bluuebunny/crossref_metadata_2025 huggingface dataset:
Elastic wave propagation in anisotropic polycrystals: inferring physical properties of glacier ice
Authors: Rathmann Nicholas M. , Grinsted Aslak , Mosegaard Klaus , Lilien David A. , Westhoff Julien , Hvidberg Christine S. , Prior David J. , Lutz Franz , Thomas Rilee E. , Dahl-Jensen Dorthe
Published: December 2022

An optimization problem is proposed for inferring physical properties of polycrystals given ultrasonic (elastic) wave velocity measurements, made across multiple sample orientations. The feasibility of the method is demonstrated by inferring both the effective grain elastic parameters and the grain

c

-axis orientation distribution function (ODF) of ice-core samples from Priestley glacier, Antarctica. The method relies on expanding the ODF in terms of a spherical harmonic series, which allows for a non-parametric estimation of the sample ODF. Moreover, any linear combination of the Voigt (strain) and Reuss (stress) homogenization scheme is allowed, although for glacier ice, the exact choice is found to matter little for bulk elastic behaviour, and thus for inferred physical properties, too. Finally, the accuracy of the inferred grain elastic parameters is discussed, including the well-posedness and shortcomings of the inverse problem, relevant for future adoptions in glaciology, geology and elsewhere.
Curvature dependences of wave propagation in reaction–diffusion models
Authors: Buenzli Pascal R. , Simpson Matthew J.
Published: December 2022

Reaction–diffusion waves in multiple spatial dimensions advance at a rate that strongly depends on the curvature of the wavefronts. These waves have important applications in many physical, ecological and biological systems. In this work, we analyse curvature dependences of travelling fronts in a single reaction–diffusion equation with general reaction term. We derive an exact, non-perturbative curvature dependence of the speed of travelling fronts that arises from transverse diffusion occurring parallel to the wavefront. Inward-propagating waves are characterized by three phases: an establishment phase dominated by initial and boundary conditions, a travelling-wave-like phase in which normal velocity matches standard results from singular perturbation theory and a dip-filling phase where the collision and interaction of fronts create additional curvature dependences to their progression rate. We analyse these behaviours and additional curvature dependences using a combination of asymptotic analyses and numerical simulations.
Many-to-one function of cat-like mandibles highlights a continuum of sabre-tooth adaptations
Authors: Chatar Narimane , Fischer Valentin , Tseng Z. Jack
Published: December 2022

Cat-like carnivorans are a textbook example of convergent evolution, with distinct morphological differences between taxa with short or elongated upper canines, the latter often being interpreted as an adaptation to bite at large angles and subdue large prey. This interpretation of the sabre-tooth condition is reinforced by a reduced taxonomic sampling in some studies, often focusing on highly derived taxa or using simplified morphological models. Moreover, most biomechanical analyses focus on biting scenarios at small gapes, ideal for modern carnivora but ill-suited to test for subduction of large prey by sabre-toothed taxa. In this contribution, we present the largest three-dimensional collection-based muscle-induced biting simulations on cat-like carnivorans by running a total of 1074 analyses on 17 different taxa at three different biting angles (30°, 60° and 90°) including both morphologies. While our results show a clear adaptation of extreme sabre-toothed taxa to bite at larger angles in terms of stress distribution, other performance variables display surprising similarities between all forms at the different angles tested, highlighting a continuous rather than bipolar spectrum of hunting methods in cat-like carnivorans and demonstrating a wide functional disparity and nuances of the sabre-tooth condition that cannot simply be characterized by specialized feeding biomechanics.
Early onset of postnatal individual vocal recognition in a highly colonial mammal species
Authors: Martin Mathilde , Gridley Tess , Elwen Simon , Charrier Isabelle
Published: December 2022

Mother–young vocal recognition is widespread in mammals. The features of vocal recognition are known to be shaped by the ecological constraints faced by each species. In some species, a rapid establishment of mother–young vocal recognition is crucial for offspring's survival. However, knowledge of the precise features of this recognition system, especially the timing of the onset in the first hours after birth, is often lacking. Here we show that Cape fur seal females can recognize their pup's voice 2–4 h after parturition and that pups develop this aptitude 4–6 h after birth. This study is the first to investigate this mechanism in a wild and free-ranging mammal from only 2 h after birth. We report the fastest establishment of mother–young vocal recognition for any mammalian species, including humans, described to date. Such early vocal identification in pups suggests an
in utero
vocal imprinting. These findings highlight the synergistic role of environmental constraints and biological traits in optimizing the timing of individual vocal recognition onset in vertebrates.
Musculoskeletal wing-actuation model of hummingbirds predicts diverse effects of primary flight muscles in hovering flight
Authors: Agrawal Suyash , Tobalske Bret W. , Anwar Zafar , Luo Haoxiang , Hedrick Tyson L. , Cheng Bo
Published: December 2022

