bluuebunny/crossref_metadata_2025 huggingface dataset:
Proposal of a simple open-source quantitative tribometric assay and its implementation for the assessment of the effects of redox-related alterations on the lubrication capacity of a commercial water-based lubricant gel
Authors: Homolak Jan
Published: July 2022

Background

Understanding molecular and biochemical mechanisms affecting biotribological properties of tissues, biological fluids, and drugs may accelerate the invention of novel drug formulations and targets and facilitate the discovery of etiopathogenetic mechanisms. Unfortunately, biotribometric equipment is expensive and unaffordable. The first aim was to assess whether PASTA, an open-source platform based on a hacked kitchen scale, can be adapted for the analysis of biotribometric properties. The second aim was to demonstrate the use of PASTA by studying the effects of oxidation on the lubricating properties of the commercial water-based lubricant.

Methods

The PASTA platform was adapted using a custom-made tribometric adapter attached to the bottom of the hacked kitchen scale connected to a computer via the NodeMCU ESP-32S. A commercial water-based lubricant was oxidized with 2,2’-azobis(2-amidinopropane) dihydrochloride and/or protected against oxidation with glutathione. The samples were analyzed using a simple tribometric assay with the PASTA platform and the ORP-146S redox microsensor.

Results

A mastPASTA custom-made adapter enables the use of PASTA for reliable quantitative tribometric studies. Oxidation of the commercial water-based lubricant does not reduce its lubrication capacity, however, the addition of the antioxidant glutathione protects against the loss of its lubrication capacity upon exposure to air by a redox-unrelated mechanism.

Conclusion

PASTA can easily be adapted for studying tribological properties. The effects of the addition of antioxidants to water-based vaginal lubricants should be explored as a possible way to enhance durability and efficacy and increase their health benefits.
Growing DAGs: Optimization Functions for Pathway Reconstruction Algorithms
Authors: Köse Tunç Başar , Li Jiarong , Ritz Anna
Published: July 2022

A major challenge in molecular systems biology is to understand how proteins work to transmit external signals to changes in gene expression. Computationally reconstructing these signaling pathways from protein interaction networks can help understand what is missing from existing pathway databases. We formulate a new pathway reconstruction problem, one that iteratively grows directed acyclic graphs (DAGs) from a set of starting proteins in a protein interaction network. We present an algorithm that provably returns the optimal DAGs for two different cost functions and evaluate the pathway reconstructions when applied to six diverse signaling pathways from the NetPath database. The optimal DAGs outperform an existingk-shortest paths method for pathway reconstruction and the new reconstructions are enriched for different biological processes. Growing DAGs is a promising step towards reconstructing pathways that provably optimize a specific cost function.
Integrative analysis of a large real-world cohort of small cell lung cancer identifies distinct genetic subtypes and insights into histological transformation
Authors: Sivakumar Smruthy , Moore Jay A. , Montesion Meagan , Sharaf Radwa , Lin Douglas I. , Fleishmann Zoe , Ebot Ericka M. , Newberg Justin , Mills Jennifer M. , Hegde Priti S. , Frampton Garrett M. , Sage Julien , Lovly Christine M.
Published: July 2022

Small cell lung cancer (SCLC) is a recalcitrant neuroendocrine carcinoma with dismal survival outcomes. A major barrier in the field has been the relative paucity of human tumors studied. Here we provide an integrated analysis of 3,600 “real-world” SCLC cases. This large cohort allowed us to identify new recurrent alterations and new genetic subtypes, including STK11-mutant tumors (1.7%) and TP53/RB1 wild-type tumors (5.5%), of which 12.7% were human papillomavirus-positive. In our cohort, gene amplifications on 4q12 are associated with increased overall survival while CCNE1 amplification is associated with decreased overall survival. We also identify more frequent alterations in the PTEN pathway in brain metastases. Finally, profiling cases of SCLC containing oncogenic drivers typically associated with NSCLC demonstrates that SCLC transformation may occur across multiple distinct molecular cohorts of NSCLC. These novel and unsuspected genetic features of SCLC may help personalize treatment approaches for this fatal form of cancer.

STATEMENT OF SIGNIFICANCE

Minimal changes in therapy and survival outcomes have occurred in SCLC for the past four decades. The identification of new genetic subtypes, novel recurrent mutations, and an improved understanding of the mechanisms of transformation to SCLC from NSCLC may guide the development of personalized therapies for subsets of patients with SCLC.
Velocity of Conduction Between Columns and Layers in Barrel Cortex Reported by Parvalbumin Interneurons
Authors: Scheuer Kate S. , Judge John , Zhao Xinyu , Jackson Meyer B.
Published: July 2022

