bluuebunny/crossref_metadata_2025 huggingface dataset:
Zebrafish models of Mucopolysaccharidosis types IIIA, B, & C show hyperactivity and changes in oligodendrocyte state
Authors: Gerken Ewan , Ahmad Syahida , Rattan Lakshay , Hemsley Kim M , Suo Shijin , Barthelson Karissa , Lardelli Michael
Published: August 2023

Sanfilippo syndrome childhood dementia, also known as mucopolysaccharidosis type III (MPS III), is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate (HS). An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete, and no effective therapies exist. We generated the hypomorphic mutationssgshS387Lfs,nagluA603EfsandhgsnatG577Sfsin the endogenous zebrafish genes orthologous to humanSGSH,NAGLU, andHGSNATthat are loci for mutations causing MPS III subtypes MPS IIIA, B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS, while behavioural analyses support anxiety and hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal, glycosaminoglycan, immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA, B and C zebrafish, supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall, our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafishs extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA, B, and C subtypes.
Insect population dynamics underWolbachia-induced cytoplasmic incompatibility: puzzle more than buzz inDrosophila suzukii
Authors: Auguste Alexandra , Ris Nicolas , Belgaidi Zainab , Kremmer Laurent , Mouton Laurence , Fauvergue Xavier
Published: August 2023

In theory, the introduction of individuals infected with an incompatible strain ofWolbachia pipientisinto a recipient host population should result in the symbiont invasion and reproductive failures caused by cytoplasmic incompatibility (CI). Modelling studies combiningWolbachiainvasion and host population dynamics show that these two processes could interact to cause a transient population decline and, in some conditions, extinction. However, these effects could be sensitive to density dependence, with the Allee effect increasing the probability of extinction, and competition reducing the demographic impact of CI. We tested these predictions with laboratory experiments in the fruit flyDrosophila suzukiiand the transinfectedWolbachiastrainwTei. Surprisingly, the introduction ofwTei intoD. suzukiipopulations at carrying capacity did not result in the expectedwTei invasion and transient population decline. In parallel, we found no Allee effect but strong negative density dependence. From these results, we propose that competition interacts in an antagonistic way withWolbachia-induced cytoplasmic incompatibility on insect population dynamics. If future models and data support this hypothesis, pest management strategies usingWolbachia-induced CI should target populations with negligible competition but a potential Allee effect, for instance at the beginning of the reproductive season.
Nitric oxide feedback to ciliary photoreceptor cells gates a UV avoidance circuit
Authors: Jokura Kei , Ueda Nobuo , Gühmann Martin , Yañez-Guerra Luis Alfonso , Słowiński Piotr , Wedgwood Kyle C. A. , Jékely Gáspár
Published: August 2023

Nitric oxide (NO) produced by nitric-oxide synthase (NOS) is a key regulator of animal physiology. Here we uncover a function for NO in the integration of UV exposure and the gating of a UV-avoidance circuit. We studied UV/violet avoidance mediated by brain ciliary photoreceptors (cPRCs) in larvae of the annelidPlatynereis dumerilii. In the larva, NOS is expressed in interneurons (INNOS) postsynaptic to cPRCs. UV stimulation of cPRCs triggers INNOS activation and NO production. NO signals retrogradely to cPRCs to induce their sustained post-stimulus activation through an unconventional guanylate cyclase. This late activation inhibits serotonergic ciliomotor neurons to induce downward swimming. InNOSmutants, retrograde signalling, circuit output and UV avoidance are defective. By mathematical modelling, we recapitulate phototransduction and circuit dynamics in wild-type and mutant larvae. Our results reveal how NO-mediated retrograde signalling gates a synaptic circuit and induces short-term memory of UV exposure to orchestrate light-avoidance behaviour.
Gorse (Ulex europeaus) wastes with 5,6-dimethyl benzimidazole supplementation can support growth of vitamin B12producing commensal gut microbes
Authors: Iyer Ajay , Soto-Martín Eva C. , Cameron Gary A. , Louis Petra , Duncan Sylvia H. , Bestwick Charles S. , Russell Wendy R.
Published: August 2023

Many commensal gut microbes are recognized for their potential to synthesize vitamin B12, offering a promising avenue to address deficiencies through probiotic supplementation. While bioinformatics tools aid in predicting B12biosynthetic potential, empirical validation remains crucial to confirm production, identify cobalamin vitamers, and establish biosynthetic yields.

