bluuebunny/crossref_metadata_2025 huggingface dataset:
The biogeography of the Mediterranean Taurus Mountains: Illustrating how complex topography and climatic conditions have shaped their biodiversity
Authors: Gür Hakan
Published: September 2021

Climate is well known as the main driver of species distributions. In this study, I focused on Geyik Mountains and surrounding areas to illustrate how complex topography and climatic conditions have shaped the distribution patterns of species/communities and therefore the biodiversity of the Mediterranean Taurus Mountains, one of the most biologically diverse areas in the Mediterranean Basin biodiversity hotspot. Accordingly, I used an ecological niche modelling approach, which has been widely used in recent biogeographic studies. I chose Taurus ground squirrels (Spermophilus taurensis) and coniferous forests as the representatives of high- and low-altitude species/communities, respectively. The results simply illustrate how complex topography and temperature and precipitation gradients have had a substantial role in shaping the distribution patterns of species/communities and therefore the biodiversity of the Mediterranean Taurus Mountains.
Viscous effects and complex local flow behaviors dominate hemolymph circulation in the living wings of locusts
Authors: Salcedo Mary K. , Jun Brian , Vlachos Pavlos , Mahadevan Lakshminarayanan , Combes Stacey A.
Published: September 2021

An insects’ living systems – circulation, respiration, and a branching nervous system – extend from the body into the wing.1,2. Hemolypmh circulation in the wing is critical for hydrating tissues, such as the highly elastic resilin3 that enhances wing flexibility, and for supplying nutrients to living systems, including sensory organs such as scent-producing patches, sound-receiving tympana, and wind-sensing sensilla distributed across the wing.4–7During flight, the presence of hemolymph in the wings reduces aerodynamic instabilities like flutter8,9, and faster hemolymph flows are induced by flapping.10 Despite the critical role of hemolymph circulation in maintaining healthy wing function, wings are often considered “lifeless” cuticle, and most measurements remain qualitative or employ coarse, bulk-flow techniques. While pioneering work in the 1960s mapped hemolymph flow direction in 100 insect species,11 half a century later we still only have quantitative measurements of flow within the wings of a few insects. Here, we focused on the North American locust Schistocerca americana, a well-studied agricultural pest species, and performed a detailed, quantitative study of global and local hemolymph flows in the densely venated fore and hind wings, along with key regions in the body and pumping organs. Through high-speed fluorescent microscopy, we measured 800 individual trajectories of neutrally buoyant fluorescent particles that move in sync with hemolymph, in the wings and body of 8 live, resting locusts. Our data show that overall flow within the wings is circuitous, but local flow behavior is highly complex, with three distinct types of flow (pulsatile, continuous, and “leaky”) occurring in various combinations in different areas of the wing. We provide the first quantitative measurements of “leaky” flow into wing regions that act as sinuses, where hemolymph flows out of tubular veins and pools within thin membranous regions. We also calculate Péclet, Reynolds, and Womersley numbers, and find that viscous effects dominate flow regimes throughout the wing. Pumping organs and wing regions closest to the body display significantly faster flows and higher Reynolds numbers, but remain within the viscous flow regime. Given the central role of wings in sustaining ecologically important insect behaviors such as pollination, migration, and mating, along with the vast diversity of insect wings seen in nature, this first detailed, quantitative map of hemolymph flows across a wing provides a template for future studies investigating the dynamics of hemolymph flows critical to sustaining wing health among insects.
An EEG study on the effect of being overweight on anticipatory and consummatory reward in response to pleasant taste stimuli
Authors: Baines Stephanie , Hensels Imca S. , Talmi Deborah
Published: September 2021

Two-thirds of adults in the United Kingdom currently suffer from overweight or obesity, making it one of the biggest contributors to health problems. Within the framework of the incentive sensitisation theory, it has been hypothesised that overweight people experience heightened reward anticipation when encountering cues that signal food, such as pictures and smells of food, but that they experience less reward from consuming food compared to normal-weight people. There is, however, little evidence for this prediction. Few studies test both anticipation and consumption in the same study, and even fewer with electroencephalography (EEG). This study sought to address this gap in the literature by measuring scalp activity when overweight and normal-weight people encountered cues signalling the imminent arrival of pleasant and neutral taste stimuli, and when they received these stimuli. The behavioural data showed that there was a smaller difference in valence ratings between the pleasant and neutral taste in the overweight than normal-weight group, in accordance with our hypothesis. However, contrary to our hypothesis, the groups did not differ in their electrophysiological response to taste stimuli. Instead, there was a reduction in N1 amplitude to both taste and picture cues in overweight relative to normal-weight participants. This suggests that reduced attention to cues may be a crucial factor in risk of overweight.
Deletion or inhibition of astrocytic transglutaminase 2 promotes functional recovery after spinal cord injury
Authors: Elahi Anissa , Emerson Jacen , Rudlong Jacob , Keillor Jeffrey W. , Salois Garrick , Visca Adam , Girardi Peter , Johnson Gail V.W. , Pröschel Christoph
Published: September 2021

