bluuebunny/crossref_metadata_2025 huggingface dataset:
Picture naming yields highly consistent cortical activation patterns: test-retest reliability of magnetoencephalography recordings
Authors: Ala-Salomäki Heidi , Kujala Jan , Liljeström Mia , Salmelin Riitta
Published: October 2020

Reliable paradigms and imaging measures of individual-level brain activity are paramount when reaching from group-level research studies to clinical assessment of individual patients. Magnetoencephalography (MEG) provides a direct, non-invasive measure of cortical processing with high spatiotemporal accuracy, and is thus well suited for assessment of functional brain damage in patients with language difficulties. This MEG study aimed to identify, in a picture naming paradigm, source-localized evoked activity and modulations of cortical oscillations that show high test-retest reliability across measurement days in healthy individuals, demonstrating their applicability in clinical settings. For patients with a severe language disorder picture naming can be a challenging task. Therefore, we also determined whether a semantic judgement task (‘is this item living’) with a spoken response (‘yes’/’no’) would suffice to induce comparably consistent activity within brain regions related to language production. The MEG data was collected from 19 healthy participants on two separate days. In picture naming, evoked activity was consistent across measurement days (intraclass correlation coefficient (ICC)>0.4) in the left frontal (400–800 ms after image onset), sensorimotor (200–800 ms), parietal (200–600 ms), temporal (200–800 ms), occipital (400–800 ms) and cingulate (600–800 ms) regions, as well as the right temporal (600–800 ms) region. In the semantic judgement task, consistent evoked activity was spatially more limited, occurring in the left temporal (200–800 ms), sensorimotor (400–800 ms), occipital (400–600 ms) and subparietal (600–800 ms) regions, and the right supramarginal cortex (600–800 ms). The naming task showed typical beta oscillatory suppression in premotor and sensorimotor regions (800–1200 ms) but other consistent modulations of oscillatory activity were mostly observed in posterior cortical regions that have not typically been associated with language processing. The high test-retest consistency of MEG evoked activity in the picture naming task testifies to its applicability in clinical evaluations of language function, as well as in longitudinal MEG studies of language production in clinical and healthy populations.
A computational grid-to-place-cell transformation model indicates a synaptic driver of place cell impairment in early-stage Alzheimer’s Disease
Authors: Ness Natalie , Schultz Simon R.
Published: October 2020

Alzheimer’s Disease (AD) is characterized by progressive neurodegeneration and cognitive impairment. Synaptic dysfunction is an established early symptom, which correlates strongly with cognitive decline, and is hypothesised to mediate the diverse neuronal network abnormalities observed in AD. However, how synaptic dysfunction contributes to network pathology and cognitive impairment in AD remains elusive. Here, we present a grid-cell-to-place-cell transformation model of long-term CA1 place cell dynamics to interrogate the effect of synaptic loss on network function and environmental representation. Synapse loss modelled after experimental observations in the APP/PS1 mouse model was found to induce firing rate alterations and place cell abnormalities that have previously been observed in AD mouse models, including enlarged place fields and lower across-session stability of place fields. Our results support the hypothesis that synaptic dysfunction underlies cognitive deficits, and demonstrate how impaired environmental representation may arise in the early stages of AD. We further propose that dysfunction of excitatory and inhibitory inputs to CA1 pyramidal cells may cause distinct impairments in place cell function, namely reduced stability and place map resolution.

Author Summary

Cognitive decline in Alzheimer’s Disease (AD) correlates most strongly with dysfunction and loss of synapses in affected brain regions. While synaptic dysfunction is a well-established early symptom of AD, how impaired synaptic transmission may lead to progressive cognitive decline, remains subject to active research. In this study, we examine the effect of synapse loss on neuronal network function using a computational model of place cells in the hippocampal network. Place cells encode a cognitive map of an animal’s environment, enabling navigation and spatial memory. This provides a useful indicator of cognitive function, as place cell function is well characterized and abnormalities in place cell firing have been shown to underlie navigational deficits in rodents. We find that synapse loss in our network is sufficient to produce progressive impairments in place cell function, which resemble those observed in mouse models of the disease, supporting the hypothesis that synaptic dysfunction may underlie the cognitive impairment in AD. Furthermore, we observe that loss of excitatory and inhibitory synapses produce distinct spatial impairments. Future experiments investigating the relative contribution of different synaptic inputs may thus allow new insights into the neuronal network alterations in AD and potentially enable the identification of new therapeutic targets.
Diets affect the age-dependent decline of associative learning inCaenorhabditis elegans
Authors: Higurashi Satoshi , Tsukada Sachio , Aleogho Binta Maria , Park Joo Hyun , Tanaka Masaru , Nakano Shunji , Mori Ikue , Noma Kentaro
Published: October 2020

