bluuebunny/crossref_metadata_2025 huggingface dataset:
Chopping techniques in cataract surgery
Authors: Lee Bryan S. , Chang David F.
Published: December 2022

Purpose of review

To explain reasons for phaco chop, outline strategies for transitioning to chop, and summarize recent articles discussing chopping techniques.

Recent findings

New variations of phaco chop may help with managing dense cataracts. Studies generally continue to show similar phaco time between traditional manual chopping and femtosecond laser-assisted cataract surgery. A nitinol ring prechopper compresses the lens similarly to horizontal chopping, which may reduce phaco energy for certain cases.

Both vertical and horizontal chopping continue to demonstrate multiple advantages over other nucleus disassembly techniques.
Dilation devices in cataract surgery
Authors: Sarnicola Enrica , Sarnicola Caterina , Sarnicola Vincenzo
Published: December 2022

Purpose of review

Cataract surgery in the setting of small pupil represent a major challenge and it is associated with a higher risk of complications. When pharmacologic pupil dilation fails, mechanical pupil expansion devices are needed to obtain and maintain sufficient intraoperative mydriasis. The purpose of this review is to assess the pupil expansion devices currently available.

Recent findings

A variety of pupil expansion devices are offered on the market. They differ for design, material, shape, size, cost, and easiness of insertion/removal, nonetheless they all seem to be effective in improving the pupil size and easing the cataract surgery.

Mechanical pupil expansion can be effectively achieved with a variety of devices, which are well tolerated and can facilitate cataract surgery in the setting of poor mydriasis.
Sequential intravesical gemcitabine and docetaxel therapy in patients with nonmuscle invasive bladder cancer: a systematic review and meta-analysis
Authors: Kawada Tatsushi , Yanagisawa Takafumi , Araki Motoo , Pradere Benjamin , Shariat Shahrokh F.
Published: December 2022

Purpose of review

Shortages in intravesical Bacillus Calmette-Guérin (BCG) immunotherapy represent a challenge in the management of high-risk nonmuscle invasive bladder cancer (HR-NMIBC). This study aimed to review the efficacy and safety of intravesical gemcitabine (GEM) and docetaxel (DOCE) for BCG-naive and unresponsive HR-NMIBC.

Recent findings

We identified six studies eligible for quantitative analysis through a systematic search according to the Preferred Reporting Items for Systematic Review and Meta-analyses (PRISMA) statement. In the two studies in the BCG-naive setting, 1-year and 2-year pooled recurrence-free survival (RFS) were 86 and 84%, respectively. In the two studies in the BCG unresponsive setting, 6-month, 1-year and 2-year pooled high-grade recurrence-free survival (HG-RFS) were 80, 66 and 51%, respectively. Cumulative data from four studies revealed that 2.3% of patients could not complete induction therapy and 6.9% experienced treatment delay or dose reduction due to adverse events.

Despite the preliminary data and based on a small sample size, intravesical GEM/DOCE therapy is a highly promising combination yielding an effective and well tolerated alternative to BCG when indicated. Further large, well designed comparative studies with BCG are needed.
Prevention and Management of Chronic Postsurgical Pain and Persistent Opioid Use Following Solid Organ Transplantation: Experiences From the Toronto General Hospital Transitional Pain Service
Authors: Yu Hai Chuan , Kleiman Valery , Kojic Katarina , Slepian P. Maxwell , Cortes Henry , McRae Karen , Katznelson Rita , Huang Alex , Tamir Diana , Fiorellino Joseph , Ganty Praveen , Cote Nathalie , Kahn Michael , Mucsi Istvan , Selzner Nazia , Rozenberg Dmitry , Chaparro Cecilia , Rao Vivek , Cypel Marcelo , Ghanekar Anand , Kona Sharath , McCluskey Stuart , Ladak Salima , Santa Mina Daniel , Karkouti Keyvan , Katz Joel , Clarke Hance
Published: December 2022

Background.

With >700 transplant surgeries performed each year, Toronto General Hospital (TGH) is currently one of the largest adult transplant centers in North America. There is a lack of literature regarding both the identification and management of chronic postsurgical pain (CPSP) after organ transplantation. Since 2014, the TGH Transitional Pain Service (TPS) has helped manage patients who developed CPSP after solid organ transplantation (SOT), including heart, lung, liver, and renal transplants.

Methods.

In this retrospective cohort study, we describe the association between opioid consumption, psychological characteristics of pain, and demographic characteristics of 140 SOT patients who participated in the multidisciplinary treatment at the TGH TPS, incorporating psychology and physiotherapy as key parts of our multimodal pain management regimen.

Results.

Treatment by the multidisciplinary TPS team was associated with significant improvement in pain severity and a reduction in opioid consumption.

Conclusions.

