bluuebunny/crossref_metadata_2025 huggingface dataset:
A Scoping Review of Mathematical Models Covering Alzheimer’s Disease Progression
Authors: Moravveji Seyedadel , Doyon Nicolas , Mashreghi Javad , Duchesne Simon
Published: December 2022

Alzheimer’s disease is a complex, multi-factorial and multi-parametric neurodegenerative etiology. Mathematical models can help understand such a complex problem by providing a way to explore and conceptualize principles, merging biological knowledge with experimental data into a model amenable to simulation and external validation, all without the need for extensive clinical trials.

We performed a scoping review of mathematical models of AD with a search strategy applied to the PubMed database which yielded 846 entries. After applying our exclusion criteria, only 17 studies remained from which we extracted data, focusing on three aspects of mathematical modeling: how authors addressed continuous time, how models were solved, and how the high dimensionality and non-linearity of models were managed. Most articles modeled AD at the cellular range of the disease process, operating on a short time scale (e.g., minutes; hours), i.e., the micro view (12/17); the rest considered regional or brain-level processes, with longer timescales (e.g., years, decades) (the macro view). Most papers were concerned primarily withAβ(n= 8), few modeled with bothAβand tau proteins (n= 3), and some considered more than these two factors in the model (n= 6). Models used partial differential equations (PDEs;n= 3), ordinary differential equations (ODEs;n= 7), both PDEs and ODEs (n= 3). Some didn’t specify the mathematical formalism (n= 4). Sensitivity analyses were performed in only a small number of papers (4/17).

Overall, we found that only two studies could be considered valid in terms of parameters and conclusions, and two more were partially valid. The majority (n= 13) either was invalid or there was insufficient information to ascertain their status. While mathematical models are powerful and useful tools for the study of AD, closer attention to reporting is necessary to gauge the quality of published studies to replicate or continue with their contributions.
Conserved Biophysical Compatibility Among the Highly Variable Germline-Encoded Regions Shapes TCR-MHC Interactions
Authors: Boughter Christopher T. , Meier-Schellersheim Martin
Published: December 2022

T cells are critically important components of the adaptive immune system primarily responsible for identifying and responding to pathogenic challenges. This recognition of pathogens is driven by the interaction between membrane-bound T cell receptors (TCRs) and antigenic peptides presented on major histocompatibility complex (MHC) molecules. The formation of the TCR-peptide-MHC complex (TCR-pMHC) involves interactions among germline-encoded and hypervariable amino acids. Germline-encoded and hypervariable regions can form contacts critical for complex formation, but only interactions between germline-encoded contacts are likely to be shared across many of all the possible productive TCR-pMHC complexes. Despite this, experimental investigation of these interactions have focused on only a small fraction of the possible interaction space. To address this, we analyzed every possible germline-encoded TCR-MHC contact in humans, thereby generating the first comprehensive characterization of these largely antigen-independent interactions. Our analysis shows that germline-encoded TCR-MHC interactions that are conserved at the sequence level are rare due to the high amino acid diversity of the TCR CDR1 and CDR2 loops, and that such conservation is unlikely to dominate the dynamic protein-protein binding interface. Instead, we find that binding properties such as the docking orientation are defined by regions of biophysical compatibility between these loops and the MHC surface.
Heterotrophic bacteria drive sulfide oxidation in coastal sediments
Authors: Cao Qun , Yang Yunyun , Lu Chuanjuan , Wang Qingda , Xia Yongzhen , Qin Qilong , Xun Luying , Liu Huaiwei
Published: December 2022

Sulfate reduction and sulfur oxidation are very active in coastal sediments. They shape the biogeochemistry and microbial ecology at hot places of organic matter metabolism. Different from the well-studied sulfate reduction, sulfur oxidation in coastal sediments is still full of questions. Herein, we investigated the distribution of reduced sulfur compounds in differently layers of coastal sediments at the Yellow sea and found that sulfide (H2S), sulfane sulfur (S0), and thiosulfate mainly accumulated in anaerobic sediments and were mostly oxidized in anoxic and oxic interface in the sediments and the sea water. Bacterial community analysis indicated that heterotrophic bacteria are dominating species in surface sediments and sea water. Metagenome analysis showed that two sulfur-oxidizing genes encoding sulfide:quinone oxidoreductases (SQR) and persufide dioxygenases (PDO), were sharply more abundant than other sulfur-oxidizing genes in the coastal sediments. Since members of the marine Roseobacter clade were dominant in coastal waters and sediments, we studied the sulfur oxidation pathway in the RoseobacterRuegeria pomeroyiDSS-3 and found that sulfide:quinone oxidoreductase, persulfide dioxygenase, and sulfite-oxidizing enzyme were the main enzymes for the oxidation of H2S, zerovalent sulfur, and sulfite/thiosulfate. This study, for the first time, clarified the dominating function of heterotrophic bacteria in sulfur oxidation in the coastal sediments and sea water.

