bluuebunny/crossref_metadata_2025 huggingface dataset:
Hypnotherapy in Pediatric Gastroenterology
Authors: Vlieger Arine M. , Assa Amit , Borrelli Osvaldo , Broekaert Ilse , Deganello Saccomani Marco , Dolinsek Jernej , Carpi de Javier‐Martin , Mas Emmanuel , Miele Erasmo , Thomson Mike , Tzivinikos Christos , Benninga Marc A. ,   Gastroenterology Committee of ESPGHAN
Published: September 2022

In several countries, gut‐directed hypnotherapy is becoming an established and evidence‐based treatment in pediatric gastroenterology. This article describes what hypnotherapy is, offers an overview of its effect in gut‐brain disorders and explains its potential mode of action. Moreover, the use of hypnotherapy in other areas of pediatric gastroenterology, as a supportive tool to reduce pain, stress, depression, and anxiety and improve quality of life, will be also discussed. Guidance toward implementing hypnotherapy in clinical practice is provided, including examples of how you can explain hypnosis to patients with gastroenterological symptoms.
Lethal Neurotoxicity in Lambda-Cyhalothrin Poisoning
Authors: Naveen Alagarasan , Sahu Manas Ranjan , Mohanty Manoj K. , Mohanty Rashmi Ranjan , Sethy Madhusmita , Velayutham Bakialakshmi
Published: September 2022

Agricultural poisons (insecticides and pesticides) are the most common types of poison implicated in the morbidity and mortality associated with acute poisoning. Suicidal ingestion is more frequent than accidental or homicidal poisonings. Pyrethroids are considered relatively safer than other insecticides. Lambda-cyhalothrin (LCH) belongs to the fourth-generation, type II synthetic pyrethroid. To the best of our knowledge, fatalities after LCH exposure have not yet been reported in the literature. Here, we describe a case of LCH poisoning in a 54-year-old male farmer after an accidental pipe burst in a sprayer while spraying in the field. The patient died 10 days after poisoning due to severe neurotoxicity resulting in bilateral parieto-occipital and brainstem infarcts. The histopathological features of the brain associated with LCH poisoning have been discussed in this report.
Assessing Community-Based Public Health Plans: An Example From US Army Injury Prevention
Authors: Courie Anna Fitch , Jones Bruce H. , Canham-Chervak Michelle
Published: September 2022

Context:

The US Army requires community health coalitions to develop action plans for their top public health priorities.

Objective:

To date, the US Army has not implemented a standardized review process for community action plans.

Design:

This project used the Plan Quality Index (PQI), an evidence-based, standardized tool, to evaluate injury prevention action plans created by injury prevention teams (IPTs).

Setting:

17 Army installations.

Participants:

17 IPT leads; 5 Health Promotion Program Officers.

Intervention:

Implementation of the PQI to evaluate the strength of injury prevention action plans and make recommendations for quality improvement to drive reductions in injuries at 17 Army installations.

Main Outcome Measure:

PQI total scores for high- (≥50 points on the PQI) and low-ranking plans (<50 points on the PQI) were assessed for differences using t tests of the mean PQI score. Chi-square tests were employed to identify differences in meeting criteria between high- and low-scoring plans.

Results:

PQI total scores ranged from 9 to 78 points out of 80. The weakest planning elements among all plans were lack of use of SMART objectives (18%), lack of identification of responsible parties (18%), absent evaluation plan (24%), and lack of timelines (35%). The mean score for the high-ranking plans (64.6 ± 9.5) was significantly higher than the mean score for the low-ranking plans (26.2 ± 12.7) (P < .001). Mean scores for clarity, effectiveness, and quality were all significantly higher for the high-ranking plans than for the low-ranking plans (P = .014, P = .002, and P < .001, respectively).

Conclusions:

The PQI tool provides a framework for objective, standardized, and evidence-based feedback and recommendations for improving community health plans. The project identified examples of high-quality action plans and provided actionable recommendations for plan improvement to facilitate sustainability of initiatives addressing injuries, which have long posed a threat to military health and readiness.
The modifications of the LICAP/LTAP flap technique in partial breast reconstruction for difficult tumor locations.
Authors: Zhygulin Andrii , Fedosov Artem , Palytsia Valentyn
Published: September 2022

We propose the modifications of the LTAP/LICAP (Lateral Thoracic Artery Perforator/Lateral Intercostal Artery Perforator) flap partial breast reconstruction that can help to achieve better aesthetic results of the procedure especially for centrally and medially located tumors. Lumpectomy is performed using the retromammary approach through lateral contour access without skin mobilization from parenchyma. This minimizes trauma and scarring of parenchyma and skin in the lateral part of the breast. In case of tumor’s central or medial location, we propose to move the flap into the tumor bed through a cut (“window”) in the m. pectoralis major. It helps to stabilize the flap in an optimal position, optimally redistribute the tissue without compression on the flap pedicle and bulge in the gland’s lateral sector. We have used this modification in 18 patients. The average tumor size was 2,8 cm (1,2-5,4 cm), the average weight of the specimens – 46,6 g (14-110 g). Two patients had a tumor in the upper-inner quadrant close to the breast meridian; the other two had a central-lateral tumor location; in fourteen cases, a tumor was located in the upper-outer quadrant. We have observed early complications in 4 cases: 2 seromas of the wound, 1 partial flap necrosis with the revision and resection of the flap, and 1 cellulite in the axillary region after axillary dissection because of long-standing lymphorrhea and drainage. The proposed modification of the LICAP/LTAP flap technique in partial breast reconstruction can lead to better aesthetic and safety results of the surgery.
Asymmetric Four Flap Breast Reconstruction with DIEP flaps and PAP flaps
Authors: Evgeniou Evgenious , Teotia Sumeet S. , Haddock Nicholas T.
Published: September 2022

