Search

MicroRNAs (miRNAs) are small post-transcriptional regulators that offer promising targets for treating complex diseases. To this end, hsa-miR-4513 is an excellent candidate as this gene harbors within its conserved heptametrical seed sequence a frequent polymorphism (rs2168518), which has previously been associated with several complex phenotypes. So far, little is known about the biological mechanism(s) underlying these associations. In an initial step, we now aimed to identify allele-specific target genes of hsa-miR-4513. We performed RNA sequencing in a miRNA overexpression model in human umbilical vein endothelial cells transfected with separated hsa-miR-4513 alleles at rs2168518, namely hsa-miR-4513-G and hsa-miR-4513-A. Genes specifically regulated by the rs2168518 alleles were independently verified by quantitative reverse transcription PCR (qRT-PCR), western blot analysis and allele-specific miRNA binding via a luciferase reporter assay. By a text-based search publicly available databases such as Online Mendelian Inheritance in Man and Mouse Genome Informatics were utilized to link target genes of hsa-miR-4513 to previously described phenotypes. Overall, we identified 23 allele-specific hsa-miR-4513 target genes and replicated 19 of those independently via qRT-PCR. Western blot analysis and luciferase reporter assays conducted for an exemplary subsample further confirmed the allele-specific regulation of these genes by hsa-miR-4513. Remarkably, multiple allele-specific target genes identified are linked via text retrieval to several phenotypes previously reported to be associated with hsa-miR-4513. These genes offer promising candidates for ongoing research on the functional pathobiological impact of hsa-miR-4513 and its seed polymorphism rs2168518. This could give rise to therapeutic applications targeting this miRNA., (© The Author(s) 2021. Published by Oxford University Press.)

Inhibition of host cell apoptosis is crucial for survival and replication of several intracellular bacterial pathogens. To interfere with apoptotic pathways, some pathogens use specialized secretion systems to inject bacterial effector proteins into the host cell cytosol. One of these pathogens is the obligate intracellular bacterium Coxiella burnetii, the etiological agent of the zoonotic disease Q fever. In this study, we analyzed the molecular activity of the anti-apoptotic T4SS effector protein AnkG (CBU0781) to understand how C. burnetii manipulates host cell viability. We demonstrate by co- and RNA-immunoprecipitation that AnkG binds to the host cell DExD box RNA helicase 21 (DDX21) as well as to the host cell 7SK small nuclear ribonucleoprotein (7SK snRNP) complex, an important regulator of the positive transcription elongation factor b (P-TEFb). The co-immunoprecipitation of AnkG with DDX21 is probably mediated by salt bridges and is independent of AnkG-7SK snRNP binding, and vice versa. It is known that DDX21 facilitates the release of P-TEFb from the 7SK snRNP complex. Consistent with the documented function of released P-TEFb in RNA Pol II pause release, RNA sequencing experiments confirmed AnkG-mediated transcriptional reprogramming and showed that expression of genes involved in apoptosis, trafficking, and transcription are influenced by AnkG. Importantly, DDX21 and P-TEFb are both essential for AnkG-mediated inhibition of host cell apoptosis, emphasizing the significance of the interaction of AnkG with both, the DDX21 protein and the 7SK RNA. In line with a critical function of AnkG in pathogenesis, the AnkG deletion C. burnetii strain was severely affected in its ability to inhibit host cell apoptosis and to generate a replicative C. burnetii-containing vacuole. In conclusion, the interference with the activity of regulatory host cell RNAs mediated by a bacterial effector protein represent a novel mechanism through which C. burnetii modulates host cell transcription, thereby enhancing permissiveness to bacterial infection., Competing Interests: The authors declare to have no competing interests.

The development of turbulence after transcatheter aortic valve (TAV) implantation may have detrimental effects on the long-term performance and durability of the valves. The characterization of turbulent flow generated after TAV implantation can provide fundamental insights to enhance implantation techniques. A self-expandable TAV was tested in a pulse replicator and the three-dimensional flow field was extracted by means of tomographic particle image velocimetry. The valve was fixed inside a silicone phantom mimicking the aortic root and the flow field was studied for two different supra-annular axial positions at peak systole. Fluctuating velocities and turbulent kinetic energy were compared between the two implantations. Velocity spectra were derived at different spatial positions in the turbulent wakes to characterize the turbulent flow. The valve presented similar overall flow topology but approximately 8% higher turbulent intensity in the lower implantation. In this configuration, axial views of the valve revealed smaller opening area and more corrugated leaflets during systole, as well as more accentuated pinwheeling during diastole. The difference arose from a lower degree of expansion of the TAV's stent inside the aortic lumen. These results suggest that the degree of expansion of the TAV in-situ is related to the onset of turbulence and that a smaller and less regular opening area might introduce flow instabilities that could be detrimental for the long-term performance of the valve. The present study highlights how implantation mismatches may affect the structure and intensity of the turbulent flow in the aortic root., 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 © 2022 Pietrasanta, Zheng, De Marinis, Hasler and Obrist.)

