bluuebunny/crossref_metadata_2025 huggingface dataset:
Tree-based automated machine learning to predict biogas production for anaerobic co-digestion of organic waste
Authors: Wang Yan , Huntington Tyler , Scown Corinne D.
Published: July 2021

The dynamics of microbial communities involved in anaerobic digestion of mixed organic waste are notoriously complex and difficult to model, yet successful operation of anaerobic digestion is critical to the goals of diverting high-moisture organic waste from landfills. Machine learning (ML) is ideally suited to capturing complex and nonlinear behavior that cannot be modeled mechanistically. This study uses 8 years of data collected from an industrial-scale anaerobic co-digestion (AcoD) operation at a municipal wastewater treatment plant in Oakland, California, combined with a powerful automated ML method, Tree-based Pipeline Optimization Tool, to develop an improved understanding of how different waste inputs and operating conditions impact biogas yield. The model inputs included daily input volumes of 31 waste streams and 5 operating parameters. Because different wastes are broken down at varying rates, the model explored a range of time lags ascribed to each waste input ranging from 0 to 30 days. The results suggest that the waste types (including rendering waste, lactose, poultry waste, and fats, oils, and greases) differ considerably in their impact on biogas yield on both a per-gallon basis and a mass of volatile solids basis, while operating parameters are not useful predictors in a carefully operated facility.
Protozoan predation drives adaptive divergence in Pseudomonas fluorescens SBW25; ecology meets experimental evolution
Authors: Golzar Farhad S. , Ferguson Gayle C. , Hendrickson Heather Lyn
Published: July 2021

Protozoan predators can affect the structure of bacterial communities, but investigations of how predation might influence bacterial evolution and antagonistic behaviours are scarce. Here, we performed a 20-day predator-prey evolution experiment on solid media to investigate the effect of continuous protozoan predation on bacterial traits using Pseudomonas fluorescens SBW25 as prey and Naegleria gruberi as an amoeboid predator. We observed the divergence of colony morphotypes coincident with an increase in bacterial grazing resistance and relative prey fitness in selected bacterial isolates. When subjected to these resistant prey, N. gruberi show reduced activity (increased encystment) and limited replication. An investigation of the mutations responsible for predation resistance reveals mutations in wspF and amrZ genes, affecting biofilm formation and motility. The bacterial mutants in the wspF gene successfully colonise the air-liquid interface and produce robust cellulose biofilms that prevent predation. The mutation in the amrZ mutant withstands predation but this variant produces low levels of cellulose and limited swarming motility. Our findings suggest that protozoan predation can profoundly influence the course of genetic and phenotypic evolution in a short period.
Trophic status and local conditions affect microbial potential for denitrification versus internal nitrogen cycling in lake sediments
Authors: Baumann K.B.L. , Thoma R. , Callbeck C.M. , Niederdorfer R. , Schubert C.J. , Müller B. , Lever M.A. , Bürgmann H.
Published: July 2021

The nitrogen (N) cycle is of global importance as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbial transformation processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates in the sediments from porewater concentration gradients. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in the sediments were reflected in distinct microbial community compositions and significant differences in the abundance of various N transformation genes. Within each lake, we observed a more pronounced spatial than seasonal variability. The eutrophic Lake Baldegg showed a higher denitrification potential with highernosZgene (N2O reductase) abundance and highernirS:nirK(nitrite reductase) ratio, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for DNRA and nitrification, and specifically a high abundance ofNitrospirae, including some capable of comammox. In general, the oligotrophic lake ecosystems had a higher microbial diversity, thus acting as an important habitat for oligotrophic microbes. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding the limitations of the N cycle response to environmental drivers.

Importance¶

Anthropogenic nitrogen (N) inputs can lead to eutrophication in aquatic systems, specifically in N limited coastal ecosystems. Lakes act as N sinks by transforming reactive N to N2through denitrification or anammox. The N cycle in lake sediments is mediated by microbial processes and affected by environmental drivers such as the amount and quality of settling organic material or nitrate concentration. However, the microbial communities mediating the different N transformation processes and their impact on N removal in freshwater lake sediments remain largely unknown. We provide the first seasonally and spatially resolved metagenomic analysis of the N cycle in the sediments of two lakes with different trophic states. We show that the trophic state of lakes provokes other microbial communities with characteristic key players and functional potential for N transformation.
PD-1 in hippocampal neurons regulates excitability, synaptic plasticity, and cognition
Authors: Zhao Junli , Bang Sangsu , McGinnis Aidan , Furutani Kenta , Jiang Changyu , Roberts Alexus , Donnelly Christopher R , He Qianru , Ko Mei-Chuan , Wang Haichen , Palmiter Richard D. , Ji Ru-Rong
Published: July 2021