INTRODUCTION:

Autologous breast reconstruction is considered superior to alloplastic options. In cases of large volume breast reconstruction, stacked flaps from a single or multiple donor areas are required. In bilateral stacked four-flap reconstructions, when a large amount of skin is required, an asymmetric reconstruction involving the use of a conjoined DIEP flap with a uniform skin paddle to reconstruct the side where most skin is required and the use of two independently perfused stacked flaps to reconstruct the side that requires less skin can provide superior aesthetic results compared with the usual hemi-DIEP/PAP four-flap configuration.

MATERIALS-METHODS:

Retrospective review of all asymmetric DIEP-PAP 4-flap breast reconstructions between March 2015 and October 2020

RESULTS:

Seven patients underwent asymmetric DIEP-PAP breast reconstructions. One of the PAP flaps was lost on post-operative day 1 due to thrombosis of the retrograde IMA/IMV. No other immediate, early or late complications were encountered.

CONCLUSIONS:

Asymmetric four-flap breast reconstruction, using a unilateral bipedicled flap combined with 2 PAP flaps, can provide superior aesthetic results, avoiding common problems associated with the classic configuration of DIEP-PAP four-flap breast reconstruction.

LEVEL OF EVIDENCE:

Therapeutic: IV Case series with post test only
Lymph Node Ratio Nomogram-Based Prognostic Model for Resected Distal Cholangiocarcinoma
Authors: Perez Marc , Hansen Carsten Palnaes , Burdio Fernando , Pellino Gianluca , Pisanu Adolfo , Salvia Roberto , Di Martino Marcello , Abu Hilal Mohammad , Aldrighetti Luca , Ielpo Benedetto ,   and the Cholangiocarcinoma Multicenter Study Coauthor Group
Published: September 2022

BACKGROUND:

Several variables have been described as prognostic factors for resected distal cholangiocarcinoma (dCC), including lymph node metastases (N status) and lymph node ratio (LNR). The present study aimed to evaluate the prognostic value of LNR on survival and to establish a novel prognostic nomogram to predict the cancer-specific recurrence-free survival (RFS) of dCC.

STUDY DESIGN:

Between December 2006 and September 2020, 415 consecutive patients who underwent pancreaticoduodenectomy (PD) for dCC in 10 centers were identified. Multivariate Cox analysis was used to identify all independent risk factors among several prognostic factors. A nomogram was then developed and assessed by integrating the independent prognostic factors into the model, and the concordance index (C-index) was used to evaluate its performance.

RESULTS:

According to Cox regression multivariate analysis, a nomogram based on independent prognostic factor for RFS was performed including LNR 15 (hazard ratio [HR] 2.442, 95% CI 1.348–4.425, p = 0.003), perineural invasion (HR 3.100, 95% CI 1.183–8.122, p = 0.025), differentiation grade (HR 2.100, 95% CI 1.172–4.143, p = 0.021), and radicality of PD (HR 2.276, 95% CI 1.223–4.234, p = 0.009). The C-index of the nomogram, tailored based on the previous significant factors, was 0.8.

CONCLUSIONS:

LNR15 yields a high prognostic efficiency for RFS. The nomogram based on LNR can provide an accurate prognosis assessment for patients with resected dCC.
A design-space minimum sampling strategy based on proper-orthogonal-decomposition projection
Authors: Lengani Davide , Petronio Daniele , Simoni Daniele , Ubaldi Marina
Published: September 2022

A proper-orthogonal-decomposition (POD)-based procedure has been developed to identify the tests/experiments strictly needed for modelling a complex system. The case here studied concerns the aerodynamic efficiency response of a low-pressure-turbine cascade to the variation of the most influencing flow parameters. A large number of experimental tests have been carried out to sample the design space. POD has been applied to reduce data dimensionality, identifying the rank of the problem and defining a vector subspace where data are as compact as possible. Lasso and Gaussian process regressions, complemented by cross-validation and marginal-likelihood criteria, have been used to learn parsimonious efficiency trends in the POD subspace. It will be shown that a model educated with the most orthogonal combination of data projected in the POD space performs as well as the model educated with the entire dataset. Then, it will be shown that the strictly needed tests can be iteratively localized (
a priori
) in the design space by means of the data-driven procedure here proposed, thus allowing for an active application. This will provide significant time reduction in the execution of tests and can be generalized to other complex systems, either of an experimental or numerical nature, even pertaining to other disciplines.
Unidirectional edge modes in time-modulated metamaterials
Authors: Ammari Habib , Cao Jinghao
Published: September 2022

