title: Production of recombinant human acid α-glucosidase with mannosidic N-glycans in α-mannosidase I mutant rice cell suspension culture

abstract: High-mannose glycans, containing 6-9 mannose residues, are favorable for in vitro mannose phosphorylation to produce Mannose-6-phosphate (M6P) residues. These are important for lysosomal enzyme targeting and essential for uptake. Golgi -mannosidase-I mediates mannose trimming in the N-glycosylation pathway. In this study, I used mutant rice with a T-DNA insertion in the Os04g0606400 ({Delta}-manI) gene to produce recombinant human acid -glucosidase (rhGAA) for enzyme replacement therapy to treat Pompe disease. After characterization of {Delta}-manI mutant rice, the gene encoding rhGAA was introduced into mutant calli by Agrobacterium-mediated transformation. Integration of the target sequence into the rice genome was detected by genomic DNA PCR. Expression of rhGAA from {Delta}-manI mutant ({Delta}-manI-GAA) and its secretion into culture media were confirmed by western blot analysis. The N-glycosylation pattern of purified {Delta}-manI-GAA was analysed by MALDI-TOF mass spectrometry. This showed that the high-mannose type N-glycan with man8 (63.8%) was the most abundant form, followed by Man7 (22.5%), GnGnXF3 (6.7%), Man6 (5.4%), and Man5 (1.6%). The results suggest the successful production of rhGAA with N-glycan containing 6-8 mannose residue in the {Delta}-manI mutant rice cell suspension culture.


title: Genetic background influences survival of infections with Salmonella enterica serovar Typhimurium in the Collaborative Cross

abstract:
Salmonella infections typically cause self-limiting gastroenteritis, but in some individuals these bacteria can spread systemically and cause disseminated disease. Salmonella Typhimurium (STm), which causes severe systemic disease in most inbred mice, has been used as a model for disseminated disease. To screen for new infection phenotypes across a range of host genetics, we orally infected 32 Collaborative Cross (CC) mouse strains with STm and monitored their disease progression for seven days by telemetry. Our data revealed a broad range of phenotypes across CC strains in many parameters including survival, bacterial colonization, tissue damage, complete blood counts (CBC), and serum cytokines. Eighteen CC strains survived to day 7, while fourteen susceptible strains succumbed to infection before day 7. Several CC strains had sex differences in survival and colonization. Surviving strains had lower pre-infection baseline temperatures and were less active during their daily active period. Core body temperature disruptions were detected earlier after STm infection than activity disruptions, making temperature a better detector of illness. All CC strains had STm in spleen and liver, but susceptible strains were more highly colonized. Tissue damage was weakly negatively correlated to survival. We identified loci associated with survival on Chromosomes (Chr) 1, 2, 4, 7. Polymorphisms in Ncf2 and Slc11a1, known to reduce survival in mice after STm infections, are located in the Chr 1 interval, and the Chr 7 association overlaps with a previously identified QTL peak called Ses2. We identified two new genetic regions on Chr 2 and 4 associated with susceptibility to STm infection. Our data reveal the diversity of responses to STm infection across a range of host genetics and identified new candidate regions for survival of STm infection.

Author SummarySalmonella Typhimurium (STm) infections typically cause self-limiting diarrheal symptoms, but in some individuals, the bacteria can spread throughout the body and cause life-threatening infection. We used a population of genetically different mice (Collaborative Cross) to identify their range of responses to STm infection. We identified a broad range of outcomes across these different mice, including a group of mice susceptible to lethal infection and a group that survived our 7 day study. We found that mice that survived STm infection had a cooler core body temperature before infection than susceptible mice, while remaining active. Thus, body temperature, rather than activity, appears to be a better predictor of poor outcomes after STm infection. We identified several regions of the mouse genome that are associated with outcome after STm infection. One of these regions, mouse Chromosome (Chr) 1 has genes that are already known to influence susceptibility to STm infection. Two other regions that we identified to influence survival after STm infection, located on mouse Chr 2 and 4, are novel and contain numerous genes of interest that may be linked to susceptibility. Our work defines the utility of exploring how host genetic diversity influences infection outcomes with bacterial pathogens.

category: genetics


title: Biologically informed deep learning to infer gene program activity in single cells

abstract: The increasing availability of large-scale single-cell datasets has enabled the detailed description of cell states across multiple biological conditions and perturbations. In parallel, recent advances in unsupervised machine learning, particularly in transfer learning, have enabled fast and scalable mapping of these new single-cell datasets onto reference atlases. The resulting large-scale machine learning models however often have millions of parameters, rendering interpretation of the newly mapped datasets challenging. Here, we propose expiMap, a deep learning model that enables interpretable reference mapping using biologically understandable entities, such as curated sets of genes and gene programs. The key concept is the substitution of the uninterpretable nodes in an autoencoders bottleneck by labeled nodes mapping to interpretable lists of genes, such as gene ontologies, biological pathways, or curated gene sets, for which activities are learned as constraints during reconstruction. This is enabled by the incorporation of predefined gene programs into the reference model, and at the same time allowing the model to learn de novo new programs and refine existing programs during reference mapping. We show that the model retains similar integration performance as existing methods while providing a biologically interpretable framework for understanding cellular behavior. We demonstrate the capabilities of expiMap by applying it to 15 datasets encompassing five different tissues and species. The interpretable nature of the mapping revealed unreported associations between interferon signaling via the RIG-I/MDA5 and GPCRs pathways, with differential behavior in CD8+ T cells and CD14+ monocytes in severe COVID-19, as well as the role of annexins in the cellular communications between lymphoid and myeloid compartments for explaining patient response to the applied drugs. Finally, expiMap enabled the direct comparison of a diverse set of pancreatic beta cells from multiple studies where we observed a strong, previously unreported correlation between the unfolded protein response and asparagine N-linked glycosylation. Altogether, expiMap enables the interpretable mapping of single cell transcriptome data sets across cohorts, disease states and other perturbations.

