Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-ß signaling.

TGF-ß receptors phosphorylate SMAD2 and SMAD3 transcription factors, which then form heterotrimeric complexes with SMAD4 and cooperate with context-specific transcription factors to activate target genes. Here we provide biochemical and structural evidence showing that binding of SMAD2 to DNA depends on the conformation of the E3 insert, a structural element unique to SMAD2 and previously thought to render SMAD2 unable to bind DNA. Based on this finding, we further delineate TGF-ß signal transduction by defining distinct roles for SMAD2 and SMAD3 with the forkhead pioneer factor FOXH1 as a partner in the regulation of differentiation genes in mouse mesendoderm precursors. FOXH1 is prebound to target sites in these loci and recruits SMAD3 independently of TGF-ß signals, whereas SMAD2 remains predominantly cytoplasmic in the basal state and set to bind SMAD4 and join SMAD3:FOXH1 at target promoters in response to Nodal TGF-ß signals. The results support a model in which signal-independent binding of SMAD3 and FOXH1 prime mesendoderm differentiation gene promoters for activation, and signal-driven SMAD2:SMAD4 binds to promoters that are preloaded with SMAD3:FOXH1 to activate transcription.

Allele-dependent interaction of LRRK2 and NOD2 in leprosy.

Leprosy, caused by Mycobacterium leprae, rarely affects children younger than 5 years. Here, we studied a multiplex leprosy family that included monozygotic twins aged 22 months suffering from paucibacillary leprosy. Whole genome sequencing identified three amino acid mutations previously associated with Crohn's disease and Parkinson's disease as candidate variants for early onset leprosy: LRRK2 N551K, R1398H and NOD2 R702W. In genome-edited macrophages, we demonstrated that cells expressing the LRRK2 mutations displayed reduced apoptosis activity following mycobacterial challenge independently of NOD2. However, employing co-immunoprecipitation and confocal microscopy we showed that LRRK2 and NOD2 proteins interacted in RAW cells and monocyte-derived macrophages, and that this interaction was substantially reduced for the NOD2 R702W mutation. Moreover, we observed a joint effect of LRRK2 and NOD2 variants on Bacillus Calmette-Guérin (BCG)-induced respiratory burst, NF-κB activation and cytokine/chemokine secretion with a strong impact for the genotypes found in the twins consistent with a role of the identified mutations in the development of early onset leprosy.

Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation.

Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.

Transposable elements alter gene expression and may impact response to cisplatin therapy in ovarian cancer.

Cisplatin is widely employed for cancer treatment; therefore, understanding resistance to this drug is critical for therapeutic practice. While studies have delved into differential gene expression in the context of cisplatin resistance, findings remain somewhat scant. We performed a comprehensive investigation of Transposable Elements (TEs) expression and their impact in host genes in two cisplatin-treated ovarian cancer cell lines. RNA-seq, ATAC-seq, and in-depth bioinformatics analysis were used to compare cisplatin-sensitive and -resistant ovarian cancer cell lines. Our results reveal that cisplatin therapy alters the expression of protein-coding genes, but also key TEs, including LINE1, Alu, and endogenous retroviruses, in both cisplatin-sensitive and -resistant cell lines. By co-expressing with downstream genes or by creating chimeric transcripts with host genes at their insertion sites, these TEs seem to control the expression of protein-coding genes, including tumor-related genes. Our model uncovers TEs influencing the expression of cancer genes and cancer pathways. Collectively, our findings indicate that TEs alterations associated with cisplatin treatment occur in critical cancer genes and cellular pathways synergically. This research highlights the importance of considering the entire spectrum of transcribed elements in the genome, especially TE expression, for a complete understanding of complex models like cancer response to treatment.

Peripheral nervous system is injured by neutrophil extracellular traps (NETs) elicited by nonstructural (NS) protein-1 from Zika virus.

