Mitochondrial Sequencing Identifies Long Non-Coding RNA Features that Promote Binding to PNPase.

Extranuclear localization of long non-coding 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 crosslinked 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, qPCR of PNPase CLIP knockout mutants (KH and S1) were performed. In vitro fluorescence assays assessed PNPase RNA binding capacity and verified with PNPase CLIP. 112 (mouse) and 1,548 (human) lncRNAs were identified in the mitochondrion with Malat1 being the most highly expressed. Most non-coding 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. Binding of lncRNAs to PNPase was decreased through 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 to bind to PNPase and undergo import into the mitochondrion.

Effect of Rootstock Genotype and Arbuscular Mycorrhizal Fungal (AMF) Species on Early Colonization of Apple.

The effect of plant cultivar on the degree of mycorrhization and the benefits mediated by arbuscular mycorrhizal fungi (AMF) have been documented in many crops. In apple, a wide variety of rootstocks are commercially available; however, it is not clear whether some rootstock genotypes are more susceptible to mycorrhization than others and/or whether AMF species identity influences rootstock compatibility. This study addresses these questions by directly testing the ability/efficacy of four different AMF species (Rhizophagus irregularis, Septoglomus deserticola, Claroideoglomus claroideum or Claroideoglomus etunicatum) to colonize a variety of commercially available Geneva apple rootstock genotypes (G.11, G.41, G.210, G.969, and G.890). Briefly, micropropagated plantlets were inoculated with individual species of AMF or were not inoculated. The effects of the rootstock genotype/AMF interaction on mycorrhization, plant growth, and/or leaf nutrient concentrations were assessed. We found that both rootstock genotype and the identity of the AMF are significant sources of variation affecting the percentage of colonization. However, these factors largely operate independently in terms of the extent of root colonization. Among the AMF tested, C. etunicatum and R. irregularis represented the most compatible fungal partners, regardless of apple rootstock genotype. Among the rootstocks tested, semi-dwarfing rootstocks appeared to have an advantage over dwarfing rootstocks in regard to establishing and maintaining associations with AMF. Nutrient uptake and plant growth outcomes were also influenced in a rootstock genotype/AMF species-specific manner. Our findings suggest that matching host genetics with compatible AMF species has the potential to enhance agricultural practices in nursery and orchard systems.

Net zero emission goals demand worldwide cooperation.

This perspective emphasizes the need for global cooperation and decisive action to address the urgent threat of climate change and achieve the net zero emissions goal before 2050.

Effect on microbial communities in apple orchard soil when exposed short-term to climate change abiotic factors and different orchard management practices.

AIM: We assessed the effect of exposing apple orchard soil to different temperatures and CO2 levels on the resident microbiome of soils from a conventionally managed and an organically managed apple orchard. The key difference between these two orchards was that synthetic fertilizers and pesticides are routinely used in the former one. METHODS AND RESULTS: To investigate the effect of CO2 and temperature, soil samples from each site at two depths were exposed to either elevated temperature (29°C) at either 5000 or 10 000 ppm for five weeks or control conditions (25°C + 400 ppm). Both bacterial and fungal communities were profiled with amplicon-sequencing. The differences between the two orchards were the most significant factor affecting the bacterial and fungal communities, contributing to 53.7-14.0% of the variance in Bray-Curtis ß diversity, respectively. Elevated CO2 concentration and increased temperature affected organic orchard microbial diversity more than the conventionally managed orchard. A number of candidate beneficial and pathogenic microorganisms had differential abundances when temperature and CO2 were elevated, but their effect on the plant is unclear. CONCLUSIONS: This study has highlighted that microbial communities in bulk soils are most significantly influenced by crop management practices compared to the climate conditions used in the study. The studied climate conditions had a more limited effect on microbial community diversity in conventionally managed soil samples than in organically managed soils.

Robotic-assisted cryothermic Cox maze for persistent atrial fibrillation: Longitudinal follow-up.