The causality and mechanism of dietary effects on brain aging are still unclear due to the long time scales of aging. The nematodeCaenorhabditis eleganshas contributed to aging research because of its short lifespan and easy genetic manipulation. When fed the standard laboratory diet,Escherichia coli,C. elegansexperiences an age-dependent decline in temperature-food associative learning, called thermotaxis. To address if diet affects this decline, we screened 35 lactic acid bacteria as alternative diets and found that animals maintained high thermotaxis ability when fed a clade ofLactobacillienriched with heterofermentative bacteria. Among them,Lactobacillusreuterimaintained the thermotaxis of aged animals without affecting their lifespan and motility. The effect ofLb. reuteridepends on the DAF-16 transcription factor functioning in neurons. Furthermore, RNA sequencing analysis revealed that differentially expressed genes between aged animals fed different bacteria were enriched with DAF-16 targets. Our results demonstrate that diet can impact brain aging in adaf-16dependent manner without changing the lifespan.
Increased amphetamine-induced hyperactivity intranslin (Tsn)KO mice is driven by elevated adiposity
Authors: Fu Xiuping , Shah Aparna P. , Keighron Jacqueline , Mou Ta-Chung M. , Ladenheim Bruce , Alt Jesse , Fukudome Daisuke , Niwa Minae , Tamashiro Kellie , Tanda Gianluigi , Sawa Akira , Cadet Jean-Lud , Rais Rana , Baraban Jay M.
Published: October 2020

The translin/trax microRNA-degrading enzyme mediates activity-induced changes in translation that underlie several long-lasting forms of cellular plasticity. As translin and trax are expressed in dopaminergic and striatal neurons, we proceeded to investigate whether deletion ofTsnblocks amphetamine sensitization, a long-lasting, translation-dependent form of behavioral plasticity,

Although we expected constitutiveTsndeletion to impair amphetamine sensitization, we found, instead, that it enhances the hyperlocomotion produced by the initial dose of amphetamine. Since these mice display elevated adiposity, which alters pharmacokinetics of many drugs, we measured brain amphetamine levels inTsnknockout mice and found that these are elevated. We also found that diet-induced increases in adiposity in WT mice correlate with elevated brain amphetamine levels. As amphetamine and its analogues are widely used to treat attention deficit disorder, which is associated with obesity, further studies are needed to assess the impact of adiposity on amphetamine levels in these patients.
Neuroinflammation alters the phenotype of lymphangiogenic vessels near the cribriform plate
Authors: Hsu Martin , Madrid Andy , Choi Yun Hwa , Laaker Collin , Herbath Melinda , Sandor Matyas , Fabry Zsuzsanna
Published: October 2020

Meningeal lymphatic vessels residing in the dural layer surrounding the dorsal regions of the brain, basal regions, and near the cribriform plate have all been implicated in the management of neuroinflammation and edema. Interestingly, only the lymphatic vessels near the cribriform plate undergo functional lymphangiogenesis in a mouse model of Multiple Sclerosis, suggesting these particular lymphatics uniquely undergo dynamic changes in response to neuroinflammation and may have distinct access to pro-lymphangiogenic factors in the CNS. However, it is unknown if these newly formed lymphangiogenic vessels are functionally similar to steady-state or if they have any other functional changes during neuroinflammation. In this study, we generated a novel protocol to isolate lymphatic endothelial cells from the cribriform plate for single cell analysis. We demonstrate that neuroinflammation-induced lymphangiogenic vessels undergo unique changes, including the capture of CNS-derived antigens, upregulation of adhesion and immune-modulatory molecules to interact with dendritic cells, and display IFN-γ dependent changes in response to the microenvironment. Single-cell trajectory analysis showed that cribriform plate lymphangiogenic vessels are post-proliferative and not generated from trans-differentiation of myeloid cells. Additionally, we show that these lymphangiogenic vessels have access to a CSF reservoir, express the water pore Aquaporin-1, and may have direct access to the CSF due to gaps in the arachnoid epithelial layer separating the dura from the subarachnoid space. These data characterize cribriform plate lymphatics and demonstrate that these vessels are dynamic structures that engage in leukocyte interactions, antigen sampling, and undergo expansion to drain excess fluid during neuroinflammation. Neuroinflammation not only induces efficient drainage of CSF but also alters the functions of lymphatic vessels near the cribriform plate.
Postharvest handling induces changes in fruit DNA methylation status and is associated with alterations in fruit quality in tomato (Solanum lycopersicumL.)
Authors: Zhou Jiaqi , Chen Bixuan , Albornoz Karin , Beckles Diane M
Published: October 2020

