Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase.

Extranuclear localization of long noncoding RNAs (lncRNAs) is poorly understood. Based on machine learning evaluations, we propose a lncRNA-mitochondrial interaction pathway where polynucleotide phosphorylase (PNPase), through domains that provide specificity for primary sequence and secondary structure, binds nuclear-encoded lncRNAs to facilitate mitochondrial import. Using FVB/NJ mouse and human cardiac tissues, RNA from isolated subcellular compartments (cytoplasmic and mitochondrial) and cross-linked immunoprecipitate (CLIP) with PNPase within the mitochondrion were sequenced on the Illumina HiSeq and MiSeq, respectively. lncRNA sequence and structure were evaluated through supervised [classification and regression trees (CART) and support vector machines (SVM)] machine learning algorithms. In HL-1 cells, quantitative PCR of PNPase CLIP knockout mutants (KH and S1) was performed. In vitro fluorescence assays assessed PNPase RNA binding capacity and verified with PNPase CLIP. One hundred twelve (mouse) and 1,548 (human) lncRNAs were identified in the mitochondrion with Malat1 being the most abundant. Most noncoding RNAs binding PNPase were lncRNAs, including Malat1. lncRNA fragments bound to PNPase compared against randomly generated sequences of similar length showed stratification with SVM and CART algorithms. The lncRNAs bound to PNPase were used to create a criterion for binding, with experimental validation revealing increased binding affinity of RNA designed to bind PNPase compared to control RNA. The binding of lncRNAs to PNPase was decreased through the knockout of RNA binding domains KH and S1. In conclusion, sequence and secondary structural features identified by machine learning enhance the likelihood of nuclear-encoded lncRNAs binding to PNPase and undergoing import into the mitochondrion.NEW & NOTEWORTHY Long noncoding RNAs (lncRNAs) are relatively novel RNAs with increasingly prominent roles in regulating genetic expression, mainly in the nucleus but more recently in regions such as the mitochondrion. This study explores how lncRNAs interact with polynucleotide phosphorylase (PNPase), a protein that regulates RNA import into the mitochondrion. Machine learning identified several RNA structural features that improved lncRNA binding to PNPase, which may be useful in targeting RNA therapeutics to the mitochondrion.

Respiratory syncytial virus in children: epidemiology and clinical impact post-COVID-19.

PURPOSE OF REVIEW: Respiratory syncytial virus (RSV) remains a leading cause of mortality and morbidity worldwide. RSV seasonality was disrupted by COVID-19-associated nonpharmaceutical interventions (NPIs). We review RSV seasonality, molecular epidemiology, clinical manifestations, and community awareness to inform future prevention strategies. RECENT FINDINGS: An initial reduction of RSV disease observed with NPIs, and subsequent global resurgence was associated with a collapse in genetic diversity. A lack of immunity is suggested to have contributed to the resurgence of RSV cases experienced post COVID-19. The median age of children admitted with RSV increased during the resurgence, likely secondary to the expanded cohort of RSV-immune naive children. The pandemic also played a role in increased community awareness, which can be utilized as part of a coordinated public health effort to introduce prevention strategies. Further education on signs and symptoms of RSV is still required. SUMMARY: mAbs and maternal vaccines targeting RSV have the potential to reduce paediatric morbidity, however this new era of RSV prevention will require ongoing research to facilitate community awareness and engagement, and better respiratory surveillance. Tackling the global burden of RSV will require a coordinated effort and measures to ensure access and affordability of new prevention strategies.

Nix Pro Color Sensor provides comparable color measurements to HunterLab colorimeter for fresh beef.

The HunterLab MiniScan (HunterLab) colorimeter is used in meat quality research worldwide for measuring meat color; however, the Nix Pro Color Sensor (Nix) could be a less expensive alternative that is easier to operate. Therefore, the objective of this study was to compare the two colorimeters to objectively evaluate fresh beef color. Longissimus thoracis muscle from one side of A maturity beef carcasses (n = 200) was evaluated using both the HunterLab (3 technical replicate scans) and Nix (3, 5, 7, and 9 technical replicate scans) colorimeters. The correlation between the HunterLab and Nix for L* (lightness), a* (redness), and b* (yellowness) values ranged between r = 0.80 to 0.85 and the Bland Altman Limits of Agreement analysis indicated good agreement between the Nix and HunterLab colorimeters for all the color parameters. These results indicated that the Nix colorimeter could be a viable alternative for HunterLab colorimeters.