Given the risk of CPSP after SOT, robust follow-up and management by a multidisciplinary team should be considered to prevent CPSP, help guide opioid weaning, and provide psychological support to these patients to improve their recovery trajectory and quality of life postoperatively.
The Vibrio vulnificus stressosome is dispensable in nutrient-replete conditions.
Authors: Cutugno Laura , Mc Cafferty Jennifer , Pané-Farré Jan , O'Byrne Conor , Boyd Aoife
Published: December 2022

The stressosome is a protein complex that has been demonstrated to sense environmental stresses and mediate the stress response in several Gram-positive bacteria, through the activation of the alternative sigma factor SigB. The in vivo characterisation of this complex has never been performed in Vibrio vulnificus or any other bacteria that do not possess SigB. The elucidation of the role of the stressosome in V. vulnificus would provide elements to elaborate a functional model of the complex in a Gram-negative bacterium and identify the regulatory output in the absence of SigB. The stressosome locus is only found in 44% of Vibrio vulnificus isolates raising the question as to whether the role of stressosome is essential or modulatory in this bacterial species. In this work, the expression of the stressosome genes was proven in nutrient-replete conditions and the co-transcription as one operonic unit of the stressosome locus and its putative downstream regulatory locus was demonstrated. Moreover, the construction of a stressosome mutant lacking the four genes constituting the stressosome complex allowed us to examine the role of this complex in vivo. The initial established mutagenesis strategy relied on rifampicin-resistant V. vulnificus to select recombinant bacteria. Our data clearly showed that the influence of the RifR allele on stress and virulence characteristics overshadowed any effects of the stressosome. Therefore, we established an alternative mutagenesis strategy with a non-modified V. vulnificus parental strain and a DAP auxotrophic E. coli donor strain. Extensive phenotypic characterisation of the successfully-generated mutant in nutrient-replete conditions showed that the stressosome does not significantly contribute to the growth, of V. vulnificus. The stressosome did not modulate the response of V. vulnificus to the range of stresses tested: Ethanol, osmolarity, temperature, and salinity. Furthermore, the stressosome is dispensable for motility and exoenzyme production of V. vulnificus.
Effect of BNT162b2 antigen dosage on protection against SARS-CoV-2 omicron infection
Authors: Chemaitelly Hiam , Ayoub Houssein H. , Coyle Peter , Tang Patrick , Yassine Hadi M. , Al Thani Asmaa A. , Al-Khatib Hebah A. , Hasan Mohammad R. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Al-Romaihi Hamad Eid , Butt Adeel A. , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J.
Published: December 2022

Background

Coronavirus Disease 2019 (COVID-19) vaccine antigen dosage may affect protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but direct evidence to quantify this effect is lacking.

Methods

A matched, retrospective, cohort study that emulated a randomized control trial was conducted in Qatar between February 3, 2022 and November 8, 2022, to provide a head-to-head, controlled comparison of protection induced by two antigen dosages of the BNT162b2 vaccine. The study compared incidence of omicron infection in the national cohort of adolescents 12 years of age who received the two-dose primary-series of the 30-µg BNT162b2 vaccine to that in the national cohort of adolescents 11 years of age who received the two-dose primary-series of the pediatric 10-µg BNT162b2 vaccine. Associations were estimated using Cox proportional-hazard regression models.

Results

Among adolescents with no record of prior infection, cumulative incidence of infection was 6.0% (95% CI: 4.9-7.3%) for the 30-µg cohort and 7.2% (95% CI: 6.1-8.5%) for the 10-µg cohort, 210 days after the start of follow-up. Incidence during follow-up was dominated by omicron subvariants including, consecutively, BA.1/BA.2, BA.4/BA.5, BA.2.75*, and XBB. The adjusted hazard ratio comparing incidence of infection in the 30-µg cohort to the 10-µg cohort was 0.77 (95% CI: 0.60-0.98). Corresponding relative effectiveness was 23.4% (95% CI: 1.6-40.4%). Relative effectiveness was -3.3% (95% CI: -68.0-27.5%) among adolescents with a record of prior infection.

Conclusions

Three-fold higher BNT162b2 dosage was associated with ∼25% higher protection against infection in infection-naïve adolescents of similar age. These findings may inform design of future COVID-19 vaccines and boosters for persons of different age groups.
Bridging Theory and Experiments of Priority Effects
Authors: Zou Heng-Xing , Rudolf Volker H. W.
Published: December 2022

Priority effects play a key role in structuring natural communities, but considerable confusion remains about how they affect different ecological systems. Synthesizing previous studies, we show that this confusion arises because the mechanisms driving priority and the temporal scale at which they operate differ among studies, leading to divergent outcomes in species interactions and biodiversity patterns. We suggest grouping priority effects into two functional categories based on their mechanisms: “frequency-dependent” priority effects that arise from positive frequency dependence, and “trait-dependent” priority effects that arise from time-dependent changes in interacting traits. Through easy quantification of these categories from experiments, we can construct community models representing diverse biological mechanisms and interactions with priority effects, therefore better predicting their consequences across ecosystems.
The Hereditary and Epigenetic Fusion Gene Signatures of Multiple Myeloma
Authors: Fei Ling , Zhuo Noah , Zhuo Degen
Published: December 2022