Postharvest handling of tomato (Solanum lycopersicumL.), specifically low-temperature storage and early harvest are used to extend shelf life, but often reduce fruit quality. Recent work suggests that DNA methylation dynamics influences fruit ripening through the demethylaseSlDML2gene. However, the influence of postharvest handling on DNA methylation in relation to fruit quality is unclear. This work aimed to clarify these issues by analyzing DNA methylation using methyl-sensitive amplification polymorphism (MSAP), semi-quantitative transcriptional analysis of marker genes for fruit quality (RIN;RIPENING INHIBITOR) and DNA methylation (SlDML2;Solanum lycopersicumL.DNA demethylase 2), and, fruit biochemical quality biomarkers. Multivariate analysis of these data supported the view that DNA methylation of fruit was influenced more by postharvest handling than ripening stage, however, fruit quality was influenced mainly by ripening. Fruit chilled postharvest were distinct in their DNA methylation state and quality characteristics, which implied that these three phenomena i.e., chilling, methylation, and quality are highly connected. In addition, different postharvest handling methods modulatedSlDML2transcript levels but had little effect on the level ofRINtranscripts in fruit that reached the Turning stage after early harvest, and cold storage. These data collectively helped to advance our interpretation of tomato fruit ripening. In conclusion, our findings revealed that postharvest-induced variation in fruit quality is in relation to DNA methylation. Long-term this work will help better connect physiological changes in tomato fruit to events happening at the molecular level.
Overcoming barriers to the registration of new varieties
Authors: Yang Chin Jian , Russell Joanne , Ramsay Luke , Thomas William , Powell Wayne , Mackay Ian
Published: October 2020

Distinctness, Uniformity and Stability (DUS) is an intellectual property system introduced in 1961 by the International Union for the Protection of New Varieties of Plants (UPOV) for safeguarding the investment and rewarding innovation in developing new plant varieties. Despite the rapid advancement in our understanding of crop biology over the past 60 years, the DUS system has not changed and is still dependent upon a set of morphological traits for testing candidate varieties. As the demand for more plant varieties increases, the barriers to registration of new varieties become more acute and thus require urgent review to the system. To highlight the challenges and remedies in the current system, we evaluated a comprehensive panel of 805 UK barley varieties that span the entire history of DUS testing. Our findings reveal the system deficiencies and provide evidence for a shift towards a robust genomics enabled registration system for new crop varieties.
The coevolution of mammae number and litter size
Authors: Stewart Thomas A. , Yoo Ihna , Upham Nathan S.
Published: October 2020

Mammals are unique in provisioning their offspring with milk, lactiferous nourishment produced in glandular organs called mammae. Mammae number is hypothesized to coevolve with litter size, acting as a constraint on offspring survival. However, predicted canonical relations between mammae number and litter size (i.e., the ‘one-half’ and ‘identity’ rules) are untested across Mammalia. Here we analyze data for 2,301 species and show how these characters coevolve. In Mammalia, mammae number approximates the maximum reported litter size of a species, and mammae number explains more variation in litter size than other species-level traits (mass, gestation length, diet, and seasonality of contemporary geographic distribution). Clades show differences in these patterns, indicating that certain life history strategies might break the ‘rules’ of mammary evolution. Mammae number is an underappreciated constraint on fecundity that has influenced the radiation of mammals.
Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data
Authors: Liang Shaoheng , Dou Jinzhuang , Iqbal Ramiz , Chen Ken
Published: October 2020

Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. Batch effect, i.e., the variability among samples gathered from different times, tissues, and patients, introduces large between-group distance and obscures the true identities of cells. To solve this problem, we introduce Batch-Corrected Distance (BCD), a metric using temporal/spatial locality of the batch effect to control for such factors. We validate BCD on a simulated data as well as applied it to a mouse retina development dataset and a lung dataset. We also found the utility of our approach in understanding the progression of the Coronavirus Disease 2019 (COVID-19). BCD achieves more accurate clusters and better visualizations than state-of-the-art batch correction methods on longitudinal datasets. BCD can be directly integrated with most clustering and visualization methods to enable more scientific findings.
Neural Network Organization for Courtship Song Feature Detection inDrosophila
Authors: Baker Christa A. , McKellar Claire , Nern Aljoscha , Dorkenwald Sven , Pacheco Diego A. , Pang Rich , Eckstein Nils , Funke Jan , Dickson Barry J. , Murthy Mala
Published: October 2020

Animals communicate using sounds in a wide range of contexts, and auditory systems must encode behaviorally relevant acoustic features to drive appropriate reactions. How feature detection emerges along auditory pathways has been difficult to solve due to challenges in mapping the underlying circuits and characterizing responses to behaviorally relevant features. Here, we study auditory activity in theDrosophila melanogasterbrain and investigate feature selectivity for the two main modes of fly courtship song, sinusoids and pulse trains. We identify 24 new cell types of the intermediate layers of the auditory pathway, and using a new connectomic resource, FlyWire, we map all synaptic connections between these cell types, in addition to connections to known early and higher-order auditory neurons - this represents the first map of the auditory pathway. We additionally determine the sign (excitatory or inhibitory) of most synapses in this auditory connectome. We find that auditory neurons display a continuum of preferences for courtship song modes, and that neurons with different song mode preferences are highly interconnected in a network that lacks hierarchical structure. Among this network, frequency tuning is centered on the range of frequencies present in song, whereas pulse rate tuning extends to rates outside of song, suggesting that these neurons form a basis set for downstream processing. Our study provides new insights into the organization of auditory coding within theDrosophilabrain.
Graph-theoretical Analysis of EEG Functional Connectivity during Balance Perturbation in Traumatic Brain Injury: A Pilot Study
Authors: Handiru Vikram Shenoy , Alivar Alaleh , Hoxha Armand , Saleh Soha , Suviseshamuthu Easter S. , Yue Guang , Allexandre Didier
Published: October 2020

