bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Functional Consequences ofGRIN2AMutations Associated with Schizophrenia and Neurodevelopmental Disorders
Authors: Shepard Nate , Baez-Nieto David , Iqbal Sumaiya , Kurganov Erkin , Budnik Nikita , Campbell Arthur J. , Pan Jen Q , Sheng Morgan , Farsi Zohreh 
Published: August 2023

AbstractHuman genetic studies have revealed rare missense and protein-truncating variants inGRIN2A, encoding for the GluN2A subunit of the NMDA receptors, that confer significant risk for schizophrenia (SCZ). Mutations inGRIN2Aare also associated with epilepsy and developmental delay/intellectual disability (DD/ID). However, it remains enigmatic how alterations to the same protein can result in diverse clinical phenotypes. Here, we performed functional characterization of human GluN1/GluN2A heteromeric NMDA receptors that contain SCZ-linked GluN2A variants, and compared them to NMDA receptors with GluN2A variants associated with epilepsy or DD/ID. Our findings demonstrate that SCZ-associatedGRIN2Avariants were predominantly loss-of-function (LoF), whereas epilepsy and DD/ID-associated variants resulted in both gain- and loss-of-function phenotypes. We additionally show that M653I and S809R, LoFGRIN2Avariants associated with DD/ID, exert a dominant-negative effect when co-expressed with a wild-type GluN2A, whereas E58Ter and Y698C, SCZ-linked LoF variants, and A727T, an epilepsy-linked LoF variant, do not. These data offer a potential mechanism by which SCZ/epilepsy and DD/ID-linked variants can cause different effects on receptor function and therefore result in divergent pathological outcomes.
Loss of synaptopodin impairs mGluR5 and protein synthesis dependent mGluR-LTD at CA3-CA1 synapses
Authors: Wu Pei You , Ji Linjia , De Sanctis Claudia , Francesconi Anna , Inglebert Yanis , McKinney R. Anne 
Published: August 2023

AbstractMetabotropic glutamate receptor-dependent long-term depression (mGluR-LTD) is an important form of synaptic plasticity that occurs in many regions of the CNS and is the underlying mechanism for several learning paradigms. In the hippocampus, mGluR-LTD is manifested by the weakening of synaptic transmission and elimination of dendritic spines. Interestingly, not all spines respond or undergo plasticity equally in response to mGluR-LTD. A subset of dendritic spines containing synaptopodin (SP), an actin-associated protein, are critical for mGluR-LTD and protect spines from elimination through mGluR1 activity. The precise cellular function of SP is still enigmatic and it is still unclear how SP contributes to the functional aspect of mGluR-LTD despite of its modulation on the structural plasticity. In the present study, we show that the lack of SP impairs mGluR-LTD by negatively affecting the mGluR5-dependent activity. Such impairment of mGluR5 activity is accompanied by a significant decrease of surface mGluR5 level in SP knockout (SPKO) mice. Intriguingly, the remaining mGluR-LTD becomes a protein synthesis-independent process in the SPKO and is mediated instead by endocannabinoid signaling. These data show for the first time that the postsynaptic protein SP can regulate the locus of expression of mGluR-LTD and provide insight to our understanding of spine/synapse-specific plasticity.Significance statementHippocampal group I metabotropic glutamate receptor dependent long-term depression (mGluR-LTD), a form of learning and memory, is misregulated in many murine models of neurodevelopmental disorders. Despite extensive studies there is a paucity of information on the molecular mechanism underlying mGluR-LTD. Previously, we reported that loss of synaptopodin, an actin-associated protein found in a subset of mature dendritic spines, impairs mGluR-LTD. In the current study, we uncover the molecular and cellular deficits involved. We find that synaptopodin is required for the mGluR5-Homer interaction and uncover synaptopodin as a molecular switch for mGluR-LTD expression, as mGluR-LTD becomes protein synthesis-independent and relies on endocannabinoid signaling in synaptopodin knock-out. This work provides insight into synaptopodin as a gatekeeper to regulate mGluR-LTD at hippocampal synapses.
GreenGate 2.0: backwards compatible addons for assembly of complex transcriptional units and their stacking with GreenGate
Authors: Piepers Marcel , Erbstein Katarina , Reyes-Hernandez Jazmin , Song Changzheng , Tessi Tomas , Petrasiunaite Vesta , Faerber Naja , Distel Kathrin , Maizel Alexis 
Published: August 2023

