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Background: Little is known about the efficacy of preexposure prophylaxis (PrEP) or what biologic factors may influence HIV transmission in transgender men (TGM). In this study, we sought to explore the effect of testosterone on the vaginal microbiome, cervicovaginal fluid (CVF) tenofovir concentrations, and levels of CVF inflammatory markers in TGM on PrEP., Methods: Cervicovaginal fluid was collected from 13 TGM (7 using testosterone) and 32 cisgender women (CGW) on PrEP. The vaginal microbiome, CVF tenofovir concentrations, and CVF inflammatory markers were determined and compared., Results: The proportion of CVF Lactobacillus was significantly higher in CGW than in TGM (78% vs 24%, P < 0.001). Among TGM, the proportion of CVF Lactobacillus was lower, though not statistically significant, in those taking testosterone than in those not taking testosterone (14% vs 35%, P-value = 0.3). Interestingly, mean CVF tenofovir concentrations were the lowest in TGM on testosterone at 884 ng/mL compared with 3150 ng/mL in TGM not on testosterone and 1932 ng/mL in CGW; however, this difference was not statistically significant. There was no statistically significant difference in any of the genital inflammatory markers between groups and no correlation between inflammation and tenofovir levels., Conclusions: Our findings suggest a potential correlation between testosterone use, Lactobacillus dominance, and lower TFV concentrations in CVF, which may have implications on HIV acquisition from vaginal sex in TGMT. Future studies with larger sample sizes are needed to further investigate these relationships., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

The average eukaryotic tRNA contains 13 posttranscriptional modifications; however, their functional impact is largely unknown. Our understanding of the complex tRNA aminoacylation machinery in metazoans also remains limited. Herein, using a series of high-resolution cryo-electron microscopy (cryo-EM) structures, we provide the mechanistic basis for recognition and aminoacylation of fully-modified cellular tRNA Lys3 by human lysyl-tRNA synthetase (h-LysRS). The tRNA Lys3 anticodon loop modifications S34 (mcm 5 s 2 U) and R37 (ms 2 t 6 A) play an integral role in recognition by h-LysRS. Modifications in the T-, variable-, and D-loops of tRNA Lys3 are critical for ordering the metazoan-specific N-terminal domain of LysRS. The two catalytic steps of tRNA Lys3 aminoacylation are structurally ordered; docking of the 3'-CCA end in the active site cannot proceed until the lysyl-adenylate intermediate is formed and the pyrophosphate byproduct is released. Association of the h-LysRS-tRNA Lys3 complex with a multi-tRNA synthetase complex-derived peptide shifts the equilibrium towards the 3'-CCA end 'docked' conformation and allosterically enhances h-LysRS catalytic efficiency. The insights presented here have broad implications for understanding the role of tRNA modifications in protein synthesis, the human aminoacylation machinery, and the growing catalog of metabolic and neurological diseases linked to it., Competing Interests: CONFLICT OF INTEREST The authors declare no competing interests.

ProXp-ala is a key component of the translational machinery in all three Domains of life. This enzyme helps to maintain the fidelity of proline codon translation through aminoacyl-tRNA Pro proofreading. In the first step of tRNA aminoacylation, the cognate aminoacyl-tRNA synthetase (aaRS) binds and activates an amino acid in the enzyme's synthetic active site. If a non-cognate amino acid passes this first selection step and is charged onto the tRNA, a distinct aaRS editing active site may recognize the mischarged tRNA and deacylate it. Alternatively, this editing reaction may be carried out by a separate enzyme that deacylates the mischarged tRNA in trans. ProXp-ala is responsible for editing Ala mischarged onto tRNA Pro . Since trans-editing domains such as ProXp-ala bind their substrates after release from the synthetase, they must recognize not only the mischarged amino acid, but also the specific tRNA. Previous studies showed that Caulobacter crescentus (Cc) ProXp-ala distinguishes tRNA Pro from tRNA Ala , in part, based on the unique tRNA Pro acceptor stem base pair C1:G72. Previous crystallographic and NMR data also revealed a role for conformational selection by the ProXp-ala α2 helix in Ala- versus Pro-tRNA Pro substrate discrimination. The α2 helix makes lattice contacts in the crystal, which left some uncertainty as to its position in solution. We report resonance assignments for the substrate-free Cc ProXp-ala and the NMR-derived three-dimensional structure of the protein. These data reveal the position of the α2 helix in solution, with implications for substrate binding and recognition., (© 2024. The Author(s).)

The provision of social care for people in prison in England has historically been lacking. Seeking to address this, the 2014 Care Act clarified that local authorities are responsible for identifying, assessing and meeting prisoners' social care needs. Against this background, in 2020 we undertook a survey to explore the emerging services for this group. Eighty-six (57%) local authorities responded. A mixed methods approach was taken. Numerical data were analysed through descriptive statistics with comparisons made to the previous survey. An inductive approach to thematic analysis was used to analyse the free text responses. The findings revealed some improvements since the 2015/16 surveys, including the wider introduction of self-referral systems, the success of peer supporters in identifying people in need of social care and greater multi-disciplinary working. However, other issues remained stubbornly persistent, including a dearth of systematic processes to identify those needing social care on release from prison, a lack of timely information sharing and disputes over the sending and receiving authorities' responsibilities. There were also particular concerns about the shortage of appropriate accommodation for people leaving prison. Perhaps the most striking finding, however, was how little most authorities knew about this population. Building on discussions in previous papers, we explore three ways in which arrangements could be strengthened for this group: the collection of better data, the wider use of release on temporary licence and the greater employment of technology in planning people's release., Competing Interests: Declarations. Ethics approval and consent to participate: The research is in accordance with the Declaration of Helsinki. The study was reviewed by Her Majesty’s Prison and Probation Service (Reference: 2019 − 371), approved by ADASS (ref RG19-12) and supported by the ADASS Care and Justice Network. There were no substantive ethical concerns associated with this study. All data included in the current study are from individuals who gave consent to participate following the provision of a participant information sheet. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

The RNA World hypothesis posits that RNA can represent a primitive life form by reproducing itself and demonstrating catalytic activity. However, this hypothesis is incapable of addressing several major origin-of-life (OoL) questions. A recently described paradox-free alternative OoL hypothesis, the Quadruplex (G4) World, is based on the ability of poly(dG) to fold into a stable architecture with an unambiguous folding pattern using G-tetrads as building elements. Because of the folding pattern of three G-tetrads and single-G loops, dG 15 is programmable and has the capability to encode biological information. Here, we address two open questions of the G4 World hypothesis: (1) Does RNA follow the same folding pattern as DNA? (2) How do stable quadruplexes evolve into the present-day system of information transfer, which is based on Watson-Crick base pair complementarity? To address these questions, we systematically studied the thermodynamic and optical properties of both DNA and RNA G15- and G3T (GGGTGGGTGGGTGGG)-derived sequences. Our study revealed that similar to DNA sequences, RNAs adopt quadruplexes with only three G-tetrads. Thus, both poly(dG) and poly(rG) possess inherent ability to fold into 3D quadruplex architecture with strictly defined folding pattern. The study also revealed that despite high stability of both DNA and RNA quadruplexes, they are vulnerable to single-nucleotide substitutions, which drop the thermal stability by ~40°C and can facilitate introduction of the complementarity principle into the G4 World., (© 2024 The Author(s). Biopolymers published by Wiley Periodicals LLC.)