Fusion transcripts are thought to be somatic and associated with cancer. However, they have been observed in healthy tissues at high recurrent frequencies. We have used SCIF (SplicingCodesIdentifyFusion Transcripts) to analyze RNA-Seq data from 727 multiple myeloma (MM) patients of the MMRF CoMMpass Study.MTG1-SCART1, SCART1-CYP2E1, andTPM4-KLF2have been detected in 96.1%, 95.7%, and 92.2% of 727 MM patients and formed fusion gene signatures.MTG1-SCART1andSCART1-CYP2E1are read-through from the same locus and the two most recurrent epigenetic fusion genes (EFGs) out of 187 EFGs detected in ≥10% of 727 MM patients.TPM4-KLF2fusion gene, which was initially thought to be somatic, has been shown by a monozygotic twin genetic model to be a hereditary fusion gene (HFG) and the dominant genetic factor associated with MM. This work provides the first line of evidence that HFGs are the genetic factors and EFGs reflect the consequences between genetics and environments during development.
Stress Combinations and their Interactions in Plants Database (SCIPDb): A one-stop resource for understanding combined stress responses in plants
Authors: Priya Piyush , Patil Mahesh , Pandey Prachi , Singh Anupriya , Babu Vishnu Sudha , Senthil-Kumar Muthappa
Published: December 2022

We have developedStressCombinations and theirInteractions inPlantsDatabase (SCIPDb;http://www.nipgr.ac.in/scipdb.php), a compendium and interactive platform offering information on both morpho-physio-biochemical (phenome) and molecular (transcriptome) responses of plants to different combinations of stresses. To delineate the effects of various stress combinations/categories on yield in major agricultural crops, global phenome data from 939 studies was analyzed and results showed that yield was affected to the greatest extent under the abiotic–abiotic stress category, followed by the biotic–biotic and abiotic–biotic stress categories. In the abiotic–abiotic stress category, drought–heat, heat–salinity, and ozone–UV are the major stress combinations causing high yield loss in barley, wheat, soybean, and quinoa crops. In the abiotic–biotic stress category, the salinity–weed stress combination causes highest yield loss in rice crop. In the biotic–biotic stress category, the nematode–fungus combination was most detrimental, causing considerable yield losses in potato, groundnut, and sugar beet crops. Transcriptome datasets from 36 studies hosted in SCIPDb identified novel genes. Thus far, these genes have not been known to play a role in combined stress. Integretome analysis under combined drought–heat stress pinpointed carbohydrate, amino acid, and energy metabolism pathways as the crucial metabolic, proteomic, and transcriptional components in plant tolerance to combined stress. These examples illustrate the application of SCIPDb in identifying novel genes and pathways involved in combined stress tolerance. Further, we showed the application of this database in identifying novel candidate genes and pathways for combined drought and pathogen stress tolerance in Arabidopsis and chickpea. To our knowledge, SCIPDb is the only publicly available platform that provides extensive information and paves the way for advancing mechanistic understanding of plant responses to combined stresses.
Recessive pathogenic variants inMCATcause combined oxidative phosphorylation deficiency
Authors: Webb Bryn D. , Nowinski Sara M. , Solmonson Ashley , Ganesh Jaya , Rodenburg Richard J. , Leandro João , Evans Anthony , Vu Hieu S. , Naidich Thomas P. , Gelb Bruce D. , DeBerardinis Ralph J. , Rutter Jared , Houten Sander M.
Published: December 2022

Malonyl-CoA-acyl carrier protein transacylase (MCAT) is an enzyme involved in mitochondrial fatty acid synthesis (mtFAS) and catalyzes the transfer of the malonyl moiety of malonyl-CoA to the mitochondrial acyl carrier protein (ACP). Previously, we showed that loss-of-function of mtFAS genes, includingMcat, is associated with severe loss of electron transport chain (ETC) complexes in mouse immortalized skeletal myoblasts (Nowinski et al., 2020). Here, we report a proband presenting with hypotonia, failure to thrive, nystagmus, and abnormal brain MRI findings. Using whole exome sequencing, we identified biallelic variants inMCAT. Protein levels for NDUFB8 and COXII, subunits of complex I and IV respectively, were markedly reduced in lymphoblasts and fibroblasts, as well as SDHB for complex II in fibroblasts. ETC enzyme activities were decreased in parallel. Reexpression of wild-typeMCATrescued the phenotype in patient fibroblasts. This is the first report of a patient withMCATpathogenic variants and combined oxidative phosphorylation deficiency.
MembraneFold: Visualising transmembrane protein structure and topology
Authors: Gutierrez Santiago , Tyczynski Wojciech G. , Boomsma Wouter , Teufel Felix , Winther Ole
Published: December 2022

Background

AlphaFold’s accuracy, which is often comparable to that of experimentally determined structures, has revolutionized protein structure research. Being a statistical method, AlphaFold implicitly infers the cellular environment, e.g. the cell membrane, from the protein sequence. Membrane protein topology prediction methods predict the cellular environment for each protein residue but not the structure. Current structure and topology tools thus provide complementary information.

