bluuebunny/crossref_metadata_2025 huggingface dataset:
An fMRI meta-analysis of the role of the striatum in everyday-life vs laboratory-developed habits
Authors: Guida Pasqualina , Michiels Mario , Redgrave Peter , Luque David , Obeso Ignacio
Published: July 2021

The dorsolateral striatum plays a critical role in the acquisition and expression of stimulus-response habits that are learned in experimental laboratories. Here, we use meta-analytic procedures to contrast the neural circuits activated by laboratory-acquired habits with those activated by stimulus-response behaviours acquired in everyday-life. We confirmed that newly learned habits rely more on the anterior putamen with activation extending into caudate and nucleus accumbens. Motor and associative components of everyday-life habits were identified. We found that motor-dominant stimulus-response associations developed outside the laboratory primarily engaged posterior dorsal putamen, supplementary motor area (SMA) and cerebellum. Importantly, associative components were also represented in the posterior putamen. Thus, common neural representations for both naturalistic and laboratory-based habits were found in the left posterior and right anterior putamen. These findings suggest a partial common striatal substrate for habitual actions that are performed predominantly by stimulus-response associations represented in the posterior striatum. The overlapping neural substrates for laboratory and everyday-life habits supports the use of both methods for the analysis of habitual behaviour.
A Population-level Strain Genotyping Method to Study Pathogen Strain Dynamics in Human Infections
Authors: Morgan Sarah J , Durfey Samantha L , Ravishankar Sumedha , Jorth Peter , Ni Wendy , Skerrett Duncan , Aitken Moira L , Mckone Edward F , Salipante Stephen J , Radey Matthew C , Singh Pradeep K
Published: July 2021

A hallmark of chronic bacterial infections is the long-term persistence of one or more pathogen species at the compromised site. Repeated detection of the same bacterial species can suggest that a single strain or lineage is continually present. However, infection with multiple strains of a given species, strain acquisition and loss, and changes in strain relative abundance can occur. Detecting strain-level changes and their effects on disease is challenging as most methods require labor intensive isolate-by-isolate analyses, thus, only a few cells from large infecting populations can be examined. Here we present a population-level method for enumerating and measuring the relative abundance of strains called “PopMLST”. The method exploits PCR amplification of strain-identifying polymorphic loci, next-generation sequencing to measure allelic variants, and informatic methods to determine whether variants arise from sequencing errors or low abundance strains. These features enable PopMLST to simultaneously interrogate hundreds of bacterial cells that are either cultured en masse from patient samples, or are present in DNA directly extracted from clinical specimens without ex vivo culture. This method could be used to detect epidemic or super-infecting strains, facilitate understanding of strain dynamics during chronic infections, and enable studies that link strain changes to clinical outcomes.
Hyperdirect connectivity of opercular speech network to the subthalamic nucleus
Authors: Jorge Ahmed , Lipski Witold J. , Wang Dengyu , Crammond Donald J. , Turner Robert S. , Richardson R. Mark
Published: July 2021

The importance of the basal ganglia in modulating cognitive and motor behaviors is well known, yet how the basal ganglia participate in the uniquely human behavior of speech is poorly understood. The subthalamic nucleus (STN) is well positioned to facilitate two basal ganglia functions critical for speech: motor learning and gain modulation. Using a novel paradigm to study cortical-subcortical interactions during speech in patients undergoing awake DBS surgery, we found evidence for a left opercular hyperdirect pathway in humans by stimulating in the STN and examining antidromic evoked activity in the left temporal, parietal and frontal opercular cortex. These high resolution cortical and subcortical mapping data provided evidence for hyperdirect connectivity between Broca’s area (typically corresponding to pars triangularis and pars opercularis of the inferior frontal gyrus) and the STN. In addition, we observed evoked potentials consistent with the presence of monosynaptic projections from areas of opercular speech cortex that are primarily sensory, including auditory cortex, to the STN. These connections may be unique to humans, evolving alongside the ability for speech.

SIGNIFICANCE

Using intracranial recordings from the basal ganglia and cortex in subjects undergoing deep brain stimulation, this study provides evidence for monosynaptic cortical inputs from motor planning, motor sensory, and auditory sensory cortices to the subthalamic nucleus. These observations suggest that in humans, the cortical-basal ganglia hyperdirect pathway is uniquely positioned to participate in speech production. Moreover, the existence of a monosynaptic connection between human sensory cortical areas and the subthalamic nucleus indicates a need to update traditional models of information transfer within cortical-basal ganglia-thalamocortical circuitry, which has significant implications for understanding other human cognitive behavior or dysfunction.
Motif-centric phosphoproteomics to target kinase-mediated signaling pathways
Authors: Tsai Chia-Feng , Ogata Kosuke , Sugiyama Naoyuki , Ishihama Yasushi
Published: July 2021

Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reaction is used to generate the targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. Over 7,000 tyrosine phosphorylation sites were quantified from several tens of µg of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.