HIV-1 must generate infectious virions to spread to new hosts and HIV-1 unspliced RNA (HIV-1 RNA) plays two central roles in this process. HIV-1 RNA serves as an mRNA that is translated to generate proteins essential for particle production and replication, and it is packaged into particles as the viral genome. HIV-1 uses several transcription start sites to generate multiple RNAs that differ by a few nucleotides at the 5' end, including those with one (1G) or three (3G) 5' guanosines. The virus relies on host machinery to translate its RNAs in a cap-dependent manner. Here, we demonstrate that the 5' context of HIV-1 RNA affects the efficiency of translation both in vitro and in cells. Although both RNAs are competent for translation, 3G RNA is translated more efficiently than 1G RNA. The 5' untranslated region (UTR) of 1G and 3G RNAs has previously been shown to fold into distinct structural ensembles. We show that HIV-1 mutants in which the 5' UTR of 1G and 3G RNAs fold into similar structures were translated at similar efficiencies. Thus, the host machinery translates two 99.9% identical HIV-1 RNAs with different efficiencies, and the translation efficiency is regulated by the 5' UTR structure.IMPORTANCEHIV-1 unspliced RNA contains all the viral genetic information and encodes virion structural proteins and enzymes. Thus, the unspliced RNA serves distinct roles as viral genome and translation template, both critical for viral replication. HIV-1 generates two major unspliced RNAs with a 2-nt difference at the 5' end (3G RNA and 1G RNA). The 1G transcript is known to be preferentially packaged over the 3G transcript. Here, we showed that 3G RNA is favorably translated over 1G RNA based on its 5' untranslated region (UTR) RNA structure. In HIV-1 mutants in which the two major transcripts have similar 5' UTR structures, 1G and 3G RNAs are translated similarly. Therefore, HIV-1 generates two 9-kb RNAs with a 2-nt difference, each serving a distinct role dictated by differential 5' UTR structures., Competing Interests: The authors declare no conflict of interest.

HIV-1, the causative agent of AIDS, is a retrovirus that packages two copies of unspliced viral RNA as a dimer into newly budding virions. The unspliced viral RNA also serves as an mRNA template for translation of two polyproteins. Recent studies suggest that the fate of the viral RNA (genome or mRNA) is determined at the level of transcription. RNA polymerase II uses heterogeneous transcription start sites to generate major transcripts that differ in only two guanosines at the 5' end. Remarkably, this two-nucleotide difference is sufficient to alter the structure of the 5'-untranslated region and generate two pools of RNA with distinct functions. The presence of both RNA species is needed for optimal viral replication and fitness., Competing Interests: Declaration of competing interest None., (Published by Elsevier Ltd.)

Many people are living in prison with a range of social care needs, for example, requiring support with washing, eating, getting around safely, and/or maintaining relationships. However, social care for this vulnerable group is generally inadequate. There is uncertainty and confusion about who is legally responsible for this and how it can best be provided, and a lack of integration with healthcare. We used realist-informed approaches to develop an initial programme theory (IPT) for identifying/assessing social care needs of, and providing care to, male adults in prison and on release. IPT development was an iterative process involving (a) an initial scoping of the international prison literature; (b) scoping prison and community social care policy documents and guidelines; (c) full systematic search of the international prison social care literature; (d) insights from the community social care literature; (e) stakeholder workshops. Information from 189 documents/sources and stakeholder feedback informed the IPT, which recommended that models of prison social care should be: trauma-informed; well integrated with health, criminal justice, third-sector services and families; and person-centred involving service-users in all aspects including co-production of care plans, goals, and staff training/awareness programmes. Our IPT provides an initial gold standard model for social care provision for people in prison and on release. The model, named Empowered Together, will be evaluated in a future trial and will be of interest to those working in the criminal justice system, care providers and commissioners, local authorities, housing authorities, voluntary groups, and service-users and their families., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Faithful mRNA decoding depends on the accuracy of aminoacyl-tRNA synthetases (ARSs). Aminoacyl-tRNA proofreading mechanisms have been well-described in bacteria, humans, and plants. However, our knowledge of translational fidelity in protozoans is limited. Trypanosoma brucei ( Tb ) is a eukaryotic, protozoan pathogen that causes Human African Trypanosomiasis, a fatal disease if untreated. Tb undergoes many physiological changes that are dictated by nutrient availability throughout its insect-mammal lifecycle. In the glucose-deprived insect vector, the tsetse fly, Tb use proline to make ATP via mitochondrial respiration. Alanine is one of the major by-products of proline consumption. We hypothesize that the elevated alanine pool challenges Tb prolyl-tRNA synthetase (ProRS), an ARS known to misactivate alanine in all three domains of life, resulting in high levels of misaminoacylated Ala-tRNA Pro . Tb encodes two domains that are members of the INS superfamily of aminoacyl-tRNA deacylases. One homolog is appended to the N-terminus of Tb ProRS, and a second is the major domain of multi-aminoacyl-tRNA synthetase complex (MSC)-associated protein 3 (MCP3). Both ProRS and MCP3 are housed in the Tb MSC. Here, we purified Tb ProRS and MCP3 and observed robust Ala-tRNA Pro deacylation activity from both enzymes in vitro . Size-exclusion chromatography multi-angle light scattering used to probe the oligomerization state of MCP3 revealed that although its unique N-terminal extension confers homodimerization in the absence of tRNA, the protein binds to tRNA as a monomer. Kinetic assays showed MCP3 alone has relaxed tRNA specificity and promiscuously hydrolyzes cognate Ala-tRNA Ala ; this activity is significantly reduced in the presence of Tb alanyl-tRNA synthetase, also housed in the MSC. Taken together, our results provide insight into translational fidelity mechanisms in Tb and lay the foundation for exploring MSC-associated proteins as novel drug targets., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Watkins, Vradi, Shulgina and Musier-Forsyth.)

