Quantifying defective and wild-type viruses from high-throughput RNA sequencing.

MOTIVATION: Defective viral genomes (DVGs) are variants of the wild-type (wt) virus that lack the ability to complete autonomously an infectious cycle. However, in the presence of their parental (helper) wt virus, DVGs can interfere with the replication, encapsidation and spread of functional genomes, acting as a significant selective force in viral evolution. DVGs also affect the host's immune responses and are linked to chronic infections and milder symptoms. Thus, identifying and characterizing DVGs is crucial for understanding infection prognosis. Quantifying DVGs is challenging due to their inability to sustain themselves, which makes it difficult to distinguish them from the helper virus, especially using high-throughput RNA sequencing (RNA-seq). An accurate quantification is essential for understanding their very dynamical interactions with the helper virus. RESULTS: We present a method to simultaneously estimate the abundances of DVGs and wt genomes within a sample by identifying genomic regions with significant deviations from the expected sequencing depth. Our approach involves reconstructing the depth profile through a linear system of equations, which provides an estimate of the number of wt and DVG genomes of each type. Until now, in silico methods have only estimated the DVG-to-wt ratio for localized genomic regions. This is the first method that simultaneously estimates the proportions of wt and DVGs genome wide from short-reads RNA sequencing. AVAILABILITY AND IMPLEMENTATION: The MATLAB code and the synthetic datasets are freely available at https://github.com/jmusan/wtDVGquantific.

High-Resolution Cryo-EM Structure Determination of α-synuclein - A Prototypical Amyloid Fibril.

The physiological role of α-synuclein (α-syn), an intrinsically disordered presynaptic neuronal protein, is believed to impact the release of neurotransmitters through interactions with the SNARE complex. However, under certain cellular conditions that are not well understood, α-syn will self-assemble into ß-sheet rich fibrils that accumulate and form insoluble neuronal inclusions. Studies of patient derived brain tissues have concluded that these inclusions are associated with Parkinson's disease, the second most common neurodegenerative disorder, and other synuclein related diseases called synucleinopathies. In addition, repetitions of and specific mutations to the SNCA gene, the gene that encodes α-syn, results in an increased disposition for synucleinopathies. The latest advances in cryo-EM structure determination and real-space helical reconstruction methods have resulted in over 60 in vitro structures of α-syn fibrils solved to date, with a handful of these reaching a resolution below 2.5 Å. Here, we provide a protocol for α-syn protein expression, purification, and fibrilization. We detail how sample quality is assessed by negative stain transmission electron microscopy (NS-TEM) analysis and followed by sample vitrification using the Vitrobot Mark IV vitrification robot. We provide a detailed step by step protocol for high resolution cryo-EM structure determination of α-syn fibrils using RELION and a series of specialized helical reconstruction tools that can be run within RELION. Finally, we detail how ChimeraX, Coot, and Phenix are used to build and refine a molecular model into the high resolution cryo-EM map. This workflow resulted in a 2.04 Å structure of α-syn fibrils with excellent resolution of residues 36 to 97 and an additional island of density for residues 15 to 22 that had not been previously reported. This workflow should serve as a starting point for individuals new to the neurodegeneration and structural biology fields. Together, this procedure lays the foundation for advanced structural studies of α-synuclein and other amyloid fibrils.

Story of an infection: Viral dynamics and host responses in the Caenorhabditis elegans-Orsay virus pathosystem.

Orsay virus (OrV) is the only known natural virus affecting Caenorhabditis elegans, with minimal impact on the animal's fitness due to its robust innate immune response. This study aimed to understand the interactions between C. elegans and OrV by tracking the infection's progression during larval development. Four distinct stages of infection were identified on the basis of viral load, with a peak in capsid-encoding RNA2 coinciding with the first signs of viral egression. Transcriptomic analysis revealed temporal changes in gene expression and functions induced by the infection. A specific set of up-regulated genes remained active throughout the infection, and genes correlated and anticorrelated with virus accumulation were identified. Responses to OrV mirrored reactions to other biotic stressors, distinguishing between virus-specific responses and broader immune responses. Moreover, mutants of early response genes and defense-related processes showed altered viral load progression, uncovering additional players in the antiviral defense response.

