bluuebunny/crossref_metadata_2025 huggingface dataset:
Pattern- based Contractility Screening (PaCS), a reference-free traction force microscopy methodology, reveals contractile differences in breast cancer cells
Authors: Ghagre Ajinkya , Amini Ali , Srivastava Luv Kishore , Tirgar Pouria , Khavari Adele , Koushki Newsha , Ehrlicher Allen
Published: May 2020

The sensing and generation of cellular forces are essential aspects of life. Traction Force Microscopy (TFM) has emerged as a standard broadly applicable methodology to measure cell contractility and its role in cell behavior. While TFM platforms have enabled diverse discoveries, their implementation remains limited in part due to various constraints, such as time-consuming substrate fabrication techniques, the need to detach cells to measure null force images, followed by complex imaging and analysis, and the unavailability of cells for post-processing. Here we introduce a reference-free technique to measure cell contractile work in real-time, with basic substrate fabrication methodologies, simple imaging, and analysis with the availability of the cells for post-processing. In this technique, we confine the cells on fluorescent adhesive protein micropatterns of a known area on compliant silicone substrates and use the cell deformed pattern area to calculate cell contractile work. We validated this approach by comparing this Pattern-based Contractility Screening (PaCS) to conventional bead-displacement TFM and show quantitative agreement between the methodologies. Using this platform, we measure the contractile work of highly metastatic MDA-MB-231 breast cancer cells is significantly higher than non-invasive MCF-7 cells. PaCS enables the broader implementation of contractile work measurements in diverse quantitative biology and biomedical applications.
Mapping Cognitive Brain Functions at Scale
Authors: Balasubramani Pragathi Priyadharsini , Ojeda Alejandro , Grennan Gillian , Maric Vojislav , Le Hortense , Alim Fahad , Zafar-Khan Mariam , Diaz-Delgado Juan , Silveira Sarita , Ramanathan Dhakshin , Mishra Jyoti
Published: May 2020

A fundamental set of cognitive abilities enable humans to efficiently process goal-relevant information, suppress irrelevant distractions, maintain information in working memory, and act flexibly in different behavioral contexts. Yet, studies of human cognition and their underlying neural mechanisms usually evaluate these cognitive constructs in silos, instead of comprehensively in-tandem within the same individual. Here, we developed a scalable, mobile platform, “BrainE” (short for Brain Engagement), to rapidly assay several essential aspects of cognition simultaneous with wireless electroencephalography (EEG) recordings. UsingBrainE, we rapidly assessed five aspects of cognition including (1) selective attention, (2) response inhibition, (3) working memory, (4) flanker interference and (5) emotion interference processing, in 102 healthy young adults. We evaluated stimulus encoding in all tasks using the EEG neural recordings, and isolated the cortical sources of the spectrotemporal EEG dynamics. Additionally, we usedBrainEin a two-visit study in 24 young adults to investigate the reliability of the neuro-cognitive data as well as its plasticity to transcranial magnetic stimulation (TMS). We found that stimulus encoding on multiple cognitive tasks could be rapidly assessed, identifying common as well as distinct task processes in both sensory and cognitive control brain regions. Event related synchronization (ERS) in the theta (3-7 Hz) and alpha (8-12 Hz) frequencies as well as event related desynchronization (ERD) in the beta frequencies (13-30 Hz) were distinctly observed in each task. The observed ERS/ERD effects were overall anticorrelated. The two-visit study confirmed high test-retest reliability for both cognitive and neural data, and neural responses showed specific TMS protocol driven modulation. We also show that the global cognitive neural responses are sensitive to mental health symptom self-reports. This first study with theBrainEplatform showcases its utility in studying neuro-cognitive dynamics in a rapid and scalable fashion.

Highlights

Rapid and scalable EEG recordings reveal common and distinct cortical activations across five core cognitive tasks.

Data acquired across visits one-week-apart show high test-retest reliability for both cognitive and neural measurements.

Evoked neural responses during emotion interference processing demonstrate specific short-term plasticity driven by type of neurostimulation.

Cognitively evoked neural responses are sensitive to variations in mental health symptoms.
The legacy of C4evolution in the hydraulics of C3and C4grasses
Authors: Zhou Haoran , Akçay Erol , Edwards Erika , Helliker Brent
Published: May 2020

The anatomical reorganization required for optimal C4photosynthesis should also impact plant hydraulics. Most C4plants possess large bundle-sheath cells and high vein density, which should also lead to higher leaf hydraulic conductance (Kleaf) and capacitance. Paradoxically, the C4pathway reduces water demand and increases water-use-efficiency, creating a potential mis-match between supply capacity and demand in C4plant water relations. We use phylogenetic analyses, physiological measurements, and models to examine the reorganization of hydraulics in closely-related C4and C3grasses. Evolutionarily young C4lineages have higher Kleaf, capacitance, turgor-loss-point, and lower stomatal conductance than their C3relatives. In contrast, species from older C4lineages show decreased Kleafand capacitance, indicating that over time, C4plants have evolved to optimize hydraulic investments while maintaining C4anatomical requirements. The initial “over-plumbing” of C4plants disrupts the positive correlation between maximal assimilation rate and Kleaf, decoupling a key relationship between hydraulics and photosynthesis generally observed in vascular plants.
Preferential synthesis of very long chain polyunsaturated fatty acids ineutreptiellasp. (eugelnozoa) revealed by chromatographic and transcriptomic analyses
Authors: Kuo Rita C. , Zhang Huan , Stuart James D. , Provatas Anthony A. , Hannick Linda , Lin Senjie
Published: May 2020