We prove the possibility of achieving unidirectional edge modes in time-modulated supercell structures. Such finite structures consist of two trimers repeated periodically. Because of their symmetry, they admit degenerate edge eigenspaces. When the trimers are time-modulated with two opposite orientations, the degenerate eigenspace splits into two one-dimensional eigenspaces described by an analytical formula, each corresponding to a mode which is localized at one edge of the structure. Our results on the localization and stability of these edge modes with respect to fluctuations in the time-modulation amplitude are illustrated by several numerical simulations.
Quantum Biology in Cellular Migration
Authors: Vecheck Amy M. , McNamee Cameron , Reijo Pera Renee , Usselman Robert J.
Published: September 2022

The impact of magnetic fields on cellular function is diverse but can be described at least in part by the Radical Pair Mechanism (RPM), where magnetic field intervention alters reactive oxygen species (ROS) populations and downstream cellular signaling. Here, cellular magnetophoresis within three-dimensional scaffolds was monitored in an applied oscillating 1.4 MHz radiofrequency (RF) magnetic field with an amplitude of 10 μT and a static 50 μT magnetic field. Given that cellular respiration or glycolysis can be increased based on the orientation of the RF magnetic field, this study focused on the parallel orientation to increase ATP synthesis. Results suggest that RF accelerated clustering and elongation after 1 day with increased levels of clustering and cellular linkage after 7 days. Electron microscopy provided additional topological information and verified the development of fibrous networks and extracellular matrix were visualized after 7 days in samples maintained in RF. Analysis of the distribution of cells within the scaffolds revealed that the clustering rate during the first day was increased nearly five times in the RF environment. This work demonstrates time-dependent cellular magnetophoresis that may be influenced by quantum biology (QB) processes and signaling that can further attenuate or enhance cellular bioenergetics and behavior.
Hydrogen Peroxide Production by Epidermal Dual Oxidase 1 Regulates Nociceptive Sensory Signals
Authors: Pató Anna , Bölcskei Kata , Donkó Ágnes , Kaszás Diána , Boros Melinda , Bodrogi Lilla , Várady György , Veronika Pape F.S. , Roux Benoit , Enyedi Balázs , Helyes Zsuzsanna , Watt Fiona M. , Sirokmány Gábor , Geiszt Miklós
Published: September 2022

Keratinocytes of the mammalian skin provide not only mechanical protection for the tissues, but also transmit mechanical, chemical, and thermal stimuli from the external environment to the sensory nerve terminals. Sensory nerve fibers penetrate the epidermal basement membrane and function in the tight intercellular space among keratinocytes. Here we show that epidermal keratinocytes produce hydrogen peroxide upon the activation of the NADPH oxidase dual oxidase 1 (DUOX1). This enzyme can be activated by increasing cytosolic calcium levels. Using DUOX1 knockout animals as a model system we found an increased sensitivity towards certain noxious stimuli in DUOX1-deficient animals, which is not due to structural changes in the skin as evidenced by detailed immunohistochemical and electron-microscopic analysis of epidermal tissue. We show that DUOX1 is expressed in keratinocytes but not in the neural sensory pathway. The release of hydrogen peroxide by activated DUOX1 alters both the activity of neuronal TRPA1 and redox-sensitive potassium channels expressed in dorsal root ganglia primary sensory neurons. We describe hydrogen peroxide, produced by DUOX1 as a paracrine mediator of nociceptive signal transmission. Our results indicate that a novel, hitherto unknown redox mechanism modulates noxious sensory signals.
An Arrayed Transposon Library of Ruegeria pomeroyi DSS-3
Authors: Mejia Catalina , Trujillo Rodriguez Lidimarie , Poudel Ravin , Ellington Adam , Rivers Adam R. , Reisch Christopher R.
Published: September 2022

The ability to construct defined genetic mutations in many bacteria is difficult and limited. Transposon mutagenesis is often highly efficient, but is not site specific, thus selections are often needed to identify mutants of interest. The construction of arrayed mutant libraries would help to fill this need, though these libraries are costly and time consuming. To enable easier construction of arrayed libraries we developed a workflow and methodology using a hierarchical barcoding scheme to identify mutants within a multiwell plate. We applied this method to the marine Alphaproteobacterium Ruegeria pomeroyi DSS-3 and created a library with over 2,800 disrupted genes.
Monitoring correlates of SARS-CoV-2 infection in cell culture using two-photon microscopy and a novel fluorescent calcium-sensitive dye
Authors: Máthé Domokos , Szalay Gergely , Cseri Levente , Kis Zoltán , Pályi Bernadett , Földes Gábor , Kovács Noémi , Fülöp Anna , Szepesi Áron , Hajdrik Polett , Csomos Attila , Zsembery Ákos , Kádár Kristóf , Katona Gergely , Mucsi Zoltán , Rózsa Balázs József , Kovács Ervin
Published: September 2022