Human T-cell leukemia virus type 1 (HTLV-1) is the only oncogenic human retrovirus discovered to date. All retroviruses are believed to use a host cell tRNA to prime reverse transcription (RT). In HTLV-1, the primer-binding site (PBS) in the genomic RNA is complementary to the 3' 18 nucleotides (nt) of human tRNA Pro The human genome encodes 20 cytoplasmic tRNA Pro genes representing seven isodecoders, all of which share the same 3' 18 nt sequence but vary elsewhere. Whether all tRNA Pro isodecoders are used to prime RT in cells is unknown. A previous study showed that a 3' 18 nt tRNA Pro -derived fragment (tRF Pro ) is packaged into HTLV-1 particles and can serve as an RT primer in vitro. The role of this tRNA fragment in the viral life cycle is unclear. In retroviruses, N1-methylation of the tRNA primer at position A58 (m 1 A) is essential for successful plus-strand transfer. Using primer-extension assays performed in chronically HTLV-1-infected cells, we found that A58 of tRNA Pro is m 1 A-modified, implying that full-length tRNA Pro is capable of facilitating successful plus-strand transfer. Analysis of HTLV-1 RT primer extension products indicated that full-length tRNA Pro is likely to be the primer. To determine which tRNA Pro isodecoder is used as the RT primer, we sequenced the minus-strand strong-stop RT product containing the intact tRNA primer and established that HTLV-1 primes RT using a specific tRNA Pro UGG isodecoder. Further studies are required to understand how this primer is annealed to the highly structured HTLV-1 PBS and to investigate the role of tRF Pro in the viral life cycle., (© 2024 Syu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)

Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular environments. A recent study with PEG crowders revealed decreased catalytic activity of Escherichia coli prolyl-tRNA synthetase (Ec ProRS), where the smaller molecular weight PEGs had the maximum impact. The molecular mechanism of the crowding effects of PEGs is not clearly understood. PEG may impact protein conformation and dynamics, thus its function. In the present study, the effects of PEG molecules of various molecular weights and concentrations on the conformation and dynamics of Ec ProRS were investigated using a combined experimental and computational approach including intrinsic tryptophan fluorescence spectroscopy, atomic force microscopy, and atomistic molecular dynamic simulations. Results of the present study suggest that lower molecular weight PEGs in the dilute regime have modest effects on the conformational dynamics of Ec ProRS but impact the catalytic function primarily via the excluded volume effect; they form large clusters blocking the active site pocket. In contrast, the larger molecular weight PEGs in dilute to semidilute regimes have a significant impact on the protein's conformational dynamics; they wrap on the protein surface through noncovalent interactions. Thus, lower-molecular-weight PEG molecules impact protein dynamics and function via crowding effects, whereas larger PEGs induce confinement effects. These results have implications for the development of inhibitors for protein targets in a crowded cellular environment.

Bordetella pertussis, which causes a respiratory disease known as pertussis ("whooping cough") remains an important global challenge, with the incidence in pertussis cases increasing in recent years. Newborns and infants are at increased risk for severe morbidity and mortality from this bacterium. Vaccination in pregnancy has become an important strategy to both passively transfer immunity as well as prevent infection in pregnant persons, who are a major source of newborn infection, thus attempting to decrease the impact of this serious disease. It is considered safe for the pregnant person, the developing fetus, and the infant, and during the first 3 months of life it has been shown to be highly effective in preventing pertussis. There are a variety of strategies, recommendations, and adherence rates associated with pertussis vaccination in pregnancy around the world. We summarize the 2021 Global Pertussis Initiative Annual Meeting that reviewed the current global status of pertussis vaccination in pregnancy and remaining medical and scientific questions, with a focus on vaccination challenges and strategies for obstetric and gynecologic healthcare providers., (© 2024 International Federation of Gynecology and Obstetrics.)

Background: As populations age globally, cooperation across multi-sector stakeholders is increasingly important to service older persons, particularly those with high and complex health and social needs. One such population is older people entering society after a period of incarceration in prison. The 'ageing epidemic' in prisons worldwide has caught the attention of researchers, governments and community organisations, who identify challenges in servicing this group as they re-enter the community. Challenges lie across multiple sectors, with inadequate support leading to dire consequences for public health, social welfare and recidivism. This is the first study to bring together multi-sector stakeholders from Australia to form recommendations for improving health and social outcomes for older people re-entering community after imprisonment., Results: A modified nominal group technique was used to produce recommendations from N = 15 key stakeholders across prison health, corrections, research, advocacy, aged care, community services, via online workshops. The importance and priority of these recommendations was validated by a broader sample of N = 44 stakeholders, using an online survey. Thirty-six recommendations for improving outcomes for this population were strongly supported. The key issues underlying the recommendations included: improved multi-stakeholder systems and services, targeted release preparation and practices that ensure continuity of care, advocacy-focused initiatives in the community, and extended funding for effective programs., Conclusions: There is consensus across stakeholders on ways forward, with intervention and policy updates required at the individual, systems and community levels. These recommendations entail two important findings about this population: (1) They are a high-needs, unique, and underserved group at risk of significant health and social inequity in the community, (2) Multi-sector stakeholder cooperation will be crucial to service this growing group., (© 2024. The Author(s).)

Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a K D ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.

Background: High rates of health inequalities and chronic non-communicable diseases exist amongst the prison population. This places people in and/or released from prison at heightened risk of multimorbidity, premature mortality, and reduced quality of life. Ensuring appropriate healthcare for people in prison to improve their health outcomes is an important aspect of social justice. This review examines the global literature on healthcare interventions to detect, monitor and manage chronic non-communicable diseases amongst the prison population and people recently released from prison., Methods: Systematic searches of EMBASE, MEDLINE, CINAHL, Web of Science, Scopus, and the Cochrane Library were conducted and supplemented by citation searching and review of the grey literature. The literature searches attempted to identify all articles describing any healthcare intervention for adults in prison, or released from prison in the past 1 year, to detect, monitor, or manage any chronic non-communicable illness. 19,061 articles were identified, of which 1058 articles were screened by abstract and 203 articles were reviewed by full text., Results: Sixty-five studies were included in the review, involving 18,311 participants from multiple countries. Most studies were quasi-experimental and/or low to moderate in quality. Numerous healthcare interventions were described in the literature including chronic disease screening, telemedicine, health education, integrated care systems, implementing specialist equipment and staff roles to manage chronic diseases in prisons, and providing enhanced primary care contact and/or support from community health workers for people recently released from prison. These interventions were associated with improvement in various measures of clinical and cost effectiveness, although comparison between different care models was not possible due to high levels of clinical heterogeneity., Conclusions: It is currently unclear which interventions are most effective at monitoring and managing chronic non-communicable diseases in prison. More research is needed to determine the most effective interventions for improving chronic disease management in prisons and how these should be implemented to ensure optimal success. Future research should examine interventions for addressing multimorbidity within prisons, since most studies tested interventions for a singular non-communicable disease., (© 2024. The Author(s).)