The involvement of innate immune mediators to the Zika virus (ZIKV)-induced neuroinflammation is not yet well known. Here, we investigated whether neutrophil extracellular traps (NETs), which are scaffolds of DNA associated with proteins, have the potential to injure peripheral nervous. The tissue lesions were evaluated after adding NETs to dorsal root ganglia (DRG) explants and to DRG constituent cells or injecting them into mouse sciatic nerves. Identification of NET harmful components was achieved by pharmacological inhibition of NET constituents. We found that ZIKV inoculation into sciatic nerves recruited neutrophils and elicited the production of the cytokines CXCL1 and IL-1ß, classical NET inducers, but did not trigger NET formation. ZIKV blocked PMA- and CXCL8-induced NET release, but, in contrast, the ZIKV nonstructural protein (NS)-1 induced NET formation. NET-enriched supernatants were toxic to DRG explants, decreasing neurite area, length, and arborization. NETs were toxic to DRG constituent cells and affected myelinating cells. Myeloperoxidase (MPO) and histones were identified as the harmful component of NETs. NS1 injection into mouse sciatic nerves recruited neutrophils and triggered NET release and caspase-3 activation, events that were also elicited by the injection of purified MPO. In summary, we found that ZIKV NS1 protein induces NET formation, which causes nervous tissue damages. Our findings reveal new mechanisms leading to neuroinflammation by ZIKV.

Interactions of mitochondrial and skeletal muscle biology in mitochondrial myopathy.

Mitochondrial dysfunction in skeletal muscle fibres occurs with both healthy aging and a range of neuromuscular diseases. The impact of mitochondrial dysfunction in skeletal muscle and the way muscle fibres adapt to this dysfunction is important to understand disease mechanisms and to develop therapeutic interventions. Furthermore, interactions between mitochondrial dysfunction and skeletal muscle biology, in mitochondrial myopathy, likely have important implications for normal muscle function and physiology. In this review, we will try to give an overview of what is known to date about these interactions including metabolic remodelling, mitochondrial morphology, mitochondrial turnover, cellular processes and muscle cell structure and function. Each of these topics is at a different stage of understanding, with some being well researched and understood, and others in their infancy. Furthermore, some of what we know comes from disease models. Whilst some findings are confirmed in humans, where this is not yet the case, we must be cautious in interpreting findings in the context of human muscle and disease. Here, our goal is to discuss what is known, highlight what is unknown and give a perspective on the future direction of research in this area.

A Survey on Data Compression Techniques for Automotive LiDAR Point Clouds.

In the evolving landscape of autonomous driving technology, Light Detection and Ranging (LiDAR) sensors have emerged as a pivotal instrument for enhancing environmental perception. They can offer precise, high-resolution, real-time 3D representations around a vehicle, and the ability for long-range measurements under low-light conditions. However, these advantages come at the cost of the large volume of data generated by the sensor, leading to several challenges in transmission, processing, and storage operations, which can be currently mitigated by employing data compression techniques to the point cloud. This article presents a survey of existing methods used to compress point cloud data for automotive LiDAR sensors. It presents a comprehensive taxonomy that categorizes these approaches into four main groups, comparing and discussing them across several important metrics.

The good, the bad and the ugly of transposable elements annotation tools.

Transposable elements are repetitive and mobile DNA segments that can be found in virtually all organisms investigated to date. Their complex structure and variable nature are particularly challenging from the genomic annotation point of view. Many softwares have been developed to automate and facilitate TEs annotation at the genomic level, but they are highly heterogeneous regarding documentation, usability and methods. In this review, we revisited the existing software for TE genomic annotation, concentrating on the most often used ones, the methodologies they apply, and usability. Building on the state of the art of TE annotation software we propose best practices and highlight the strengths and weaknesses from the available solutions.

Hallux Valgus: The Influence of Intersesamoid Crista's Osteoarthritis on Frontal Plane Pronation.

A frontal plane metatarsal rotational (pronation) has been documented in a high percentage of hallux valgus patients. Pathoanatomical concepts leading to pronation are still debated. Nevertheless, there is no consensus on how to measure this component of the deformity. The aim of the present study was to find potential associations between sesamoid's crista osteoarthritis and the frontal plane deformity in HV cases. Our study showed a moderate correlation between the crista's OA and the intermetatarsal angle (IMA), the hallux valgus angle (HVA) and the alpha angle. In severe hallux vulgus deformed specimens, with an eroded intersesamoid crista, frontal plane pronation was not as prevalent nor severe as in those without osteoarthritic degeneration. Severe hallux valgus cases with a completely eroded crista, showed lower pronation, and higher IMA, when compared to specimens with a preserved anatomy. This brings to light the intersesamoid crista's unique function in retaining the IMA. Understanding the role the frontal plane plays in hallux valgus' biomechanics and in its radiographic appearance is vital to change the current paradigm.