Immunotherapy using monoclonal antibodies against programmed cell death protein 1 (PD-1) demonstrated improved survival in cancer patients through immune activation. Here we show that functional PD-1 is expressed in mouse and primate hippocampal neurons and PD-1 inhibition improves cognition in physiological and pathological conditions. Mice lacking the Pdcd1 gene encoding PD-1 exhibit enhanced long-term potentiation (LTP) and learning and memory. These behavioral and cellular changes can be recapitulated by selective deletion of Pdcd1 in hippocampal excitatory neurons but not in microglia. Perfusion of mouse or nonhuman primate brain slices with anti-PD-1 antibody is sufficient to increase excitability in CA1 hippocampal neurons. Conversely, re-expression of Pdcd1 in PD-1 deficient hippocampal neurons suppresses memory and LTP. Traumatic brain injury impairs learning and memory, which is improved by intraventricular administration of anti-PD-1. These findings suggest that anti-PD-1 treatment has therapeutic potential to counteract cognitive decline.

Highlights

Adult mice lacking Pdcd1 in hippocampal neurons exhibit enhanced memory and LTP

Anti-PD-1 antibody treatment increases CA1 neuron excitability in brain slices of mice and primates

Re-expression of Pdcd1 in PD-1 deficient hippocampal neurons impairs memory and LTP

Cognitive deficits after traumatic brain injury are improved by anti-PD-1 treatment
Multiplex base editing to convert TAG into TAA codons in the human genome
Authors: Chen Yuting , Hysolli Eriona , Chen Anlu , Casper Stephen , Liu Songlei , Yang Kevin , Liu Chenli , Church George
Published: July 2021

Large-scale recoding has been shown to enable novel amino acids, biocontainment and viral resistance in bacteria only so far. Here we extend this to human cells demonstrating exceptional base editing to convert TAG to TAA for 33 essential genes via a single transfection, and examine base-editing genome-wide (observing ~ 40 C-to-T off-target events in essential gene exons). We also introduce GRIT, a computational tool for recoding. This demonstrates the feasibility of recoding, and multiplex editing in mammalian cells.
Image-based assessment of plant disease progression identifies new genetic loci for resistance
Authors: Méline Valérian , Caldwell Denise L. , Kim Bong-Suk , Baireddy Sriram , Yang Changye , Sparks Erin E. , Delp Edward J. , Iyer-Pascuzzi Anjali S.
Published: July 2021

A major challenge in global crop production is mitigating yield loss due to plant diseases. One of the best means of disease control is plant resistance, but the identification of genes that promote resistance has been limited by the subjective quantification of disease, which is typically scored by the human eye. We hypothesized that image-based, non-destructive quantification of disease phenotypes would enable the rapid identification of new disease resistance loci. We tested this using the interaction between tomato andRalstonia solanacearum, a soilborne pathogen that causes bacterial wilt disease. We acquired over 40,000 time-series images of disease progression in a tomato recombinant inbred line population, and developed an image analysis pipeline providing a suite of ten traits to quantify wilt disease based on plant shape and size. Quantitative trait loci (QTL) analyses using image-based phenotyping identified QTL that were both unique and shared compared with those identified by human assessment of wilting. When shared loci were identified, image-based phenotyping could detect some QTL several days earlier than human assessment. Thus, expanding the phenotypic space of disease with image-based, non- destructive phenotyping allowed both earlier detection and identified new genetic components of resistance.
Capsaicin alters human NaV1.5 mechanosensitivity
Authors: Cowan Luke M. , Strege Peter R. , Rusinova Radda , Andersen Olaf S. , Beyder Arthur , Farrugia Gianrico
Published: July 2021

SCN5A-encoded NaV1.5 is a voltage-gated Na+ channel expressed in cardiac myocytes and human gastrointestinal (GI) smooth muscle cells (SMCs). NaV1.5 contributes to electrical excitability in the heart and slow waves in the gut. NaV1.5 is also mechanosensitive, and mechanical force modulates several modes of NaV1.5’s voltage-dependent function. NaV1.5 mutations in patients with cardiac arrhythmias and gastrointestinal diseases lead to abnormal mechano- and voltage-sensitivity. Membrane permeable amphipathic drugs that target NaV1.5 in the heart and GI tract alter NaV1.5 mechanosensitivity (MS), suggesting that amphipaths may be a viable therapeutic option for modulating NaV1.5 function. We therefore searched for membrane-permeable amphipathic agents that would modulate NaV1.5 MS with minimal effect on NaV1.5 voltage-gating intact to more selectively target mechanosensitivity. We used two methods to assess NaV1.5 MS: (1) membrane suction in cell-attached macroscopic patches and (2) fluid shear stress on whole cells. We tested the effect of capsaicin on NaV1.5 MS by examining macropatch and whole-cell Na+ current parameters with and without force. The pressure- and shear-mediated peak current increase and acceleration were effectively abolished by capsaicin. Capsaicin abolished the mechanosensitive shifts in the voltage-dependence of activation (shear) and inactivation (pressure and shear). Exploring the recovery from inactivation and use-dependent entry into inactivation, we found divergent stimulus-dependent effects that could potentiate or mitigate the effect of capsaicin, suggesting that mechanical stimuli may differentially modulate NaV1.5 MS. We conclude that selective modulation of MS makes capsaicin is a novel modulator of NaV1.5 MS and a promising therapeutic candidate.
Long-read transcriptome sequencing analysis with IsoTools
Authors: Lienhard Matthias , van den Beucken Twan , Timmermann Bernd , Hochradel Myriam , Boerno Stefan , Caiment Florian , Vingron Martin , Herwig Ralf
Published: July 2021