IMPORTANCE

Coastal sediments are the most productive ecosystems. We performed the microbial community diversity and metagenomic analysis of seawater and coastal sediments of the Yellow Sea and explored the sulfur oxidation process in them. We found that heterotrophic bacteria are dominating species in surface sediments and sea water, sulfide and sulfane sulfur were mostly oxidized in surface sediments, and the genes encoding SQR, PDO, and SOE are abundant. UsingRuegeria pomeroyiDSS-3 as the model strain, we studied how these enzymes cooperate to oxidize H2S to sulfate. Thus, this research revealed the critical role of heterotrophic bacteria in sulfur oxidation in coastal sediments and sea water.
Species-specific LUBAC-mediated M1 ubiquitination regulates necroptosis by segregating the cellular distribution and fate of activated MLKL
Authors: Weinelt Nadine , Wächtershäuser Kaja Nicole , Smith Sonja , Andrieux Geoffroy , Das Tonmoy , Jeiler Birte , Roedig Jens , Feist Leonard , Rotter Björn , Boerries Melanie , Pampaloni Francesco , van Wijk Sjoerd J. L.
Published: December 2022

Plasma membrane accumulation of phosphorylated mixed lineage kinase domain-like (MLKL) is a hallmark of necroptosis, leading to membrane rupture and inflammatory cell death. Pro-death functions of MLKL are tightly controlled by several checkpoints, including phosphorylation. Endocytosis and exocytosis limit MLKL membrane accumulation and counteract necroptosis, but the exact mechanisms remain poorly understood. Here, we identify linear ubiquitin chain assembly complex (LUBAC)-mediated M1 poly-ubiquitination (poly-Ub) as novel checkpoint for necroptosis regulation downstream of activated MLKL in human cells. Loss of LUBAC activity inhibits necroptosis, without affecting necroptotic signaling, but by preventing membrane accumulation of activated MLKL. Flotillin-1/2 act as putative necroptotic M1 poly-Ub targets that inhibit necroptosis suppression induced by LUBAC inhibition. Finally, we confirm LUBAC-dependent activation of necroptosis in primary human pancreatic organoids. Our findings identify LUBAC as species-specific regulator of necroptosis which promotes MLKL membrane accumulation and pioneer primary human organoids to model necroptosis in near-physiological settings.
Multi-omics approach reveals dysregulated genes during hESCs neuronal differentiation exposure to paracetamol
Authors: Spildrejorde Mari , Samara Athina , Sharma Ankush , Leithaug Magnus , Falck Martin , Modafferi Stefania , Sundaram Arvind Y. M. , Acharya Ganesh , Nordeng Hedvig , Eskeland Ragnhild , Gervin Kristina , Lyle Robert
Published: December 2022

Prenatal paracetamol exposure has been associated with neurodevelopmental outcomes in childhood. Pharmacoepigenetic studies show differences in cord blood DNA methylation between paracetamol exposed and unexposed neonates. However, causal implications and impact of long-term prenatal long-term paracetamol exposure on brain development remain unclear. Using a multi-omics approach, we investigated the effects of paracetamol on a model of early human brain development. We exposed human embryonic stem cells undergoing in vitro neuronal differentiation to daily media changes with paracetamol concentrations corresponding to maternal therapeutic doses. Single-cell RNA-seq and ATAC-seq integration identified paracetamol-induced chromatin-opening changes linked to gene expression. Differentially methylated and/or expressed genes were involved in signalling, neurotransmission, and cell fate-determination trajectories. Some genes involved in neuronal injury and development-specific pathways, such asKCNE3, overlapped with differentially methylated genes previously identified in cord blood associated with prenatal paracetamol exposure. Our data suggest that paracetamol may play a causal role in impaired neurodevelopment.

Graphical Abstract
Evidence implicating sequential commitment of the founder lineages in the human blastocyst by order of hypoblast gene activation
Authors: Corujo-Simon Elena , Radley Arthur H. , Nichols Jennifer
Published: December 2022

Successful human pregnancy depends upon rapid establishment of three founder lineages: trophectoderm, epiblast and hypoblast, which together form the blastocyst. Each plays an essential role in preparing the embryo for implantation and subsequent development. Several models are proposed to define the lineage segregation. The first suggests that all specify simultaneously; the second favours differentiation of trophectoderm before separation of epiblast and hypoblast, either via differentiation of hypoblast from established epiblast, or production of both tissues from the inner cell mass precursor. To begin to resolve this discrepancy and thereby understand the sequential process for production of viable human embryos, we investigated the expression order of genes associated with emergence of hypoblast. Based upon published data and immunofluorescence analysis for candidate genes, we present a basic blueprint for human hypoblast differentiation, lending support to the proposed model of sequential segregation of the founder lineages of the human blastocyst. The first characterised marker, specific initially to the early inner cell mass, and subsequently identifying presumptive hypoblast is PDGFRA, followed by SOX17, FOXA2 and GATA4 in sequence as the hypoblast becomes committed.

Summary Statement

Optimal segregation of human blastocyst founder lineages is essential to establish healthy human pregnancies. Mapping activation of hypoblast marker genes over time helps understand how the yolk sac is regulated.
NewAequoreafluorescent proteins for cell-free bioengineering
Authors: Deich Christopher , Gaut Nathaniel J. , Sato Wakana , Engelhart Aaron E. , Adamala Katarzyna P.
Published: December 2022

Recently, a new subset of fluorescent proteins has been identified from the Aequorea species of jellyfish. These fluorescent proteins were characterizedin vivo; however, there has not been validation of these proteins within cell-free systems. Cell-free systems and technology development is a rapidly expanding field, encompassing foundational research, synthetic cells, bioengineering, biomanufacturing and drug development. Cell-free systems rely heavily on fluorescent proteins as reporters. Here we characterize and validate this new set of Aequorea proteins for use in a variety of cell-free and synthetic cell expression platforms.

