bluuebunny/crossref_metadata_2025 huggingface dataset:
Pre- and post-synaptic roles for DCC in memory consolidation in the adult mouse hippocampus
Authors: Glasgow Stephen D. , Wong Edwin W. , Thompson-Steckel Greta , Séguéla Philippe , Ruthazer Edward S. , Kennedy Timothy E.
Published: July 2019

The receptor deleted in colorectal cancer (DCC) and its ligand netrin-1 are essential for axon guidance during development and are expressed by neurons in the mature brain. Netrin-1 recruits GluA1-containing α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) and is critical for long-term potentiation (LTP) at CA3-CA1 hippocampal Schaffer collateral synapses, while conditional DCC deletion from glutamatergic neurons impairs hippocampal-dependent spatial memory and severely disrupts LTP induction. DCC co-fractionates with the detergent-resistant component of the postsynaptic density, yet is enriched in axonal growth cones that differentiate into presynaptic terminals during development. Specific presynaptic and postsynaptic contributions of DCC to the function of mature neural circuits have yet to be identified. Employing hippocampal subregion-specific conditional deletion of DCC, we show that DCC loss from CA1 hippocampal pyramidal neurons results in deficits in spatial memory, increased resting membrane potential, abnormal dendritic spine morphology, and weaker spontaneous excitatory postsynaptic activity. In contrast, deletion of DCC from CA3 neurons did not induce detectable changes in spine morphology or intrinsic electrophysiological properties of CA1 pyramidal neurons, but resulted in impaired performance on the novel object place recognition task as well as compromised excitatory synaptic transmission and long-term potentiation (LTP) at the Schaffer collateral synapse. Together, these findings reveal that DCC makes specific pre- and post-synaptic contributions to hippocampal synaptic plasticity underlying spatial memory.
AAV mediated delivery of a novel anti-BACE1 VHH reduces Abeta in an Alzheimer’s disease mouse model
Authors: Rincon Melvin Y. , Zhou Lujia , Marneffe Catherine , Voytyuk Iryna , Wouters Yessica , Dewilde Maarten , Duqué Sandra I. , Vincke Cécile , Levites Yona , Golde Todd E. , Muyldermans Serge , De Strooper Bart , Holt Matthew G.
Published: July 2019

Single domain antibodies (VHH) are potentially disruptive therapeutics, with important biological value for treatment of several diseases, including neurological disorders. However, VHH have not been widely used in the central nervous system (CNS), as it is hard to reach therapeutic levels, both because of their restricted blood-brain-barrier penetration and their apparent rapid clearance from the parenchyma. Here, we propose a gene transfer strategy based on adeno-associated virus (AAV)-based vectors to deliver VHH directly into the CNS, ensuring continuous production at therapeutic levels. As a proof-of-concept, we explored the potential of AAV-delivered VHH to inhibit BACE1, a well-characterized target in Alzheimer’s disease. First, we generated a panel of VHHs targeting BACE1. One of them, VHH-B9, showed high selectivity for BACE1 and efficacy in lowering BACE1 activity in vitro. We then went on to demonstrate significant reductions in amyloid beta (Aβ) levels after AAV-based delivery of VHH-B9 into the CNS of a mouse model of cerebral amyloidosis. These results constitute a novel therapeutic approach for neurodegenerative diseases, which is applicable to a range of CNS disease targets.
Transfer of Septin Rings to Cytokinetic Remnants Directs Age-Sensitive ER stress Surveillance Cell Cycle Re-entry
Authors: Chao Jesse T. , Piña Francisco , Onishi Masayuki , Cohen Yifat , Schuldiner Maya , Niwa Maho
Published: July 2019

During cell division, cells must actively pass on organelles. Previously, we discovered the endoplasmic reticulum (ER) stress surveillance (ERSU) pathway that ensures the inheritance of functional ER. Activation of the ERSU causes the septin ring to mislocalize, which blocks ER inheritance and cytokinesis. Here, we found that the septin ring mislocalizes to previously utilized cell division sites called cytokinetic remnants (CRMs). The transfer of the septin ring to CRMs requires Nba1, a negative polarity component that normally prevents septin ring formation at CRMs. Furthermore, septin ring movement to CRMs relies on the ERSU component Slt2, which is recruited by binding Bem1. During ER stress, Bem1 also binds the GTP exchange factor Cdc24, without activating Cdc42, a GTPase that normally establishes polarized growth. Failure to translocate septin rings to CRMs delays the cell’s ability to re-enter cell division when ER homeostasis is re-established. Thus, ER stress considers the history of previous cell cycle for future cell cycle re-entry upon ER stress recovery.
Metabolic dependency of chorismate in Plasmodium falciparum
Authors: Valenciano Ana Lisa , Fernández-Murga Maria L. , Merino Emilio F. , Holderman Nicole R. , Butschek Grant J. , Shaffer Karl J. , Tyler Peter C. , Cassera Maria Belen
Published: July 2019