Inhibitory interneurons that express parvalbumin (PV) play critical roles throughout the brain. Their rapid-spiking characteristics enable them to control the dynamics of neural circuits across a range of time scales, but the timing of their activation by different cortical pathways remains unclear. Here, we use a genetically encoded hybrid voltage sensor, hVOS, to image PV interneuron voltage changes with sub-millisecond precision in primary somatosensory barrel cortex (BC) of adult male and female mice. Electrical stimulation evoked depolarizing responses with a latency that increased with distance from the stimulating electrode, allowing us to determine conduction velocity. By focusing on conduction between cortical layers or between barrel columns we were able to measure interlaminar or intralaminar conduction velocity, respectively. Velocities ranged from 74 to 473 μm/msec depending on trajectory, and we found that interlaminar conduction velocity was about 71% faster than intralaminar conduction velocity. This suggests that computations within columns can be processed more rapidly than between columns. BC circuitry integrates thalamic and intracortical input for a variety of functions including texture discrimination and sensory tuning. The difference in timing between intra- and interlaminar activation of PV interneurons could impact these functions. This study illustrates how hVOS imaging of PV interneuron electrical activity can reveal differences in the dynamics of signaling within different elements of cortical circuitry, and this approach offers a unique opportunity to investigate conduction in populations of axons based on their targeting specificity.
MEPSi: A tool for simulating tomograms of membrane-embedded proteins
Authors: de Francisco Borja Rodríguez , Bezault Armel , Xu Xiao-Ping , Hanein Dorit , Volkmann Niels
Published: July 2022

The throughput and fidelity of cryogenic cellular electron tomography (cryo-ET) is constantly increasing through advances in cryogenic electron microscope hardware, direct electron detection devices, and powerful image processing algorithms. However, the need for careful optimization of sample preparations and for access to expensive, high-end equipment, make cryo-ET a costly and time-consuming technique. Generally, only after the last step of the cryo-ET workflow, when reconstructed tomograms are available, it becomes clear whether the chosen imaging parameters were suitable for a specific type of sample in order to answer a specific biological question. Tools for a-priory assessment of the feasibility of samples to answer biological questions and how to optimize imaging parameters to do so would be a major advantage. Here we describe MEPSi (Membrane Embedded Protein Simulator), a simulation tool aimed at rapid and convenient evaluation and optimization of cryo-ET data acquisition parameters for studies of transmembrane proteins in their native environment. We demonstrate the utility of MEPSi by showing how to detangle the influence of different data collection parameters and different orientations in respect to tilt axis and electron beam for two examples: (1) simulated plasma membranes with embedded single-pass transmembrane αIIbβ3 integrin receptors and (2) simulated virus membranes with embedded SARS-CoV-2 spike proteins.

HIGHLIGHTS

Tool to simulate tomograms of membrane-embedded proteins

Detangles influence of data acquisition parameters from sample quality issues

Rapid evaluation and optimization of cryo-ET data acquisition parameters

Proof-of-concept provided with integrins and SARS-CoV-2 spike simulations

GRAPHICAL ABSTRACT
GCDPipe: risk gene, cell type, and drug ranking for complex traits
Authors: Pinakhina Daria , Loboda Alexander , Sergushichev Alexey , Artomov Mykyta
Published: July 2022

We introduce a user-friendly machine learning tool for risk gene, cell type, and drug ranking for complex traits - GCDPipe. It uses gene-level GWAS-derived data and publicly available expression data to train a model for prediction of disease risk genes and relevant cell types. Gene-ranking information is then coupled with known drug targets data to prioritize drugs based on their estimated functional effects associated with identified risk genes. The pipeline was tested in two case studies: inflammatory bowel disease (IBD) and schizophrenia, then it was applied to Alzheimer’s disease to investigate potential options for drug repurposing. The results show that GCDPipe is an effective tool to unify genetic risk factors with cellular context and known drug targets.
Towards 3D-bioprinting of osseous tissue of pre-defined shape using single-matrix cell-bioink constructs
Authors: Gu Yawei , Pigeot Sebastian , Ahrens Lucas , Tribukait-Riemenschneider Fabian , Sarem Melika , Wolf Francine , Barbero Andrea , Martin Ivan , Shastri V. Prasad
Published: July 2022

Engineering living bone tissue of defined shape on-demand has remained a challenge. 3D-bioprinting (3DBP), a biofabrication process capable of yielding cell constructs of defined shape, when combined with developmental engineering can provide a possible path forward. Through the development of a bioink possessing appropriate rheological properties to carry a high cell load and concurrently yield physically stable structures, printing of stable, cell-laden, single-matrix constructs of anatomical shapes was realized without the need for fugitive or support phases. Using this bioink system, constructs of hypertrophic cartilage of predesigned geometry were engineered in vitro by printing human MSCs at a high density to drive spontaneous condensation and implanted in nude mice to evoke endochondral ossification. The implanted constructs retained their prescribed shape over a 12-week period and underwent remodeling to yield ossicles of the designed shape with neovascularization. Micro-CT, histological and immunohistochemistry assessments confirmed bone tissue characteristics and the presence of human cells. These results demonstrate the potential of 3DBP to fabricate complex bone tissue for clinical application.
MISPEL: A supervised deep learning harmonization method for multi-scanner neuroimaging data
Authors: Torbati Mahbaneh Eshaghzadeh , Minhas Davneet S. , Laymon Charles M. , Maillard Pauline , Wilson James D. , Chen Chang-Le , Crainiceanu Ciprian M. , DeCarli Charles S. , Hwang Seong Jae , Tudorascu Dana L.
Published: July 2022

