bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing Optimization Criteria in Antibiotic Allocation Protocols
Authors: Jamieson-Lane Alastair , Friedrich Alexander , Blasius Bernd
Published: November 2021

Clinicians prescribing antibiotics in a hospital context follow one of several possible “treatment protocols” -heuristic rules designed to balance the immediate needs of patients against the long term threat posed by the evolution of antibiotic resistance and multi-resistant bacteria. Several criteria have been proposed for assessing these protocols, unfortunately these criteria frequently conflict with one another, each providing a different recommendation as to which treatment protocol is best. Here we review and compare these optimization criteria. We are able to demonstrate that criteria focused primarily on slowing evolution of resistance are directly antagonistic to patient health both in the short and long term. We provide a new optimization criteria of our own, intended to more meaningfully balance the needs of the future and present. Asymptotic methods allow us to evaluate this criteria and provide insights not readily available through the numerical methods used previously in the literature. When cycling antibiotics, we find an antibiotic switching time which proves close to optimal across a wide range of modelling assumptions.
Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir (PF-07321332)
Authors: Ullrich Sven , Ekanayake Kasuni B. , Otting Gottfried , Nitsche Christoph
Published: November 2021

The COVID-19 pandemic continues to be a public health threat. Multiple mutations in the spike protein of emerging variants of SARS-CoV-2 appear to impact on the effectiveness of available vaccines. Specific antiviral agents are keenly anticipated but their efficacy may also be compromised in emerging variants. One of the most attractive coronaviral drug targets is the main protease (Mpro). A promising Mpro inhibitor of clinical relevance is the peptidomimetic nirmatrelvir (PF-07321332). We expressed Mpro of six SARS-CoV-2 lineages (C.37 Lambda, B.1.1.318, B.1.2, B.1.351 Beta, B.1.1.529 Omicron, P.2 Zeta), each of which carries a strongly prevalent missense mutation (G15S, T21I, L89F, K90R, P132H, L205V). Enzyme kinetics showed that these Mpro variants are similarly catalytically competent as the wildtype. We show that nirmatrelvir has similar potency against the variants as against the wildtype. Our in vitro data suggest that the efficacy of the specific Mpro inhibitor nirmatrelvir is not compromised in current COVID-19 variants.

Graphical abstract
Rate discrimination training may partially restore temporal processing abilities from age-related deficits
Authors: Anderson Samira , DeVries Lindsay , Smith Edward , Goupell Matthew J. , Gordon-Salant Sandra
Published: November 2021

The ability to understand speech in complex environments depends on the brain’s ability to preserve the precise timing characteristics of the speech signal. Age-related declines in temporal processing may contribute to the older adult’s experience of communication difficulty in challenging listening conditions. This study’s purpose was to evaluate the effects of rate discrimination training on auditory temporal processing. A double-blind, randomized control design assigned 77 young normal-hearing, older normal-hearing, and older hearing-impaired listeners to one of two treatment groups: experimental (rate discrimination for 100-Hz and 300-Hz pulse trains) and active control (tone detection in noise). All listeners were evaluated during pre-and post-training sessions using perceptual rate discrimination of 100-, 200-, 300-, and 400-Hz band-limited pulse trains and auditory steady-state responses (ASSRs) to the same stimuli. Training generalization was evaluated using several temporal processing measures and sentence recognition tests that included time-compressed and reverberant speech stimuli. Results demonstrated a session × training group interaction for perceptual and ASSR testing to the trained frequencies (100 and 300 Hz), driven by greater improvements in the training group than in the active control group. Further, post-test rate discrimination of the older listeners reached levels that were equivalent to those of the younger listeners at pre-test. The training-specific gains generalized to untrained frequencies (200 and 400 Hz), but not to other temporal processing or sentence recognition measures. Further, non-auditory inhibition/attention performance predicted training-related improvement in rate discrimination. Overall, the results demonstrate the potential for auditory training to partially restore temporal processing in older listeners and highlight the role of cognitive function in these gains.
COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme
Authors: Fasching Clare L. , Servellita Venice , McKay Bridget , Nagesh Vaishnavi , Broughton James P. , Sotomayor-Gonzalez Alicia , Wang Baolin , Brazer Noah , Reyes Kevin , Streithorst Jessica , Deraney Rachel N. , Stanfield Emma , Hendriks Carley G. , Miller Steve , Ching Jesus , Chen Janice S. , Chiu Charles Y.
Published: November 2021

Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here we present the development and validation of a rapid COVID-19 variant DETECTR®assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene. This assay targets the L452R, E484K/Q/A, and N501Y mutations that are associated with nearly all circulating viral lineages and identifies the two circulating variants of concern, Delta and Omicron. In a comparison of three different Cas12 enzymes, only the newly identified enzyme CasDx1 was able to accurately identify all targeted SNP mutations. An analysis pipeline for CRISPR-based SNP identification from 139 clinical samples yielded an overall SNP concordance of 98% and agreement with SARS-CoV-2 lineage classification of 138/139 compared to viral whole-genome sequencing. We also showed that detection of the single E484A mutation was necessary and sufficient to accurately identify Omicron from other major circulating variants in patient samples. These findings demonstrate the utility of CRISPR-based DETECTR®as a faster and simpler diagnostic than sequencing for SARS-CoV-2 variant identification in clinical and public health laboratories.
Mutation-related apparent myelin, not axon density, drives white matter differences in premanifest Huntington’s disease: Evidence from in vivo ultra-strong gradient MRI
Authors: Casella Chiara , Chamberland Maxime , Laguna Pedro Luque , Parker Greg D. , Rosser Anne E. , Coulthard Elizabeth , Rickards Hugh , Berry Samuel C. , Jones Derek K. , Metzler-Baddeley Claudia
Published: November 2021