The organism-wide effects of viral infection SARS-CoV-2 are well studied, but little is known about the dynamics of how the infection spreads in time among or within cells due to the scarcity of suitable high-resolution experimental systems. Two-photon (2P) imaging combined with a proper subcellular staining technique has been an effective tool for studying mechanisms at such resolutions and organelle levels. Herein, we report the development of a novel calcium sensor molecule along with a 2P-technique for identifying imaging patterns associated with cellular correlates of infection damage within the cells. The method works as a cell viability assay and also provides valuable information on how the calcium level and intracellular distribution are perturbed by the virus. Moreover, it allows the quantitative analysis of infection dynamics. This novel approach facilitates the study of the infection progression and the quantification of the effects caused by viral variants and viral load.
CimpleG: Finding simple CpG methylation signatures
Authors: Maié Tiago , Schmidt Marco , Erz Myriam , Wagner Wolfgang , Costa Ivan G.
Published: September 2022

DNA methylation (DNAm) at specific CG dinucleotides (CpG sites) in the genome provides powerful biomarkers for a wide range of applications, such as epigenetic clocks, cell type deconvolution, and stratification of cancer patients. Such epigenetic signatures are usually based on multivariate approaches that require hundreds of DNAm sites for predictions. In contrast, targeted assays for only a few selected CpGs may facilitate faster turnover, better standardisation, and reduced costs. Here, we propose a computational framework named CimpleG for the detection of small CpG methylation signatures, exemplarily used for cell type classification. We evaluate the performance of CimpleG and competing methods on two distinct datasets in regard to the cell-type classification of blood cells and of other somatic cells. Furthermore, we evaluate how well these classifiers perform cellular deconvolution of blood cell mixtures. We show that CimpleG is both time efficient and performs as well as Elastic Net, while basing its prediction on a single DNAm site per cell type. Altogether, CimpleG provides a complete computational framework for the delineation of DNAm signatures and cellular deconvolution.
Far-red light increases maize volatile emissions in response to volatile cues from neighboring plants
Authors: Escobar-Bravo Rocío , Schimmel Bernardus C.J. , Zhang Yaqin , Wang Lei , Robert Christelle A.M. , Glauser Gaétan , Ballaré Carlos L. , Erb Matthias
Published: September 2022

Plants perceive the presence and defense status of their neighbors through light and volatile cues, but how plants integrate both stimuli is poorly understood. We investigated if and how low Red to Far red light (R:FR) ratios, indicative of shading or canopy closure, affect maize (Zea mays) responses to herbivore-induced plant volatiles (HIPVs), including the green leaf volatile (Z)-3-hexenyl acetate. We modulated light signaling and perception by using FR supplementation and aphyB1phyB2mutant, and we determined volatile release as a response readout. To gain mechanistic insights, we examined expression of volatile biosynthesis genes, hormone accumulation, and photosynthesis. Exposure to a full blend of HIPVs or (Z)-3-hexenyl acetate induced maize volatile release. Short-term FR supplementation increased this response. In contrast, prolonged FR supplementation or constitutive phytochrome B inactivation inphyB1phyB2plants showed the opposite response. Short-term FR supplementation enhanced photosynthesis and stomatal conductance and (Z)-3-hexenyl acetate-induced JA-Ile levels. We conclude that a FR-enriched light environment can prompt maize plants to respond more strongly to HIPVs emitted by neighbors, which might be explained by changes in photosynthetic processes and phytochrome B signaling. Our findings reveal interactive responses to light and volatile cues with potentially important consequences for plant-plant and plant-herbivore interactions.
Quantification of membrane binding and diffusion using Fluorescence Correlation Spectroscopy diffusion laws
Authors: Mouttou Anita , Bremaud Erwan , Noero Julien , Dibsy Rayane , Arone Coline , Mak Johnson , Muriaux Delphine , Berry Hugues , Favard Cyril
Published: September 2022

Many transient processes in cells arise from the binding of cytosolic proteins to membranes. Quantifying this membrane binding and its associated diffusion in the living cell is therefore of primary importance. Dynamic photonic microscopies, e.g. single/multiple particle tracking, fluorescence recovery after photobleaching and fluorescence correlation spectroscopy (FCS) enable noninvasive measurement of molecular mobility in living cells and their plasma membranes. However, FCS with a single beam waist is of limited applicability with complex, non Brownian, motions. Recently, the development of FCS diffusion laws methods has given access to the characterization of these complex motions, although none of them is applicable to the membrane binding case at the moment. In this study, we combined computer simulations and FCS experiments to propose an FCS diffusion law for membrane binding. First, we generated computer simulations of spot-variation FCS (svFCS) measurements for a membrane binding process combined to 2D and 3D diffusion at the membrane and in the bulk/cytosol, respectively. Then, using these simulations as a learning set, we derived an empirical diffusion law with three free parameters: the apparent binding constant KDapp, the diffusion coefficient on the membrane D2D and the diffusion coefficient in the bulk/cytosol, D3D. Finally, we monitored, using svFCS, the dynamics of retroviral Gag proteins and associated mutants during their binding to supported lipid bilayers of different lipid composition or at plasma membranes of living cells and we quantified KDapp and D2D in these conditions using our empirical diffusion law. Based on these experiments and numerical simulations, we conclude that this new approach enables correct estimation of membrane partitioning and membrane diffusion properties (KDapp and D2D) for peripheral membrane molecules.
Mapping the Constrained Coding Regions in the human genome to their corresponding proteins
Authors: Hasenahuer Marcia A. , Sanchis-Juan Alba , Laskowski Roman A. , Baker James A. , Stephenson James D. , Orengo Christine A. , Raymond F. Lucy , Thornton Janet M.
Published: September 2022