Deficits in maximal and explosive knee extensor strength, which are usually assessed with unilateral tasks, are substantial in patients with knee osteoarthritis (KOA). The aim of this study was to investigate the clinical relevance of unilateral vs. bilateral tasks for assessing knee extensor strength in patients with KOA. This was achieved primarily by comparing unilateral and bilateral inter-limb strength asymmetries and secondarily by examining the relationship between unilaterally and bilaterally measured strength, and performance-based and self-reported function. Twenty-four patients with unilateral KOA (mean age: 65 ± 7 years) performed isometric gradual and explosive maximal voluntary contractions to assess, respectively their maximal and explosive strength. Performance-based and self-reported function were also evaluated with standard functional tests and questionnaires, respectively. Inter-limb asymmetries of maximal and explosive strength did not differ significantly between unilateral (mean asymmetry: 26 ± 15%) and bilateral tasks (22 ± 21%). In the same way, the relationships between knee extensor strength-measured either unilaterally or bilaterally-and performance-based or self-reported function were not influenced by the type of task. In conclusion, it does not seem to make a difference in terms of clinical relevance whether maximal and explosive knee extensor strength are evaluated with unilateral or bilateral tasks in KOA patients.

La and La-related proteins (LARPs) are characterized by a common RNA interaction platform termed the La module. This structural hallmark allows LARPs to pervade various aspects of RNA biology. The metazoan LARP7 protein binds to the 7SK RNA as part of a 7SK small nuclear ribonucleoprotein (7SK snRNP), which inhibits the transcriptional activity of RNA polymerase II (Pol II). Additionally, recent findings revealed unanticipated roles of LARP7 in the assembly of other RNPs, as well as in the modification, processing and cellular transport of RNA molecules. Reduced levels of functional LARP7 have been linked to cancer and Alazami syndrome, two seemingly unrelated human diseases characterized either by hyperproliferation or growth retardation. Here, we review the intricate regulatory networks centered on LARP7 and assess how malfunction of these networks may relate to the etiology of LARP7-linked diseases.

Background: Postoperative readmission rates following radical cystectomy remain significant. Early identification of emerging complications could potentially allow for immediate institution of therapy., Objective: To intensify postoperative patient-physician communication via a cellphone-based health care application (CHA) and to evaluate its potential for early detection of complications., Design Setting and Participants: This was a pilot study involving 18 radical cystectomy patients. During the first 30 d, patients received a push cellphone notification twice a week requesting data input into the CHA. This was reduced to once a week from day 31 to day 90. De-identified recorded data were reviewed by the surgeon involved. If deemed necessary, patients were contacted by the surgeon via telephone to obtain more detailed clinical information., Outcome Measurements and Statistical Analysis: Descriptive statistics were used., Results and Limitations: Of the 18 patients enrolled, all completed the 90-d reporting period. On two occasions, interventions were necessary on the basis of data recorded on the CHA. One neobladder patient was given antibiotic therapy for pyelonephritis. Another patient reported weight loss and nausea with clinical suspicion of metabolic acidosis, and his sodium bicarbonate and fluid intake were increased. Limitations include the small number of cases from a single low-volume center., Conclusions: CHA-based monitoring of clinical parameters within the crucial 90-d postoperative period following radical cystectomy provides meaningful information. In this pilot study, two potential readmissions were possibly avoided on the basis of recorded basic vital signs and early intervention., Patient Summary: Besides regular clinic follow-up visits after radical cystectomy, additional aids such as a cellphone-based health care application can provide treating physicians with relevant clinical information and may help to identify imminent deviations from normal postoperative recovery at an early stage., (© 2020 The Author(s).)