Algal lipids are important fuel storage molecules in algae and a currency for energy transfer in the marine food chain as well as materials for biofuel production, but their production and regulation are not well understood in many species including the common coastal phytoplanktonEutreptiellaspp. Here, using gas chromatography-tandem mass spectrometry (GC/MS/MS), we discovered 24 types of fatty acids (FAs) inEutreptiellasp. with a relatively high proportion of long chain unsaturated FAs. The abundances of C16, C18 and saturated FAs decreased when phosphate in the culture medium was depleted. Among the 24 FAs, docosahexaenoic acid (22:6) and eicosapentaenoic acid (20:5) were the most abundant, suggesting thatEutreptiellasp. preferentially invests in the synthesis of very long chain polyunsaturated fatty acids (VLCPFA). Further transcriptomic analysis revealed thatEutreptiellasp. likely synthesizes VLCPFA via Δ8 pathway and uses type I and II fatty acid synthases. Using RT-qPCR, we found that some of the lipid production genes, such as β-ketoacyl-ACP reductase, fatty acid desaturase, acetyl-CoA carboxylase, acyl carrier protein, Δ8 desaturase, and Acyl-ACP thioesterase, were more actively expressed during light period. Besides, two carbon-fixation genes were more highly expressed in the high lipid illuminated cultures, suggesting a linkage between photosynthesis and lipid production.
Cross-attractor repertoire provides new perspective on structure-function relationship in the brain
Authors: Zhang Mengsen , Sun Yinming , Saggar Manish
Published: May 2020

The brain is a complex system exhibiting ever-evolving activity patterns without any external inputs or tasks. Such intrinsic dynamics (or lack thereof) are thought to play crucial roles in typical as well as atypical cognitive functioning. Linking the ever-changing intrinsic dynamics to the rather static anatomy is a challenging endeavor. Dynamical systems models are important tools for understanding how structure and function are linked in the brain. Here, we provide a novel modeling framework to examine such structure-function relations. Our deterministic approach complements previous modeling frameworks, which typically focus on noise-driven (or stochastic) dynamics near a single attractor. We examine the overall organizations of and coordination between all putative attractors. Using our approach, we first provide evidence that examining cross-attractor coordination between brain regions could better predict human functional connectivity than examining noise-driven near-attractor dynamics. Further, we observed that structural connections across scales modulate the energy costs of such cross-attractor coordination. Overall, our work provides a systematic framework for characterizing intrinsic brain dynamics as a web of cross-attractor transitions and associated energy costs. The framework may be used to predict transitions and energy costs associated with experimental or clinical interventions.
Three distinct neural mechanisms support movement-induced analgesia
Authors: Lu Xuejing , Yao Xinru , Thompson William Forde , Hu Li
Published: May 2020

Pain is essential for our survival by protecting us from severe injuries. Pain signals may be exacerbated by continued physical activities but can also be interrupted or over-ridden by physical movements, a process called movement-induced analgesia. A number of neural mechanisms have been proposed to account for this effect, including the reafference principle, the gate control theory of pain, and the top-down psychological modulation. Given that the analgesic effects of these mechanisms are temporally overlapping, it is unclear whether movement-induced analgesia results from a single neural mechanism or the joint action of multiple neural mechanisms. To address this question, we conducted five experiments on 130 healthy human subjects. First, the frequency of hand shaking was manipulated in order to quantify the relationship between the strength of the voluntary movement and the analgesic effect. Second, the temporal delay (between hand shaking and nociceptive laser stimuli) and the stimulated side (nociceptive laser stimuli were delivered on the hand ipsilateral or contralateral to the shaken one) were manipulated to quantify the temporal and spatial characteristics of the analgesic effect induced by voluntary movement. Combining psychophysics and electroencephalographic recordings, we demonstrated that movement-induced analgesia is a result of the joint action of multiple neural mechanisms. This investigation is the first to disentangle the distinct contributions of different neural mechanisms to the analgesic effect of voluntary movement. These findings extend our understanding of sensory attenuation arising from voluntary movement and may prove instrumental in the development of new strategies in pain management.
Elevated dietary ω-6 polyunsaturated fatty acids induce reversible peripheral nerve dysfunction that exacerbates comorbid pain conditions
Authors: Boyd Jacob T. , LoCoco Peter M. , Furr Ashley R. , Bendele Michelle R. , Tram Meilinn , Li Qun , Chang Fang-Mei , Colley Madeline E. , Arris Dominic A. , Locke Erin E. , Bach Stephan B.H. , Tobon Alejandro , Ruparel Shivani B. , Hargreaves Kenneth M.
Published: May 2020