Constrained Coding Regions (CCRs) in the human genome have been derived from DNA sequencing data of large cohorts of healthy control populations, available in the Genome Aggregation Database (gnomAD) [1]. They identify regions depleted of protein-changing variants and thus identify segments of the genome that have been constrained during human evolution. By mapping these DNA-defined regions from genomic coordinates onto the corresponding protein positions and combining this information with protein annotations, we have explored the distribution of CCRs and compared their co-occurrence with different protein functional features, previously annotated at the amino acid level in public databases. As expected, our results reveal that functional amino acids involved in interactions with DNA/RNA, protein-protein contacts and catalytic sites are the protein features most likely to be highly constrained for variation in the control population. More surprisingly, we also found that linear motifs, linear interacting peptides (LIPs), disorder-order transitions upon binding with other protein partners and liquid-liquid phase separating (LLPS) regions are also strongly associated with high constraint for variability. We also compared intra-species constraints in the human CCRs with inter-species conservation and functional residues to explore how such CCRs may contribute to the analysis of protein variants. As has been previously observed, CCRs are only weakly correlated with conservation, suggesting that intraspecies constraints complement interspecies conservation and can provide more information to interpret variant effects.
A protocol for rapid generation cycling (speed breeding) of hemp (Cannabis sativa) for research and agriculture
Authors: Schilling Susanne , Melzer Rainer , Dowling Caroline A. , Shi Jiaqi , Muldoon Shaun , McCabe Paul F.
Published: September 2022

Hemp (Cannabis sativa) is a highly versatile multi-purpose crop with a multitude of applications, from textiles, biofuel and building material to high-value food products for consumer markets. Furthermore, non-hallucinogenic cannabinoids like cannabidiol (CBD), which can be extracted from female hemp flowers, are potentially valuable pharmacological compounds. In addition, hemp has high carbon sequestration potential due to its rapid growth rate. Therefore, the hemp industry is gaining more traction and breeding hemp cultivars adapted to local climate conditions or bred for specific applications is becoming increasingly important.

Here, we present a method for rapid generation cycling (speed breeding) for hemp. The speed breeding protocol makes use of the photoperiod sensitivity of Cannabis. It encompasses vegetative growth of the plants for two weeks under continuous light, followed by flower induction, pollination and seed development for four weeks under short-day conditions and a seed ripening phase under continuous light and water stress. With the protocol introduced here, a generation time of under nine weeks (61 days) from seed to seed can be achieved. Our method furthermore synchronises flowering time of different hemp cultivars, thus facilitating crosses between cultivars. The extremely short generation time will enable hemp researchers and breeders to perform crosses in a time-efficient way and generate new hemp cultivars with defined genetic characteristics in a shorter amount of time.
Evolutionary metabolomics of specialized metabolism diversification in the genusNicotianahighlights allopolyploidy-mediated innovations inN-acylnornicotine metabolism
Authors: Elser David , Pflieger David , Villette Claire , Moegle Baptiste , Miesch Laurence , Gaquerel Emmanuel
Published: September 2022

Specialized metabolite (SM) diversification is a core process to plants’ adaptation to diverse ecological niches. Here we implemented a computational mass spectrometry (MS)-based metabolomics approach to explore SM diversification in tissues of 20 species coveringNicotianaphylogenetics sections. To drastically increase metabolite annotation, we created a largein silicofragmentation database, comprising more than 1 million structures, and scripts for connecting class prediction to consensus substructures. Altogether, the approach provides an unprecedented cartography of SM diversity and section-specific innovations in this genus. As a case-study, and in combination with NMR and MS imaging, we explored the distribution ofN-acyl nornicotines, alkaloids predicted to be specific toRepandaeallopolyploids, and revealed their prevalence in the genus, albeit at much lower magnitude, as well as a greater structural diversity than previously thought. Altogether, the novel data integration approaches provided here should act as a resource for future research in plant SM evolution.

Teaser

Computational metabolomics delineates main trends in the diversification of specialized metabolism in the genusNicotiana
Measuring Capillary Flow Dynamics using Interlaced Two-Photon Volumetric Scanning
Authors: Giblin John T , Park Seong-Wook , Jiang John , Kılıç Kıvılcım , Kura Sreekanth , Boas David A. , Chen Ichun A.
Published: September 2022