Motivation

Sensitivity for detecting phosphopeptides with a particular phosphorylation motif is limited, especially for tyrosine phosphopeptides.
ENDO-Pore: High-throughput linked-end mapping of single DNA cleavage events using nanopore sequencing
Authors: Torres Montaguth Oscar E. , Cross Stephen J. , Ingram Kincaid W.A. , Lee Laura , Diffin Fiona M. , Szczelkun Mark D.
Published: July 2021

Mapping the precise position of DNA cleavage events plays a key role in determining the mechanism and function of endonucleases. ENDO-Pore is a high-throughput nanopore-based method that allows the time resolved mapping single molecule DNA cleavage events in vitro. Following linearisation of a circular DNA substrate by the endonuclease, a resistance cassette is ligated recording the position of the cleavage event. A library of single cleavage events is constructed and subjected to rolling circle amplification to generate concatemers. These are sequenced and used to produce accurate consensus sequences. To identify the cleavage site(s), we developed CSI (Cleavage Site Investigator). CSI recognizes the ends of the cassette ligated into the cleaved substrate and triangulates the position of the dsDNA break. We firstly benchmarked ENDO-Pore using Type II restriction endonucleases. Secondly, we analysed the effect of crRNA length on the cleavage pattern of CRISPR Cas12a. Finally, we mapped the time-resolved DNA cleavage by the Type ISP restriction endonuclease LlaGI that introduces random double-strand breaks into its DNA substrates.
Systems Biology Analysis of Human Genomes Points to Key Pathways Conferring Spina Bifida Risk
Authors: Aguiar-Pulido Vanessa , Wolujewicz Paul , Martinez-Fundichely Alexander , Elhaik Eran , Thareja Gaurav , AbdelAleem Alice , Chalhoub Nader , Cuykendall Tawny , Al-Zamer Jamel , Lei Yunping , El-Bashir Haitham , Musser James M. , Al-Kaabi Abdulla , Shaw Gary M. , Khurana Ekta , Suhre Karsten , Mason Christopher E. , Elemento Olivier , Finnell Richard H. , Ross M. Elizabeth
Published: July 2021

Spina bifida (SB) is a debilitating birth defect caused by multiple gene and environment interactions. Though SB shows non-Mendelian inheritance, genetic factors contribute to an estimated 70% of cases. Nevertheless, identifying human mutations conferring SB risk is challenging due to its relative rarity, genetic heterogeneity, incomplete penetrance and environmental influences that hamper GWAS approaches to untargeted discovery. Thus, SB genetic studies may suffer from population substructure and/or selection bias introduced by typical candidate gene searches. We report a population based, ancestry-matched whole-genome sequence analysis of SB genetic predisposition using a systems biology strategy to interrogate 298 case-control subject genomes (149 pairs). Genes that were enriched in likely gene disrupting (LGD), rare protein-coding variants were subjected to machine learning analysis to identify genes in which LGD variants occur with a different frequency in cases vs. controls and so discriminate between these groups. Those genes with high discriminatory potential for SB significantly enriched pathways pertaining to carbon metabolism, inflammation, innate immunity, cytoskeletal regulation and essential transcriptional regulation, indicating their impact on the pathogenesis of human SB. Additionally, interrogation of conserved non-coding sequences identified robust variant enrichment in regulatory regions of several transcription factors critical to embryonic development. This genome-wide perspective offers an effective approach to interrogation of coding and non-coding sequence variant contributions to rare complex genetic disorders.
The role of feedback in the production of skilled finger sequences
Authors: Popp Nicola J. , Hernandez-Castillo Carlos R. , Gribble Paul L. , Diedrichsen Jörn
Published: July 2021

Actions involving fine control of the hand, for example grasping an object, rely heavily on sensory information from the fingertips. While the integration of feedback during execution of individual movements is well understood, less is known about the use of sensory feedback in the control of skilled movement sequences. To address this gap, we trained participants to produce sequences of finger movements on a keyboard-like device over a four-day training period. Participants received haptic, visual, and auditory feedback indicating the occurrence of each finger press. We then either transiently delayed or advanced the feedback for a single press by a small amount of time (30 or 60 ms). We observed that participants rapidly adjusted their ongoing finger press by either accelerating or prolonging the ongoing press, in accordance with the direction of the perturbation. Furthermore, we could show that this rapid behavioural modulation was driven by haptic feedback. While these feedback-driven adjustments reduced in size with practice, they were still clearly present at the end of training. In contrast to the directionally-specific effect we observed on the perturbed press, a feedback perturbation resulted in a delayed onset of the subsequent presses irrespective of perturbation direction or feedback modality. This observation is consistent with a hierarchical organization of skilled movement sequences, with different levels reacting distinctly to sensory perturbations.
A Novel Art of Electrocardiogram Assessment in Zebrafish for Cardiovascular Disease Studies and Drug Screening
Authors: Le Tai , Zhang Jimmy , Nguyen Anh Hung , Torres Ramses Seferino Trigo , Vo Khuong , Dutt Nikil , Lee Juhyun , Ding Yonghe , Xu Xiaolei , Lau Michael P.H. , Cao Hung
Published: July 2021