category: bioinformatics


title: Mechanistic origin of different binding affinities of SARS-CoV and SARS-CoV-2 spike RBDs to human ACE2

abstract: The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein mediates viral entry into host cells through binding to the cell-surface receptor angiotensin-converting enzyme 2 (ACE2). It has been shown that SARS-CoV-2 RBD (RBDCoV2) has a higher binding affinity to human ACE2 than its highly homologous SARS-CoV RBD (RBDCoV), for which the mechanistic reasons still remain to be elucidated. Here, we used the multiple-replica molecular dynamics (MD) simulations, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations, and interface residue contact network (IRCN) analysis approach to explore the mechanistic origin of different ACE2 binding affinities of these two RBDs. The results demonstrate that, when compared to the RBDCoV2-ACE2 complex, the RBDCoV-ACE2 complex features the enhanced overall structural fluctuations and inter-protein positional movements and increased conformational entropy and diversity. The inter-protein electrostatic attractive interactions are a dominant force in determining the high ACE2 affinities of both RBDs, while the significantly strengthened electrostatic forces of attraction of ACE2 to RBDCoV2 determine the higher ACE2 binding affinity of RBDCoV2 than of RBDCoV. Comprehensive comparative analyses of the residue binding free energy components and IRCNs reveal that, although any RBD residue substitution involved in the charge change can significantly impact the inter-protein electrostatic interaction strength, it is the substitutions at the RBD interface that lead to the overall stronger electrostatic attractive force of RBDCoV2-ACE2, which in turn not only tightens the interface packing and suppresses the dynamics of RBDCoV2-ACE2, but also enhances the ACE2 binding affinity of RBDCoV2 compared to that of RBDCoV. Since the RBD residue substitutions involving gain/loss of the positively/negatively charged residues, in particular those near/at the binding interfaces with the potential to form hydrogen bonds and/or salt bridges with ACE2, can greatly enhance the ACE2 binding affinity, the SARS-CoV-2 variants carrying such mutations should be paid special attention to.

category: biophysics


title: An mRNA vaccine candidate for the SARS-CoV-2 Omicron variant

abstract: The newly emerged Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains more than 30 mutations on the spike protein, 15 of which are located within the receptor binding domain (RBD). Consequently, Omicron is able to extensively escape existing neutralizing antibodies and may therefore compromise the efficacy of current vaccines based on the original strain, highlighting the importance and urgency of developing effective vaccines against Omicron. Here we report the rapid generation and evaluation of an mRNA vaccine candidate specific to Omicron. This mRNA vaccine encodes the RBD of Omicron (designated RBD-O) and is formulated with lipid nanoparticle. Two doses of the RBD-O mRNA vaccine efficiently induce neutralizing antibodies in mice; however, the antisera are effective only on the Omicron variant but not on the wildtype and Delta strains, indicating a narrow neutralization spectrum. It is noted that the neutralization profile of the RBD-O mRNA vaccine is opposite to that observed for the mRNA vaccine expressing the wildtype RBD (RBD-WT). Our work demonstrates the feasibility and potency of an RBD-based mRNA vaccine specific to Omicron, providing important information for further development of bivalent or multivalent SARS-CoV-2 vaccines with broad-spectrum efficacy.

category: microbiology


title: A potent SARS-CoV-2 neutralizing antibody recognizing a conserved epitope with broad mutant variant and SARS-CoV activity.

abstract: COVID-19 is the deadliest respiratory virus pandemic since 1918 and the latest of several coronavirus epidemics and pandemics in recent years. Despite the unprecedented response by both the government and private sectors to develop vaccines and therapies, the evolution of SARS-CoV-2 variants resistant to these interventions reveals a crucial need for therapeutics that maintain their efficacy against current and future mutant variants. Here we describe a SARS-CoV-2 neutralizing antibody, ABP-310, with potent activity against all variants tested including the Omicron variant. ABP-310 also displays potent neutralizing activity against SARS-CoV, highlighting the conserved nature of the ABP-310 epitope. By targeting a conserved epitope, we believe that ABP-310 has therapeutic promise not only against the current SARS-CoV-2 variants but would be expected to maintain efficacy against future variants and possibly even novel coronaviruses.


title: Vaccine Protection Against the SARS-CoV-2 Omicron Variant in Macaques

abstract:
BackgroundThe rapid spread of the SARS-CoV-2 Omicron (B.1.1.529) variant, including in highly vaccinated populations, has raised important questions about the efficacy of current vaccines. Immune correlates of vaccine protection against Omicron are not known.

Methods30 cynomolgus macaques were immunized with homologous and heterologous prime-boost regimens with the mRNA-based BNT162b2 vaccine and the adenovirus vector-based Ad26.COV2.S vaccine. Following vaccination, animals were challenged with the SARS-CoV-2 Omicron variant by the intranasal and intratracheal routes.

ResultsOmicron neutralizing antibodies were observed following the boost immunization and were higher in animals that received BNT162b2, whereas Omicron CD8+ T cell responses were higher in animals that received Ad26.COV2.S. Following Omicron challenge, sham controls showed more prolonged virus in nasal swabs than in bronchoalveolar lavage. Vaccinated macaques demonstrated rapid control of virus in bronchoalveolar lavage, and most vaccinated animals also controlled virus in nasal swabs, showing that current vaccines provide substantial protection against Omicron in this model. However, vaccinated animals that had moderate levels of Omicron neutralizing antibodies but negligible Omicron CD8+ T cell responses failed to control virus in the upper respiratory tract. Virologic control correlated with both antibody and T cell responses.

ConclusionsBNT162b2 and Ad26.COV2.S provided robust protection against high-dose challenge with the SARS-CoV-2 Omicron variant in macaques. Protection against this highly mutated SARS-CoV-2 variant correlated with both humoral and cellular immune responses.


title: Predicting Schrödinger's range-shifting cat: Analytic results for the impact of asymmetric environmental dependence on species responses to climate change

abstract: Analytic models for how species will respond to climate change can highlight key parameter dependencies. By mapping equations for population dynamics onto corresponding problems from quantum mechanics with known solutions we derive analytical results for the frequently observed case of asymmetric environmental response curves. We derive expressions in terms of parameters representing climate velocity, dispersal rate, maximum growth rate, niche width, high-frequency climate variability and environmental performance curve skew for three key responses: 1) population persistence, 2) lag between range displacement and climate displacement, 3) location of maximum population sensitivity. Surprisingly, under our model assumptions, the direction of performance curve asymmetry does not strongly contribute to either persistence or lags. A simple metapopulation simulation corroborated this result. Measures to support range-shifting populations may have most benefit where the environmental dependence is shallow, irrespective of whether this is the  leading or  trailing edge. Our results introduce new tools to ecology and illustrate the continued role of analytic theory.

category: ecology


title: Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures

abstract:
Machine learning has proven to be a powerful tool for the identification of distinctive genomic signatures among viral sequences. Such signatures are motifs present in the viral genome that differentiate species or variants. In the context of SARS-CoV-2, the identification of such signatures can contribute to taxonomic and phylogenetic studies, help in recognizing and defining distinct emerging variants, and focus the characterization of functional properties of polymorphic gene products. Here, we study KEVOLVE, an approach based on a genetic algorithm with a machine learning kernel, to identify several genomic signatures based on minimal sets of k-mers. In a comparative study, in which we analyzed large SARS-CoV-2 genome dataset, KEVOLVE performed better in identifying variant-discriminative signatures than several gold-standard reference statistical tools. Subsequently, these signatures were characterized to highlight potential biological functions. The majority were associated with known mutations among the different variants, with respect to functional and pathological impact based on available literature. Notably, we found show evidence of new motifs, specifically in the Omicron variant, some of which include silent mutations, indicating potentially novel, variant-specific virulence determinants. The source code of the method and additional resources are available at: https://github.com/bioinfoUQAM/KEVOLVE.