Two photon microscopy and optical coherence tomography (OCT) are two standard methods for measuring flow speeds of red blood cells in microvessels, particularly in animal models. However, traditional two photon microscopy lacks the depth of field to adequately capture the full volumetric complexity of the cerebral microvasculature and OCT lacks the specificity offered by fluorescent labeling. In addition, the traditional raster scanning technique utilized in both modalities requires a balance of image frame rate and field of view, which severely limits the study of RBC velocities in the microvascular network. Here, we overcome this by using a custom two photon system with an axicon based Bessel beam to obtain volumetric images of the microvascular network with fluorescent specificity. We combine this with a novel scan pattern that generates pairs of frames with short time delay sufficient for tracking red blood cell flow in capillaries. We track flow speed in 10 or more capillaries simultaneously at 1 Hz in a 237 μm x 237μm x 120 μm volume and quantify both spatial and temporal variability in speed. We also demonstrate the ability to track flow speed changes around stalls in capillary flow.
Genozip 14 - advances in compression of BAM and CRAM files
Authors: Lan Divon , Llamas Bastien
Published: September 2022

Genozip performs compression of a wide range of genomic data, including widely used FASTQ, BAM and VCF file formats. Here, we introduce the latest advancement in Genozip technology, focused on compression of BAM and CRAM files. We demonstrate Genozip’s ability to compress data generated by a variety of study types (e.g., whole genome sequencing, DNA methylation, RNASeq), sequencing technologies and aligners, up to 2.7 times better than the current state of the art compressor, CRAM version 3.1.

Availability and implementation

Genozip is freely available for academic research use and has been tested for Linux, Mac and Windows. Installation instructions are available at https://genozip.com/installing.html. A user manual is available at https://genozip.com/manual.html.

Supplementary information

Supplementary data are available.
The Ecosystem Pressure-Volume Curve
Authors: Binks Oliver , Meir Patrick , Mencuccini Maurizio
Published: September 2022

The ecosystem pressure-volume curve (EPV) is the relationship between vegetation water content and a representative value of water potential applied on a ground-area basis. The EPV attempts to reconcile our detailed and physically rigorous understanding of small-scale field-measureable processes to the spatial scale applicable to ecosystem and climate science. Successfully bridging that gap in scale potentially allows us to use field measurements to interpret remote sensing data, and then remote sensing data to inform our understanding of vegetation-climate interactions. Here we clearly define the idea of the EPV, evaluate the limitations of applying values of water content and water potential to ecosystems on a ground area basis, and discuss practical ways to construct the EPV with existing data. We also present the first EPVs based on data from nine different plots, including tropical rainforest, savanna, temperate forest, and a long-term drought experiment in Amazonian rainforest (Caxiuanã, State of Pará, Brazil). The initial findings suggest high levels of consistency among sites. In particular, the ratio of water to biomass across ecosystems appears to be constrained to around 1:3. Seven of nine sites had closely converging ‘relative maximum water storage’ (the proportion of total stored water than can be lost before an ecosystem succumbs to physiological damage) at 9.1% +/-1.8 standard deviation. Relative ecosystem capacitance may increase with site biomass (P = 0.091), but varied little across sites with a mean of 0.068 MPa−1 +/-0.029 standard deviation. These first estimates suggest that the EPV idea may reveal useful trends across ecosystems, potentially paving the way to increasing the ecophysiological significance of remote sensing data, and enabling an alternative method for modelling long-term ecosystem-climate feedbacks based on equilibrium thermodynamics.
MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization
Authors: Zhang Yuwen , Cao Xuan , Gao Zehua , Ma Xuying , Wang Qianfeng , Cai Xiumei , Zhang Yan , Zhang Zhao , Wei Gang , Wen Bo
Published: September 2022

Long interspersed nuclear elements (LINEs) play essential role in shaping chromatin state, while the factors that cooperate with LINEs and their roles in higher-order chromatin organization remain poorly understood. Here we show that MATR3, a nuclear matrix protein, interplays with antisense LINE1 (AS L1) RNAs to form into a gel-like meshwork via phase-separation, providing a partially dynamic platform for chromatin spatial organization. Either depletion of MATR3 or AS L1 RNAs changes nuclear distribution of each other and leads to chromatin reorganization in the nucleus. After MATR3 depletion, topologically associating domains (TADs) that highly transcribed MATR3-associated AS L1 RNAs showed a decrease on local chromatin interactions. Furthermore, amyotrophic lateral sclerosis (ALS)-associated MATR3 mutants alter biophysical features of the MATR3-AS L1 RNA meshwork and cause chromatin reorganization. Collectively, we revealed an essential role of meshwork formed by nuclear matrix and retrotransposon-derived RNAs in gathering chromatin in the nucleus.
Neutrophils regulate ITPR2 levels in epithelia by direct injection of elastase
Authors: Ogino N , Leite M Fatima , Kruglov E , Asashima H , Hafler DA , Ehrlich BE , Nathanson MH
Published: September 2022

The destructive role of neutrophils in inflammation is well known1 but they also have less damaging effects such as tissue remodeling and modulation of metabolism2, 3. Usually, neutrophils in tissues release toxic or digestive compounds into the extracellular region4–8. Here we report that neutrophils can inject their granule contents directly into hepatocytes. Neutrophil elastase within the hepatocytes selectively degrades the inositol trisphosphate receptor (ITPR), especially the type 2 isoform which is the predominant intracellular calcium release channel in these cells9. This action reduces calcium signals and cell proliferation without cellular damage. In response, the hepatocytes increase expression of serpins E2 and A3, which block the effect of elastase. This phenomenon is also observed in liver biopsies from patients with alcoholic hepatitis, a condition characterized by infiltration of neutrophils10, 11. This non-destructive and reversible effect on hepatocytes defines a previously unappreciated role of neutrophils in transiently regulating signaling mechanisms in epithelia.
Vowel and formant representation in human auditory speech cortex
Authors: Oganian Yulia , Bhaya-Grossman Ilina , Johnson Keith , Chang Edward F.
Published: September 2022