Abstract Figure
Genetic Variants of Phospholipase C-γ2 Confer Altered Microglial Phenotypes and Differential Risk for Alzheimer’s Disease
Authors: Tsai Andy P. , Dong Chuanpeng , Lin Peter Bor-Chian , Oblak Adrian L. , Di Prisco Gonzalo Viana , Wang Nian , Hajicek Nicole , Carr Adam J. , Lendy Emma K. , Hahn Oliver , Atkins Micaiah , Foltz Aulden G. , Patel Jheel , Xu Guixiang , Moutinho Miguel , Sondek John , Zhang Qisheng , Mesecar Andrew D. , Liu Yunlong , Atwood Brady K. , Wyss-Coray Tony , Nho Kwangsik , Bissel Stephanie J. , Lamb Bruce T. , Landreth Gary E.
Published: December 2022

Genetic association studies have demonstrated the critical involvement of the microglial immune response in Alzheimer’s disease (AD) pathogenesis. Phospholipase C-gamma-2 (PLCG2) is selectively expressed by microglia and acts in many immune receptor signaling pathways. In AD, PLCG2 is induced uniquely in plaque-associated microglia. A genetic variant ofPLCG2, PLCG2P522R, is a mild hypermorph that attenuates AD risk. We report the identification of aPLCG2variant,PLCG2M28L, associated with loss-of-function and confers increased AD risk. PLCG2P522Rattenuates disease in an amyloidogenic murine AD model, whereasPLCG2M28Lexacerbates the plaque burden associated with altered phagocytosis and Aβ clearance. The variants bidirectionally modulate disease pathology by inducing distinct transcriptional programs that identify microglial subpopulations associated with protective or detrimental phenotypes. In summary, these findings identify PLCG2M28Las a new AD risk variant and demonstrate that PLCG2 variants can differentially orchestrate microglial responses in AD pathogenesis that can be therapeutically targeted.

Graphical abstract

Highlights

A genetic variant of PLCG2, M28L, is associated with an increased risk for Alzheimer’s disease (AD)

In an amyloidogenic AD mouse model, PLCG2M28L exacerbates disease pathogenesis

Conversely, PLCG2P522R, a protective PLCG2 variant, attenuates AD pathogenesis

The PLCG2 variants uniquely alter the microglial transcriptome and phenotypes
Capabilities of the CCi-Mobile Cochlear Implant Research Platform for Real-Time Sound Coding
Authors: Azadpour Mahan , Saba Juliana , Hansen John H.L. , Svirsky Mario A.
Published: December 2022

One important obstacle to optimizing fitting and sound coding for auditory implants is lack of flexible, powerful and portable platforms that can be used in real-world listening environments by implanted patients. The clinical processors and the typically available research tools either do not have sufficient computational power and flexibility or are not portable. In response to this need, the Center for Robust Speech Systems (CRSS) at the University of Texas at Dallas has developed CCI-Mobile, in collaboration with the Laboratory for Translational Auditory Research at New York University School of Medicine and the Binaural Hearing and Speech Laboratory at the University of Wisconsin-Madison. The CCI-Mobile platform provides unique flexibility to implement a variety of real-time sound coding algorithms in real-world environments, including algorithms that require synchronized binaural stimulation. In this paper, we will describe the overall architecture of the CCI-Mobile platform and provide practical considerations for designing real-time sound coding algorithms with this platform. CCI-Mobile is under development and future generations may provide further functionality, beyond what is described in this paper.
Structural basis for translation inhibition by the glycosylated antimicrobial peptide Drosocin fromDrosophila melanogaster
Authors: Koller Timm O. , Morici Martino , Berger Max , Safdari Haaris A. , Lele Deepti S. , Beckert Bertrand , Kaur Kanwal J. , Wilson Daniel N.
Published: December 2022

The proline-rich antimicrobial peptide (PrAMP) drosocin is produced byDrosophilaspecies to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation influences not only cellular uptake of the peptide, but also interacts with its intracellular target, the ribosome. Cryo-electron microscopy structures of glycosylated drosocin on the ribosome at 2.1-2.8 Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base-pair with A752. Collectively, our study provides novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provides a structural basis for future development of this class of antimicrobials.
Neisseria gonorrhoeaeco-opts C4b-binding protein to enhance complement-independent survival from neutrophils
Authors: Werner Lacie M. , Alcott Allison , Mohlin Frida , Ray Jocelyn C. , Dufrisne Meagan Belcher , Smirnov Asya , Columbus Linda , Blom Anna M. , Criss Alison K.
Published: December 2022

Neisseria gonorrhoeae(Gc) is a human-specific pathogen that causes the sexually transmitted infection gonorrhea. Gc survives in neutrophil-rich gonorrheal secretions, and recovered bacteria predominantly express phase-variable, surface-expressed opacity-associated (Opa) proteins (Opa+). However, expression of Opa proteins like OpaD decreases Gc survival when exposed to human neutrophilsex vivo. Here, we made the unexpected observation that incubation with normal human serum, which is found in inflamed mucosal secretions, enhances survival of Opa+ Gc from primary human neutrophils. We directly linked this phenomenon to a novel complement-independent function for C4b-binding protein (C4BP). When bound to the bacteria, C4BP was necessary and sufficient to suppress Gc-induced neutrophil reactive oxygen species production and prevent neutrophil phagocytosis of Opa+ Gc. This research identifies for the first time a complement-independent role for C4BP in enhancing the survival of a pathogenic bacterium from phagocytes, thereby revealing how Gc exploits inflammatory conditions to persist at human mucosal surfaces.