Author summaryAdvances in cloning and sequencing technologies have yielded a vast repository of viral genomic sequence data. To analyze this complex and massive data, Machine learning, which refers to the development and application of computer algorithms that improve with experience, has proven to be efficient. Although many methods have been developed to classify viruses into different characteristic groups, it is often difficult to explain the predictions of these methods. To overcome this, we are working in our laboratory on the design of machine learning based methods for discriminative signatures identification within viral genomic sequences. These signatures which are a specific motifs to groups of viruses known to be pervasive in their genome, are used to 1) build accurate and explainable prediction tools for pathogens and 2) highlight mutations potentially associated with functional changes. In this paper we present the potential of our latest approach KEVOLVE. We first compare it to three discriminating motif identification tools with data sets covering several SARS-CoV-2 variant genomes. We then focus on the identified motifs by KEVOLVE to analyze the mutations associated with the different variants and the potential changes in biological functions that they may involve.


title: Preclinical Pharmacokinetics and In Vitro Properties of GS-441524, A Potential Oral Drug Candidate for COVID-19 Treatment

abstract: Preclinical pharmacokinetics (PK) and in vitro ADME properties of GS-441524, a potential oral agent for the treatment of Covid-19, were studied. GS-441524 was stable in vitro in liver microsomes, cytosols, and hepatocytes of mice, rats, monkeys, dogs, and humans. The plasma free fractions of GS-441524 were 62-78% across all studied species. The in vitro transporter study results showed that GS-441524 was a substrate of MDR1, BCRP, CNT3, ENT1, and ENT2; but not a substrate of CNT1, CNT2, and ENT4. GS-441524 had a low to moderate plasma clearance (CLp), ranging from 4.1 mL/min/kg in dogs to 26 mL/min/kg in mice; the steady state volume distribution (Vdss) ranged from 0.9 L/kg in dogs to 2.2 L/kg in mice after IV administration. Urinary excretion appeared to be the major elimination process for GS-441524. Following oral administration, the oral bioavailability was 8.3% in monkeys, 33% in rats, 39% in mice, and 85% in dogs. The PK and ADME properties of GS-441524 support its further development as an oral drug candidate.

category: pharmacology and toxicology


title: Comprehensive Epitope Mapping of Broad Sarbecovirus Neutralizing Antibodies

abstract: Omicron sub-lineage BA.2 has rapidly surged globally, accounting for over 60% of recent SARS-CoV-2 infections. Newly acquired RBD mutations and high transmission advantage over BA.1 urge the investigation of BA.2s immune evasion capability. Here, we show that BA.2 causes strong neutralization resistance, comparable to BA.1, in vaccinated individuals plasma. However, BA.2 displays more severe antibody evasion in BA.1 convalescents, and most prominently, in vaccinated SARS convalescents plasma, suggesting a substantial antigenicity difference between BA.2 and BA.1. To specify, we determined the escaping mutation profiles1,2 of 714 SARS-CoV-2 RBD neutralizing antibodies, including 241 broad sarbecovirus neutralizing antibodies isolated from SARS convalescents, and measured their neutralization efficacy against BA.1, BA.1.1, BA.2. Importantly, BA.2 specifically induces large-scale escape of BA.1/BA.1.1-effective broad sarbecovirus neutralizing antibodies via novel mutations T376A, D405N, and R408S. These sites were highly conserved across sarbecoviruses, suggesting that Omicron BA.2 arose from immune pressure selection instead of zoonotic spillover. Moreover, BA.2 reduces the efficacy of S309 (Sotrovimab)3,4 and broad sarbecovirus neutralizing antibodies targeting the similar epitope region, including BD55-5840. Structural comparisons of BD55-5840 in complexes with BA.1 and BA.2 spike suggest that BA.2 could hinder antibody binding through S371F-induced N343-glycan displacement. Intriguingly, the absence of G446S mutation in BA.2 enabled a proportion of 440-449 linear epitope targeting antibodies to retain neutralizing efficacy, including COV2-2130 (Cilgavimab)5. Together, we showed that BA.2 exhibits distinct antigenicity compared to BA.1 and provided a comprehensive profile of SARS-CoV-2 antibody escaping mutations. Our study offers critical insights into the humoral immune evading mechanism of current and future variants.

category: immunology


title: Omicron BA.2 specifically evades broad sarbecovirus neutralizing antibodies


title: EMoMiS: A Pipeline for Epitope-based Molecular Mimicry Search in Protein Structures with Applications to SARS-CoV-2

abstract:
MotivationEpitope-based molecular mimicry occurs when an antibody cross-reacts with two different antigens due to structural and chemical similarities. Molecular mimicry between proteins from two viruses can lead to beneficial cross-protection when the antibodies produced by exposure to one also react with the other. On the other hand, mimicry between a protein from a pathogen and a human protein can lead to auto-immune disorders if the antibodies resulting from exposure to the virus end up interacting with host proteins. While cross-protection can suggest the possible reuse of vaccines developed for other pathogens, cross-reaction with host proteins may explain side effects. There are no computational tools available to date for a large-scale search of antibody cross-reactivity.

ResultsWe present a comprehensive Epitope-based Molecular Mimicry Search (EMoMiS) pipeline for computational molecular mimicry searches. EMoMiS, when applied to the SARS-CoV-2 Spike protein, identified eight examples of molecular mimicry with viral and human proteins. These findings provide possible explanations for (a) differential severity of COVID-19 caused by cross-protection due to prior vaccinations and/or exposure to other viruses, and (b) commonly seen COVID-19 side effects such as thrombocytopenia and thrombophilia. Our findings are supported by previously reported research but need validation with laboratory experiments. The developed pipeline is generic and can be applied to find mimicry for novel pathogens. It has applications in improving vaccine design.

AvailabilityThe developed Epitope-based Molecular Mimicry Search Pipeline (EMoMiS) is available from https://biorg.cs.fiu.edu/emomis/.

Contactgiri@cs.fiu.edu


title: OCTA observation of changes in macular vessel density in diabetic patients and its correlation with diabetic retinopathy staging

abstract:
ObjectiveTo investigate the association between disease progression and OCTA vessel density and other indices in patients with diabetic retinopathy.

MethodsParticipants were selected with the following criteria: 63 patients (100 eyes) diagnosed with type 2 diabetes mellitus, which included 44 patients (72 eyes) with diabetic retinopathy and 19 patients (28 eyes) with type 2 diabetes mellitus and non-diabetic retinopathy (NDR), who were seen at the Eye Hospital China Academy of Chinese Medical Sciences from September 2020 to July 2021. All patients underwent OCTA examination, and FAZ, PERIM, AI, FD, SVD, DVD and other indices were counted.