The shikimate pathway, a metabolic pathway absent in humans, is responsible for the production of chorismate, a branch point metabolite. In the malaria parasite, chorismate is postulated to be a direct precursor in the synthesis of p-aminobenzoic acid (folate biosynthesis), p-hydroxybenzoic acid (ubiquinone biosynthesis), menaquinone, and aromatic amino acids. While the potential value of the shikimate pathway as a drug target is debatable, the metabolic dependency of chorismate in P. falciparum remains unclear. Current evidence suggests that the main role of chorismate is folate biosynthesis despite ubiquinone biosynthesis being active and essential in the malaria parasite. Our goal in the present work was to expand our knowledge of the ubiquinone head group biosynthesis and its potential metabolic dependency on chorismate in P. falciparum. These data led us to further characterize the mechanism of action of MMV688345, a compound from the open-access “Pathogen Box” collection from Medicine for Malaria Venture. We systematically assessed the development of both asexual and sexual stages of P. falciparum in a defined medium in the absence of an exogenous supply of chorismate end-products and present biochemical evidence suggesting that the benzoquinone ring of ubiquinones in this parasite may be synthesized through a yet unidentified route.
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets
Authors: Singh Urminder , Hur Manhoi , Dorman Karin , Wurtele Eve
Published: July 2019

The diverse and growing omics data in public domains provide researchers with a tremendous opportunity to extract hidden knowledge. However, the challenge of providing domain experts with easy access to these big data has resulted in the vast majority of archived data remaining unused. Here, we present MetaOmGraph (MOG), a free, open-source, standalone software for exploratory data analysis of massive datasets by scientific researchers. Using MOG, a researcher can interactively visualize and statistically analyze the data, in the context of its metadata. Researchers can interactively hone-in on groups of experiments or genes based on attributes such as expression values, statistical results, metadata terms, and ontology annotations. MOG’s statistical tools include coexpression, differential expression, and differential correlation analysis, with permutation test-based options for significance assessments. Multithreading and indexing enable efficient data analysis on a personal computer, with no need for writing code. Data can be visualized as line charts, box plots, scatter plots, and volcano plots. A researcher can create new MOG projects from any data or analyze an existing one. An R-wrapper lets a researcher select and send smaller data subsets to R for additional analyses. A researcher can save MOG projects with a history of the exploratory progress and later reopen or share them. We illustrate MOG by case studies of large curated datasets from human cancer RNA-Seq, in which we assembled a list of novel putative biomarker genes in different tumors, and microarray and metabolomics from A. thaliana.
Rectus femoris hyperreflexia predicts knee flexion angle in Stiff-Knee gait after stroke
Authors: Akbas Tunc , Kim Kyoungsoon , Doyle Kathleen , Manella Kathleen , Lee Robert , Spicer Patrick , Knikou Maria , Sulzer James
Published: July 2019

Stiff-knee gait (SKG) after stroke is often accompanied by decreased knee flexion angle during the swing phase. The decreased knee flexion has been hypothesized to originate from excessive quadriceps activation. However, it is unclear whether this activation is due to poor timing or hyperreflexia, both common post-stroke impairments. The goal of this study was to investigate the relation between quadriceps hyperreflexia in post-stroke SKG with knee flexion angle during walking. The rectus femoris (RF) H-reflex was recorded in eleven participants with post-stroke SKG and ten healthy controls during standing and walking during toe-off. In order to separate the effects of poorly timed quadriceps muscle activation from hyperreflexia, healthy individuals voluntarily increased quadriceps activity using RF electromyographic (EMG) biofeedback during standing and pre-swing upon H-reflex stimulation. We observed a negative correlation (R = −0.92, p=0.001) between knee flexion angle and RF H-reflexes in post-stroke SKG. In contrast, H-reflex amplitude in healthy individuals in presence (R = 0.47, p = 0.23) or absence (R = −0.17, p = 0.46) of increased RF activity had no correlation with knee flexion angle. The RF H-reflex amplitude differed between standing and walking in healthy individuals, including when RF activity was increased voluntarily (d = 2.86, p = 0.007), but was not observed post-stroke (d =0.73, p = 0.296). Thus, RF reflex modulation is impaired in post-stroke SKG. Further, RF hyperreflexia, as opposed to overactivity, may play a role in knee flexion kinematics in post-stroke SKG. Interventions targeting self-regulated quadriceps hyperreflexia may be effective in promoting better neural control of the knee joint and thus better quality of walking post-stroke.
souporcell: Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes
Authors: Heaton Haynes , Talman Arthur M. , Knights Andrew , Imaz Maria , Gaffney Daniel , Durbin Richard , Hemberg Martin , Lawniczak Mara
Published: July 2019