Hummingbirds have evolved to hover and manoeuvre with exceptional flight control. This is enabled by their musculoskeletal system that successfully exploits the agile motion of flapping wings. Here, we synthesize existing empirical and modelling data to generate novel hypotheses for principles of hummingbird wing actuation. These may help guide future experimental work and provide insights into the evolution and robotic emulation of hummingbird flight. We develop a functional model of the hummingbird musculoskeletal system, which predicts instantaneous, three-dimensional torque produced by primary (pectoralis and supracoracoideus) and combined secondary muscles. The model also predicts primary muscle contractile behaviour, including stress, strain, elasticity and work. Results suggest that the primary muscles (i.e. the flight ‘engine’) function as diverse effectors, as they do not simply power the stroke, but also actively deviate and pitch the wing with comparable actuation torque. The results also suggest that the secondary muscles produce controlled-tightening effects by acting against primary muscles in deviation and pitching. The diverse effects of the pectoralis are associated with the evolution of a comparatively enormous bicipital crest on the humerus.
Environment and genotype predict the genomic nature of domestication of salmonids as revealed by gene expression
Authors: Bull James K. , Stanford Brenna C. M. , Bokvist Jessy K. , Josephson Matthew P. , Rogers Sean M.
Published: December 2022

Billions of salmonids are produced annually by artificial reproduction for harvest and conservation. Morphologically, behaviourally and physiologically these fish differ from wild-born fish, including in ways consistent with domestication. Unlike most studied domesticates, which diverged from wild ancestors millennia ago, salmonids offer a tractable model for early-stage domestication. Here, we review a fundamental mechanism for domestication-driven differences in early-stage domestication, differentially expressed genes (DEGs), in salmonids. We found 34 publications examining DEGs under domestication driven by environment and genotype, covering six species, over a range of life-history stages and tissues. Three trends emerged. First, domesticated genotypes have increased expression of growth hormone and related metabolic genes, with differences magnified under artificial environments with increased food. Regulatory consequences of these DEGs potentially drive overall DEG patterns. Second, immune genes are often DEGs under domestication and not simply owing to release from growth-immune trade-offs under increased food. Third, domesticated genotypes exhibit reduced gene expression plasticity, with plasticity further reduced in low-complexity environments typical of production systems. Recommendations for experimental design improvements, coupled with tissue-specific expression and emerging analytical approaches for DEGs present tractable avenues to understand the evolution of domestication in salmonids and other species.
Shewanella putrefaciens: a rare cause of purulent otorrhoea
Authors: Benaissa Elmostafa , Maleb Adil , Elouennass Mostafa
Published: December 2022

Shewanella putrefaciens

is a Gram-negative, non-fermenting, motile and oxidase-positive bacillus. Its incrimination in human pathology is very rare, although there has been a resurgence in

Shewanella

infections in recent years. We report the first case in Morocco of a purulent otorrhoea caused by

S. putrefaciens

, resistant to conventional treatment, occurring in a 25-year-old female, afebrile, without deterioration of the general state and possibly acquired during sea bathing. We also describe the bacteriological characteristics of and antibiotic susceptibility results for the isolate.
Large-scale comparative genomics to refine the organization of the global Salmonella enterica population structure
Authors: Liu Chao Chun , Hsiao William W. L.
Published: December 2022

The White–Kauffmann–Le Minor (WKL) scheme is the most widely used

Salmonella

typing scheme for reporting the disease prevalence of the enteric pathogen. With the advent of whole-genome sequencing (WGS), in silico methods have increasingly replaced traditional serotyping due to reproducibility, speed and coverage. However, despite integrating genomic-based typing by in silico serotyping tools such as SISTR, in silico serotyping in certain contexts remains ambiguous and insufficiently informative. Specifically, in silico serotyping does not attempt to resolve polyphyly. Furthermore, in spite of the widespread acknowledgement of polyphyly from genomic studies, the prevalence of polyphyletic serovars is not well characterized. Here, we applied a genomics approach to acquire the necessary resolution to classify genetically discordant serovars and propose an alternative typing scheme that consistently reflect natural

Salmonella

populations. By accessing the unprecedented volume of bacterial genomic data publicly available in GenomeTrakr and PubMLST databases (>180 000 genomes representing 723 serovars), we characterized the global

Salmonella

population structure and systematically identified putative non-monophyletic serovars. The proportion of putative non-monophyletic serovars was estimated higher than previous reports, reinforcing the inability of antigenic determinants to depict the complexity of

Salmonella

evolutionary history. We explored the extent of genetic diversity masked by serotyping labels and found significant intra-serovar molecular differences across many clinically important serovars. To avoid false discovery due to incorrect in silico serotyping calls, we cross-referenced reported serovar labels and concluded a low error rate in in silico serotyping. The combined application of clustering statistics and genome-wide association methods demonstrated effective characterization of stable bacterial populations and explained functional differences. The collective methods adopted in our study have practical values in establishing genomic-based typing nomenclatures for an entire microbial species or closely related subpopulations. Ultimately, we foresee an improved typing scheme to be a hybrid that integrates both genomic and antigenic information such that the resolution from WGS is leveraged to improve the precision of subpopulation classification while preserving the common names defined by the WKL scheme.
Molecular Dynamics Simulation as a Promising Approach for Computational Study of Liquid Crystal-based Aptasensors
Authors: Zahraee Hamed , Arab Seyed Shahriar , Khoshbin Zahra , Taghdisi Seyed Mohammad , Abnous Khalil
Published: December 2022