This study investigates vitamin B12production in three human colonic bacterial species:Anaerobu-tyricum halliiDSM 3353,Roseburia faecisDSM 16840, andAnaerostipes caccaeDSM 14662, along withPropionibacterium freudenreichiiDSM 4902 as a positive control. These strains were selected for their potential use as probiotics, based on speculated B12production from prior bioinformatic analyses. Cultures were grown in M2GSC, chemically defined media (CDM), and Gorse extract medium (GEM). The composition of GEM was similar to CDM, expect that the carbon and nitrogen source was replaced with protein-depleted liquid wastes obtained after subjecting Gorse to a leaf protein extraction process. B12yields were quantified using liquid chromatography with tandem mass spectrophotometry.

The results suggest that the three butyrate-producing strains could indeed produce B12, although the yields were notably low, and with no B12being detected in the extracellular media. Next, GEM outperformed the conventional M2GSC growth medium in enhancing B12production. The positive control,P. freudenreichiiDSM 4902 produced B12at concentrations ranging from 7 ng·mL−1to 12 ng·mL−1. Univariate-scaled Principal Component Analysis of data from previous publications investigating B12production inP. freudenreichiirevealed that B12yields diminished when the carbon source concentration was≤30 g·L−1.

In conclusion, the protein-depleted wastes from the leaf protein extraction process from Gorse can be valorised as a viable substrate for culturing B12-producing colonic gut microbes. Furthermore, this is the first report attesting to the ability ofA. hallii, R. faecis, andA. caccaeto produce B12. However, these microbes seem unsuitable for industrial applications owing to low B12yields.
Assessment of tobacco andN. benthamianaas biofactories of irregular monoterpenes for sustainable crop protection
Authors: Mateos-Fernández Rubén , Vacas Sandra , Navarro-Fuertes Ismael , Navarro-Llopis Vicente , Orzáez Diego , Gianoglio Silvia
Published: August 2023

Irregular monoterpenes are important precursors of different compounds employed in pest control such as insecticides and insect sex pheromones. Metabolically engineered plants are appealing as biofactories of such compounds, but specially as potential live biodispensers of related bioactive volatiles, which could be continuously emitted to the environment from different plant tissues. Here we assess the use of cultivated tobacco and Nicotiana benthamiana as biofactories for the irregular monoterpenes chrysanthemol and lavandulol. We evaluate the impact of high levels of constitutive metabolite production on the plant physiology and biomass, and their biosynthetic dynamics for different plant tissues and developmental stages. As an example of an active pheromone compound, we super-transformed the best lavandulol-producing tobacco line with an acetyl transferase gene to obtain a tobacco lavandulyl acetate biodispenser emitting up to 0.63 mg of lavandulyl acetate per plant every day. We estimate that with these volatile emission levels, between 200 and 500 plants per hectare would be sufficient to ensure a daily emission of pheromones comparable to commercial lures. This is an important step towards plant-based sustainable solutions for pest control, and it lays the ground for further developing biofactories for other irregular monoterpenoid pheromones, whose biosynthetic genes are yet unknown.
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

Human 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

Metabotropic 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 statement

Hippocampal 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

Molecular 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

Cholera 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

Formate 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

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A recombinant MeFDH1 from an inducible expression system

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Structural characterization of recombinant MeFDH1 for its catalytic activity

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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

Abstract

Why 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

An 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

Microbial 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

Background

Deficient 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.

Purpose

The aim of this study was to create a human disease model to define the role ofNFKB2in human pituitary development.

Methods

We 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.

Results

Analysis 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.

Conclusion

We 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

Introduction

Public 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).

Methods

In 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.

Results

We 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.

Conclusion

This 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 implementation

All 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

Thanks 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

No. 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

MITF, 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.
Interpreting SNP heritability in admixed populations
Authors: Huang Jinguo , Kleman Nicole , Basu Saonli , Shriver Mark D. , Zaidi Arslan A.
Published: August 2023

SNP heritabilityis defined as the proportion of phenotypic variance explained by genotyped SNPs and is believed to be a lower bound of heritability (h2), being equal to it if all causal variants are known. Despite the simple intuition behind, its interpretation and equivalence toh2is unclear, particularly in the presence of population structure and assortative mating. It is well known that population structure can lead to inflation inestimates because of confounding due to linkage disequilibrium (LD) or shared environment. Here we use analytical theory and simulations to demonstrate thatestimates can be biased in admixed populations, even in the absence of confounding and even if all causal variants are known. This is because admixture generates LD, which contributes to the genetic variance, and therefore to heritability. Genome-wide restricted maximum likelihood (GREML) does not capture this contribution leading to under-or over-estimates ofrelative toh2, depending on the genetic architecture. In contrast, Haseman-Elston (HE) regression exaggerates the LD contribution leading to biases in the opposite direction. For the same reason, GREML and HE estimates of local ancestry heritabilityare also biased. We describe this bias inandas a function of admixture history and the genetic architecture of the trait and show that it can be recovered under some conditions. We clarify the interpretation ofin admixed populations and discuss its implication for genome-wide association studies and polygenic prediction.
Machine learning-based meta-analysis of colorectal cancer and inflammatory bowel disease
Authors: Sardari Aria , Usefi Hamid
Published: August 2023

