculated by Poisson–Boltzmann methods. Our results show rigid-body docking that includes a rigorous treatment of the electrostatic interaction energy can be effective in predicting protein–DNA interactions. Proteins 2004. © 2004 Wiley-Liss, Inc.

The aim of this study was to characterize cellular responses to muscle-stageTrichinella spiralis. From its intracellular habitat in muscle,T. spiralissecretes potent glycoprotein antigens that elicit a strong systemic host immune response. Despite the magnitude and prolonged nature of this response, nurse cells are rarely destroyed by infiltrating cells. We tested the hypothesis that the anti-inflammatory cytokine interleukin-10 (IL-10) moderates cellular responses to muscle-stage parasites.Trichinellalarvae colonize the diaphragm in large numbers, prompting us to evaluate regional responses in body cavities in addition to local responses in muscle. Mice deficient in IL-10 demonstrated an exaggerated inflammatory response around nurse cells and in the pleural cavity. The effect of IL-10 was most evident 20 days following muscle infection. The increased intensity of the response in IL-10-deficient mice did not affect parasite establishment or survival. Between 20 and 50 days postinfection, the inflammatory response was diminished in both wild-type and IL-10-deficient mice. Muscle infection also elicited an antibody response, characterized initially by mixed isotypes directed at somatic larval antigens and changing to an immunoglobulin G1-dominated response directed at tyvelose-bearing excreted or secreted antigens. We conclude that IL-10 limits local and regional inflammation during the early stages of muscle infection but that chronic inflammation is controlled by an IL-10-independent mechanism that is coincident with a Th2 response.

protein to form chromatin, the fundamental unit of which is the nucleosome core particle (NCP). An NCP consists of two copies each of the four core histones H2A, H2B, H3, and H4. This histone octamer binds 147 base pairs of DNA around its outer surface in 1.65 tight superhelical turns (Fig. 1A) (Luger et al. 1997; Richmond and Davey 2003). Linker histones and other nonhistone proteins promote or stabilize the folding of nucleosomal arrays into superstructures of increasing complexity and largely unknown architecture (Hansen 2002). Covalent modification of the core histones and variations in the fundamental biochemical composition of nucleosomes distinguish transcriptionally active from inactive chromatin regions, by either changing the structure of the nucleosomes, altering their ability to interact with other protein factors, or modifying their propensity to fold into varying degrees of higher-order structures (or by any combination of the above). Studying the mechanism for establishing distinct chromatin domains is essential to understanding differential regulation of gene expression and all other DNA-dependent processes. Much progress has been made in this direction in the past few years. Substitution of one or more of the core histones with the corresponding histone variants has the potential to exert considerable influence on the structure and function of chromatin. Histone variants are distinct nonallelic forms of conventional, major-type histones that form the bulk of nucleosomes during replication and whose synthesis is tightly coupled to S phase. Histone variants are characterized by a completely different expression pattern that is not restricted to S phase. They are found in most eukaryotic organisms and are expressed in all tissue types (unlike some H2B isoforms that are found only in specialized tissues such as testes). Compared to their majortype counterparts, histone variants exhibit moderate to significant degrees of sequence homology (Fig. 1B). H2A.X (82%) and H3.3 (~96%) are the least divergent of all histone variants. H2A.Z (~60%), macroH2A (~65%), H2A.Bbd (40%), and CenpA, which has a 93 amino acid domain that is 62% identical to H3 (Palmer et al. 1991; Sullivan et al. 1994), are increasingly divergent in their Structural Characterization of Histone H2A Variants

We present an evaluation of our results for the first Critical Assessment of PRedicted Interaction (CAPRI). The methods used include the molecular docking program DOT, shape analysis tool FADE, cluster analysis and filtering based on biological data. Good results were obtained for most of the seven CAPRI targets, and for two systems, submissions having the highest number of correctly predicted contacts were produced.

Cryptochrome flavoproteins, which share sequence homology with light-dependent DNA repair photolyases, function as photoreceptors in plants and circadian clock components in animals. Here, we coupled sequencing of an Arabidopsis cryptochrome gene with phylogenetic, structural, and functional analyses to identify a new cryptochrome class (cryptochrome DASH) in bacteria and plants, suggesting that cryptochromes evolved before the divergence of eukaryotes and prokaryotes. The cryptochrome crystallographic structure, reported here for Synechocystis cryptochrome DASH, reveals commonalities with photolyases in DNA binding and redox-dependent function, despite distinct active-site and interaction surface features. Whole genome transcriptional profiling together with experimental confirmation of DNA binding indicated that Synechocystis cryptochrome DASH functions as a transcriptional repressor.