Author Summary

Gonorrhea is considered an urgent threat to public health with an estimated 98 million cases occurring annually worldwide, growing antimicrobial resistance, and the absence of a gonococcal vaccine. Currently, we do not understand howN. gonorrhoeaeexpressing opacity (Opa) proteins survive neutrophil defenses and are recovered viable from infected patients. Here, we investigated how soluble elements of gonorrhea infection, present in human serum, contribute toN. gonorrhoeaesurvival from neutrophils. We found that the serum component C4b-binding protein (C4BP) protectsN. gonorrhoeaefrom neutrophil killing and suppresses neutrophil activation. C4BP limited neutrophil phagocytosis ofN. gonorrhoeaethat expressed Opa proteins that bound to neutrophil receptors of the CEACAM family. This work provides novel insight into the interplay between the noncellular and cellular aspects of the innate immune response toN. gonorrhoeae.
Incidence, antifungal resistance properties, and virulence traits of candida species isolated from HIV/AIDS Patients from the hospital system in Kenya
Authors: Miruka Haron N. , Eric Omwenga O. , Musyoki Stanslaus , Awuor Silas O.
Published: December 2022

Candidiasis is the most common fungal infection in hospitalized patients with acquired immune deficiency syndrome resulting to morbidity and mortality. This study aimed at characterizing, incidence, susceptibility, resistance genes, antibiofilm activity, and virulence traits ofCandidaspecies isolated from HIV-Infected patients. One hundred and eighty-one samples were collected and cultured on Sabouraud Dextrose Agar, biochemical tests and confirmed using automated Vitek-2®Compact bioMérieux followed by susceptibility tests. were done by use of various conventional antifungals against the isolates using standard procedures. Virulence factors, biofilm formations and resistance genes of Candida strains were determined. Out of the 181 samples, 46 were identified asCandida spp., 20C. albicans(43.5%), 6C. tropicalis(13.0%), 8C. krusei(17.4%), 4C. glabrata(8.7%), 3C. famata(6.5%), 3C. parapsilosis(6.5%), and2 C. guilliermondii(4.3%). All theCandida albicansisolated were both Gram positive and Germ test tube test positive. Eighteen (90%) of the isolates were susceptible to Clotrimazole at a concentration of 5 μg/mL – 10μg/mL followed by 17 (85%) isolates to Panosoconazole at a concentration of 0.002 μg/mL – 5μg/mL. Eight (40.0 %) of theCandida albicansisolates possessed the gene (cdr1) that was observed at 286 bp. Virulence enzymes was determined in which 100% produced Haemolysin, followed by proteinase (75.0%), phospholipase (50%), coagulase at (50%) and lastly capsulase (25.0%). Fluconazole and Clotrimazole did not inhibit growth ofC. albicansat high concentrations but from our study, it was deduced that they inhibit biofilm formation at lower concentrations.C. albicansisolates were resistant to multiple antifungal including those commonly used in the management on HIV/AIDs patient. This attributed to resistant genes and produced various virulence factors that were found to be present in the isolates. Therefore, there is a need to carry out regular surveillance on antifungal drug resistance.
Endosomal egress and intercellular transmission of hepatic ApoE-containing lipoproteins and its exploitation by the hepatitis C virus
Authors: Pham Minh-Tu , Lee Ji-Young , Ritter Christian , Thielemann Roman , Haselmann Uta , Funaya Charlotta , Laketa Vibor , Rohr Karl , Bartenschlager Ralf
Published: December 2022

Liver-generated plasma Apolipoprotein E (ApoE)-containing lipoproteins (LPs) (ApoE-LPs) play central roles in lipid transport and metabolism. Perturbations of ApoE can result in several metabolic disorders and ApoE genotypes have been associated with multiple diseases. ApoE is synthesized at the endoplasmic reticulum and transported to the Golgi apparatus for LP assembly; however, ApoE-LPs transport from there to the plasma membrane is largely unknown. Here, we established an integrative imaging approach based on a fully functional fluorescently tagged ApoE. We found that ApoE-LPs accumulate in CD63-positive endosomes of hepatocytes. In addition, we observed the co-egress of ApoE-LPs and extracellular vesicles (EVs) along the late endosomal trafficking route. Moreover, complexes of ApoE-LPs and CD63-positive EVs were found to be transmitted from cell to cell. Given the important role of ApoE in viral infections, we studied the hepatitis C virus (HCV) and found that the viral replicase protein NS5A is enriched in ApoE-containing intraluminal vesicles. Interaction between NS5A and ApoE is required for the efficient release of EVs containing viral RNA. These vesicles are transported along the endosomal ApoE egress pathway. Taken together, our data argue for endosomal egress and transmission of hepatic ApoE-LPs, a pathway that is hijacked by HCV. Given the more general role of EV-mediated cell-to-cell communication, these insights provide new starting points for research into the pathophysiology of ApoE-related metabolic and infection-related disorders.