Chronic pain is the leading cause of disability worldwide1 and commonly associated with comorbid disorders2. However, the role of diet in chronic pain is poorly understood. Of particular interest is the Western-style diet, enriched with ω-6 polyunsaturated fatty acids (PUFAs) that accumulate in membrane phospholipids and oxidize into pronociceptive oxylipins3,4. Here we report that mice administered a diet enriched with ω-6 PUFAs develop persistent nociceptive hypersensitivities, spontaneously-active and hyper-responsive glabrous afferent fibers, and histologic markers of peripheral nerve damage reminiscent of a peripheral neuropathy. Linoleic and arachidonic acids accumulate in lumbar dorsal root ganglia, with increased liberation via elevated PLA2 activity. Pharmacological and molecular inhibition of PLA2g7 or diet reversal with high ω-3 PUFAs attenuate nociceptive behaviors, neurophysiologic abnormalities, and afferent histopathology induced by high ω-6 intake. In addition, ω-6 accumulation exacerbates the intensity or duration of allodynia observed in preclinical inflammatory and neuropathic pain models, as well as in clinical diabetic neuropathy. Collectively, these data reveal diet as a novel etiology of peripheral neuropathy and risk factor for chronic pain, and implicate multiple therapeutic considerations for clinical pain management.
Evaluation of cerebellar function scores in relation to cerebellar axonal loss in multiple sclerosis
Authors: Boonstra F. , Gajamange S. , Noffs G. , Perera T. , Strik M. , Vogel A. , Butzkueven H. , Evans A. , van der Walt A. , Kolbe S.
Published: May 2020

Background

Cerebellar damage is common in people with multiple sclerosis (pwMS) and is associated with worse progression and relapse recovery. Studies into the importance of the cerebellum in pwMS are hampered by limited understanding of cerebellar damage and its relation to cerebellar function in pwMS.

Objective

Examine axonal loss, as a primary driver of progressive neurological decline, in the cerebellum using advanced diffusion MRI and compare axonal loss with cerebellar dysfunction in pwMS

Methods

We recruited 55 pwMS and 14 healthy controls. Clinical assessments included scale for the assessment and rating of ataxia (SARA), and Bain tremor ratings. Subjects underwent FLAIR, T1-weighted and diffusion MRI. Cerebellar grey and white matter and lesion volume were calculated. Cerebellar axonal loss was examined with fibre-specific markers. Fibre density and cross-section (FDC) accounts for microscopic and macroscopic changes in a fibre bundle.

Results

Loss of cerebellar FDC was associated with increased SARA (r=-0.42, p<0.01) and tremor severity (rho=-0.35, p=0.01). Cerebellar lesion volume correlated with SARA (r=0.49, p<0.01) and tremor severity (rho=0.41, p=0.01).

Conclusion

Fibre-specific measures of cerebellar pathology could provide a functionally relevant marker of cerebellar damage in MS. Future trials using fibre-specific markers are needed to further characterize cerebellar pathology in pwMS and understand its significance in disease progression.
Comparative genomics of ocularPseudomonas aeruginosastrains from keratitis patients with different clinical outcomes
Authors: Kandasamy Kathirvel , Thirumalmuthu Kannan , Prajna Namperumalsamy Venkatesh , Lalitha Prajna , Mohankumar Vidyarani , Devarajan Bharanidharan
Published: May 2020

Bacterial keratitis caused byPseudomonas aeruginosais a destructive disease of cornea. Pseudomonas keratitis progresses rapidly and leads to vision loss if untreated. Even with adequate treatment, many patients show poor visual outcomes. The virulence factors or multiple drug-resistant (MDR) mechanisms of the ocular strains responsible for poor clinical outcomes remain largely unknown. Here, we performed whole-genome sequencing of fiveP. aeruginosastrains cultured from corneal scrapings of the healed and corneal buttons of the poor outcome keratitis patients. We investigated the distribution of virulence factors, resistance genes and resistance-associated mutations, the efflux-pump system in all five genomes, and as groups between poor and good clinical outcome as well as MDR vs. non-MDR. We detected several resistance genes and mutations associated with drug resistance in MDR groups; however, a large number of virulence genes were detected in all our genomes. Among the virulence genes, exoU and exoS exotoxin of the Type III secretion system detected in MDR and non-MDR strains, respectively, considered as main virulence contributors of keratitis pathogenesis. Despite this fact, this study did not show an association between MDR with exoU and poor clinical outcomes. However, strain-specific resistance and virulence genes were observed in this study, suggesting their role in the clinical outcome. Mainly, the flagellar genes fliC and fliD, reported to altering the host immune response, might impact the clinical outcome. This comparative study may provide new insights into the genome of ocular strains and requires further functional studies.
Acute Exercise Following Skill Practice Promotes Motor Memory Consolidation in Parkinson’s Disease
Authors: Wanner Philipp , Winterholler Martin , Gaßner Heiko , Winkler Jürgen , Klucken Jochen , Pfeifer Klaus , Steib Simon
Published: May 2020

Acute cardiovascular exercise has shown to promote neuroplastic processes, and thus to improve the consolidation of newly acquired motor skills in healthy adults. First results suggest that this concept may be transferred to populations with motor and cognitive dysfunctions. In this context, Parkinson’s disease (PD) is highly relevant since patients demonstrate deficits in motor learning. Hence, in the present study we sought to explore the effect of a single post-practice exercise bout on motor memory consolidation in PD patients.

For this purpose, 17 PD patients (Hoehn and Yahr: 1 – 2.5, age: 60.1 ± 7.9 y) practiced a whole-body task followed by either (i) a moderate-intense bout of cycling, or (ii) seated rest for a total of 30 minutes. The motor task required the participants to balance on a tiltable platform (stabilometer) for 30 seconds. During skill practice, patients performed 15 trials followed by a retention test 1 day and 7 days later. We calculated time in balance (platform within ± 5° from horizontal) for each trial and within- and between-group differences in memory consolidation (i.e. offline learning = skill change from last acquisition block to retention tests) were analyzed.