Methods to deconvolve single-cell RNA sequencing (scRNAseq) data are necessary for samples containing a natural mixture of genotypes and for scRNAseq experiments that multiplex cells from different donors1. Multiplexing across donors is a popular experimental design with many benefits including avoiding batch effects2, reducing costs, and improving doublet detection. Using variants detected in the RNAseq reads, it is possible to assign cells to the individuals from which they arose. These variants can also be used to identify and remove cross-genotype doublet cells that may have highly similar transcriptional profiles precluding detection by transcriptional profile. More subtle cross-genotype variant contamination can be used to estimate the amount of ambient RNA in the system. Ambient RNA is caused by cell lysis prior to droplet partitioning and is an important confounder of scRNAseq analysis3. Souporcell is a novel method to cluster cells using only the genetic variants detected within the scRNAseq reads. We show that it achieves high accuracy on genotype clustering, doublet detection, and ambient RNA estimation as demonstrated across a wide range of challenging scenarios.
Enhancing rigor and reproducibility in maternal immune activation models: practical considerations and predicting resilience and susceptibility using baseline immune responsiveness before pregnancy
Authors: Estes Myka L. , Farrelly Kathleen , Cameron Scott , Aboubechara John Paul , Haapanen Lori , Schauer Joseph D. , Horta Aurora , Prendergast Kathryn , MacMahon Jeremy A. , Shaffer Christine I. , Le Catherine T. , Kincheloe Greg N. , Tan Danielle John , van der List Deborah , Bauman Melissa D. , Carter Cameron S. , Van de Water Judy , McAllister A. Kimberley
Published: July 2019

Despite the potential of rodent models of maternal immune activation (MIA) to identify new biomarkers and therapeutic interventions for a range of psychiatric disorders, their value is currently limited by issues of scientific rigor and reproducibility. Here, we report three sources of variability—the immunogenicity of the poly(I:C), the baseline immune responsiveness (BIR) of the females prior to pregnancy, and differences in immune responses in C57/B6 dams across vendors. Similar to the variable effects of human maternal infection, MIA in mice does not cause disease-related phenotypes in all offspring and the magnitude and type of maternal response, determined by a combination of poly(I:C) dose and BIR, predicts offspring outcome. Together, our results provide recommendations for optimization of MIA protocols to enhance rigor and reproducibility and reveal new factors that drive susceptibility of some pregnancies and resilience of others to MIA-induced abnormalities in offspring.
In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome
Authors: Lanz Michael Charles , Yugandhar Kumar , Gupta Shagun , Sanford Ethan , Faça Vitor , Vega Stephanie , Joiner Aaron , Fromme Chris , Yu Haiyuan , Smolka Marcus Bustamante
Published: July 2019

Phosphorylation is one of the most dynamic and widespread post-translational modifications regulating virtually every aspect of eukaryotic cell biology. Here we present a comprehensive phosphoproteomic dataset for budding yeast, comprised of over 30,000 high confidence phosphorylation sites identified by mass spectrometry. This single dataset nearly doubles the size of the known phosphoproteome in budding yeast and defines a set of cell cycle-regulated phosphorylation events. With the goal of enhancing the identification of functional phosphorylation events, we performed computational positioning of phosphorylation sites on available 3D protein structures and systematically identified events predicted to regulate protein complex architecture. Results reveal a large number of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic “clashes” predicted to disrupt the interaction. Phosphorylation site mutants experimentally validate our predictions and support a role for phosphorylation in negatively regulating protein-protein interactions. With the advancement of Cryo-EM and the increasing number of available structures, our approach should help drive the functional and spatial exploration of the phosphoproteome.
Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure
Authors: Koch Hillary , DeGiorgio Michael
Published: July 2019

Though large multilocus genomic datasets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI, that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI’s performance in the four-taxon setting, and demonstrate the application of TASTI on a six-species Afrotropical mosquito dataset. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community.
P38α Regulates Expression of DUX4 in Facioscapulohumeral Muscular Dystrophy
Authors: Rojas L. Alejandro , Valentine Erin , Accorsi Anthony , Maglio Joseph , Shen Ning , Robertson Alan , Kazmirski Steven , Rahl Peter , Tawil Rabi , Cadavid Diego , Thompson Lorin A. , Ronco Lucienne , Chang Aaron N. , Cacace Angela M. , Wallace Owen
Published: July 2019

FSHD is caused by the loss of repression at the D4Z4 locus leading to DUX4 expression in skeletal muscle, activation of its early embryonic transcriptional program and muscle fiber death. While progress toward understanding the signals driving DUX4 expression has been made, the factors and pathways involved in the transcriptional activation of this gene remain largely unknown. Here, we describe the identification and characterization of p38α as a novel regulator of DUX4 expression in FSHD myotubes. By using multiple highly characterized, potent and specific inhibitors of p38α/β, we show a robust reduction of DUX4 expression, activity and cell death across FSHD1 and FSHD2 patient-derived lines. RNA-seq profiling reveals that a small number of genes are differentially expressed upon p38α/β inhibition, the vast majority of which are DUX4 target genes. Our results reveal a novel and apparently critical role for p38α in the aberrant activation of DUX4 in FSHD and support the potential of p38α/β inhibitors as effective therapeutics to treat FSHD at its root cause.