Following CNS injury astrocytes become “reactive” and exhibit pro-regenerative or harmful properties. However, the molecular mechanisms that cause astrocytes to adopt either phenotype are not well understood. Transglutaminase 2 (TG2) plays a key role in regulating the response of astrocytes to insults. Here we used mice in which TG2 was specifically deleted in astrocytes (Gfap-Cre+/-TG2fl/fl, referred to here as TG2-A-cKO) in a spinal cord contusion injury (SCI) model. Deletion of TG2 from astrocytes resulted in a significant improvement in motor function following SCI. GFAP and NG2 immunoreactivity, as well as number of SOX9 positive cells, were significantly reduced in TG2-A-cKO_mice. RNA-seq analysis of spinal cords from TG2-A-cKO and control mice 3 days postinjury identified thirty-seven differentially expressed genes, all of which were increased in TG2-A-cKO mice. Pathway analysis reveals a prevalence for fatty acid metabolism, lipid storage and energy pathways, which play essential roles in neuron-astrocyte metabolic coupling. Excitingly, treatment of wild type mice with the selective TG2 inhibitor VA4 significantly improved functional recovery after SCI, similar to what was observed using the genetic model. These findings indicate the use of TG2 inhibitors as a novel strategy for the treatment of SCI and other CNS injuries.
Episodic memory precision and reality monitoring following stimulation of angular gyrus
Authors: Kwon S. , Richter F.R. , Siena M. J. , Simons J.S.
Published: September 2021

The qualities of remembered experiences are often used to inform ‘reality monitoring’ judgments, our ability to distinguish real and imagined events (Johnson & Raye, 1981). Previous experiments have tended to investigate only whether reality monitoring decisions are accurate or not, providing little insight into the extent to which reality monitoring may be affected by qualities of the underlying mnemonic representations. We used a continuous-response memory precision task to measure the quality of remembered experiences that underlie two different types of reality monitoring decisions: agency decisions that distinguish actions performed by participants and the experimenter, and perceptual decisions that distinguish perceived and imagined experiences. The data revealed memory precision to be associated with higher accuracy in both agency and perceptual reality monitoring decisions, with reduced precision linked with a tendency to misattribute self-generated experiences to external sources. We then sought to investigate the possible neurocognitive basis of these observed associations by applying brain stimulation to a region that has been implicated in precise recollection of personal events, left angular gyrus. Stimulation of angular gyrus selectively reduced the association between memory precision and self-referential reality monitoring decisions, relative to control site stimulation. Angular gyrus may, therefore, be important for the ability to imbue remembered experiences with a sense of self-agency, a key component of ‘autonoetic consciousness’ that characterises episodic memory (Tulving, 1985).
Environmental correlates and functional consequences of bill divergence in island song sparrows
Authors: Gamboa Maybellene P. , Ghalambor Cameron K. , Sillett T. Scott , Funk W. Chris , Furbush Ross A. , Husak Jerry F. , Danner Raymond M.
Published: September 2021

Inferring the environmental selection pressures responsible for phenotypic variation is a challenge in adaptation studies as traits often have multiple functions and are shaped by complex selection regimes. We provide experimental evidence that morphology of the multifunctional avian bill is related to climate, not foraging efficiency, in song sparrows (Melospiza melodia) on the California Channel Islands. Our research builds on a study in song sparrow museum specimens that demonstrated a positive correlation between bill surface area and maximum temperature, suggesting a greater demand for dry heat dissipation in hotter, xeric environments. We sampled contemporary sparrow populations across three climatically distinct islands to test the alternate hypotheses that song sparrow bill morphology is either a product of vegetative differences with functional consequences for foraging efficiency or related to maximum temperature and, consequently, important for thermoregulation. Measurements of >500 live individuals indicated a significant, positive relationship between maximum temperature and bill surface area when correcting for body size. In contrast, maximum bite force, seed extraction time, and vegetation on breeding territories (a proxy for food resources) were not significantly associated with bill dimensions. While we cannot exclude the influence of foraging ability and diet on bill morphology, our results are consistent with the hypothesis that variation in song sparrows’ need for thermoregulatory capacity across the northern Channel Islands selects for divergence in bill surface area.