Vowel sounds are a fundamental component of human speech across all languages. Vowels are cued acoustically by formants, the resonance frequencies determined by the shape of the vocal tract during speaking. An outstanding question in neurolinguistics is how the human brain processes vowel formants during speech perception. We used high-density intracranial recordings from the human speech cortex on the superior temporal gyrus (STG) while participants listened to natural continuous speech to address this question. We derived two-dimensional receptive fields based on the first and second formants to characterize tuning to vowel sounds. We found that neural activity at single STG sites was highly selective for particular zones in the formant space. Furthermore, this formant tuning shifted dynamically to adjust for speaker-specific spectral context. Despite this formant selectivity, local cortical responses were not sufficient to reliably discriminate between vowel categories. Instead, vowel category representations could be accurately decoded when using the entire population of formant encoding electrodes. Together, our results reveal that vowels are locally encoded in STG with complex acoustic tuning in two-dimensional formant space. As a population code this gives rise to phonological vowel perception.
ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development
Authors: Graham-Paquin Adda-Lee , Saini Deepak , Sirois Jacinthe , Hossain Ishtiaque , Katz Megan S. , Zhuang Qinwei Kim-Wee , Kwon Sin Young , Yamanaka Yojiro , Bourque Guillaume , Bouchard Maxime , Pastor William A.
Published: September 2022

ZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found thatZmym2-/-mice show embryonic lethality by E10.5. Molecular characterization ofZmym2-/-embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice.Zmym2-/-embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. Interaction and colocalization data indicate that ZMYM2 homes to germline genes via binding to the non-canonical polycomb complex PRC1.6 and to transposons via the TRIM28 complex. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation.ZMYM2-/-human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.
Steric-free bioorthogonal profiling of cellular acetylation and glycosylation via a fluorine-selenol displacement reaction (FSeDR)
Authors: Zhao Yue , Zhao Mi , Lyu Zhigang , Gorman Nicole , Lewis Todd R. , Goldman Aaron R. , Tang Hsin-Yao , Wang Rongsheng E.
Published: September 2022

Global detection and identification of protein post-translational modification (PTM) is a major bottleneck due to its dynamic property and rather low abundance. Tremendous efforts have been since made to develop antibody-based immunoaffinity enrichment or bioorthogonal chemistry-based chemical reporter approach but both suffer from inherent limitations. Following our previously reported steric-free tagging strategy, we hereby report the invention of selenol as a new generation of fluorine-displacement probe. The fluorine-selenol based displacement reaction enabled us to efficiently label and image acetylation and glycosylation at cellular level. We further pursued FSeDR in tandem with SILAC based quantitative proteomics to globally profile acetylation substrate proteins in a representative prostate cancer cell line PC3. Our results unraveled the fluorine-based toolbox for powerful chemical biology probing and allow for the future study of PTMs in a systemic manner.
Real-time TIRF imaging of single adiponectin vesicle exocytosis in 3T3-L1 adipocytes stably expressing mCherry fused to human adiponectin
Authors: Shrestha Man Mohan , Barg Sebastian , Olofsson Charlotta S.
Published: September 2022

Adiponectin is a peptide hormone abundantly released from adipocytes, and reduced circulating levels are associated with obesity-related diseases, such as type 2 diabetes, insulin resistance and cardiovascular disease. Adiponectin is released by regulated exocytosis of secretory vesicles, but traditional molecular biology and imaging techniques lack the specificity and time resolution to adequately quantify exocytosis and trafficking of adiponectin-containing vesicles. Here we generated 3T3-L1 adipocytes that stably express mCherry-tagged human adiponectin, resulting in robust labelling of small adiponectin vesicles with a diameter of 200-300 nm, in live cells. Total internal reflection fluorescence (TIRF) microscopy was used to visualise and quantify exocytosis and adiponectin release in real-time, observed as rapid disappearance of the fluorescence of individual vesicles. Bulk adiponectin secretion measurements confirmed that the labelled adiponectin was secreted to the surrounding solution under these conditions, and expressed in the same vesicle population as endogenous adiponectin. In contrast to previous electrophysiological results, elevation of cytosolic Ca2+alone was sufficient to induce exocytosis, although at a lower rate compared to elevated cytosolic cAMP. We conclude that the adiponectin-mCherry-labelled cells are useful for studying adiponectin exocytosis at the single vesicle level, and that an intracellular elevation of either cAMP or Ca2+can trigger adiponectin vesicle release.
A flexible and efficient microfluidics platform for the characterization and isolation of novel bacteriophages
Authors: Mabrouk Adam Sidi , Ongenae Véronique , Claessen Dennis , Brenzinger Susanne , Briegel Ariane
Published: September 2022