White matter (WM) alterations have been observed early in Huntington’s disease (HD) progression but their role in the disease-pathophysiology remains unknown. We exploited ultra-strong-gradient MRI to tease apart contributions of myelin (with the magnetization transfer ratio), and axon density (with the restricted volume fraction from the Composite Hindered and Restricted Model of Diffusion) to WM differences between premanifest HD patients and age- and sex-matched controls. Diffusion tensor MRI (DT-MRI) measures were also assessed. We used tractometry to investigate region-specific changes across callosal segments with well-characterized early- and late-myelinating axonal populations, while brain-wise alterations were explored with tract-based cluster analysis (TBCA). Behavioural measures were included to explore disease-associated brain-function relationships. We detected lower myelin in the rostrum of patients (tractometry: p = 0.0343; TBCA: p = 0.030), but higher myelin in their splenium (p = 0.016). Importantly, patients’ myelin and mutation size were positively associated (all p-values < 0.01), indicating that increased myelination might be a direct result of the mutation. Finally, myelin was higher than controls in younger patients but lower in older patients (p = 0.003), suggesting detrimental effects of increased myelination later in the course of the disease. Higher FR in patients’ left cortico-spinal tract (CST) (p = 0.03) was detected, and was found to be positively associated with MTR in the posterior callosum (p = 0.033), possibly suggesting compensation to myelin alterations. This comprehensive, ultra-strong gradient MRI investigation provides novel evidence of CAG-driven myelin alterations in premanifest HD which may reflect neurodevelopmental, rather than neurodegenerative disease-associated changes.
The Astrin-SKAP Complex Reduces Friction at the Kinetochore-Microtubule Interface
Authors: Rosas-Salvans Miquel , Sutanto Renaldo , Suresh Pooja , Dumont Sophie
Published: November 2021

The kinetochore links chromosomes to spindle microtubules to drive chromosome segregation at cell division. While we know nearly all mammalian kinetochore proteins, how these give rise to the strong yet dynamic microtubule attachments required for function remains poorly understood. Here, we focus on the Astrin-SKAP complex, which localizes to bioriented kinetochores and is essential for chromosome segregation, but whose mechanical role is unclear. Live imaging reveals that SKAP depletion dampens movement and decreases coordination of metaphase sister kinetochores, and increases tension between them. Using laser ablation to isolate kinetochores bound to polymerizing vs depolymerizing microtubules, we show that without SKAP kinetochores move slower on both polymerizing and depolymerizing microtubules, and that more force is needed to rescue microtubules to polymerize. Thus, in contrast to previously described kinetochore proteins that increase grip on microtubules under force, Astrin-SKAP reduces grip, increasing attachment dynamics and force responsiveness and reducing friction. Together, our findings suggest a model where the Astrin-SKAP complex effectively “lubricates” correct, bioriented attachments to help preserve them.
Oxidative Modification of LHC II Associated with Photosystem II and PS I-LHC I-LHC II Membranes
Authors: Kale Ravindra S. , Seep Jacob , Sallans Larry , Frankel Laurie K. , Bricker Terry M.
Published: November 2021

Under aerobic conditions the production of Reactive Oxygen Species (ROS) by electron transport chains is unavoidable, and occurs in both autotrophic and heterotrophic organisms. In photosynthetic organisms both Photosystem II (PS II) and Photosystem I (PS I), in addition to the cytochrome b6/f complex, are demonstrated sources of ROS. All of these membrane protein complexes exhibit oxidative damage when isolated from field-grown plant material. An additional possible source of ROS in PS I and PS II is the distal, chlorophyll-containing light-harvesting array LHC II, which is present in both photosystems. These serve as possible sources of 1O2 produced by the interaction of 3O2 with 3chl* produced by intersystem crossing. We have hypothesized that amino acid residues close to the sites of ROS generation will be more susceptible to oxidative modification than distant residues. In this study, we have identified oxidized amino acid residues in a subset of the spinach LHC II proteins (Lhcb1 and Lhcb2) that were associated with either PS II membranes (i.e. BBYs) or PS I-LHC I-LHC II membranes, both of which were isolated from field-grown spinach. We identified oxidatively modified residues by high-resolution tandem mass spectrometry. Interestingly, two different patterns of oxidative modification were evident for the Lhcb1 and Lhcb2 proteins from these different sources. In the LHC II associated with PS II membranes, oxidized residues were identified to be located on the stromal surface of Lhcb1 and, to a much lesser extent, Lhcb2. Relatively few oxidized residues were identified as buried in the hydrophobic core of these proteins. The LHC II associated with PS I-LHC I-LHC II membranes, however, exhibited fewer surface-oxidized residues but, rather a large number of oxidative modifications buried in the hydrophobic core regions of both Lhcb1 and Lhcb2, adjacent to the chlorophyll prosthetic groups. These results appear to indicate that ROS, specifically 1O2, can modify the Lhcb proteins associated with both photosystems and that the LHC II associated with PS II membranes represent a different population from the LHC II associated with PS I-LHC I-LHC II membranes.
Asking the Wrong Questions About American Science Education: Insights from a Longitudinal Study of High School Biotechnology Lab Instruction
Authors: Micklos Dave , Barone Lindsay
Published: November 2021