From the disruption of RNA metabolism to the targeting of RNA-binding proteins: The case of polyglutamine spinocerebellar ataxias.

Polyglutamine spinocerebellar ataxias (PolyQ SCAs) represent a group of monogenetic diseases in which the expanded polyglutamine repeats give rise to a mutated protein. The abnormally expanded polyglutamine protein produces aggregates and toxic species, causing neuronal dysfunction and neuronal death. The main symptoms of these disorders include progressive ataxia, motor dysfunction, oculomotor impairment, and swallowing problems. Nowadays, the current treatments are restricted to symptomatic alleviation, and no existing therapeutic strategies can reduce or stop the disease progression. Even though the origin of these disorders has been associated with polyglutamine-induced toxicity, RNA toxicity has recently gained relevance in polyQ SCAs molecular pathogenesis. Therefore, the research's focus on RNA metabolism has been increasing, especially on RNA-binding proteins (RBPs). The present review summarizes RNA metabolism, exposing the different processes and the main RBPs involved. We also explore the mechanisms by which RBPs are dysregulated in PolyQ SCAs. Finally, possible therapies targeting the RNA metabolism are presented as strategies to reverse neuropathological anomalies and mitigate physical symptoms.

Mitochondrial DNA disorders: from pathogenic variants to preventing transmission.

Mitochondrial DNA (mtDNA) disorders are recognized as one of the most common causes of inherited metabolic disorders. The mitochondrial genome occurs in multiple copies resulting in both homoplasmic and heteroplasmic pathogenic mtDNA variants. A biochemical defect arises when the pathogenic variant level reaches a threshold, which differs between variants. Moreover, variants can segregate, clonally expand, or be lost from cellular populations resulting in a dynamic and tissue-specific mosaic pattern of oxidative deficiency. MtDNA is maternally inherited but transmission patterns of heteroplasmic pathogenic variants are complex. During oogenesis, a mitochondrial bottleneck results in offspring with widely differing variant levels to their mother, whilst highly deleterious variants, such as deletions, are not transmitted. Complemented by a complex interplay between mitochondrial and nuclear genomes, these peculiar genetics produce marked phenotypic variation, posing challenges to the diagnosis and clinical management of patients. Novel therapeutic compounds and several genetic therapies are currently under investigation, but proven disease-modifying therapies remain elusive. Women who carry pathogenic mtDNA variants require bespoke genetic counselling to determine their reproductive options. Recent advances in in vitro fertilization techniques, have greatly improved reproductive choices, but are not without their challenges. Since the first pathogenic mtDNA variants were identified over 30 years ago, there has been remarkable progress in our understanding of these diseases. However, many questions remain unanswered and future studies are required to investigate the mechanisms of disease progression and to identify new disease-specific therapeutic targets.

A Survey on Ground Segmentation Methods for Automotive LiDAR Sensors.

In the near future, autonomous vehicles with full self-driving features will populate our public roads. However, fully autonomous cars will require robust perception systems to safely navigate the environment, which includes cameras, RADAR devices, and Light Detection and Ranging (LiDAR) sensors. LiDAR is currently a key sensor for the future of autonomous driving since it can read the vehicle's vicinity and provide a real-time 3D visualization of the surroundings through a point cloud representation. These features can assist the autonomous vehicle in several tasks, such as object identification and obstacle avoidance, accurate speed and distance measurements, road navigation, and more. However, it is crucial to detect the ground plane and road limits to safely navigate the environment, which requires extracting information from the point cloud to accurately detect common road boundaries. This article presents a survey of existing methods used to detect and extract ground points from LiDAR point clouds. It summarizes the already extensive literature and proposes a comprehensive taxonomy to help understand the current ground segmentation methods that can be used in automotive LiDAR sensors.

Development of an Open-Source Injection Mold Monitoring System.