Purification and Cryo-Electron Microscopy Analysis of Bacterial Appendages.

A number of extracellular helical protein polymers are crucial for supporting bacterial motility. The bacterial flagellum is a polymeric appendage used to support cellular motility. Historically, structural studies of flagellar and other filaments were limited to those present as or locked into straightened states. Here, we present a robust workflow that produces biologically relevant high-resolution cryo-electron microscopy (cryo-EM) structures of bacterial flagellar filaments. We highlight how a simple purification method, centered around several centrifugation steps, exploits the process of filament ejection in Caulobacter crescentus and results in isolated filaments amenable to transmission electron microscopy (TEM) studies. The quality of the sample is validated by SDS-PAGE and negative stain TEM analysis before a sample is vitrified for cryogenic electron microscopy (cryo-EM) data collection. We provide a detailed protocol for reconstructing either straight or curved flagellar filaments by cryo-EM helical reconstruction methods, followed by an overview of model building and validation. In our hands, this workflow resulted in several flagellar structures below 3 Å resolution, with one data set reaching a global resolution of 2.1 Å. The application of this workflow supports structure-function studies to better understand the molecular interactions that regulate filament architecture in biologically relevant states. Future work will not only examine interactions that regulate bacterial flagellar and other filament organization but also provide a foundation for developing new helical biopolymers for biotech applications. Key features • Rapid high-quality purification of bacterial flagella via simple bacterial culturing, centrifugation, and resuspension methods. • High-throughput cryo-EM data collection of filamentous objects. • Use of cryoSPARC implementations of helical reconstruction algorithms to generate high-resolution 3D structures of bacterial flagella or other helical polymers.

Quality of care assessment for non-small cell lung cancer patients: transforming routine care data into a continuous improvement system.

PURPOSE: The complexity of cancer care requires planning and analysis to achieve the highest level of quality. We aim to measure the quality of care provided to patients with non-small cell lung cancer (NSCLC) using the data contained in the hospital's information systems, in order to establish a system of continuous quality improvement. METHODS/PATIENTS: Retrospective observational cohort study conducted in a university hospital in Spain, consecutively including all patients with NSCLC treated between 2016 and 2020. A total of 34 quality indicators were selected based on a literature review and clinical practice guideline recommendations, covering care processes, timeliness, and outcomes. Applying data science methods, an analysis algorithm, based on clinical guideline recommendations, was set up to integrate activity and administrative data extracted from the Electronic Patient Record along with clinical data from a lung cancer registry. RESULTS: Through data generated in routine practice, it has been feasible to reconstruct the therapeutic trajectory and automatically calculate quality indicators using an algorithm based on clinical practice guidelines. Process indicators revealed high adherence to guideline recommendations, and outcome indicators showed favorable survival rates compared to previous data. CONCLUSIONS: Our study proposes a methodology to take advantage of the data contained in hospital information sources, allowing feedback and repeated measurement over time, developing a tool to understand quality metrics in accordance with evidence-based recommendations, ultimately seeking a system of continuous improvement of the quality of health care.

The pericapsular nerve group block, a highly selective blockage for intracapsular hip fractures: A case series.

Hip fracture is a very frequent clinical situation in the elderly and frail patient. The Pericapsular Nerve Group (PENG) has emerged as a highly selective block for the intracapsular hip fractures. We describe 44 patients with intracapsular hip fractures who underwent a PENG block in addition to spinal anaesthesia with. The main objective was to assess post-surgical pain control at the recovery room and after 24 h. Also, we considered the need for first of second analgesic rescue during the first 24 h after surgery. Only 10 patients presented mild pain at the recovery room. Up to 30 of them had pain after 24 h. However, 25 of these patients reported having mild pain. Only 9 patients required analgesic rescue for postoperative pain control. In conclusion, PENG block is a locoregional technique that allows good postoperative pain control and low opioid consumption during the postoperative period of intracapsular hip fractures.