Long-read transcriptome sequencing (LRTS) holds the promise to boost our understanding of alternative splicing. Recent advances in accuracy and throughput have diminished the major limitations and enabled the direct quantification of isoforms. Considering the complexity of the data and the broad range of potential applications, it is clear that highly flexible, accurate analysis tools are crucial. Here, we present IsoTools, a comprehensive Python-based analysis package, for the improvement of alternative and differential splicing analysis. Iso-Tools provides a comprehensive data structure that integrates genomic information from LRTS transcripts together with the reference annotation, and enables broad functionality to quality control, visualize and analyze the data. Additionally, we implemented a graph-based method for the identification of alternative splicing events and a statistical approach based on the beta binomial distribution for the detection of differential events. To demonstrate our methods, we generated PacBio Iso-Seq data of human hepatocytes treated with the HDAC inhibitor valproic acid, a compound known to induce widespread transcriptional changes. Contrasted with short read RNA-Seq of the same samples, this analysis shows that LRTS provides valuable additional insights for a better understanding of alternative splicing, in particular with respect to complex novel and differential splicing events. IsoTools is made available for the community along with extensive documentation at https://github.com/MatthiasLienhard/isotools.
IL7Rα is required for hematopoietic stem cell reconstitution of tissue-resident lymphoid cells
Authors: Worthington Atesh K. , Cool Taylor S. , Poscablo Donna M. , Hussaini Adeel , Beaudin Anna E. , Forsberg E. Camilla
Published: July 2021

Traditional, adult-derived lymphocytes that circulate provide adaptive immunity to infection and pathogens. However, subsets of lymphoid cells are also found in non-lymphoid tissues and are called tissue-resident lymphoid cells (TLCs). TLCs encompass a wide array of cell types that span the spectrum of innate-to-adaptive immune function. Unlike traditional lymphocytes that are continuously generated from hematopoietic stem cells (HSCs), many TLCs are of fetal origin and poorly generated from adult HSCs. Here, we sought to understand the development of murine TLCs across multiple tissues and therefore probed the roles of Flk2 and IL7Rα, two cytokine receptors with known roles in traditional lymphopoiesis. Using Flk2- and Il7r-Cre lineage tracing models, we found that peritoneal B1a cells, splenic marginal zone B (MZB) cells, lung ILC2s and regulatory T cells (Tregs) were highly labeled in both models. Despite this high labeling, highly quantitative, in vivo functional approaches showed that the loss of Flk2 minimally affected the generation of these cells in situ. In contrast, the loss of IL7Rα, or combined deletion of Flk2 and IL7Rα, dramatically reduced the cell numbers of B1a cells, MZBs, ILC2s, and Tregs both in situ and upon transplantation, indicating an intrinsic and more essential role for IL7Rα. Surprisingly, reciprocal transplants of WT HSCs showed that an IL7Rα-/- environment selectively impaired reconstitution of TLCs when compared to TLC numbers in situ. Taken together, our data revealed functional roles of Flk2 and IL7Rα in the establishment of tissue-resident lymphoid cells.
Citrus photosynthesis and morphology acclimate to phloem-affecting huanglongbing disease at the leaf and shoot levels
Authors: Keeley Mark , Rowland Diane , Vincent Christopher
Published: July 2021