The La-related protein 7 (LARP7) forms a complex with the nuclear 7SK RNA to regulate RNA polymerase II transcription. It has been implicated in cancer and the Alazami syndrome, a severe developmental disorder. Here, we report a so far unknown role of this protein in RNA modification. We show that LARP7 physically connects the spliceosomal U6 small nuclear RNA (snRNA) with a distinct subset of box C/D small nucleolar RNAs (snoRNAs) guiding U6 2'-O-methylation. Consistently, these modifications are severely compromised in the absence of LARP7. Although general splicing remains largely unaffected, transcriptome-wide analysis revealed perturbations in alternative splicing in LARP7-depleted cells. Importantly, we identified defects in 2'-O-methylation of the U6 snRNA in Alazami syndrome siblings carrying a LARP7 mutation. Our data identify LARP7 as a bridging factor for snoRNA-guided modification of the U6 snRNA and suggest that alterations in splicing fidelity contribute to the etiology of the Alazami syndrome., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

U6 snRNA, as an essential component of the catalytic core of the pre-mRNA processing spliceosome, is heavily modified post-transcriptionally, with 2'-O-methylation being most common. The role of these modifications in pre-mRNA splicing as well as their physiological function in mammals have remained largely unclear. Here we report that the La-related protein LARP7 functions as a critical cofactor for 2'-O-methylation of U6 in mouse male germ cells. Mechanistically, LARP7 promotes U6 loading onto box C/D snoRNP, facilitating U6 2'-O-methylation by box C/D snoRNP. Importantly, ablation of LARP7 in the male germline causes defective U6 2'-O-methylation, massive alterations in pre-mRNA splicing, and spermatogenic failure in mice, which can be rescued by ectopic expression of wild-type LARP7 but not an U6-loading-deficient mutant LARP7. Our data uncover a novel role of LARP7 in regulating U6 2'-O-methylation and demonstrate the functional requirement of such modification for splicing fidelity and spermatogenesis in mice., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The multiple-breath washout (MBW) is a lung function test that measures the degree of ventilation inhomogeneity (VI). The test is used to identify small airway impairment in patients with lung diseases like cystic fibrosis. However, the physical and physiological factors that influence the test outcomes and differentiate health from disease are not well understood. Computational models have been used to better understand the interaction between anatomical structure and physiological properties of the lung, but none of them has dealt in depth with the tracer gas washout test in a whole. Thus, our aim was to create a lung model that simulates the entire MBW and investigate the role of lung morphology and tissue mechanics on the tracer gas washout procedure. To this end, we developed a multi-scale lung model to simulate the inert gas transport in airways of all size. We then applied systematically different modifications to geometrical and mechanical properties of the lung model (compliance, residual airway volume and flow resistance) which have been associated with VI. The modifications were applied to distinct parts of the model, and their effects on the gas distribution within the lung and on the gas concentration profile were assessed. We found that variability in compliance and residual volume of the airways, as well as the spatial distribution of this variability in the lung had a direct influence on gas distribution among airways and on the MBW pattern (washout duration, characteristic concentration profile during each expiration), while the effects of variable flow resistance were negligible. Based on these findings, it is possible to classify different types of inhomogeneities in the lung and relate them to specific features of the MBW pattern, which builds the basis for a more detailed association of lung function and structure., Competing Interests: The authors have declared that no competing interests exist.

Objectives: Bioprosthetic valve thrombosis has been considered uncommon, but recent studies have shown that it is more frequent than previously thought. Insufficient washout of the aortic sinus is believed to be a risk factor for bioprosthetic valve thrombosis. The objective of this in vitro experiment was to investigate the impact of aortic root morphology on blood flow in the aortic sinus and to relate these results to in vivo data obtained in patients with a transcatheter aortic valve implant., Methods: Two compliant aortic root phantoms with different morphologies (symmetrical and patient-specific) were fabricated with silicone. A bioprosthetic aortic valve was inserted in both phantoms. Haemodynamic measurements were performed in a pulsatile flow-loop replicating physiological flow and pressure conditions. The flow in the aortic root was visualized by injecting contrast agent (CA). The distribution of the CA was captured by a high-speed camera, and image post-processing was performed to quantify CA distribution in the aortic sinus. The results were compared with angiographic images after a transcatheter aortic valve implant., Results: Blood flow in the aortic root and the washout of the sinus portion are significantly affected by aortic root morphology. CA arrives at the aortic sinus of the 2 phantoms at 0.09 s and 0.16 s after the valve opens in the symmetrical and the patient-specific phantoms, respectively. Delayed CA arrival was also observed in the patients with a transcatheter aortic valve implant., Conclusions: Aortic root morphology affects the blood flow in the aortic sinus and may be a factor in bioprosthetic valve thrombosis. Therefore, patient-specific aortic root morphology should be considered when selecting and positioning a prosthesis.