Groups revealed similar improvements during skill practice (F4,60= .316, p = .866), but showed differences in offline learning, which was only evident after 7 days (F1,14= 5.602, p = .033).

Our results suggest that a single post-practice exercise bout is effective in enhancing long-term motor memory consolidation in a population with motor learning impairments. This may point at unique promoting effects of exercise on dopamine neurotransmission involved in memory formation. Future studies should investigate the potential role of exercise-induced effects on the dopaminergic system.

Highlights

Acute exercise enhanced motor memory consolidation in PD

Effects were evident only at 7-day retention

Results may indicate unique exercise-effects on the dopaminergic system

Findings show promising potential of exercise for motor rehabilitation
GALA: gap-free chromosome-scale assembly with long reads
Authors: Awad Mohamed , Gan Xiangchao
Published: May 2020

High-quality genome assembly has wide applications in genetics and medical studies. However, it is still very challenging to achieve gap-free chromosome-scale assemblies using current workflows for long-read platforms. Here we propose GALA (Gap-freelong-readassembler), a chromosome-by-chromosome assembly method implemented through a multi-layer computer graph that identifies mis-assemblies within preliminary assemblies or chimeric raw reads and partitions the data into chromosome-scale linkage groups. The subsequent independent assembly of each linkage group generates a gap-free assembly free from the mis-assembly errors which usually hamper existing workflows. This flexible framework also allows us to integrate data from various technologies, such as Hi-C, genetic maps, a reference genome and even motif analyses, to generate gap-free chromosome-scale assemblies. Wede novoassembled theC. elegansandA. thalianagenomes using combined Pacbio and Nanopore sequencing data from publicly available datasets. We also demonstrated the new method’s applicability with a gap-free assembly of a human genome with the help a reference genome. In addition, GALA showed promising performance for Pacbio high-fidelity long reads. Thus, our method enables straightforward assembly of genomes with multiple data sources and overcomes barriers that at present restrict the application ofde novogenome assembly technology.
HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping
Authors: Charles OJ , Venturini C , Goldstein RA , Breuer J
Published: May 2020

The prevention and treatment of many herpesvirus associated diseases is based on the utilization of antiviral therapies, however therapeutic success is limited by the development of drug resistance. A comprehensive point of truth of resistance conferring mutations has been missing but would be important to aid the development of antiviral drugs and in management of infections. We therefore developed HerpesDRG, a drug resistance mutation database for all the known important genes and current treatment options, built from a systematic review of available genotype to phenotype literature. The database is released along with an R package to provide a low barrier of entry to variant resistance annotation and clinical implication analysis from common sanger and NGS sequence data. This represents the first openly available and community maintainable knowledgebase of drug resistance mutations for the human herpes viruses (HHV), developed for the community of researchers and clinicians tackling HHV drug resistance.

Availability

The HerpesDRG database is available at github.com/ojcharles/herpesdrg-db. The R package for resistance genotyping data is available at github.com/ojcharles/herpesdrg. A user-friendly webserver is available at cmv-resistance.ucl.ac.uk/herpesdrg
Community-scale Synchronization and Temporal Partitioning of Gene Expression, Metabolism, and Lipid Biosynthesis in Oligotrophic Ocean Surface Waters
Authors: Muratore Daniel , Boysen Angie K. , Harke Matthew J. , Becker Kevin W. , Casey John R. , Coesel Sacha N. , Mende Daniel R. , Wilson Samuel T. , Aylward Frank O. , Eppley John M. , Vislova Alice , Peng Shengyun , Rodriguez-Gonzalez Rogelio A. , Beckett Stephen J. , Armbrust E. Virginia , DeLong Edward F. , Karl David M. , White Angelicque E. , Zehr Jonathan P. , Van Mooy Benjamin A.S. , Dyhrman Sonya T. , Ingalls Anitra E. , Weitz Joshua S.
Published: May 2020

Sunlight drives daily rhythms of photosynthesis, growth, and division of photoautotrophs throughout the surface oceans. However, the cascading impacts of oscillatory light input on diverse microbial communities and community-scale metabolism remains unclear. Here we use an unsupervised machine learning approach to show that a small number of diel archetypes can explain pervasive periodic dynamics amongst more than 65,000 distinct time series, including transcriptional activity, macromolecules, lipids, and metabolites from the North Pacific Subtropical Gyre. Overall, we find evidence for synchronous timing of carbon-cycle gene expression that underlie daily oscillations in the concentrations of particulate organic carbon. In contrast, we find evidence of asynchronous timing in gene transcription related to nitrogen metabolism and related metabolic processes consistent with temporal niche partitioning amongst microorganisms in the bacterial and eukaryotic domains.
Molecular and clinical characterization of 5mC regulators in glioma: results of a multicenter study
Authors: Zhao Liang , Zhang Jiayue , Liu Zhiyuan , Wang Yu , Xuan Shurui , Zhao Peng
Published: May 2020