VISUAL ABSTRACT
Can the microbiome influence host evolutionary trajectories?
Authors: Henry Lucas P. , Bruijning Marjolein , Forsberg Simon K.G. , Ayroles Julien F.
Published: July 2019

The microbiome shapes many traits in hosts, but we still do not understand how it influences host evolution. To impact host evolution, the microbiome must be heritable and have phenotypic effects on the host. However, the complex inheritance and context-dependence of the microbiome challenges traditional models of organismal evolution. Here, we take a multifaceted approach to identify conditions in which the microbiome influences host evolutionary trajectories. We explore quantitative genetic models to highlight how microbial inheritance and phenotypic effects can modulate host evolutionary responses to selection. We synthesize the literature across diverse taxa to find common scenarios of microbiome driven host evolution. First, hosts may leverage locally adapted microbes, increasing survivorship in stressful environments. Second, microbial variation may increase host phenotypic variation, enabling exploration of novel fitness landscapes. We further illustrate these effects by performing a meta-analysis of artificial selection in Drosophila, finding that bacterial diversity also frequently responds to host selection. We conclude by outlining key avenues of research and experimental procedures to improve our understanding of the complex interplay between hosts and microbiomes. By synthesizing perspectives through multiple conceptual and analytical approaches, we show how microbiomes can influence the evolutionary trajectories of hosts.
Foot shock stress generates persistent widespread hypersensitivity and anhedonic behavior in an anxiety-prone strain of mice
Authors: Wu Pau Yen , Yang Xiaofang , Wright Douglas E. , Christianson Julie A.
Published: July 2019

A significant subset of patients with urologic chronic pelvic pain syndrome (UCPPS) suffer from widespread, as well as pelvic, pain and experience mood-related disorders, including anxiety, depression, and panic disorder. Stress is a commonly-reported trigger for symptom onset and exacerbation within these patients. The link between stress and pain is thought to arise, in part, from the hypothalamic-pituitary-adrenal (HPA) axis, which regulates the response to stress and can influence the perception of pain. Previous studies have shown that stress exposure in anxiety-prone rats can induce both pelvic and widespread hypersensitivity. Here, we exposed female A/J mice, an anxiety-prone inbred murine strain, to 10 days of foot shock stress to determine stress-induced effects on sensitivity, anhedonia, and HPA axis regulation and output in. At 1- and 28-days post-foot shock, A/J mice displayed significantly increased bladder sensitivity and hind paw mechanical allodynia. They also displayed anhedonic behavior, measured as reduced nest building scores and a decrease in sucrose preference during the 10-day foot shock exposure. Serum corticosterone was significantly increased at 1-day post-foot shock and bladder mast cell degranulation rates were similarly high in both sham- and shock-exposed mice. Bladder cytokine and growth factor mRNA levels indicated a persistent shift toward a pro-inflammatory environment following foot shock exposure. Together, these data suggest that chronic stress exposure in an anxiety-prone mouse strain may provide a useful translational model for understanding mechanisms that contribute to widespreadness of pain and increased comorbidity in a subset of UCPPS patients.
Zero-shot neural decoding of visual categories without prior exemplars
Authors: O’Connell Thomas P. , Chun Marvin M. , Kreiman Gabriel
Published: July 2019

Decoding information from neural responses in visual cortex demonstrates interpolation across repetitions or exemplars. Is it possible to decode novel categories from neural activity without any prior training on activity from those categories? We built zero-shot neural decoders by mapping responses from macaque inferior temporal cortex onto a deep neural network. The resulting models correctly interpreted responses to novel categories, even extrapolating from a single category.
Janggu - Deep learning for genomics
Authors: Kopp Wolfgang , Monti Remo , Tamburrini Annalaura , Ohler Uwe , Akalin Altuna
Published: July 2019

Motivation

In recent years, numerous applications have demonstrated the potential of deep learning for an improved understanding of biological processes. However, most deep learning tools developed so far are designed to address a specific question on a fixed dataset and/or by a fixed model architecture. Adapting these models to integrate new datasets or to address different hypotheses can lead to considerable software engineering effort. To address this aspect we have built Janggu, a python library that facilitates deep learning for genomics applications.

Results

Janggu aims to ease data acquisition and model evaluation in multiple ways. Among its key features are special dataset objects, which form a unified and flexible data acquisition and pre-processing framework for genomics data that enables streamlining of future research applications through reusable components. Through a numpy-like interface, the dataset objects are directly compatible with popular deep learning libraries, including keras. Furthermore, Janggu offers the possibility to visualize predictions as genomic tracks or by exporting them to the BIGWIG format. We illustrate the functionality of Janggu on several deep learning genomics applications. First, we evaluate different model topologies for the task of predicting binding sites for the transcription factor JunD. Second, we demonstrate the framework on published models for predicting chromatin effects. Third, we show that promoter usage measured by CAGE can be predicted using DNase hyper-sensitivity, histone modifications and DNA sequence features. We improve the performance of these models due to a novel feature in Janggu that allows us to include high-order sequence features. We believe that Janggu will help to significantly reduce repetitive programming overhead for deep learning applications in genomics, while at the same time enabling computational biologists to assess biological hypotheses more rapidly.