Results

We introduce the web server MembraneFold. MembraneFold combines protein structure (from an uploaded PDB file/AlphaFold DB/OmegaFold) and topology (DeepTMHMM) prediction in one server. The output is shown both as a structure with topology superimposed and as a sequence annotation. MembraneFold uses structures predicted by OmegaFold if neither a PDB file is uploaded nor the structure is available in AlphaFold DB.

Conclusion

MembraneFold is a user-friendly web server that provides practitioners with fast and accurate information about membrane proteins. It is available athttps://ku.biolib.com/MembraneFold/.
Discovering Haematoma-Stimulated Circuits for Secondary Brain Injury after Intraventricular Haemorrhage by Spatial Transcriptome Analysis
Authors: Zhang Le , Badai Jiayidaer , Wang Guan , Ru Xufang , Song Wenkai , You Yujie , He Jiaojiao , Huang Suna , Feng Hua , Chen Runsheng , Zhao Yi , Chen Yujie
Published: December 2022

Central nervous system (CNS) diseases, such as neurodegenerative disorders and brain diseases caused by acute injuries, are important yet challenging to study due to disease leisions’ locations and other complexities. Utilizing the powerful spatial transcriptome analysis together with novel algorithms we developed for the study, we report here for the first time a 3D trajectory map of gene expression changes in the brain following acute neural injury using a mouse model of intraventricular haemorrhage (IVH). IVH is a common and representative complication after various acute brain injuries with severe mortality and mobility implications. Our data identified three main 3D global pseudospace-time trajectory bundles which represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex induced by experimental intraventricular haematoma stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH. These results are informative in understanding the pathophysiological changes, including the spatial and temporal patterns of gene expression changes, in IVH patients after acute brain injuries and strategizing more effective clinical management regimens. The bioinformatics strategies will also be useful for the study of other CNS diseases.
Prospecting for zoonotic pathogens using targeted DNA enrichment
Authors: Enabulele Egie E. , Le Clec’h Winka , Roberts Emma K. , Thompson Cody W. , McDonough Molly M. , Ferguson Adam W. , Bradley Robert D. , Anderson Timothy J. C. , Platt Roy N.
Published: December 2022

There are over 60 zoonoses linked to small mammals, including some of the most devastating pathogens in human history. Meanwhile, millions of museum-archived tissues are available to understand natural history of these pathogens. Our goal is to maximize the value of museum collections for pathogen-based research using targeted sequence capture. To this end, we have generated a probe panel that includes 39,916, 80bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Lab generated, mock control samples show that we are capable of enriching targeted loci from pathogen DNA 2,882 to 6,746-fold. Further, we were able to identify bacterial species in museum-archived samples, includingBartonella, a known human zoonosis. These results show that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.
Multiscale Mechanical Characterization and Computational Modeling of Fibrin Gels
Authors: Jimenez Julian M. , Tuttle Tyler , Guo Yifan , Miles Dalton , Buganza-Tepole Adrian , Calve Sarah
Published: December 2022

Fibrin is a naturally occurring protein network that forms a temporary structure to enable remodeling during wound healing. It is also a common tissue engineering scaffold because the structural properties can be controlled. However, to fully characterize the wound healing process and improve the design of regenerative scaffolds, understanding fibrin mechanics at multiple scales is necessary. Here, we present a strategy to quantify both the macroscale (1 – 10 mm) stress-strain response and the deformation of the mesoscale (10 – 1000 μm) network structure during unidirectional tensile tests. The experimental data is then used to inform a computational model to accurately capture the mechanical response of fibrin gels. Simultaneous mechanical testing and confocal microscopy imaging of fluorophore-conjugated fibrin gels revealed up to an 88% decrease in volume coupled with increase in volume fraction in deformed gels, and non-affine fiber alignment in the direction of deformation. Combination of the computational model with finite element analysis enabled us to predict the strain fields that were observed experimentally within heterogenous fibrin gels with spatial variations in material properties. These strategies can be expanded to characterize and predict the macroscale mechanics and mesoscale network organization of other heterogeneous biological tissues and matrices.

Statement of Significance

Fibrin is a naturally-occurring scaffold that supports cellular growth and assembly ofde novotissue and has tunable material properties. Characterization of meso- and macro-scale mechanics of fibrin gel networks can advance understanding of the wound healing process and impact future tissue engineering approaches. Using structural and mechanical characteristics of fibrin gels, a theoretical and computational model that can predict multiscale fibrin network mechanics was developed. These data and model can be used to design gels with tunable properties.
Rapid, high-throughput phenotypic profiling of endosymbiotic dinoflagellates (Symbiodiniaceae) using benchtop flow cytometry
Authors: Anthony Colin J. , Lock Colin , Bentlage Bastian
Published: December 2022