OBJECTIVES: Surgical ablation of atrial fibrillation (AF) is recommended as a stand-alone therapy for patients refractory to medical or catheter-based treatment, or as a concomitant therapy when associated with structural disease. We report a single-therapy robotic approach to the Cox maze with longitudinal follow-up. METHODS: Consecutive patients who underwent robotic biatrial cryothermic Cox maze for nonparoxysmal AF between November 2016 and January 2022 were examined at 1, 2, 3, 6, 9, 12, 18, 24, 36, 48, and 60 months. Freedom from atrial tachyarrhythmia was assessed with 24-hour continuous electrocardiogram or pacemaker interrogation in all patients after 6 months. Mean follow-up was 17 ± 14.5 months (range, 1-60 months). Time to event analysis with competing risks was used to determine risk-adjusted associations with late outcomes. RESULTS: Patients (n = 135) had a median AF duration of 4.0 years (interquartile range, 0.8-7.0), with 29.6% in whom 1 or more catheter ablations had failed. Stand-alone maze was performed in 25.2%, whereas 61.4% underwent concomitant robotic mitral valve surgery, 7.4% tricuspid valve repair, and 4.4% aortic valve replacement. No patients were discharged in AF. There were 3 operative mortalities (2.2%), none in stand-alone patients. One patient required catheter ablation at 8 months postoperatively, and one had a nonembolic stroke at 18 months. There were 9 late deaths. Freedom from atrial tachyarrhythmia and antiarrhythmic drugs at 9, 12, 18, 24, 36, and 48 months was 97.0%, 96.7%, 98.1%, 97.1%, and 100%, respectively. Lower ejection fraction and need for concomitant mitral valve replacement and/or aortic valve replacement were independently associated with worse survival. CONCLUSIONS: For persistent AF, robotic biatrial cryothermic Cox maze offered greater than 90% 1-year longitudinal freedom from stroke, oral anticoagulation, repeat ablation, and recurrent AF without the need for antiarrhythmic drugs.

Inter-row cropping and rootstock genotype selection in a UK cider orchard to combat apple replant disease.

Apple rootstock genotypes confer different levels of tolerance to apple replant disease (ARD) and vigour to a newly replanted apple tree. A hybrid management system of rotating the rootstock genotype planted between successive generations and inter-row planting in the alleyways of orchards may minimise the severity of ARD symptoms. High-throughput sequencing of the fungal ITS and bacterial 16S rDNA regions was used to investigate the diversity, and differential taxa present in soils displaying symptoms of ARD. Candidate pathogens and beneficial microorganisms were correlated with the above-ground establishment of each rootstock genotype in a UK cider orchard. Our results suggest that the same rootstock or rootstock with closely related parentage to the previous rootstock had more severe ARD symptoms. Planting in the alleyway appeared an effective strategy to minimise the severity of symptoms irrespective of rootstock genotype. The planting location effect had a higher contribution to the variation in the rhizosphere microbiome than that of the rootstock genotype. No predicted causal agents for ARD could be identified to a taxonomic level to predict their function but two species associated with mycorrhizae, Pteridiospora spinosispora and Paraglomus laccatum were identified as inversely correlated with ARD severity and could be candidate beneficial species for apple, warranting further investigation and research. Our findings suggest that planting in the alleyways and planting rootstocks genetically dissimilar to the previously planted rootstock can be beneficial for tree establishment. We have also identified species inversely associated with ARD severity, making candidates for future research to test the antagonistic effect of the species against ARD pathogens in apple roots. Supplementary Information: The online version contains supplementary material available at 10.1186/s42483-023-00184-y.

The hypothalamic RFamide, QRFP, increases feeding and locomotor activity: The role of Gpr103 and orexin receptors.

Here we show that central administration of pyroglutamylated arginine-phenylamine-amide peptide (QRFP/26RFa) increases both food intake and locomotor activity, without any significant effect on energy expenditure, thermogenesis or reward. Germline knock out of either of the mouse QRFP receptor orthologs, Gpr103a and Gpr103b, did not produce a metabolic phenotype. However, both receptors are required for the effect of centrally administered QRFP to increase feeding and locomotor activity. As central injection of QRFP activated orexin/hypocretin neurons in the lateral hypothalamus, we compared the action of QRFP and orexin on behaviour. Both peptides increased arousal and locomotor activity. However, while orexin increased consummatory behaviour, QRFP also affected other appetitive behaviours. Furthermore, the feeding but not the locomotor response to QRFP, was blocked by co-administration of an orexin receptor 1 antagonist. These results suggest that QRFP agonism induces both appetitive and consummatory behaviour, but only the latter is dependent on orexin/hypocretin receptor signalling.