The zebrafish (Dario rerio) has proven to be an excellent animal model for biological research owing to its small size, low cost for maintenance, short generation time, amenable genetics, and optical transparency. Zebrafish have been extensively used in cardiovascular studies in which mutant lines with cardiovascular defects were introduced and analyzed. Despite the small size, technological advances have paved the way to effectively assess cardiac functions of zebrafish. Here, we present a novel art for long-term simultaneous monitoring and analysis of electrocardiogram (ECG) in multiple zebrafish with controlled environment. The system helps minimize the effect of anesthetic drug and temperature to cardiac rhythm side effects as well as save time and efforts by 40-50 fold compared with the conventional approach. We further employed the system to study the Na+ sensitivity in the development of sinus arrest in Tg(SCN5A-D1275N) fish, a study model of the sick sinus syndrome, as well as the relationship between this variant and drug administration. The novel ECG system developed in this study holds promise to greatly accelerate other cardiovascular studies and drug screening using zebrafish.
Experimental and Bioinformatic upgrade for genome-wide mapping of nucleosomes in Trypanosoma cruzi
Authors: Beati Paula , Stepñicka Milena Massimino , Larrea Salomé Vilchez , Alonso Guillermo Daniel , Ocampo Josefina
Published: July 2021

1

In Trypanosoma cruzi, as in every eukaryotic cell, DNA is packaged into chromatin by octamers of histone proteins that constitute nucleosomes. Besides compacting DNA, nucleosomes control DNA dependent processes by modulating the access of DNA binding proteins to regulatory elements on the DNA; or by providing the platform for additional layers of regulation given by histone variants and histone post-translational modifications. In trypanosomes, protein coding genes are constitutively transcribed as polycistronic units. Therefore, gene expression is controlled mainly post transcriptionally. However, chromatin organization and the histone code influence transcription, cell cycle progression, replication and DNA repair. Hence, determining nucleosome position is of uppermost importance to understand the peculiarities of these processes in trypanosomes. Digestion of chromatin with micrococcal nuclease followed by deep sequencing has been widely applied for genome-wide mapping of nucleosomes in several organisms. Nonetheless, this parasite presents numerous singularities. On one hand, special growth conditions and cell manipulation are required. On the other hand, chromatin organization shows some uniqueness that demands a specially designed analytical approach. An additional entanglement is given by the nature of its genome harboring a large content of repetitive sequences and the poor quality of the genome assembly and annotation of many strains. Here, we adapted this broadly used method to the hybrid reference strain, CL Brener. Particularly, we developed an exhaustive and thorough computational workflow for data analysis, highlighting the relevance of using its whole genome as a reference instead of the commonly used Esmeraldo-like haplotype. Moreover, the performance of two aligners, Bowtie2 and HISAT2 was tested to find the most appropriate tool to map any genomic read to reference genomes bearing this complexity.
Repopulation of a 3D-simulated periapical lesion cavity with triggered osteoblastic-differentiated dental pulp stem cell spheroids
Authors: Ribeiro Vítor Luís , Dernowsek Janaína A. , Fernandes Roger R. , Pitol Dimitrius L. , Issa João Paulo Mardegan , Mazzi-Chaves Jardel F. , Bombonato-Prado Karina Fittipaldi , Sousa-Neto Manoel Damião , Passos Geraldo Aleixo
Published: July 2021

We established a proof of concept model system for the biological repair of periapical lesions using stem cell spheroids. A mesenchymal stem cell line isolated from the dental pulp of deciduous teeth (shed cells) was cultured in a 2D monolayer and then in 3D multicellular spheroids. An image of a periapical lesion of an upper lateral incisor tooth was obtained by computed micro tomography, which was used as a model for photopolymer resin 3D printing to generate a negative frame of the lesion. The negative model served to prepare a positive model of the periapical lesion cavity in an agarose gel. Shed cells cultured in monolayers or as spheroids were seeded in the positive lesion mold before or after osteoblastic differentiation. The results showed that compared to cells cultured in monolayers, the spheroids featured uniform cellularity and had a greater viability within the lesion cavity, accompanied by a temporal reduction in the expression of mRNAs typically expressed by stem cells (Cd13, Cd29, Cd44, Cd73, and Cd90). Concomitantly, there was an increase in the expression of protein markers that characterize osteoblastic differentiation (RUNX2, ALP, and BGLAP). These results provide a new perspective for regenerative endodontics with the use of spheroids prepared with shed cells to repair periapical lesions.
Making BrainWaves: Portable Brain Technology in Biology Education
Authors: Davidesco Ido , Azeka Steven , Carter Steven , Laurent Emma , Valk Henry , Naipaul Jimmy , Dikker Suzanne , Suzuki Wendy A
Published: July 2021