Large-scale data obtained from aggregation of already collected multi-site neuroimaging datasets has brought benefits such as higher statistical power, reliability, and robustness to the studies. Despite these promises from growth in sample size, substantial technical variability stemming from differences in scanner specifications exists in the aggregated data and could inadvertently bias any downstream analyses on it. Such a challenge calls for data normalization and/or harmonization frameworks, in addition to comprehensive criteria to estimate the scanner-related variability and evaluate the harmonization frameworks. In this study, we propose MISPEL (Multi-scanner Image harmonization via Structure Preserving Embedding Learning), a supervised multi-scanner harmonization method that is naturally extendable to more than two scanners. We also designed a set of criteria to investigate the scanner-related technical variability and evaluate the harmonization techniques. As an essential requirement of our criteria, we introduced a multi-scanner matched dataset of 3T T1 images across four scanners, which, to the best of our knowledge is one of the few datasets of this kind. We also investigated our evaluations using two popular segmentation frameworks: FSL and segmentation in statistical parametric mapping (SPM). Lastly, we compared MISPEL to popular methods of normalization and harmonization, namely White Stripe, RAVEL, and CALAMITI. MISPEL outperformed these methods and is promising for many other neuroimaging modalities.
A developmental atlas of the mouse brain by single-cell mass cytometry
Authors: Van Deusen Amy L. , Goggin Sarah M. , Williams Corey M. , Keeler Austin B. , Fread Kristen I. , Cheng Irene , Deppmann Christopher D. , Zunder Eli R.
Published: July 2022

Development of the mammalian brain requires precisely controlled differentiation of neurons, glia, and nonneural cells. To investigate protein-level changes in these diverse cell types and their progenitors, we performed single-cell mass cytometry on whole brain (E11.5/E12.5) and microdissected telencephalon, diencephalon, mesencephalon, and rhombencephalon (E13.5–P4) collected at daily timepoints from C57/BL6 mice. Measuring 24,290,787 cells from 112 sample replicates with a 40-antibody panel, we quantified 85 molecularly distinct cell populations across embryonic and postnatal development, including microglia putatively phagocytosing neurites, neural cells, and myelin. Differentiation trajectory analysis also identified two separate pathways for producing oligodendrocyte precursor cells. Comparison with previous studies revealed considerable discrepancies between protein and mRNA abundances in the developing brain, demonstrating the value of protein-level measurements for identifying functional cell states. Overall, our findings demonstrate the utility of mass cytometry as a high-throughput, scalable platform for single-cell profiling of brain tissue.
Analysis of Phylogeny of Agrocybe Genus Based on Nucleotide Database in NCBI
Authors: Wang Long , Zhou Qingping , Li Lingli
Published: July 2022

The study of the phylogeny of species is a basic discipline for the effective protection, development, and utilization of their germplasm resources. Since this century, the fungi of the Agrocybe genus have become the most successful class of medium and high-grade edible and medicinal fungi that have been artificially domesticated and grown on a large scale, and have high commercial value. However, there are few reports on its germplasm resources. To clarify the genetic and developmental relationship at the genus level of the Agrocybe in the world. In this paper, based on the NCBI Nucleotide database(National Center for Biotechnology Information), taking the single gene ITS sequence as the research object, the T92 (Tamura 3-parameters) parameter model was used to calculate the genetic distance, and the neighbor joining method was used to construct the genus-level phylogenetic tree of the Agrocybe. The results showed that the phylogenetic tree constructed by 192 ITS single gene sequences of 43 species of the Agrocybe (including 31 known species and 12 undetermined species) in the NCBI Nucleotide database was roughly divided into 6 branches and belonged to different groups, and 17 undetermined species of the Agrocybe sp. was preliminarily identified. This study has a certain reference value for the genetic relationship among different species of Agrocybe all over the world, as well as the selection of the parent bank and the protection of germplasm resources of each species of the genus.
Impact of bilayer composition on the dimerization properties of the Slg1 stress sensor TMD from a multiscale analysis †
Authors: Keller Fabian , Alavizargar Azadeh , Wedlich-Söldner Roland , Heuer Andreas
Published: July 2022

Mutual interactions between the transmembrane domains of membrane proteins and lipids on the bilayer properties has gained major interest. Most simulation studies of membranes rely on the Martini force field, which has proven extremely helpful in providing molecular insights into realistic systems. Accordingly, an evaluation of the accuracy of Martini is crucial to be able to correctly interpret the reported data. In this study, we combine atomistic and coarse-grained Martini simulations to investigate the properties of transmembrane domains (TMDs) in a model yeast membrane. The results show that the TMD binding state (monomeric, dimeric with positive or negative crossing angle) and the membrane composition significantly influence the properties around the TMDs and change TMD-TMD and TMD-lipid affinities. Furthermore, ergosterol (ERG) exhibits strong affinity to TMD dimers. Importantly, the right-handed TMD dimer configuration is stabilized via TMD-TMD contacts by addition of asymmetric anionic PS. The CG simulations corroborate many of these findings, with two notable exceptions: a systematic overestimation of TMD-ERG interaction and lack of stabilization of the right-handed TMD dimers with the addition of PS. Atomistic simulation results suggest that a meaningful comparison of dimer formation and experimentally-determined network factor may require to additionally take into account the precise conformation and thermodynamic relevance of multimeric TMD clusters.
Hypothalamic extraretinal photoreceptor Opsin3 regulates water balance, body temperature and motor activity
Authors: Bárez-López Soledad , Elsamad Ghadir , Bishop Paul , Searby Daniel , Kershaw Yvonne , Conway-Campbell Becky , Murphy David , Greenwood Michael P
Published: July 2022