Availability

Janggu is freely available under a GPL-v3 license on https://github.com/BIMSBbioinfo/janggu or via https://pypi.org/project/janggu
Cryptic genetic variation underpins rapid adaptation to ocean acidification
Authors: Bitter M. C. , Kapsenberg L. , Gattuso J.-P. , Pfister C. A.
Published: July 2019

Global climate change has intensified the need to assess the capacity for natural populations to adapt to abrupt shifts in the environment. Reductions in seawater pH constitute a conspicuous stressor associated with increasing atmospheric carbon dioxide that is affecting ecosystems throughout the world’s oceans. Here, we quantify the phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the marine mussel,Mytilus galloprovincialis. We reared a genetically diverse larval population in ambient and extreme low pH conditions (pHT8.1 and 7.4) and tracked changes in the larval size and allele frequency distributions through settlement. Additionally, we separated larvae by size to link a fitness-related trait to its underlying genetic background in each treatment. Both phenotypic and genetic data show thatM. galloprovincialiscan evolve in response to a decrease in seawater pH. This process is polygenic and characterized by genotype-environment interactions, suggesting the role of cryptic genetic variation in adaptation to future climate change. Holistically, this work provides insight into the processes underpinning rapid evolution, and demonstrates the importance of maintaining standing variation within natural populations to bolster species’ adaptive capacity as global change progresses.
A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level
Authors: Mair Florian , Erickson Jami R. , Voillet Valentin , Simoni Yannick , Bi Timothy , Tyznik Aaron J. , Martin Jody , Gottardo Raphael , Newell Evan W. , Prlic Martin
Published: July 2019

High throughput single-cell RNA sequencing (sc-RNAseq) has become a frequently used tool to assess immune cell function and heterogeneity. Recently, the combined measurement of RNA and protein expression by sequencing was developed, which is commonly known as CITE-Seq. Acquisition of protein expression data along with transcriptome data resolves some of the limitations inherent to only assessing transcript, but also nearly doubles the sequencing read depth required per single cell. Furthermore, there is still a paucity of analysis tools to visualize combined transcript-protein datasets.

Here, we describe a novel targeted transcriptomics approach that combines analysis of over 400 genes with simultaneous measurement of over 40 proteins on more than 25,000 cells. This targeted approach requires only about 1/10 of the read depth compared to a whole transcriptome approach while retaining high sensitivity for low abundance transcripts. To analyze these multi-omic transcript-protein datasets, we adapted One-SENSE for intuitive visualization of the relationship of proteins and transcripts on a single-cell level.
A nanobody that recognizes a 14-residue peptide epitope in the E2 ubiquitin-conjugating enzyme UBC6e modulates its activity
Authors: Ling Jingjing , Cheloha Ross W. , McCaul Nicholas , Sun Zhen-Yu J. , Wagner Gerhard , Ploegh Hidde L.
Published: July 2019

A substantial fraction of eukaryotic proteins is folded and modified in the endoplasmic reticulum (ER) prior to export and secretion. Proteins that enter the ER but fail to fold correctly must be degraded, mostly in a process termed ER-associated degradation (ERAD). Both protein folding in the ER and ERAD are essential for proper immune function. Several E2 and E3 enzymes localize to the ER and are essential for various aspects of ERAD, but their functions and regulation are incompletely understood. Here we identify and characterize single domain antibody fragments derived from the variable domain of alpaca heavy chain-only antibodies (VHHs or nanobodies) that bind to the ER-localized E2 UBC6e, an enzyme implicated in ERAD. One such VHH, VHH05 recognizes a 14 residue stretch and enhances the rate of E1-catalyzed ubiquitin E2 loading in vitro and interferes with phosphorylation of UBC6e in response to cell stress. Identification of the peptide epitope recognized by VHH05 places it outside the E2 catalytic core, close to the position of activation-induced phosphorylation on Ser184. Our data thus suggests a site involved in allosteric regulation of UBC6e’s activity. This VHH should be useful not only to dissect the participation of UBC6e in ERAD and in response to cell stress, but also as a high affinity epitope tag-specific reagent of more general utility.

Highlights

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Identified single domain antibodies (VHHs) that bind to UBC6e with high affinity

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VHH binds to a short linear epitope near a phosphorylation site

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VHH binding to UBC6e enhances enzymatic activity

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VHH binding inhibits UBC6e phosphorylation in cells
Light-sheet engineering using the Field Synthesis theorem
Authors: Chang Bo-Jui , Fiolka Reto
Published: July 2019

Recent advances in light-sheet microscopy have enabled sensitive imaging with high spatiotemporal resolution. However, the creation of thin light-sheets for high axial resolution is challenging, as the thickness of the sheet, field of view and confinement of the excitation need to be carefully balanced. Some of the thinnest light-sheets created so far have found little practical use as they excite too much out-of-focus fluorescence. In contrast, the most commonly used lightsheet for subcellular imaging, the square lattice, has excellent excitation confinement at the cost of lower axial resolving power. Here we leverage the recently discovered Field Synthesis theorem to create light-sheets where thickness and illumination confinement can be continuously tuned. Explicitly, we scan a line beam across a portion of an annulus mask on the back focal plane of the illumination objective, which we call it C-light-sheets. We experimentally characterize these light-sheets and their application on biological samples.
Too much, too young? Altered corticolimbic axonal innervation and resting state functional connectivity suggests sex-dependent outcomes in a rat model of early life adversity
Authors: Honeycutt Jennifer A. , Demaestri Camila , Peterzell Shayna , Silveri Marisa M. , Cai Xuezhu , Kulkarni Praveen , Cunningham Miles G. , Ferris Craig F. , Brenhouse Heather C.
Published: July 2019