AbstractMolecular cloning is a crucial technique in genetic engineering that enables the precise design of synthetic transcriptional units (TUs) and the manipulation of genomes. GreenGate and several other modular molecular cloning systems were developed about ten years ago and are widely used in plant research. All these systems define grammars for assembling transcriptional units from building blocks, cloned as Level 0 modules flanked by four-base pair overhangs and recognition sites for a particular Type IIs endonuclease. Modules are efficiently assembled into Level 1 TUs in a hierarchical assembly process, and Level 2 multigene constructs are assembled by stacking Level 1 TUs. GreenGate is highly popular but has three main limitations. First, using ad-hoc overhangs added by PCR and classical restriction/ligation prevents the efficient use of a one-pot, one-step reaction to generate entry clones and domesticate internal sites; second, a Level 1 TU is assembled from a maximum of six modules, which may be limiting for applications such as multiplex genome editing; third, the generation of Level 2 assemblies is sequential and inefficient. GreenGate 2.0 (GG2.0) expands GreenGate features. It introduces additional overhangs, allowing for the combination of up to 12 Level 0 modules in a Level 1 TU. It includes a Universal Entry Generator plasmid (pUEG) to streamline the generation of Level 0 modules. GG2.0 introduces GreenBraid, a convenient method for stacking transcriptional units iteratively for multigene assemblies. Importantly, GG2.0 is backwards compatible with most existing GreenGate modules. Additionally, GG2.0 includes Level 0 modules for multiplex expression of guide RNAs for CRISPR/Cas9 genome editing and pre-assembled Level 1 vectors for dexamethasone-inducible gene expression and ubiquitous expression of plasma membrane and nuclear fluorescent markers. GG2.0 streamlines and increases the versatility of assembling complex transcriptional units and their combination.
Fucosylated glycoproteins and fucosylated glycolipids play opposing roles in cholera intoxication
Authors: Ghorashi Atossa C. , Boucher Andrew , Archer-Hartmann Stephanie A. , Murray Nathan B. , Konada Rohit Sai Reddy , Zhang Xunzhi , Xing Chao , Azadi Parastoo , Yrlid Ulf , Kohler Jennifer J. 
Published: August 2023

SUMMARYCholera toxin (CT) is the etiological agent of cholera. Here we report that multiple classes of fucosylated glycoconjugates function in CT binding and intoxication of intestinal epithelial cells. In Colo205 cells, knockout of B3GNT5, the enzyme required for synthesis of lacto- and neolacto-series glycosphingolipids (GSLs), reduces CT binding but sensitizes cells to intoxication. Overexpressing B3GNT5 to generate more fucosylated GSLs confers protection against intoxication, indicating that fucosylated GSLs act as decoy receptors for CT. Knockout (KO) of B3GALT5 causes increased production of fucosylated O-linked and N-linked glycoproteins, and leads to increased CT binding and intoxication. Knockout of B3GNT5 in B3GALT5 KO cells eliminates production of fucosylated GSLs but increases intoxication, identifying fucosylated glycoproteins as functional receptors for CT. These findings provide insight into molecular determinants regulating CT sensitivity of host cells.
Structure of recombinant formate dehydrogenase fromMethylobacterium extorquens(MeFDH1)
Authors: Park Junsun , Heo Yoonyoung , Jeon Byoung Wook , Jung Mingyu , Kim Yong Hwan , Lee Hyung Ho , Roh Soung-Hun 
Published: August 2023