The discussion of American science education is often framed by the questions: Why do American precollege students do poorly on international science assessments and what we are doing wrong? Rather we need to ask: Why do so many international students come to US universities for science, what are we doing right in science, and how do we stay ahead in science education? Poor scores on international assessments belie the fact that the U.S. has the best science education system in the world. Our study of 6,200 high school teachers in 1998 and 2018 documented striking success in retooling classrooms for labbased instruction in biotechnology and provided a pre-COVID-19 snapshot of what is right with American biology education. However, it also highlights the need revitalize our precollege teaching resource with a renewed National Science Foundation commitment to in-service training.
A framework for multiplex imaging optimization and reproducible analysis
Authors: Eng Jennifer , Bucher Elmar , Hu Zhi , Zheng Ting , Gibbs Summer L. , Chin Koei , Gray Joe W.
Published: November 2021

Multiplex imaging technologies are increasingly used for single-cell phenotyping and spatial characterization of tissues; however, transparent methods are needed for comparing the performance of platforms, protocols and analytical pipelines. We developed a python software, mplexable, for reproducible image processing and utilize Jupyter notebooks to share our optimization of signal removal, antibody specificity, background correction and batch normalization of the multiplex imaging with a focus on cyclic immunofluorescence (CyCIF). Our work both improves the CyCIF methodology and provides a framework for multiplexed image analytics that can be easily shared and reproduced.
A Binary Matrix Method to Enumerate, Hierarchically Order and Structurally Classify Peptide Aggregation
Authors: Tagad Amol , Singh Reman Kumar , Patwari G. Naresh
Published: November 2021

Protein aggregation is a common and complex phenomenon in biological processes, yet a robust analysis of this aggregation process remains elusive. The commonly used methods such as center-of-mass to center-of-mass (COM–COM) distance, the radius of gyration (Rg), hydrogen bonding (HB) and solvent accessible surface area (SASA) do not quantify the aggregation accurately. Herein, a new and robust method that uses an aggregation matrix (AM) approach to investigate peptide aggregation in a MD simulation trajectory is presented. A nxn two-dimensional aggregation matrix (AM) is created by using the inter-peptide Cα–Cα cut-off distances which are binarily encoded (0 or 1). These aggregation matrices are analyzed to enumerate, hierarchically order and structurally classify the aggregates. Comparison of the present AM method suggests that it is superior to the HB method since it can incorporate non-specific interactions and Rg, COM–COM methods since the cut-off distance is independent of the length of the peptide. More importantly, the present method can structurally classify the peptide aggregates, which the conventional Rg, COM– COM and HB methods fail. The unique selling point of this method is its ability to structurally classify peptide aggregates using two-dimensional matrices.

Abstract Figure
Regional opportunities for Siberian tundra conservation in the next 1000 years
Authors: Kruse Stefan , Herzschuh Ulrike
Published: November 2021

The biodiversity of tundra areas in northern high latitudes is threatened by invasion of forests under global warming. However, poorly understood nonlinear responses of the treeline ecotone mean the timing and extent of tundra losses are unclear but policymakers need such information to optimize conservation efforts. Our individual based model LAVESI, developed for the Siberian tundra-taiga ecotone, can help improve our understanding. Consequently, we simulated treeline migration trajectories until the end of the millennium, causing a loss of tundra area when advancing north. Our simulations reveal that the treeline follows climate warming with a severe, century-long time lag, which is overcompensated by infilling of stands in the long run even when temperatures cool again. Our simulations reveal that only under ambitious mitigation strategies (RCP 2.6) will ~30% of original tundra areas remain in the north but separated into two disjunct refugia.
Dexamethasone induces senescence of lung epithelial cells and augments TGF-β1-mediated production of the fibrosis mediator serpin E1 (plasminogen activator inhibitor-1)
Authors: Longhorne Francesca. L. , Wilkinson Holly N. , Hardman Matthew J. , Hart Simon P.
Published: November 2021

Background

Idiopathic pulmonary fibrosis (IPF) is a progressive, incurable scarring disease of the lungs with a prognosis worse than most cancers. Pathologically, IPF is characterised by upregulation of the pro-fibrotic cytokine transforming growth factor-β1 (TGF-β1), activation of fibroblasts, and deposition of collagen in the alveolar interstitium. Recent evidence has highlighted the role of senescent type 2 alveolar epithelial cells in the pathogenesis of IPF. In a clinical trial, a treatment regimen containing a corticosteroid drug accelerated pulmonary fibrosis leading to more hospitalizations and deaths, particularly in patients with telomere shortening which drives cellular senescence.