Huanglongbing (HLB) is a phloem-affecting disease of citrus that reduces growth and has impacted global citrus production. HLB is caused by a phloem-limited bacterium (CandidatusLiberibacter asiaticus;CLas). By inhibiting phloem function, HLB stunts sink growth, including reducing production of new shoots and leaves, and induces hyperaccumulation of foliar starch. HLB induces feedback inhibition of photosynthesis by reducing foliar carbohydrate export. In this work we assessed the relationship of bacterial distribution within the foliage, foliar starch accumulation, and net CO2assimilation (Anet). Because HLB impacts canopy morphology, we developed a chamber to measure whole-shootAnetto test the effects of HLB at both leaf and shoot levels. Whole-shoot-levelAnetsaturated at high irradiance, and green stems had high photosynthetic rates compared to leaves. Starch accumulation was correlated with bacterial population, and starch was negatively correlated withAnetat the leaf level but not at the shoot level. Starch increased initially after infection, then decreased progressively with increasing length of infection. HLB infection reducedAnetat the leaf level, but increased it at the whole shoot level, in association with reduced leaf size and greater relative contribution of stems to photosynthetic surface area. Although HLB-increased photosynthetic efficiency, total carbon fixed per shoot decreased because photosynthetic surface area was reduced. We conclude that the localized effects of infection on photosynthesis are mitigated by whole shoot morphological acclimation over time. Stems contribute important proportions of whole shootAnet, and these contributions are likely increased by the morphological acclimation induced by HLB.
Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers
Authors: Wibisana Johannes N. , Inaba Takehiko , Shinohara Hisaaki , Yumoto Noriko , Hayashi Tetsutaro , Umeda Mana , Ebisawa Masashi , Nikaido Itoshi , Sako Yasushi , Okada Mariko
Published: July 2021

The transcription factor NF-κB, which plays an important role in cell fate determination, is involved in the activation of super-enhancers (SEs). However, the biological functions of the NF-κB SEs in gene control are not fully elucidated. We investigated the characteristics of NF-κB-mediated SE activity using fluorescence live-cell imaging of RelA, single-cell transcriptome, and chromatin accessibility analyses in anti-IgM-stimulated B cells. Cell stimulation induced nuclear foci formation of RelA and gene expression in a switch-like manner. The gained SEs induced a higher fold-change expression and enhanced cell-to-cell variability in transcriptional response. These properties were correlated with the number of gained cis-regulatory interactions, while switch-like gene induction was associated with the number of NF-κB binding sites in SE. Our study suggests that NF-κB SEs have unique roles for quantitative control of gene expression through direct binding to accessible DNA and enhanced DNA contacts.
Interaction between SARS-CoV-2 spike glycoprotein and human skin models: a molecular dynamics study
Authors: Domingo Marc , Faraudo Jordi
Published: July 2021

The possibility of contamination of human skin by infectious virions plays an important role in indirect transmission of respiratory viruses but little is known about the fundamental physico-chemical aspects of the virus-skin interactions. In the case of coronaviruses, the interaction with surfaces (including the skin surface) is mediated by their large glycoprotein spikes that protrude from (and cover) the viral envelope. Here, we perform all atomic simulations between the SARS-CoV-2 spike glycoprotein and human skin models. We consider an “oily” skin covered by sebum and a “clean” skin exposing the stratum corneum. The simulations show that the spike tries to maximize the contacts with stratum corneum lipids, particularly ceramides, with substantial hydrogen bonding. In the case of “oily” skin, the spike is able to retain its structure, orientation and hydration over sebum with little interaction with sebum components. Comparison of these results with our previous simulations of the interaction of SARS-CoV-2 spike with hydrophilic and hydrophobic solid surfaces, suggests that the”soft” or “hard” nature of the surface plays an essential role in the interaction of the spike protein with materials.
The role of reading experience in atypical cortical tracking of speech and speech-in-noise in dyslexia
Authors: Destoky Florian , Bertels Julie , Niesen Maxime , Wens Vincent , Ghinst Marc Vander , Rovai Antonin , Trotta Nicola , Lallier Marie , De Tiège Xavier , Bourguignon Mathieu
Published: July 2021

Dyslexia is a frequent developmental disorder in which reading acquisition is delayed and that is usually associated with difficulties understanding speech in noise. At the neuronal level, children with dyslexia were reported to display abnormal cortical tracking of speech (CTS) at phrasal rate. Here, we aimed to determine if abnormal tracking is a cause or a consequence of dyslexia and if it is modulated by the severity of dyslexia or the presence of acoustic noise.

We included 26 school-age children with dyslexia, 26 age-matched controls and 26 reading-level matched controls. All were native French speakers. Children’s brain activity was recorded with magnetoencephalography while they listened to continuous speech in noiseless and multiple noise conditions. CTS values were compared between groups, conditions and hemispheres, and also within groups, between children with best and worse reading performance.

Syllabic CTS was significantly reduced in the right superior temporal gyrus in children with dyslexia compared with controls matched for age but not for reading level. Among children with dyslexia, phrasal CTS tended to lateralize to the left hemisphere in severe dyslexia and lateralized to the right hemisphere in children with mild dyslexia and in all control groups. Finally, phrasal CTS was lower in children with dyslexia compared with age-matched controls, but only in informational noise conditions. No such effect was seen in comparison with reading-level matched controls.

Overall, our results confirmed the finding of altered neuronal basis of speech perception in noiseless and babble noise conditions in dyslexia compared with age-matched peers. However, the absence of alteration in comparison with reading-level matched controls suggests that such alterations are a consequence of reduced reading experience rather than a cause of dyslexia.