Human lysyl-tRNA synthetase (LysRS) was previously shown to be re-localized from its normal cytoplasmic location in a multi-aminoacyl-tRNA synthetase complex (MSC) to the nucleus of HIV-1 infected cells. Nuclear localization depends on S207 phosphorylation but the nuclear function of pS207-LysRS in the HIV-1 lifecycle is unknown. Here, we show that HIV-1 replication was severely reduced in a S207A-LysRS knock-in cell line generated by CRISPR/Cas9; this effect was rescued by S207D-LysRS. LysRS phosphorylation up-regulated HIV-1 transcription, as did direct transfection of Ap4A, an upstream transcription factor 2 (USF2) activator that is synthesized by pS207-LysRS. Overexpressing an MSC-derived peptide known to stabilize LysRS MSC binding inhibited HIV-1 replication. Transcription of HIV-1 proviral DNA and other USF2 target genes was reduced in peptide-expressing cells. We propose that nuclear pS207-LysRS generates Ap4A, leading to activation of HIV-1 transcription. Our results suggest a new role for nuclear LysRS in facilitating HIV-1 replication and new avenues for antiviral therapy., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Single-nucleotide variants (SNVs) in the gene encoding Kinesin Family Member 5A (KIF5A), a neuronal motor protein involved in anterograde transport along microtubules, have been associated with amyotrophic lateral sclerosis (ALS). ALS is a rapidly progressive and fatal neurodegenerative disease that primarily affects the motor neurons. Numerous ALS-associated KIF5A SNVs are clustered near the splice-site junctions of the penultimate exon 27 and are predicted to alter the carboxy-terminal (C-term) cargo-binding domain of KIF5A. Mis-splicing of exon 27, resulting in exon exclusion, is proposed to be the mechanism by which these SNVs cause ALS. Whether all SNVs proximal to exon 27 result in exon exclusion is unclear. To address this question, we designed an in vitro minigene splicing assay in human embryonic kidney 293 cells, which revealed heterogeneous site-specific effects on splicing: only 5' splice-site (5'ss) SNVs resulted in exon skipping. We also quantified splicing in select clustered, regularly interspaced, short palindromic repeats-edited human stem cells, differentiated to motor neurons, and in neuronal tissues from a 5'ss SNV knock-in mouse, which showed the same result. Moreover, the survival of representative 3' splice site, 5'ss, and truncated C-term variant KIF5A (v-KIF5A) motor neurons was severely reduced compared with wild-type motor neurons, and overt morphological changes were apparent. While the total KIF5A mRNA levels were comparable across the cell lines, the total KIF5A protein levels were decreased for v-KIF5A lines, suggesting an impairment of protein synthesis or stability. Thus, despite the heterogeneous effect on ribonucleic acid splicing, KIF5A SNVs similarly reduce the availability of the KIF5A protein, leading to axonal transport defects and motor neuron pathology., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Transfer RNAs are the adaptors in protein synthesis that provide the key link between the nucleic acid-based genetic blueprint and proteins. While the central role of tRNAs in protein synthesis has been known for over 60 years, recent discoveries of their many non-canonical functions and therapeutic potential have heightened interest in tRNAs. In this thematic series, we highlight some of the developments presented at the recent biennial "International tRNA Workshop". The topics chosen reflect advances that were enabled by the latest technological breakthroughs in structure determination and small RNA sequencing and emphasize the prospects and challenges of tRNA-based medicines to treat human diseases., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

HTLV-1 is an oncogenic human retrovirus and the etiologic agent of the highly aggressive ATL malignancy. Two viral genes, Tax and Hbz , are individually linked to oncogenic transformation and play an important role in the pathogenic process. Consequently, regulation of HTLV-1 gene expression is a central feature in the viral lifecycle and directly contributes to its pathogenic potential. Herein, we identified the cellular transcription factor YBX1 as a binding partner for HBZ. We found YBX1 activated transcription and enhanced Tax-mediated transcription from the viral 5' LTR promoter. Interestingly, YBX1 also interacted with Tax. shRNA-mediated loss of YBX1 decreased transcript and protein abundance of both Tax and HBZ in HTLV-1-transformed T-cell lines, as well as Tax association with the 5' LTR. Conversely, YBX1 transcriptional activation of the 5' LTR promoter was increased in the absence of HBZ. YBX1 was found to be associated with both the 5' and 3' LTRs in HTLV-1-transformed and ATL-derived T-cell lines. Together, these data suggest that YBX1 positively influences transcription from both the 5' and 3' promoter elements. YBX1 is able to interact with Tax and help recruit Tax to the 5' LTR. However, through interactions with HBZ, YBX1 transcriptional activation of the 5' LTR is repressed.

Background: Developed as an environment assessment informed by the Model of Human Occupation, the Residential Environment Impact Survey considered the physical, social and activity features of the environment, evaluating the impact of the environment on resident's quality of life. Clinicians reported that the Residential Environment Impact Survey was a useful tool; however, it had not been structured to be a measurement tool and did not have established psychometric properties., Aims/objectives: This study examines the psychometric properties of the restructured Residential Environment Impact Scale Version 4.0 (REIS), which measures the level of environment support provided to residents., Material and Methods: The REIS was completed across residential sites for people with complex mental health needs. A many facets Rasch analysis was conducted to establish the reliability and validity of the REIS., Results: The REIS demonstrated reasonable psychometric properties, with items demonstrating internal scale validity and scale items following an expected pattern of increasingly challenging environment support., Conclusions and Significance: Initial evidence suggests that the REIS provides a valid and reliable measure of environment support, providing a detailed assessment of how physical, social and activity elements of the environment support or inhibit participation and can be applied across a range of living environments.

HIV-1 relies on host RNA polymeraseII (Pol II) to transcribe its genome and uses multiple transcription start sites (TSS), including three consecutive guanosines located near the U3-R junction, to generate transcripts containing three, two, and one guanosine at the 5' end, referred to as 3G, 2G, and 1G RNA, respectively. The 1G RNA is preferentially selected for packaging, indicating that these 99.9% identical RNAs exhibit functional differences and highlighting the importance of TSS selection. Here, we demonstrate that TSS selection is regulated by sequences between the CATA/TATA box and the beginning of R. Furthermore, we have generated two HIV-1 mutants with distinct 2-nucleotide modifications that predominantly express 3G RNA or 1G RNA. Both mutants can generate infectious viruses and undergo multiple rounds of replication in T cells. However, both mutants exhibit replication defects compared to the wild-type virus. The 3G-RNA-expressing mutant displays an RNA genome-packaging defect and delayed replication kinetics, whereas the 1G-RNA-expressing mutant exhibits reduced Gag expression and a replication fitness defect. Additionally, reversion of the latter mutant is frequently observed, consistent with sequence correction by plus-strand DNA transfer during reverse transcription. These findings demonstrate that HIV-1 maximizes its replication fitness by usurping the TSS heterogeneity of host RNA Pol II to generate unspliced RNAs with different specialized roles in viral replication. The three consecutive guanosines at the junction of U3 and R may also maintain HIV-1 genome integrity during reverse transcription. These studies reveal the intricate regulation of HIV-1 RNA and complex replication strategy.