Aim

To investigate the potential pro-fibrotic actions of corticosteroids on lung epithelial cellsin vitro, including effects on cellular senescence and interactions with TGF-β1.

Methods

The synthetic glucocorticoid dexamethasone (DEX) was incubated with A549 and BEAS-2B human lung epithelial cells in the presence or absence of TGF-β1. Cellular senescence was assessed by morphology, senescence-associated beta-galactosidase (SA β-Gal) expression, and qPCR for transcription of senescence-associated molecular markers. Conditioned media were screened for growth factors and cytokines and cultured with human lung fibroblasts. An IPF lung tissue RNA array dataset was re-analysed with a focus on senescence markers.

Results

DEX induced senescence in lung epithelial cells associated with increased p21 (CDKN1A) expression independently of p16 (CDKN2A) or p53 (TP53). DEX amplified upregulation of the pro-fibrotic mediator serpin E1/plasminogen activator inhibitor-1 (PAI-1) in the presence of TGF-β1. The senescence-associated secretory phenotype from lung epithelial cells treated with DEX plus TGF-β1-treated contained increased concentrations of GM-CSF and IL-6 and when incubated with primary human lung fibroblasts there were trends to increased senescence and production of fibrosis markers. Upregulation of senescence markers was demonstrated by analysis of an IPF transcriptomic dataset.

Discussion

DEX induces senescence in lung epithelial cell linesin vitroand interacts with TGF-β1 to amplify production of the pro-fibrotic mediator serpin E1 (PAI-1). This may be a mechanism by which corticosteroids promote pulmonary fibrosis in susceptible individuals. Serpin E1/PAI-1 is a potential druggable target in pulmonary fibrosis.
Design of novel specific primers for helicobacter detection with diagnostic utility evaluation of different 16srRNA genus-specific primers: A comparative study
Authors: Abdelmalek Shaymaa , Shokry Karim , Hamed Wafy , Abdelnalser Mohammed , Aboubakr Ashraf , Elenin Sameh Abou , Ali Mohamed , Mostafa Mohamed , Abou-Okada Mahmoud
Published: November 2021

Molecular diagnosis of helicobacters by PCR is simpler, more accurate, and feasible compared to other diagnostic methods. Validity and accuracy are highly dependent on the PCR primer design, diffusion time, and mutation rate of helicobacters. This study aimed to design 16srRNA -specific primers for Helicobacter spp. and H. pylori. Application of comparative statistical analysis of the diagnostic utility of the most available 16srRNA genus-specific primers. The new primers were designed using bioinformatics tools (MAFFT MSA and Gblocks command line). A comparative study was applied on nine genus-specific 16srRNA primers in comparison to the ConsH using Insilco and laboratory evaluation. The results demonstrated that the best specificity and sensitivity of the primers designed for this study compared to other primers. The comparative study revealed that the heminested outer/inner primers were the worst. Although H276,16srRNA(a), HeliS/Heli-nest, and Hcom had acceptable diagnostic utility, false positive and false negative results were obtained. Specificity testing on clinical samples indicated a surprising result; that H. pylori was not the sole enemy that we were looking for, but the NPH should be considered as a real risk prognostic for gastric diseases, consequently, a specific diagnosis and treatment should be developed. This study concluded that our designed primers were the most specific and sensitive in comparison with other primers. in addition, Insilco evaluation is not accurate enough for primer assessment and that the laboratory evaluation is mandatory.
General factors of white matter microstructure from DTI and NODDI in the developing brain
Authors: Vaher Kadi , Galdi Paola , Cabez Manuel Blesa , Sullivan Gemma , Stoye David Q , Quigley Alan J , Thrippleton Michael J , Bogaert Debby , Bastin Mark E , Cox Simon R , Boardman James P
Published: November 2021

Preterm birth is closely associated with diffuse white matter dysmaturation inferred from diffusion MRI and neurocognitive impairment in childhood. Diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) are distinct dMRI modalities, yet metrics derived from these two methods share variance across tracts. This raises the hypothesis that dimensionality reduction approaches may provide efficient whole-brain estimates of white matter microstructure that capture (dys)maturational processes. To investigate the optimal model for accurate classification of generalised white matter dysmaturation in preterm infants we assessed variation in DTI and NODDI metrics across 16 major white matter tracts using principal component analysis and structural equation modelling, in 79 term and 141 preterm infants at term equivalent age. We used logistic regression models to evaluate performances of single-metric and multimodality general factor frameworks for efficient classification of preterm infants based on variation in white matter microstructure. Single-metric general factors from DTI and NODDI capture substantial shared variance (41.8-72.5%) across 16 white matter tracts, and two multimodality factors captured 93.9% of variance shared between DTI and NODDI metrics themselves. General factors associate with preterm birth and a single model that includes all seven DTI and NODDI metrics provides the most accurate prediction of microstructural variations associated with preterm birth. This suggests that despite global covariance of dMRI metrics in neonates, each metric represents information about specific (and additive) aspects of the underlying microstructure that differ in preterm compared to term subjects.