Highlights

The cortical tracking of speech (CTS) was assessed in dyslexia and proper controls

Phrasal CTS and its resistance to noise were altered in dyslexia

Such alterations were not found in comparison with controls matched for reading level

The severity of dyslexia modulated the hemispheric lateralization of phrasal CTS
Turnover Regulation of the Rho GTPase Cdc42 by Heat Shock Protein Chaperones and the MAPK Pathway Scaffold Bem4
Authors: González Beatriz , Cullen Paul J.
Published: July 2021

All cells maintain an axis of polarity that directs the orientation of growth. Cell polarity can be reorganized during development and in response to extrinsic cues to produce new cell types. Rho GTPases are central regulators of cell polarity and signal-dependent cell differentiation. We show here that one of the best understood Rho GTPases, the highly conserved yeast Cdc42p, is turned over by members of the Heat Shock family of Proteins (HSPs). The Hsp40p chaperone, Ydj1p, was required for turnover of Cdc42p by the NEDD4 E3 ubiquitin ligase, Rsp5p, in the proteosome. Cdc42p turnover was regulated by HSPs at high temperatures, and in aging cells where the protein formed aggregates, implicating HSPs in Rho GTPase quality control. We also show that Cdc42pQ61L, which mimics the active (GTP-bound) conformation of the protein, was turned over at elevated levels by Ydj1p and Rsp5p. A turnover-defective version of Cdc42pQ61L led to multibudding phenotypes, implicating Cdc42 turnover in singularity in cell polarization. Cdc42p turnover also impacted MAP kinase pathway specificity. A pathway-specific scaffold, Bem4p, stabilized Cdc42p levels, which biased Cdc42p function in one MAPK pathway over another. Turnover regulation of Rho GTPases by HSPs and scaffolds provides new dimensions to the regulation of cell polarity and signal-dependent morphogenesis.

Significance Statement

Rho GTPases are switch-like proteins that govern major decisions in cell polarity and signaling in eukaryotes. We elucidate here a pathway that turns over the yeast Rho GTPase Cdc42p, which is mediated by the heat-shock family of proteins (HSPs) and the NEDD4-type E3 ubiquitin ligase Rsp5p. This finding provides a way for HSPs to exert their widespread effects on morphogenetic responses, phenotypic plasticity, and signaling pathways. We also found that turnover of an active version of Cdc42p is critical for modulating cell polarity. Cdc42p turnover also impacted its function in a pathway specific setting, as stabilization of Cdc42p by Bem4p (SmgGDS-type scaffold) influenced the activity of a specific MAPK pathway. HSPs may regulate Rho GTPase turnover in many systems.
Global change differentially modulates coral physiology and suggests future shifts in Caribbean reef assemblages
Authors: Bove Colleen B , Davies Sarah W , Ries Justin B , Umbanhowar James , Thomasson Bailey C , Farquhar Elizabeth B , McCoppin Jessica A , Castillo Karl D
Published: July 2021

Global change driven by anthropogenic carbon emissions is altering ecosystems at unprecedented rates, especially coral reefs, whose symbiosis with algal endosymbionts ise particularly vulnerable to increasing ocean temperatures and altered carbonate chemistry. Here, we assess the physiological responses of the coral holobiont (animal host + algal symbiont) of three Caribbean coral species from two reef environments after exposure to simulated ocean warming (28, 31 °C), acidification (300 - 3290 μatm), and the combination of stressors for 93 days. We used multidimensional analyses to assess how multiple coral holobiont physiological parameters respond to ocean acidification and warming. Our results demonstrate significantly diminishing holobiont physiology in S. siderea and P. astreoides in response to projected ocean acidification, while future warming elicited severe declines in P. strigosa. Offshore S. siderea fragments exhibited higher physiological plasticity than inshore counterparts, suggesting that this offshore population has the capacity to modulate their physiology in response to changing conditions, but at a cost to the holobiont. Plasticity of P. strigosa and P. astreoides was not clearly different between natal reef environments, however, temperature evoked a greater plastic response in both species. Interestingly, while these species exhibit unique physiological responses to ocean acidification and warming, when data from all three species are modeled together, convergent stress responses to these conditions are observed, highlighting the overall sensitivities of tropical corals to these stressors. Our results demonstrate that while ocean warming is a severe acute stressor that will have dire consequences for coral reefs globally, chronic exposure to acidification may also impact coral physiology to a greater extent than previously assumed. The variety of responses to global change we observe across species will likely manifest in altered Caribbean reef assemblages in the future.
Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos)
Authors: Tseng Elizabeth , Underwood Jason G. , Evans Hutzenbiler Brandon D. , Trojahn Shawn , Kingham Brewster , Shevchenko Olga , Bernberg Erin , Vierra Michelle , Robbins Charles T. , Jansen Heiko T. , Kelley Joanna L.
Published: July 2021