Accumulation Dynamics of Defective Genomes during Experimental Evolution of Two Betacoronaviruses.

Virus-encoded replicases often generate aberrant RNA genomes, known as defective viral genomes (DVGs). When co-infected with a helper virus providing necessary proteins, DVGs can multiply and spread. While DVGs depend on the helper virus for propagation, they can in some cases disrupt infectious virus replication, impact immune responses, and affect viral persistence or evolution. Understanding the dynamics of DVGs alongside standard viral genomes during infection remains unclear. To address this, we conducted a long-term experimental evolution of two betacoronaviruses, the human coronavirus OC43 (HCoV-OC43) and the murine hepatitis virus (MHV), in cell culture at both high and low multiplicities of infection (MOI). We then performed RNA-seq at regular time intervals, reconstructed DVGs, and analyzed their accumulation dynamics. Our findings indicate that DVGs evolved to exhibit greater diversity and abundance, with deletions and insertions being the most common types. Notably, some high MOI deletions showed very limited temporary existence, while others became prevalent over time. We observed differences in DVG abundance between high and low MOI conditions in HCoV-OC43 samples. The size distribution of HCoV-OC43 genomes with deletions differed between high and low MOI passages. In low MOI lineages, short and long DVGs were the most common, with an additional cluster in high MOI lineages which became more prevalent along evolutionary time. MHV also showed variations in DVG size distribution at different MOI conditions, though they were less pronounced compared to HCoV-OC43, suggesting a more random distribution of DVG sizes. We identified hotspot regions for deletions that evolved at a high MOI, primarily within cistrons encoding structural and accessory proteins. In conclusion, our study illustrates the widespread formation of DVGs during betacoronavirus evolution, influenced by MOI and cell- and virus-specific factors.

Capture of Group A Streptococcus by Open-Microfluidic CandyCollect Device in Pediatric Patients.

State the purpose: Obtaining high-quality samples to diagnose streptococcal pharyngitis in pediatric patients is challenging due to discomfort associated with traditional pharyngeal swabs. This may cause reluctance to go to the clinic, inaccurate diagnosis, or inappropriate treatment for children with sore throat. Here, we determined the efficacy of CandyCollect, a lollipop-inspired open-microfluidic pathogen collection device, to capture Group A Streptococcus (GAS) and compare user preference for CandyCollect, conventional pharyngeal swabs, or mouth swabs in children with pharyngitis and their caregivers. Results: All child participants (30/30) were positive for GAS by qPCR on both the mouth swab and CandyCollect. Caregivers ranked CandyCollect as a good sampling method overall (27/30), and all caregivers (30/30) would recommend CandyCollect for children 5 years and older. Twenty-three of 30 children "really like" the taste and 24/30 would prefer to use CandyCollect if a future test were needed. All caregivers (30/30) and most children (28/30) would be willing to use CandyCollect at home. Conclusion: All participants tested positive for GAS on all three collection methods (pharyngeal swab, mouth swab, and CandyCollect). While both caregivers and children like CandyCollect, some caregivers would prefer a shorter collection time. Future work includes additional studies with larger cohorts presenting with pharyngitis of unknown etiology and shortening collection time while maintaining the attractive form of the device. Translational Impact Statement: Obtaining oral samples for the diagnosis of streptococcal pharyngitis is of great importance for children. To address the challenges associated with traditional pharyngeal swab sampling, we developed the CandyCollect device, a lollipop-inspired open mesofluidic saliva sampling system. In this study, saliva samples were collected from children, aged 5-14 years, with CandyCollect and mouth swabs and analyzed via qPCR. The results show CandyCollect is the child preferred collection tool and had 100% concordance with the results from traditional diagnosis methods as part of their clinical care.