ABSTRACTFormate dehydrogenase (FDH) is critical for the conversion between formate and carbon dioxide. Despite its importance, the structural complexity of FDH and difficulties in the production of the enzyme have made it difficult to elucidate its unique physicochemical properties. Here, we purified recombinantMethylobacterium extorquensAM1 FDH (MeFDH1) and used cryo-electron microscopy to determine its structure. We resolved a heterodimeric MeFDH1 structure at a resolution of 2.8 Å, showing a noncanonical active site and a well-embedded Fe-S redox chain relay. In particular, the tungsten bis-molybdopterin guanine dinucleotide active site showed an open configuration with the flexible C-terminal cap domain, suggesting structural and dynamic heterogeneity in the enzyme.SIGNIFICANCE-A recombinant MeFDH1 from an inducible expression system-Structural characterization of recombinant MeFDH1 for its catalytic activity-A dynamic, open configuration of the C-terminal cap domain
Transposable element expression with variation in sex chromosome number: insights into a toxic Y effect on human longevity
Authors: Teoli Jordan , Merenciano Miriam , Fablet Marie , Necsulea Anamaria , Siqueira-de-Oliveira Daniel , Brandulas-Cammarata Alessandro , Labalme Audrey , Lejeune Hervé , Lemaitre Jean-François , Gueyffier François , Sanlaville Damien , Bardel Claire , Vieira Cristina , Marais Gabriel AB , Plotton Ingrid 
Published: August 2023

AbstractWhy women live longer than men is still an open question in human biology. Sex chromosomes have been proposed to play a role in the observed sex gap in longevity, and the Y male chromosome has been suspected of having a potential toxic genomic impact on male longevity. It has been hypothesized that in aging individuals, TE repression is diminished, which could lead to detrimental effects (e.g. somatic mutations, perturbed gene expression) and to an acceleration of the aging process. As the Y chromosome is typically enriched in transposable elements (TE), this could explain why the presence of a Y chromosome is associated with shorter longevity. Using transcriptomic data from humans with atypical karyotypes, we found an association between TE expression and the presence and number of Y chromosomes. These findings are consistent with the existence of a toxic Y effect on men's longevity.
Aggregation of Disrupted in Schizophrenia 1 arises from a central region of the protein
Authors: Zaharija Beti , Bradshaw Nicholas J. 
Published: August 2023

AbstractAn emerging approach to studying major mental illness is through proteostasis, with the identification of several proteins that form insoluble aggregates in the brains of patients. One of these is Disrupted in Schizophrenia 1 (DISC1), a neurodevelopmentally-important scaffold protein, and the product of a classic schizophrenia risk gene. DISC1 was seen to aggregate in post mortem tissue from patients with schizophrenia, bipolar disorder and major depressive disorder, as well as in a variety of model systems, although the mechanism by which it does so is still unclear. Aggregation of two other proteins implicated in mental illness, TRIOBP-1 and NPAS3, was shown to be dependent on very specific structural regions of the protein. We therefore looked to the recently determined domain structure of DISC1, and investigated which structural elements were key for its aggregation. While none of the known DISC1 regions (named D, I, S and C respectively) formed aggregates individually when expressed in neuroblastoma cells, the combination of the D and I regions, plus the linker region between them, formed visible aggregates. Further refinement revealed that a region of approximately 30 amino acids between these two regions is critical to aggregation, with deletion of this region from full length DISC1 sufficient to abolish its aggregation propensity. This finding from mammalian cell culture contrasts with the recent determination that the extreme C-terminal of DISC1 can aggregatein vitro, although we did see some indication that combinations of C-terminal DISC1 regions can also aggregate in our system. It therefore appears likely that DISC1 aggregation, implicated in mental illness, can occur through at least two distinct mechanisms.
Metabolic complexity drives divergence in microbial communities
Authors: Silverstein Michael , Bhatnagar Jennifer M. , Segrè Daniel 
Published: August 2023