DNA methylation has been widely reported to associate with the progression of glioma. DNA methylation at the 5 position of cytosine (5-methylcytosine, 5mC), which is regulated by 5mC regulators (“writers”, “erasers” and “readers”), is the most critical modification pattern. However, a systematic study on the role of these regulators in glioma is still lacking. In this study, we collected gene expression profiles and corresponding clinical information of gliomas from three independent public datasets. Gene expression of 21 5mC regulators was analyzed and linked to clinicopathological features. A novel molecular classification of glioma was developed using consensus non-negative matrix factorization (CNMF) algorithm, and the tight association with molecular characteristics as well as tumor immune microenvironment was clarified. Sixteen prognostic factors were identified using univariate Cox regression analysis, and a 5mC regulator-based gene signature was further constructed via the least absolute shrinkage and selection operator (LASSO) cox analysis. This risk model was proved as an efficient predictor of overall survival for diffuse glioma, glioblastoma (GBM), and low-grade glioma (LGG) patients in three glioma cohorts. The significant correlation between risk score and intratumoral infiltrated immune cells, as well as immunosuppressive pathways, was found, which explained the difference in clinical outcomes between high and low-risk groups. Finally, a nomogram incorporating the gene signature and other clinicopathological risk factors was established, which might direct clinical decision making. In summary, our work highlights the potential clinical application value of 5mC regulators in prognostic stratification of glioma and their potentialities for developing novel treatment strategies.
Diet-Induced Vitamin D Deficiency Results in Reduced Skeletal Muscle Mitochondrial Respiration in C57BL/6J Mice
Authors: Ashcroft Stephen P. , Fletcher Gareth , Philp Ashleigh M. , Atherton Philip J. , Philp Andrew
Published: May 2020

Vitamin D deficiency is known to be associated with symptoms of skeletal muscle myopathy including muscle weakness and fatigue. Recently, vitamin D related metabolites have been linked to the maintenance of mitochondrial function within skeletal muscle. However, current evidence is limited toin vitromodels and the effects of diet-induced vitamin D deficiency upon skeletal muscle mitochondrial functionin vivohave received little attention. In order to examine the role of vitamin D in the maintenance of mitochondrial functionin vivo, we utilised an established model of diet-induced vitamin D deficiency in C57BL/6J mice. Mice were fed either a control (2,200 IU/kg) or a vitamin D deplete (0 IU/kg) diet for periods of 1-, 2- and 3-months. Skeletal muscle mitochondrial function and ADP sensitivity were assessed via high-resolution respirometry and mitochondrial protein content via immunoblotting. As a result of 3-month of diet-induced vitamin D deficiency, respiration supported via CI+IIPand ETC were 35% and 37% lower when compared to vitamin D replete mice (P< 0.05). Despite functional alterations, the protein expression of electron transfer chain subunits remained unchanged in response to dietary intervention (P> 0.05). In conclusion, we report that 3-months of diet-induced vitamin D deficiency reduced skeletal muscle mitochondrial function in C57BL/6J mice. Our data, when combined with previousin vitroobservations, suggests that vitamin D mediated regulation of mitochondrial function may underlie the exacerbated muscle fatigue and performance deficits observed during vitamin D deficiency.
ER Proteostasis Regulators Reduce Amyloidogenic Light Chain Secretion Through an On-Target, ATF6-Independent Mechanism
Authors: Rius Bibiana , Mesgarzadeh Jaleh S. , Romine Isabelle C. , Paxman Ryan J. , Kelly Jeffery W. , Wiseman R. Luke
Published: May 2020

The plasma cell secretion and toxic aggregation of amyloidogenic immunoglobulin light chains (LCs) causes proteotoxicity in Light Chain Amyloidosis (AL). We recently identified endoplasmic reticulum (ER) proteostasis regulators such as compound147that reduce secretion and aggregation of LCs implicated in AL (Plate, Cooley et al., 2016). Compound147promotes adaptive ER proteostasis remodeling through a mechanism involving covalent modification of multiple protein disulfide isomerases (PDIs) and subsequent activation of the ATF6 unfolded protein response (UPR) -associated transcriptional signaling pathway (Paxman, Plate et al., 2018). Here, we show that the147-dependent reduction in amyloidogenic LC secretion from AL patient plasma cells is independent of ATF6 activation, but instead requires on-target PDI modification. Our results reveal pharmacologic targeting of PDIs as a potential strategy to ameliorate AL-associated proteotoxicity and demonstrate that147can influence ER proteostasis through multiple on-target mechanisms including ATF6 activation and PDI modification.

IMPACT STATEMENT

This study demonstrates the broad potential for endoplasmic reticulum proteostasis regulator compounds such as147to influence secretory proteostasis of disease-associated proteins through multiple on target mechanisms.
Algorithms for the selection of fluorescent reporters
Authors: Vaidyanathan Prashant , Appleton Evan , Tran David , Vahid Alexander , Church George , Densmore Douglas
Published: May 2020

Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as excitation and emission spectra, brightness) and require similar equipment for data acquisition. Selecting an ideal set of fluorophores for a particular measurement technology or vice versa is a multidimensional problem that is difficult to solve withad hocmethods due to the enormous solution space of possible fluorophore panels. Choosing sub-optimal fluorophore panels can result in unreliable or erroneous measurements of biochemical properties in model systems. Here, we describe a set of algorithms, implemented in an open-source software tool, for solving these problems efficiently to arrive at fluorophore panels optimized for maximal signal and minimal bleed-through.
Multidimensional trophic niche revealed by complementary approaches: gut content, digestive enzymes, fatty acids and stable isotopes in soil fauna
Authors: Potapov Anton M. , Pollierer Melanie M. , Salmon Sandrine , Šustr Vladimír , Chen Ting-Wen
Published: May 2020

The trophic niche of an organism is tightly related to its role in the ecosystem and to interactions with other species. Thousands of species of soil animals feed on detritus and co-exist with apparently low specialisation in food resource use. Trophic niche differentiation may explain species coexistence in such a cryptic environment. However, most of the existing studies provide only few and isolated evidence on food resources, thus simplifying the multidimensional nature of the trophic niches available in soil.