High fidelity tRNA aminoacylation by aminoacyl-tRNA synthetases is essential for cell viability. ProXp-ala is a trans-editing protein that is present in all three domains of life and is responsible for hydrolyzing mischarged Ala-tRNAPro and preventing mistranslation of proline codons. Previous studies have shown that, like bacterial prolyl-tRNA synthetase, Caulobacter crescentus ProXp-ala recognizes the unique C1:G72 terminal base pair of the tRNAPro acceptor stem, helping to ensure deacylation of Ala-tRNAPro but not Ala-tRNAAla. The structural basis for C1:G72 recognition by ProXp-ala is still unknown and was investigated here. NMR spectroscopy, binding, and activity assays revealed two conserved residues, K50 and R80, that likely interact with the first base pair, stabilizing the initial protein-RNA encounter complex. Modeling studies are consistent with direct interaction between R80 and the major groove of G72. A third key contact between A76 of tRNAPro and K45 of ProXp-ala was essential for binding and accommodating the CCA-3' end in the active site. We also demonstrated the essential role that the 2'OH of A76 plays in catalysis. Eukaryotic ProXp-ala proteins recognize the same acceptor stem positions as their bacterial counterparts, albeit with different nucleotide base identities. ProXp-ala is encoded in some human pathogens; thus, these results have the potential to inform new antibiotic drug design., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

While vaccines have markedly reduced the incidence of pertussis, a resurgence has occurred in many countries. Until recently, pertussis has not been recognized as an important public health challenge in India due to its successful infant immunization program. However, India still accounts for a large proportion of the world's cases, and increasing reports of pertussis in other countries and in neonates have regenerated interest in pertussis among Indian authorities. The Global Pertussis Initiative (GPI) Annual Meeting was held virtually in October 2020, in part, to gain a better understanding of the epidemiology and disease burden of pertussis and to explore opportunities to improve its prevention in India. There was a consensus that pertussis cases are being underestimated in India due to multiple factors, such as a reliance on passive surveillance and diagnostic challenges. India offers both whole-cell pertussis and acellular pertussis vaccines, but vaccine coverage is inconsistent across regions due to differences in vaccine availability, access to health care, and regional administrative challenges. This report summarizes the outcomes and considers the key clinical implications of this meeting. The GPI agreed that active surveillance of pertussis in India would be optimal and recommended several studies, including serosurveillance among women of reproductive age to assess the prevalence of recent pertussis infection and to enable policy changes that will enhance the rational use of acellular and whole-cell vaccines. It also recommended engagement with nongovernmental organizations in order to encourage pregnancy immunization in the public sector. To achieve effective control of pertussis in the future, the GPI recognizes there are opportunities to characterize the burden of pertussis in India appropriately and increase vaccination coverage in multiple age groups., (© 2022. The Author(s), under exclusive licence to Dr. K C Chaudhuri Foundation.)

Aminoacyl-tRNA synthetases are enzymes that ensure accurate protein synthesis. Variants of the dual-functional cytoplasmic human glutamyl-prolyl-tRNA synthetase, EPRS1, have been associated with leukodystrophy, diabetes and bone disease. Here, we report compound heterozygous variants in EPRS1 in a 4-year-old female patient presenting with psychomotor developmental delay, seizures and deafness. Functional studies of these two missense mutations support major defects in enzymatic function in vitro and contributed to confirmation of the diagnosis., (© 2022 The Authors. Clinical Genetics published by John Wiley & Sons Ltd.)

Host factor tRNAs facilitate the replication of retroviruses such as human immunodeficiency virus type 1 (HIV-1). HIV-1 uses human tRNA Lys3 as the primer for reverse transcription, and the assembly of HIV-1 structural protein Gag at the plasma membrane (PM) is regulated by matrix (MA) domain-tRNA interactions. A large, dynamic multi-aminoacyl-tRNA synthetase complex (MSC) exists in the cytosol and consists of eight aminoacyl-tRNA synthetases (ARSs) and three other cellular proteins. Proteomic studies to identify HIV-host interactions have identified the MSC as part of the HIV-1 Gag and MA interactomes. Here, we confirmed that the MA domain of HIV-1 Gag forms a stable complex with the MSC, mapped the primary interaction site to the linker domain of bi-functional human glutamyl-prolyl-tRNA synthetase (EPRS), and showed that the MA-EPRS interaction was RNA dependent. MA mutations that significantly reduced the EPRS interaction reduced viral infectivity and mapped to MA residues that also interact with phosphatidylinositol-(4,5)-bisphosphate. Overexpression of EPRS or EPRS fragments did not affect susceptibility to HIV-1 infection, and knockdown of EPRS reduced both a control reporter gene and HIV-1 protein translation. EPRS knockdown resulted in decreased progeny virion production, but the decrease could not be attributed to selective effects on virus gene expression, and the specific infectivity of the virions remained unchanged. While the precise function of the Gag-EPRS interaction remains uncertain, we discuss possible effects of the interaction on either virus or host activities.

Infants are at high risk for severe morbidity and mortality from pertussis disease during early infancy. Vaccination against pertussis in pregnancy has emerged as the ideal strategy to protect infants during these early, vulnerable, first months of life. On 30 November and 1 December 2021, the Global Pertussis Initiative held a meeting that aimed to discuss and review the most up-to-date scientific literature supporting vaccination against pertussis in pregnancy and outstanding scientific questions. Herein, we review the current and historically published literature and summarize the findings as consensus statements on vaccination against pertussis in pregnancy on behalf of the Global Pertussis Initiative.

Background and Objectives: Global policy emphasizes the need to promote healthy aging through supporting inclusivity, safety, and functional independence. Research indicates that efforts to enhance resilience can contribute to meeting these objectives. We employed a meta-analytical approach to examine evidence on resilience in community-living older adults., Research Design and Methods: We searched electronic databases until January 13, 2020 for observational studies investigating factors associated with resilience in this population. Articles had to provide quantitative data based on standardized assessment and include samples where mean participants' age and lower 95% confidence interval were more than 55 years. We included 49 studies reported in 43 articles and completed 38 independent meta-analyses, 27 for personal and 11 for contextual factors associated with resilience., Results: A range of personal and contextual factors were significantly associated with resilience, with effects sizes predominantly small to moderate (0.1 < r < 0.49). Factors reflecting psychological and physical well-being and access to/quality of social support were associated with higher resilience. Factors indicative of poorer psychological well-being and social challenges were associated with lower resilience. Longitudinal evidence was limited. The level of between-study heterogeneity was substantial to considerable. Where relevant analysis was possible, the identified publication bias was also considerable., Discussion and Implications: The quality of the available evidence, as well as issues related to measurement of resilience, indicates the need for further work relative to its conceptualization and assessment. The presented findings have important clinical implications, particularly within the context of the coronavirus disease 2019 impact on resilience in older adults., (© The Author(s) 2021. Published by Oxford University Press on behalf of The Gerontological Society of America.)