Bacteriophages are viruses that infect bacteria. This property makes them highly suitable for varied uses in industry or in the development of the treatment of bacterial infections. However, the conventional methods that are used to isolate and analyze these bacteriophages from the environment are generally cumbersome and time-consuming. Here, we adapted a high-throughput microfluidic setup for long-term analysis of bacteriophage-bacteria interaction and demonstrate isolation of phages from environmental samples.
CTNND2 regulation by the SRGAP2 protein family links human evolution to synaptic neoteny
Authors: Assendorp Nora , Fossati Matteo , Libé-Philippot Baptiste , Christopoulou Eirini , Depp Marine , Rapone Roberta , Dingli Florent , Loew Damarys , Vanderhaeghen Pierre , Charrier Cécile
Published: September 2022

Human-specific genes are potential drivers of brain evolution. Among them, SRGAP2C has contributed to the emergence of features characterizing human cortical synapses, including their extended period of maturation. SRGAP2C inhibits its ancestral copy, the postsynaptic protein SRGAP2A; yet the synaptic molecular pathways differentially regulated in humans by SRGAP2 proteins remain largely unknown. Here, we identify CTNND2, a protein implicated in severe intellectual disability (ID) in the Cri-du-Chat syndrome, as an SRGAP2 effector. We demonstrate that CTNND2 slows down synaptic maturation and promotes neuronal homeostasis. During postnatal development, CTNND2 moderates neuronal excitation and excitability. In adults, it supports synapse maintenance. While CTNND2 deficiency is deleterious and results in the synaptic loss of SYNGAP1, another major ID-associated protein, the human-specific protein SRGAP2C enhances CTNND2 synaptic accumulation in human neurons. Our findings reveal that CTNND2 regulation by SRGAP2C contributes to synaptic neoteny in humans, and link human-specific and ID genes at the synapse.
The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution
Authors: Moulana Alief , Dupic Thomas , Phillips Angela M. , Chang Jeffrey , Roffler Anne A. , Greaney Allison J. , Starr Tyler N. , Bloom Jesse D. , Desai Michael M.
Published: September 2022

The Omicron BA.1 variant of SARS-CoV-2 escapes convalescent sera and monoclonal antibodies that are effective against earlier strains of the virus. This immune evasion is largely a consequence of mutations in the BA.1 receptor binding domain (RBD), the major antigenic target of SARS-CoV-2. Previous studies have identified several key RBD mutations leading to escape from most antibodies. However, little is known about how these escape mutations interact with each other and with other mutations in the RBD. Here, we systematically map these interactions by measuring the binding affinity of all possible combinations of these 15 RBD mutations (215= 32,768 genotypes) to four monoclonal antibodies (LY-CoV016, LY-CoV555, REGN10987, and S309) with distinct epitopes. We find that BA.1 can lose affinity to diverse antibodies by acquiring a few large-effect mutations and can reduce affinity to others through several small-effect mutations. However, our results also reveal alternative pathways to antibody escape that do not include every large-effect mutation. Moreover, epistatic interactions are shown to constrain affinity decline in S309 but only modestly shape the affinity landscapes of other antibodies. Together with previous work on the ACE2 affinity landscape, our results suggest that escape of each antibody is mediated by distinct groups of mutations, whose deleterious effects on ACE2 affinity are compensated by another distinct group of mutations (most notably Q498R and N501Y).
Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides
Authors: O’Brien Darragh P , Jones Hannah BL , Guenther Franziska , Murphy Emma J , England Katherine S , Anderson Malcolm , Brennan Paul , Davis John B , Pinto-Fernández Adán , Turnbull Andrew P , Kessler Benedikt M
Published: September 2022

Dampening functional levels of the mitochondrial deubiquitylating enzyme USP30 has been suggested as an effective therapeutic strategy against neurodegenerative disorders such as Parkinson’s Disease. USP30 inhibition may counteract the deleterious effects of impaired turnover of damaged mitochondria which is inherent to both familial and sporadic forms of the disease. Small-molecule inhibitors targeting USP30 are currently in development, but little is known about their precise nature of binding to the protein. We have integrated biochemical and structural approaches to gain novel mechanistic insights into USP30 inhibition by a small-molecule benzosulfonamide containing compound,39. Activity-based protein profiling (ABPP) mass spectrometry confirmed target engagement, the high selectivity, and potency of39for USP30 against 49 other deubiquitylating enzymes in a neuroblastoma cell line.In vitrocharacterization of39enzyme kinetics infers slow and tight binding behavior, which is comparable with features of covalent modification of USP30. Finally, we blended hydrogen-deuterium exchange mass spectrometry and computational docking to elucidate the molecular architecture and geometry of USP30 complex formation with39, identifying structural rearrangements at the cleft of the USP30 thumb and palm subdomains. These studies suggest that39binds to the thumb-palm cleft that guides the ubiquitin C-terminus into the active site, thereby preventing ubiquitin binding and isopeptide bond cleavage, and confirming its importance in the inhibitory process. Our data will pave the way for the design and development of next-generation inhibitors targeting USP30 and associated deubiquitinylases.