SUMMARY STATEMENT

Island song sparrow bill differences are correlated with climate, not vegetation, and experimental evidence finds no functional effect on foraging efficiency. This suggests many factors shape this multifunctional trait.
Classifying the Unknown: Identification of Insects by Deep Open-set Bayesian Learning
Authors: Badirli Sarkhan , Picard Christine J. , Mohler George , Akata Zeynep , Dundar Murat
Published: September 2021

Insects represent a large majority of biodiversity on Earth, yet only 20% of the estimated 5.5 million insect species are currently described (1). While describing new species typically requires specific taxonomic expertise to identify morphological characters that distinguish it from other potential species, DNA-based methods have aided in providing additional evidence of separate species (2). Machine learning (ML) is emerging as a potential new approach in identifying new species, given that this analysis may be more sensitive to subtle differences humans may not process. Existing ML algorithms are limited by image repositories that do not include undescribed species. We developed a Bayesian deep learning method for the open-set classification of species. The proposed approach forms a Bayesian hierarchy of species around corresponding genera and uses deep embeddings of images and barcodes together to identify insects at the lowest level of abstraction possible. To demonstrate proof of concept, we used a database of 32,848 insect instances from 1,040 described species split into training and test data. The test data included 243 species not present in the training data. Our results demonstrate that using DNA sequences and images together, insect instances of described species can be classified with 96.66% accuracy while achieving accuracy of 81.39% in identifying genera of insect instances of undescribed species. The proposed deep open-set Bayesian model demonstrates a powerful new approach that can be used for the gargantuan task of identifying new insect species.
Tourmaline: a containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake
Authors: Thompson Luke R. , Anderson Sean R. , Den Uyl Paul A. , Patin Nastassia V. , Lim Shen Jean , Sanderson Grant , Goodwin Kelly D.
Published: September 2021

Background

Amplicon sequencing (metabarcoding) is a common method to survey diversity of environmental communities whereby a single genetic locus is amplified and sequenced from the DNA of whole or partial organisms, organismal traces (e.g., skin, mucus, feces), or microbes in an environmental sample. Several software packages exist for analyzing amplicon data, among which QIIME 2 has emerged as a popular option because of its broad functionality, plugin architecture, provenance tracking, and interactive visualizations. However, each new analysis requires the user to keep track of input and output file names, parameters, and commands; this lack of automation and standardization is inefficient and creates barriers to meta-analysis and sharing of results.

Findings

We developed Tourmaline, a Python-based workflow that implements QIIME 2 and is built using the Snakemake workflow management system. Starting from a configuration file that defines parameters and input files—a reference database, a sample metadata file, and a manifest or archive of FASTQ sequences—it uses QIIME 2 to run either the DADA2 or Deblur denoising algorithm, assigns taxonomy to the resulting representative sequences, performs analyses of taxonomic, alpha, and beta diversity, and generates an HTML report summarizing and linking to the output files. Features include support for multiple cores, automatic determination of trimming parameters using quality scores, representative sequence filtering (taxonomy, length, abundance, prevalence, or ID), support for multiple taxonomic classification and sequence alignment methods, outlier detection, and automated initialization of a new analysis using previous settings. The workflow runs natively on Linux and macOS or via a Docker container. We ran Tourmaline on a 16S rRNA amplicon dataset from Lake Erie surface water, showing its utility for parameter optimization and the ability to easily view interactive visualizations through the HTML report, QIIME 2 viewer, and R- and Python-based Jupyter notebooks.

Conclusions

Automated workflows like Tourmaline enable rapid analysis of environmental and biomedical amplicon data, decreasing the time from data generation to actionable results. Tourmaline is available for download at github.com/aomlomics/tourmaline.
Effect of tag attachment on the flight performance of five raptor species
Authors: Longarini Arianna , Duriez Olivier , Shepard Emily , Safi Kamran , Wikelski Martin , Scacco Martina
Published: September 2021

Bio-logging devices play a fundamental and indispensable role in movement ecology studies, particularly in the wild. However, researchers are becoming increasingly aware of the influence that attaching devices can have on animals, particularly on their behaviour, energy expenditure and survival. The way a device is attached to an animal’s body has also potential consequences for the collected data, and quantifying the type and magnitude of such potential effects is fundamental to enable researchers to combine and compare data from different studies, as much as it is to improve animal welfare.

For over two decades, large terrestrial birds have been in the focus of long-term movement ecology research, employing bio-logging devices attached with different types of harnesses. However, comparative studies investigating the effects of different harness types used on these species are scarce.

In this study, we tested for potential differences in data collected by two commonly used harness types, backpack and leg-loop, on the flight performance of 10 individuals from five raptor species, equipped with high resolution bio-logging devices, in the same area and time. We explored the effect of harness type on vertical speed, horizontal speed, glide ratio, height above sea level, distance travelled, proportion of soaring and flapping behaviour, and VeDBA (a proxy for energy expenditure) between and within individuals, all used as fine-scale measures of flight performance. Birds equipped with leg-loops climbed up to 0.65 ms−1 faster, reached 19% greater heights while soaring, and spent less time in active flight compared to birds equipped with backpacks, suggesting that backpack harnesses, compared to leg-loops, might cause additional drag affecting the birds’ flight performance. A lower rate of sinking while gliding, a slightly higher glide ratio, higher horizontal speed while soaring, and lower VeDBA, were also indicative of less drag using leg-loops. Our results add to the existing literature highlighting the design-related advantages of leg-loops, and support the use of leg-loops as a better alternative to backpack harnesses for large soaring birds, when possible. Our study also highlights how apparently small changes in device attachment can lead to notable improvements in tagging practice, with implications for animal welfare, data interpretation and comparability.
Relationships between individual differences in dual process and electrophysiological signatures of familiarity and recollection during retrieval
Authors: Dimsdale-Zucker Halle R. , Maciejewska Karina , Kim Kamin , Yonelinas Andrew P. , Ranganath Charan
Published: September 2021