In the highly competitive injection molding industry, the ability to effectively collect information from various sensors installed in molds and machines is of the utmost relevance, enabling the development of data-based Industry 4.0 algorithms. In this work, an alternative to commercially available monitoring systems used in the industry was developed and tested in the scope of the TOOLING 4G project. The novelty of this system is its affordability, simplicity, real-time data acquisition and display in an intuitive Graphical User Interface (GUI), while being open-source firmware and software-based. These characteristics, and their combinations have been present in previous works, but, to the authors' knowledge, not all of them simultaneously. The system used an Arduino microcontroller-based data acquisition module that can be connected to any computer via a USB port. Software was developed, including a GUI, prepared to receive data from both the Arduino module and a second module. In the current state of development, data corresponding to a maximum of six sensors can be visualized, at a rate of 10 Hz, and recorded for later usage. These capabilities were verified under real-world conditions for monitoring an injection mold with the objective of creating the basis of a platform to deploy predictive maintenance. Mold temperature, cavity pressure, 3-axis acceleration, and extraction force data showed the system can successfully monitor the mold and allowed the clear distinction between normal and abnormal operating patterns.

Characterization of Functional Coatings on Cork Stoppers with Laser-Induced Breakdown Spectroscopy Imaging.

Evaluating the efficiency of surface treatments is a problem of paramount importance for the cork stopper industry. Generically, these treatments create coatings that aim to enhance the impermeability and lubrification of cork stoppers. Yet, current methods of surface analysis are typically time-consuming, destructive, have poor representativity or rely on indirect approaches. In this work, the use of a laser-induced breakdown spectroscopy (LIBS) imaging solution is explored for evaluating the presence of coating along the cylindrical surface and in depth. To test it, several cork stoppers with different shaped areas of untreated surface were analyzed by LIBS, making a rectangular grid of spots with multiple shots per spot, to try to identify the correspondent shape. Results show that this technique can detect the untreated area along with other features, such as leakage and holes, allowing for a high success rate of identification and for its performance at different depths, paving the way for future industry-grade quality control solutions with more complex surface analysis.

Pediatric androgenetic alopecia: an updated review.

Pediatric androgenetic alopecia is an underrecognized disorder. A clinical evaluation with trichoscopy should be made in children and adolescents with hair loss and/or reduced hair density. Diagnosis is usually clinical, by observation of the hair loss pattern and performance of trichoscopy. In some cases, hyperandrogenism should be excluded. Although there is no approved therapy for androgenetic alopecia in pediatric age, topical minoxidil, oral minoxidil and topical finasteride may be very useful. Hair transplant may be an option for girls in selected cases. This article is a review of the current state of evidence concerning pediatric androgenetic alopecia.

Radiological and Anatomical Evaluation of First Metatarsal Pronation in Hallux Valgus Deformity: A Comparison Between Three Different Methods.

A frontal plane metatarsal rotational (pronation) has been documented in a high percentage of hallux valgus patients. Pathoanatomical concepts leading to pronation are still debated. Nevertheless, there is no consensus on how to measure this component of the deformity. The aim of the present study was to compare three commonly used radiographic methods to measure the frontal plane deformity in hallux valgus deformity, such as 1. Round sign of the lateral edge of the first metatarsal head on anterior-posterior radiograph, 2. Non-weightbearing CT-scan and 3. Bernard's axial projection of the first metatarsal head. Afterwards, feet were dissected, and a direct measurement of the pronation was done. Our data showed that alpha angle measurements made through the Bernard's axial projection were closer with those obtained during the dissection compared to those made through the CT-scan. The main finding of our study is that osteoarthritic changes at the metatarso-sesamoid joint play an important role in severe hallux valgus cases. The proposed radiographic methods allow surgeons to verify whether rotation can be corrected during Hallux Valgus procedures and to determine which procedure may be the best for each patient.

Complications after total ankle arthroplasty- A systematic review.