Neuroscience is one of the fastest growing STEM fields, yet its presence in K-12 science education is very limited, partially due to the lack of accessible teaching materials and tools. Here, we describe a new high school neuroscience curriculum (“BrainWaves”), where students utilize recent advances in low-cost, portable Electroencephalography (EEG) technology to investigate their own brain activity. This semester-long curriculum is supported by science mentors and an educational application that guides students through the process of recording and analyzing their own brain activity. Evaluation data collected in 5 public New York City schools in 2018/19 indicate significant positive shifts in content knowledge and self-efficacy among students who participated inBrainWavescompared to students in other courses of the same teacher. The quantitative findings are supported by interviews, where students reported increased appreciation for neuroscience and college readiness and discussed the benefits of collaborating with scientists and using portable brain technology in classrooms.
APRILE: Exploring the Molecular Mechanisms of Drug Side Effects with Explainable Graph Neural Networks
Authors: Xu Hao , Sang Shengqi , Yao Herbert , Herghelegiu Alexandra I. , Lu Haiping , Yurkovich James T. , Yang Laurence
Published: July 2021

The majority of people over the age of 65 take two or more medications. While many individual drug side effects are known, polypharmacy side effects due to novel drug combinations poses great risk. Here, we present APRILE: an explainable artificial intelligence (XAI) framework that uses graph neural networks to explore the molecular mechanisms underlying polypharmacy side effects. Given a list of side effects and the pairs of drugs causing them, APRILE identifies a set of proteins (drug targets or non-targets) and associated Gene Ontology (GO) terms as mechanistic ‘explanations’ of associated side effects. Using APRILE, we generate such explanations for 843,318 (learned) and 93,966 (novel) side effect–drug pair events, spanning 861 side effects (472 diseases, 485 symptoms and 9 mental disorders) and 20 disease cate-gories. We show that our two new metrics—pharmacogenomic information utilization and protein-protein interaction information utilization—provide quantitative estimates of mechanism complexity. Explanations were significantly consistent with state of the art disease-gene associations for 232/239 (97%) side effects. Further, APRILE generated new insights into molecular mechanisms of four diverse categories of adverse drug reactions: infection, metabolic diseases, gastrointestinal diseases, and mental disorders, including paradoxical side effects. We demonstrate the viability of discovering polypharmacy side effect mechanisms by training an XAI framework on massive biomedical data. Consequently, it facilitates wider and more reliable use of AI in healthcare.
Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation
Authors: Di Santo Lionel N. , Hoban Sean , Parchman Thomas L. , Wright Jessica W. , Hamilton Jill A.
Published: July 2021

Understanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world’s rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species’ evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 SNPs candidates for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates that natural selection has likely contributed to population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effect of rarity, divergent selection between populations indicates that genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.
Discovery ofUPSTREAM OF FLOWERING LOCUS C(UFC) andFLOWERING LOCUS C EXPRESSOR(FLX) inGladiolus ×hybridus,G. dalenii
Authors: Aljaser Jaser A. , Anderson Neil O. , Noyszewski Andrzej
Published: July 2021

Gladiolus is a geophytic floricultural crop, cultivated for cut flower and garden ornamental uses. Ornamental geophytes such as gladiolus, lily, tulip and daffodil are examples of floral crops that are currently being investigated to understand the flowering pathway. While the environmental and hormonal factors leading to flowering are established inArabidopsis. However, the lack of genetic regulation is poorly understood. Thus, the importance of such an ornamental crop that relies on flowers (flowering) for economic purposes encourages researchers to discover the flowering genes to breed vigorous flowering cultivars. The understanding of the flowering mechanisms in the flowering pathway is also paramount. Herein we show the discovery ofUPSTREAM OF FLOWERING LOCUS C(UFC) andFLOWERING LOCUS C EXPRESSOR(FLX) genes inGladiolus ×hybridus and G. dalenii. TheUFCgene is adjacent toFLOWERING LOCUS C(FLC) which is a floral repressor in many temperate species.FLXgene upregulatesFRIGIDA(FRI) which upregulatesFLCexpression. The discovery of both genes is a step forward in finding theFLCgene in gladiolus, provided they are linked. Seventeen gladiolus genotypes, consisting of early flowering and commercial cultivars, have theUFCgene, consisting of four exons in two allelic forms. TheUFCgene sequenced when translated into amino acid sequence and set in pair-alignment to other species, has up to 57% in amino acid identity toMusa acuminata. TheUFCprotein ranges in identity with pair-alignment to other species, reaching up to 57% in amino acid identity toMusa acuminata. TheFLXgene in gladiolus has 3/5 (60%) exons in relative toAnanas comosus, i.e. lacking 2 exons and a partially complete gene sequence; the pair-alignment of the three exons shows up over all ~65% identity ofFLXtoAnanas comosus. TheUFCprotein consists of a conserved domain, DUF966, which is higher in identity and pair-alignment, with up to 86% identity inElaeis guineensis. The discoveredFLXgene in gladiolus has 3/5 (60%) exons, i.e. lacking 2 exons and a partially complete gene sequence; the pair-alignment of the 3 exons shows up to ~65% of identity ofFLXtoAnanas comosus. These discovered two genes in gladiolus provide insight to further our understanding of the flowering and vernalization response in ornamental geophytes.