Traumatic Brain Injury (TBI) often results in balance impairment, increasing the risk of falls, and the chances of further injuries. However, the underlying neurophysiological mechanisms of postural control after TBI are not well understood. To this end, we conducted a pilot study with a multimodal approach of EEG, MRI, and Diffusion Tensor Imaging (DTI) to explore the neural mechanisms of unpredictable balance perturbations in 17 chronic TBI participants and 15 matched Healthy Controls (HC). As quantitative measures of the functional integration and segregation of the brain networks during the postural task, we computed the global graph-theoretic network measures (global efficiency and modularity) of brain functional connectivity derived from source-space EEG in different frequency bands. We observed that the TBI group showed a lower balance performance as measured by the Center of Pressure (COP) displacement during the task, and the Berg Balance Scale. They also showed altered brain activation and connectivity during the balance task. In particular, the task modulation of brain network segregation in alpha-band was reduced in TBI. Moreover, the DTI findings revealed that the structural damage is associated with reduced network connectivity and integration. In terms of the neural correlates, we observed a distinct role played by different frequency bands; greater theta-band modularity during the task was strongly correlated with the BBS in TBI group; alpha-band and beta-band graph-theoretic measures were associated with the measures of white matter structural integrity. Our future studies will focus on how postural training will modulate the functional brain networks in TBI.
Possible transmission flow of SARS-CoV-2 based on ACE2 features
Authors: Hassan Sk. Sarif , Ghosh Shinjini , Attrish Diksha , Choudhury Pabitra Pal , Uversky Vladimir N. , Uhal Bruce D. , Lundstrom Kenneth , Rezaei Nima , Aljabali Alaa A. A. , Seyran Murat , Pizzol Damiano , Adadi Parise , Soares Antonio , El-Aziz Tarek Mohamed Abd , Kandimalla Ramesh , Tambuwala Murtaza , Azad Gajendra Kumar , Sherchan Samendra P. , Baetas-da-Cruz Wagner , Takayama Kazuo , Serrano-Aroca Ángel , Chauhan Gaurav , Palu Giorgio , Brufsky Adam M.
Published: October 2020

Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22-42, aa 79-84, and aa 330-393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species.
Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant
Authors: Lee Cheryl Yi-Pin , Amrun Siti Naqiah , Chee Rhonda Sin-Ling , Goh Yun Shan , Mak Tze-Minn , Octavia Sophie , Yeo Nicholas Kim-Wah , Chang Zi Wei , Tay Matthew Zirui , Torres-Ruesta Anthony , Carissimo Guillaume , Poh Chek Meng , Fong Siew-Wai , Bei Wang , Lee Sandy , Young Barnaby Edward , Tan Seow-Yen , Leo Yee-Sin , Lye David C. , Lin Raymond T. P. , Maurer-Stroh Sebastien , Lee Bernett , Cheng-I Wang , Renia Laurent , Ng Lisa F.P.
Published: October 2020

The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. With an increased infection and transmission rate, it is imperative to determine whether antibodies induced against the D614 isolate may cross-neutralize against the G614 variant. In this report, profiling of the anti-SARS-CoV-2 humoral immunity reveals similar neutralization profiles against both S protein variants, albeit waning neutralizing antibody capacity at the later phase of infection. These findings provide further insights towards the validity of current immune-based interventions.

IMPORTANCE

Random mutations in the viral genome is a naturally occurring event that may lead to enhanced viral fitness and immunological resistance, while heavily impacting the validity of licensed therapeutics. A single point mutation from aspartic acid (D) to glycine (G) at position 614 of the SARS-CoV-2 spike (S) protein, termed D614G, has garnered global attention due to the observed increase in transmissibility and infection rate. Given that a majority of the developing antibody-mediated therapies and serological assays are based on the S antigen of the original Wuhan reference sequence, it is crucial to determine if humoral immunity acquired from the original SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against the novel prevailing D614G variant.
Reliability of retinal pathology quantification in age-related macular degeneration: Implications for clinical trials and machine learning applications
Authors: Müller Philipp L. , Liefers Bart , Treis Tim , Rodrigues Filipa Gomes , Olvera-Barrios Abraham , Paul Bobby , Dhingra Narendra , Lotery Andrew , Bailey Clare , Taylor Paul , Sánchez Clarisa I. , Tufail Adnan
Published: October 2020

Purpose

To investigate the inter-reader agreement for grading of retinal alterations in age-related macular degeneration (AMD) using a reading center setting.