Our everyday memories can vary in terms of accuracy and phenomenology. According to one theoretical account, these differences hinge on whether the memories contain information about both an item itself as well as associated details (remember) versus those that are devoid of these associated contextual details (familiar). This distinction has been supported by computational modeling of behavior, studies in patients, and neuroimaging work including differences both in electrophysiological and functional magnetic resonance imaging. At present, however, little evidence has emerged to suggest that neurophysiological measures track individual differences in estimates of recollection and familiarity. Here, we conducted electrophysiological recordings of brain activity during a recognition memory task designed to differentiate between behavioral indices of recollection and familiarity. Non-parametric cluster-based permutation analyses revealed associations between electrophysiological signatures of familiarity and recollection with their respective behavioral estimates. These results support the idea that recollection and familiarity are distinct phenomena and is the first, to our knowledge, to identify distinct electrophysiological signatures that track individual differences in these processes.
Metabolic Derangement in Polycystic Kidney Disease Mouse Models Is Ameliorated by Mitochondrial-Targeted Antioxidants
Authors: Daneshgar Nastaran , Baguley Andrew W , Liang Peir-In , Wu Fei , Chu Yi , Kinter Michael T. , Benavides Gloria A. , Johnson Michelle S. , Darley-Usmar Victor , Zhang Jianhua , Chan Kung-Sik , Dai Dao-Fu
Published: September 2021

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressively enlarging cysts. Here we elucidate the interplay between oxidative stress, mitochondrial dysfunction, and metabolic derangement using two mouse models of PKD1 mutation, PKD1RC/nulland PKD1RC/RC. Mouse kidneys with PKD1 mutation have decreased mitochondrial complexes activity. Targeted proteomics analysis shows a significant decrease in proteins involved in the TCA cycle, fatty acid oxidation (FAO), respiratory complexes, and endogenous antioxidants. Overexpressing mitochondrial-targeted catalase (mCAT) using adeno-associated virus reduces mitochondrial ROS, oxidative damage, ameliorates the progression of PKD and partially restores expression of proteins involved in FAO and the TCA cycle. In human ADPKD cells, inducing mitochondrial ROS increased ERK1/2 phosphorylation and decreased AMPK phosphorylation, whereas the converse was observed with increased scavenging of ROS in the mitochondria. Treatment with the mitochondrial protective peptide, SS31, recapitulates the beneficial effects of mCAT, supporting its potential application as a novel therapeutic for ADPKD.
Environment-dependence of the expression of mutational load and species’ range limits
Authors: Perrier Antoine , Sánchez-Castro Darío , Willi Yvonne
Published: September 2021

Theoretical and empirical research on the causes of species’ range limits suggests the contribution of several intrinsic and extrinsic factors, with potentially complex interactions among them. An intrinsic factor proposed by recent theory is mutational load increasing towards range edges because of genetic drift. Furthermore, environmental quality may decline toward range edges and enhance the expression of load. Here we tested whether the expression of mutational load associated with range limits in the North American plantArabidopsis lyratais enhanced under stressful environmental conditions by comparing the performance of within-versusbetween-population crosses at common garden sites across the species’ distribution and beyond. Heterosis, reflecting the expression of load, increased with heightened estimates of genomic load and with environmental stress caused by warming, but the interaction was not significant. We conclude that range-edge populations suffer from a twofold genetic Allee effect caused by increased mutational load and stress-dependent load linked to general heterozygote deficiency, but no synergistic effect between them.
A biologically accurate model of directional hearing in the parasitoid flyOrmia ochracea
Authors: Mikel-Stites Max R. , Salcedo Mary K. , Socha John J. , Marek Paul E. , Staples Anne E.
Published: September 2021

This manuscript was compiled on October 5, 2021 Although most binaural organisms localize sound sources using neurological structures to amplify the sounds they hear, some animals use mechanically coupled hearing organs instead. One of these animals, the parasitoid flyOrmia ochracea,has astoundingly accurate sound localization abilities and can locate objects in the azimuthal plane with a precision of 2°, equal to that of humans. This is accomplished despite an intertympanal distance of only 0.5 mm, which is less than 1/100th of the wavelength of the sound emitted by the crickets that it parasitizes. In 1995, Mileset al.developed a model of hearing mechanics in O.ochracea,which works well for incoming sound angles of less than ±30°, but suffers from reduced accuracy (up to 60% error) at higher angles. Even with this limitation, it has served as the basis for multiple bio-inspired microphone designs for decades. Here, we present critical improvements to the classicO. ochraceahearing model based on information from 3D reconstructions ofO. ochracea’stympana. The 3D images reveal that the tympanal organ has curved lateral faces in addition to the flat front-facing prosternal membranes represented in the Miles model. To mimic these faces, we incorporated spatially-varying spring and damper coefficients that respond asymmetrically to incident sound waves, making a new quasi-two-dimensional (q2D) model. The q2D model has high accuracy (average errors of less than 10%) for the entire range of incoming sound angles. This improved biomechanical hearing model can inform the development of new technologies and may help to play a key role in developing improved hearing aids.