Identifying Future High Cost Individuals within an Intermediate Cost Population.

BACKGROUND: Improving health and controlling healthcare costs requires better tools for predicting future health needs across populations. We sought to identify factors associated with transitioning of enrollees in an indigent care program from an intermediate cost segment to a high cost segment of this population. METHODS: We analyzed data from 9,624 enrollees of the Virginia Coordinated Care program between 2010 and 2013. Each fiscal year included all enrollees who were classified in intermediate cost segment in the preceding year and also enrolled in the program in the following year. Using information from the preceding year, we built logistic regression models to identify the individuals in the top 10% of expenditures in the following year. The effect of demographics, count of chronic conditions, presence of the prevalent chronic conditions, and utilization indicators were evaluated and compared. Models were compared via the Bayesian information criterion and c-statistic. RESULTS: The count of chronic conditions, diagnosis of congestive heart failure, and numbers of total hospital visits and prescriptions were significantly and independently associated with being in the future high cost segment. Overall, the model that included demographics and utilization indicators had a reasonable discrimination (c=0.67). CONCLUSIONS: A simple model including demographics and health utilization indicators predicted high future costs. The count of chronic conditions and certain medical diagnoses added additional predictive value. With further validation, the approach could be used to identify high-risk individuals and target interventions that decrease utilization and improve health.

More than the SRY: The Non-Coding Landscape of the Y Chromosome and Its Importance in Human Disease.

Historically, the Y chromosome has presented challenges to classical methodology and philosophy of understanding the differences between males and females. A genetic unsolved puzzle, the Y chromosome was the last chromosome to be fully sequenced. With the advent of the Human Genome Project came a realization that the human genome is more than just genes encoding proteins, and an entire universe of RNA was discovered. This dark matter of biology and the black box surrounding the Y chromosome have collided over the last few years, as increasing numbers of non-coding RNAs have been identified across the length of the Y chromosome, many of which have played significant roles in disease. In this review, we will uncover what is known about the connections between the Y chromosome and the non-coding RNA universe that originates from it, particularly as it relates to long non-coding RNAs, microRNAs and circular RNAs.

Characterizing the Palliative Care Physician Workforce: A Retrospective Cross-Sectional Study With Population-Based Data in Ontario, Canada.

OBJECTIVES: Because of an increasing need to build capacity for end-of-life care, improving access to palliative care is a priority. Where a physician practices (eg, hospital, outpatient clinic, home) directly relates to the type of service and the stage of illness at which care is provided. In this study, we describe the physician palliative care specialist workforce and the settings of care within which they practice. DESIGN: A retrospective cohort. SETTING AND PARTICIPANTS: All physicians with palliative care billing codes who were practicing between April 1, 2018, and March 31, 2019, in Ontario, Canada. METHODS: Descriptive statistics of physician billing location and frequency using linked population-based health administrative data. RESULTS: We identified 8883 physicians who provided palliative care during the study period. Of those, 723 (8.1%) were classified as palliative care specialists (>10% of their billings encounters were palliative care). The majority (57.4%) of palliative care specialists worked in 1 setting more than 90% of their time, across home visits (27.1%), indirect care (22.4%), and office (7.9%). There were 61 palliative care specialists practicing in mixed locations who provided home visits, meaning 310 (42.9%) of the palliative care specialists delivered some home-based care. CONCLUSIONS AND IMPLICATIONS: This research provides a comprehensive description of the current palliative care specialist physician workforce that can support efforts to build capacity for high-quality end-of-life care.

Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities.

Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cancer hallmarks remain unclear. We employ pooled CRISPR deletion to perturb 831 lncRNAs detected in KRAS-mutant non-small cell lung cancer (NSCLC) and measure their contribution to proliferation, chemoresistance, and migration across two cell backgrounds. Integrative analysis of these data outperforms conventional "dropout" screens in identifying cancer genes while prioritizing disease-relevant lncRNAs with pleiotropic and background-independent roles. Altogether, 80 high-confidence oncogenic lncRNAs are active in NSCLC, which tend to be amplified and overexpressed in tumors. A follow-up antisense oligonucleotide (ASO) screen shortlisted two candidates, Cancer Hallmarks in Lung LncRNA 1 (CHiLL1) and GCAWKR, whose knockdown consistently suppressed cancer hallmarks in two- and three-dimension tumor models. Molecular phenotyping reveals that CHiLL1 and GCAWKR control cellular-level phenotypes via distinct transcriptional networks. This work reveals a multi-dimensional functional lncRNA landscape underlying NSCLC that contains potential therapeutic vulnerabilities.

Prenatal Cadmium Exposure Alters Proliferation in Mouse CD4+ T Cells via LncRNA Snhg7.

Objective: Prenatal cadmium (Cd) exposure leads to immunotoxic phenotypes in the offspring affecting coding and non-coding genes. Recent studies have shown that long non-coding RNAs (lncRNAs) are integral to T cell regulation. Here, we investigated the role of long non-coding RNA small nucleolar RNA host gene 7 (lncSnhg7) in T cell proliferation. Methods: RNA sequencing was used to analyze the expression of lncRNAs in splenic CD4+ T cells with and without CD3/CD28 stimulation. Next, T cells isolated from offspring exposed to control or Cd water throughout mating and gestation were analyzed with and without stimulation with anti-CD3/CD28 beads. Quantitative qPCR and western blotting were used to detect RNA and protein levels of specific genes. Overexpression of a miR-34a mimic was achieved using nucleofection. Apoptosis was measured using flow cytometry and luminescence assays. Flow cytometry was also used to measure T cell proliferation in culture. Finally, lncSnhg7 was knocked down in splenic CD4+ T cells with lentivirus to assess its effect on proliferation. Results: We identified 23 lncRNAs that were differentially expressed in stimulated versus unstimulated T cells, including lncSnhg7. LncSnhg7 and a downstream protein, GALNT7, are upregulated in T cells from offspring exposed to Cd during gestation. Overexpression of miR-34a, a regulator of lncSnhg7 and GALNT7, suppresses GALNT7 protein levels in primary T cells, but not in a mouse T lymphocyte cell line. The T cells isolated from Cd-exposed offspring exhibit increased proliferation after activation in vitro, but Treg suppression and CD4+ T cell apoptosis are not affected by prenatal Cd exposure. Knockdown on lncSnhg7 inhibits proliferation of CD4+ T cells. Conclusion: Prenatal Cd exposure alters the expression of lncRNAs during T cell activation. The induction of lncSnhg7 is enhanced in splenic T cells from Cd offspring resulting in the upregulation of GALNT7 protein and increased proliferation following activation. miR-34a overexpression decreased GALNT7 expression and knockdown of lncSnhg7 inhibited proliferation suggesting that the lncSnhg7/miR-34a/GALNT7 is an important pathway in primary CD4+ T cells. These data highlight the need to understand the consequences of environmental exposures on lncRNA functions in non-cancerous cells as well as the effects in utero.

Flower lose, a cell fitness marker, predicts COVID-19 prognosis.