Understanding hibernation in brown bears (Ursus arctos) can provide insight into many human diseases. During hibernation, brown bears experience states of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic human diseases such as type 2 diabetes, muscle atrophy, renal and heart failure, cachexia, and obesity. The reversibility of these states from hibernation to active season allows for the identification of novel mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, we performed full-length RNA-sequencing (Iso-Seq) on three tissue types from three individuals sampled during both active and hibernation seasons. We combined the long-read data with the reference annotation for an improved transcriptome and mapped RNA-seq data from six individuals to the improved transcriptome to quantify differential isoform usage between tissues and seasons. We identified differentially expressed isoforms in all study tissues and showed that adipose has a high level of differential isoform usage with isoform switching, regardless of whether the genes were differentially expressed. Our analyses provide a comprehensive evaluation of isoform usage between active and hibernation states, revealing that differential isoform usage, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.
Apo and ligand-bound high resolution Cryo-EM structures of the human Kv3.1 reveal a novel binding site for positive modulators
Authors: Botte Mathieu , Huber Sophie , Bucher Denis , Klint Julie K. , Rodríguez David , Tagmose Lena , Chami Mohamed , Cheng Robert , Hennig Michael , Rahman Wassim Abdul
Published: July 2021

Kv3 ion-channels constitute a class of functionally distinct voltage gated ion channels characterized by their ability to fire at a high frequency. Several disease relevant mutants, together with biological data, suggest the importance of this class of ion channels as drug targets for CNS disorders, and several drug discovery efforts have been reported. Despite the increasing interest for this class of ion channels, no structure of a Kv3 channel has been reported yet. We have determined the cryo-EM structure of Kv3.1 at 2.6 Å resolution using full length wild type protein. When compared to known structures for potassium channels from other classes, a novel domain organization is observed with the cytoplasmic T1 domain, containing a well resolved Zinc site and displaying a rotation by 35°. This suggests a distinct cytoplasmic regulation mechanism for the Kv3.1 channel. A high resolution structure was obtained for Kv3.1 in complex with a novel positive modulator Lu AG00563. The structure reveals a novel ligand binding site for the Kv class of ion channels located between the voltage sensory domain and the channel pore, a region which constitutes a hotspot for disease causing mutations. The discovery of a novel binding site for a positive modulator of a voltage gated potassium channel could shed light on the mechanism of action for these small molecule potentiators. This finding could enable structure-based drug design on these targets with high therapeutic potential for the treatment of multiple CNS disorders.
Motor memories of object dynamics are categorically organized
Authors: Cesanek Evan , Zhang Zhaoran , Ingram James N. , Wolpert Daniel M. , Flanagan J. Randall
Published: July 2021

The ability to predict the dynamics of objects, linking applied force to motion, underlies our capacity to perform many of the tasks we carry out on a daily basis. Thus, a fundamental question is how the dynamics of the myriad objects we interact with are organized in memory. Using a custom-built three-dimensional robotic interface that allowed us to simulate objects of varying appearance and weight, we examined how participants learned the weights of sets of objects that they repeatedly lifted. We find strong support for the novel hypothesis that motor memories of object dynamics are organized categorically, in terms of families, based on covariation in their visual and mechanical properties. A striking prediction of this hypothesis, supported by our findings and not predicted by standard associative map models, is that outlier objects with weights that deviate from the family-predicted weight will never be learned despite causing repeated lifting errors.
Quantifying the size and healing of volumetric muscle wounds using 3D Slicer on CT scans in a canine model
Authors: Larie Dale , An Gary , Johnson Scott , Hoffman Kelly , Vodovotz Yoram , Badylak Stephen , Cockrell Chase
Published: July 2021

Volumetric soft tissue and muscle wounds can arise from trauma or necrotizing soft tissue infection. Quantifying the size of these wounds can be challenging, as they often have irregular borders and contours and invariably involve skin loss. 3-dimensional Computed Tomography (3dCT) has been used to characterize the volume of numerous tissue structures, but these use cases invariably involve structures for which clear anatomic borders exist. This is not the case for volumetric soft tissue or muscle wounds, where the volume of the wound being assessed, which is actually a void representing the absence of tissue, does not contain an explicit border at the superficial surface. We present a method that allows quantification of the void size of volumetric muscle wounds using CT scans processed with the software package 3D Slicer. This quantification allows us to chart the progression of healing in such wounds with sequential scans. The development of a means to quantify wound size and healing rate is a necessary capability in order to assess the efficacy of potential therapeutic interventions aimed at enhancing healing of such wounds.
Disentangling temporal associations in marine microbial networks
Authors: Deutschmann Ina Maria , Krabberød Anders K. , Latorre Francisco , Delage Erwan , Marrasé Cèlia , Balagué Vanessa , Gasol Josep M. , Massana Ramon , Eveillard Damien , Chaffron Samuel , Logares Ramiro
Published: July 2021

Background

Microbial interactions are fundamental for Earth’s ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network.