Significance Statement

The ability to identify the location of sound sources is critical to organismal survival and for technologies that minimize unwanted background noise, such as directional microphones for hearing aids. Because of its exceptional auditory system, the parasitoid flyOrmia ochraceahas served as an important model for binaural hearing and a source of bioinspiration for building tiny directional microphones with outsized sound localization abilities. Here, we performed 3D imaging of the fly’s tympanal organs and used the morphological information to improve the current model for hearing inO. ochracea.This model greatly expands the range of biological accuracy from ±30° to all incoming sound angles, providing a new avenue for studies of binaural hearing and further inspiration for fly-inspired technologies.
DYNAMICS OF NEUROMUSCULAR TRANSMISSION REPRODUCED BY CALCIUM-DEPENDENT SERIAL TRANSITIONS IN THE VESICLE FUSION COMPLEX
Authors: Martínez-Valencia Alejandro , Ramírez-Santiago Guillermo , De-Miguel Francisco F.
Published: September 2021

Neuromuscular transmission, from spontaneous release to facilitation and depression was accurately reproduced by a mechanistic kinetic model of sequential maturation transitions in the molecular fusion complex. The model incorporates three predictions. First, sequential calcium-dependent forward transitions take vesicles from docked to pre-primed to primed states, followed by fusion. Second, pre-priming and priming are reversible. Third, fusion and recycling are unidirectional. The model was fed with experimental data from previous studies while the backward (β) and recycling (ρ) rate constant values were fitted. Classical experiments were successfully reproduced when every forward (α) rate constant had the same value, and both backward rate constants were 50-100 times larger. Such disproportion originated an abruptly decreasing gradient of resting vesicles from docked to primed states. Simulations also predict that: i. Spontaneous release reflects primed to fusion spontaneous transitions. ii. Calcium elevations synchronize the series of forward transitions that lead to fusion. iii Facilitation reflects a transient increase of priming following calcium-dependent transitions. iv. Backward transitions and recycling restore the resting state. v. Depression reflects backward transitions and slow recycling after intense release. Such finely-tuned kinetics offers a mechanism for collective non-linear transitional adaptations of a homogeneous vesicle pool to an ever-changing pattern of electrical activity.
Acute Glucagon-Like Peptide-1 Receptor Agonist Liraglutide Prevents Drug-Induced Heroin Seeking in Rats
Authors: Douton Joaquin E. , Acharya Nikhil K. , Stoltzfus Brooke , Sun Dongxiao , Grigson Patricia S. , Nyland Jennifer E.
Published: September 2021

Substance use disorder is a difficult disease to treat due to its relapsing nature. In the last decade, opioid use disorder has been a threat to public health, being declared an epidemic by the Centers for Disease Control and Prevention. This is a tragic situation, considering there are currently effective, yet not ideal, treatments to prevent relapse. Recent research has shown that hormones that modulate hunger and satiety also can modulate motivated behavior for drugs of abuse. For example, the short-acting analog of glucagon-like peptide-1 (GLP-1), an incretin hormone that regulates homeostatic feeding, has been shown to reduce responding for rewarding stimuli such as food, cocaine, heroin and nicotine. Here, we tested the acute effects of the long-acting GLP-1 analog, liraglutide, on heroin seeking. We found that, in rats with heroin self-administration experience, subcutaneous (sc) administration of an acute dose of 0.3 mg/kg liraglutide was effective in preventing relapse after exposure to three major precipitators: drug-associated cues, stress, and the drug itself. However, the effects of the drug were contingent upon the pretreatment time, with the drug being fully effective when administered using a 6 h, rather than a 4 h pretreatment time. Finally, we confirmed that the reduction in drug seeking is not due to a locomotor impairment, as liraglutide did not significantly alter performance in a rotarod test. As such, this acute non-opioid treatment may serve as a new and effective bridge to treatment.
Evolutionary association of receptor-wide amino acids with G protein coupling selectivity in aminergic GPCRs
Authors: Selçuk Berkay , Erol Ismail , Durdağı Serdar , Adebali Ogun
Published: September 2021