Eco-Friendly Natural Rubber-Jute Composites for the Footwear Industry.

Nowadays, biocomposites represent a new generation of materials that are environmentally friendly, cost-effective, low-density, and not derived from petroleum. They have been widely used to protect the environment and generate new alternatives in the polymer industry. In this study, we incorporated untreated jute fibers (UJFs) and alkaline-treated jute fibers (TJFs) at 1-5 and 10 phr into TSR 10 natural rubber as reinforcement fillers. These composites were produced to be used in countersole shoes manufacturing. Untreated fibers were compared to those treated with 10% sodium hydroxide. The alkali treatment allowed the incorporation of fibers without compromising their mechanical properties. The TJF samples exhibited 8% less hardness, 70% more tensile strength, and the same flexibility compared to their pure rubber counterparts. Thanks to their properties and ergonomic appearance, the composites obtained here can be useful in many applications: construction materials (sound insulating boards, and flooring materials), the automotive industry (interior moldings), the footwear industry (shoe soles), and anti-static moldings. These new compounds can be employed in innovative processes to reduce their carbon footprint and negative impact on our planet. Using the Lorenz-Park equation, the loaded composites examined in this study exhibited values above 0.7, which means a competitive load-rubber interaction. Scanning electron microscopy (SEM) was used to investigate the morphology of the composites in detail.

Patterns and outcome of unplanned care in lung cancer patients: an observational study in a medical oncology department.

Background: There is increasing interest in unplanned care utilization among lung cancer patients and its evaluation should allow the identification of areas for quality improvement. Being a major priority for transformation in oncology, we aim to measure the risk and burden of unplanned care in a medical oncology department and identify factors that determine acute care. Methods: This was an observational retrospective cohort study that included all lung cancer patients treated at Puerta de Hierro-Majadahonda University Hospital between January 1st 2016 and December 31st 2020. Data cut off: June 30th, 2021. The main objective was to assess the incidence of unplanned care, emergency department (ED) visits and unplanned hospital admissions, from the first visit to the medical oncology service and its potential conditioning variables, considering patient death as a competitive event. As secondary objectives, a description and a quality of unplanned care evaluation was carried out. Results: A total of 821 lung cancer patients, all histologies and stages, were included (median follow-up: 32.8 months). Six hundred and eighty-one patients required consultation in the ED (82.9%), and 558 required an unplanned admission (68%). Eighty-six percent of ED consultations and 80.9% of unplanned hospital admissions were related to cancer or its treatment. The 1-year cumulative incidence for ED consultation and for unplanned hospital admission was 71.3% (95% CI: 67.8-74.5%) and 56.7% (95% CI: 53-60%), respectively. In the multivariable analysis, a higher tumor stage increased the risk of consultation in the ED, while a higher stage, Eastern Cooperative Oncology Group performance status (ECOG PS) 2 compared to ECOG PS 0, male sex, opioid or steroid use at first consultation increased the risk of unplanned admission. Conclusions: Our study shows that lung cancer patients have an extremely high demand for unplanned care. It is an early need and related to cancer in the majority of consultations and admissions and therefore a key issue for the management of oncology departments. We must optimize the follow-up of patients with a higher risk of unplanned care, advanced lung cancer or symptomatic patients, incorporating remote monitoring strategies and early interventions, as developing specific urgent care pathways for a better comprehensive cancer care.

Correlative montage parallel array cryo-tomography for in situ structural cell biology.

Imaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here we present robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens. The combination of correlative cryo-fluorescence microscopy, focused-ion-beam milling, substrate micropatterning, and MPACT supports studies that contextually define the three-dimensional architecture of cells. To further extend the flexibility of MPACT, tilt series may be processed in their entirety or as individual tiles suitable for sub-tomogram averaging, enabling efficient data processing and analysis.