Results(1) The correlation coefficients of SVD, paracentric SVD, DVD, paracentric DVD and DR processes were: -0.525, -0.586, -0.323, and -0.424 (P< 0.05), respectively, and all were moderately negatively correlated. (2) The correlation coefficients of FAZ and PERIM with DR process were: -0.031, 0.084 (P>0.05), respectively, and not correlated. The correlation coefficients of AI and FD with DR process were: 0.307, -0.459 (P<0.05), and with moderate positive and negative correlations, respectively. (3) The correlation coefficients of FAZ, PERIM, AI and FD with age were: -0.124, -0.052, 0.113, -0.170 (P>0.05), and no correlation, respectively.

ConclusionThe disease progression of DR was moderately correlated with OCTA superficial vessel density and deep vessel density; and moderately correlated with AI and FD. OCTA could assist in the assessment of DR disease progression.

category: neuroscience


title: High-throughput widefield fluorescence imaging of 3D samples using deep learning for 2D projection image restoration

abstract: Fluorescence microscopy has become a core tool for visualizing and quantifying the spatial and temporal dynamics of complex biological processes. Thanks to its low cost and ease-of-use, widefield fluorescent imaging remains one of the most widely used fluorescence microscopy imaging modalities. To accomplish imaging of 3D samples, conventional fluorescence imaging entails acquiring a sequence of 2D images spaced along the z-dimension, typically called a z-stack. Oftentimes, the next step is to project the 3D volume into a single 2D image, as 3D image data can be cumbersome to manage and challenging to analyze and interpret, effectively limiting the utlity of z-dimensional information. Furthermore, z-stack acquisition is often time-consuming and consequently may induce photodamage to the biological sample, which are both major hurdles for its application in experiments that require high-throughput, such as drug screening. As an alternative to z-stacks, axial sweep acquisition schemes have been proposed to circumvent these drawbacks and offers potential of 100-fold faster image acquisition for 3D-samples compared to z-stack acquisition but unfortunately results in blurry, low-quality raw 2D z-projected images. We propose a novel workflow to combine axial z-sweep acquisition with deep learning-based image restoration, ultimately enabling high-throughput and high-quality imaging of complex 3D-samples using 2D projection images. To demonstrate the capabilities of our proposed workflow, we apply it to live-cell imaging of 3D tumor spheroids and find we can produce high-fidelity images appropriate for quantitative analysis. Therefore, we conclude that combining axial z-sweep image acquisition with deep learning-based image restoration enables high-throughput and high-quality fluorescence imaging of complex 3D biological samples.

category: cell biology


title: Control of neocortical memory by long-range inhibition in layer 1

abstract: Mounting evidence identifies layer 1 (L1) as a central site of memory in sensory neocortex. While this work revealed plasticity in several excitatory brain-wide afferent systems, the existence, connectivity and memory-related signaling of long-range inhibitory input to L1 remains elusive. We report that inhibitory afferents from zona incerta project specifically to auditory cortex L1, where they connect selectively to interneurons to disinhibit the cortical circuit and facilitate behavioral memory. Chronic calcium imaging of these synapses identifies a balanced form of plasticity that develops rapidly during threat learning and is characterized by the de novo appearance of negative stimulus responses which transmit most information. Our results therefore pinpoint malleability of long-range (dis)inhibitory afferents to L1 as a key factor for the exquisite computational flexibility of this unique layer.


title: Let's face it: The lateralization of the face perception network as measured with fMRI is not clearly right dominant

abstract: The neural face perception network is distributed across both hemispheres. However, the dominant role in humans is virtually unanimously attributed to the right hemisphere. Interestingly, there are, to our knowledge, no imaging studies that systematically describe the distribution of hemispheric lateralization in the core system of face perception across subjects in large cohorts so far. To address this, we determined the hemispheric lateralization of all core system regions (i.e., occipital face area (OFA), fusiform face area (FFA), posterior superior temporal sulcus (pSTS)) in 108 healthy subjects using functional magnetic resonance imaging (fMRI). We were particularly interested in the variability of hemispheric lateralization across subjects and explored how many subjects can be classified as right-dominant based on the fMRI activation pattern. We further assessed lateralization differences between different regions of the core system and analyzed the influence of handedness and sex on the lateralization with a generalized mixed effects regression model. As expected, brain activity was on average stronger in right-hemispheric brain regions than in their left-hemispheric homologues. This asymmetry was, however, only weakly pronounced in comparison to other lateralized brain functions (such as language and spatial attention) and strongly varied between individuals. Only half of the subjects in the present study could be classified as right-hemispheric dominant. Additionally, we did not detect significant lateralization differences between core system regions. Our data did also not support a general leftward shift of hemispheric lateralization in left-handers. Only the interaction of handedness and sex in the FFA revealed that specifically left-handed men were significantly more left-lateralized compared to right-handed males. In essence, our fMRI data did not support a clear right-hemispheric dominance of the face perception network. Our findings thus ultimately question the dogma that the face perception network - as measured with fMRI - can be characterized as "typically right lateralized".


title: Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence

abstract:
Changes in gene regulation were a major driver of the divergence of archaic hominins (AHs)--Neanderthals and Denisovans--and modern humans (MHs). The three-dimensional (3D) folding of the genome is critical for regulating gene expression; however, its role in recent human evolution has not been explored because the degradation of ancient samples does not permit experimental determination of AH 3D genome folding. To fill this gap, we apply novel deep learning methods for inferring 3D genome organization from DNA sequence to Neanderthal, Denisovan, and diverse MH genomes. Using the resulting 3D contact maps across the genome, we identify 167 distinct regions with diverged 3D genome organization between AHs and MHs. We show that these 3D-diverged loci are enriched for genes related to the function and morphology of the eye, supra-orbital ridges, hair, lungs, immune response, and cognition. Despite these specific diverged loci, the 3D genome of AHs and MHs is more similar than expected based on sequence divergence, suggesting that the pressure to maintain 3D genome organization constrained hominin sequence evolution. We also find that 3D genome organization constrained the landscape of AH ancestry in MHs today: regions more tolerant of 3D variation are enriched for introgression in modern Eurasians. Finally, we identify loci where modern Eurasians have inherited novel 3D genome folding from AH ancestors, which provides a putative molecular mechanism for phenotypes associated with these introgressed haplotypes. In summary, our application of deep learning to predict archaic 3D genome organization illustrates the potential of inferring molecular phenotypes from ancient DNA to reveal previously unobservable biological differences.