G protein-coupled receptors (GPCRs) induce signal transduction pathways through coupling to four main subtypes of G proteins (Gs, Gi, Gq, G12/13), selectively. However, G protein selective activation mechanisms and residual determinants in GPCRs have remained obscure. Herein, we performed an extensive phylogenetic analysis and identified specifically conserved residues for the receptors having similar coupling profiles in each aminergic receptor. By integrating our methodology of differential evolutionary conservation of G protein-specific amino acids with structural analyses, we identified selective activation networks for Gs, Gi1, Go, and Gq. To validate that these networks could determine coupling selectivity we further analyzed Gs specific activation network and associated it with the larger TM6 tilt which is a signature of Gs-coupled receptors. Through molecular dynamics simulations, we showed that previously uncharacterized Glycine at position 7×41 plays an important role in both receptor activation and Gs coupling selectivity by inducing a larger TM6 movement. Finally, we gathered our results into a comprehensive model of G protein selectivity called “sequential switches of activation” describing three main molecular switches controlling GPCR activation: ligand binding, G protein selective activation mechanisms and G protein contact.
Correlated variability in primate superior colliculus depends on functional class
Authors: Katz Leor N. , Yu Gongchen , Herman James P. , Krauzlis Richard J.
Published: September 2021

Correlated variability (spike count correlations, rSC) in a population of neurons can constrain how information is read out, depending on behavioral task and neuronal tuning. Here we tested whether rSC also depends on neuronal functional class. We recorded from populations of neurons in macaque superior colliculus (SC), a structure that contains well-defined functional classes. We found that during a guided saccade task, different classes of neurons exhibited differing degrees of rSC. “Delay class” neurons displayed the highest rSC, especially during the delay epoch of saccade tasks that relied on working memory. This was only present among Delay class neurons within the same hemisphere. The dependence of rSC on functional class indicates that subpopulations of SC neurons occupy distinct circuit niches with distinct inputs. Such subpopulations should be accounted for differentially when attempting to model or infer population coding principles in the SC, or elsewhere in the primate brain.
Circuit contributions to sensory-driven glutamatergic drive of olfactory bulb mitral and tufted cells during odorant inhalation
Authors: Moran Andrew K. , Eiting Thomas P. , Wachowiak Matt
Published: September 2021

In the mammalian olfactory bulb (OB), mitral/tufted (MT) cells respond to odorant inhalation with diverse temporal patterns that are thought to encode odor information. Much of this diversity is already apparent at the level of glutamatergic input to MT cells, which receive direct, monosynaptic excitatory input from olfactory sensory neurons (OSNs) as well as multisynaptic excitatory drive via glutamatergic interneurons. Both pathways are also subject to modulation by inhibitory circuits in the glomerular layer of the OB. To understand the role of direct OSN input versus postsynaptic OB circuit mechanisms in shaping diverse dynamics of glutamatergic drive to MT cells, we imaged glutamate signaling onto MT cell dendrites in anesthetized mice while blocking multisynaptic excitatory drive with ionotropic glutamate receptor antagonists and blocking presynaptic modulation of glutamate release from OSNs with GABAB receptor antagonists. GABAB receptor blockade increased the magnitude of inhalation-linked glutamate transients onto MT cell apical dendrites without altering their inhalation-linked dynamics, confirming that presynaptic inhibition impacts the gain of OSN inputs to the OB. Surprisingly, blockade of multisynaptic excitation only modestly impacted glutamatergic input to MT cells, causing a slight reduction in the amplitude of inhalation-linked glutamate transients in response to low odorant concentrations and no change in the dynamics of each transient. Postsynaptic blockade also modestly impacted glutamate dynamics over a slower timescale, mainly by reducing adaptation of the glutamate response across multiple inhalations of odorant. These results suggest that direct glutamatergic input from OSNs provides the bulk of excitatory drive to MT cells, and that diversity in the dynamics of this input may be a primary determinant of the temporal diversity in MT cell responses that underlies odor representations at this stage.
Accurate Name Entity Recognition for Biomedical Literatures: A Combined High-quality Manual Annotation and Deep-learning Natural Language Processing Study
Authors: Huang Dao-Ling , Zeng Quanlei , Xiong Yun , Liu Shuixia , Pang Chaoqun , Xia Menglei , Fang Ting , Ma Yanli , Qiang Cuicui , Zhang Yi , Zhang Yu , Li Hong , Yuan Yuying
Published: September 2021