BACKGROUND: Total ankle arthroplasty was developed as an alternative option to ankle arthrodesis in patients with end-stage ankle osteoarthritis. Multiple trials have assessed the outcomes of ankle arthroplasty, but complication risk or relative effectiveness is not systematized in literature. AIM: Review complications of new designs of total ankle arthroplasty and the relationship between their severity and failure rates. METHODS: We reviewed complications and revision rates of prospective studies of primary total ankle arthroplasty that included more than 50 patients and with minimum 2 years follow-up. RESULTS: We included 22 studies (4412 ankles, median age of 61.9 years) with an adjusted mean follow-up time of 66.6 ± 40.9 months. The adjusted mean complication rate was 23.7 % (2.4-52 %), mostly high-grade complications (35.6 %). We found a statistically significant positive correlation between high- and medium-grade complications and revision rates. CONCLUSION: Patient selection is crucial to successfully treat end-stage ankle osteoarthritis. Further multicenter clinical trials with consistent reporting of complications are warranted.

Temporal characterization of broadband femtosecond laser pulses by surface third-harmonic dispersion scan with ptychographic retrieval.

We present a new, to the best of our knowledge, variant of dispersion scan (d-scan) based on surface third-harmonic generation (STHG) and a ptychographic algorithm tailored for full retrieval (amplitude and phase) of broadband laser pulses. We demonstrate the technique by temporally measuring and compressing few-cycle pulses with 7 fs and 2.5 nJ from a Ti:sapphire oscillator, using a sapphire window as the nonlinear medium. The results are in very good agreement with standard second-harmonic d-scan measurements based on a nonlinear crystal. The intrinsically broadband and phase-matching-independent nature of STHG make this technique very suitable for the characterization of ultrashort laser pulses over a broad wavelength range extending into the mid-infrared.

Cost of healthcare utilization associated with incident cardiovascular and renal disease in individuals with type 2 diabetes: A multinational, observational study across 12 countries.

AIM: To examine how the development of cardiovascular and renal disease (CVRD) translates to hospital healthcare costs in individuals with type 2 diabetes (T2D) initially free from CVRD. METHODS: Data were obtained from the digital healthcare systems of 12 nations using a prespecified protocol. A fixed country-specific index date of 1 January was chosen to secure sufficient cohort disease history and maximal follow-up, varying between each nation from 2006 to 2017. At index, all individuals were free from any diagnoses of CVRD (including heart failure [HF], chronic kidney disease [CKD], coronary ischaemic disease, stroke, myocardial infarction [MI], or peripheral artery disease [PAD]). Outcomes during follow-up were hospital visits for CKD, HF, MI, stroke, and PAD. Hospital healthcare costs obtained from six countries, representing 68% of the total study population, were cumulatively summarized for CVRD events occurring during follow-up. RESULTS: In total, 1.2 million CVRD-free individuals with T2D were identified and followed for 4.5 years (mean), that is, 4.9 million patient-years. The proportion of individuals indexed before 2010 was 18% (n = 207 137); 2010-2015, 31% (361 175); and after 2015, 52% (609 095). Overall, 184 420 (15.7%) developed CVRD, of which cardiorenal disease was most frequently the first disease to develop (59.7%), consisting of 23.0% HF and 36.7% CKD, and more common than stroke (16.9%), MI (13.7%), and PAD (9.7%). The total cumulative cost for CVRD was US$1 billion, of which 59.0% was attributed to cardiorenal disease, 3-, 5-, and 6-fold times greater than the costs for stroke, MI, and PAD, respectively. CONCLUSION: Across all nations, HF or CKD was the most frequent CVRD manifestation to develop in a low-risk population with T2D, accounting for the highest proportion of hospital healthcare costs. These novel findings highlight the importance of cardiorenal awareness when planning healthcare.

Stress does not induce a general transcription of transposable elements in Drosophila.

Transposable elements, also known as "jumping genes," have the ability to hop within the host genome. Nonetheless, this capacity is kept in check by the host cell defense systems to avoid unbridled TE mobilization. Different types of stressors can activate TEs in Drosophila, suggesting that TEs may play an adaptive role in the stress response, especially in generating genetic variability for adaptive evolution. TE activation by stressors may also lead to the notion, usually found in the literature, that any form of stress could activate all or the majority of TEs. In this review, we define what stress is. We then present and discuss RNA sequencing results from several studies demonstrating that stress does not trigger TE transcription broadly in Drosophila. An explanation for the LTR order of TEs being the most overexpressed is also proposed.