1 HighlightsO_LIThe 3D genome organization of archaic hominins can be inferred from sequence to facilitate comparisons to modern humans.
C_LIO_LILoci with 3D genome folding divergence between humans and Neanderthals highlight functional differences in the eye, supra-orbital ridges, hair, lungs, immune response, and cognition.
C_LIO_LI3D genome organization constrained recent human evolution.
C_LIO_LITolerance to variation in 3D genome organization shaped the landscape of Neanderthal ancestry in modern humans.
C_LIO_LINeanderthal introgression contributed novel 3D genome folding patterns to Eurasians.
C_LI

category: evolutionary biology


title: Assessing human genome-wide variation in the Massim region of Papua New Guinea and implications for the Kula trading tradition

abstract: The Massim, a cultural region encompassing the southeastern tip of mainland Papua New Guinea (PNG) and nearby islands, is famous for the Kula trading network, in which different valuables circulate in different directions among the islands. To explore Massim genetic history, we generated genome-wide data from across the region and found variable levels of Papuan-related (indigenous) ancestry, including a novel ancestry associated with Rossel Island, and Austronesian-related ancestry that arrived later. We find genetic evidence for different patterns of contact across PNG, the Massim, and the Bismarck and Solomon Archipelagoes for Austronesian-related vs. Papuan-related ancestry, with more geographic restriction for the latter. Moreover, Kula-practicing groups share more genetic similarity than do other groups, and this likely predates the origin of Kula, suggesting that high between-group contact facilitated the formation of Kula. Our study provides the first comprehensive genome-wide assessment of Massim inhabitants and new insights into the fascinating Kula system.

category: genomics


title: Atypical and distinct microtubule radial symmetries in the centriole and the axoneme of Lecudina tuzetae.

abstract: The centriole is a minute cylindrical organelle present in a wide range of eukaryotic species. Most centrioles have a signature 9-fold radial symmetry of microtubules that is imparted onto the axoneme of the cilia and flagella they template, with 9 centriolar microtubule doublets growing into 9 axonemal microtubule doublets. There are exceptions to the 9-fold symmetrical arrangement of axonemal microtubules, with lower or higher fold symmetries in some species. In the few cases where this has been examined, such alterations in axonemal symmetries are grounded in likewise alterations in centriolar symmetries. Here, we examine the question of microtubule number continuity between centriole and axoneme in flagellated gametes of the gregarine Lecudina tuzetae, which have been reported to exhibit a 6-fold radial symmetry of axonemal microtubules. We used time-lapse differential interference microscopy to identify the stage at which flagellated gametes are present. Thereafter, using electron microscopy and ultrastructure-expansion microscopy coupled to STimulated Emission Depletion (STED) super-resolution imaging, we uncover that a 6- or 5-fold radial symmetry in the axoneme is accompanied by an 8-fold radial symmetry in the centriole. We conclude that there can be plasticity in the transition between centriolar and axonemal microtubules.


title: The Motor Wisdom of the Crowd

abstract:
Wisdom of the Crowd is the aggregation of many individual estimates to obtain a better collective one. This effect has an enormous potential from the social point of view, as it means that a decision may be taken more effectively by vote among a large crowd than by a small minority of experts. Wisdom of the Crowd has been demonstrated in a wide range of cognitive tasks, all of which involve rational thinking. Here we tested this effect in the context of drawing simple geometrical shapes which, while still enacting cognitive processes, mainly involved visuo-motor control. We asked more than 700 school students to trace with their finger a predefined pattern shown on a touchscreen, and analyzed whether their individual trajectories could be aggregated in a way that improved the match with the original pattern. We found that this task has all the characteristics of the strongest examples of Wisdom of the Crowd: First, the aggregate trajectory can be up to 5 times more accurate than the individual ones. Second, this great improvement requires aggregating trajectories from different individuals (rather than different trials from the same individual). Third, the aggregate trajectory outperforms >99% of the individual trajectories. Fourth, when we split our dataset between young children (<10.5 years old) and older children, we find that older individuals outperform younger ones, as naively expected. However, a crowd of young children outperforms the average older individual. In sum, we demonstrate for the first time the Wisdom of the Crowd phenomenon in the realm of motor control, opening the door to further studies of human but also animal behavioral trajectories and their mechanistic underpinnings.

Significance statementWisdom of the Crowd is the aggregation of many individual estimates to obtain a better collective one. Thanks to a combination of mathematical, psychological and social factors, this collective estimate can be surprisingly accurate, even when it comes from a crowd of poorly informed individuals. Originally proposed in the context of simple tasks (such as estimating a number), a general version of this concept now pervades our society, from being a key reason behind the success of democracies to being explicitly used to generate collective high-quality knowledge, from Wikipedia to Stack Exchange. Despite this enormous practical success, academic research lags behind, with most studies focusing on simple and narrow tasks. Here we apply the concept for the first time to a sensory-motor task, testing whether the combination of many drawings traced by different subjects resembles the original template. This type of task is wildly different from previous studies of Wisdom of the Crowd, as it depends on continuous sensory-motor control, rather than explicit reasoning or discrete decision-making. We demonstrate that the effect is strong: The aggregate trajectories are more accurate than an overwhelming majority of the individual ones, and a crowd of young children outperforms the average teenager with more mature motor skills.

category: animal behavior and cognition


title: Pre-B cell receptor acts as a selectivity switch for Galectin-1 at the pre-B cell surface

abstract: Galectins are glycan binding proteins translating the sugar-encoded information of cellular glycoconjugates into many physiological activities including immunity, cell migration, and signaling. During early B lymphocytes (BL) development at the pre-B cell stage, BL express the pre-B cell receptor (pre-BCR) and are supported by mesenchymal stromal cells secreting Galectin-1 (Gal-1). Gal-1 interacts with glycosylated receptors from stromal and pre-B cell surfaces but also with the pre-BCR through a direct carbohydrate-independent contact. How this interaction might interplay with the glycan-decoding function of Gal-1 is unknown. Here, we investigated Gal-1 binding to cell surface ligands using NMR spectroscopy on native membranes. We showed that pre-BCR regulates Gal-1 binding to specifically target 2,3-sialylated receptors on pre-B cells. Upon pre-BCR interaction, dynamic changes resulted in additional contacts with 2,3-sialylated glycans converting Gal-1 from an exo- to an endo-type lectin. Remarkably, this selectivity switch is able to promote pre-B cell survival. Altogether, we shed light on a new mechanism allowing fine-tuning of Galectin specificity at the cell surfaces.

category: biochemistry


title: Comparative assessment of quantification methods for tumor tissue phosphoproteomics

abstract: With increasing sensitivity and accuracy in mass spectrometry, the tumor phosphoproteome is getting into reach. However, the selection of quantitation techniques best-suited to the biomedical question and diagnostic requirements remains a trial and error decision as no study has directly compared their performance for tumor tissue phosphoproteomics. We compared label-free quantification (LFQ), spike-in-SILAC (stable isotope labeling by amino acids in cell culture) and TMT isobaric tandem mass tags technology for quantitative phosphosite profiling in tumor tissue. TMT offered the lowest accuracy and the highest precision and robustness towards different phosphosite abundances and matrices. Spike-in-SILAC offered the best compromise between these features but suffered from a low phosphosite coverage. LFQ offered the lowest precision but the highest number of identifications. Both spike-in-SILAC and LFQ presented susceptibility to matrix effects. Match between run (MBR)-based analysis enhanced the phosphosite coverage across technical replicates in LFQ and spike-in-SILAC but further reduced the precision and robustness of quantification. The choice of quantitative methodology is critical for both study design such as sample size in sample groups and quantified phosphosites, and comparison of published cancer phosphoproteomes. Using ovarian cancer tissue as an example, our study builds a resource for the design and analysis of quantitative phosphoproteomic studies in cancer research and diagnostics.