Endosymbiotic dinoflagellates (Family Symbiodiniaceae) are the primary producer of energy for many cnidarians, including corals. The intricate coral-dinoflagellate symbiotic relationship is becoming increasingly important under climate change, as its breakdown leads to mass coral bleaching and often mortality. Despite methodological progress, assessing the phenotypic traits of Symbiodiniaceaein-hospiteremains a complex task. Bio-optics, biochemistry, or “-omics” techniques are expensive, often inaccessible to investigators, or lack the resolution required to understand single-cell phenotypic states within endosymbiotic dinoflagellate assemblages. To help address this issue, we developed a protocol that collects information on cell autofluorescence, shape, and size to simultaneously generate phenotypic profiles for thousands of Symbiodiniaceae cells, thus revealing phenotypic variance of the Symbiodiniaceae assemblage to the resolution of single cells. As flow cytometry is adopted as a robust and efficient method for cell counting, integration of our protocol into existing workflows allows researchers to acquire a new level of resolution for studies examining the acclimation and adaptation strategies of Symbiodiniaceae assemblages.
The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation
Authors: Yu Ji-Gao , Tang Jun-Yong , Wei Ran , Lan Mei-Fang , Xiang Rui-Chen , Xiang Qiao-Ping , Zhang Xian-Chun
Published: December 2022

Lycophytes and euphyllophytes (ferns and seed plants) are the two surviving lineages of vascular plants. The modern lycophytes (clubmosses) are herbaceous found either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). The contrasting genome size between homosporous and heterosporous plants has long been an attractive topic. Most clubmosses are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimer’s disease, but the evolutionary trajectory of which in land plants is unexplored. To better understand these fundamental questions, the genome data of a homosporous lycophyte is urgently required. We generated theLycopodium clavatumL. genome by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is LTR. Two whole genome duplications (WGDs) are rigorously detected. The content of LTR-RTs was more than ten times higher in homosporous lycophytes than heterosporous ones, although most appeared within one Mya. Then, we find that the LTR-RTs’ birth-death mode (a much greater birth and extremely slower death) contributes the accumulation of LTR-RTs resulting homosporous lycophyte genome expansion, while in heterosporous lycophytes, the mode is exactly the opposite. Furthermore, the five necessary enzymes of the HupA biosynthetic pathway were identified in theL. clavatumgenome, but absent in the other land plants. This decoded genome data will be a key cornerstone to elucidating the fundamental aspects of lycophyte biology and land plant evolution.
Stratified tissue biofabrication by rotational internal flow layer engineering
Authors: Holland Ian , Shu Wenmiao , Davies Jamie A.
Published: December 2022

The bioassembly of layered tissue that closely mimics human histology presents challenges for tissue engineering. Existing bioprinting technologies lack the resolution and cell densities necessary to form the microscale cell-width layers commonly observed in stratified tissue, particularly when using low-viscosity hydrogels, such as collagen. Here we present rotational internal flow layer engineering (RIFLE), a novel biofabrication technology for assembling tuneable, multi-layered tissue-like structures. Using high-speed rotating tubular moulds, small volumes of cell-laden liquids added to the inner surface were transitioned into thin layers and gelled, progressively building macroscale tubes composed of discrete microscale strata with thicknesses a function of rotational speed. Cell encapsulation enabled the patterning of high-density layers (108cells/ml) into heterogenous constructs. RIFLE versatility was demonstrated through tunica media assembly, encapsulating human smooth muscle cells in cell-width (12.5μm) collagen layers. This enabling technology has the potential to allow researchers to economically create a range of representative stratified tissue.
Competitive, connective and allosteric Nanobodies that modulate the SOS1•RAS protein-protein interactions and tune the nucleotide exchange rate as a starting point for drug design
Authors: Fischer Baptiste , Uchański Tomasz , Sheryazdanova Aidana , Gonzalez Simon , Volkov Alexander N. , Brosens Elke , Zögg Thomas , Kalichuk Valentina , Ballet Steven , Versées Wim , Sablina Anna A. , Pardon Els , Wohlkönig Alexandre , Steyaert Jan
Published: December 2022

Protein-protein interactions (PPIs) are central in cell metabolism but research tools for the structural and functional characterization of these PPIs are often missing. Here we introduce novel and broadly applicable immunization (Cross-link PPIs andimmunizellamas, ChILL) and selection strategies (Display andco-selection, DisCO) for the discovery of diverse Nanobodies that either stabilize or disrupt PPIs in a single experiment. We applied ChILL and DisCO to identify competitive, connective or fully allosteric Nanobodies that inhibit or facilitate the formation of the SOS1•RAS complex and modulate the nucleotide exchange rate on this pivotal GTPasein vitroand RAS signallingin cellulo. One of these connective Nanobodies fills a cavity that was previously identified as the binding pocket for a series of therapeutic lead compounds. The long complementarity-determining region (CDR3) that penetrates this binding pocket serves as an innovative pharmacophore for extending the repertoire of potential leads.
Learning the differences: a transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity
Authors: Bravi Barbara , Di Gioacchino Andrea , Fernandez-de-Cossio-Diaz Jorge , Walczak Aleksandra M. , Mora Thierry , Cocco Simona , Monasson Rémi
Published: December 2022