The flow field past a prosthetic aortic valve comprises many details that indicate whether the prosthesis is functioning well or not. It is, however, not yet fully understood how an optimal flow scenario would look, i.e. which subtleties of the fluid dynamics in place are essential regarding the durability and compatibility of a prosthetic valve. In this study, we measured and analyzed the 3D flow field in the vicinity of a bio-prosthetic heart valve in function of the aortic root size. The measurements were conducted within aortic root phantoms of different size, mounted in a custom-built hydraulic setup, which mimicked physiological flow conditions in the aorta. Tomographic particle image velocimetry was used to measure the 3D instantaneous velocity field at various instances. Several 3D fields (e.g. instantaneous and mean velocity, 3D shear rate) were analyzed and compared focusing on the impact of the aortic root size, but also in order to gain general insight in the 3D flow structure past the bio-prosthetic valve. We found that the diameter of the aortic jet relative to the diameter of the ascending aorta is the most important parameter in determining the characteristics of the flow. A large aortic cross-section, relative to the cross-section of the aortic jet, was associated with higher levels of turbulence intensity and higher retrograde flow in the ascending aorta.

Although RNA are synthesized as single-stranded molecules, most of them are characterized by extensive secondary structures. Two RNA that require distinct folding for biogenesis and function are miRNA and tRNA. While miRNA are processed from hairpin-containing precursors, tRNA are folded into characteristic L-shaped structures. In addition, tRNA and their precursors are a rich source of RNA fragments. Recent findings suggest that their production might be determined by structural characteristics of the tRNA substrates. Importantly, correct folding of pre-tRNA is assisted by the Lupus autoantigen La, an RNA chaperone. In this context, La interacts with pre-tRNA to prevent alternative foldings leading to mis-channeling into the miRNA pathway. Thus, RNA chaperones also function as gatekeepers for correct RNA pathway selection., (© 2016 Federation of European Biochemical Societies.)

The Lupus autoantigen La is an RNA-binding protein that stabilizes RNA polymerase III (Pol III) transcripts and supports RNA folding and has in addition been implicated in the mammalian microRNA (miRNA) pathway. Here, we have analyzed effects of La depletion on Argonaute (Ago)-bound small RNAs in human cells. We find that in the absence of La, distinct tRNA fragments are loaded into Ago proteins. Thus, La functions as gatekeeper ensuring correct tRNA maturation and protecting the miRNA pathway from potentially functional tRNA fragments. However, one specific isoleucin pre-tRNA produces both a functional tRNA and a miRNA even when La is present. We demonstrate that the fully complementary 5' leader and 3' trailer of the pre-tRNA-Ile form a double-stranded RNA molecule that has low affinity to La. Instead, Exportin-5 (Xpo5) recognizes it as miRNA precursor and transports it into the cytoplasm for Dicer processing and Ago loading., (Copyright © 2016 Elsevier Inc. All rights reserved.)

The oncogenic Epstein-Barr virus (EBV) expresses 44 mature microRNAs and two non-coding EBER RNAs of 167 (EBER1) and 172 (EBER2) nt length. MiRNA profiling of NK/T cell lines and primary cells and Northern blotting of EBV-infected cell lines and primary tumors revealed processing of EBER1 to short 5'-derived RNAs of approximately 23, 52 and 70 nt (EBER123, EBER152, and EBER170) and of EBER2 to 3' fragments. The biogenesis of these species is independent of Dicer, and EBER123 does not act like a miRNA OPEN ACCESS Non-Coding RNA 2015, 1 171 to target its complementary sequence. EBER1, EBER2 and EBER123 were bound by the lupus antigen (La), a nuclear and cytoplasmic protein that facilitates RNAi. Consistent with this, the EBERs affect regulation of interleukin 1alpha (IL1α) and RAC1 reporters harboring miR target sequences, targets of miR-142-3p. However, the EBERs have no effect upon another target of miR-142-3p, ADCY9, nor on TOMM22, a target of ebv-miR-BART16, indicative of selective modulation of gene expression by the EBERs.