As a potent computational methodology, molecular dynamics (MD) simulation provides advantageous knowledge about biological compounds from the molecular viewpoint. In particular, MD simulation gives exact information about aptamer strands, such as the short synthetic oligomers, their orientation, binding sites, folding-unfolding state, and conformational re-arrangement. Also, the effect of the different chemicals and biochemicals as the components of aptamer-based sensors (aptasensors) on the aptamer-target interaction can be investigated by MD simulation. Liquid crystals (LCs) as soft substances with characteristics of both solid anisotropy and liquid fluidity are new candidates for designing label-free aptasensors. To now, diverse aptasensors have been developed experimentally based on the optical anisotropy, fluidity, and long-range orientational order of LCs. Here, we represent a computational model of an LC-based aptasensor through a detailed MD simulation study. The different parameters are defined and studied to achieve a comprehensive understanding of the computational design of the LC-based aptasensor, including the density of LCs, their orientation angle, and lognormal distribution in the absence and presence of aptamer strands, both aptamer and target molecules with various concentrations, and interfering substance. As a case study, the tobramycin antibiotic is considered the target molecule for the computational model of the LC-based aptasensor.
A thermodynamical model of non-deterministic computation in cortical neural networks
Authors: Stoll Elizabeth A
Published: December 2022

Neuronal populations in the cerebral cortex engage in probabilistic coding, effectively encoding the state of the surrounding environment with high accuracy and extraordinary energy efficiency. A new approach models the inherently probabilistic nature of cortical neuron signaling outcomes as a thermodynamic process of non-deterministic computation. A mean field approach is used, with the trial Hamiltonian maximizing free energy and minimizing the net quantity of temperature-entropy, compared with a reference Hamiltonian. Thermodynamic quantities are always conserved during the computation; free energy must be expended to produce information, and free energy is released during information compression, as correlations are identified between the encoding system and its surrounding environment. Due to the relationship between the Gibbs free energy equation and the Nernst equation, any increase in free energy is paired with a local decrease in membrane potential. As a result, this process of thermodynamic computation adjusts the likelihood of each neuron firing an action potential. This model shows that non-deterministic signaling outcomes can be achieved by noisy cortical neurons, through an energy-efficient computational process that involves optimally redistributing a Hamiltonian over some time evolution. Calculations demonstrate that the energy efficiency of the human brain is consistent with this model of non-deterministic computation, with net entropy production far too low to retain the assumptions of a classical system.
Rewiring Cancer Drivers to Activate Apoptosis
Authors: Gourisankar Sai , Krokhotin Andrey , Ji Wenzhi , Liu Xiaofan , Chang Chiung-ying , Kim Samuel H. , Li Zhengnian , Wenderski Wendy , Simanauskaite Juste M. , Zhang Tinghu , Gray Nathanael S. , Crabtree Gerald R.
Published: December 2022

Genes that drive the proliferation, survival, invasion and metastasis of malignant cells have been identified for many human cancers1–6. Independent studies have identified cell death pathways that eliminate cells for the good of the organism7–10. The coexistence of the cell death pathways with the driver mutations suggest that the cancer driver could be rewired to activate cell death. We have invented a new class of molecules: TCIPs (Transcriptional/Epigenetic Chemical Inducers of Proximity) that recruit the endogenous cancer driver, or a downstream transcription factor, to the promoters of cell death genes thereby activating their expression. To develop this concept, we have focused on diffuse large B cell lymphoma (DLBCL), in which BCL6 is amplified or mutated11. BCL6 binds to the promoters of cell death genes and epigenetically suppresses their expression12. We produced the first TCIPs by chemically linking BCL6 inhibitors to small molecules that bind transcriptional activators. Several of these molecules robustly kill DLBCL at single-digit nanomolar concentrations, including chemotherapy-resistant, TP53-mutant lines. The dominant gain-of-function approach provided by TCIPs captures the combinatorial specificity inherit to transcription and can thereby accesses new therapeutic space. TCIPs are relatively non-toxic to normal cells and mice, apparently reflecting their need for coincident expression of both target proteins for effective killing. The general TCIP concept has applications in elimination of senescent cells, enhancing expression of therapeutic genes, treatment of diseases produced by haploinsufficiency, and activation of immunogens for immunotherapy.
Constraining the global niche suitability of the Eusuchia clade across the Cretaceous-Paleogene boundary
Authors: Harper Morgan , Farnsworth Alexander , Valdes Paul J. , Markwick Paul J. , Stockdale Maximilian T.
Published: December 2022

The crocodiles and their close relatives, the alligators and gharials, have a compelling evolutionary history. They are a clade of great antiquity, with their most recent common ancestor emerging within the Mesozoic. However, unlike many groups of such a great age, the crocodilians have an extensive crown-group, with around two dozen extant examples. They have a limited ecomorphology, which has varied little since their inception, and their biogeography has been shown to interact closely with climate. The biogeography of crocodilians in deep time remains an outstanding question, which is complicated further by the limitations of the fossil record. The fossil record is fundamentally incomplete yet represents the most common method used to infer biogeography of organisms. The scarcity of fossil remains makes apparent absences difficult to confirm. Preservation bias will promote fossil occurrences in areas with a high sedimentation rate, which may not be the true ecological niche for a given taxon. This study uses species distribution models of extant crocodilians to infer the ecological niche of related taxa in the Maastrichtian and Danian. Models indicate a much wider latitudinal range than is observed among extant examples, and the invasion of new ecospace following the end-Cretaceous mass extinction. In addition, we find that while temperature is of significance to crocodilian biogeography, it is precipitation that is the most influential climatic variable.
Efficacy of a bivalent (D614 + B.1.351) SARS-CoV-2 Protein Vaccine
Authors: Dayan Gustavo H. , Rouphael Nadine , Walsh Stephen R. , Chen Aiying , Grunenberg Nicole , Allen Mary , Antony Johannes , Asante Kwaku Poku , Suresh Bhate Amit , Beresnev Tatiana , Bonaparte Matthew I , Angeles Ceregido Maria , Dobrianskyi Dmytro , Fu Bo , Grillet Marie-Helene , Keshtkar-Jahromi Maryam , Juraska Michal , Jin Kee Jia , Kibuuka Hannah , Koutsoukos Marguerite , Masotti Roger , Michael Nelson L. , Reynales Humberto , Robb Merlin L. , Villagómez Martínez Sandra M. , Sawe Fredrick , Schuerman Lode , Tong Tina , Treanor John , Wartel T. Anh , Diazgranados Carlos A. , Chicz Roman M. , Gurunathan Sanjay , Savarino Stephen , Sridhar Saranya ,   the VAT00008 study team
Published: December 2022