Background: Compare outcomes of early laparoscopic cholecystectomy (ELC) and percutaneous trans-hepatic drainage of gallbladder (PTGBD) as an initial intervention for AC and to compare operative outcomes of ELC and delayed laparoscopic cholecystectomy (DLC)., Methods: English-language studies published until December 2020 were searched. Randomised controlled trials (RCTs) and observational studies compared EC and PTGBD with delayed cholecystectomy for patients presented with acute cholecystitis were considered. Main outcomes were mortality, conversion to open, complications and length of hospital stay., Results: Out of 1347 records, 14 studies were included. 205,361 (94.7%) patients had EC and 11,565 (5.3%) patients had PTGBD as an initial intervention for AC. Mortality was higher in PTGBD; HR, 95% CI: [3.68 (2.13, 6.38)]. In contrast, complication rate was significantly higher in EC group (47%) vs PTGBD group (8.7%) in patients admitted to ICU; P-value = 0.011. Patients who had ELC were at higher risk of post-operative complications compared to DLC; RR [95% CI]: 2.88 [1.78, 4.65]. Risk of bile duct injury was six folds more in ELC; RR [95% CI]: 6.07 [1.67, 21.99]., Conclusion: ELC may be a preferred treatment option over PTGBD in AC. However, patient and disease specific factors should be considered to avoid unfavourable outcomes with ELC., (Crown Copyright © 2022. Published by Elsevier Ltd. All rights reserved.)

Faithful translation of the genetic code is critical for the viability of all living organisms. The trans-editing enzyme ProXp-ala prevents Pro to Ala mutations during translation by hydrolyzing misacylated Ala-tRNA Pro that has been synthesized by prolyl-tRNA synthetase. Plant ProXp-ala sequences contain a conserved C-terminal domain (CTD) that is absent in other organisms; the origin, structure, and function of this extra domain are unknown. To characterize the plant-specific CTD, we performed bioinformatics and computational analyses that provided a model consistent with a conserved α-helical structure. We also expressed and purified wildtype Arabidopsis thaliana (At) ProXp-ala in Escherichia coli, as well as variants lacking the CTD or containing only the CTD. Circular dichroism spectroscopy confirmed a loss of α-helical signal intensity upon CTD truncation. Size-exclusion chromatography with multiangle laser-light scattering revealed that wildtype At ProXp-ala was primarily dimeric and CTD truncation abolished dimerization in vitro. Furthermore, bimolecular fluorescence complementation assays in At protoplasts support a role for the CTD in homodimerization in vivo. The deacylation rate of Ala-tRNA Pro by At ProXp-ala was also significantly reduced in the absence of the CTD, and kinetic assays indicated that the reduction in activity is primarily due to a tRNA binding defect. Overall, these results broaden our understanding of eukaryotic translational fidelity in the plant kingdom. Our study reveals that the plant-specific CTD plays a significant role in substrate binding and canonical editing function. Through its ability to facilitate protein-protein interactions, we propose the CTD may also provide expanded functional potential for trans-editing enzymes in plants., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Adults with neurodevelopmental disorders frequently present to, but fit uneasily into, adult mental health services. We offer definitions of important terms related to neurodevelopmental disorders through unifying research data, medical and other viewpoints. This may improve understanding, clinical practice and development of neurodevelopmental disorder pathways within adult mental health services.

Written and oral communication are skills graduate students often request training in and supervisors often bemoan the lack of. We describe an approach to address this training gap using an instructional model that integrates experienced research-active PIs with an expert in the study and teaching of technical writing., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Interactions between lysyl-tRNA synthetase (LysRS) and HIV-1 Gag facilitate selective packaging of the HIV-1 reverse transcription primer, tRNA Lys3 . During HIV-1 infection, LysRS is phosphorylated at S207, released from a multi-aminoacyl-tRNA synthetase complex and packaged into progeny virions. LysRS is critical for proper targeting of tRNA Lys3 to the primer-binding site (PBS) by specifically binding a PBS-adjacent tRNA-like element (TLE), which promotes release of the tRNA proximal to the PBS. However, whether LysRS phosphorylation plays a role in this process remains unknown. Here, we used a combination of binding assays, RNA chemical probing, and small-angle X-ray scattering to show that both wild-type (WT) and a phosphomimetic S207D LysRS mutant bind similarly to the HIV-1 genomic RNA (gRNA) 5'UTR via direct interactions with the TLE and stem loop 1 (SL1) and have a modest preference for binding dimeric gRNA. Unlike WT, S207D LysRS bound in an open conformation and increased the dynamics of both the PBS region and SL1. A new working model is proposed wherein a dimeric phosphorylated LysRS/tRNA complex binds to a gRNA dimer to facilitate tRNA primer release and placement onto the PBS. Future anti-viral strategies that prevent this host factor-gRNA interaction are envisioned.

Aim: To explore concurrent validity, convergent validity, interrater reliability, test-retest reliability, and Rasch model analysis of the School Participation Questionnaire (SPQ), a tool for teachers to assess personal and environmental determinants of school participation., Method: Teachers of children with additional support needs, including intellectual disability, autism, and learning difficulties completed measures. Data were collected using the SPQ and the Participation and Environment Measure for Children and Youth (PEM-CY). Test-retest and interrater reliability were assessed using intraclass correlation coefficients (ICCs). Internal consistency was assessed with Cronbach's alpha. Concurrent and convergent validity were explored via correlations with the PEM-CY. Further psychometrics were examined using a Rasch model., Results: One hundred and eighty-seven children (136 [72.7%] male; mean age 9y [range 5y 6mo-12y 10mo, SD 2y]) were assessed by 67 teachers. Cronbach's alpha, test-retest, and interrater reliability were acceptable-excellent across each SPQ scale (alphas=0.89, 0.9, 0.94, 0.79; test-retest ICCs=0.64, 0.61, 0.78, 0.62; interrater ICCs=0.85, 0.71, 0.90, 0.81). Concurrent and convergent validity were confirmed with significant positive correlations between SPQ and PEM-CY. After Mokken and Rasch model analysis, person and item reliability were good, and unidimensionality was confirmed. Mean administration time was 8.2 minutes., Interpretation: The results suggest that the SPQ is a rapid, reliable, and valid tool for assessment of participation-related indicators in schools., (© 2022 Mac Keith Press.)