Adverse early experiences significantly alter behavioral and neural trajectories via aberrant brain maturation. Children with a history of early life stress (ELS) exhibit maladaptive behaviors and increased risk of mental illness later in life. Evidence in ELS-exposed humans identifies a role of atypical corticolimbic development; specifically, within amygdala-prefrontal cortex (PFC) circuits, and show precocially mature task-based corticolimbic functional connectivity (FC). However, the neurobiological substrates of such ELS-driven developmental changes remain unknown. Here, we identify putative neurobiological changes to determine the timeline of developmental perturbations following ELS in rats. Anterograde axonal tracing from basolateral amygdala (BLA) to pre- and infralimbic (PL, IL) PFC was quantified at postnatal days (PD)28, 38, and 48, along with anxiety-like behavior, in maternally separated (ELS) or control reared (CON) male and female rats. Resting state (rs)FC was assessed at PD28 and PD48 in a separate cohort. We report that ELS-exposed female rats show early maturation of BLA-PFC innervation at PD28, with ELS-related changes in males not appearing until PD38. ELS disrupted the maturation of rsFC from PD28 to PD48 in females, with enduring relationships between early rsFC and later anxiety-like behavior. Only transient ELS-related changes in rsFC were seen in male PL. Together, these data provide evidence that female rats may be more vulnerable to the effects of ELS via precocial BLA-PFC innervation, which may drive altered corticolimbic rsFC. These data also provide evidence that increased BLA-IL rsFC is associated with behavioral resiliency following ELS in female rats, providing mechanistic insight into the underlying etiology of adversity-induced vulnerability and resiliency.
Phenylacetyl-CoA, not phenylacetic acid, attenuates CepIR-regulated virulence inBurkholderia cenocepacia
Authors: Lightly Tasia Joy , Frejuk Kara L. , Groleau Marie-Christine , Chiarelli Laurent R. , Ras Cor , Buroni Silvia , Déziel Eric , Sorensen John L. , Cardona Silvia T.
Published: July 2019

During phenylalanine catabolism, phenylacetic acid (PAA) is converted to phenylacetyl-CoA (PAA-CoA) by a ligase, PaaK, and then epoxidized by a multicomponent monooxygenase, PaaABCDE, before further degradation to the TCA cycle. In the opportunistic pathogenBurkholderia cenocepacia,loss ofpaaABCDEattenuates virulence factor expression, which is under control of the LuxIR-like quorum sensing system, CepIR. To further investigate the link between CepIR-regulated virulence and PAA catabolism, we created knockout mutants of the first step of the pathway (PAA-CoA synthesis by PaaK) and characterized them in comparison to apaaABCDEmutant using liquid chromatography/mass spectrometry (LC-MS/MS) and virulence assays. We found that while loss of PaaABCDE decreased virulence, deletion of thepaaKgenes resulted in a more virulent phenotype than the wild type strain. Deletion of eitherpaaKorpaaABCDEled to higher levels of released PAA but no differences in internal accumulation, compared to wild type. While we found no evidence of directcepIRdownregulation by PAA-CoA or PAA, a low virulencecepRmutant reverted to a virulent phenotype upon removal of thepaaKgenes. On the other hand, removal ofpaaABCDEin thecepRmutant did not impact its attenuated phenotype. Together, our results suggest an indirect role for PAA-CoA in supressingB. cenocepaciaCepIR-activated virulence.

Importance

The opportunistic pathogenBurkholderia cenocepaciauses a chemical signal process called quorum sensing (QS) to produce virulence factors. InB. cenocepacia, QS relies on the presence of the transcriptional regulator CepR, which upon binding QS signal molecules, activates virulence. In this work, we found that even in the absence of CepR,B. cenocepaciacan elicit a pathogenic response if phenylacetyl-CoA, an intermediate of the phenylacetic acid degradation pathway, is not produced. Instead, accumulation of phenylacetyl-CoA appears to attenuate pathogenicity. Therefore, we have discovered that it is possible to trigger virulence in the absence of CepR, challenging the classical view of activation of virulence by this QS mechanism. Our work provides new insight into the relationship between metabolism and virulence in opportunistic bacteria. We propose that, in the event that QS signaling molecules cannot accumulate to trigger a pathogenic response, a metabolic signal can still activate virulence inB. cenocepacia.
The Creative Mind: Blending Oxytocinergic, Dopaminergic and Personality
Authors: Chong Anne , Becker Benjamin , Angeles Dario Cruz , Matos Maria Gutierrez , Yue Xiong , Lai Poh San , Cheung Mike , Lei Zhen , Malavasi Fabio , Chew Soo Hong , Ebstein Richard P.
Published: July 2019

