Proline residues within spacer peptide p1 are important for human immunodeficiency virus type 1 infectivity, protein processing, and genomic RNA dimer stability

The full-length human immunodeficiency virus type 1 (HIV-1) mRNA encodes two precursor polyproteins, Gag and GagProPol. An infrequent ribosomal frameshifting event allows these proteins to be synthesized from the same mRNA in a predetermined ratio of 20 Gag proteins for each GagProPol. The RNA frameshift signal consists of a slippery sequence and a hairpin stem-loop whose thermodynamic stability has been shown in in vitro translation systems to be critical to frameshifting efficiency. In this study we examined the frameshift region of HIV-1, investigating the effects of altering stem-loop stability in the context of the complete viral genome and assessing the role of the Gag spacer peptide p1 and the GagProPol transframe (TF) protein that are encoded in this region. By creating a series of frameshift region mutants that systematically altered the stability of the frameshift stem-loop and the protein sequences of the p1 spacer peptide and TF protein, we have demonstrated the importance of stem-loop thermodynamic stability in frameshifting efficiency and viral infectivity. Multiple changes to the amino acid sequence of p1 resulted in altered protein processing, reduced genomic RNA dimer stability, and abolished viral infectivity. The role of the two highly conserved proline residues in p1 (position 7 and 13) was also investigated. Replacement of the two proline residues by leucines resulted in mutants with altered protein processing and reduced genomic RNA dimer stability that were also noninfectious. The unique ability of proline to confer conformational constraints on a peptide suggests that the correct folding of p1 may be important for viral function.<br /

Publishing and sharing multi-dimensional image data with OMERO

Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org

Triggered Escalating Real-Time Adherence Intervention to Promote Rapid HIV Viral Suppression Among Youth Living With HIV Failing Antiretroviral Therapy: Protocol for a Triggered Escalating Real-Time Adherence Intervention

BACKGROUND: Youth living with HIV (YLWH) are confronted with many self-care challenges that can be experienced as overwhelming in the context of normal developmental processes that characterize adolescence and young adulthood. A sizable minority of YLWH have unsuppressed viral loads in the United States attributable to antiretroviral therapy (ART) nonadherence. Interventions to promote sustained viral suppression in YLWH are needed. OBJECTIVE: The aim of this study is to evaluate the efficacy of the Triggered Escalating Real-Time Adherence (TERA) intervention in comparison with standard of care (SOC) in YLWH (aged 13-24 years) failing ART on (1) primary outcome measures-HIV viral suppression (VLS), defined as both &lt;200 copies/ml and &lt;50 copies/ml at 12 weeks, and (2) secondary outcome measures-VLS rates and rates of ART adherence at 24, 36, and 48 weeks as well as patterns of adherence over time as measured by an electronic dose monitoring (EDM) device. METHODS: The TERA study is a phase 2, multisite clinical trial conducted with 120 YLWH failing ART (randomized 1:1 to TERA or SOC) at participating clinical sites within the Adolescent Medicine Trials Network for HIV/AIDS Interventions (ATN). Participants are followed for a total of 48 weeks. For TERA arm participants, the first 12 weeks involve delivery of the intervention. For all participants, clinical outcomes are collected throughout follow-up, and adherence is assessed using EDM over the full 48 weeks. During the 12-week intervention period, TERA arm participants receive 3 remote coaching sessions delivered in clinic via videoconferencing timed to coincide with baseline and follow-up clinical visits, text message reminders when the EDM has not been opened at dose time (which escalate to 2-way theory-informed short message service coaching interactions in response to real-time nonadherence), and review of dosing graphs produced by EDM at follow-up visits. RESULTS: Launch dates for enrollment varied by site. Enrollment began in April 2018 and is expected to be completed by August 2019, with results presented by the second quarter of 2021. CONCLUSIONS: Effective, generalizable, and scalable approaches to rapidly assist YLWH failing to achieve and sustain VLS may have a substantial impact on individual health and efforts to curb transmission. Coaching for a brief but intensive period from remote coaches and using communication channels common to youth may offer multiple unique advantages in promoting self-care

Probing biological nanotopology via diffusion of weakly constrained plasmonic nanorods with optical coherence tomography

Many diseases are characterized by nanostructural changes in connective fibers and soluble proteins, which can indicate or drive disease progression. Noninvasive methods sensitive to nanotopological changes in 3D tissue models can elucidate biophysical changes associated with disease progression. Nanoparticles probe their environment via their diffusion, which is impacted by the size and connectivity of pores into which they freely diffuse. Here, we show that optical coherence tomography provides depth-resolved imaging of gold nanorods (GNRs) to infer local biological nanotopology. We demonstrate the broad potential of this method by sensing changes in diffusion of GNRs in 3D models of mammary ECM and pulmonary mucus

Ethnic inequalities in cancer incidence and mortality: census-linked cohort studies with 87 million years of person-time follow-up