title: PBRM1 BD2 and BD4 associate with RNA to facilitate chromatin association

abstract: PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Here we demonstrate that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.


title: High Fat Diet Blunts Stress-Induced Hypophagia and Activation of Glp1r Dorsal Lateral Septum Neurons in Male but not in Female Mice

abstract: While stress typically reduces caloric intake (hypophagia) in chow-fed rodents, presentation of palatable, high calorie substances during stress can increase caloric consumption (i.e. "comfort feeding") and promote obesity. However, little is known about how obesity itself affects feeding behavior in response to stress and the mechanisms that can influence stress-associated feeding in the context of obesity. We show that lean male mice display the expected hypophagic response following acute restraint stress, but obese male mice are resistant to this acute stress-induced hypophagia. Activation of the glucagon-like peptide-1 (Glp1) receptor (Glp1r) in various brain regions leads to hypophagia in response to stress. Here we show that Glp1r-positive neurons in the dorsal lateral septum (dLS) are robustly activated during acute restraint stress in lean but not in obese male mice. This raises the possibility that activation of dLS Glp1r neurons during restraint stress contributes to subsequent hypophagia. Supporting this, we show that chemogenetic inhibition of dLS Glp1r neurons attenuates acute restraint stress hypophagia in male mice. Surprisingly, we show that both lean and obese female mice are resistant to acute restraint stress-induced hypophagia and activation of dLS Glp1r neurons. Taken together, these results suggest that dLS Glp1r neurons contribute to the hypophagic response to acute restraint stress in male mice, but not in female mice, and that obesity disrupts this response in male mice. Broadly, these findings show sexually dimorphic mechanisms and feeding behaviors in lean vs. obese mice in response to acute stress.


title: ACh signaling modulates activity of the GABAergic signaling network in the basolateral amygdala and behavior in stress-relevant paradigms.

abstract: Balance between excitatory and inhibitory (E/I) signaling is important for maintaining homeostatic function in the brain. Indeed, dysregulation of inhibitory GABA interneurons in the amygdala has been implicated in human mood disorders. We hypothesized that acetylcholine (ACh) signaling in the basolateral amygdala (BLA) might alter E/I balance resulting in changes in stress-sensitive behaviors. We therefore measured ACh release as well as activity of calmodulin-dependent protein kinase II (CAMKII)-, parvalbumin (PV)-, somatostatin (SOM)- and vasoactive intestinal protein (VIP)-expressing neurons in the BLA of awake, behaving mice. ACh levels and activity of both excitatory and inhibitory BLA neurons increased when animals were actively coping, and decreased during passive coping, in the light-dark box, tail suspension and social defeat. Changes in neuronal activity preceded behavioral state transitions, suggesting that BLA activity may drive the shift in coping strategy. In contrast to exposure to escapable stressors, prolonging ACh signaling with a cholinesterase antagonist changed the balance of activity among BLA cell types, significantly increasing activity of VIP neurons and decreasing activity of SOM cells, with little effect on CaMKII or PV neurons. Knockdown of 7 or {beta}2-containing nAChR subtypes in PV and SOM, but not CaMKII or VIP, BLA neurons altered behavioral responses to stressors, suggesting that ACh signaling through nAChRs on GABA neuron subtypes contributes to stress-induced changes in behavior. These studies show that ACh modulates the GABAergic signaling network in the BLA, shifting the balance between SOM, PV, VIP and CaMKII neurons, which are normally activated coordinately during active coping in response to stress. Thus, prolonging ACh signaling, as occurs in response to chronic stress, may contribute to maladaptive behaviors by shifting the balance of inhibitory signaling in the BLA.


title: Neuronal growth regulator 1 (NEGR1) promotes synaptic targeting of glutamic acid decarboxylase 65 (GAD65)

abstract: Neuronal growth regulator 1 (NEGR1) is a glycosylphosphatidylinositol-anchored cell adhesion molecule encoded by an obesity susceptibility gene. We demonstrate that NEGR1 accumulates in GABAergic inhibitory synapses in hypothalamic neurons, a GABA-synthesizing enzyme GAD65 attaches to the plasma membrane, and NEGR1 promotes clustering of GAD65 at the synaptic plasma membrane. GAD65 is removed from the plasma membrane with newly formed vesicles. The association of GAD65 with vesicles results in increased GABA synthesis. In NEGR1 deficient mice, the synaptic targeting of GAD65 is decreased, the GABAergic synapse densities are reduced, and the reinforcing effects of food rewards are blunted. In mice fed a high fat diet, levels of NEGR1 are increased and GAD65 abnormally accumulates at the synaptic plasma membrane. Our results indicate that NEGR1 regulates a previously unknown step required for synaptic targeting and functioning of GAD65, which can be affected by bidirectional changes in NEGR1 levels causing disruptions in the GABAergic signaling controlling feeding behavior.


title: Synaptic vesicle proteins are selectively delivered to axons in mammalian neurons

abstract: Neurotransmitter-filled synaptic vesicles (SV) mediate synaptic transmission and are a hallmark specialization in neuronal axons. Yet, how SV proteins are sorted to presynaptic nerve terminals remains the subject of debate. The leading models posit that these proteins are randomly trafficked throughout neurons and are selectively retained in presynaptic boutons. Here, we used the RUSH system, in conjunction with HaloTag labeling approaches, to study the egress of two distinct SV proteins from the soma of cultured neurons. In sharp contrast to the selective retention model, both proteins selectively and specifically entered axons and did not traffic through dendrites; only upon overexpression do SV proteins spillover into other compartments. Moreover, we observed that SV constituents were first delivered to the presynaptic plasma membrane before incorporation into SVs. These experiments reveal a new-found membrane trafficking pathway in classically polarized mammalian neurons and provide a glimpse at the first steps of SV biogenesis.