Antigen immunogenicity and the specificity of binding of T-cell receptors to antigens are key properties underlying effective immune responses. Here we propose diffRBM, an approach based on transfer learning and Restricted Boltzmann Machines, to build sequence-based predictive models of these properties. DiffRBM is designed to learn the distinctive patterns in amino acid composition that, one the one hand, underlie the antigen’s probability of triggering a response, and on the other hand the T-cell receptor’s ability to bind to a given antigen. We show that the patterns learnt by diffRBM allow us to predict putative contact sites of the antigen-receptor complex. We also discriminate immunogenic and non-immunogenic antigens, antigen-specific and generic receptors, reaching performances that compare favorably to existing sequence-based predictors of antigen immunogenicity and T-cell receptor specificity. More broadly, diffRBM provides a general framework to detect, interpret and leverage selected features in biological data.
First biodegradable bioactive glass-based humidity sensor
Authors: Gharbi Amina , Kallel Ahmed Yahia , Kanoun Olfa , Cheikhrouhou-Koubaa Wissem , Contag Christopher H. , Antoniac Iulian , Derbel Nabil , Ashammakhi Nureddin
Published: December 2022

Monitoring changes in edema-associated intracranial pressure that complicates trauma or surgery would lead to improved outcomes. Implantable pressure sensors have been explored, but, these sensors require post-surgical removal leading to risks of injury to brain tissue. Biodegradable implantable sensors would eliminate the risks while providing sensing when needed. Here, we demonstrate a bioactive glass (BaG)-based hydration sensor. A fluorine (CaF2) containing BaG (BaG-F) was produced using a melting manufacturing technique. The structure and electrical properties of the resulting constructs were evaluated to understand the electrical behaviors of this BaG-based sensor. The synthetic process of producing the BaG-F-based sensor was validated by assessing the electrical properties. We demonstrated that this BaG-F chemical composition is highly sensitive to hydration, and that electrical activity (resistive-capacitive) is induced by hydration and reversed by dehydration. These properties make BaG-F suitable for use as a humidity sensor to monitor brain edema and consequently provide an alert for increasing intracranial pressure.
Matrix Gla Protein acts as a driver of stemness and tumor initiation in ovarian cancer
Authors: Nieddu V. , Melocchi V. , Battistini C. , Franciosa G. , Lupia M. , Stellato C. , Bertalot G. , Olsen J.V. , Colombo N. , Bianchi F. , Cavallaro U.
Published: December 2022

Ovarian cancer (OC) displays the highest mortality among gynecological tumors, mainly due to early peritoneal dissemination, the high frequency of tumor relapse following primary debulking and the development of chemoresistance. All these events are thought to be initiated and sustained by a subpopulation of neoplastic cells, termed ovarian cancer stem cells (OCSC), that are endowed with self-renewing and tumor-initiating properties. This implies that interfering with OCSC function should offer novel therapeutic perspectives to defeat OC progression. To this aim, a better understanding of the molecular and functional makeup of OCSC in clinically relevant model systems is essential.

We have profiled the transcriptome of OCSC vs. their bulk cell counterpart from a panel of patient-derived OC cell cultures. This revealed that Matrix Gla Protein (MGP), classically known as a calcification-preventing factor in cartilage and blood vessels, is markedly enriched in OCSC. Functional assays showed that MGP confers several stemness-associated traits to OC cells, including a transcriptional reprogramming. Patient-derived organotypic cultures pointed to the peritoneal microenvironment as a major inducer of MGP expression in OC cells. Furthermore, MGP was found to be necessary and sufficient for tumor initiation in OC mouse models, by shortening tumor latency and increasing dramatically the frequency of tumor-initiating cells. Mechanistically, MGP-driven OC stemness was mediated by the stimulation of Hedgehog signaling, in particular through the induction of the Hedgehog effector GLI1, thus highlighting a novel MGP/Hedgehog pathway axis in OCSC. Finally, MGP expression was found to correlate with poor prognosis in OC patients, and was increased in tumor tissue after chemotherapy, supporting the clinical relevance of our findings.

Thus, MGP is a novel driver in OCSC pathophysiology, with a major role in stemness and in tumor initiation.
Exploring the intricacies and pitfalls of the ATN framework: An assessment across cohorts and thresholding methodologies
Authors: Salimi Yasamin , Domingo-Fernández Daniel , Hofmann-Apitius Martin , Birkenbihl Colin ,   the Alzheimer’s Disease Neuroimaging Initiative,   the Japanese Alzheimer’s Disease Neuroimaging Initiative,   the Alzheimer’s Disease Repository Without Borders Investigators,   the European Prevention of Alzheimer’s Disease (EPAD) Consortium
Published: December 2022