A Real-Time FPGA-Based Metaheuristic Processor to Efficiently Simulate a New Variant of the PSO Algorithm.

Nowadays, high-performance audio communication devices demand superior audio quality. To improve the audio quality, several authors have developed acoustic echo cancellers based on particle swarm optimization algorithms (PSO). However, its performance is reduced significantly since the PSO algorithm suffers from premature convergence. To overcome this issue, we propose a new variant of the PSO algorithm based on the Markovian switching technique. Furthermore, the proposed algorithm has a mechanism to dynamically adjust the population size over the filtering process. In this way, the proposed algorithm exhibits great performance by reducing its computational cost significantly. To adequately implement the proposed algorithm in a Stratix IV GX EP4SGX530 FPGA, we present for the first time, the development of a parallel metaheuristic processor, in which each processing core simulates the different number of particles by using the time-multiplexing technique. In this way, the variation of the size of the population can be effective. Therefore, the properties of the proposed algorithm along with the proposed parallel hardware architecture potentially allow the development of high-performance acoustic echo canceller (AEC) systems.

Vegetable Cellulose Fibers in Natural Rubber Composites.

In the last decade, natural fibers have had a significant impact on the research and development of innovative composites made with natural rubber, improving their properties over those of their counterparts that incorporate polluting synthetic fibers. In recent years, this fact has stimulated the research into several modified natural rubber composites reinforced with vegetable fibers. This paper reviews the scientific literature published in the last decade about the properties and characteristics of natural vegetable fibers and natural rubber used in composites. Nowadays the use of alternative materials has become necessary, considering that synthetic materials have caused irreversible damage to the environment, being associated with global warming, for this reason research and development with materials that print a lower carbon footprint during the manufacturing process and subsequent product manufacturing. This review is an invitation to the use of vegetable fibers, as well as vegetable-type matrices, in this case natural rubber as a binder system, it is fantastic to know the different works carried out by other scientists and engineers, in this way to project new compounds linked to innovation in processes that reduce the carbon footprint and its negative impact on our planet.

Atomic-level architecture of Caulobacter crescentus flagellar filaments provide evidence for multi-flagellin filament stabilization.

Flagella are dynamic, ion-powered machines with assembly pathways that are optimized for efficient flagella production. In bacteria, dozens of genes are coordinated at specific times in the cell lifecycle to generate each component of the flagellum. This is the case for Caulobacter crescentus, but little is known about why this species encodes six different flagellin genes. Furthermore, little is known about the benefits multi-flagellin species possess over single flagellin species, if any, or what molecular properties allow for multi-flagellin filaments to assemble. Here we present an in-depth analysis of several single flagellin filaments from C. crescentus, including an extremely well-resolved structure of a bacterial flagellar filament. We highlight key molecular interactions that differ between each bacterial strain and speculate how these interactions may alleviate or impose helical strain on the overall architecture of the filament. We detail conserved residues within the flagellin subunit that allow for the synthesis of multi-flagellin filaments. We further comment on how these molecular differences impact bacterial motility and highlight how no single flagellin filament achieves wild-type levels of motility, suggesting C. crescentus has evolved to produce a filament optimized for motility comprised of six flagellins. Finally, we highlight an ordered arrangement of glycosylation sites on the surface of the filaments and speculate how these sites may protect the ß-hairpin located on the surface exposed domain of the flagellin subunit.

Advances in the development of tailor-made color alcoholic beverages based on an accelerated maturation process.