AbstractMicrobial communities are shaped by the metabolites available in their environment, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. To this end, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the diverse assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively smaller ones, is necessary and sufficient to recapitulate all of our experimental observations. In addition to pointing to a fundamental principle of community assembly, the divergence-complexity effect has important implications for microbiome engineering applications, as it can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions.
Modeling corticotroph deficiency with pituitary organoids supports the functional role ofNFKB2in human pituitary differentiation
Authors: Mac Thi Thom , Fauquier Teddy , Jullien Nicolas , Romanet Pauline , Etchevers Heather C. , Barlier Anne , Castinetti Frederic , Brue Thierry 
Published: August 2023

AbstractBackgroundDeficient Anterior pituitary with common Variable Immune Deficiency (DAVID) syndrome, combining adrenocorticotropic hormone deficiency (ACTHD) and primary hypogammaglobulinemia, is caused byNFKB2heterozygous mutations. Nuclear factor kappa B (NFKB) signaling is a key regulator of the immune system; however, the underlying mechanism of its association with endocrine symptoms remains unknown. The role of NFKB2 in the development of the human pituitary was called into question byNfkb2-deficientLym1mice, which have normal pituitary functions.PurposeThe aim of this study was to create a human disease model to define the role ofNFKB2in human pituitary development.MethodsWe established pituitary organoids in three-dimensional (3D) culture after directed differentiation from CRISPR/Cas9-edited human induced pluripotent stem cells (hiPSC). First, we conducted a proof-of-concept study, introducing a homozygousTBX19K146R/K146Rmissense pathogenic variant in hiPSC, an allele found in patients with congenital isolated ACTHD. We then used the same method to produceNFKB2D865G/D865Gmutant organoids, harboring the pathogenic missense variant previously identified in DAVID patients. This mutation causes a failure of NFKB2 p100 phosphorylation that blocks processing to form active NFKB2 p52. We further characterized pituitary organoid development with bulk RNA sequencing and validated findings with quantitative RT-PCR and by immunofluorescence in section and whole organoids.ResultsAnalysis of wild-type (WT) organoids demonstrated that thisin vitromodel recapitulates corticotroph cell differentiation.TBX19K146R/K146Rorganoids conserved early expression ofHESX1, but had significantly decreasedPITX1,TBX19,LHX3,andPOMCtranscription. NFKB2D865G/D865Gorganoids also had dramatically reduced corticotrophs. Furthermore,NFKB2D865G/D865Gsignificantly perturbs the expression of 67 genes known to contribute to pituitary development, among which 39 transcription factors. Differential expression was found for several growth factor genes or genes associated with the epithelial-to-mesenchymal transition and terminal endocrine differentiation.ConclusionWe used a combination of CRISPR/Cas9 editing and refinement of a 3D organoid culture protocol to model human ACTHD due toTBX19orNFKB2mutations. TheNFKB2variant studied induced a significant decrease in corticotroph differentiation, confirming the causative role of NFKB2 in isolated or syndromic ACTHD and demonstrating for the first time a direct functional role of NFKB2 in human pituitary development.
Single-linkage molecular clustering of viral pathogens
Authors: Miranda Maryelba Soto , Narváez Romo Ramiro , Moshiri Niema 
Published: August 2023

ABSTRACTIntroductionPublic health faces the ongoing mission of safeguarding the population’s health against various infectious diseases caused by a great number of pathogens. Epidemiology is an essential discipline in this field. With the rise of more advanced technologies, new tools are emerging to enhance the capability to intervene and control an epidemic. Among these approaches, molecular clustering comes forth as a promising option. However, appropriate genetic distance thresholds for defining clusters are poorly explored in contexts outside of Human Immunodeficiency Virus-1 (HIV-1).MethodsIn this work, using the well-used pairwise Tamura-Nei 93 (TN93) distance threshold of 0.015 for HIV-1 as a point of reference for molecular cluster properties of interest, we perform molecular clustering on whole genome sequence datasets from HIV-1, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Zaire ebolavirus, and Mpox virus, to explore potential pairwise distances thresholds for these other viruses.ResultsWe found the following pairwise TN93 distance thresholds as potential candidates for use in molecular clustering: 0.00016 (3 mutations) for Ebola, 0.00014 (4 mutations) for SARS-CoV-2, and 0.0000051 (1 mutation) for Mpox.ConclusionThis study provides valuable information for epidemic control strategies, and public health efforts in managing infectious diseases caused by these viruses. The identified pairwise distance thresholds for molecular clustering can serve as a foundation for future research and intervention to combat epidemics effectively.Availability and implementationAll relevant data and results can be found in the following repository:https://github.com/Niema-Lab/ENLACE-2023
Asynchronous and slow-wave oscillatory states in connectome-based models of mouse, monkey and human cerebral cortex
Authors: Sacha Maria , Goldman Jennifer S. , Kusch Lionel , Destexhe Alain 
Published: August 2023