Background

COVID-19 vaccines with alternative strain compositions are needed to provide broad protection against newly emergent SARS-CoV-2 variants of concern.

Methods

We conducted a global Phase 3, multi-stage efficacy study (NCT04904549) among adults aged ≥18 years. Participants were randomized 1:1 to receive two intramuscular injections 21 days apart of a bivalent SARS-CoV-2 recombinant protein vaccine with AS03-adjuvant (5 μg of ancestral (D614) and 5 μg of B.1.351 [beta] variant spike protein) or placebo. Symptomatic COVID-19 was defined as laboratory-confirmed COVID-19 with COVID-19-like illness (CLI) symptoms. The primary efficacy endpoint was the prevention of symptomatic COVID-19 ≥14 days after the second injection (post-dose 2 [PD2]).

Results

Between 19 Oct 2021 and 15 Feb 2022, 12,924 participants received ≥1 study injection. 75% of participants were SARS-CoV-2 non-naïve. 11,416 participants received both study injections (efficacy-evaluable population [vaccine, n=5,736; placebo, n=5,680]). Up to 15 March 2022, 121 symptomatic COVID-19 cases were reported (32 in the vaccine group and 89 in the placebo group) ≥14 days PD2 with a vaccine efficacy (VE) of 64.7% (95% confidence interval [CI] 46.6; 77.2%). VE was 75.1% (95% CI 56.3; 86.6%) in non-naïve and 30.9% (95% CI -39.3; 66.7%) in naïve participants. Viral genome sequencing identified the infecting strain in 68 cases (Omicron [BA.1 and BA.2 subvariants]: 63; Delta: 4; Omicron and Delta: 1). The vaccine was well-tolerated and had an acceptable safety profile.

Conclusions

A bivalent vaccine conferred heterologous protection against symptomatic infection with newly emergent Omicron (BA.1 and BA.2) in non-naïve adults 18–59 years of age.

ClinicalTrials.gov

NCT04904549
The large GTPase Sey1/atlastin mediates lipid droplet- and FadL-dependent intracellular fatty acid metabolism ofLegionella pneumophila
Authors: Hüsler Dario , Stauffer Pia , Keller Bernhard , Böck Desirée , Steiner Thomas , Ostrzinski Anne , Striednig Bianca , Swart A. Leoni , Letourneur François , Maaß Sandra , Becher Dörte , Eisenreich Wolfgang , Pilhofer Martin , Hilbi Hubert
Published: December 2022

The facultative intracellular bacteriumLegionella pneumophilaemploys the Icm/Dot type IV secretion system (T4SS) to replicate in a unique membrane-bound compartment, theLegionella-containing vacuole (LCV). The endoplasmic reticulum (ER)-resident large fusion GTPase Sey1/atlastin promotes remodeling and expansion of LCVs, and the GTPase is also implicated in the formation of ER-derived lipid droplets (LDs). Here we show that LCVs intimately interact with palmitate-induced LDs inDictyostelium discoideumamoeba. Comparative proteomics of LDs isolated from theD. discoideumparental strain Ax3 or ⊗sey1revealed 144 differentially produced proteins, of which 7 or 22 were exclusively detected in LDs isolated from strain Ax3 or ⊗sey1, respectively. Using dually fluorescence-labeled amoeba producing the LCV marker P4C-GFP or AmtA-GFP and the LD marker mCherry-perilipin, we discovered that Sey1 and theL. pneumophilaIcm/Dot T4SS as well as the effector LegG1 promote LCV-LD interactions.In vitroreconstitution of the LCV-LD interactions using purified LCVs and LDs fromD. discoideumAx3 or ⊗sey1revealed that Sey1 and GTP promote this process. The LCV-LD interactions were impaired for ⊗sey1-derived LDs, suggesting that Sey1 regulates LD composition. Palmitate promoted the growth of (i)L. pneumophilawild-type inD. discoideumAx3 but not in ⊗sey1mutant amoeba and (ii)L. pneumophilawild-type but not ⊗fadLmutant bacteria lacking a homologue of theE. colifatty acid transporter FadL. Finally, isotopologue profiling indicated that intracellularL. pneumophilametabolizes13C-palmitate, and its catabolism was reduced inD. discoideum⊗sey1andL. pneumophila⊗fadL. Taken together, our results reveal that Sey1 mediates LD- and FadL-dependent fatty acid metabolism of intracellularL. pneumophila.
The establishment of locally adaptive inversions in structured populations
Authors: Mackintosh Carl , Scott Michael F , Reuter Max , Pomiankowski Andrew
Published: December 2022