Results

A single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions.

Conclusions

Our results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems.
Life history traits and dispersal shape neutral genetic diversity in metapopulations
Authors: Garnier Jimmy , Lafontaine Pierre
Published: July 2021

Genetic diversity at population scale, depends on species life-history traits, population dynamics and local and global environmental factors. We first investigate the effect of life-history traits on the neutral genetic diversity of a single population using a deterministic mathematical model. When the population is stable, we show that semelparous species with precocious maturation and iteroparous species with delayed maturation exhibit higher diversity because their life history traits tend to balance the lifetimes of non reproductive individuals (juveniles) and adults which reproduce. Then, we extend our model to a metapopulation to investigate the additional effect of dispersal on diversity. We show that dispersal may truly modify the local effect of life history on diversity. As a result, the diversity at the global scale of the metapopulation differ from the local diversity which is only described through local life history traits of the populations. In particular, dispersal usually promotes diversity at the global metapopulation scale.
Morphological integration during postnatal ontogeny: implications for evolutionary biology
Authors: Hubbe Alex , Machado Fabio A. , Melo Diogo , Garcia Guilherme , Sebastião Harley , Porto Arthur , Cheverud James , Marroig Gabriel
Published: July 2021

How covariance patterns of phenotypes change during development is fundamental for a broader understanding of evolution. There is compelling evidence that mammalian skull covariance patterns change during ontogeny. However, it is unclear to what extent variation in covariance patterns during ontogeny can impact the response to selection. To tackle this question we explored: i) the extent to which covariance patterns change during postnatal ontogeny; ii) in which ontogenetic stages covariance patterns differ the most, and iii) the extent to which the phenotypic covariance pattern at different ontogenetic stages can be explained by the same processes determining additive genetic covariance. We sampled postnatal ontogenetic series for both marsupials, and placentals. Within each ontogenetic series, we compared covariance matrices (P-matrices) at different ontogenetic stages. Furthermore, we compared these P-matrices to two target matrices [adult P-matrix and an additive genetic covariance matrix (G-matrix)]. Our results show that for all ontogenetic series, covariance patterns from weaning onward are conserved and probably shaped by the same processes determining the G-matrix. We conclude that irrespective of eventual differences in how selection operates during most of postnatal ontogeny, the net response to such pressures will probably not be affected by ontogenetic differences in the covariance pattern.
PAC: Highly accurate quantification of allelic gene expression for population and disease genetics
Authors: Saukkonen Anna , Kilpinen Helena , Hodgkinson Alan
Published: July 2021

Analysis of allele-specific gene expression (ASE) is a powerful approach for studying gene regulation. However, detection of ASE events relies on accurate alignment of RNA-sequencing reads, where challenges still remain. We have developed PAC, a method that combines multiple steps to improve the quantification of allelic reads, including personalised (i.e. diploid) read alignment with improved allocation of multi-mapping reads. We show that PAC outperforms standard alignment approaches for ASE detection in both accuracy and in the number of sites it can reliably quantify.
The roles of NADPH oxidases during adult zebrafish fin regeneration
Authors: Chopra Kunal , Folkmanaitė Milda , Stockdale Liam , Shathish Vishali , Ishibashi Shoko , Bergin Rachel , Amich Jorge , Amaya Enrique
Published: July 2021

Sustained elevated levels of reactive oxygen species (ROS) have been shown to be essential for whole body, appendage and organ regeneration in various organisms, including planarians, Hydra, zebrafish, axolotl, Xenopus, geckos and mice. In the majority of cases these roles have been shown via the use of NADPH oxidase pharmacological inhibitors, which generally target all NAPDH oxidases (NOXes). To identify the specific NOX or NOXes essential for ROS production during adult fin regeneration in zebrafish, we generated nox mutants for duox, nox5 and cyba (a key subunit of NOXes 1-4). We also crossed these mutant lines to a transgenic line ubiquitously expressing HyPer, which permits the measurement of ROS levels in adult zebrafish fins. Using this approach, we found that homozygous duox mutants have significantly attenuated ROS levels following fin amputation, and this correlated with a significantly diminished rate of fin regeneration. While the other nox homozygous mutants (nox5 and cyba) showed less of an effect on ROS levels or adult fin regeneration, duox/cyba double mutants showed a more diminished rate of fin regeneration than duox mutants alone, suggesting that Nox1-4 do play a role during regeneration, but one that is secondary to that of Duox. This work also serendipitously found that ROS levels in amputated adult zebrafish fins oscillate during the day with a circadian rhythm.
gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit
Authors: Guebila Marouen Ben , Morgan Daniel C , Glass Kimberly , Kuijjer Marieke L. , DeMeo Dawn L. , Quackenbush John
Published: July 2021