Highlights

We measured variation of 7 DTI and NODDI metrics across 16 major tracts

General factors for DTI and NODDI capture substantial shared variance across tracts

General factors also capture substantial shared variance between DTI and NODDI

Single-metric and multimodality factors associate with gestational age at birth

The best preterm prediction model contains all 7 single-metric g-factors
Kv3 channels contribute to the excitability of sub-populations of spinal cord neurons in lamina VII
Authors: Mullen Pierce , Pilati Nadia , Large Charles H. , Deuchars Jim , Deuchars Susan
Published: November 2021

Autonomic parasympathetic preganglionic neurons (PGN) drive contraction of the bladder during micturition but remain quiescent during bladder filling. This quiescence is postulated to be due to recurrent inhibition of PGN by fast-firing adjoining interneurons. Here, we defined four distinct neuronal types within lamina VII of the lumbosacral spinal cord, where PGN are situated, by combining whole cell patch clamp recordings with k-means clustering of a range of electrophysiological parameters. Additional morphological analysis separated these neuronal classes into parasympathetic preganglionic populations (PGN) and a fast firing interneuronal population. Kv3 channels are voltage-gated potassium channels (Kv) that allow fast and precise firing of neurons. We found that blockade of Kv3 channels by tetraethylammonium (TEA) reduced neuronal firing frequency and isolated high-voltage-activated Kv currents in the fast-firing population but had no effect in PGN populations. Furthermore, Kv3 blockade potentiated the local and descending inhibitory inputs to PGN indicating that Kv3-expressing inhibitory neurons are synaptically connected to PGN. Taken together, our data reveal that Kv3 channels are crucial for fast and regulated neuronal output of a defined population that may be involved in intrinsic spinal bladder circuits that underpin recurrent inhibition of PGN.

Significance statement

Neural circuits in the spinal cord and pons mediate the micturition reflex. The spinal cord drives bladder contraction during micturition through the activation of parasympathetic preganglionic neurons in lamina VII of the lumbosacral spinal cord. Despite the significant contribution of these neurons to a crucial physiological reflex, neurons in this region have been under-characterised. This study therefore elucidated and thoroughly characterised distinct neuronal populations in this lamina; we propose that these populations included a fast firing interneuron and subtypes of parasympathetic preganglionic neurons. Further investigation revealed the critical importance of Kv3 channels in the fast firing ability of the interneurons, as well as in synaptic release onto parasympathetic preganglionic neurons.
Priority conservation areas and a global population estimate for the Critically Endangered Philippine Eagle derived from modelled range metrics using remote sensing habitat characteristics
Authors: Sutton Luke J. , Ibañez Jayson C. , Salvador Dennis I. , Taraya Rowell L. , Opiso Guiller S. , Senarillos Tristan Luap P. , McClure Christopher J.W.
Published: November 2021

Many range-restricted taxa are currently experiencing population declines yet lack fundamental information regarding distribution and population size. Establishing baseline estimates for both these key biological parameters is however critical for directing conservation planning for at-risk range-restricted species. The International Union for the Conservation of Nature (IUCN) Red List uses three range metrics that define species distributions and inform extinction risk assessments: extent of occurrence (EOO), area of occupancy (AOO) and area of habitat (AOH). However, calculating all three metrics using standard IUCN approaches relies on a geographically representative sample of locations, which for rare species is often spatially biased. Here, we apply model-based interpolation using Species Distribution Models (SDMs), correlating occurrences with remote-sensing covariates, to calculate IUCN range metrics, protected area coverage and a global population estimate for the Critically Endangered Philippine Eagle (Pithecophaga jefferyi). Our final range wide continuous SDM had high predictive accuracy (Continuous Boyce Index = 0.927) and when converted to a binary model estimated an AOH = 23,185 km2, a maximum EOO = 605,759 km2, a minimum EOO = 272,272 km2, with an AOO = 53,867 km2. Based on inferred habitat from the AOH metric, we estimate a global population of 318 breeding pairs (range: 258-362 pairs), or 636 mature individuals, across the Philippine Eagle global range. Protected areas covered 34 % of AOH, 15 % less than the target representation, with the continuous model identifying key habitat as priority conservation areas. We demonstrate that even when occurrences are geographically biased, robust habitat models can be built that enable quantification of baseline IUCN range metrics, protected area coverage, and a population size estimate. In the absence of adequate location data for many rare and threatened taxa, our method is a promising spatial modelling tool with widespread applications, in particular for island endemics facing high extinction risk.
The Endosomal Sorting Complex, ESCRT, has diverse roles in blood progenitor maintenance, lineage choice and immune response
Authors: Ray Arindam , Rai Yashashwinee , Inamdar Maneesha S
Published: November 2021