Methods

In this cross-sectional case series, spectral domain optical coherence tomography (OCT, Topcon 3D OCT, Tokyo, Japan) scans of 112 eyes of 112 patients with neovascular AMD (56 treatment-naive, 56 after three anti-vascular endothelial growth factor injections) were analyzed by four independent readers. Imaging features specific for AMD were annotated using a novel custom-built annotation platform. Dice score, Bland-Altman plots, coefficients of repeatability (CR), coefficients of variation (CV), and intraclass correlation coefficients (ICC) were assessed.

Results

Loss of ellipsoid zone, pigment epithelium detachment, subretinal fluid, and Drusen were the most abundant features in our cohort. The features subretinal fluid, intraretinal fluid, hypertransmission, descent of the outer plexiform layer, and pigment epithelium detachment showed highest inter-reader agreement, while detection and measures of loss of ellipsoid zone and retinal pigment epithelium were more variable. The agreement on the size and location of the respective annotation was more consistent throughout all features.

Conclusions

The inter-reader agreement depended on the respective OCT-based feature. A selection of reliable features might provide suitable surrogate markers for disease progression and possible treatment effects focusing on different disease stages.

Translational Relevance

This might give opportunities to a more time- and cost-effective patient assessment and improved decision-making as well as have implications for clinical trials and training machine learning algorithms.
Expanding the Galaxy’s reference data
Authors: VijayKrishna Nagampalli , Joshi Jayadev , Coraor Nate , Hillman-Jackson Jennifer , Bouvier Dave , van den Beek Marius , Eguinoa Ignacio , Coppens Frederik , Golitsynskiy Sergey , Stolarczyk Michał , Sheffield Nathan C. , Gladman Simon , Cuccuru Gianmauro , Grüning Björn , Soranzo Nicola , Rasche Helena , Langhorst Bradley W. , Bernt Matthias , Fornika Dan , de Lima Morais David Anderson , Barrette Michel , van Heusden Peter , Petrillo Mauro , Puertas-Gallardo Antonio , Patak Alex , Hotz Hans-Rudolf , Blankenberg Daniel
Published: October 2020

Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows to easily organize, retrieve, and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. Additionally, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie’s remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS repository from GalaxyProject.org, with mirrors across the United States, Canada, Europe, and Australia, enabling easy use outside of Galaxy.

Availability and implementation

The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 20.05, which is available fromhttps://github.com/galaxyproject/galaxyunder the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed athttps://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pulland released using an MIT license.
A mobile genetic element increases bacterial host fitness by manipulating development
Authors: Jones Joshua M. , Grinberg Ilana , Eldar Avigdor , Grossman Alan D.
Published: October 2020

Horizontal gene transfer is a major force in bacterial evolution. Mobile genetic elements are responsible for much of horizontal gene transfer and also carry beneficial cargo genes. Uncovering strategies used by mobile genetic elements to benefit host cells is crucial for understanding their stability and spread in populations. We describe a benefit that ICEBs1, an integrative and conjugative element ofBacillus subtilis, provides to its host cells. Activation of ICEBs1conferred a frequency-dependent selective advantage to host cells during two different developmental processes: biofilm formation and sporulation. These benefits were due to inhibition of biofilm-associated gene expression and delayed sporulation by ICEBs1-containing cells, enabling them to exploit their neighbors and grow more prior to development. A single ICEBs1gene,devI(formerlyydcO), was both necessary and sufficient for inhibition of development. Manipulation of host developmental programs allows ICEBs1to increase host fitness, thereby increasing propagation of the element.
A red fluorescent protein with improved monomericity enables ratiometric voltage imaging with ASAP3
Authors: Kim Benjamin B. , Wu Haodi , Hao Yukun A. , Pan Michael , Chavarha Mariya , Westberg Michael , St-Pierre Francois , Wu Joseph C. , Lin Michael Z.
Published: October 2020

A ratiometric genetically encoded voltage indicator (GEVI) would be desirable for tracking transmembrane voltage changes in cells that are undergoing motion. To create a high-performance ratiometric GEVI, we explored the possibility of adding a voltage-independent red fluorophore to ASAP3, a high-gain green fluorescent GEVI. We performed combinatorial multi-site mutagenesis on the cyan-excitable red fluorescent protein mCyRFP1 to enhance brightness and monomericity, creating mCyRFP3. Among red fluorescent proteins tested, mCyRFP3 proved to be the least perturbing when fused to ASAP3. We demonstrate that the red fluorescence of ASAP3-mCyRFP3 (ASAP3-R3) provides an effective reference channel to remove motion artifacts from voltage-induced changes in green fluorescence. Finally we use ASAP3-R3 to visualize membrane voltage changes throughout the cell cycle of motile cells.
Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations
Authors: Johnson Milo S. , Gopalakrishnan Shreyas , Goyal Juhee , Dillingham Megan E. , Bakerlee Christopher W. , Humphrey Parris T. , Jagdish Tanush , Jerison Elizabeth R. , Kosheleva Katya , Lawrence Katherine R. , Min Jiseon , Moulana Alief , Phillips Angela M. , Piper Julia C. , Purkanti Ramya , Rego-Costa Artur , McDonald Michael J. , Ba Alex N. Nguyen , Desai Michael M.
Published: October 2020