Gene regulatory network inference allows for the study of transcriptional control to identify the alteration of cellular processes in human diseases. Our group has developed several tools to model a variety of regulatory processes, including transcriptional (PANDA, SPIDER) and post-transcriptional (PUMA) gene regulation, and gene regulation in individual samples (LIONESS). These methods work by performing repeated operations on data matrices in order to integrate information across multiple lines of biological evidence. This limits their use for large-scale genomic studies due to the associated high computational burden. To address this limitation, we developed gpuZoo, which includes GPU-accelerated implementations of these algorithms. The runtime of the gpuZoo implementation in MATLAB and Python is up to 61 times faster and 28 times less expensive than the multi-core CPU implementation of the same methods. gpuZoo takes advantage of the modern multi-GPU device architecture to build a population of sample-specific gene regulatory networks with similar runtime and cost improvements by combining GPU acceleration with an efficient on-line derivation. Taken together, gpuZoo allows parallel and on-line gene regulatory network inference in large-scale genomic studies with cost-effective performance.

gpuZoo is available in MATLAB through the netZooM package https://github.com/netZoo/netZooM and in Python through the netZooPy package https://github.com/netZoo/netZooPy.
Co-translational assembly counteracts promiscuous interactions
Authors: Seidel Maximilian , Becker Anja , Pereira Filipa , Landry Jonathan J. M. , de Azevedo Nayara Trevisan Doimo , Fusco Claudia M. , Kaindl Eva , Baumbach Janina , Langer Julian D. , Schuman Erin M. , Patil Kiran Raosaheb , Hummer Gerhard , Benes Vladimir , Beck Martin
Published: July 2021

During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examined structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally tested candidate structural motifs and identified several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assembled co-translationally in only one but not all of the relevant assembly pathways. Our results highlight the regulatory complexity of assembly pathways.
Calorie Restriction Maintains Mitochondrial Function and Redox Balance Avoiding Lipidomic Reprogramming during Isoproterenol-Induced Cardiac Hypertrophy
Authors: David Cícera Edna Barbosa , Lucas Aline Maria Brito , Cunha Pedro Lourenzo Oliveira , Viana Yuana Ivia Ponte , Yoshinaga Marcos Yukio , Miyamoto Sayuri , Filho Adriano Brito Chaves , Varela Anna Lídia Nunes , Kowaltowski Alicia Juliana , Facundo Heberty Tarso
Published: July 2021

Cardiac hypertrophy induces a metabolic shift, leading to a preferential consumption of glucose (over fatty acids) to support the high energetic demand. Typically, health cardiac tissue utilizes more fat than any other organ. Calorie restriction is a dietary procedure that induces health benefits and lifespan extension in many organisms. Given the beneficial effects of calorie restriction and the metabolic dysregulation seen during cardiac hypertrophy, we hypothesized that calorie restriction prevents cardiac hypertrophy, lipid, mitochondrial, and redox dysregulations. Strikingly, calorie restriction reversed isoproterenol-induced cardiac hypertrophy, lowered succinate driven mitochondrial H2O2 production, improved mitochondrial function (indicated as a higher Respiratory Control Ratio – RCR) and avoided mitochondrial superoxide dismutase (MnSOD) and glutathione peroxidase (GPX) repression. To gain insight into how calorie restriction could interfere with the metabolic changes induced by cardiac hypertrophy, we performed lipidomic profiling. Calorie restriction protected against the consumption of several triglycerides (TG) linked to unsaturated fatty acids, and the accumulation of TGs containing saturated fatty acids observed in hypertrophic samples. Cardiac hypertrophy induced an increase in ceramides, phosphoethanolamines and acylcarnitines (12:0, 14:0, 16:0 and 18:0) that were also reversed by calorie restriction. Altogether, our data demonstrate that hypertrophy changes the cardiac lipidome, causes mitochondrial disturbances and oxidative stress. All these changes are prevented by calorie restriction intervention in vivo. This study uncovers calorie restriction as a resource protect cardiac tissue and prevent cardiac hypertrophy-induced lipidomic remodeling.
Experimental evidence that network topology can accelerate the spread of beneficial mutations
Authors: Chakraborty Partha Pratim , Nemzer Louis R. , Kassen Rees
Published: July 2021

Whether the spatial arrangement of a population influences adaptive evolution has puzzled evolutionary biologists. Theoretical models make contrasting predictions about the probability a beneficial mutation will become fixed in a population for certain topologies like stars, where leaf populations are connected through a hub. To date, these predictions have not been evaluated under realistic conditions. Here, we test the prediction that topology can change the fixation probability bothin vitroandin silicoby tracking the dynamics of a beneficial mutant under positive selection as it spreads through networks of different topologies. Our results provide empirical support that metapopulation topology can increase the likelihood that a beneficial mutation spreads, broadens the conditions under which this phenomenon is thought to occur, and points the way towards using network topology to amplify the effects of weakly favored mutations under directed evolution in industrial applications.