The study of the evolution of color of alcoholic beverages subjected to accelerate maturation process using heat-treated French oak wood fragments is presented. The results show that it is possible to obtain tonalities like aged beverages in 4 weeks. In this sense, the fragments conditioned at 150 °C (light toasted) proportionated colors like white wine, pale straw, and pale gold. On the other hand, the fragments that received a heat treatment at 200 °C (medium toasted) present yellow tones such as old gold, amber, and deep gold. Finally, the fragments treated at 250 °C (heavily toasted) are those with the most intense yellow tones, classified as sweet chestnut, sherry, russet, muscat, and tawny. The studies of kinetic maturation concluded that the mathematical model of parabolic diffusion could correctly describe the process. Based on this, it is concluded that the heat treatment increases the cavities of the most exposed surface of the wood, increasing the maximum humidity of the materials by 20 %; in such a way that during the first two weeks, there is a diffusion of the solution to the active sites. Wood bioactive compounds on the outer surface achieve a rapid extraction, such as flavonoids, which oxidize rapidly within the solution, generating an increase in yellow color. The previous results were corroborated in a real case analysis using Tequila which can be concluded that the proposed process can give the beverage similar colors to an aged, extra-aged, and ultra-aged class in less than 4 weeks.

Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B-cell lymphomas.

Histone methylation-modifiers, such as EZH2 and KMT2D, are recurrently altered in B-cell lymphomas. To comprehensively describe the landscape of alterations affecting genes encoding histone methylation-modifiers in lymphomagenesis we investigated whole genome and transcriptome data of 186 mature B-cell lymphomas sequenced in the ICGC MMML-Seq project. Besides confirming common alterations of KMT2D (47% of cases), EZH2 (17%), SETD1B (5%), PRDM9 (4%), KMT2C (4%), and SETD2 (4%), also identified by prior exome or RNA-sequencing studies, we here found recurrent alterations to KDM4C in chromosome 9p24, encoding a histone demethylase. Focal structural variation was the main mechanism of KDM4C alterations, and was independent from 9p24 amplification. We also identified KDM4C alterations in lymphoma cell lines including a focal homozygous deletion in a classical Hodgkin lymphoma cell line. By integrating RNA-sequencing and genome sequencing data we predict that KDM4C structural variants result in loss-offunction. By functional reconstitution studies in cell lines, we provide evidence that KDM4C can act as a tumor suppressor. Thus, we show that identification of structural variants in whole genome sequencing data adds to the comprehensive description of the mutational landscape of lymphomas and, moreover, establish KDM4C as a putative tumor suppressive gene recurrently altered in subsets of B-cell derived lymphomas.

A novel hydro-pneumatic fluid percussion device for inducing traumatic brain injury: assessment of sensory, motor, cognitive, molecular, and morphological outcomes in rodents.

Introduction: The fluid percussion method is widely used to induce brain injury in rodents. However, this approach has several limitations, including variability in the resulting damage, which is attributed to factors such as manual control of the mass used to generate the desired pressure. To address these issues, several modifications to the original method have been proposed. Methods: In this study, we present a novel device called the Hydro-pneumatic Fluid Percussion Device, which delivers fluid directly to a lateral region of the brain to induce injury. To validate this model, three groups of male and female rats were subjected to lateral fluid percussion using our device, and the resulting damage was evaluated using sensory, motor, and cognitive tests, measurements of serum injury biomarkers, and morphological analysis via cresyl violet staining. Results: Our results demonstrate that this new approach induced significant alterations in all parameters evaluated. Discussion: This novel device for inducing TBI may be a valuable alternative for modeling brain injury and studying its consequences.

DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data.

The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing (HTS) data has become an interesting computational problem. Several algorithms have been proposed to accomplish this goal, though all incur false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. We present a metasearch tool, DVGfinder, that wraps the two most commonly used DVG search algorithms in a single workflow for the identification of the DVGs in HTS data. DVGfinder processes the results of ViReMa-a and DI-tector and uses a gradient boosting classifier machine learning algorithm to reduce the number of false-positive events. The program also generates output files in user-friendly HTML format, which can help users to explore the DVGs identified in the sample. We evaluated the performance of DVGfinder compared to the two search algorithms used separately and found that it slightly improves sensitivities for low-coverage synthetic HTS data and DI-tector precision for high-coverage samples. The metasearch program also showed higher sensitivity on a real sample for which a set of copy-backs were previously validated.