The amyloid/tau/neurodegeneration (ATN) framework has redefined Alzheimer’s disease (AD) toward a primarily biological entity. While it has found wide application in AD research, it was so far typically applied to single cohort studies using distinct data-driven thresholding methods. This poses the question of how concordant thresholds obtained using distinct methods are within the same dataset as well as whether thresholds derived by the same technique are interchangeable across cohorts. Given potential differences in cohort data-derived thresholds, it remains unclear whether individuals of one cohort are actually comparable with regard to their exhibited disease patterns to individuals of another cohort, even when they are assigned to the same ATN profile. If such comparability is not evident, the generalizability of results obtained using the ATN framework is at question. In this work, we evaluated the impact of selecting specific thresholding methods on ATN profiles by applying five commonly-used methodologies across eleven AD cohort studies. Our findings revealed high variability among the obtained thresholds, both across methods and datasets, linking the choice of thresholding method directly to the type I and type II error rate of ATN profiling. Moreover, we assessed the generalizability of primarily Magnetic Resonance Imaging (MRI) derived biological patterns discovered within ATN profiles by simultaneously clustering participants of different cohorts who were assigned to the same ATN profile. In only two out of seven investigated ATN profiles, we observed a significant association between individuals’ assigned clusters and cohort origin for thresholds defined using Gaussian Mixture Models, while no significant associations were found for K-means-derived thresholds. Consequently, in the majority of profiles, biological signals governed the clustering rather than systematic cohort differences resulting from distinct biomarker thresholds. Our work revealed that: 1) the thresholding method selection is a decision of statistical relevance that will inevitably bias the resulting profiling, 2) obtained thresholds are most likely not directly interchangeably across two independent cohorts, and 3) MRI-based biological patterns derived from distinctly thresholded ATN profiles can generalize across cohort datasets. Conclusively, in order to appropriately apply the ATN framework as an actionable and robust biological profiling scheme, a comprehensive understanding of the impact of used thresholding methods, their statistical implications, and the validation of achieved results is crucial.
DRAGin situbarcoding reveals an increased number of HSPCs contributing to myelopoiesis with age
Authors: Urbanus Jos , Cosgrove Jason , Beltman Joost , Elhanati Yuval , de Andrade Moral Rafael , Conrad Cecile , van Heijst Jeroen W , Tubeuf Emilie , Velds Arno , Kok Lianne , Merle Candice , Magnusson Jens P , Frisén Jonas , Fre Silvia , Walczak Aleksandra M , Mora Thierry , Jacobs Heinz , Schumacher Ton N. , Perié Leïla
Published: December 2022

Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their regenerative capacity. However, HSPC function has been mostly assessed using transplantation assays, and it remains unclear how HSPCs age in the native bone marrow niche. To address this issue, we developed a novel in situ single cell lineage tracing technology to quantify the clonal composition and cell production of single cells in their native niche. Our results demonstrate that a pool of HSPCs with unequal output maintains myelopoiesis through overlapping waves of cell production throughout adult life. During ageing, the increased frequency of myeloid cells is explained by greater numbers of HSPCs contributing to myelopoiesis, rather than increased myeloid output of individual HSPCs. Strikingly, the myeloid output of HSPCs remained constant over time despite accumulating significant transcriptomic changes throughout adulthood. Together, these results show that, unlike emergency myelopoiesis post-transplantation, aged HSPCs in their native microenvironment do not functionally decline in their regenerative capacity.
PDX3 is important for carbon/nitrogen balance in Arabidopsis associated with distinct environmental conditions
Authors: Steensma Priscille , Eisenhut Marion , Colinas Maite , Rosado-Souza Laise , Fernie Alisdair R. , Weber Andreas P. M. , Fitzpatrick Teresa B.
Published: December 2022

To survive and proliferate in diverse environments with varying climate and nutrient availability, plants modulate their metabolism. Achieving a balance between carbon (C) and nitrogen (N) use such that growth and defense mechanisms can be appropriately controlled is critical for plant fitness. The identification of factors that regulate C/N utilization in plants can make a significant contribution to optimization of plant health. Here we show that pyridox(am)ine 5’-phosphate oxidase (PDX3), which regulates vitamin B6homeostasis, influences C/N balance. The B6vitamer imbalance resulting from loss of PDX3 leads to over-accumulation of nitrogenous compounds. A combination of increased glutamate dehydrogenase activity, impairment in the photorespiratory cycle and inappropriate use of endogenous ammonium fuel the metabolic imbalance. Growth at elevated CO2levels further exacerbates thepdx3phenotypes. Interestingly, serine supplementation rescues growth under high CO2likely bypassing the phosphorylated pathway of biosynthesis suggesting that this amino acid is an important commodity. We show that PDX3 function appears dispensable upon thermomorphogenesis, a condition that favors C metabolism. Furthermore, while a low ammonium to nitrate ratio likely accounts for overstimulation of salicylic acid (SA) defense responses inpdx3lines that compromises growth, a basal level of SA protects against loss of PDX3 biochemical function. Overall, the study highlights environmental scenarios where vitamin B6homeostasis, as managed by the salvage pathway enzyme PDX3, is critical and provides insight into how plants reprogram their metabolism under such conditions.
Coupled carbon and nitrogen cycling regulates the cnidarian-algal symbiosis
Authors: Rädecker Nils , Escrig Stéphane , Spangenberg Jorge E. , Voolstra Christian R. , Meibom Anders
Published: December 2022