AbstractThanks to the availability of connectome data that map connectivity between multiple brain areas, it is now possible to build models of whole brain activity. At the same time, advances in mean-field techniques have led to biologically based population models that integrate biophysical features such as membrane conductances or synaptic conductances. In this paper, we show that this approach can lead to brain-wide models of mouse, macaque, and human. We illustrate this approach by showing the transition from wakefulness to sleep simulated with multi-scale models in the three species. We compare the level of synchrony between the three species and found that the mouse brain displays a higher overall synchrony of slow-waves compared to monkey and human brains. We show that these differences are due to the different delays of axonal signal propagation between regions associated to brain-size differences between the species. We also make the program code publicly available, which provides a set of open-source tools for simulating large-scale activity in the cerebral cortex of mouse, monkey, and human.
Can a Sparse 29× 29Pixel Chaos Game Representation Predict Protein Binding Sites using Fine-Tuned State-of-the-Art Deep Learning Semantic Segmentation Models?
Authors: Dick Kevin , Green James R. 
Published: August 2023

AbstractNo. While our experiments ultimately failed, this work was motivated by the seemingly reasonable hypothesis that encoding protein sequences as a fractal-based image in combination with a binary mask identifying those pixels representative of the protein binding interface could effectively be used to fine-tune a semantic segmentation model. We were wrong.Despite the shortcomings of this work, a number of insights were drawn, inspiring discussion about how this fractal-based space may be exploited to generate effective protein binding site predictors in the future. Furthermore, these realizations promise to orient complimentary studies leveraging fractal-based representations, whether in the field of bioinformatics, or more broadly within disparate fields leveraging sequence-type data, such as Natural Language Processing.In a non-traditional way, this work presents the experimental design undertaken and interleaves various insights and limitations. It is the hope of this work that those interested in leveraging fractal-based representations and deep learning architectures as part of their work will benefit from the insights arising from this work.
Novel mechanisms of MITF regulation and melanoma predisposition identified in a mouse suppressor screen
Authors: Vu Hong Nhung , Valdimarsson Matti Már , Sigurbjörnsdóttir Sara , Bergsteinsdóttir Kristín , Debbache Julien , Bismuth Keren , Swing Deborah A. , Hallsson Jón H. , Larue Lionel , Arnheiter Heinz , Copeland Neal G. , Jenkins Nancy A. , Heidarsson Petur O. , Steingrímsson Eiríkur 
Published: August 2023

AbstractMITF, a basic-Helix-Loop-Helix Zipper (bHLHZip) transcription factor, plays vital roles in melanocyte development and functions as an oncogene. To explore MITF regulation and its role in melanoma, we conducted a genetic screen for suppressors of the Mitf-associated pigmentation phenotype. An intragenic Mitf mutation was identified, leading to termination of MITF at the K316 SUMOylation site and loss of the C-end intrinsically disordered region (IDR). The resulting protein is more nuclear but less stable than wild-type MITF and retains DNA-binding ability. Interestingly, as a dimer, it can translocate wild-type and mutant MITF partners into the nucleus, improving its own stability and ensuring an active nuclear MITF supply. Interactions between K316 SUMOylation and S409 phosphorylation sites across monomers largely explain the observed effects. Notably, the recurrent melanoma-associated E318K mutation in MITF, which affects K316 SUMOylation, also alters protein regulation in concert with S409, unraveling a novel regulatory mechanism with unexpected disease insights.