Summary Statement

Two gladiolus flowering genes (UFC; FLX) were discovered which will aid research in understanding flowering and vernalization in geophytes
The HAPPE plus Event-Related (HAPPE+ER) Software: A Standardized Processing Pipeline for Event-Related Potential Analyses
Authors: Monachino A.D. , Lopez K.L. , Pierce L.J. , Gabard-Durnam L.J.
Published: July 2021

Event-Related Potential (ERP) designs are a common method for interrogating neurocognitive function with electroencephalography (EEG). However, the gold standard of preprocessing ERP data is manual-editing – a subjective, time-consuming processes. A number of automated pipelines have recently been created to address the need for standardization, automation, and quantification of EEG data processing; however, few are optimized for ERP analyses (especially in developmental or clinical populations). To fill this need, we propose and validate the HAPPE plus Event-Related (HAPPE+ER) software, a standardized and automated processing pipeline optimized for ERP analyses in EEG data. HAPPE+ER processes event- related potential data from raw files through a series of filtering, line noise reduction, bad channel detection, artifact rejection from continuous data, segmentation, and bad segment rejection methods. HAPPE+ER also includes post-processing reports of both data quality and pipeline quality metrics to facilitate the evaluation and reporting of data processing in a standardized manner. Finally, HAPPE+ER includes a post-processing script to facilitate generating ERP figures and measures for statistical analysis. We describe multiple approaches with both adult and developmental data to optimize and validate pipeline performance. HAPPE+ER software is freely available under the terms of GNU General Public License athttps://github.com/PINE-Lab/HAPPE.
Truncation of IFT80 causes early embryonic loss in cattle
Authors: Ortega M. Sofía , Bickhart Derek M. , Lockhart Kelsey N. , Null Daniel J. , Hutchison Jana L. , McClure Jennifer C. , Cole John B.
Published: July 2021

Recessive alleles represent a risk in populations that have undergone bottleneck events. We present a comprehensive framework for identification and validation of these genetic defects, including haplotype-based detection, variant selection from sequence data, and validation using knockout embryos. Holstein haplotype 2 (HH2), which causes embryonic death, was used to demonstrate the approach. HH2 was identified using a deficiency-of-homozygotes approach and confirmed to negatively affect conception rate and stillbirths. Five carriers were present in a group of 183 sequenced Holstein bulls selected to maximize the coverage of unique haplotypes. Three variants concordant with haplotype calls were found in HH2: a high-priority frameshift mutation resulting in a deletion, and two low-priority variants (1 synonymous variant, 1 premature stop codon). The frameshift in intraflagellar protein 80 (IFT80) was confirmed in a separate group of Holsteins from the 1000 Bull Genomes Project that shared no animals with the discovery set. IFT80-null embryos were generated by truncating the IFT80 transcript at exon 2 or 11 using a CRISPR-Cas9 system. Abattoir-derived oocytes were fertilized in vitro and embryos were injected at the one-cell stage either with CRISPR-Cas9 complex (n=100) or Cas9 mRNA (control, n=100) before return to culture, and replicated 3 times. IFT80 is activated at the 8-cell stage, and IFT80-null embryos arrested at this stage of development, which is consistent with data from mouse hypomorphs and HH2 carrier-to-carrier matings. This frameshift in IFT80 on chromosome 1 at 107,172,615 bp (p.Leu381fs) disrupts WNT and hedgehog signaling, and is responsible for the death of homozygous embryos.

Significance Statement

Holstein haplotype 2 is an embryonic lethal present in 1.21% of the US Holstein cattle population, and unrecognized carrier-to-carrier matings are responsible for >$2 million/year in additional breeding expenses. A high-impact frameshift mutation in exon 11 of intraflagellar protein 80 (IFT80) was identified as the putative causal variant. Biallelic IFT80 knockout embryos were produced in vitro and compared to wild-type embryos. IFT80-null embryos consistently arrested at the 8-cell stage of development. The IFT80 protein expressed in knockout embryos had substantially altered protein structure, resulting in a loss of functional domains. These results validate the putative causal mutation observed in Holsteins. This system is a good model for investigating possible causal variants that affect livestock fertility early in development.
Out of rhythm: Compromised precision of theta-gamma coupling impairs associative memory in old age
Authors: Karlsson Anna E. , Lindenberger Ulman , Sander Myriam C.
Published: July 2021