Opsin 3 (Opn3) is a light-sensitive protein present throughout the mammalian brain, although its functions in this organ are currently unknown. SinceOpn3encoded mRNA increases in the supraoptic nucleus (SON) of the hypothalamus in response to hyperosmotic stimuli, we have explored the role of Opn3 in this nucleus. Byin situhybridization, we have demonstrated thatOpn3is expressed in neurones expressing both arginine vasopressin and oxytocin in the rat SON, suggesting that OPN3 functions in both neuronal types. Gene profiling analysis by RNA-seq suggested that neuropeptide production is impaired when knocking downOpn3in the rat SON, as confirmed by quantitative PCR and immunolabelling. Knocking down Opn3 in the rat SON altered physiological parameters including water intake, body temperature and motor activity. Altogether the data indicates that Opn3 in the SON is involved in the regulation of a number of neuropeptides and other proteins that participate in water homeostasis, body temperature and motor activity.
CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana
Authors: Bakirbas Ahmet , Walker Elsbeth L.
Published: July 2022

Long non-coding RNAs (lncRNAs) are RNA molecules with functions independent of any protein-coding potential. A whole transcriptome (RNA-seq) study of Arabidopsis shoots under iron sufficient and deficient conditions was carried out to determine the genes that are iron-regulated in the shoots. We identified two previously unannotated transcripts on chromosome 1 that are significantly iron-regulated. We have called this iron-regulated lncRNA, CAN OF SPINACH (COS). cos mutants have altered iron levels in leaves and seeds. Despite the low iron levels in the leaves, cos mutants have higher chlorophyll levels than WT plants. Moreover, cos mutants have abnormal development during iron deficiency. Roots of cos mutants are longer than those of WT plants, when grown on iron deficient medium. In addition, cos mutant plants accumulate singlet oxygen during iron deficiency. The mechanism through which COS affects iron deficiency responses is unclear, but small regions of sequence similarity to several genes involved in iron deficiency responses occur in COS, and small RNAs from these regions have been detected. We hypothesize that COS is required for normal adaptation to iron deficiency conditions.
Improved Nanopore full-length cDNA sequencing by PCR-suppression
Authors: Bayega Anthony , Oikonomopoulos Spyros , Wang Yu Chang , Ragoussis Jiannis
Published: July 2022

Full-length transcript sequencing remains a main goal of RNA sequencing. However, even the application of long-read sequencing technologies such as Oxford Nanopore Technologies still fail to yield full-length transcript sequencing for a significant portion of sequenced reads. Since these technologies can sequence reads that are far longer than the longest known processed transcripts, the lack of efficiency to obtain full-length transcripts from good quality RNAs stems from library preparation inefficiency rather than the presence of degraded RNA molecules. It has previously been shown that addition of inverted terminal repeats in cDNA during reverse transcription followed by single-primer PCR creates a PCR suppression effect that prevents amplification of short molecules thus enriching the library for longer transcripts. We adapted this method for Nanopore cDNA library preparation and show that not only is PCR efficiency increased but gene body coverage is dramatically improved. The results show that implementation of this simple strategy will result in better quality full-length RNA sequencing data and make full-length transcript sequencing possible for most of sequenced reads.

Contribution to the field

Long-read RNA sequencing aims to sequence expressed transcripts in their entirety. However, this has remained a challenge, mainly due to inherent inefficiencies in cDNA library preparation. Herein, we provide a new Nanopore cDNA library preparation protocol, termed Panhandle, that improves the efficiency of cDNA PCR with yields 2 – 8 times the yields obtained with ordinary PCR. This is key, as this should in turn reflect in the possibility of lowering the number of PCR cycles needed to obtain ample sequencing material, which in turn could reduce PCR biases, PCR artifacts, turnaround time, reagents, and could increase general quality of the library. Further, transcripts generated using the Panhandle method show better gene body coverage and more accurate transcription start site mapping than regular methods. This represents an important step towards full-length cDNA sequencing by Nanopore.
Pathogen effector-associated nuclear-localization of RPW8.2 amplifies its expression to boost immunity in Arabidopsis
Authors: Zhao Jing-hao , Huang Yan-yan , Wang He , Yang Xue-mei , Fan Jing , Li Yan , Pu Mei , Zhou Shi-xin , Zhang Ji-wei , Zhao Zhi-xue , Li Guo-bang , Hassan Beenish , Hu Xiao-hong , Chen Xue-wei , Xiao Shunyuan , Wu Xian-jun , Wang Wen-ming
Published: July 2022