A combined high-quality manual annotation and deep-learning natural language processing study is reported to make accurate name entity recognition (NER) for biomedical literatures. A home-made version of entity annotation guidelines on biomedical literatures was constructed. Our manual annotations have an overall over 92% consistency for all the four entity types — gene, variant, disease and species —with the same publicly available annotated corpora from other experts previously. A total of 400 full biomedical articles from PubMed are annotated based on our home-made entity annotation guidelines. Both a BERT-based large model and a DistilBERT-based simplified model were constructed, trained and optimized for offline and online inference, respectively. The F1-scores of NER of gene, variant, disease and species for the BERT-based model are 97.28%, 93.52%, 92.54% and 95.76%, respectively, while those for the DistilBERT-based model are 95.14%, 86.26%, 91.37% and 89.92%, respectively. The F1 scores of the DistilBERT-based NER model retains 97.8%, 92.2%, 98.7% and 93.9% of those of BERT-based NER for gene, variant, disease and species, respectively. Moreover, the performance for both our BERT-based NER model and DistilBERT-based NER model outperforms that of the state-of-art model—BioBERT, indicating the significance to train an NER model on biomedical-domain literatures jointly with high-quality annotated datasets.
A B73 x Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize
Authors: Perez-Limón Sergio , Li Meng , Carolina Cintora-Martinez G. , Rocio Aguilar-Rangel M , Nancy Salazar-Vidal M. , González-Segovia Eric , Blöcher-Juárez Karla , Guerrero-Zavala Alejandro , Barrales-Gamez Benjamin , Carcaño-Macias Jessica , Costich Denise E. , Nieto-Sotelo Jorge , de la Vega Octavio Martinez , Simpson June , Hufford Matthew B. , Ross-Ibarra Jeffrey , Flint-Garcia Sherry , Diaz-Garcia Luis , Rellán-Álvarez Rubén , Sawers Ruairidh J. H.
Published: September 2021

Generations of farmer selection have produced a unique collection of traditional maize varieties adapted to the environmental challenges of the central Mexican highlands. In addition to agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterized a recombinant inbred line population derived from the cross of the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. Evaluation over multiple years in lowland and highland field sites in Mexico identified genomic regions linked to yield components and putatively adaptive morphological traits. A region on chromosome 7 associated with ear weight showed antagonistic allelic effects in lowland and highland fields, suggesting a trade-off consistent with local adaptation. We identified several alleles of highland origin associated with characteristic highland traits, including reduced tassel branching, increased stem pigmentation and the presence of stem macrohairs. The oligogenic architecture of characteristic morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role ofde novomutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.
Alzheimer’s disease alters astrocytic functions related to neuronal support and transcellular internalization of mitochondria
Authors: Lampinen Riikka , Belaya Irina , Saveleva Liudmila , Liddell Jeffrey R , Rait Dzhessi , Huuskonen Mikko T , Giniatullina Raisa , Sorvari Annika , Soppela Liisi , Mikhailov Nikita , Boccuni Isabella , Giniatullin Rashid , Cruz-Haces Marcela , Konovalova Julia , Koskuvi Marja , Rauramaa Tuomas , Domanskyi Andrii , Hämäläinen Riikka H , Goldsteins Gundars , Koistinaho Jari , Malm Tarja , Chew Sweelin , Rilla Kirsi , White Anthony R , Marsh-Armstrong Nicholas , Kanninen Katja M
Published: September 2021

Under physiological conditionsin vivoastrocytes internalize and degrade neuronal mitochondria in a process called transmitophagy. Mitophagy is widely reported to be impaired in neurodegeneration but it is unknown whether and how transmitophagy is altered in Alzheimer’s disease (AD). Here we report that the internalization and degradation of neuronal mitochondria are significantly increased in astrocytes isolated from aged AD mouse brains. We also demonstrate for the first time a similar phenomenon between human neurons and AD astrocytes, and in murine hippocampiin vivo. The results suggest the involvement of S100a4 in impaired mitochondrial transfer between neurons and aged AD astrocytes. Significant increases in the mitophagy regulator Ambra1 were observed in the aged AD astrocytes. These findings demonstrate altered neuron-supporting functions of aged AD astrocytes and provide a starting point for studying the molecular mechanisms of transmitophagy in AD.
Global chromosome topology and the two-component systems in concerted manner regulate transcription in Streptomyces
Authors: Gongerowska-Jac Martyna , Szafran Marcin J. , Mikołajczyk Jakub , Szymczak Justyna , Bartyńska Magda , Gierlikowska Anna , Biały Sylwia , Elliot Marie A. , Jakimowicz Dagmara
Published: September 2021

Bacterial gene expression is controlled at multiple levels, with chromosome supercoiling being one of the most global regulators. Global DNA supercoiling is maintained by the orchestrated action of topoisomerases. In Streptomyces, mycelial soil bacteria with a complex life cycle, topoisomerase I depletion led to elevated chromosome supercoiling, changed expression of significant fraction of genes, delayed growth and blocked sporulation. To identify supercoiling-induced sporulation regulators, we searched for S. coelicolor transposon mutants that were able to restore sporulation despite high chromosome supercoiling. We established that transposon insertion in genes encoding a novel two-component system named SatKR reversed the sporulation blockage resulting from topoisomerase I depletion. Transposition in satKR abolished the transcriptional induction of the genes within the so-called supercoiling-hypersensitive cluster (SHC). Moreover, we found that activated SatR also induced the same set of SHC genes under normal supercoiling conditions. We determined that the expression of genes in this region impacted S. coelicolor growth and sporulation. Interestingly, among the associated products is another two-component system (SitKR), indicating the potential for cascading regulatory effects driven by the SatKR and SitKR two-component systems. Thus, we demonstrated the concerted activity of chromosome supercoiling and a hierarchical two-component signalling system that impacts gene activity governing Streptomyces growth and sporulation.