Transition to adulthood can be a challenging developmental task for adolescents with common mental health problems and is linked to adverse outcomes such as 'not in education, employment or training' (NEET). This study investigated longitudinal associations between adolescent psychosocial factors (e.g., self-esteem, aspirations, bullying, physical activity) and later NEET status among individuals with common mental health problems (i.e., depression and anxiety). A secondary data analysis of the Next Steps cohort study was completed using waves 2 and 8. Psychosocial factors, mental health, and background characteristics were captured when participants were aged 15-16 years (wave 2) while still in compulsory education. The 12-item General Health Questionnaire was used to identify adolescents with common mental health problems. The study population consisted of 2224 participants (females 66.8%) of which 1473 (66.2%) were aged 15 years and 751 (33.8%) were aged 16 years in wave 2. The outcome was NEET status at ages 25-26 years (wave 8). The results showed that after adjusting for background characteristics, adolescent self-esteem, locus of control, bullying, physical activity, job aspirations, and attitudes to school predicted NEET status. Educational aspirations, substance use, and behavioural problems were not significantly associated with NEET status. These findings provide new insights into the role of adolescent psychosocial factors in the context of education and employment outcomes for youth at risk and highlight the necessity of targeted mental health support to improve life chances., (© 2022. The Author(s).)

Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K + or Sr 2+ . TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines., (© 2022 The Authors. Published by Wiley-VCH GmbH.)

Plasma-membrane-specific localization of Gag, an essential step in HIV-1 particle assembly, is regulated by the interaction of the Gag MA domain with PI(4,5)P 2 and tRNA-mediated inhibition of non-specific or premature membrane binding. Different tRNAs inhibit PI(4,5)P 2 -independent membrane binding to varying degrees in vitro; however, the structural determinants for this difference remain unknown. Here we demonstrate that membrane binding of full-length Gag synthesized in vitro using reticulocyte lysates is inhibited when RNAs that contain the anticodon arm of tRNA Pro , but not that of tRNA Lys3 , are added exogenously. In contrast, in the context of a liposome binding assay in which the effects of tRNAs on purified MA were tested, full-length tRNA Lys3 showed greater inhibition of MA membrane binding than full-length tRNA Pro . While transplantation of the D loop sequence of tRNA Lys3 into tRNA Pro resulted in a modest increase in the inhibitory effect relative to WT tRNA Pro , replacing the entire D arm sequence with that of tRNA Lys3 was necessary to confer the full inhibitory effects upon tRNA Pro . Together, these results demonstrate that the D arm of tRNA Lys3 is a major determinant of strong inhibition of MA membrane binding and that this inhibitory effect requires not only the D loop, which was recently reported to contact the MA highly basic region, but the loop sequence in the context of the D arm structure., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

We previously reported a tetrahelical monomolecular architecture of DNA, tmDNA, which employs G-quartets and an all-parallel GGGTGGGTGGGTGGG (G3T) quadruplex as the repeating unit. Based on thermodynamic and kinetic studies, we proposed that covalently joined (G3T) n units formed an uninterrupted programmable homopolymer; however, structural evidence for the tmDNA architecture was lacking. Here, we used NMR spectroscopy of wild-type and single-inosine-substituted constructs to characterize both monomolecular (G3T) 2 and bimolecular quadruplex-Mg-coupled versions of tmDNA. The NMR results support an architecture consisting of uninterrupted stacked G-tetrads in both the monomolecular constructs and bimolecular assemblies. Taken together, these data support the formation of a stable programmable homopolymeric tmDNA architecture, which may have been a precursor to the modern-day Watson-Crick DNA duplex., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

The HIV-1 nucleocapsid protein (NC) is a multi-functional protein necessary for viral replication. Recent studies have demonstrated reverse transcription occurs inside the fully intact viral capsid and that the timing of reverse transcription and uncoating are correlated. How a nearly 10 kbp viral DNA genome is stably contained within a narrow capsid with diameter similar to the persistence length of double-stranded (ds) DNA, and the role of NC in this process, are not well understood. In this study, we use optical tweezers, fluorescence imaging, and atomic force microscopy to observe NC binding a single long DNA substrate in multiple modes. We find that NC binds and saturates the DNA substrate in a non-specific binding mode that triggers uniform DNA self-attraction, condensing the DNA into a tight globule at a constant force up to 10 pN. When NC is removed from solution, the globule dissipates over time, but specifically-bound NC maintains long-range DNA looping that is less compact but highly stable. Both binding modes are additionally observed using AFM imaging. These results suggest multiple binding modes of NC compact DNA into a conformation compatible with reverse transcription, regulating the genomic pressure on the capsid and preventing premature uncoating.

Respiratory motion (i.e., motion pattern and rate) can provide valuable information for many medical situations. This information may help in the diagnosis of different health disorders and diseases. Wi-Fi-based respiratory monitoring schemes utilizing commercial off-the-shelf (COTS) devices can provide contactless, low-cost, simple, and scalable respiratory monitoring without requiring specialized hardware. Despite intense research efforts, an in-depth investigation on how to evaluate this type of technology is missing. We demonstrated and assessed the feasibility of monitoring and extracting human respiratory motion from Wi-Fi channel state information (CSI) data. This demonstration involves implementing an end-to-end system for a COTS-based hardware platform, control software, data acquisition, and a proposed processing algorithm. The processing algorithm is a novel deep-learning-based approach that exploits small changes in both CSI amplitude and phase information to learn high-level abstractions of breathing-induced chest movements and to reveal the unique characteristics of their difference. We also conducted extensive laboratory experiments demonstrating an assessment technique that can be replicated when quantifying the performance of similar systems. The results indicate that the proposed scheme can classify respiratory patterns and rates with an accuracy of 99.54% and 98.69%, respectively, in moderately degraded RF channels. Comprehensive data acquisition revealed the capability of the proposed system in detecting and classifying respiratory motions. Understanding the feasible limits and potential failure factors of Wi-Fi CSI-based respiratory monitoring scheme - and how to evaluate them - is an essential step toward the practical deployment of this technology. This study discusses ideas for further expansion of this technology.

To generate infectious virus, HIV-1 must package two copies of its full-length RNA into particles. HIV-1 transcription initiates from multiple, neighboring sites, generating RNA species that only differ by a few nucleotides at the 5' end, including those with one (1G) or three (3G) 5' guanosines. Strikingly, 1G RNA is preferentially packaged into virions over 3G RNA. We investigated how HIV-1 distinguishes between these nearly identical RNAs using in-gel chemical probing combined with recently developed computational tools for determining RNA conformational ensembles, as well as cell-based assays to quantify the efficiency of RNA packaging into viral particles. We found that 1G and 3G RNAs fold into distinct structural ensembles. The 1G RNA, but not the 3G RNA, primarily adopts conformations with an intact polyA stem, exposed dimerization initiation site, and multiple, unpaired guanosines known to mediate Gag binding. Furthermore, we identified mutants that exhibited altered genome selectivity and packaged 3G RNA efficiently. In these mutants, both 1G and 3G RNAs fold into similar conformational ensembles, such that they can no longer be distinguished. Our findings demonstrate that polyA stem stability guides RNA-packaging selectivity. These studies also uncover the mechanism by which HIV-1 selects its genome for packaging: 1G RNA is preferentially packaged because it exposes structural elements that promote RNA dimerization and Gag binding., Competing Interests: The authors declare no competing interest.