Inversions have been proposed to facilitate local adaptation, by linking together locally coadapted alleles at different loci. Classic prior work addressing this question theoretically has considered the spread of inversions in “continent-island” models in which there is a unidirectional flow of maladapted migrants into the island population. In this setting, inversions are most likely to establish when selection is weak, because stronger local selection more effectively purges maladaptive alleles, thus lessening the advantage of inversions. Here, we show this finding only holds under limited conditions. We study the establishment of inversions in a “two-deme” model, which explicitly considers the dynamics of allele frequencies in both populations linked by bidirectional migration. For symmetric selection and migration, we find that stronger local selection increases the flow of maladaptive alleles and favours inversions, the opposite of the pattern seen in the asymmetric continent-island model. Furthermore, we show that the strength and symmetry of selection also change the likelihood that an inversion captures an adaptive haplotype in the first place. Considering the combined process of invasion and capture shows that inversions are most likely to be found when locally adaptive loci experience strong selection. In addition, inversions that establish in one deme also protect adaptive allele combinations in the other, leading to differentiation between demes. Stronger selection in either deme once again makes differentiation between populations more likely. In contrast, differentiation is less likely when migration rates are high because adaptive haplotypes become less common. Overall, this analysis of evolutionary dynamics across a structured population shows that established inversions are most likely to have captured strongly selected local adaptation alleles.
The Axin scaffold protects the kinase GSK3β from cross-pathway inhibition
Authors: Gavagan Maire , Jameson Noel , Zalatan Jesse G.
Published: December 2022

Multiple signaling pathways regulate the kinase GSK3β by inhibitory phosphorylation at Ser9, which then occupies the GSK3β priming pocket and blocks substrate binding. Since this mechanism should affect GSK3β activity towards all primed substrates, it is unclear why Ser9 phosphorylation does not affect other GSK3β-dependent pathways, such as Wnt signaling. We used biochemical reconstitution and cell culture assays to evaluate how Wnt-associated GSK3β is insulated from cross-activation by other signals. We found that the Wnt-specific scaffold protein Axin allosterically protects GSK3β from phosphorylation at Ser9 by upstream kinases, which prevents accumulation of pS9-GSK3β in the Axin-GSK3β complex. Scaffold proteins that protect bound proteins from alternative pathway reactions could provide a general mechanism to insulate signaling pathways from improper crosstalk.
Cross-species analysis reveals unique and shared roles of Sox9 and Sox10 (SOXE family) transcription factors in melanoma
Authors: Kramer Eva T. , Godoy Paula M. , Kaufman Charles K.
Published: December 2022

SOX9 and SOX10 are two highly similar transcription factors with nearly 100% identity at their DNA binding domains. Both transcription factors play key but distinct roles in neural crest cell fate specification and melanoma formation. High expression of SOX9 and SOX10 appear to be mutually exclusive, with high SOX10 characteristic of proliferative melanoma and high SOX9 characteristic of metastatic melanoma. To further elucidate the role of SOX9 in melanoma, we over-express SOX9 in a zebrafish melanoma model and a human melanoma cell line. Analysis of tumor onset, binding dynamics, and transcriptional identities supports the notion of SOX9 driving a more mesenchymal signature, which is important for metastasis. Additionally, we identified a potential mechanism of SOX9 down-regulation via analysis of a functional and recurrent non-coding variant in human melanoma. Altogether, our results present a dosage-dependent role of SOX9 and, likely, SOX10 in the melanoma lifespan.
Unexpected finding ofFusobacterium variumabundance in cattle rumen: implications for liver abscess interventions
Authors: Schwarz Cory , Mathieu Jacques , Gomez Jenny Laverde , Miller Megan R. , Tikhonova Marina , Nagaraja T.G. , Alvarez Pedro J.J.
Published: December 2022

Fusobacterium variumhas been generally overlooked in cattle rumen microbiome studies relative to the presumably more abundant, liver abscess-causingFusobacterium necrophorum. Here, we revisit that conventional wisdom and report greater relative abundance ofF. variumthanF. necrophorumin both raw rumen samples and in lactate-supplemented enrichments tailored forF. necrophorumgrowth, despite its consistent inadvertence in past ruminal surveys and putative inability to metabolize lactate. Our observation thatF. variumgrows under restrictive conditions used to enumerateF. necrophorumsuggests that previous estimations were inaccurate andF. variumis an underestimated player within the ruminal community. Exposure to tylosin, the current gold standard among prophylactic liver abscess prevention strategies in cattle, consistently reduced growth of allF. necrophorumstrains screened by greater than 67% relative to unexposed controls. In contrast,F. variumstrains were completely or highly resistant (0 - 11% reduction in maximum yield). Monensin, an ionophore fed to cattle to improve feed efficiency also had stronger inhibitory activity againstF. necrophorumthan againstF. varium. Finally, preliminary genomic analysis of twoF. variumbovine isolates revealed the presence of virulence genes related to those of pathogenicF. variumhuman isolates associated with active invasion of mammalian cells.