RESISTANCE TO POWDERY MILDEW 8 (RPW8) defines a unique N-terminal coiled-coil domain of nucleotide-binding and leucine-rich repeat immune receptors required for immune signaling in plants. Arabidopsis RPW8.2 is specifically induced by the powdery mildew (PM) fungus (Golovinomyces cichoracearum) in the infected epidermal cells to activate immunity. The mechanism of RPW8.2-induction is not well understood. Here, we identify aG. cichoracearumfactor delivered to the nucleus of the host cell, named Gc-RPW8.2 interacting protein 1 (GcR8IP1). Ectopic expression of GcR8IP1 in Arabidopsis orNicotiana benthamianasuppressed host immune responses and enhanced susceptibility to PM. Host-induced gene silencing ofGcR8IP1compromised PM infectivity in susceptible Arabidopsis plants. Co-expression of GcR8IP1 with RPW8.2 increased nuclear localization of RPW8.2, which in turn, promoted transcriptional amplification ofRPW8.2. Thus, RPW8.2-dependent defense strengthening is due to altered partitioning of RPW8.2 by an effector of a PM fungus, which exemplifies an atypical form of effector-triggered immunity.
PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue
Authors: Nobori Tatsuya , Oliva Marina , Lister Ryan , Ecker Joseph R.
Published: July 2022

Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (Plant HYbridization-based Targeted Observation of gene expression Map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. We applied PHYTOMap to simultaneously analyze 28 cell type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-seq datasets in complex plant tissue.
The porcine cGAS-STING pathway exerts an unusual antiviral function independent of IFN and autophagy
Authors: Jiang Sen , Xia Nengwen , Luo Jia , Zhang Youwen , Cao Qi , Zhang Jiajia , Wang Yuening , Zheng Wanglong , Chen Nanhua , Meurens François , Zhu Jianzhong
Published: July 2022

The innate immune DNA sensing cGAS-STING pathway exerts strong antiviral activity through the downstream interferon (IFN) production; however, it has been recently recognized that IFN independent activity of STING also plays an important role in antiviral functions. Nevertheless, the IFN independent antiviral activity of STING is not fully understood. In this study, we showed that porcine STING (pSTING) played a critical role in anti-HSV1 and anti-VSV infections, and IFN defective mutants including pSTING pLxIS sub, S365A and ΔCTT all exhibited similar antiviral functions to wild type (WT) pSTING. Further, all these IFN defective pSTING mutants possessed a comparable autophagy activity relative to WT pSTING as expected. From pSTING WT, S365A and ΔCTT, the residues responsible for autophagy were mutated, which included L333A/R334A, Y167A/L170A and Y245A/L248A, respectively. Surprisingly, all these autophagy defective pSTING mutants still resisted from the two viral infections, demonstrating the pSTING antiviral function independent of IFN as well as autophagy. On the other hand, all the autophagy defective pSTING mutants triggered cell apoptosis, which was associated with the antiviral functions. Additionally, pSTING lost its antiviral activity in TBK1-/- and IRF3-/- porcine macrophages, indicating the involvement of TBK1 and IRF3 in other STING activity such as apoptosis. Collectively, our results revealed that STING exerts both IFN and autophagy independent antiviral activity, and also suggested that STING triggered cell apoptosis might resist from virus infections.
Identification of Mycobacterium abscessus subspecies by MALDI-TOF Mass Spectrometry and Machine Learning
Authors: Rodríguez-Temporal David , Herrera Laura , Alcaide Fernando , Domingo Diego , Vila Neus , Arroyo Manuel J. , Méndez Gema , Muñoz Patricia , Mancera Luis , Ruiz-Serrano María Jesús , Rodríguez-Sánchez Belén
Published: July 2022

Mycobacterium abscessus complex is one of the most common and pathogenic nontuberculous mycobacteria (NTM) isolated in clinical laboratories. It consists of three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. bolletii and M. abscessus subsp. massiliense. Due to their different antibiotic susceptibility pattern, a rapid and accurate identification method is necessary for their differentiation. Although matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has proven useful for NTM identification, the differentiation of M. abscessus subspecies is challenging. In this study, a collection of 244 clinical isolates of M. abscessus complex was used for MALDI-TOF MS analysis and for the development of machine learning predictive models. Overall, using a Random Forest model with several confidence criteria (samples by triplicate and similarity values >60%), a total of 95.8% of isolates were correctly identified at subspecies level. In addition, differences in culture media, colony morphology and geographic origin of the strains were evaluated, showing that the latter most affected the mass spectra of isolates. Finally, after studying all protein peaks previously reported for this complex, two novel peaks with potential for subspecies differentiation were found. Therefore, machine learning methodology has proven to be a promising approach for rapid and accurate identification of subspecies of the M. abscessus complex using MALDI-TOF MS.
Enveloped viruses show increased propensity to cross-species transmission and zoonosis
Authors: Valero-Rello Ana , Sanjuán Rafael
Published: July 2022