Author Summary

The post-Golgi egress pathway of hepatocyte-derived ApoE-containing lipoproteins (ApoE-LPs) is largely unknown. By using integrative imaging analyses, we show that ApoE-LPs are enriched in CD63-positive endosomes suggesting that these endosomes might be a central hub for the storage of ApoE-LPs from which they are released into the circulation. In addition, we provide evidence for the co-egress of ApoE-LPs with extracellular vesicles (EVs) along the late endosomal route and their transfer from cell to cell. This pathway is hijacked by the hepatitis C virus that induces the production of ApoE-associated EVs containing viral RNA. Given the important role of ApoE in multiple metabolic, degenerative and infectious diseases, and the role of EVs in cell-to-cell communication, these results provide important information how perturbations of ApoE might contribute to various pathophysiologies.
ESCRT pathway-dependent MVBs contribute to the morphogenesis of the fungusArthrobotrys oligospora
Authors: Tian Mengqing , Huang Jinrong , Cui Peijie , Li Guohong , Zhang Keqin , Wang Xin
Published: December 2022

Ammonia opens trap formation in the nematode-trapping (NT) fungusArthrobotrys oligospora, an intriguing morphological switch in NT fungi, where saprophytic mycelia are converted to pathogenic organs. Endocytosis plays a prominent role in nutrient uptake, signaling cascades, and maintenance of cellular homeostasis in higher eukaryotes. Here, we demonstrate that ammonia efficiently promotes endocytosis via the formation of 3D-adhesive mycelial nets inA. oligospora. Trap production is followed by the presence of massive multivesicular bodies (MVBs) and membrane rupture and repair. Additionally, both the ubiquitin-proteasome system and the endosomal sorting complex for transport (ESCRT) pathway are immediately linked to endocytosis regulation and MVB formation in ammonia-induced trap formation. Moreover, disruption of the ESCRT-1 complex subunit proteins AoHse and AoVps27 led to the complete loss of membrane endocytosis and trap formation. Finally, the deletion of the deubiquitinase AoSst2 caused a significant reduction in the number of trap structures produced in response to exposure to ammonia or nematodes. Overall, our results increase our knowledge of the molecular mechanisms underlying the phenotypic changes in the NT fungal group, demonstrating that the endocytosis-ESCRT-MVB pathway participates in the regulation of trapping organs.

Author Summary

The lifestyle switch of nematode-trapping (NT) fungi is a significant event that increases their pathogenicity to nematode prey, which has resulted in large losses to agricultural crops worldwide. Here, we describe the molecular mechanism underlying how this fungal group forms a NT structure in response to ammonia, a widely preferred nitrogen source in soil niches. Ammonia enhances the endocytosis process, ubiquitin-proteasome system, and endosomal sorting complex for transport (ESCRT) pathway of the model NT fungusA. oligospora, thereby generating enriched multivesicular bodies (MVBs) during trap formation. In this process, the cell membrane morphology is remarkably damaged and then repaired. We further found that disruption of the ESCRT-0 subcomplex or ubiquitinase severely blocked trap production and membrane reorganization. Our study provides a new understanding of endocytosis-ESCRT-MVB flux in the transition of fungal NT organs.
Phylogenetic inference using Generative Adversarial Networks
Authors: Smith Megan L. , Hahn Matthew W.
Published: December 2022

Motivation

The application of machine learning approaches in phylogenetics has been impeded by the vast model space associated with inference. Supervised machine learning approaches require data from across this space to train models. Because of this, previous approaches have typically been limited to inferring relationships among unrooted quartets of taxa, where there are only three possible topologies. Here, we explore the potential of generative adversarial networks (GANs) to address this limitation. GANs consist of a generator and a discriminator: at each step, the generator aims to create data that is similar to real data, while the discriminator attempts to distinguish generated and real data. By using an evolutionary model as the generator, we use GANs to make evolutionary inferences. Since a new model can be considered at each iteration, heuristic searches of complex model spaces are possible. Thus, GANs offer a potential solution to the challenges of applying machine learning in phylogenetics.

Results

We developed phyloGAN, a GAN that infers phylogenetic relationships among species. phy-loGAN takes as input a concatenated alignment, or a set of gene alignments, and infers a phylogenetic tree either considering or ignoring gene tree heterogeneity. We explored the performance of phyloGAN for up to fifteen taxa in the concatenation case and six taxa when considering gene tree heterogeneity. Error rates are relatively low in these simple cases. However, run times are slow and performance metrics suggest issues during training. Future work should explore novel architectures that may result in more stable and efficient GANs for phylogenetics.

Availability

phyloGAN is available on github:https://github.com/meganlsmith/phyloGAN/.