Importance

Judicious antibiotic use is essential to mitigate the spread of antimicrobial resistance. Dogmatic prophylactic use of in-feed tylosin to control cattle liver abscesses hinges on the assumption thatF. necrophorumin the rumen is the main etiologic agent. However, our unexpected finding of abundance ofF. variumin the rumen and its resistance to antibiotics, in hand with the potential pathogenicity of this species, calls for increased attention toF. varium. Further investigation intoF. variumis necessary to better understand bovine liver abscess development and devise higher-precision alternatives to antibiotic treatment.
Lack of effectiveness of Bebtelovimab Monoclonal Antibody Among High-Risk Patients with SARS-Cov-2 Omicron During BA.2, BA.2.12.1 and BA.5 Subvariants Dominated Era
Authors: Sridhara Srilekha , Gungor Ahmet B. , Erol Halil K. , Al-Obaidi Mohanad , Zangeneh Tirdad T. , Bedrick Edward J. , Ariyamuthu Venkatesh K. , Shetty Aneesha , Qannus Abd A. , Mendoza Katherine , Murugapandian Sangeetha , Gupta Gaurav , Tanriover Bekir
Published: December 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants are expected to be resistant to Bebtelovimab (BEB) monoclonal antibody (MAb) and the real-world experience regarding its effectiveness is scarce. This retrospective cohort study reports a data analysis in Banner Healthcare System (a large not-for-profit organization) between 4/5/2022 and 8/1/2022 and included 19,778 Coronavirus disease-19 (COVID-19) positive (by PCR or direct antigen testing) patients who were selected from Cerner-Electronic Health Record after the exclusions criteria were met. The study index date for cohort was determined as the date of BEB MAb administration or the date of the first positive COVID-19 testing. The cohort consist of COVID-19 infected patients who received BEB MAb (N=1,091) compared to propensity score (PS) matched control (N=1,091). The primary outcome was the incidence of 30-day all-cause hospitalization and/or mortality. All statistical analyses were conducted on the paired (matched) dataset. For the primary outcome, the event counts and percentages were reported. Ninety-five percent Clopper-Pearson confidence intervals for percentages were computed. The study cohorts were 1:1 propensity matched without replacement across 26 covariates using an optimal matching algorithm that minimizes the sum of absolute pairwise distance across the matched sample after fitting and using logistic regression as the distance function. The pairs were matched exactly on patient vaccination status, BMI group, age group and diabetes status. Compared to the PS matched control group (2.6%; 95% confidence interval [CI]: 1.7%, 3.7%), BEB MAb use (2.2%; 95% CI: 1.4%, 3.3%) did not significantly reduce the incidence of the primary outcome (p=0.67). In the subgroup analysis, we observed similar no-difference trends regarding the primary outcomes for the propensity rematched BEB MAb treated and untreated groups, stratified by patient vaccination status, age (<65 years or ≥65), and immunocompromised status (patients with HIV/AIDS or solid organ transplants or malignancy including lymphoproliferative disorder). The number needed to treat (1/0.026-0.022) with BEB MAb was 250 to avoid one hospitalization and/or death over 30 days. The BEB MAb use lacked efficacy in patients with SARS-CoV-2 Omicron subvariants (mainly BA.2, BA.2.12.1, and BA.5) in the Banner Healthcare System in the Southwestern United States.
Preferences of health care workers using tongue swabs for tuberculosis diagnosis during COVID-19
Authors: Codsi Renée , Errett Nicole A. , Luabeya Angelique K. , Hatherill Mark , Shapiro Adrienne E. , Lochner Katherine A. , Vingino Alexandria R. , Kohn Marlena J. , Cangelosi Gerard A.
Published: December 2022

Healthcare workers (HCW) who come into contact with tuberculosis (TB) patients are at elevated risk of TB infection and disease. The collection and handling of sputum samples for TB diagnosis poses exposure risks to HCW, particularly in settings where aerosol containment is limited. An alternative sample collection method, tongue swabbing, was designed to help mitigate this risk, and is under evaluation in multiple settings. This study assessed risk perceptions among South African HCW who used tongue swabbing in TB diagnostic research during the COVID-19 pandemic. We characterized their context-specific preferences as well as the facilitators and barriers of tongue swab use in clinical and community settings. Participants (n=18) were HCW with experience using experimental tongue swabbing methods at the South African Tuberculosis Vaccine Initiative (SATVI). We used key informant semi-structured interviews to assess attitudes toward two tongue swab strategies: Provider-collected swabbing (PS) and supervised self-swabbing (SSS). Responses from these interviews were analyzed by rapid qualitative analysis and thematic analysis methods. Facilitators included aversion to sputum (PS and SSS), perceived safety of the method (SSS), and educational resources to train patients (SSS). Barriers included cultural stigmas, as well as personal security and control of their work environment when collecting swabs in community settings. COVID-19 risk perception was a significant barrier to the PS method. Motivators for HCW use of tongue swabbing differed substantially by use case, and whether the HCW has the authority and agency to implement safety precautions in specific settings. These findings point to a need for contextually specific educational resources to enhance safety of and adherence to the SSS collection method.
A high-resolution single-particle cryo-EM hydrated structure ofStreptococcus pyogenesenolase offers insights into its function as a plasminogen receptor
Authors: Tjia-Fleck Sheiny , Readnour Bradley M. , Ayinuola Yetunde A. , Castellino Francis J.
Published: December 2022