Most hematological malignancies are associated with reduced expression of one or more components of the Endosomal Sorting Complex Required for Transport (ESCRT). However, the roles of ESCRT in stem cell and progenitor maintenance are not resolved. The difficulty in parsing signaling pathway roles in relation to their canonical cargo sorting function poses a challenge. TheDrosophilahematopoietic organ, the larval lymph gland, provides a path to dissect the roles of cellular trafficking pathways such as ESCRT in blood development and maintenance.Drosophilahas 13 core ESCRT components. Knockdown of individual ESCRTs showed that only Vps28 and Vp36 were required in all lymph gland progenitors. Using the well-conserved ESCRT-II complex (Vps22, Vps25 and Vps36) as an example of the range of phenotypes seen upon ESCRT depletion, we show that ESCRTs have cell autonomous as well as non-autonomous roles in progenitor maintenance and differentiation. ESCRT depletion also sensitized posterior lymph gland progenitors to respond to immunogenic cues such as wasp infestation. We also identify key heterotypic roles for ESCRT in position-dependent control of Notch activation to suppress crystal cell differentiation. Our study shows that the cargo sorting machinery can determine progenitor identity and capacity to adapt to the dynamic environments that blood cells are exposed to. These mechanisms for control of cell fate may tailor developmental diversity in multiple contexts.
Distractibility and impulsivity neural states are distinct from attention states and modulate the implementation of attention
Authors: Amengual JL , Di Bello F , Ben Hadj Hassen S , Hamed Suliann Ben
Published: November 2021

In the context of visual attention, it has been classically assumed that missing the response to a target or erroneously selecting a distractor occurs as a consequence of the (miss)allocation of attention in space. In the present paper, we challenge this view and provide evidence that, in addition to encoding spatial attention, prefrontal neurons also encode a distractibility-to-impulsivity state. Using supervised dimensionality reduction techniques, we identify two partially overlapped neuronal subpopulations associated either with attention or overt behaviour. The degree of overlap accounts for the behavioural gain associated with the good allocation of attention. We further describe the neural variability accounting for distractibility-to-impulsivity behaviour by a two dimensional state associated with optimality in task and responsiveness. Overall, we thus show that behavioural performance arises from the integration of task-specific neuronal processes and pre-existing neuronal states describing task-independent behavioural states, shedding new light on attention disorders such as ADHD.
Transposon Extermination Reveals Their Adaptive Fitness Contribution
Authors: Cranz-Mileva Susanne , Reilly Eve , Chalhoub Noor , Patel Rohan , Atanassova Tania , Cao Weihuan , Ellison Christopher , Zaratiegui Mikel
Published: November 2021

Transposable Elements are molecular parasites that persist in their host genome by generating new copies to outpace natural selection. Here we measure the parameters governing the copy number dynamics of the fission yeast Tf2 retrotransposons, using experimental and natural populations and a strain where all Tf2 copies are removed. Natural population genomes display active and persistent Tf2 colonies, but in the absence of selection mitotic recombination deletes Tf2 elements at rates that far exceed transposition. We show that Tf2 elements provide a fitness contribution to their host by dynamically rewiring the transcriptional response to metabolic stress. Therefore, Tf2 elements exhibit a mutualistic rather than parasitic behavior toward their host.
Metabolic strategies of sharing pioneer bacteria mediating fresh macroalgae breakdown
Authors: Brunet Maéva , Duff Nolwen Le , Barbeyron Tristan , Thomas François
Published: November 2021

Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of “pioneer” bacteria within the flavobacterial genusZobelliato initiate the degradation of fresh brown macroalgae, which has received little attention compared to the degradation of isolated polysaccharides.Zobellia galactanivoransDsijTcould use macroalgae as a sole carbon source and extensively degrade algal tissues without requiring physical contact,viathe secretion of extracellular enzymes. This indicated a sharing behaviour, whereby pioneers release public goods that can fuel other bacteria. Comparisons of eightZobelliastrains, and strong transcriptomic shifts inZ. galactanivoranscells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include stress resistance proteins, type IX secretion system proteins and novel uncharacterized Polysaccharide Utilization Loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the niche, metabolism and evolution of pioneer degraders, as well as their cooperative interactions within microbial communities, as key players in macroalgal biomass turnover.
OPTN limits herpes stromal keratitis severity and demyelination through negative regulation of IL-17 and hyperinflammatory T-cell response
Authors: Ames Joshua , Yadavalli Tejabjiram , Patil Chandrashekhar , Hopkins James , Bhattacharya Ilina , Shukla Deepak
Published: November 2021

Herpes stromal keratitis (HSK) is a result of the inflammatory sequelae following primary and recurrent Herpes simplex virus type-1 (HSV-1) infections. This pathology is known to be mediated by immunopathogenic T cell responses against viral antigens, however most individuals infected with HSV-1 never exhibit signs of this immunopathology. Recent studies have identified the host restriction factor, optineurin (OPTN), as an inhibitor of viral spread in the central nervous system, protecting hosts from viral encephalopathy. In an HSV-1 corneal infection mouse model on OPTN knockout mice, we assess the contribution of OPTN to ameliorating the clinical manifestations of HSK. We identify that OPTN protects the host from loss of ocular and whisker sensitivity and opacification of the cornea. scRNA-seq of the trigeminal ganglion (TG) reveals that transcription changes to the peripheral neurons and immune cell populations drive the expression of Il-17A in CD4 and CD8 T cells, as well as increased infiltration of T cells into the TG. This leads to demyelination and the observed HSK pathology.
TractoInferno: A large-scale, open-source, multi-site database for machine learning dMRI tractography
Authors: Poulin Philippe , Theaud Guillaume , Rheault Francois , St-Onge Etienne , Bore Arnaud , Renauld Emmanuelle , de Beaumont Louis , Guay Samuel , Jodoin Pierre-Marc , Descoteaux Maxime
Published: November 2021