In a fast-changing world, creative thinking (CT) is an extraordinary currency. Oxytocin (OT) is associated with CT and release of OT depends on ADP ribosyl-cyclases (CD38 and CD157). Moreover, CT as well as OT’s mechanism of action are mediated via central dopaminergic pathways. Consequently, we evaluate the roles of CD38, CD157, dopamine receptor D2 (DRD2) and catechol-O-methyltransferase (COMT) peripheral gene expression in CT. Two principal domains of CT, divergent thinking and insight solving problems, were assessed using validated behavioral assessments. To facilitate discriminant validity, two established correlates of CT, trait Openness and fluid intelligence as well as age and sex were included in the regression model. In women, significant main effects (p<0.01) were positively associated with the expression CD38, CD15, and their interaction CD38 x CD157 controlling for Openness, fluid intelligence and age. Subsequent analysis on the subscale-level revealed significant main effects for CD157 and CD38 x CD157 in men specifically for divergent thinking. In women, significant (p<0.01) results are also observed for dopaminergic expression (DRD2, COMT, DRD2 x COMT). The full model (oxytocinergic and dopaminergic gene expressions, Openness, and fluid intelligence) explains a sizable 39% of the variance in females. Significant main effects are observed for CD38, CD157, DRD2 and COMT as well as their interactions (CD38xCD157 and DRD2xCOMT). In conclusion, we show that oxytocinergic and dopaminergic gene expression contribute significantly to the complex CT phenotype suggesting the notion that the perspective gained from examining the peripheral transcriptome meaningfully adds to understanding the landscape of creative thinking.

Significance Statement

Creative thinking (CT) is a powerful driving force galvanizing progress and civilization. Towards better understanding the neurobiology of CT, we implement a gene expression strategy that is considered to capture not only genomic elements but also environmental signatures. We employ laboratory measures of CT (alternative uses test and insight problem solving), controlling for fluid intelligence and the personality trait of Openness. We focus on oxytocinergic and dopaminergic genes that contribute to the molecular architecture of CT. Oxytocinergic and dopaminergic gene expression significantly explains a robust 39% of the variance in CT. Notably, this study demonstrates the potential of the peripheral transcriptome towards tracing gene pathways underlying some complex cognitive behaviors such as creative thinking.
Detecting task-dependent modulation of spatiotemporal module via tensor decomposition: application to kinematics and EMG data for walking and running at various speed
Authors: Takiyama Ken , Yokoyama Hikaru , Kaneko Naotsugu , Nakazawa Kimitaka
Published: July 2019

How the central nervous system (CNS) controls many joints and muscles is a fundamental question in motor neuroscience and related research areas. An attractive hypothesis is the module hypothesis: the CNS controls groups of joints or muscles (i.e., spatial modules) while providing time-varying motor commands (i.e., temporal modules) to the spatial modules rather than controlling each joint or muscle separately. Another fundamental question is how the CNS generates numerous repertories of movement patterns. One hypothesis is that the CNS modulates the spatial and/or temporal modules depending on the required tasks. It is thus essential to quantify the spatial module, the temporal module, and the task-dependent modulation of those modules. Although previous methods attempted to quantify these aspects, they considered the modulation in only the spatial or temporal module. These limitations were possibly due to the constraints inherent to conventional methods for quantifying the spatial and temporal modules. Here, we demonstrate the effectiveness of tensor decomposition in quantifying the spatial module, the temporal module, and the task-dependent modulation of these modules without such limitations. We further demonstrate that the tensor decomposition provides a new perspective on the task-dependent modulation of spatiotemporal modules: in switching from walking to running, the CNS modulates the peak timing in the temporal module while recruiting proximal muscles in the corresponding spatial module.

Author summary

There are at least two fundamental questions in motor neuroscience and related research areas: 1) how does the central nervous system (CNS) control many joints and muscles and 2) how does the CNS generate numerous repertories of movement patterns. One possible answer to question 1) is that the CNS controls groups of joints or muscles (i.e., spatial modules) while providing time-varying motor commands (i.e., temporal modules) to the spatial modules rather than controlling each joint or muscle separately. One possible answer to question 2) is that the CNS modulates the spatial and/or temporal module depending on the required tasks. It is thus essential to quantify the spatial module, the temporal module, and the task-dependent modulation of those modules. Here, we demonstrate the effectiveness of tensor decomposition in quantifying the modules and those task-dependent modulations while overcoming the shortcomings inherent to previous methods. We further show that the tensor decomposition provides a new perspective on how the CNS switches between walking and running. The CNS modulated the peak timing in the temporal module while recruiting proximal muscles in the corresponding spatial module.
Temporal regulation of prenatal embryonic development by paternal imprinted loci
Authors: Li Qing , Li Yuanyuan , Yin Qi , Huang Shuo , Wang Kai , Zhuo Liangchai , Li Wei , Chang Boran , Li Jinsong
Published: July 2019

H19andGtl2are paternal imprinted genes that are pivotal for prenatal embryonic development. Meanwhile, mouse nongrowing oocytes and sperm- or oocyte-originated haploid embryonic stem cells (haESCs) carrying bothH19andIG-DMR (differentially DNA-methylated region) deletions (DKO) that partially mimic paternal imprinting ofH19-Igf2andDlk1-Dio3can be employed as sperm replacement to efficiently support full-term embryonic development. However, howH19-DMR andIG-DMR act together to regulate embryonic development is still largely unknown. Here, using androgenetic haESC (AG-haESC)-mediated semi-cloned (SC) technology, we showed that paternalH19-DMR andIG-DMR are not essential for pre-implantation development of SC embryos generated through injection of AG-haESCs into oocytes.H19-DMR plays critical roles before 12.5 days of gestation whileIG-DMR is essential for late-gestation of SC embryos. Interestingly, we found that combined deletions ofH19andH19-DMR can further improve the efficiency of normal development of SC embryos at mid-gestation compared to DKO SC embryos. Transcriptome and histology analyses revealed thatH19andH19-DMR combined deletions rescue the placental defects. Furthermore, we showed thatH19,H19-DMR andIG-DMR deletions (TKO) give rise to better prenatal and postnatal embryonic development of SC embryos compared to DKO. Together, our results indicate the temporal regulation of paternal imprinted loci during embryonic development.
Exploring the Complexity of Protein-Level Dosage Compensation that Fine-Tunes Stoichiometry of Multiprotein Complexes
Authors: Ishikawa Koji , Ishihara Akari , Moriya Hisao
Published: July 2019