Cellular plasminogen (Pg) receptors (PgR) are utilized to recruit Pg, stimulate its activation to the serine protease, plasmin (Pm), and sterically protect the generated Pm from inactivation by natural host inhibitors. The net result is that cells contain a stable proteolytic surface used for biological mechanisms involved in cell migration. One such PgR is the moonlighting enzyme, enolase, some of which leaves the cytoplasm and resides at the cell surface to potentially function as a PgR. Since microbes employ conscription of host Pg by PgRs as one virulence mechanism, we explored the structural basis of the ability ofStreptococcus pyogenesenolase (Sen) to function in this regard. Employing single-particle cryo-electron microscopy (cryo-EM), recombinant Sen fromS. pyogeneswas modeled at 2.6 Å as a stable symmetrical homooctamer displaying point group 422 (D4) symmetry, with a monomeric subunit molecular weight of ~49 kDa. Subunit-subunit interactions showed four major and four minor interfaces in the octamer. Binding sites for hPg were previously proposed to include the COOH-terminal K434,435residues of Sen, but in native Sen these residues are buried within the minor interfaces of the octamer and do not function as a Pg binding epitope. Whereas Sen and hPg do not interact in solution, when Sen is bound to a surface, hPg interacts with Sen independently of K434,434. We propose that the octameric structure of Sen is important to its ability to interact with hPg, but disruption of its overall octameric conformation without dissociation of the octamer exposes neoepitopes for hPg binding.
Mega-scale experimental analysis of protein folding stability in biology and protein design
Authors: Tsuboyama Kotaro , Dauparas Justas , Chen Jonathan , Laine Elodie , Mohseni Behbahani Yasser , Weinstein Jonathan J. , Mangan Niall M. , Ovchinnikov Sergey , Rocklin Gabriel J.
Published: December 2022

Advances in DNA sequencing and machine learning are illuminating protein sequences and structures on an enormous scale. However, the energetics driving folding are invisible in these structures and remain largely unknown. The hidden thermodynamics of folding can drive disease, shape protein evolution, and guide protein engineering, and new approaches are needed to reveal these thermodynamics for every sequence and structure. We present cDNA display proteolysis, a new method for measuring thermodynamic folding stability for up to 900,000 protein domains in a one-week experiment. From 1.8 million measurements in total, we curated a set of ~850,000 high-quality folding stabilities covering all single amino acid variants and selected double mutants of 354 natural and 188 de novo designed protein domains 40-72 amino acids in length. Using this immense dataset, we quantified (1) environmental factors influencing amino acid fitness, (2) thermodynamic couplings (including unexpected interactions) between protein sites, and (3) the global divergence between evolutionary amino acid usage and protein folding stability. We also examined how our approach could identify stability determinants in designed proteins and evaluate design methods. The cDNA display proteolysis method is fast, accurate, and uniquely scalable, and promises to reveal the quantitative rules for how amino acid sequences encode folding stability.

One-Sentence Summary

Massively parallel measurement of protein folding stability by cDNA display proteolysis
Astrocytic engagement of the corticostriatal synaptic cleft is disrupted in a mouse model of Huntington disease
Authors: Villanueva Carlos Benitez , Stephensen Hans J. T. , Mokso Rajmund , Benraiss Abdellatif , Sporring Jon , Goldman Steven A.
Published: December 2022

Astroglial dysfunction contributes to the pathogenesis of Huntington’s disease (HD), and glial replacement can ameliorate disease course. To establish the topographic relationship of diseased astrocytes to medium spiny neuron (MSN) synapses in HD, we used 2-photon imaging to map the relationship of tRFP-tagged striatal astrocytes and rabies-traced, EGFP-tagged coupled neuronal pairs, in R6/2 HD and wild-type (WT) mice. The tagged, prospectively-identified corticostriatal synapses were then studied by correlated light electron microscopy followed by serial block-face scanning EM, allowing nm scale assessment of synaptic structure in 3D. By this means, we compared the astrocytic engagement of single striatal synapses in HD and WT brains. R6/2 HD astrocytes exhibited constricted domains, with significantly less coverage of mature dendritic spines than WT astrocytes, despite enhanced engagement of immature, thin spines. These data suggest that disease-dependent changes in astroglial engagement and sequestration of MSN synapses enable the high synaptic and extrasynaptic levels of glutamate and K+that underlie the striatal hyperexcitability of HD. As such, these data suggest that astrocytic structural pathology may causally contribute to the synaptic dysfunction and disease phenotype of those neurodegenerative disorders characterized by network overexcitation.

Significance Statement

Astrocytic physiological dysfunction contributes to development of the neurodegenerative phenotype in Huntington’s disease (HD), but the structural correlates to this dysfunction are unclear. Here, we used a combination of viral tracing, phenotype-specific tagging, and ultrastructural modalities to reconstruct and study HD synapses at nm scale, in the neostriata of HD mice. We discovered significant impairment in the glial engagement of mature striatal synapses. In light of the known deficiencies in glutamate and potassium uptake by HD astrocytes, these findings suggest the potential for leakage of excitatory synaptic contents during neurotransmission, and hance a structural basis for neuronal hyperexcitability in HD. More broadly, our data suggest that astrocytic structural pathology may causally contribute to those neurodegenerative disorders associated with central hyperexcitability.
Fractions strategy differences in those born extremely preterm
Authors: Carr Sarah , Babinchak W. Michael , Istrate Ana , Martyn-Dow Blaine , Wang George , Chen Weicong , Fondran Jeremy , Zhang Jing , Wien Michael , Yoon Seo Yeon , Birnbaum Anne , Roth Elizabeth , Gross Carol , Minich Nori , Thompson Lee , Kim Won Hwa , Stern Yaakov , Nosarti Chiara , Taylor H. Gerry , Tatsuoka Curtis
Published: December 2022

Introduction

To investigate the effects of different strategies and cognitive load we explored brain hemodynamic responses associated with the use of different strategies to solve subtraction of fractions. We focused on those born extremely preterm (EPT; <28 weeks’ gestation) as they are known to have cognitive challenges and struggle with mathematics. We also included a group of full-term (FT) peers for comparison.