Steep rise in drug use-associated infective endocarditis in West Virginia: Characteristics and healthcare utilization.

INTRODUCTION: Life-threatening infections such as infective endocarditis (IE) are increasing simultaneously with the injection drug use epidemic in West Virginia (WV). We utilized a newly developed, statewide database to describe epidemiologic characteristics and healthcare utilization among patients with (DU-IE) and without (non-DU-IE) drug use-associated IE in WV over five years. MATERIALS AND METHODS: This retrospective, observational study, incorporating manual review of electronic medical records, included all patients aged 18-90 years who had their first admission for IE in any of the four university-affiliated referral hospitals in WV during 2014-2018. IE was identified using ICD-10-CM codes and confirmed by chart review. Demographics, clinical characteristics, and healthcare utilization were compared between patients with DU-IE and non-DU-IE using Chi-square/Fisher's exact test or Wilcoxon rank sum test. Multivariable logistic regression analysis was conducted with discharge against medical advice/in-hospital mortality vs. discharge alive as the outcome variable and drug use as the predictor variable. RESULTS: Overall 780 unique patients had confirmed first IE admission, with a six-fold increase during study period (p = .004). Most patients (70.9%) had used drugs before hospital admission, primarily by injection. Compared to patients with non-DU-IE, patients with DU-IE were significantly younger (median age: 33.9 vs. 64.1 years; p < .001); were hospitalized longer (median: 25.5 vs. 15 days; p < .001); had a higher proportion of methicillin-resistant Staphylococcus aureus (MRSA) isolates (42.7% vs. 29.9%; p < .001), psychiatric disorders (51.2% vs. 17.3%; p < .001), cardiac surgeries (42.9% vs. 26.6%; p < .001), and discharges against medical advice (19.9% vs. 1.4%; p < .001). Multivariable regression analysis showed drug use was an independent predictor of the combined outcome of discharge against medical advice/in-hospital mortality (OR: 2.99; 95% CI: 1.67-5.64). DISCUSSION AND CONCLUSION: This multisite study reveals a 681% increase in IE admissions in WV over five years primarily attributable to injection drug use, underscoring the urgent need for both prevention efforts and specialized strategies to improve outcomes.

Sex Differences in Characteristics of Patients with Infective Endocarditis: A Multicenter Study.

Infectious diseases like infective endocarditis (IE) may manifest or progress differently between sexes. This study sought to identify the differences in demographic and clinical characteristics among male and female patients with IE. Data were obtained from a newly developed registry comprising all adult patients with first IE admission at the four major tertiary cardiovascular centers in West Virginia, USA during 2014−2018. Patient characteristics were compared between males and females using Chi-square test, Fisher's exact test, and Wilcoxon rank-sum test. A secondary analysis was restricted to IE patients with drug use only. Among 780 unique patients (390 males, 390 females), significantly more women (a) were younger than males (median age 34.9 vs. 41.4, p < 0.001); (b) reported drug use (77.7% vs. 64.1%, p < 0.001); (c) had tricuspid valve endocarditis (46.4% vs. 30.8%, p < 0.001); and (d) were discharged against medical advice (20% vs. 9.5%, p < 0.001). These differences persisted even within the subgroup of patients with drug use-associated IE. In a state with one of the highest incidences of drug use and overdose deaths, the significantly higher incident IE cases in younger women and higher proportion of women leaving treatment against medical advice are striking. Differential characteristics between male and female patients are important to inform strategies for specialized treatment and care.

Manipulation of the miR-378a/mt-ATP6 regulatory axis rescues ATP synthase in the diabetic heart and offers a novel role for lncRNA Kcnq1ot1.