Laboratory experimental evolution provides a window into the details of the evolutionary process. To investigate the consequences of long-term adaptation, we evolved 205 S. cerevisiae populations (124 haploid and 81 diploid) for ∼10,000 generations in three environments. We measured the dynamics of fitness changes over time, finding repeatable patterns of declining adaptability. Sequencing revealed that this phenotypic adaptation is coupled with a steady accumulation of mutations, widespread genetic parallelism, and historical contingency. In contrast to long-term evolution in E. coli, we do not observe long-term coexistence or populations with highly elevated mutation rates. We find that evolution in diploid populations involves both fixation of heterozygous mutations and frequent loss-of-heterozygosity events. Together, these results help distinguish aspects of evolutionary dynamics that are likely to be general features of adaptation across many systems from those that are specific to individual organisms and environmental conditions.
Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
Authors: Ohno Ayumu , Umezawa Kazuo , Asai Satomi , Kryukov Kirill , Nakagawa So , Miyachi Hayato , Imanishi Tadashi
Published: October 2020

Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria.
Calcium signaling through a Transient Receptor Channel is important forToxoplasma gondiigrowth
Authors: Márquez-Nogueras Karla M. , Chasen Nathan M. , Hortua Triana Myriam A. , Kuo Ivana Y. , Moreno Silvia N.J.
Published: October 2020

Transient Receptor Potential (TRP) channels participate in ion calcium (Ca2+) influx and intracellular Ca2+release. TRP channels have not been studied inToxoplasma gondiior any other Apicomplexan parasite. We characterized a protein predicted to possess a TRP domain (TgTRPPL-2) and determined its role in Ca2+signaling inT. gondii, the causative agent of toxoplasmosis. TgTRPPL-2 localized to the plasma membrane and the endoplasmic reticulum ofT. gondii. TheΔTgTRPPL-2mutant was defective in growth and Ca2+influx. Heterologous expression of TgTRPPL-2 in HEK-3KO cells allowed its functional characterization. Patching of ER-nuclear membranes demonstrated that TgTRPPL-2 is a non-selective cation channel that conducts Ca2+. Pharmacological blockers of TgTRPPL-2 inhibited Ca2+influx and parasite growth. This is the first report of an Apicomplexan channel that conducts Ca2+and initiates the Ca2+signaling cascade that culminates in the stimulation of motility, invasion and egress. TgTRPPL-2 is a potential target for combating toxoplasmosis.
Transcriptome Analysis of the Eggplant Fruits Overexpressing a Gene of Chlorogenic Acid Pathway
Authors: Kaushik Prashant
Published: October 2020

Chlorogenic acid is the primary phenolic acids present in Eggplant fruits. For the generation of chlorogenic acid in the eggplant hydroxycinnamoyl CoA-quinate transferase (SmHQT), is a central enzyme that catalyzes the reaction to the chlorogenic acid production. Although a precise function of SmHQT is not well defined in the eggplant fruit. In this study, the overexpression of SmHQT in the eggplant fruit’s flesh was studied using the agroinfiltration technique. Furthermore, to determine the differences at the genomic level RNA-seq analysis was performed, and its results showed that 415 genes of the phenylpropanoid pathway were upregulated in the transgenic fruit. Also, it was determined that the differentially expressed genes were dominantly related to phenylpropanoid pathway along with cell expansion, and cytokinin. The agroinfiltrated fruit exhibited more than twice the chlorogenic content in the normal fruit. Overall, the result provides new insight into the eggplant chlorogenic content increment at the molecular level and unseal the opportunities to design new strategies for the improvement of chlorogenic content as nutrition in eggplant.
Cross-Linking of T cell to B cell lymphoma by the T cell bispecific antibody CD20-TCB induces IFNγ/CXCL10-dependent peripheral T cell recruitment in humanized murine model
Authors: Cremasco Floriana , Menietti Elena , Speziale Dario , Sam Johannes , Sammicheli Stefano , Richard Marine , Varol Ahmet , Klein Christian , Umana Pablo , Bacac Marina , Colombetti Sara , Perro Mario
Published: October 2020