Focusing on one of the most diverse soil taxa – springtails (Collembola) – we aimed to reveal the additional value of information provided by four complementary methods: visual gut content-, digestive enzyme-, fatty acid- and stable isotope analyses, and to demonstrate the multidimensional nature of trophic niches.

From 40 studies, we compiled fifteen key trophic niche parameters for 125 species, each analysed with at least one method. Focusing on interspecific variability, we explored correlations of trophic niche parameters and described variation of these parameters in different Collembola species, taxonomic groups and life forms.

Correlation between trophic niche parameters of different methods was weak in 45 out of 64 pairwise comparisons, reflecting the complementarity of the multidimensional trophic niche approach. Gut content and fatty acids provided comparable information on fungivory and plant feeding in Collembola. Information provided by digestive enzymes differed from that gained by the other methods, suggesting its high additional value. Stable isotopes were mainly related to plant versus microbial feeding. Many parameters were affected by taxonomic affiliation but not life form. Furthermore, we showed evidence of bacterial feeding, which may be more common in Collembola than usually assumed.

Different methods reveal different feeding dimensions, together drawing a comprehensive picture of the trophic niche in taxa with diverse feeding habits. Food web studies will benefit from simultaneously applying several joint approaches, allowing to trace trophic complexity. Future studies on the multidimensional trophic niche may improve understanding of food-web functioning and help to explain species coexistence in cryptic environments such as soil.
Multi-channel intraneural vagus nerve recordings with a novel high-density carbon fiber microelectrode array
Authors: Jiman Ahmad A. , Ratze David C. , Welle Elissa J. , Patel Paras R. , Richie Julianna M. , Bottorff Elizabeth C. , Seymour John P. , Chestek Cynthia A. , Bruns Tim M.
Published: May 2020

Autonomic nerves convey essential neural signals that regulate vital body functions. Recording clearly distinctive physiological neural signals from autonomic nerves will help develop new treatments for restoring regulatory functions. However, this is very challenging due to the small nature of autonomic nerves and the low-amplitude signals from their small axons. We developed a multi-channel, high-density, intraneural carbon fiber microelectrode array (CFMA) with ultra-small electrodes (8-9 μm in diameter, 150-250 μm in length) for recording physiological action potentials from small autonomic nerves. In this study, we inserted CFMA with up to 16 recording carbon fibers in the cervical vagus nerve of 22 isoflurane-anesthetized rats. We recorded action potentials with peak-to-peak amplitudes of 15.1-91.7 μV and signal-to-noise ratios of 2.0-8.3 on multiple carbon fibers per experiment, determined conduction velocities of some vagal signals in the afferent (0.7-4.4 m/sec) and efferent (0.7-8.8 m/sec) directions, and monitored firing rate changes in breathing and blood glucose modulated conditions. Overall, these experiments demonstrated that CFMA is a novel interface for in-vivo intraneural action potential recordings. This work is considerable progress towards the comprehensive understanding of physiological neural signaling in vital regulatory functions controlled by autonomic nerves.
Stress induces divergent gene expression among lateral habenula efferent pathways
Authors: Levinstein Marjorie R. , Coffey Kevin R. , Marx Russell G. , Lesiak Atom J. , Neumaier John F.
Published: May 2020

The lateral habenula (LHb) integrates critical information regarding aversive stimuli that shapes decision making and behavioral responses. The three major LHb outputs innervate dorsal raphe nucleus (DRN), ventral tegmental area (VTA), and the rostromedial tegmental nucleus (RMTg). LHb neurons that project to these targets are segregated and nonoverlapping, and this led us to consider whether they have distinct molecular phenotypes and adaptations to stress exposure. In order to capture a time-locked profile of gene expression after repeated forced swim stress, we used intersectional expression of RiboTag in rat LHb neurons and next-gen RNA sequencing to interrogate the RNAs actively undergoing translation from each of these pathways. The “translatome” in the neurons comprising these pathways was similar at baseline, but diverged after stress, especially in the neurons projecting to the RMTg. Using weighted gene co-expression network analysis, we found one module comprising genes downregulated after stress in the RMTg-projecting LHb neurons; there was an overrepresentation of genes associated with phosphoinositide 3 kinase (PI3K) signaling in this module. Reduced PI3K signaling in RMTg-projecting LHb neurons may be a compensatory adaptation that alters the functional balance of LHb outputs to GABAergic vs. monoaminergic neurons following repeated stress exposure.
AFTERHYPERPOLARIZATION AMPLITUDE IN CA1 PYRAMIDAL CELLS OF AGED LONG-EVANS RATS CHARACTERIZED FOR INDIVIDUAL DIFFERENCES
Authors: Severin Daniel , Gallagher Michela , Kirkwood Alfredo
Published: May 2020