Efficient nutrient recycling underpins the ecological success of the cnidarian-algal symbiosis in oligotrophic waters. In a stable symbiosis, nitrogen limitation restricts the growth of algal endosymbionts and stimulates their release of photosynthates to the cnidarian animal host. However, the detailed mechanisms controlling nitrogen availabilityin hospiteand their role in symbiosis regulation remain poorly understood. Here, we studied the metabolic regulation of symbiotic nitrogen cycling in the sea anemone Aiptasia by experimentally altering labile carbon availability in a series of experiments. Combining13C and15N stable isotope labeling experiments with physiological analyses and NanoSIMS imaging, we show that the competition for environmental ammonium between the host and its algal symbionts is regulated by labile carbon availability. Light regimes optimal for algal photosynthesis increased carbon availability in the holobiont and stimulated nitrogen assimilation in the host metabolism. Consequently, algal symbiont densities were lowest under optimal environmental conditions and increased toward the symbiosis’s lower and upper light tolerance limits. This metabolic regulation promotes efficient carbon recycling in a stable symbiosis across a wide range of environmental conditions. At the same time, the dependence on resource competition may favor parasitic interactions explaining the instability of the symbiosis as the environmental conditions in the Anthropocene shift towards its tolerance limits.
No supergene despite social polymorphism in the big-headed antPheidole pallidula
Authors: Favreau Emeline , Lebas Claude , Stolle Eckart , Priyam Anurag , Pracana Rodrigo , Aron Serge , Wurm Yannick
Published: December 2022

Ant colonies ancestrally contained one queen and her non-reproductive workers. This is also the case for many but not all colonies of the Mediterranean big-headed antPheidole pallidula. Indeed, this species also has a derived form of social organization with multiple reproductive queens in the colony. The co-existence of two social forms also independently evolved in three other lineages of ants. In each of those lineages, variants of a supergene region of suppressed recombination determine social form. This is likely because supergene regions can link advantageous combinations of alleles from multiple loci. We thus hypothesized that a supergene region also determines colony queen number in the big-headed ant. To test this, we performed extensive population genetic analyses and genomic comparisons. We find no evidence of a supergene-like region with differentiation between single- and multiple-queen colonies. Our results show that a complex social polymorphism can evolve and be maintained without supergenes.
Improvement of protein tertiary and quaternary structure predictions using the ReFOLD4 refinement method and the AlphaFold2 recycling process
Authors: Adiyaman Recep , Edmunds Nicholas S. , Genc Ahmet G. , Alharbi Shuaa M. A. , McGuffin Liam J.
Published: December 2022

Motivation

The accuracy gap between predicted and experimental structures has been significantly reduced following the development of AlphaFold2. However, for further studies, such as drug discovery and protein design, AlphaFold2 structures need to be representative of proteins in solution, yet AlphaFold2 was trained to generate only a few structural conformations rather than a conformational landscape. In previous CASP experiments, MD simulation-based methods have been widely used to improve the accuracy of single 3D models. However, these methods are highly computationally intensive and less applicable for practical use in large-scale applications. Despite this, the refinement concept can still provide a better understanding of conformational dynamics and improve the quality of 3D models at a modest computational cost. Here, our ReFOLD4 pipeline was adopted to provide the conformational landscape of AlphaFold2 predictions while maintaining high model accuracy. In addition, the AlphaFold2 recycling process was utilised to improve 3D models by using them as custom template inputs for tertiary and quaternary structure predictions.

Results

According to the Molprobity score, 94% of the generated 3D models by ReFOLD4 were improved. As measured by average change in lDDT, AlphaFold2 recycling showed an improvement rate of 87.5% (using MSAs) and 81.25% (using single sequences) for monomeric AF2 models and 100% (MSA) and 97.8% (single sequence) for monomeric non-AF2 models. By the same measure, the recycling of multimeric models showed an improvement rate of as much as 80% for AF2 models and 94% for non-AF2 models. The AlphaFold2 recycling processes and ReFOLD4 method can be combined very efficiently to provide conformational landscapes at the AlphaFold2-accuracy level, while also significantly improving the global quality of 3D models for both tertiary and quaternary structures, with much less computational complexity than traditional refinement methods.
A bioelectrical phase transition patterns the first beats of a vertebrate heart
Authors: Jia Bill Z. , Qi Yitong , Wong-Campos J. David , Megason Sean G. , Cohen Adam E.
Published: December 2022

The heart is among the first organs to function in vertebrate development, but its transition from silent to beating has not been directly characterized. Using all-optical electrophysiology, we captured the very first zebrafish heartbeat and analyzed the development of cardiac excitability around this singular event. The first beats appeared suddenly and propagated coherently across the primordial heart. Targeted optogenetic perturbations mapped the development of excitability and conduction before and after the first heartbeats. Measured bioelectrical dynamics support a noisy saddle-node on invariant circle (SNIC) bifurcation as the critical phase transition that starts the heart. Simple models of this bifurcation quantitatively capture cardiac dynamics in space and time through early development, including coherent beating before transcriptional specification of pacemakers. Our work shows how gradual and largely asynchronous development of single-cell bioelectrical properties produces a stereotyped and robust tissue-scale transition from quiescence to coordinated beating.