IMPORTANCE

Streptomyces, soil bacteria with complex life cycle, are the producers of a broad range of biologically active compounds (e.g. antibiotics). Streptomyces respond to various environmental signals using complex transcriptional regulation mechanism. Understanding regulation of their gene expression is crucial for Streptomyces application as industrial organisms. Here, based on extensive transcriptomics analyses, we describe the concerted regulation of genes crucial for growth and development by global DNA supercoiling and novel two-component system. Our data indicate that regulated genes encode growth and sporulation regulator. Thus, we demonstrate that Streptomyces link the global regulatory strategies to adjusts life cycle to unfavourable conditions.
Collective dynamics support group drumming, reduce variability, and stabilize tempo drift
Authors: Dotov Dobromir , Delasanta Lana , Cameron Daniel J , Large Edward , Trainor Laurel J
Published: September 2021

Humans are social animals who engage in a variety of collective activities requiring coordinated action. Among these, music is a defining and ancient aspect of human sociality. Human social interaction has largely been addressed in dyadic paradigms and it is yet to be determined whether the ensuing conclusions generalize to larger groups. Studied more extensively in nonhuman animal behaviour, the presence of multiple agents engaged in the same task space creates different constraints and possibilities than in simpler dyadic interactions. We addressed whether collective dynamics play a role in human circle drumming. The task was to synchronize in a group with an initial reference pattern and then maintain synchronization after it was muted. We varied the number of drummers, from solo to dyad, quartet, and octet. The observed lower variability, lack of speeding up, smoother individual dynamics, and leader-less inter-personal coordination indicated that stability increased as group size increased, a sort of temporal wisdom of crowds. We propose a hybrid continuous-discrete Kuramoto model for emergent group synchronization with pulse-based coupling that exhibits a mean field positive feedback loop. This research suggests that collective phenomena are among the factors that play a role in social cognition.
Movement shapes the structure of fish communities along a cross-shore section in the California Current
Authors: Guiet Jérôme , Bianchi Daniele , Maury Olivier , Barrier Nicolas , Kessouri Fayçal
Published: September 2021

Pelagic fish communities are shaped by bottom-up and top-down processes, transport by currents, and active swimming. However, the interaction of these processes remains poorly understood. Here, we use a regional implementation of the APex ECOSystem Model (APECOSM), a mechanistic model of the pelagic food web, to investigate these processes in the California Current, a highly productive upwelling system characterized by vigorous mesoscale circulation. The model is coupled with an eddy-resolving representation of ocean currents and lower trophic levels, and is tuned to reproduce observed fish biomass from fisheries independent trawls. Several emergent properties of the model compare realistically with observations. First, the epipelagic community accounts for one order of magnitude less biomass than the vertically migratory community, and is composed by smaller species. Second, the abundance of small fish decreases from the coast to the open ocean, while the abundance of large fish remains relatively uniform. This in turn leads to flattening of biomass size-spectra away from the coast for both communities. Third, the model reproduces a cross-shore succession of small to large sizes moving offshore, consistent with observations of species occurrence. These cross-shore variations emerge in the model from a combination of: (1) passive offshore advection by the mean current, (2) active swimming towards coastal productive regions to counterbalance this transport, and (3) mesoscale heterogeneity that reduces the ability of organisms to return to coastal waters. Our results highlight the importance of passive and active movement in structuring the pelagic food web, and suggest that a correct representation of these processes is needed for realistic simulations with marine ecosystem models.
Increased temporal discounting and reduced model-based control in problem gambling are not substantially modulated by exposure to virtual gambling environments
Authors: Bruder Luca R. , Wagner Ben , Mathar David , Peters Jan
Published: September 2021

High-performance virtual reality (VR) technology has opened new possibilities for the examination of the reactivity towards addiction-related cues (cue-reactivity) in addiction. In this preregistered study (https://osf.io/4mrta), we investigated the subjective, physiological, and behavioral effects of gambling-related VR environment exposure in participants reporting frequent or pathological gambling (n=31) as well as non-gambling controls (n=29). On two separate days, participants explored two rich and navigable VR-environments (neutral: café vs. gambling-related: casino/sports-betting facility), while electrodermal activity and heart rate were continuously measured using remote sensors. Within VR, participants performed a temporal discounting task and a sequential decision-making task designed to assess model-based and model-free contributions to behavior. Replicating previous findings, we found strong evidence for increased temporal discounting and reduced model-based control in participants reporting frequent or pathological gambling. Although VR gambling environment exposure increased subjective craving, there was if anything inconclusive evidence for further behavioral or physiological effects. Instead, VR exposure substantially increased physiological arousal (electrodermal activity), across groups and conditions. VR is a promising tool for the investigation of context effects in addiction, but some caution is warranted since effects of real gambling environments might not generally replicate in VR. Future studies should delineate how factors such as cognitive load and ecological validity could be balanced to create a more naturalistic VR experience.