Colorectal cancer (CRC) is a major global health concern, resulting in numerous cancer-related deaths. CRC detection, treatment, and prevention can be improved by identifying genes and biomarkers. Despite extensive research, the underlying mechanisms of CRC remain elusive, and previously identified biomarkers have not yielded satisfactory insights. This shortfall may be attributed to the predominance of univariate analysis methods, which overlook potential combinations of variants and genes contributing to disease development. Here, we address this knowledge gap by presenting a novel multivariate machine-learning strategy to pinpoint genes associated with CRC. Additionally, we applied our analysis pipeline to Inflammatory Bowel Disease (IBD), as IBD patients face substantial CRC risk. The importance of the identified genes was substantiated by rigorous validation across numerous independent datasets. Several of the discovered genes have been previously linked to CRC, while others represent novel findings warranting further investigation.
Balance of Activity during a Critical Period Tunes a Developing Network
Authors: Hunter Iain , Coulson Bramwell , Pettini Tom , Davies Jacob J. , Parkin Jill , Landgraf Matthias , Baines Richard A.
Published: August 2023

Developing neural circuits are influenced by activity and are especially sensitive to changes in activity during critical periods (CPs) of development. Changes occurring during a CP often become ‘locked-in’ so that they affect the mature network. Indeed, several neurodevelopmental disorders have been linked to excessive activity during such periods. It is, therefore, important to identify those aspects of neural circuit development that are influenced by neural activity during a CP. In this study, we take advantage of the genetic tractability ofDrosophilato show that activity perturbation during an embryonic CP permanently alters properties of the locomotor circuit. Specific changes we identify include increased synchronicity of motoneuron activity, and greater strengthening of excitatory over inhibitory synaptic drive to motoneurons. These changes are sufficient to reduce network robustness, evidenced by increased sensitivity to induced seizure. We also show that we can rescue these changes when increased activity is mitigated by inhibition provided by mechanosensory neurons. Similarly, we demonstrate a dose-dependent relationship between inhibition experienced during the CP, and the extent to which it is possible to rescue the hyperexcitable phenotype characteristic of theparabssmutation. This suggests that developing circuits must be exposed to a properly balanced sum of excitation and inhibition during the CP to achieve normal mature network function. Our results, therefore, provide novel insight into how activity during a CP shapes specific elements of a circuit, and how activity during this period is integrated to tune neural circuits to the environment in which they will likely function.
ECM degradation in the stump region induced by Fgf during functional joint regeneration in frogs
Authors: Matsubara Haruka , Inoue Takeshi , Agata Kiyokazu
Published: August 2023

Previous studies indicated the importance of the reciprocal interactions between residual tissues in the stump and the newly formed blastema for achieving functional joint regeneration after amputation at the joint level in newts. This reciprocal interaction during regeneration was named “reintegration”. When this reintegration mechanism was evoked inXenopus leavis, regeneration of a functional joint was induced in frogs. Interestingly, degradation of extracellular matrix (ECM) in the remaining joint cartilage was observed during regeneration in both newts and frogs. Histological and gene expression analyses suggested that the degradation of Type II collagen in the cartilage of the articular head might be performed by matrix metalloproteases (Mmps) which were transiently expressed after amputation. We found that fibroblast growth factor (Fgf) induced Mmps expression in the cartilage of the articular head. These results support the possibility that the Fgf signal induces ECM degradation in joint tissues via Mmps expression and that the ECM degradation and subsequent bone morphogenetic protein (Bmp) secretion promote cell proliferation, migration, and differentiation of the cells in the blastema to achieve functional joint regeneration.
Menin regulates androgen receptor- and MLL-driven condensation, upsetting regulation of cellular AR-driven transcription
Authors: Ahmed Junaid , Claridge Jolyon K , Meszaros Attila , Tompa Peter
Published: August 2023