Episodic memory declines with advancing adult age. This decline is particularly pronounced when associations between items and their contexts need to be formed. According to theories of neural communication, the precise coupling of gamma power to the phase of the theta rhythm supports associative memory formation. To investigate whether age differences in associative memory are related to compromised theta–gamma coupling, we took electroencephalographic (EEG) recordings during the encoding phase of an item-context association task. Fifty-eight younger and 55 older adults studied pictures of objects superimposed on background scenes. In a recognition test, objects were presented on old or new backgrounds, and participants responded if they had seen (1) the object and (2) the object–scene pair. Theta–gamma coupling supported pair memory formation in both age groups. Whereas pair memory was associated with coupling closer to the peak of the theta rhythm, item-only memory was associated with a deviation in phase angle relative to pair memory. Furthermore, a stable relation between coupling phase and pair memory performance demonstrated that coupling closer to the peak is beneficial for associative memory. Critically, older adults’ lower pair memory was accompanied by a shift in coupling phase relative to younger adults. In concert, the present results are consistent with the hypothesis that decrements in the precision with which gamma power is coupled to the theta phase underlie the decline of associative memory in normal cognitive aging.

Significance Statement

According to prominent theories of neural communication, the precise coordination of oscillatory activity enables the formation of associative memories. We propose that normal cognitive aging impairs associative memory formation by compromising the precision of neural communication. We show that the coupling of high-frequency gamma power to low-frequency theta phase supports associative memory formation in both younger and older adults, with coupling closer to the theta peak benefitting memory performance. However, compared to younger adults, the coupling phase angle is shifted and more variable in older adults. We conclude that alterations in the precision of theta–gamma coupling contribute to adult age differences in associative memory.
Signatures of rapid synaptic learning in the hippocampus during novel experiences
Authors: Priestley James B. , Bowler John C. , Rolotti Sebi V. , Fusi Stefano , Losonczy Attila
Published: July 2021

Neurons in the hippocampus exhibit striking selectivity for specific combinations of sensory features, forming representations which are thought to subserve episodic memory. Even during a completely novel experience, ensembles of hippocampal “place cells” are rapidly configured such that the population sparsely encodes visited locations, stabilizing within minutes of the first exposure to a new environment. What cellular mechanisms enable this fast encoding of experience? Here we leverage virtual reality and large scale neural recordings to dissect the effects of novelty and experience on the dynamics of place field formation. We show that the place fields of many CA1 neurons transiently shift locations and modulate the amplitude of their activity immediately after place field formation, consistent with rapid plasticity mechanisms driven by plateau potentials and somatic burst spiking. These motifs were particularly enriched during initial exploration of a novel context and decayed with experience. Our data suggest that novelty modulates the effective learning rate in CA1, favoring burst-driven field formation to support fast synaptic updating during new experience.
Using Progressive Context Encoders for Anomaly Detection in Digital Pathology Images
Authors: Gillard Ryan , Meroueh Chady , Gu Qiangqiang , Prodduturi Naresh , Patil Sandhya , Flotte Thomas J , Hart Steven N
Published: July 2021

Whole slide imaging (WSI) is transforming the practice of pathology, converting a qualitative discipline into a quantitative one. However, one must exercise caution in interpreting algorithm assertions, particularly in pathology where an incorrect classification could have profound impacts on a patient, and rare classes exist that may not have been seen by the algorithm during training. A more robust approach would be to identify areas of an image for which the pathologist should concentrate their effort to make a final diagnosis. This anomaly detection strategy would be ideal for WSI, but given the extremely high resolution and large file sizes, such an approach is difficult. Here, we combine progressive generative adversarial networks with a flexible adversarial autoencoder architecture capable of learning the “normal distribution” of WSIs of normal skin tissue at extremely high resolution and demonstrate its anomaly detection performance. Our approach yielded pixel-level accuracy of 89% for identifying melanoma, suggesting that our label-free anomaly detection pipeline is a viable strategy for generating high quality annotations - without tedious manual segmentation by pathologists. The code is publicly available athttps://github.com/Steven-N-Hart/P-CEAD.
SARS-CoV-2 Lambda Variant Remains Susceptible to Neutralization by mRNA Vaccine-elicited Antibodies and Convalescent Serum
Authors: Tada Takuya , Zhou Hao , Dcosta Belinda M. , Samanovic Marie I. , Mulligan Mark J. , Landau Nathaniel R.
Published: July 2021

The SARS-CoV-2 lambda variant (lineage C.37) was designated by the World Health Organization as a variant of interest and is currently increasing in prevalence in South American and other countries. The lambda spike protein contains novel mutations within the receptor binding domain (L452Q and F490S) that may contribute to its increased transmissibility and could result in susceptibility to re-infection or a reduction in protection provided by current vaccines. In this study, the infectivity and susceptibility of viruses with the lambda variant spike protein to neutralization by convalescent sera and vaccine-elicited antibodies was tested. Virus with the lambda spike had higher infectivity and was neutralized by convalescent sera and vaccine-elicited antibodies with a relatively minor 2.3-3.3-fold decrease in titer on average. The virus was neutralized by the Regeneron therapeutic monoclonal antibody cocktail with no loss of titer. The results suggest that vaccines in current use will remain protective against the lambda variant and that monoclonal antibody therapy will remain effective.
Pharmacokinetics and Central Accumulation of Delta-9-Tetrahydrocannabinol (THC) and its Bioactive Metabolites Are Influenced by Route of Administration and Sex
Authors: Baglot Samantha L. , Hume Catherine , Petrie Gavin N. , Aukema Robert J. , Lightfoot Savannah H.M. , Grace Laine M. , Zhou Ruokun , Parker Linda , Rho Jong M. , Borgland Stephanie L. , McLaughlin Ryan J. , Brechenmacher Laurent , Hill Matthew N.
Published: July 2021