title: Non-synaptic alterations in striatal excitability and cholinergic modulation in a SAPAP3 mouse model of compulsive motor behavior

abstract: Deletion of the OCD-associated gene SAP90/PSD-95-associated protein 3 (Sapap3), which encodes a postsynaptic anchoring protein at corticostriatal synapses, causes OCD-like motor behaviors in mice. While corticostriatal synaptic dysfunction is central to this phenotype, the striatum efficiently adapts to pathological changes, often in ways that expand upon the original circuit impairment. Here we show that SAPAP3 deletion causes non-synaptic and pathwayspecific alterations in dorsolateral striatum circuit function. While somatic excitability was elevated in striatal projection neurons (SPNs), dendritic excitability was exclusively enhanced in direct pathway SPNs. Layered on top of this, cholinergic modulation was altered in opposing ways: striatal cholinergic interneuron density and evoked acetylcholine release were elevated, while basal muscarinic modulation of SPNs was reduced. These data describe how SAPAP3 deletion alters the striatal landscape upon which impaired corticostriatal inputs will act, offering a basis for how pathological synaptic integration and unbalanced striatal output underlying OCD-like behaviors may be shaped.


title: Entrainment to sleep spindles reflects dissociable patterns of connectivity between cortex and basal ganglia

abstract: Communication between the basal ganglia (BG) and cortex is crucial for behavior as it allows learning through external reinforcement. Non-REM sleep benefits learning in the corticostriatal system through the sleep spindle-associated reactivation of previously active neuronal ensembles and the subsequent modification of synaptic weights. However, how sleep spindles coordinate cross-region spiking, and whether spindle-driven reactivation occurs in other BG structures, remains unknown. We recorded field potentials (FP) and spiking activity in cortex and BG during sleep in two non-human primates immediately following a task that involved the learning of new cue-reward contingencies. FP sleep spindles were widespread in the BG, and they were similar to cortical spindles in morphology, spectral content and response to learning prior to sleep. Further, BG FP spindles were concordant with EEG spindles and associated with increased cortico-BG correlation. However, spindles across the BG differed markedly in their entrainment of local spiking. The spiking activity of striatal projection neurons exhibited consistent phase locking to striatal FP spindles and EEG spindles, producing phase windows of peaked cross-region spindling. In contrast, in the subthalamic nucleus (STN), which like the striatum receives substantial thalamocortical input, and in BG nuclei downstream to the striatum and STN, neuronal firing was not entrained to either local or EEG sleep spindles. These results dissociate striatal projection neurons from the rest of the BG, and suggest corticostriatal synapses as the main hub for offline communication between cortex and BG.


title: Can DyeCycling break the photobleaching limit in single-molecule FRET?

abstract: Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a prohibitively narrow temporal bandwidth of [≤] 3 orders of magnitude. Here, we introduce  DyeCycling, a measurement scheme with which we aim to break the photobleaching limit in single-molecule FRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide >100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range.


title: Fingerprinting of brain disease: Connectome identifiability in cognitive decline and neurodegeneration

abstract: In analogy to the friction ridges of a human finger, the functional connectivity patterns of the human brain can be used to identify a given individual from a population. In other words, functional connectivity patterns constitute a marker of human identity, or a  brain fingerprint. Notably, very little is known about whether brain fingerprints are preserved in brain ageing and in the presence of cognitive decline. Using fMRI data of 96 memory clinic subjects, here we show that individuals functional connectivity profiles remain unique even when cognitive impairment occurs. Yet, the patterns of functional connectivity that make the healthy subjects more identifiable change during cognitive decline, suggesting that the brain undergoes functional reconfiguration. Notably, the functional connections that were the most reliable in healthy cohorts disappeared during cognitive decline, leaving room for other stable connections, adapting to the process of neurodegeneration. We believe that these findings could help in moving towards a more personalised medicine and treatment during cognitive decline, and we hope they will set the ground for clinical fingerprinting of brain disease.


title: Vertical HIV-1 transmission in the setting of maternal broad and potent antibody responses

abstract:
Despite the worldwide availability of antiretroviral therapy (ART), approximately 150,000 pediatric HIV infections continue to occur annually. ART can dramatically reduce HIV mother-to-child transmission (MTCT), but inconsistent drug access and adherence, as well as primary maternal HIV infection during pregnancy and lactation are major barriers to eliminating vertical HIV transmission. Thus, immunologic strategies to prevent MTCT, such as an HIV vaccine, will be required to attain an HIV-free generation. A primary goal of HIV vaccine research has been to elicit broadly neutralizing antibodies (bnAbs) given the ability of passive bnAb immunization to protect against sensitive strains, yet we previously observed that HIV-transmitting mothers have more plasma neutralization breadth than non-transmitting mothers. Additionally, we have identified infant transmitted/founder (T/F) viruses that escape maternal bnAb responses. In this study, we examine a cohort of postpartum HIV-transmitting women with neutralization breadth to determine if certain maternal bnAb specificities drive the selection of infant T/F viruses. Using HIV pseudoviruses that are resistant to neutralizing antibodies targeting common bnAb epitopes, we mapped the plasma bnAb specificities of this cohort. Significantly more transmitting women with plasma bnAb activity had a mappable plasma bnAb specificity (six of seven, or 85.7%), compared to that of non-transmitting women with plasma bnAb activity (seven of twenty-one, or 33.3%, p=0.029 by 2-sided Fisher exact test). Our study suggests that having multispecific broad activity and/or uncommon epitope-specific bnAbs in plasma may be associated with protection against the vertical HIV transmission in the setting of maternal bnAb responses.

ImportanceAs mother to child transmission (MTCT) of HIV plays a major part in the persistence of the HIV/AIDS epidemic and bnAb-based passive and active vaccines are a primary strategy for HIV prevention, research in this field is of great importance. While previous MTCT research has investigated the neutralizing antibody activity of HIV-infected women, this is to our knowledge the largest study identifying differences in bnAb specificity of maternal plasma between transmitting and non-transmitting women. Here, we show that among HIV-infected women with broad and potent neutralization activity, more postpartum-transmitting women had a mappable plasma broadly neutralizing antibody (bnAb) specificity, compared to that of non-transmitting women, suggesting that the non-transmitting women more often have multi-specific bnAb responses or bnAb responses that target uncommon epitopes. Such responses may be required for protection against vertical HIV transmission in the setting of maternal bnAb responses.


title: Tracing genetic connections of ancient Hungarians to the 6-14th century populations of the Volga-Ural region

abstract:
Most of the early Hungarian tribes originated from the Volga-Kama and South-Ural regions, where they were composed of a mixed population based on historical, philological, and archaeological data. We present here the uniparental genetic makeup of the medieval era of these regions that served as a melting pot for ethnic groups with different linguistic and historical backgrounds. Representing diverse cultural contexts, the new genetic data originates from ancient proto-Ob-Ugric people from Western Siberia (6th-13th century), the pre-Conquest period, and subsisting Hungarians from the Volga-Ural region (6th-14th century) and their neighbours. By examining the eastern archaeology traits of Hungarian prehistory, we also study their genetic composition and origin in an interdisciplinary framework.