Menin is a protein that is regulated via protein-protein interactions by different binding partners, such as mixed lineage leukemia protein (MLL) and androgen receptor (AR). We observed that menin-AR and menin-MLL interactions are regulated by concentration-dependent dimerization of menin, and its interaction with cancer-related AR. As a result of its oligomerization-dependent interaction with both AR and MLL, menin is recruited into AR-RNA and MLL-RNA condensates formed by liquid-liquid phase separation (LLPS), with different outcomes under AR-overexpression or MLL-overexpression conditions representing different cancer types. At high concentrations promoting menin dimerization, it inhibits MLL-RNA LLPS, while making AR-RNA condensates less dynamic, i.e., more gel-like. Regions of AR show both negative/positive cooperativity in menin binding. AR contains a specific menin-binding region (MBR) in its intrinsically disordered N-terminal domain (NTD), menin binding of which is inhibited by the adjacent DNA-binding domain (DBD), but facilitated by a hinge region located between its DBD and ligand-binding domain (LBD) as well as by N terminus of AR. Interestingly, the hinge region reduces the propensity of full-length AR to undergo LLPS in the presence of RNA, which is facilitated by an alternative hinge region present in the tumor-specific AR isoform, AR-v7. As both menin and MLL are recruited into AR-driven, functional cellular condensates aggravated in the case of AR-v7, we posit that the menin-AR-MLL system represents a fine-tuned condensate module of transcription regulation that is balanced toward the tumor-suppressor activity of menin. Our results suggest that this balance can be upset by prevalent oncogenic events, such as menin upregulation and/or AR-v7 overexpression, in cancer.
The Influenza B Virus Victoria and Yamagata Lineages Display Distinct Cell Tropism and Infection Induced Host Gene Expression in Human Nasal Epithelial Cell Cultures
Authors: Wilson Jo L. , Akin Elgin , Zhou Ruifeng , Jedlicka Anne , Dziedzic Amanda , Liu Hsuan , Fenstermacher Katherine Z. , Rothman Richard , Pekosz Andrew
Published: August 2023

Understanding Influenza B virus infections is of critical importance in our efforts to control severe influenza and influenza-related disease. Until 2020, two genetic lineages of influenza B virus – Yamagata and Victoria – circulated in the population. These lineages are antigenically distinct but differences in virus replication or the induction of host cell responses after infection have not been carefully studied. Recent IBV clinical isolates of both lineages were obtained from influenza surveillance efforts of the Johns Hopkins Center of Excellence in Influenza Research and Response and characterizedin vitro. B/Victoria and B/Yamagata clinical isolates were recognized less efficiently by serum from influenza-vaccinated individuals in comparison to the vaccine strains. B/Victoria lineages formed smaller plaques on MDCK cells compared to B/Yamagata, but infectious virus production in primary human nasal epithelial cell (hNEC) cultures showed no differences. While ciliated epithelial cells were the dominant cell type infected by both lineages, B/Victoria lineages had a slight preference for MUC5AC-positive cells, while B/Yamagata lineages infected more basal cells. Finally, while both lineages induced a strong interferon response 48 hours after infection of hNEC cultures, the B/Victoria lineages showed a much stronger induction of interferon related signaling pathways compared to B/Yamagata. This demonstrates that the two influenza B virus lineages differ not only in their antigenic structure but in their ability to induce host innate immune responses.
Is Inappropriate Pulse Timing Responsible for Poor Binaural Hearing with Cochlear Implants?
Authors: Schnupp Jan W. H. , Buchholz Sarah , Buck Alexa N. , Budig Henrike , Khurana Lakshay , Rosskothen-Kuhl Nicole
Published: August 2023

Cochlear implants (CIs) have restored enough of a sense of hearing to around one million severely hearing impaired patients to enable speech understanding in quiet. However, several aspects of hearing with CIs remain very poor. This includes a severely limited ability of CI patients to make use of interaural time difference (ITD) cues for spatial hearing and noise reduction. A major cause for this poor ITD sensitivity could be that current clinical devices fail to deliver ITD information in a manner that is accessible to the auditory pathway. CI processors measure the envelopes of incoming sounds and then stimulate the auditory nerve with electrical pulse trains which are amplitude modulated to reflect incoming sound envelopes. The timing of the pulses generated by the devices is largely or entirely independent of the incoming sounds. Consequently, bilateral CIs (biCIs) provide veridical envelope (ENV) ITDs but largely or entirely replace the “fine structure” ITDs that naturally occur in sounds with completely arbitrary electrical pulse timing (PT) ITDs. To assess the extent to which this matters, we devised experiments that measured the sensitivity of deafened rats to precisely and independently controlled PT and ENV ITDs for a variety of different CI pulse rates and envelope shapes. We observed that PT ITDs completely dominate ITD perception, while the sensitivity to ENV ITDs was almost negligible in comparison. This strongly suggests that the confusing yet powerful PT ITDs that contemporary clinical devices deliver to biCI patients may be a major cause of poor binaural hearing outcomes with biCIs.