Up to a third of North Americans over 16 years old report using cannabis in the prior month, most commonly through inhalation. Animal models that reflect human cannabis consumption are critical to study its impacts on brain and behaviour. Nevertheless, most animal studies to date examine effects of cannabis through injection of delta-9-tetrahydrocannabinol (THC; primary psychoactive component of cannabis). THC injections produce markedly different physiological and behavioural effects than inhalation, likely due to distinctive pharmacokinetics of each administration route. The current study directly examined if administration route (injection versus inhalation), with dosing being matched on peak THC blood levels, alters the metabolism of THC, and the central accumulation of THC and its metabolites over time. Adult male and female Sprague-Dawley rats received either a single intraperitoneal injection of THC (2.5 mg/kg) or a single (15 min) session of inhaled exposure to THC distillate (100 mg/mL) vapour. Blood and brains were collected at 15, 30, 60, 90 and 240 minutes post-exposure for analysis of THC and metabolites through mass spectrometry-liquid chromatography. Inhalation results in immediate hypothermia, whereas injection results in delayed hypothermia. Despite achieving comparable peak concentrations of blood THC in both groups, our results indicate higher initial brain THC concentration following inhalation, whereas injection resulted in dramatically higher 11-OH-THC concentrations, a potent THC metabolite, in blood and brain that increased over time. Our results provide evidence that THC and its metabolites exhibit different pharmacokinetic profiles following inhalation versus injection, which could have significant impacts for data interpretation and generalizability. Accordingly, we suggest that translational work in the realm of THC and cannabis strongly consider using inhalation models over those that employ injection.

Highlights

Body temperature as well as blood and brain levels of THC and metabolites differ based on administration route

THC inhalation results in immediate hypothermia, whereas THC injection results in delayed hypothermia

THC inhalation results in higher initial brain THC levels than injection

THC injection results in higher blood & brain 11-OH-THC levels than inhalation

Translational cannabis work should strongly consider using inhalation over injection
Kinetic Properties of Microbial Exoenzymes Vary with Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile
Authors: Alves Ricardo J. Eloy , Callejas Ileana A. , Marschmann Gianna L. , Mooshammer Maria , Singh Hans W. , Whitney Bizuayehu , Torn Margaret S. , Brodie Eoin L.
Published: July 2021

Current knowledge of the mechanisms and responses of soil organic matter (SOM) turnover to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of microbial exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate coniferous forest, and their temperature sensitivity based on Arrhenius and Macromolecular Rate Theory (MMRT) models over six temperatures between 4-50°C. Maximal enzyme velocity (Vmax) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results indicated that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, likely reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. Warming consistently led to increasedVmaxand catalytic efficiency of all enzymes, and thus to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar through the soil profile based on both Arrhenius/Q10and MMRT models. Nevertheless, temperature directly affected the kinetic properties of different enzyme types in a depth-dependent manner, and thus the relative depolymerization potential of different compounds. Our results indicate that kinetic and thermal properties of exoenzymes are intrinsic traits of soil microbiomes adapted to distinct physicochemical conditions associated with different soil depths, and improve our conceptual understanding of critical mechanisms underlying SOM dynamics and responses to warming through the soil profile.
The blood vasculature instructs lymphatics patterning in a SOX7 dependent manner
Authors: Chiang Ivy Kim-Ni , Luu Winnie , Jiang Key , Kirschnick Nils , Moustaqil Mehdi , Davidson Tara , Lesieur Emmanuelle , Skoczylas Renae , Kouskoff Valerie , Kazenwadel Jan , Arriola-Martinez Luis , Sierecki Emma , Gambin Yann , Alitalo Kari , Kiefer Friedmann , Harvey Natasha L. , Francois Mathias
Published: July 2021