Diabetes mellitus has been linked to an increase in mitochondrial microRNA-378a (miR-378a) content. Enhanced miR-378a content has been associated with a reduction in mitochondrial genome-encoded mt-ATP6 abundance, supporting the hypothesis that miR-378a inhibition may be a therapeutic option for maintaining ATP synthase functionality during diabetes mellitus. Evidence also suggests that long noncoding RNAs (lncRNAs), including lncRNA potassium voltage-gated channel subfamily Q member 1 overlapping transcript 1 (Kcnq1ot1), participate in regulatory axes with microRNAs (miRs). Prediction analyses indicate that Kcnq1ot1 has the potential to bind miR-378a. This study aimed to determine if loss of miR-378a in a genetic mouse model could ameliorate cardiac dysfunction in type 2 diabetes mellitus (T2DM) and to ascertain whether Kcnq1ot1 interacts with miR-378a to impact ATP synthase functionality by preserving mt-ATP6 levels. MiR-378a was significantly higher in patients with T2DM and 25-wk-old Db/Db mouse mitochondria, whereas mt-ATP6 and Kcnq1ot1 levels were significantly reduced when compared with controls. Twenty-five-week-old miR-378a knockout Db/Db mice displayed preserved mt-ATP6 and ATP synthase protein content, ATP synthase activity, and preserved cardiac function, implicating miR-378a as a potential therapeutic target in T2DM. Assessments following overexpression of the 500-bp Kcnq1ot1 fragment in established mouse cardiomyocyte cell line (HL-1) cardiomyocytes overexpressing miR-378a revealed that Kcnq1ot1 may bind and significantly reduce miR-378a levels, and rescue mt-ATP6 and ATP synthase protein content. Together, these data suggest that Kcnq1ot1 and miR-378a may act as constituents in an axis that regulates mt-ATP6 content, and that manipulation of this axis may provide benefit to ATP synthase functionality in type 2 diabetic heart.

Robotic Aortic Valve Replacement: First 50 Cases.

BACKGROUND: Existing management challenges in selecting transcatheter vs surgical aortic valve replacement (SAVR) include bicuspid stenosis, low clinical risk, horizontal valve position, aortic insufficiency (AI), and need for concomitant procedures or mechanical valves. To address these gaps, we present our early experience with fully robotic-assisted aortic valve replacement (RAVR). METHODS: Between January 2020 and February 2021, 50 consecutive RAVR operations were performed using a 3- to 4-cm lateral mini-thoracotomy 3-port technique with transthoracic aortic clamping, similar to our robotic mitral platform. Conventional SAVR prostheses were implanted with interrupted braided sutures in all cases. RESULTS: The 50 patients were a median age of 67.5 years, body mass index was 29 kg/m2, calcified bicuspid disease was present in 28 (56%), and severe AI in 8 (16%). Ejection fraction was 0.55 ± 0.08 (mean ± SD), and The Society of Thoracic Surgeons predicted risk of mortality was 1.54% ± 0.7%. Mechanical prostheses were used in 16 of 50 (32%), and 7 required concomitant procedures, including Cox maze in 3, aortic root enlargement in 2, and left atrial appendage clipping, mitral repair, and left atrial myxoma excision in 1 each. Median times (minutes) were 166 for cardiopulmonary bypass, 117 for cross-clamp, 4 for valvectomy, 20 for annular sutures, and 31 for aortotomy closure. All times plateaued after the initial 5 cases. Extubation occurred in 42 of 50 patients (84%) in the operating room, and within 4 hours in the remaining 8 (16%). There was no 30-day operative mortality or stroke. All had 30-day echocardiography demonstrating no valvular or perivalvular abnormalities. CONCLUSIONS: RAVR appears to have procedural safety and short-term outcomes to rival alternatives. Incremental experience may facilitate the safe performance of concomitant procedures as deemed necessary.

Robotic assisted cryothermic biatrial Cox-Maze.

INTRODUCTION: Robotic cryothermic Cox-Maze (CM) IV is a minimally invasive procedure that reliably replicates the biatrial lesion set of the CM III by utilizing cryothermia as a single power source. METHODS: Herein we describe a step by step creation of the biatrial CM III lesion sets utilizing the minimally invasive robotic platform. RESULTS: Technical details are reviewed for this single incision, single stage, highly effective option for stand-alone or concomitant surgical ablation of atrial fibrillation (AF). CONCLUSION: Robotic cryothermic CM IV can be safely performed as a stand-alone or concomitant procedure, and offers a comprehensive surgical ablation solution for patients with AF.