Diffuse large B cell lymphomas (DLBCL) are a highly heterogeneous subtype of Non Hodgkin Lymphoma (NHL), accounting for about 25% of NHL [1]. Despite an increased progression-free survival upon therapy, 40-50% of patients develop relapse/refractory disease, therefore there remains an important medical need [2]. T cell recruiting therapies, such as the CD20xCD3 T cell bi-specific antibody CD20-TCB (RG6026 or glofitamab), represent a novel approach to target all stages of DLBCL, especially those that fail to respond to multiple lines of treatment [3, 4]. We aimed for a better understanding of the molecular features related to the mode of action (MoA) of CD20-TCB in inducing Target/T cell synapse formation and human T cell recruitment to the tumor. To directly evaluate the correlation between synapse, cytokine production and anti-tumor efficacy using CD20-TCB, we developed an innovative preclinical human DLBCLin vivomodel that allowed trackingin vivohuman T cell dynamics by multiphoton intravital microscopy (MP-IVM). Byex vivoandin vivoapproaches, we revealed that CD20-TCB is inducing strong and stable synapses between human T cell and tumor cells, which are dependent on the dose of CD20-TCB and on LFA-1 activity but not on FAS-L. Moreover, despite CD20-TCB being a large molecule (194.342 kDa), we observed that intra-tumor CD20-TCB-mediated human T cell-tumor cell synapses occur within 1 hour upon CD20-TCB administration. These tight interactions, observed for at least 72 hours post TCB administration, result in tumor cell cytotoxicity, resident T cell proliferation and peripheral blood T cell recruitment into tumor. By blocking the IFNγ-CXCL10 axis, the recruitment of peripheral T cells was abrogated, partially affecting the efficacy of CD20-TCB treatment which rely only on resident T cell proliferation. Altogether these data reveal that CD20-TCB’s anti-tumor activity relies on a triple effect: i) fast formation of stable T cell-tumor cell synapses which induce tumor cytotoxicity and cytokine production, ii) resident T cell proliferation and iii) recruitment of fresh peripheral T cells to the tumor core to allow a positive enhancement of the anti-tumor effect.
Natural Oil Blend Formulation (NOBF) as an anti- African Swine Fever Virus (ASFV) agent in Primary Porcine Alveolar Macrophases (PAM) cells of Swine
Authors: Babikian Haig Yousef , Jha Rajeev Kumar , Truong Quang Lam , Nguyen Lan Thi , Nguyen Hoa Thi , To Thanh Long
Published: October 2020

African swine fever is one of the severe pathogens of swine. It has a significant impact on production and on economics. So far, there are no known remedies, such as vaccines or drugs, reported. The natural oil blend formulation (NOBF) successfully tested against the African swine fever virus (ASFV) inin vitroconditions. The natural oil blend formulation (NOBF) combinesEucalyptus globulus,Pinus sylvestris, andLavandula latifolia. We used a two-fold serial dilution to test the NOBF formulation dose. Thein vitrotrial results demonstrated that NOBF up to dilution 13 or 0.000625 ml deactivates the lethal dose 105HAD50 of ASFV. There was no hemadsorption (Rosetta formation) up to dilution 12 or 0.00125 ml of NOBF. The Ct value of the NOBF group at 96 hours post-infection was the same as the initial value or lower (25), whereas the Ct value of positive controls increased several folds (17.84). Thein vitrotrial demonstrated that NOBF can deactivate the African swine fever virus.

HIGHLIGHTS

The natural oil blend formulation (NOBF) was formulated using three natural oils, i.e.,Eucalyptus globulus,Pinus sylvestris, andLavandula latifolia.

The in vitro trial was conducted using porcine alveolar macrophages (PAMs) and further passaged in the PAMs; the stock used in the present study was that obtained after the 15th passage.

The natural oil blend formulation (NOBF) showed protection against ASF virus up to a dilution of 13 or 0.000625 of a dilution of 16 or 0.000078 ml that was tried.

The real-time PCR analysis showed that the virus did not replicate in the NOBF group, which implies that either ASFV growth was inhibited in the presence of NOBF or that it was inactivated.

Thein vitrotrial outcome showed that NOBF has anti-ASFV properties.
Mendelian randomization identifies the potential causal impact of dietary patterns on circulating blood metabolites
Authors: Taba Nele , Valge Hanna-Kristel , Metspalu Andres , Esko Tõnu , Wilson James F. , Fischer Krista , Pirastu Nicola
Published: October 2020

Nutrition plays an important role in the development and progress of several health conditions, but the exact mechanism is often still unclear. Blood metabolites are likely candidates to be mediating these relationships, as their levels are strongly dependent on the frequency of consumption of several foods/drinks. Understanding the causal effect of food on metabolites is thus of extreme importance. To establish these effects we utilized Two-sample Mendelian randomization using the genetic variants associated with dietary traits as instrumental variables. The estimates of single-nucleotide polymorphisms’ effects on exposures were obtained from a recent genome-wide association study (GWAS) of 25 individual and 15 principal-component dietary traits, whereas the ones for outcomes were obtained from a GWAS of 123 blood metabolites measured by nuclear magnetic resonance spectroscopy. We identified 417 potentially causal links between food and metabolites, replicating previous findings, such as the association between increased oily fish consumption and higher DHA, and highlighting several novel associations. Most of the associations were related to very-low-density, intermediate-density (IDL) and low-density lipoproteins (LDL). For example, we found that constituents of IDL particles and large LDL particles were raised by coffee and alcohol while lowered by an overall healthier diet and fruit consumption. Our results represent one of the first examples of the estimates of long-term causal effects of diet on metabolites and start bridging the gap in the mechanistic understanding linking food consumption to its health consequences.
Sex-specific maturational trajectory of endocannabinoid plasticity in the rat prefrontal cortex
Authors: Bernabeu Axel , Bara Anissa , Manduca Antonia , Borsoi Milene , Lassalle Olivier , Pelissier-Alicot Anne-Laure , Manzoni Olivier JJ
Published: October 2020