Despite a growing catalogue of secreted factors critical for lymphatic network assembly, little is known about the mechanisms that modulate the expression level of these molecular cues in blood vascular endothelial cells (BECs). Here, we show that a BEC-specific transcription factor, SOX7, plays a crucial role in lymphatic vessel patterning by modulating the transcription of lymphangiocrine signals. While SOX7 is not expressed in lymphatic endothelial cells (LECs), loss of SOX7 function in mouse embryos causes a dysmorphic dermal lymphatic phenotype. We identify novel distant regulatory regions in mice and humans that contribute to directly repressing the transcription of a major lymphangiogenic growth factor (Vegfc) in a SOX7-dependent manner. Further, we show that SOX7 directly binds HEY1, a canonical repressor of the Notch pathway, suggesting that transcriptional repression may also be modulated by the recruitment of this protein partner at Vegfc genomic regulatory regions. Our work unveils a role for SOX7 in modulating downstream signalling events crucial for lymphatic patterning, at least in part via the transcriptional repression of VEGFC levels in the blood vascular endothelium.
Fatty acid binding proteins shape the cellular response to activation of the glucocorticoid receptor
Authors: Liu Bonan , Chandrashekaran Indu R. , Ilyichova Olga , Valour Damien , Melchiore Fabien , Bourrier Chantal , Giganti Adeline , Stephan Jean-Philippe , Dacquet Catherine , Genissel Patrick , Gosgnach Willy , Weaver Richard J. , Porter Christopher J.H. , Scanlon Martin J. , Halls Michelle L.
Published: July 2021

Glucocorticoids are steroid hormones that are essential for life in mammals. Therapeutically, they are some of the most cost-effective drugs for the treatment of inflammatory diseases ranging from skin rashes to COVID-19, but their use is limited by adverse effects. Glucocorticoids exert their effects via the glucocorticoid receptor, a type I nuclear hormone receptor which modulates gene expression. The transcriptional activity of some related, but nuclear restricted, type II nuclear hormone receptors can be enhanced by a family of intracellular transport proteins, the fatty acid binding proteins (FABPs). We find that the transcriptional activity of the GR can be altered by a sub-set of FABP family members dependent on the GR-ligand. The ability of some FABPs to selectively promote or limit the transcriptional activity of the GR in a ligand-dependent manner could facilitate the discovery of drugs that narrow GR activity to only the desired subset of therapeutically relevant genes.
A scalable, multi-wavelength, broad bandwidth frequency-domain near-infrared spectroscopy platform for real-time quantitative tissue optical imaging
Authors: Stillwell Roy A. , Kitsmiller Vincent J. , Wei Alicia Y. , Chong Alyssa , Senn Lyla , O’Sullivan Thomas D.
Published: July 2021

Frequency-domain near-infrared spectroscopy (FD-NIRS) provides quantitative noninvasive measurements of tissue optical absorption and scattering, and provides a safe and accurate method for characterizing tissue composition and metabolism. However, the poor scalability and high complexity of most FD-NIRS systems assembled to date have contributed to its limited clinical impact. To address these shortcomings, we present a scalable, digital-based FD-NIRS platform capable of measuring optical properties and tissue chromophore concentrations in real-time. The system provides single-channel FD-NIRS amplitude/phase, optical property, and chromophore data at a maximum display rate of 36.6 kHz, 17.9 kHz, and 10.2 kHz, respectively, and can be scaled to multiple channels as well as integrated into a handheld format. The entire system is enabled by several innovations including an ultra-high-speed k-nearest neighbor lookup table method (maximum of 250,000 inversions/s for large 2500×700 table of absorption and reduced scattering coefficients), embedded FPGA and CPU high-speed co-processing, and high-speed data transfer (due to on-board processing). We show that our 6-wavelength, broad modulation bandwidth (1-400 MHz) system can be used to perform 2D high-density spatial mapping of optical properties.
MAGI2-AS3 modulates proliferation, apoptosis and glycolysis in acute lymphoblastic leukemia via miR-452-5p/FOXN3 axis
Authors: Chen Xiao-Guang , Dou Bing-Hua , An Jin-Dou , Feng Song , Liu Na , Sheng Guang-Yao
Published: July 2021

Background

Long non-coding RNA MAGI2 antisense RNA 3 (MAGI2-AS3) has been identified as a tumor suppressor in various cancers. Acute lymphoblastic leukemia (ALL) is a prevalent kind of leukemia among children. In this study, we aimed at evaluate the role of MAGI2-AS3 in ALL and its underlying mechanisms.

Methods

qPCR was adopted to determine MAGI2-AS3, miR-452-5p, and FOXN3 expression. The malignant properties of ALL cells were assessed by CCK8 assay and flow cytometry analysis. The glucose uptake, lactate production, and ATP level were measured to evaluate glycolysis. Western blotting was performed to detect PCNA, Bcl-2, Bax, and HK2 protein levels. The interaction between MAGI2-AS3/FOXN3 and miR-452-5p was validated by luciferase reporter assay. The in vivo growth of ALL cells was determined in xenograft model.

Results

MAGI2-AS3 was strikingly down-regulated in ALL samples and cells. Overexpression of MAGI2-AS3 restrained growth, glycolysis and triggered apoptosis of ALL cells. Mechanistically, MAGI2-AS3 could sponge miR-452-5p to up-regulate FOXN3. Silencing of FOXN3 abolished the anti-tumor effect of MAGI2-AS3. Finally, MAGI2-AS3 suppressed the in vivo growth of ALL cells via modulating miR-452-5p/FOXN3 axis.

Conclusion

Our findings demonstrate that MAGI2-AS3 delays the progression of ALL by regulating miR-452-5p/FOXN3 signaling pathway.