Contact

mls16@indiana.edu
Golgi fragmentation - One of the earliest organelle phenotypes in Alzheimer’s disease neurons
Authors: Haukedal Henriette , Corsi Giulia I. , Gadekar Veerendra P. , Doncheva Nadezhda T. , Kedia Shekhar , de Haan Noortje , Chandrasekaran Abinaya , Jensen Pia , Schiønning Pernille , Vallin Sarah , Marlet Frederik Ravnkilde , Poon Anna , Pires Carlota , Agha Fawzi Khoder , Wandall Hans H. , Cirera Susanna , Simonsen Anja Hviid , Nielsen Troels Tolstrup , Nielsen Jørgen Erik , Hyttel Poul , Muddashetty Ravi , Aldana Blanca I. , Gorodkin Jan , Nair Deepak , Meyer Morten , Larsen Martin Røssel , Freude Kristine
Published: December 2022

Alzheimer’s disease (AD) is the most common cause of dementia, with no current cure. Consequently, alternative approaches focusing on early pathological events in specific neuronal populations, besides targeting the well-studied Amyloid beta (Aβ) accumulations and Tau tangles, are needed. In this study, we have investigated disease phenotypes specific to glutamatergic forebrain neurons and mapped the timeline of their occurrence, by implementing familial and sporadic human induced pluripotent stem cell models as well as the 5xFAD mouse model. We recapitulated characteristic late AD disease phenotypes, such as increased Aβ secretion and Tau hyperphosphorylation, as well as previously well documented mitochondrial and synaptic deficits. Intriguingly, we identified Golgi fragmentation as one of the earliest AD phenotypes, indicating potential impairments in protein processing and post-translational modifications. Computational analysis of RNA sequencing data revealed differentially expressed genes involved in glycosylation and glycan patterns, whilst total glycan profiling revealed minor glycosylation differences. This indicates general robustness of glycosylation besides the observed fragmented morphology. Importantly, we identified that genetic variants in Sortilin-related receptor 1 (SORL1) associated with AD could aggravate the Golgi fragmentation and subsequent glycosylation changes. In summary, we identified Golgi fragmentation as one of the earliest disease phenotypes in AD neurons in variousin vivoandin vitrocomplementary disease models, which can be exacerbated via additional risk variants inSORL1.

Abstract Figure
Genetic validation ofPfFKBP35 as an antimalarial drug target
Authors: Thommen Basil T. , Dziekan Jerzy M. , Achcar Fiona , Tjia Seth , Passecker Armin , Buczak Katarzyna , Gumpp Christin , Schmidt Alexander , Rottmann Matthias , Grüring Christof , Marti Matthias , Bozdech Zbynek , Brancucci Nicolas M. B.
Published: December 2022

Plasmodium falciparumaccounts for the majority of over 600’000 malaria-associated deaths annually. Parasites resistant to nearly all antimalarials have emerged and the need for drugs with alternative modes of action is thus undoubted. The FK506-binding proteinPfFKBP35 has gained attention as a promising drug target due to its high affinity to the macrolide compound FK506 (tacrolimus). Whilst there is considerable interest in targetingPfFKBP35 with small molecules, a genetic validation of this factor as a drug target is missing and its function in parasite biology remains elusive. Here, we show that limitingPfFKBP35 levels are lethal toP. falciparumand result in a delayed death-like phenotype that is characterized by defective ribosome homeostasis and stalled protein synthesis. Our data furthermore suggest that FK506, unlike the action of this drug in model organisms, exerts its anti-proliferative activity in aPfFKBP35-independent manner and, using cellular thermal shift assays, we identify putative FK506-targets beyondPfFKBP35. In addition to revealing first insights into the function ofPfFKBP35, our results show that FKBP-binding drugs can adopt non-canonical modes of action – with major implications for the development of FK506-derived molecules active againstPlasmodiumparasites and other eukaryotic pathogens.
5-HT1Aand 5-HT2Breceptor interaction and co-clustering regulates serotonergic neuron excitability
Authors: Benhadda Amina , Delhaye Célia , Moutkine Imane , Marques Xavier , Russeau Marion , Magueresse Corentin Le , Roumier Anne , Lévi Sabine , Maroteaux Luc
Published: December 2022

Many psychiatric diseases including depression, schizophrenia and anxiety have been associated with serotonin (5-HT) neuron dysfunction. Pacemaker-like firing of raphe 5-HT neurons was proposed to be under unique 5-HT1Areceptor-mediated autoinhibition. We previously showed that 5-HT2Breceptors were expressed by 5-HT neurons together with 5-HT1Areceptors. However, functional consequences on 5-HT neurons of putative interaction between these receptors are unknown. Using co-immunoprecipitation, BRET, confocal and super-resolution microscopy in hippocampal and 5-HT neurons, we present converging evidence that 5-HT1Aand 5-HT2Breceptors can form heterodimers and co-cluster at the surface of dendrites. 5-HT2Breceptor clusters were redistributed upon 5-HT1Areceptor expression supporting functional interactions between the two receptors. Furthermore, 5-HT2Breceptor expression prevented agonist-induced internalization of 5-HT1Areceptors, whereas 5-HT1Areceptors mimicked the clustering effect of 5-HT2Breceptor stimulation on its surface expression. The functional impact of this interactionin-vivowas assessed by recording 5-HT neuron excitability from mice lacking 5-HT2Breceptors in 5-HT neurons. Upon 5-HT1Areceptor stimulation, the firing activity of 5-HT neurons was increased in the absence of 5-HT2Breceptors and decreased in their presence through regulation of SK channels, thus demonstrating functional output of this interaction in controlling 5-HT neuron firing activity.
Effect of ethanol exposurein uteroon infant mice gut microbiotas assessed by nanopore and illumina sequencing
Authors: Pedroso-Roussado Cristiano , Guppy Fergus , Brissett Nigel , Bowler Lucas , Inacio Joao
Published: December 2022