Altered neural excitability is considered a prominent contributing factor to cognitive decline during aging. A clear example is the excess neural activity observed in several temporal lobe structures of cognitively impaired older individuals in rodents and humans. At a cellular level, aging-related changes in mechanisms regulating intrinsic excitability have been well examined in pyramidal cells of the CA1 hippocampal subfield. Studies in the inbred Fisher 344 rat strain document an age-related increase in the slow afterhyperpolarization (AHP) that normally occurs after a burst of action potentials, and serves to reduce subsequent firing. We evaluated the status of the AHP in the outbred Long-Evans rat, a well-established model for studing individual differences in neurocognitive aging. In contrast to the findings reported in the Fisher 344 rats, in the Long-Evan rats we detected a selective reduction in AHP in cognitively impaired aged individuals. We discuss plausible scenarios to account for these differences and also discuss possible implications of these differences.
Dopaminergic neuromodulation of spike timing dependent plasticity in mature adult rodent and human cortical neurons
Authors: Louth Emma Louise , Jørgensen Rasmus Langelund , Korshøj Anders Rosendal , Sørensen Jens Christian Hedemann , Capogna Marco
Published: May 2020

Synapses in the cerebral cortex constantly change and this dynamic property regulated by the action of neuromodulators such as dopamine (DA), is essential for reward learning and memory. DA modulates spike-timing-dependent plasticity (STDP), a cellular model of learning and memory, in juvenile rodent cortical neurons. However, it is unknown whether this neuromodulation also occurs at excitatory synapses of cortical neurons in mature adult mice or in humans. Cortical layer V pyramidal neurons were recorded with whole cell patch clamp electrophysiology and an extracellular stimulating electrode was used to induce STDP. DA was either bath-applied or optogenetically released in slices from mice. Classical STDP induction protocols triggered non-Hebbian excitatory synaptic depression in the mouse or no plasticity at human cortical synapses. DA reverted long term synaptic depression to baseline in mouse or elicited long term synaptic potentiation in human cortical synapses. Furthermore, when DA was applied during a STDP protocol it depressed presynaptic inhibition in the mouse but not in the human cortex. Thus, DA modulates excitatory synaptic plasticity differently in humanversusmouse cortex. The data strengthens the importance of DA in gating cognition in humans, and may inform on therapeutic interventions to recover brain function from diseases.
Lipopolysaccharide stimulation of RAW264.7 cells is a model for identifying novel clients of Hsc70
Authors: Rakus John F. , Kegley Nicholas R. , Ashley Alex J. , Parsons Michael A. , Takeuchi Megumi
Published: May 2020

Heat shock cognate protein 71 kDa (Hsc70, Hspa8, Hspa10, Hsp73) is a member of the heat shock protein 70 kDa family of molecular chaperones. These chaperones function to aid the correct folding of client proteins using an ATP-dependent mechanism. Though Hsc70 is accepted to be a constitutively expressed protein, it has a well-documented function in modulating the induction of the pro-inflammatory cytokine TNFα by the LPS/TLR4 pathway. In this work we attempt to identify protein clients of Hsc70 to gain insight into those which may be responsible for this regulatory effect. RAW264.7 cells were cultured in the absence or presence of 1 μg/mL LPS for 0 to 24 hours. Herein we describe of a large number of newly-categorized Hsc70 clients using immunoprecipitation and nanoLC-MS/MS and we validate several novel Hsc70/client interactions using co-immunoprecipitation. After performing immunoprecipitation using a commercially available antibody, eluted fractions were proteolytically digested either immediately after immunoprecipitation or after separation by SDS-PAGE and sequence analyzed using nanoLC-MS/MS with a Q-Exactive Plus triple-quadrupole/orbitrap mass spectrometer. Using these methods, 292 total unique protein hits were identified with high confidence; 34 of which were only detected in LPS-treated cells.
Phylogenomics ofBrosimumSw. (Moraceae) and allied genera, including a revised subgeneric system
Authors: Gardner Elliot M. , Audi Lauren , Zhang Qian , Sauquet Hervé , Monro Alexandre K. , Zerega Nyree J.C.
Published: May 2020

We present a phylogenomic study ofBrosimumand the allied generaTrymatococcusandHelianthostylis, with near-complete taxon sampling. Distributed from Mexico and the Greater Antilles to the Amazon, this clade contains the underutilized crop ramón (bread nut) (Brosimum alicastrum) as well as other species valued for timber or medicinal uses. Target enrichment for 333 genes produced a well-resolved phylogenetic tree and showed thatTrymatoccocusandHelianthostylisare nested withinBrosimum. We present a revised subgeneric classification ofBrosimumbased on phylogenetic and morphological considerations, including the reduction ofTrymatococcusandHelianthostylisto subgenera. The monophyletic subgenera can be diagnosed based on stipule, pistillode, and cotyledon synapomorphies. Divergence date estimates suggest a Miocene origin forBrosimum, and ancestral area reconstruction indicated that all four subgenera originated and initially diversified in Amazonia before dispersing into other parts of South and Central America.

Presentamos un estudio filogenómico del géneroBrosimumy sus aliados,TrymatococcusyHelianthostylis, y que incluye prácticamente todas las especies descritas. Su distribución va desde México y las Antillas Mayores hasta el Amazonas y comprende especies como el ramón (B. alicastrum), un cultivo infrautilizado, y otras especies empleadas como madera o en medicina. La secuenciación masiva dirigida de 333 marcadores nucleares de copia única permitió la reconstrucción de una filogenia bien resuelta, en la que se demuestra queTrymatococcusyHelianthostylisestán anidados enBrosimum. Presentamos, por lo tanto, una clasificación revisada a nivel de especies, teniendo en cuenta los resultados moleculares y las características morfológicas, y dondeTrymatococcusyHelianthostylispasan a ser subgéneros deBrosimum. Estos subgéneros monofiléticos pueden ser identificados por caracteres de las estípulas y de los pistilodios.
Astrocytes close a critical period of motor circuit plasticity
Authors: Ackerman Sarah D. , Perez-Catalan Nelson A. , Freeman Marc R. , Doe Chris Q.
Published: May 2020