Proper control of gene expression levels upon various perturbations is a fundamental aspect of cellular robustness. Protein-level dosage compensation is one mechanism buffering perturbations to stoichiometry of multiprotein complexes through accelerated proteolysis of unassembled subunits. Although N-terminal acetylation- and ubiquitin-mediated proteasomal degradation by the Ac/N-end rule pathway enables selective compensation of excess subunits, it is unclear how dominant this pathway contributes to stoichiometry control. Here we report that dosage compensation depends only partially on the Ac/N-end rule pathway. Our analysis of genetic interactions between 18 subunits and 10 quality control factors in budding yeast demonstrated that multiple E3 ubiquitin ligases and N-acetyltransferases are involved in dosage compensation. We find that N-acetyltransferases-mediated compensation is not simply predictable from N-terminal sequence despite their sequence specificity for N-acetylation. We also find that the compensation of Pop3 and Bet4 is due in large part to a minor N-acetyltransferase NatD. Furthermore, canonical NatD substrates histone H2A/H4 were compensated even in its absence, suggesting N-acetylation-independent compensation. Our study reveals the complexity and robustness of the stoichiometry control system.
Selection against expression noise explains the origin of the hourglass pattern of Evo-Devo
Authors: Liu Jialin , Frochaux Michael , Gardeux Vincent , Deplancke Bart , Robinson-Rechavi Marc
Published: July 2019

The evolution of embryological development has long been characterized by deep conservation. Both morphological and transcriptomic surveys have proposed a “hourglass” model of Evo-Devo1,2. A stage in mid-embryonic development, the phylotypic stage, is highly conserved among species within the same phylum3–7. However, the reason for this phylotypic stage is still elusive. Here we hypothesize that the phylotypic stage might be characterized by selection for robustness to noise and environmental perturbations. This could lead to mutational robustness, thus evolutionary conservation of expression and the hourglass pattern. To test this, we quantified expression variability of single embryo transcriptomes throughout flyDrosophila melanogasterembryogenesis. We found that indeed expression variability is lower at extended germband, the phylotypic stage. We explain this pattern by stronger histone modification mediated transcriptional noise control at this stage. In addition, we find evidence that histone modifications can also contribute to mutational robustness in regulatory elements. Thus, the robustness to noise does indeed contributes to robustness of gene expression to genetic variations, and to the conserved phylotypic stage.
Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk traits in Chinese buffalo breeds
Authors: Lu Xing-Rong , Duan An-Qin , Liang Sha-Sha , Ma Xiao-Ya , Liang Xian-Wei , Deng Ting-Xian
Published: July 2019

Water buffalo holds the tremendous potential of milk and meat that widespread throughout central and southern China. However, characterization of the population genetics of Chinese buffalo is poorly understood. Using Axiom®buffalo genotyping array, we performed the genetic diversity, linkage disequilibrium (LD) pattern and signature of selection in the 176 Chinese buffaloes from thirteen breeds. A total of 35,547 SNPs passed quality control and were used for further analyses. Population genetic analysis revealed a clear separation between the swamp and river types. Ten Chinese indigenous breeds clustered into the swamp group, Murrah and Nili-Ravi breeds were the river group, and the crossbred breed was closer to the river group. Genetic diversity analysis showed that the swamp group had a lower average expected heterozygosities compared to the river group. LD decay distance was much shorter in the swamp group compared with the river group withvalue of approximately 50 Kb. Analysis of runs of homozygosity indicated that extensive remote and recent inbreeding activity was respectively found within swamp and river groups. Moreover, a total of 12 genomic regions under selection were detected between river and swamp groups. Further, 12 QTL regions were found associated with buffalo milk production traits. Some candidate genes within these QTLs were predicted to be involved in the cell structure and function, suggesting that these genes might play vital roles in the buffalo milk performance. Our data contribute to our understanding of the characterization of population genetics in Chinese buffaloes, which in turn may be utilized in buffalo breeding programs.

Author Summary

Identifying the causal genes or markers associated with important economic traits in livestock is critical to increasing the production level on the species. However, current understanding of the genetic basis for milk production traits in buffalo is limited. Here, we confirmed the divergent evolution, distinct population structure, and LD extent among Chinese buffalo breeds. We also identified 12 QTL regions associated with milk production traits in buffaloes using the selective sweeps and haplotype analysis. Further, a total of 7 genes involved in the cell structure and function were predicted within the identified QTLs. These findings suggested that these genes can serve as the candidate genes associated with buffalo milk production, which hold a vital role in the milk trait improvement of dairy buffalo industry.