Age-related macular degeneration (AMD) is the leading cause of severe vision impairment in Western populations over 55 years. A growing number of gene variants have been identified which are strongly associated with an altered risk to develop AMD. Nevertheless, gene-based biomarkers which could be dysregulated at defined stages of AMD may point toward key processes in disease mechanism and thus may support efforts to design novel treatment regimens for this blinding disorder. Circulating microRNAs (cmiRNAs) which are carried by nanosized exosomes or microvesicles in blood plasma or serum, have been recognized as valuable indicators for various age-related diseases. We therefore aimed to elucidate the role of cmiRNAs in AMD by genome-wide miRNA expression profiling and replication analyses in 147 controls and 129 neovascular AMD patients. We identified three microRNAs differentially secreted in neovascular (NV) AMD (hsa-mir-301-3p, pcorrected = 5.6*10-5, hsa-mir-361-5p, pcorrected = 8.0*10-4 and hsa-mir-424-5p, pcorrected = 9.6*10-3). A combined profile of the three miRNAs revealed an area under the curve (AUC) value of 0.727 and was highly associated with NV AMD (p = 1.2*10-8). To evaluate subtype-specificity, an additional 59 AMD cases with pure unilateral or bilateral geographic atrophy (GA) were analyzed for microRNAs hsa-mir-301-3p, hsa-mir-361-5p, and hsa-mir-424-5p. While we found no significant differences between GA AMD and controls neither individually nor for a combined microRNAs profile, hsa-mir-424-5p levels remained significantly higher in GA AMD when compared to NV (pcorrected<0.005). Pathway enrichment analysis on genes predicted to be regulated by microRNAs hsa-mir-301-3p, hsa-mir-361-5p, and hsa-mir-424-5p, suggests canonical TGFβ, mTOR and related pathways to be involved in NV AMD. In addition, knockdown of hsa-mir-361-5p resulted in increased neovascularization in an in vitro angiogenesis assay.

Argonaute proteins are the mediators of small RNA-guided gene silencing pathways. In this issue, Couvillion and coworkers (Couvillion et al., 2012) found an unexpected function for a Tetrahymena Argonaute protein: It forms a complex with tRNA fragments and is required for nuclear Xrn2 localization and function., (Copyright © 2012 Elsevier Inc. All rights reserved.)

We propose a new learning strategy for object detection. The proposed scheme forgoes the need to train a collection of detectors dedicated to homogeneous families of poses, and instead learns a single classifier that has the inherent ability to deform based on the signal of interest. We train a detector with a standard AdaBoost procedure by using combinations of pose-indexed features and pose estimators. This allows the learning process to select and combine various estimates of the pose with features able to compensate for variations in pose without the need to label data for training or explore the pose space in testing. We validate our framework on three types of data: hand video sequences, aerial images of cars, and face images. We compare our method to a standard boosting framework, with access to the same ground truth, and show a reduction in the false alarm rate of up to an order of magnitude. Where possible, we compare our method to the state of the art, which requires pose annotations of the training data, and demonstrate comparable performance.

The precision of five instruments (Coag-A-Mate, Auto-Fi, Coagulyzer, Electra 600 and Fibrometer) in performing activated partial thrmboplastin time (PTT) assays were compared using three different coagulation reagent systems (Ortho, Dade, and General Diagnostics) utilizing normal and abnormal control reagents. There were wide variations in mean PTT values and co-efficient of variation (CV) among all instruments and for each instrument utilizing different reagents. The smallest CV was noted for The Coagulyzer using Dade reagents, the Coag-A-Mate using Dade and General Diagnostic reagents and the Auto-Fi using General Diagnostic reagents. Auto-Fi values were always longer than those determined with the Fibrometer whereas the optical detection instruments usually gave shorter values. The range of normal values for the prothrombin time (PT) and PTT assay was recorded simultaneously on blood samples of 52 healthy donors utilizing the Coagulyzer with Ortho reagents, the Coag-A-Mate with General Diagnostic reagents nd the Auto-Fi with Dade reagents. No differences were noted between male and female donors. There was a poor correlation among PT results recorded by all instruments. For the PTT assay, results obtained with the Coag-A-Mate and the Auto-Fi had a correlation of 0.84. The normal mean plus 2 or 3 standard deviations determined by the Auto-Fi and the Coag-A-Mate were used to classify blood samples from 263 patients as normal or abnormal when assayed by each instrument. For the PTT assay, coincidence was attained in 91.2% of the samples and discrepancies (a blood classified abnormal by one instrument and normal by the other) were evenly distributed for both instruments. For the PT assay, coincidence occurred in 85.1% of the cases and there was a statistically significant trend (P < 0.05) for the Auto-Fi in classifying abnormal samples categorized normal by the Coag-A-Mate.

The platelet aggregation responses induced by adenosine diphosphate (ADP) and collagen were characterized by parameters defining rate and extent of reaction. Values were compared on the basis of platelet concentration, time elapsed between sample collection and test performance, and sex of donors. Rate and extent of aggregation varied as a function of platelet concentration. Maximal responses were obtained for platelet concentrations greater than 100,000/microliter. Results from samples processed after 90 min of incubation at room temperature were consistently and significantly lower than those obtained from samples processed immediately. ADP-induced aggregation responses elicited by samples from male and female normal donors differed significantly. This indicates that comparisons between normal and patient results should be made with sex-matched individuals to avoid erroneous interpretations.