BACKGROUND: Cancer makes up a large and increasing proportion of excess mortality for indigenous, marginalised and socioeconomically deprived populations, and much of this inequality is preventable. This study aimed to determine which cancers give rise to changing ethnic inequalities over time. METHODS: New Zealand census data from 1981, 1986, 1991, 1996, 2001, and 2006, were all probabilistically linked to three to five subsequent years of mortality (68 million person-years) and cancer registrations (87 million person years) and weighted for linkage bias. Age-standardised rate differences (SRDs) for Māori (indigenous) and Pacific peoples, each compared to European/Other, were decomposed by cancer type. RESULTS: The absolute size and percentage of the cancer contribution to excess mortality increased from 1981-86 to 2006-11 in Māori males (SRD 72.5 to 102.0 per 100,000) and females (SRD 72.2 to 109.4), and Pacific females (SRD -9.8 to 42.2) each compared to European/Other. Specifically, excess mortality (SRDs) increased for breast cancer in Māori females (linear trend p < 0.01) and prostate (p < 0.01) and colorectal cancers (p < 0.01) in Māori males. The incidence gap (SRDs) increased for breast (Māori and Pacific females p < 0.01), endometrial (Pacific females p < 0.01) and liver cancers (Māori males p = 0.04), and for cervical cancer it decreased (Māori females p = 0.03). The colorectal cancer incidence gap which formerly favoured Māori, decreased for Māori males and females (p < 0.01). The greatest contributors to absolute inequalities (SRDs) in mortality in 2006-11 were lung cancer (Māori males 50 %, Māori females 44 %, Pacific males 81 %), breast cancer (Māori females 18 %, Pacific females 23 %) and stomach cancers (Māori males 9 %, Pacific males 16 %, Pacific females 20 %). The top contributors to the ethnic gap in cancer incidence were lung, breast, stomach, endometrial and liver cancer. CONCLUSIONS: A transition is occurring in what diseases contribute to inequalities. The increasing excess incidence and mortality rates in several obesity- and health care access-related cancers provide a sentinel warning of the emerging drivers of ethnic inequalities. Action to further address inequalities in cancer burden needs to be multi-pronged with attention to enhanced control of tobacco, obesity, and carcinogenic infectious agents, and focus on addressing access to effective screening and quality health care

Detectability of Plasmodium falciparum clones

BACKGROUND: In areas of high transmission people often harbour multiple clones of Plasmodium falciparum, but even PCR-based diagnostic methods can only detect a fraction (the detectability, q) of all clones present in a host. Accurate measurements of detectability are desirable since it affects estimates of multiplicity of infection, prevalence, and frequency of breakthrough infections in clinical drug trials. Detectability can be estimated by typing repeated samples from the same host but it has been unclear what should be the time interval between the samples and how the data should be analysed. METHODS: A longitudinal molecular study was conducted in the Kassena-Nankana district in northern Ghana. From each of the 80 participants, four finger prick samples were collected over a period of 8 days, and tested for presence of different Merozoite Surface Protein (msp) 2 genotypes. Implications for estimating q were derived from these data by comparing the fit of statistical models of serial dependence and over-dispersion. RESULTS: The distribution of the frequencies of detection for msp2 genotypes was close to binomial if the time span between consecutive blood samples was at least 7 days. For shorter intervals the probabilities of detection were positively correlated, i.e. the shorter the interval between two blood collections, the more likely the diagnostic results matched for a particular genotype. Estimates of q were rather insensitive to the statistical model fitted. CONCLUSIONS: A simple algorithm based on analysing blood samples collected 7 days apart is justified for generating robust estimates of detectability. The finding of positive correlation of detection probabilities for short time intervals argues against imperfect detection being directly linked to the 48-hour periodicity of P. falciparum. The results suggest that the detectability of a given parasite clone changes over time, at an unknown rate, but fast enough to regard blood samples taken one week apart as statistically independent

NCCN Guidelines Insights: Survivorship, Version 2.2020.

The NCCN Guidelines for Survivorship provide screening, evaluation, and treatment recommendations for consequences of adult-onset cancer and its treatment, with the goal of helping healthcare professionals who work with survivors, including those in primary care. The guidelines also provide recommendations to help clinicians promote physical activity, weight management, and proper immunizations in survivors and facilitate care coordination to ensure that all of the survivors needs are addressed. These NCCN Guidelines Insights summarize additions and changes made to the guidelines in 2020 regarding cardiovascular disease risk assessment and screening for subsequent primary malignancies

Molecular Evolution of the Rice Blast Resistance Gene Pi-ta in Invasive Weedy Rice in the USA

The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing

Heterozygous FOXN1 Variants Cause Low TRECs and Severe T Cell Lymphopenia, Revealing a Crucial Role of FOXN1 in Supporting Early Thymopoiesis

FOXN1 is the master regulatory gene of thymic epithelium development. FOXN1 deficiency leads to thymic aplasia, alopecia, and nail dystrophy, accounting for the nude/severe combined immunodeficiency (nu/SCID) phenotype in humans and mice. We identified several newborns with low levels of T cell receptor excision circles (TRECs) and T cell lymphopenia at birth, who carried heterozygous loss-of-function FOXN1 variants. Longitudinal analysis showed persistent T cell lymphopenia during infancy, often associated with nail dystrophy. Adult individuals with heterozygous FOXN1 variants had in most cases normal CD4+ but lower than normal CD8+ cell counts. We hypothesized a FOXN1 gene dosage effect on the function of thymic epithelial cells (TECs) and thymopoiesis and postulated that these effects would be more prominent early in life. To test this hypothesis, we analyzed TEC subset frequency and phenotype, early thymic progenitor (ETP) cell count, and expression of FOXN1 target genes (Ccl25, Cxcl12, Dll4, Scf, Psmb11, Prss16, and Cd83) in Foxn1nu/+ (nu/+) mice and age-matched wild-type (+/+) littermate controls. Both the frequency and the absolute count of ETP were significantly reduced in nu/+ mice up to 3 weeks of age. Analysis of the TEC compartment showed reduced expression of FOXN1 target genes and delayed maturation of the medullary TEC compartment in nu/+ mice. These observations establish a FOXN1 gene dosage effect on thymic function and identify FOXN1 haploinsufficiency as an important genetic determinant of T cell lymphopenia at birth