The transmission of viruses between different host species is a major source of emerging diseases and is of particular concern in the case of zoonotic transmission from mammals to humans. Several zoonosis risk factors have been identified, but it is currently unclear which viral traits primarily influence this process, as previous work has focused on a few hundred viruses that are not representative of the actual viral diversity. Here we investigate fundamental virological traits that influence cross-species transmissibility and zoonotic propensity by interrogating a database of over 12,000 mammalian virus-host associations, obtained mainly from recent viral metagenomics projects. Our analysis reveals that enveloped viruses tend to infect more host species and are more likely to infect humans than non-enveloped viruses, while other viral traits such as genome composition, structure, size or the viral replication compartment play a minor role. This contrasts with the previous notion that viral envelopes did not significantly impact or even reduced zoonotic risk, and should help better prioritize outbreak prevention efforts. We suggest several mechanisms by which viral envelopes could promote cross-species transmissibility, including structural flexibility and evasion of viral entry barriers.
Microbiota colonization tunes the antigen threshold of microbiota-specific T cell activation in the gut
Authors: Hoces Daniel , Corak Basak , Estrada Brull Anna , Berent Sara , Faccin Erica , Moresi Claudia , Keys Tim , Joller Nicole , Slack Emma
Published: July 2022

Harnessing the potential of commensal bacteria for immunomodulatory therapy in the gut requires the identification of conditions that modulate immune activation towards incoming colonizing bacteria. In this study, we used the commensal Bacteroides thetaiotaomicron (B.theta) and combined it with B.theta-specific transgenic T cells, in the context of defined colonization of gnotobiotic and immunodeficiency mouse models, to probe the factors modulating bacteria-specific T cell activation against newly colonizing bacteria. After colonizing germ-free (GF) and conventionally raised (SPF) mice with B.theta, we only observed proliferation of B.theta-specific T cells in GF mice. Using simple gnotobiotic communities we could further demonstrate that T-cell activation against newly colonizing gut bacteria is restricted by previous bacteria colonization in GF mice. However, this restriction requires a functional adaptive immune system as Rag1-/- allowed B.theta-specific T cell proliferation even after previous colonization. Interestingly, this phenomenon seems to be dependent on the type of TCR-transgenic model used. B.theta-specific transgenic T cells also proliferated after gut colonization with an E.coli strain carrying the B.theta-specific epitope. However, this was not the case for the SM-1 transgenic T cells as they did not proliferate after similar gut colonization with an E.coli strain expressing the cognate epitope. In summary, we found that activation of T cells towards incoming bacteria in the gut is modulated by the influence of colonizing bacteria on the adaptive immune system of the host.
Development and optimization of biologically contained Marburg virus for high-throughput antiviral screening
Authors: Vanmechelen Bert , Stroobants Joren , Chiu Winston , Naesens Lieve , Schepers Joost , Vermeire Kurt , Maes Piet
Published: July 2022

Comparable to the related Ebola virus, Marburg virus is an emerging zoonotic pathogen that causes hemorrhagic fever with a high mortality rate. Therefore, handling of Ebola virus and Marburg virus is limited to biosafety level 4 facilities, of which only a limited number exists worldwide. However, researchers have developed several virus alternatives that are safe to handle in lower biosafety settings. One particularly interesting approach is the engineering of biologically contained Ebola virus by removing an essential gene from the virus genome and providing this missing gene in trans in a specific cell line. Because the virus is confined to this specific cell line, this results in a system that is safe to handle. So far, Ebola virus is the only virus for which biological containment has been reported. Here, we describe the first successful rescue of biologically contained Marburg virus and demonstrate that biological containment is also feasible for other filoviruses. Specifically, we describe the development of containment cell lines for Marburg virus through lentiviral transduction and show the growth and safety characteristics of eGFP-expressing, biologically contained Marburg virus in these cell lines. Additionally, we exploited this newly established Marburg virus system to screen over 500 compounds from available libraries. Lastly, we also validated the applicability of our biologically contained Marburg virus system in a 384-well format, to further illustrate the usefulness of this novel system as an alternative for high-throughput MARV screening of compound libraries.
Establishing Physalis as a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
Authors: He Jia , Alonge Michael , Ramakrishnan Srividya , Benoit Matthias , Soyk Sebastian , Reem Nathan T. , Hendelman Anat , Eck Joyce Van , Schatz Michael C. , Lippman Zachary B.
Published: July 2022

The highly diverse Solanaceae family contains several widely studied model and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking Inflated Calyx Syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative P. pruinosa and use these resources to study natural and engineered variation in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9 targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system, and establish a new paradigm for the search of factors driving ICS.
A characterization of the neural representation of confidence during probabilistic learning
Authors: Bounmy Tiffany , Eger Evelyn , Meyniel Florent
Published: July 2022