TractoInferno is the world’s largest open-source multi-site tractography database, including both research- and clinical-like human acquisitions, aimed specifically at machine learning tractography approaches and related ML algorithms. It provides 284 datasets acquired from 3T scanners across 6 different sites. Available data includes T1-weighted images, single-shell diffusion MRI (dMRI) acquisitions, spherical harmonics fitted to the dMRI signal, fiber ODFs, and reference streamlines for 30 delineated bundles generated using 4 tractography algorithms, as well as masks needed to run tractography algorithms. Manual quality control was additionally performed at multiple steps of the pipeline. We showcase TractoInferno by benchmarking the learn2track algorithm and 5 variations of the same recurrent neural network architecture. Creating the TractoInferno database required approximately 20,000 CPU-hours of processing power, 200 man-hours of manual QC, 3,000 GPU-hours of training baseline models, and 4 Tb of storage, to produce a final database of 350 Gb. By providing a standardized training dataset and evaluation protocol, TractoInferno is an excellent tool to address common issues in machine learning tractography.
Non-uniform distribution of dendritic nonlinearities differentially engages thalamostriatal and corticostriatal inputs onto cholinergic interneurons
Authors: Oz Osnat , Matityahu Lior , Mizrahi-Kliger Aviv , Kaplan Alexander , Berkowitz Noa , Tiroshi Lior , Bergman Hagai , Goldberg Joshua A.
Published: November 2021

The tonic activity of striatal cholinergic interneurons (CINs) is modified differentially by their afferent inputs. Although their unitary synaptic currents are identical, in most CINs cortical inputs onto distal dendrites only weakly entrain them, whereas proximal thalamic inputs trigger abrupt pauses in discharge in response to salient external stimuli. To test whether the dendritic expression of the active conductances that drive autonomous discharge contribute to the CINs’ capacity to dissociate cortical from thalamic inputs, we used an optogenetics-based method to quantify dendritic excitability. We found that the persistent sodium (NaP) current gave rise to dendritic boosting, and that the hyperpolarization-activated cyclic nucleotide-gated (HCN) current gave rise to a subhertz membrane resonance. This resonance may underlie our novel finding of an association between CIN pauses and internally-generated slow wave events in sleeping non-human primates. Moreover, our method indicated that dendritic NaP and HCN currents were preferentially expressed in proximal dendrites. We validated the non-uniform distribution of NaP currents pharmacologically; with two-photon imaging of dendritic back-propagating action potentials; and by demonstrating boosting of thalamic, but not cortical, inputs by NaP currents. Thus, the localization of active dendritic conductances in CIN dendrites mirrors the spatial distribution of afferent terminals and may promote their differential responses to thalamic vs. cortical inputs.
Differential EDS1 requirement for cell death activities of plant TIR-domain proteins
Authors: Johanndrees Oliver , Baggs Erin L. , Uhlmann Charles , Locci Federica , Läßle Henriette L. , Melkonian Katharina , Käufer Kiara , Dongus Joram A. , Nakagami Hirofumi , Krasileva Ksenia V. , Parker Jane E. , Lapin Dmitry
Published: November 2021

Toll/interleukin-1 Receptor (TIR) domains are integral to immune systems across all domains of life. TIRs exist as single-domain and as larger receptor or adaptor proteins. In plants, TIRs constitute N-terminal domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors. Although TIR-NLR and TIR signaling requires the Enhanced disease susceptibility 1 (EDS1) protein family, TIR domains persist in species that have incomplete or no EDS1 members. To assess whether particular TIR groups appear with EDS1, we searched for TIR-EDS1 co-occurrence patterns. Using a large-scale phylogenetic analysis of TIR domains from 39 algae and land plant species, we identify four conserved TIR groups, two of which are TIR-NLRs present in eudicots and two are more widespread. Presence of one TIR-only protein group is highly correlated with EDS1 and members of this group elicit EDS1-dependent cell death. By contrast, a more widely represented TIR group of TIR-NB-WD40/TPR (TNP) proteins (formerly called XTNX) has at least one member which can induce EDS1-independent cell death. Our data provide a new phylogeny-based plant TIR classification and identify TIR groups that appear to have evolved with and are dependent on EDS1, while others have EDS1-independent activity.