Significance Statement

CIs deliver spectro-temporal envelopes, including speech formants, to severely deaf patients, but they do little to cater to the brain’s ability to process temporal sound features with sub-millisecond precision. CIs “sample” sound envelope signals rapidly and accurately, and thus provide information which should make it possible in principle for CI listeners to detect envelope ITDs in a similar way to normal listeners. However, here we demonstrate through behavioral experiments on CI implanted rats trained to detect sub-millisecond ITDs that pulse timing ITDs completely dominate binaural hearing. This provides the strongest confirmation to date that the arbitrary pulse timing widely used in current clinical CIs is a critical obstacle to good binaural hearing through prosthetic devices.
Effects of sex and gestational exercise on pain perception, BDNF and irisin levels in an animal model of ADHD
Authors: Tosta Andréa , Fonseca Ariene S. , Messender Débora , Ferreira Sérgio T. , Lourenco Mychael V. , Pandolfo Pablo
Published: August 2023

Abnormal cognitive and sensorial properties have been reported in patients with psychiatric and neurodevelopmental conditions, such as attention deficit hyperactivity disorder (ADHD). ADHD patients exhibit impaired dopaminergic signaling and plasticity in brain areas related to cognitive and sensory processing. The spontaneous hypertensive rat (SHR), in comparison to the Wistar Kyoto rat (WKY), is the most used genetic animal model to study ADHD. Brain neurotrophic factor (BDNF), critical for midbrain and hippocampal dopaminergic neuron survival and differentiation, is reduced in both ADHD subjects and SHR. Physical exercise (e.g. swimming) promotes neuroplasticity and improves cognition by increasing BDNF and irisin. Here we investigate the effects of gestational swimming on sensorial and behavioral phenotypes, striatal dopaminergic parameters, and hippocampal FNDC5/irisin and BDNF levels observed in WKY and SHR. Gestational swimming improved nociceptive reflex impairment in SHR rats and increased hippocampal BDNF levels in a sex-dependent manner in adolescent offspring. Sex differences were observed in hippocampal FNDC5/irisin levels, with females presenting lower levels than males. Our results contribute to the notion that swimming during pregnancy is a promising alternative to improve ADHD phenotypes in the offspring.

Graphical abstract
Multi-color live-cell optical nanoscopy using phasor analysis
Authors: Zhang Zhimin , Huang Yuran , Tao Wenli , Wei Yunfei , Xu Liang , Gong Wenwen , Zhang Yuhui , Zhou Jiaqiang , Cao Liangcai , Liu Yong , Han Yubing , Kuang Cuifang , Liu Xu
Published: August 2023

Stimulated emission depletion microscopy (STED) is a powerful tool for studying nanoscale cell structure and activity, but the difficulties it encounters in multicolor imaging limit its application in biological research. To overcome the disadvantages of limited number of channels and high cost of multicolor STED imaging based on spectral identity, we introduced lifetime into live-cell multicolor STED imaging by separating selected dyes of the same spectrum by phasor analysis. Experimental results show that our method enables live-cell STED imaging with at least 4 colors, enabling observation of cellular activity beyond the diffraction limit.
Structure of the imine reductase from Ajellomyces dermatitidis in three crystal forms
Authors: Sharma Mahima , Cuetos Anibal , Willliams Adam , González-Martínez Daniel , Grogan Gideon
Published: August 2023

The NADPH-dependent imine reductase from Ajellomyces dermatitidis (AdRedAm) catalyzes the reductive amination of certain ketones with amine donors supplied in an equimolar ratio. The structure of AdRedAm has been determined in three forms. The first form, which belongs to space group P3121 and was refined to 2.01 Å resolution, features two molecules (one dimer) in the asymmetric unit in complex with the redox-inactive cofactor NADPH4. The second form, which belongs to space group C21 and was refined to 1.73 Å resolution, has nine molecules (four and a half dimers) in the asymmetric unit, each complexed with NADP+. The third form, which belongs to space group P3121 and was refined to 1.52 Å resolution, has one molecule (one half-dimer) in the asymmetric unit. This structure was again complexed with NADP+ and also with the substrate 2,2-difluoroacetophenone. The different data sets permit the analysis of AdRedAm in different conformational states and also reveal the molecular basis of stereoselectivity in the transformation of fluorinated acetophenone substrates by the enzyme.