Background: During HIV-1 maturation, Gag and Gag-Pol polyproteins are proteolytically cleaved and the capsid protein polymerizes to form the honeycomb capsid lattice. HIV-1 integrase (IN) binds the viral genomic RNA (gRNA) and impairment of IN-gRNA binding leads to mis-localization of the nucleocapsid protein (NC)-condensed viral ribonucleoprotein complex outside the capsid core. IN and NC were previously demonstrated to bind to the gRNA in an orthogonal manner in virio; however, the effect of IN binding alone or simultaneous binding of both proteins on gRNA structure is not yet well understood., Results: Using crosslinking-coupled selective 2'-hydroxyl acylation analyzed by primer extension (XL-SHAPE), we characterized the interaction of IN and NC with the HIV-1 gRNA 5'-untranslated region (5'-UTR). NC preferentially bound to the packaging signal (Psi) and a UG-rich region in U5, irrespective of the presence of IN. IN alone also bound to Psi but pre-incubation with NC largely abolished this interaction. In contrast, IN specifically bound to and affected the nucleotide (nt) dynamics of the apical loop of the transactivation response element (TAR) and the polyA hairpin even in the presence of NC. SHAPE probing of the 5'-UTR RNA in virions produced from allosteric IN inhibitor (ALLINI)-treated cells revealed that while the global secondary structure of the 5'-UTR remained unaltered, the inhibitor treatment induced local reactivity differences, including changes in the apical loop of TAR that are consistent with the in vitro results., Conclusions: Overall, the binding interactions of NC and IN with the 5'-UTR are largely orthogonal in vitro. This study, together with previous probing experiments, suggests that IN and NC binding in vitro and in virio lead to only local structural changes in the regions of the 5'-UTR probed here. Accordingly, disruption of IN-gRNA binding by ALLINI treatment results in local rather than global secondary structure changes of the 5'-UTR in eccentric virus particles., (© 2021. The Author(s).)

There is a variable standard of access to quality neurodevelopmental assessment and diagnosis. People may have negative experiences, encountering lengthy waiting times, and inconsistent practices. Practitioners need guidance on standards and practices for assessment and diagnosis matched to new ways of working. In this paper, we present a new pathway and recommendations for multidisciplinary neurodevelopmental assessment and diagnosis for children and young people (<19 years), developed by the Scottish Government funded National Autism Implementation Team (NAIT). Our research used the Medical Research Council guidance for the development of complex interventions and included several iterative stages. Stage 1: n = 44 stakeholders attended an event on developing new practices for diagnosis and assessment. Stage 2: a literature synthesis was completed by the research team of clinical guidelines and diagnosis and assessment tools. Stage 3: an event with n = 127 stakeholders included discussion and debate of the data from stages 1 and 2. Recommendations and a draft pathway were written. Stage 4: successive drafts of recommendations and the pathway documentation were circulated among an advisory group, including multidisciplinary clinical experts and people with lived experience, until the final pathway was agreed upon. The finalised pathway includes guidance on terminology, assessment, diagnosis, triage, time standards and engagement of people with lived experience. The new pathway has been adopted by the Scottish Government. The pathway and associated documentation are freely available online for use by others.

Background: Older people are the fastest-growing demographic group among prisoners in England and Wales and they have complex health and social care needs. Their care is frequently ad hoc and uncoordinated. No previous research has explored how to identify and appropriately address the needs of older adults in prison. We hypothesised that the Older prisoner Health and Social Care Assessment and Plan (OHSCAP) would significantly increase the proportion of met health and social care needs 3 months after prison entry, compared to treatment as usual (TAU)., Methods: The study was a parallel randomised controlled trial (RCT) recruiting male prisoners aged 50 and over from 10 prisons in northern England. Participants received the OHSCAP or TAU. A clinical trials unit used minimisation with a random element as the allocation procedure. Data analysis was conducted blind to allocation status. The intervention group had their needs assessed using the OHSCAP tool and care plans were devised; processes that lasted approximately 30 min in total per prisoner. TAU included the standard prison health assessment and care. The intention to treat principle was followed. The trial was registered with the UK Clinical Research Network Portfolio (ISRCTN ID: 11841493) and was closed on 30 November 2016., Results: Data were collected between 28 January 2014 and 06 April 2016. Two hundred and forty nine older prisoners were assigned TAU of which 32 transferred prison; 12 were released; 2 withdrew and 1 was deemed unsafe to interview. Two hundred and fifty three 3 prisoners were assigned the OHSCAP of which 33 transferred prison; 11 were released; 6 withdrew and 1 was deemed unsafe to interview. Consequently, data from 202 participants were analysed in each of the two groups. There were no significant differences in the number of unmet needs as measured by the Camberwell Assessment of Needs - Forensic Short Version (CANFOR-S). The mean number of unmet needs for the OHSCAP group at follow-up was 2.03 (SD = 2.07) and 2.06 (SD = 2.11) for the TAU group (mean difference = 0.088; 95% CI - 0.276 to 0.449, p = 0.621). No adverse events were reported., Conclusion: The OHSCAP was fundamentally not implemented as planned, partly due to the national prison staffing crisis that ensued during the study period. Therefore, those receiving the OHSCAP did not experience improved outcomes compared to those who received TAU., Trial Registration: Current Controlled Trials: ISRCTN11841493 , 25/10/2012., (© 2021. The Author(s).)

Aim: The review aimed to identify and explore the association of level of support received by people with severe mental illness in supported accommodation and participation., Method: The authors conducted a systematic search in MEDLINE, PsychINFO, PsychARTICLES, CINAHL Plus and ASSIA. Searches were restricted to articles published in English and participants aged 18 years and over with severe mental illness. Articles were included based on level of support received in mental health supported accommodation, classified according to the Simple Taxonomy for Supported Accommodation, and three factors of participation: social participation, daily living functioning and personal empowerment. Studies of in-patient settings and nursing homes were excluded. The review protocol is registered on PROSPERO (registration number: CRD42019161808)., Results: Six articles were included in the review from USA, Australia, Sweden and Taiwan. Factors of participation for people living in accommodation with moderate support and accommodation with high support were explored. Data indicated an association between level of support and participation showing that people living in accommodation with moderate support had increased participation compared to people living in accommodation with high support., Conclusion: This review identified an association between level of formal support and participation. People with SMI living in accommodation with medium support participated in more community occupations, more activities and had a higher level of personal empowerment than people living in accommodation with high support.