Risk stratification of COVID-19 patients is essential for pandemic management. Changes in the cell fitness marker, hFwe-Lose, can precede the host immune response to infection, potentially making such a biomarker an earlier triage tool. Here, we evaluate whether hFwe-Lose gene expression can outperform conventional methods in predicting outcomes (e.g., death and hospitalization) in COVID-19 patients. We performed a post-mortem examination of infected lung tissue in deceased COVID-19 patients to determine hFwe-Lose's biological role in acute lung injury. We then performed an observational study (n = 283) to evaluate whether hFwe-Lose expression (in nasopharyngeal samples) could accurately predict hospitalization or death in COVID-19 patients. In COVID-19 patients with acute lung injury, hFwe-Lose is highly expressed in the lower respiratory tract and is co-localized to areas of cell death. In patients presenting in the early phase of COVID-19 illness, hFwe-Lose expression accurately predicts subsequent hospitalization or death with positive predictive values of 87.8-100% and a negative predictive value of 64.1-93.2%. hFwe-Lose outperforms conventional inflammatory biomarkers and patient age and comorbidities, with an area under the receiver operating characteristic curve (AUROC) 0.93-0.97 in predicting hospitalization/death. Specifically, this is significantly higher than the prognostic value of combining biomarkers (serum ferritin, D-dimer, C-reactive protein, and neutrophil-lymphocyte ratio), patient age and comorbidities (AUROC of 0.67-0.92). The cell fitness marker, hFwe-Lose, accurately predicts outcomes in COVID-19 patients. This finding demonstrates how tissue fitness pathways dictate the response to infection and disease and their utility in managing the current COVID-19 pandemic.

Effects of space allowance and marketing strategy on growth performance of pigs raised to 165 kg.

A total of 976 pigs (PIC 327 × Camborough; PIC, Hendersonville, TN; initially 22.0 ± 1.53 kg body weight [BW]) were used in a 160-d growth study to evaluate the effects of increasing space allowance and varying marketing strategies on growth performance of pigs raised to market weights of ~165 kg. Pens of pigs were blocked by location within the barn and allotted to one of six treatments. Pen served as the experimental unit, and there were eight replicate pens per treatment. The first four treatments consisted of increased initial stocking density and did not utilize topping strategies: (1) 14 pigs/pen (1.17 m2/pig), (2) 17 pigs/pen (0.97 m2/pig), (3) 20 pigs/pen (0.82 m2/pig), and (4) 23 pigs/pen (0.71 m2/pig). The fifth treatment began with 25 pigs/pen (0.66 m2/pig) and had four marketing events with the heaviest 3 pigs/pen removed on day 93, and additional pigs removed to a common inventory of 20 pigs/pen on day 122 and 17 pigs/pen on day 147 with final marketing on day 160. The final treatment began the experiment with 23 pigs/pen (0.71 m2/pig) with three marketing events to achieve a common inventory of 20 pigs/pen on day 108 and 17 pigs/pen on day 147. Pens of pigs were weighed and feed disappearance measured on days 0, 55, 93, 108, 122, 135, 147, and 160. As space allowance decreased from 1.17 to 0.71 m2/pig via increased initial pen inventory (treatments 1 to 4), overall average daily gain (ADG) and average daily feed intake (ADFI) decreased (linear, P < 0.001), while gain:feed ratio (G:F) did not differ (P > 0.05). The treatments with multiple marketing events were compared with each other and with the treatment that began with 0.71 m2/pig and only marketed once at the end of the study. Overall ADG and ADFI were not different (P > 0.05) among these three treatments. Marketing pigs three or four times improved (P < 0.05) G:F compared with the treatment that began the study with 0.71 m2/pig and marketed only once. Reducing floor space allowance for heavy weight pigs decreased intake, which resulted in lower growth rate and final BW, with these reductions occurring before the critical k-value was reached. Total weight gain per pen was maximized with the lowest space allowance and the multiple marketing treatments. Thus, strategic use of pig removals prior to final marketing may allow producers to maximize both number of pigs and total weight marketed through a barn when feeding to heavy weights.

Evaluation of marbling and enhancement's abilities to compensate for reduced beef palatability at elevated degrees of doneness.