Critical periods – brief intervals where neural circuits can be modified by sensory input – are necessary for proper neural circuit assembly. Extended critical periods are associated with neurodevelopmental disorders, including schizophrenia and autism; however, the mechanisms that ensure timely critical period closure remain unknown. Here, we define the extent of a critical period in the developingDrosophilamotor circuit, and identify astrocytes as essential for proper critical period termination. During the critical period, decreased activity produces larger motor dendrites with fewer inhibitory inputs; conversely, increased motor neuron activity produces smaller motor dendrites with fewer excitatory inputs. Importantly, activity has little effect on dendrite morphology after critical period closure. Astrocytes invade the neuropil just prior to critical period closure, and astrocyte ablation prolongs the critical period. Finally, we use a genetic screen to identify astrocyte-motor neuron signaling pathways that close the critical period, including Neuroligin-Neurexin signaling. Reduced signaling destabilizes dendritic microtubules, increases dendrite dynamicity, and impairs locomotor behavior, underscoring the importance of critical period closure. Previous work defines astroglia as regulators of plasticity at individual synapses; here, we show that astrocytes also regulate large-scale structural plasticity to motor dendrite, and thus, circuit architecture to ensure proper locomotor behavior.
Quantitativein vivobioluminescence imaging of orthotopic patient-derived glioblastoma xenografts
Authors: Koessinger Anna L. , Koessinger Dominik , Stevenson Katrina , Cloix Catherine , Mitchell Louise , Chalmers Anthony J. , Norman Jim C. , Tait Stephen W.G
Published: May 2020

Despite extensive research, little progress has been made in glioblastoma therapy, owing in part to a lack of adequate preclinicalin vivomodels to study this disease. To mitigate this, primary patient-derived cell lines, which maintain their specific stem-like phenotypes, have replaced established glioblastoma cell lines. However, due to heterogenous tumour growth inherent in glioblastoma, the use of primary cells for orthotopicin vivostudies often requires large experimental group sizes. Therefore, when using intracranial patient-derived xenograft (PDX) approaches, it is advantageous to deploy imaging techniques to monitor tumour growth and allow stratification of mice. Here we show that stable expression of near-infrared fluorescent protein (iRFP) in patient-derived glioblastoma cells enables rapid direct non-invasive monitoring of tumour development without compromising tumour stemness or tumorigenicity. Moreover, as this approach does not depend on the use of agents like luciferin, which can cause variability due to changing bioavailability, it can be used for quantitative longitudinal monitoring of tumour growth. Notably, we show that this technique also allows quantitative assessment of tumour burden in highly invasive models spreading throughout the brain. Thus, iRFP transduction of primary patient-derived glioblastoma cells is a reliable, cost- and time-effective way to monitor heterogenous orthotopic PDX growth.
Hsp70 chaperone blocks α-synuclein oligomer formation via a novel engagement mechanism
Authors: Tao Jiahui , Berthet Amandine , Citron Rose , Stanley Robert , Gestwicki Jason , Agard David A. , McConlogue Lisa
Published: May 2020

Over-expression and aggregation of α-synuclein (ASyn) are linked to the onset and pathology of Parkinson’s disease and related synucleinopathies. Elevated levels of the stress induced chaperone, Hsp70, protects against ASyn misfolding and ASyn-driven neurodegeneration in cell and animal models, yet there is minimal mechanistic understanding of this important protective pathway. It is generally assumed that Hsp70 binds to ASyn using its canonical and promiscuous substrate-binding cleft to limit aggregation. Here we report that this activity is due to a novel and unexpected mode of Hsp70 action, involving neither ATP nor the typical substrate-binding cleft. We use novel ASyn oligomerization assays to show that Hsp70 directly blocks ASyn oligomerization, an early event in ASyn misfolding. Using truncations, mutations and inhibitors, we confirmed that Hsp70 interacts with ASyn via an as yet unidentified, non-canonical interaction site in the C-terminal domain. Finally, a biological role for a non-canonical interaction was observed in H4 neuroglioma cells. Together, these findings suggest that new chemical approaches will be required to target Hsp70-ASyn interaction in synucleinopathies. Such approaches are likely to be more specific than targeting Hsp70 canonical actions. Additionally, these results raise the question of whether other misfolded proteins might also engage via the same non-canonical mechanism.
intern: Integrated Toolkit for Extensible and Reproducible Neuroscience
Authors: Matelsky Jordan , Rodriguez Luis , Xenes Daniel , Gion Timothy , Hider Robert , Wester Brock , Gray-Roncal William
Published: May 2020

As neuroscience datasets continue to grow in size, the complexity of data analyses can require a detailed understanding and implementation of systems computer science for storage, access, processing, and sharing. Currently, several general data standards (e.g., Zarr, HDF5, precompute, tensorstore) and purpose-built ecosystems (e.g., BossDB, CloudVolume, DVID, and Knossos) exist. Each of these systems has advantages and limitations and is most appropriate for different use cases. Using datasets that don’t fit into RAM in this heterogeneous environment is challenging, and significant barriers exist to leverage underlying research investments. In this manuscript, we outline our perspective for how to approach this challenge through the use of community provided, standardized interfaces that unify various computational backends and abstract computer science challenges from the scientist. We introduce desirable design patterns and our reference implementation called intern.