Methods

Functional MRI was acquired while the participants mentally solved fraction equations using either a strategy based on improper or mixed fractions. Different fraction item types were given, which affected respective required cognitive loads per strategy. Diffusion and T1-weighted structural images were also acquired.

Results

The EPT and FT groups differed in terms of task-related hemodynamic responses. Functional group differences were greatest when strategies were applied to item types that result in high cognitive load. Other findings showed reduced white and grey matter volume and reduced white matter connectivity in widespread areas in the EPT group compared to the FT group.

Conclusion

The understanding of function and structure presented here may help inform pedagogical practices by allowing for tailoring of mathematical education through identifying suitable strategy adoption that depends on item type, to circumvent weaknesses in cognitive skills.
Substrate profiling of the metalloproteinase ovastacin – Implications for its physiological function in mammalian fertilization
Authors: Felten Matthias , Distler Ute , Wiegen Nele v. , Łącki Mateusz , Behl Christian , Tenzer Stefan , Stöcker Walter , Körschgen Hagen
Published: December 2022

The metalloproteinase ovastacin is released by the mammalian egg upon fertilization and cleaves a distinct peptide bond in zona pellucida protein 2, a component of the enveloping extracellular matrix. This limited proteolysis causes zona pellucida hardening, abolishes sperm binding and thereby regulates fertility. Accordingly, this process is tightly controlled by the plasma protein fetuin-B, an endogenous competitive inhibitor. At present, little is known about how the cleavage characteristics of ovastacin differ from closely related proteases. Physiological implications of ovastacin beyond ZP2 cleavage are still obscure. In this study, we employed N-terminal amine isotopic labeling of substrates (N-TAILS) contained in the secretome of mouse embryonic fibroblasts to elucidate the substrate specificity and the precise cleavage site specificity. Furthermore, we were able to unravel the physicochemical properties governing enzyme-substrate interactions. Eventually, we identified several potential physiological substrates with significance for mammalian fertilization. These data suggest that ovastacin might regulate sperm-oocyte interaction and fertility beyond zona pellucida hardening.

Graphical Abstract
Interactions betweenMycoplasma mycoidessubsp.mycoidesand bovine macrophages under physiological conditions
Authors: Totté Philippe , Bonnefois Tiffany , Manso-Silván Lucia
Published: December 2022

Abstract

We investigated the interactions of unopsonized and opsonizedMycoplasma mycoidessubsp.mycoides(Mmm) with bovine macrophagesin vitro. Mmmsurvived and proliferated extracellularly on bovine macrophage cell layers in the absence ofMmm-specific antisera. Bovine complement used at non-bactericidal concentrations did neither have opsonizing effect nor promoted intracellular survival, whereasMmm-specific antisera substantially increased phagocytosis andMmmkilling. A phagocytosis-independent uptake ofMmmby macrophages occurred at a high multiplicity of infection, also found to induce the production of TNF, and both responses were unaffected by non-bactericidal doses of bovine complement. Bovine complement used at higher doses killedMmmin cell-free cultures and completely abrogated TNF responses by macrophages. These results provide a framework to identifyMmmantigens involved in interactions with macrophages and targeted by potentially protective antibodies and point towards a pivotal role of complement in the control of inflammatory responses in contagious bovine pleuropneumonia.
EEG correlates of olfactory processing during an instructed-delay task
Authors: Ninenko Ivan , Kleeva Daria F. , Bukreev Nikita , Lebedev Mikhail A.
Published: December 2022

EEG correlates of olfaction are of fundamental and practical interest for many reasons. In the field of neural technologies, olfactory-based brain-computer interfaces (BCIs) represent an approach that could be useful for neurorehabilitation of anosmia, dysosmia and hyposmia. While the idea of a BCI that decodes neural responses to different odors and/or enables odor-based neurofeedback is appealing, the results of previous EEG investigations into the olfactory domain are rather inconsistent, particularly when non-primary processing of olfactory signals is concerned. Here we report the results from an EEG study where an olfaction-based instructed-delay task was implemented. We utilized an olfactory display and a sensor of respiration to present odors in a strictly controlled fashion. Spatio-spectral EEG properties were analyzed to assess the olfactory-related components. Under these experimental conditions, EEG components representing processing of olfactory information were found around channel C4, where changes were detected for the 12-Hz spectral component. Additionally, significant differences in EEG patterns were observed when responses to odors were compared to the responses to odorless stimuli. We conclude EEG recordings are suitable for detecting active processing of odors. As such they could be integrated in a BCI that strives to rehabilitate olfactory disabilities or uses odors for hedonistic purposes.