One sentence summary

Land plants have evolved four conserved TIR groups
Bet-hedging antimicrobial strategies in macrophage phagosome acidification drive the dynamics ofCryptococcus neoformansintracellular escape mechanisms
Authors: Dragotakes Quigly , Jacobs Ella , Ramirez Lia Sanchez , Yoon Insun , Perez-Stable Caitlin , Eden Hope , Pagnotta Jenlu , Vij Raghav , Bergman Aviv , D’Alessio Franco , Casadevall Arturo
Published: November 2021

The fungusCryptococcus neoformansis a major human pathogen with a remarkable intracellular survival strategy that includes exiting macrophages through non-lytic exocytosis (Vomocytosis) and transferring between macrophages (Dragotcytosis) by a mechanism that involves sequential events of non-lytic exocytosis and phagocytosis. Vomocytosis and Dragotcytosis are fungal driven processes, but their triggers are not understood. We hypothesized that the dynamics of Dragotcytosis could inherit the stochasticity of phagolysosome acidification and that Dragotcytosis was triggered by fungal cell stress. Consistent with this view, fungal cells involved in Dragotcytosis reside in phagolysosomes characterized by low pH and/or high oxidative stress. Using fluorescent microscopy, qPCR, live cell video microscopy, and fungal growth assays we found that the that mitigating pH or oxidative stress abrogated Dragotcytosis frequency, that ROS susceptible mutants ofC. neoformansunderwent Dragotcytosis more frequently. Dragotcytosis initiation was linked to phagolysosomal pH and oxidative stresses and correlated with the macrophage polarization state. Dragotcytosis manifested stochastic dynamics thus paralleling the dynamics of phagosomal acidification, which correlated with the inhospitality of phagolysosomes in differently polarized macrophages. Hence, randomness in phagosomal acidification randomly created a population of inhospitable phagosomes where fungal cell stress triggered stochasticC. neoformansnon-lytic exocytosis dynamics to escape a non-permissive intracellular macrophage environment.
Structured connectivity in the cerebellum enables noise-resilient pattern separation
Authors: Nguyen Tri M. , Thomas Logan A. , Rhoades Jeff L. , Ricchi Ilaria , Yuan Xintong Cindy , Sheridan Arlo , Hildebrand David G. C. , Funke Jan , Regehr Wade G. , Lee Wei-Chung Allen
Published: November 2021

The cerebellum is thought to detect and correct errors between intended and executed commands1–3 and is critical for social behaviors, cognition and emotion4–6. Computations for motor control must be performed quickly to correct errors in real time and should be sensitive to small differences between patterns for fine error correction while being resilient to noise7. Influential theories of cerebellar information processing have largely assumed random network connectivity, which increases the encoding capacity of the network’s first layer8–13. However, maximizing encoding capacity reduces resiliency to noise7. To understand how neuronal circuits address this fundamental tradeoff, we mapped the feedforward connectivity in the mouse cerebellar cortex using automated large-scale transmission electron microscopy (EM) and convolutional neural network-based image segmentation. We found that both the input and output layers of the circuit exhibit redundant and selective connectivity motifs, which contrast with prevailing models. Numerical simulations suggest these redundant, non-random connectivity motifs increase discriminability of similar input patterns at a minimal cost to the network’s overall encoding capacity. This work reveals how neuronal network structure can balance encoding capacity and redundancy, unveiling principles of biological network architecture with implications for artificial neural network design.
Modeling Alternate Conformations with Alphafold2 via Modification of the Multiple Sequence Alignment
Authors: Stein Richard A. , Mchaourab Hassane S.
Published: November 2021

The unprecedented performance of Deepmind’s Alphafold2 in predicting protein structure in CASP XIV and the creation of a database of structures for multiple proteomes is reshaping structural biology. Moreover, the availability of Alphafold2’s architecture and code has stimulated a number of questions on how to harness the capabilities of this remarkable tool. A question of central importance is whether Alphafold2’s architecture is amenable to predict the intrinsic conformational heterogeneity of proteins. A general approach presented here builds on a simple manipulation of the multiple sequence alignment, via in silico mutagenesis, and subsequent modeling by Alphafold2. The approach is based in the concept that the multiple sequence alignment encodes for the structural heterogeneity, thus its rational manipulation will enable Alphafold2 to sample alternate conformations and potentially structural alterations due to point mutations. This modeling pipeline is benchmarked against canonical examples of protein conformational flexibility and applied to interrogate the conformational landscape of membrane proteins. This work broadens the applicability of Alphafold2 by generating multiple protein conformations to be tested biologically, biochemically, biophysically, and for use in structure-based drug design.
TRPA1: A Potential Prognostic Indicator for Oral Squamous Cell Carcinoma
Authors: Chakraborty Rajdeep , Jabeen Amara , Hu Honghua , Darido Charbel , Vickery Karen , Ranganathan Shoba
Published: November 2021

Introduction

Transient receptors are related to oral cancer pain. Previously capsaicin (TRPV1 agonist) was shown to induce cell death in oral cancer cells. We hypothesised that these receptors are present in oral cancer.

Method

We examined the presence of cannabinoid receptors (CB1 and CB2) and targets (TRPV1, TRPA1, CaV 3.1, CaV 3.2, CaV 3.3) via quantitative polymerase chain reaction (qPCR) in oral cancer cells SCC4, SCC9, SCC25, Cal27, and normal oral cell line OKF6.

Result

Cannabinoid receptors are absent in all the cell lines, while TRPA1 is only present in normal cells, but absent in all the oral cancer cell lines. Voltage-gated calcium channels are present in all the cell lines.

Conclusion and Future Aspects

TRPA1 could be the possible future prognostic indicator of oral squamous cell carcinoma. Future functionality assays could use precancerous cell lines to follow the loss of TRPA1.