The gut microbiome plays a vital role in host homeostasis and understanding of its biology is essential for a better comprehension of the etiology of disorders such as Foetal Alcohol Spectrum Disorder. Foetal Alcohol Spectrum Disorder represents a cluster of abnormalities including growth deficiencies and neurological impairments, which are not easily diagnosed nor treated. Here the effect of ethanol exposurein uteroon the gut microbial profiles of 16 infant mice (nine exposedin uteroand seven non-exposed) was assessed by targeted nanopore sequencing and Illumina sequencing approaches. The nanopore sequencing was implemented using MinION system targeting PCR-amplified amplicons made from the full-length 16S rRNA gene. The Illumina sequencing was performed using Miseq system targeting the V3-V4 region of the 16S rRNA gene. Ethanol exposure did not affect the microbial profiles. Several low prevalent taxa, likeAkkermansia muciniphila, were detected but further studies must be performed to detail the effect of ethanol exposure to these taxa since no clear pattern was detected throughout this study.

Importance

Detailed knowledge about the interactions between gut microbes and the developing nervous system is still scarce. Foetal Alcohol Spectrum Disorder represents a clinically relevant set of conditions with cumbersome diagnostic and treatment. In this work the microbial profiles of infant mice gut exposed to ethanolin uterowere analysed through third-generation Illumina and optimized next-generation nanopore sequencing technologies. The fungal (albeit not detected) and bacterial microbial profiles here obtained through nanopore and Illumina sequencing represent a technological and biological advancement towards a better comprehension of the microbial landscape in Foetal Alcohol Spectrum Disorder at early post-natal periods.
Molecular basis and design principles of a system for switchable front-rear polarity and directional migration
Authors: Menezes Carreira Luís António , Szadkowski Dobromir , Lometto Stefano , Hochberg Georg K.A. , Søgaard-Andersen Lotte
Published: December 2022

During cell migration, front-rear polarity is spatiotemporally regulated; however, the underlying design of regulatory interactions vary. In rod-shapedMyxococcus xanthuscells, a spatial toggle switch dynamically regulates front-rear polarity. The polarity module establishes front-rear polarity by guaranteeing front pole-localization of the small GTPase MglA. Conversely, the Frz chemosensory system, by acting on the polarity module, causes polarity inversions. MglA localization depends on the RomR/RomX GEF and MglB/RomY GAP complexes that localize asymmetrically to the poles by unknown mechanisms. Here, we show that RomR and the MglB and MglC roadblock domain proteins generate a positive feedback by forming a RomR/MglC/MglB complex, thereby establishing the rear pole with high GAP activity that is non-permissive to MglA. MglA at the front engages in negative feedback that inhibits the RomR/MglC/MglB positive feedback allosterically, thus ensuring low GAP activity at this pole. These findings unravel the design principles of a system for switchable front-rear polarity.
Conformational restriction shapes inhibition of a multidrug efflux adaptor protein
Authors: Lewis Benjamin Russell , Uddin Muhammad R. , Moniruzzaman Mohammad , Kuo Katie M. , Higgins Anna J. , Shah Laila M. N. , Sobott Frank , Parks Jerry M. , Hammerschmid Dietmar , Gumbart James C. , Zgurskaya Helen I. , Reading Eamonn
Published: December 2022

Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system fromEscherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.
Color and gloss constancy under diverse lighting environments
Authors: Morimoto Takuma , Akbarinia Arash , Storrs Katherine , Cheeseman Jacob R. , Smithson Hannah E. , Gegenfurtner Karl R. , Fleming Roland W.
Published: December 2022

When we look at an object, we simultaneously see how glossy or matte it is, how light or dark, and what color. Yet, at each point on the object’s surface, both diffuse and specular reflections are mixed in different proportions, resulting in substantial spatial chromatic and luminance variations. To further complicate matters, this pattern changes radically when the object is viewed under different lighting conditions. The purpose of this study was to simultaneously measure our ability to judge color and gloss using an image set capturing diverse object and illuminant properties. Participants adjusted the hue, lightness, chroma, and specular reflectance of a reference object so that it appeared to be made of the same material as a test object. Critically, the two objects were presented under different lighting environments. We found that hue matches were highly accurate, except for under a chromatically atypical illuminant. Chroma and lightness constancy were generally poor, but these failures correlated well with simple image statistics. Gloss constancy was particularly poor, and these failures were only partially explained by reflection contrast. Importantly, across all measures, participants were highly consistent with one another in their deviations from constancy. Although color and gloss constancy hold well in simple conditions, the variety of lighting and shape in the real world presents significant challenges to our visual system’s ability to judge intrinsic material properties.
Wnt-associated adult stem cell marker Lgr6 is required for osteogenesis and fracture healing
Authors: Doherty Laura , Wan Matthew , Peterson Anna , Youngstrom Daniel W. , King Justin S. , Kalajzic Ivo , Hankenson Kurt D. , Sanjay Archana
Published: December 2022