Learning in a stochastic and changing environment is a difficult task. Models of learning typically postulate that observations that deviate from the learned predictions are surprising and used to update those predictions. Bayesian accounts further posit the existence of a confidence-weighting mechanism: learning should be modulated by the confidence level that accompanies those predictions. However, the neural bases of this confidence are much less known than the ones of surprise. Here, we used a dynamic probability learning task and high-field MRI to identify putative cortical regions involved in the representation of confidence about predictions during human learning. We devised a stringent test based on the conjunction of four criteria. We localized several regions in parietal and frontal cortices whose activity is sensitive to the confidence of an ideal observer, specifically so with respect to potential confounds (surprise and predictability), and in a way that is invariant to which item is predicted. We also tested for functionality in two ways. First, we localized regions whose activity patterns at the subject level showed an effect of both confidence and surprise in qualitative agreement with the confidence-weighting principle. Second, we found neural representations of ideal confidence that also accounted for subjective confidence. Taken together, those results identify a set of cortical regions potentially implicated in the confidence-weighting of learning.
Dynein functions in galectin-3 mediated processes of clathrin-independent endocytosis
Authors: Mayya Chaithra , Naveena Hema , Sinha Pankhuri , Bhatia Dhiraj
Published: July 2022

Multiple endocytic processes operate in cells in tandem for the uptake of multiple cargoes, metabolites, and signaling molecules that are involved in diverse cellular functions including cell adhesion and migration. The best studied endocytic process involves the formation of a well-defined cytoplasmic coat at sites of uptake made of clathrin and its interacting partners. Galectin-3 (Gal3), an endogenous lectin, binds to glycosylated membrane receptors and glycosphingolipids (GSLs) to drive membrane bending, leading to the formation of tubular membrane invaginations which undergo scission to form a morphologically distinct class of uptake structures, termed clathrin-independent carriers (CLICs). This mechanism has been termed the GlycoLipid-Lectin (GL-Lect) hypothesis. Which components from cytoskeletal machinery are involved in the scission of CLICs remains yet to be explored. In this study, we propose that dynein, a retrograde motor protein, is recruited onto Gal3-induced tubular endocytic pits and provides the pulling force to for friction driven scission. Uptake of Gal3 and its cargoes (CD98/CD147) is significantly dependent on dynein activity, whereas the uptake of transferrin (a marker for clathrin-mediated endocytosis) is only slightly affected upon dynein inhibition. Dynein inhibition also affects cellular organelle distribution, 3D cell invasion and wound healing. Our study thereby reveals functions of dynein in individual and collective cell migration in 2D and 3D that are tightly coupled to endocytic processes in cells.
OM-85 reduces SARS-COV-2 viral RNA expression in nasopharyngeal cells from COVID-19 patients
Authors: Cassão Gisele , Antunes Krist Helen , Gonçalvez João Ismael Budelon , Santos Leonardo Duarte , Abbadi Bruno Lopes , Bizarro Cristiano Valim , Machado Pablo , Basso Luiz Augusto , Pasquali Christian , Stein Renato T. , Souza Ana Paula Duarte de
Published: July 2022

OM-85 is a bacterial lysate from common respiratory tract pathogens, with an excellent safety profile, widely used to prevent recurrent respiratory tract infections. Several studies have been reporting the antiviral roles of OM-85. Here we demonstrated the effect of ex-vivo OM-85 exposure in nasopharyngeal cells collected from COVID-19 patients. OM-85 decreased the SARS-CoV-2 N1 gene expression and increased RIG-I (DDX58) gene expression in these cells. These data support the antiviral effect of OM-85 against SARS-CoV-2.
Infection- or vaccine mediated immunity reduces SARS-CoV-2 transmission, but increases competitiveness of Omicron in hamsters
Authors: Port Julia R. , Yinda Claude Kwe , Riopelle Jade C. , Weishampel Zachary A. , Saturday Taylor A. , Avanzato Victoria A. , Schulz Jonathan E. , Holbrook Myndi G. , Barbian Kent , Perry-Gottschalk Rose , Haddock Elaine , Martens Craig , Shaia Carl. I. , Lambe Teresa , Gilbert Sarah C. , van Doremalen Neeltje , Munster Vincent J.
Published: July 2022

Omicron has demonstrated a competitive advantage over Delta in vaccinated people. To understand this, we designed a transmission chain experiment using naïve, intranasally (IN) or intramuscularly (IM) vaccinated, and previously infected (PI) hamsters. Vaccination and previous infection protected animals from disease and virus replication after Delta and Omicron dual challenge. A gradient in transmission blockage was observed: IM vaccination displayed moderate transmission blockage potential over three airborne chains (approx. 70%), whereas, IN vaccination and PI blocked airborne transmission in >90%. In naïve hamsters, Delta completely outcompeted Omicron within and between hosts after dual infection in onward transmission. Although Delta also outcompeted Omicron in the vaccinated and PI transmission chains, an increase in Omicron competitiveness was observed in these groups. This correlated with the increase in the strength of the humoral response against Delta, with the strongest response seen in PI animals. These data highlight the continuous need to assess the emergence and spread of novel variants in populations with pre-existing immunity and address the additional evolutionary pressure this may exert on the virus.
Evolution of the Growth Hormone Gene Duplication in Passerine Birds
Authors: Rasband Shauna A. , Bolton Peri E. , Fang Qi , Johnson Philip L. F. , Braun Michael J.
Published: July 2022