The prefrontal cortex (PFC) develops until early adulthood in rodents and humans, but how synaptic plasticity evolves throughout postnatal development is not known. Here, we used a cross-sectional approach to establish the postnatal maturational trajectories of intrinsic properties and synaptic plasticity in the PFC of rats of both sexes. We found that while layer 5 PFC pyramidal neurons from rats of both sexes displayed similar current-voltage relationships, rheobases and resting potentials across all age groups, excitability was lower in female adults compared to the other developmental stages. NMDAR-dependent long-term potentiation and mGluR2/3-mediated long-term depression (LTD) were equally expressed at the juvenile, pubescent and adult developmental stages in animals of both sexes. However, the developmental course of endocannabinoid (eCB)-mediated LTD was sexually dimorphic. First, eCB-LTD emerged during the juvenile period in females. However, although CB1Rs were functional in both sexes at all developmental stages, eCB-LTD’s first emerged during pubescence in male. Second, eCB-LTD engaged distinct receptors in males and females depending on their developmental stages. Female rats employ both CB1R and TRPV1R to produce eCB-LTD at the juvenile stage but solely CB1R at pubescence followed by only TRPV1R at adulthood. In contrast, in pubescent and adult males eCB-LTD always and exclusively depended on CB1R. Pharmacological blockade of 2AG’s principal degrading enzyme allowed incompetent male juvenile synapses to express eCB-LTD. The data reveal different maturational trajectories in the PFC of male and female rats and provide new cellular substrates to the sex-specific behavioral and synaptic abnormalities caused by adolescent exposure to cannabinoids.
Machine learning (decision tree analysis) identifies ecological selectivity patterns across the end-Permian mass extinction
Authors: Foster William J. , Ayzel Georgy , Isson Terry T. , Mutti Maria , Aberhan Martin
Published: October 2020

Decision tree algorithms are rarely utilized in paleontological research, and here we show that machine learning algorithms can be used to identify determinants of extinction as well as predict extinction risk. This application of decision tree algorithms is important because the ecological selectivity of mass extinctions can reveal critical information on organismic traits as key determinants of extinction and hence the causes of extinction. To understand which factors led to the mass extinction of life during an extreme global warming event, we quantified the ecological selectivity of marine extinctions in the well-studied South China region during the end-Permian mass extinction using the categorized gradient boosting algorithm. We find that extinction selectivity varies between different groups of organisms and that a synergy of multiple environmental stressors best explains the overall end-Permian extinction selectivity pattern. Extinction risk was greater for genera that were limited to deep-water habitats, had a stationary mode of life, possessed a siliceous skeleton or, less critically, had calcitic skeletons. These selective losses directly link the extinction to the environmental effects of rapid injections of carbon dioxide into the ocean-atmosphere system, specifically the combined effects of expanded oxygen minimum zones, rapid warming, and ocean acidification.
Evolutionary diversification of tiny ocean predators
Authors: Latorre Francisco , Deutschmann Ina M. , Labarre Aurelie , Obiol Aleix , Krabberød Anders , Pelletier Eric , Sieracki Michael E. , Cruaud Corinne , Jaillon Olivier , Massana Ramon , Logares Ramiro
Published: October 2020

Unicellular eukaryotic predators have a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionary-diverse organisms have been combined into a single functional group (Heterotrophic flagellates), overlooking their organismal differences. Here we investigate four evolutionary related species belonging to one cosmopolitan family of uncultured marine picoeukaryotic predators: MAST-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A & C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using Single-Cell Genomics. Analyses of 69 single-cells recovered 66-83% of the MAST-4A/B/C/E genomes, which displayed substantial inter-species divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition co-excluded each other (A & C) in the surface global ocean, while species with a different set of GHs appeared to be able to co-exist (species B & C) suggesting further niche diversification associated to prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. Altogether, we show that minute ocean predators from the same family may have different biogeography and genomic content, which need to be accounted to better comprehend marine food webs.
Mirage: A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model
Authors: Fukunaga Tsukasa , Iwasaki Wataru
Published: October 2020

Reconstruction of gene-content evolutionary history is an essential approach for understanding how complex biological systems have been organized. However, the existing gene-content evolutionary models cannot formulate complex and heterogeneous gene gain/loss processes, which reflect diverse evolutionary events and greatly depend on gene families. In this study, we developed Mirage (MIxture model with aRealistic evolutionary rate model forAncestralGenomeEstimation), which allows different gene families to have flexible gene gain/loss rates, but reasonably limits the number of parameters to be estimated by the expectation-maximization algorithm. Simulation analysis showed that Mirage can accurately estimate complex and heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that our evolutionary model better fits genome data from various taxonomic groups than other models. Using Mirage, we revealed that gene families of metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated. The source code of Mirage is freely available athttps://github.com/fukunagatsu/Mirage.