The objectives of this study were to evaluate the extent marbling compensates for reduced beef palatability at elevated degrees of doneness and to determine the relationship of residual moisture and fat in cooked steaks to beef palatability, specifically beef juiciness. Paired strip loins (IMPS # 180) were collected to equally represent five quality treatments [Prime, Top Choice (modest and moderate marbling), Low Choice, Select, and Select Enhanced (110% of raw weight)]. Steaks were grouped into sets of three consecutively cut steaks and randomly assigned a degree of doneness (DOD): very-rare (VR; 55 °C), rare (R; 60 °C), medium-rare (MR; 63 °C), medium (M; 71 °C), well done (WD; 77 °C), or very well done (VWD; 82 °C). Samples were subjected to consumer and trained sensory evaluation, Warner-Braztler shear force (WBSF), slice shear force (SSF), pressed juice percentage (PJP) evaluation, and raw and cooked proximate analysis. There were no (P > 0.05) quality treatment × DOD interactions for consumer sensory ratings, indicating increased DOD had the same negative impact regardless of marbling level. There was a quality treatment × DOD interaction (P < 0.05) for the percentage of steaks rated acceptable by consumers for juiciness. Increased marbling modified the point in which steaks became unacceptable for juiciness. Similarly, there was a quality treatment × DOD interaction (P < 0.05) for trained juiciness ratings. When cooked to MR and lower, Prime was rated only 8% to 18% higher (P < 0.05) than Select for trained juiciness ratings, but was rated 38% to 123% higher (P < 0.05) than Select when cooked to M and higher. Besides cooking loss, combined cooked moisture and fat percentage was more highly associated (P < 0.01) to consumer juiciness (r = 0.69) and trained initial (r = 0.84) and sustained (r = 0.85) juiciness ratings than all other objective evaluations. Using regression analyses, cooked moisture and fat percentages, alone, were poor indicators of consumer and trained juiciness ratings. However, when combined, the regression equations explained 45%, 74%, and 69% of the variation in consumer, trained initial, and trained sustained juiciness ratings, respectively. These results indicate that increased marbling levels only offer "insurance" for juiciness of steaks that are cooked to high degrees of doneness, but not for other palatability traits. Additionally, cooked residual moisture and fat percentages, when combined, are a good indicator of sensory juiciness ratings.

Pseudoexon activation increases phenotype severity in a Becker muscular dystrophy patient.

We report a dystrophinopathy patient with an in-frame deletion of DMD exons 45-47, and therefore a genetic diagnosis of Becker muscular dystrophy, who presented with a more severe than expected phenotype. Analysis of the patient DMD mRNA revealed an 82 bp pseudoexon, derived from intron 44, that disrupts the reading frame and is expected to yield a nonfunctional dystrophin. Since the sequence of the pseudoexon and canonical splice sites does not differ from the reference sequence, we concluded that the genomic rearrangement promoted recognition of the pseudoexon, causing a severe dystrophic phenotype. We characterized the deletion breakpoints and identified motifs that might influence selection of the pseudoexon. We concluded that the donor splice site was strengthened by juxtaposition of intron 47, and loss of intron 44 silencer elements, normally located downstream of the pseudoexon donor splice site, further enhanced pseudoexon selection and inclusion in the DMD transcript in this patient.

2MASS J035523.37+113343.7: A YOUNG, DUSTY, NEARBY, ISOLATED BROWN DWARF RESEMBLING A GIANT EXOPLANET.

We present parallax and proper motion measurements, near-infrared spectra, and WISE photometry for the low surface gravity L5γ dwarf 2MASSJ035523.37+113343.7 (2M0355). We use these data to evaluate photometric, spectral, and kinematic signatures of youth as 2M0355 is the reddest isolated L dwarf yet classified. We confirm its low-gravity spectral morphology and find a strong resemblance to the sharp triangular shaped H-band spectrum of the ∼10 Myr planetary-mass object 2M1207b. We find that 2M0355 is underluminous compared to a normal field L5 dwarf in the optical and MKO J, H, and K bands and transitions to being overluminous from 3-12 µm, indicating that enhanced photospheric dust shifts flux to longer wavelengths for young, low-gravity objects, creating a red spectral energy distribution. Investigating the near-infrared color magnitude diagram for brown dwarfs confirms that 2M0355 is redder and underluminous compared to the known brown dwarf population, similar to the peculiarities of directly imaged exoplanets 2M1207b and HR8799bcd. We calculate UVW space velocities and find that the motion of 2M0355 is consistent with young disk objects (< 2-3 Gyr) and it shows a high likelihood of membership in the AB Doradus association.