Birds of the order Passeriformes represent the most speciose radiation of land vertebrates, yet the cause or causes of their elevated species richness have not been satisfactorily explained. One potential key adaptation is their sole lineage-specific gene, a duplicate copy of growth hormone (GH), present in all major lineages of passerines, but in no other group of birds. Growth hormone genes plausibly influence extreme life history traits that passerines exhibit, including the shortest embryo-to-fledging developmental period of any avian order. To unravel the implications of this GH duplication, we investigated the molecular evolution of the ancestral avian GH gene (GH or GH1) and the novel passerine GH paralog (GH2), using 497 gene sequences extracted from 342 genomes. Passerine GH1 and GH2 are reciprocally monophyletic, consistent with a single duplication event from a microchromosome onto a macrochromosome in a common ancestor of extant passerines. Additional chromosomal rearrangements have changed the syntenic and potential regulatory context of these genes. Both passerine GH1 and GH2 paralogs display substantially higher rates of nonsynonymous codon change than non-passerine avian GH, suggesting positive selection following duplication. A site involved in signal peptide cleavage is under selection in both paralogs. Other sites under positive selection differ between the two paralogs, but many are clustered in one region of a 3D model of the protein. Both paralogs retain key functional features and are actively but differentially expressed in two major passerine suborders. These phenomena suggest that growth hormone genes may be evolving novel adaptive roles in passerine birds.
Investigating the mediating role of sustainability disclosure in the relationship between corporate governance and firm performance in Jordan
Authors: Alodat Ahmad Yuosef , Salleh Zalailah , Hashim Hafiza Aishah , Sulong Farizah
Published: July 2022

Purpose

This study aimed to investigate the effect of sustainability disclosure (SD) as a mediator for the relationship between corporate governance (CG) and the performance of firms listed on the Amman Stock Exchange (ASE).

Design/methodology/approach

The study analysed 405 reports of firms listed on the ASE from 2014 to 2018. The direct and indirect impact of governance mechanisms on the firms' performance was examined using STATA 15. A four-step procedure for testing mediation was used to determine the mediating role of SD.

Findings

The results demonstrated that the board and audit committees' effectiveness positively and significantly influences the firm's performance. Additionally, the results demonstrated that SD partially mediates the relationship between CG and the firm's performance.

Research limitations/implications

Research implications – This study supported the assumptions of agency, resource dependence and stakeholder theories as the basis to explain the relationship among board’s effectiveness, audit committee’s effectiveness, sustainability report and firm performance in developing economies. In addition, the results suggested that CG helps to enhance the firm's performance and sustainability reporting. Firms providing sustainable report are deemed more responsible and attract more returns to firms. Research limitations – The study only focused on reports from five years for non-financial firms listed on the ASE to test the assumed relationship between the variables.

Practical implications

This study contributed to the body of knowledge by examining the mediating role of SD between CG and firm performance. Investors, managers and regulators can obtain further insights, especially those seeking to improve a firm's performance in the emerging markets, through a sound CG system and extensive sustainability reporting.

Originality/value

This study focused on the direct and indirect impacts of CG and firm performance in an emerging and developing economy. The study used SD as the mediating variable in examining the indirect effect.
Melanocytic matricoma with atypical features: A case of malignant melanocytic matricoma?
Authors: Melson Gabriella J. , Hong Sophiette G. , Brem Candice E.
Published: July 2022

Melanocytic matricoma is a rarely reported, benign cutaneous adnexal neoplasm composed of epithelial cells exhibiting differentiation towards hair matrix as well as admixed, pigmented, dendritic melanocytes. The proposed malignant counterpart to melanocytic matricoma, malignant melanocytic matricoma (MMM), is even more rare. Here we report a case of a melanocytic matricoma with atypical features in a 92‐year‐old female with a 1.2‐cm pigmented nodule on the right nasal sidewall. Histopathology revealed a well‐circumscribed dermal tumor composed of atypical matrical cells with scattered aggregates of anucleate keratinocytes (ghost cells), prominent intratumoral pigment, numerous mitotic figures (88 mitosis/10 high‐power field [HPF]), and intermixed dendritic melanocytes. A literature review was performed for MMM to determine if the current case fit diagnostic criteria for this entity. Including the current case, 12 cases of MMM were identified and analyzed to investigate common clinical and histopathologic features. MMM commonly occurred on the head and neck (7/12 cases) of older individuals (median age of 80) with a slight male predominance (male‐to‐female ratio of 3:1) and on histopathology presented as a multinodular dermal tumor composed of mitotically active (average mitotic rate of >50 mitoses/10 HPF) pleomorphic epithelial cells with foci of ghost cells. Dendritic melanocytes were found throughout the tumor lobules in all cases. Given that only two of 12 cases have exhibited locally aggressive behavior, further study is warranted to determine the true malignant potential of MMM.