Despite the remarkable regenerative capacity of skeletal tissues, nonunion of bone and failure of fractures to heal properly presents a significant clinical concern. Stem and progenitor cells are present in bone and become activated following injury; thus, elucidating mechanisms that promote adult stem cell-mediated healing is important. Wnt-associated adult stem marker Lgr6 is implicated in the regeneration of tissues with well-defined stem cell niches in stem cell-reliant organs. Here, we demonstrate that Lgr6 is dynamically expressed in osteoprogenitors in response to fracture injury. Using anLgr6-null mouse model, we find thatLgr6expression is necessary for maintaining bone volume and efficient postnatal bone regeneration in adult mice. Skeletal progenitors isolated fromLgr6-nullmice have reduced colony-forming potential and reduced osteogenic differentiation capacity due to attenuated cWnt signaling.Lgr6-null mice consist of a lower proportion of self-renewing stem cells. In response to fracture injury,Lgr6-nullmice have deficient proliferation of periosteal progenitors and reduced ALP activity. Further, analysis of bone regeneration phase and remodeling phase of fracture healing in Lgr6-null mice showed impaired endochondral ossification and reduced mineralization. We propose that in contrast to not being required for successful skeletal development Lgr6-positive cells have a direct role in endochondral bone repair.
Protein-protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning
Authors: MacRae Mark R. , Puvanendran Dhenesh , Haase Max A. B. , Coudray Nicolas , Kolich Ljuvica , Lam Cherry , Baek Minkyung , Bhabha Gira , Ekiert Damian C.
Published: December 2022

The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer that protects the cell from various external stressors, such as antibiotics. The Mla transport system is implicated in theMaintenance of outer membraneLipidAsymmetry and is thought to mediate retrograde phospholipid transport across the cell envelope. This system uses a shuttle-like mechanism to move lipids between the MlaFEDB inner membrane complex and the MlaA-OmpF/C OM complex, via a periplasmic lipid-binding protein, MlaC. MlaC binds to MlaD and MlaA, but the underlying protein-protein interactions that facilitate lipid transfer are not well understood. Here, we take an unbiased deep mutational scanning approach to map the fitness landscape of MlaC, which provides insights into important functional sites. Combining this analysis with AlphaFold2 structure predictions and binding experiments, we map the MlaC-MlaA and MlaC-MlaD protein-protein interfaces. Our results suggest that the MlaD and MlaA binding surfaces on MlaC overlap to a large extent, leading to a model in which MlaC can only bind one of these proteins at a time. Low-resolution cryo-electron microscopy (cryo-EM) maps of MlaC bound to MlaFEDB suggest that at least two MlaC molecules can bind to MlaD at once, in a conformation consistent with AlphaFold2 predictions. These data lead us to a model for MlaC interaction with its binding partners and insights into lipid transfer steps that underlie phospholipid transport between the inner and outer membranes.
ATP diffusional gradients are sufficient to maintain bioenergetic homeostasis in synaptic boutons lacking mitochondria
Authors: Kuznetsov Ivan A. , Kuznetsov Andrey V.
Published: December 2022

Previous work on mitochondrial distribution in axons has shown that approximately half of the presynaptic release sites do not contain mitochondria, raising the question of how the boutons that do not contain mitochondria are supplied with ATP. Here, we develop and apply a mathematical model to study this question. Specifically, we investigate whether diffusive transport of ATP is sufficient to support the exocytic functionality in synaptic boutons which lack mitochondria. Our results demonstrate that the difference in ATP concentration between a bouton containing a mitochondrion and a neighboring bouton lacking a mitochondrion is only approximately 0.4%, which is still 3.75 times larger than the ATP concentration minimally required to support synaptic vesicle release. This work therefore suggests that passive diffusion of ATP is sufficient to maintain the functionality of boutons which do not contain mitochondria.
Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models
Authors: Watson Joseph L. , Juergens David , Bennett Nathaniel R. , Trippe Brian L. , Yim Jason , Eisenach Helen E. , Ahern Woody , Borst Andrew J. , Ragotte Robert J. , Milles Lukas F. , Wicky Basile I. M. , Hanikel Nikita , Pellock Samuel J. , Courbet Alexis , Sheffler William , Wang Jue , Venkatesh Preetham , Sappington Isaac , Torres Susana Vázquez , Lauko Anna , De Bortoli Valentin , Mathieu Emile , Barzilay Regina , Jaakkola Tommi S. , DiMaio Frank , Baek Minkyung , Baker David
Published: December 2022

There has been considerable recent progress in designing new proteins using deep learning methods1–9. Despite this progress, a general deep learning framework for protein design that enables solution of a wide range of design challenges, includingde novobinder design and design of higher order symmetric architectures, has yet to be described. Diffusion models10,11have had considerable success in image and language generative modeling but limited success when applied to protein modeling, likely due to the complexity of protein backbone geometry and sequence-structure relationships. Here we show that by fine tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding, and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold Diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of new designs. In a manner analogous to networks which produce images from user-specified inputs, RFdiffusionenables the design of diverse, complex, functional proteins from simple molecular specifications.