We analysed 110 deep-sequenced mitogenomes and 42 Y-chromosome haplotypes from 18 archaeological sites in Russia. The results support the studied groups genetic relationships regardless of geographical distances, suggesting large-scale mobility. We detected long-lasting genetic connections between the sites representing the Kushnarenkovo and Chiyalik cultures and the Carpathian Basin Hungarians and confirmed the Uralic transmission of several East-Eurasian uniparental lineages in their genepool. Based on phylogenetics, we demonstrate and model the connections and splits of the studied Volga-Ural and conqueror groups.

Early Hungarians and their alliances conquered the Carpathian Basin around 890 AD. Re-analysis of the Hungarian conquerors maternal genepool reveals numerous surviving maternal relationships in both sexes; therefore, we conclude that men and women came to the Carpathian Basin together, and although they were subsequently genetically fused into the local population, certain eastern lineages survived for centuries.


title: Motivational trade-offs in bumblebees

abstract: Mammals can supress their nociceptive responses to prioritise other important responses via endogenous modulation from the brain. It is well established that insects display nociception, but not whether the insect brain can modulate nociceptive processing. To address this question, we investigated whether bumblebees (Bombus terrestris) attraction to higher sucrose solution concentrations reduces their avoidance of noxious heat. Bees were given the choice between either unheated or noxiously-heated (55{degrees}C) feeders with different sucrose concentrations. The feeders were associated with colour stimuli to act as conditioned cues. Bees fed more from higher sucrose concentration heated feeders than lower sucrose concentration unheated feeders. Further, bees "testing out" of feeders (landing but not feeding) reduced as the experiment progressed, demonstrating that conditioned colour cues informed the bees behaviour. Therefore, bees trade off competing conditioned motivational stimuli to modulate nocifensive behaviour, suggesting a form of pain perception.


title: Brain strain rate response: addressing computational ambiguity and experimental data for model validation

abstract:
Traumatic brain injury (TBI) is an alarming global public health issue with high morbidity and mortality rates. Although the causal link between external insults and consequent brain injury remains largely elusive, both strain and strain rate are generally recognized as crucial factors for brain injury development. With respect to the flourishment of strain-based exploration, concerning ambiguity and inconsistency are noted in the scheme for strain rate calculation within the TBI research community. Furthermore, there is no experimental data that can be used to validate the strain rate responses of finite element (FE) models of the human brain. Thus, the current work presented a theoretical clarification of two commonly used strain rate computational schemes: the strain rate was either calculated as the time derivative of strain or derived from the rate of deformation tensor. To further substantiate this theoretical disparity, these two schemes were respectively implemented to estimate the strain rate responses from a previous-published cadaveric experiment and an FE brain model secondary to a concussive impact. The results clearly showed scheme-dependent responses, both in the experimentally determined principal strain rate and FE-derived principal and tract-oriented strain rates. The results suggest that cross-scheme comparison of strain rate responses is inappropriate, and the utilized strain rate computational scheme needs to be reported in future studies. The newly calculated experimental strain rate curves can be used for strain rate validation of FE head models.

HighlightsO_LIA theoretical clarification of two strain rate computational schemes was presented, in which the strain rate was respectively calculated as the time derivative of strain or derived from the rate of deformation tensor.
C_LIO_LIDiscordant cross-scheme responses were substantiated by experimental principal strain rate and computational principal and tract-oriented strain rates.
C_LIO_LICross-scheme comparison of strain rate responses is inappropriate.
C_LIO_LIThe newly calculated experimental strain rate curves can be used for strain rate validation of FE head model
C_LI

Graphic abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/478773v2_ufig1.gif" ALT="Figure 1">
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category: bioengineering


title: Cell Type Composition Analysis: Comparison of statistical methods

abstract: Measuring changes in cell type composition between conditions (disease vs not, knockout vs wild type, treated vs not, etc) is fast becoming a standard step in single cell RNA-Seq analysis. Despite that, there is no agreement on the best approach for this type of analysis. As such, we decided to test numerous methods for cell type composition analysis, seeing how they performed in terms of false positive rate and power. Though there is not one clear winner, we do find two method (the propeller method with asin normalization and Dirichlet regression with the alternative parameterization) perform well in most situations. Most importantly, consistent with results in differential expression analysis, we see that it is important to take into account sample to sample (mouse to mouse, person to person, etc) variability to avoid high false positive rates. We also see evidence that aggregation (aka pseudobulk) based method slightly outperform the mixed model methods we tested.


title: Specific Peptides Predict Protein Classification.

abstract: The methodology of Specific Peptides (SP) has been introduced within the context of enzymes. It is based on an unsupervised machine leaning (ML) tool for motif extraction, followed by supervised annotation of the motifs. In the case of enzymes, the classifier is the Enzyme Classification (EC) number. Here we demonstrate that this method reaches precision of 96.5% and recall of 89.1% on presently available protein sequences. We also apply this method to two other protein families, GPCR and ZF, find their corresponding SPs, and provide the code for searching any protein sequence for its classification under any such family.


title: Beta HPV8 E6 Induces Micronuclei Formation and Promotes Chromothripsis

abstract:
Cutaneous beta genus human papillomaviruses ({beta}-HPV) are suspected to promote the development of non-melanoma skin cancer (NMSC) by destabilizing the host genome. Multiple studies have established the genome destabilizing capacities of {beta}-HPV proteins E6 and E7 as a co-factor with UV. However, the E6 protein from {beta}-HPV8 (HPV8 E6) induces tumors in mice without UV exposure. Here, we examined a UV-independent mechanism of HPV8 E6-induced genome destabilization. We showed that HPV8 E6 reduced the abundance of anaphase bridge resolving helicase, Bloom syndrome protein (BLM). The diminished BLM was associated with increased segregation errors and micronuclei. These HPV8 E6-induced micronuclei had disordered micronuclear envelopes yet retained replication and transcription competence. HPV8 E6 decreased antiproliferative responses to micronuclei and time-lapse imaging revealed HPV8 E6 promoted cells with micronuclei to complete mitosis. Finally, whole genome sequencing revealed that HPV8 E6 induced chromothripsis in 9 chromosomes. These data provide insight into mechanisms by which HPV8 E6-induces genome instability independent of UV exposure.

ImportanceSome beta genus human papillomaviruses ({beta}-HPVs) may promote skin carcinogenesis by inducing mutations in the host genome. Supporting this, the E6 protein from {beta}-HPV8 (8E6) promotes skin cancer in mice with or without UV exposure. Many mechanisms by which 8E6 increases mutations caused by UV have been elucidated, but less is known about how 8E6 induces mutations without UV. We address that knowledge gap by showing 8E6 causes mutations stemming from mitotic errors. Specifically, 8E6 reduces the abundance of BLM, a helicase that resolves and prevents anaphase bridges. This hinders anaphase bridge resolution and increases their frequency. 8E6 makes the micronuclei that can result from anaphase bridges more common. These micronuclei often have disrupted envelopes yet retain localization of nuclear-trafficked proteins. 8E6 promotes the growth of cells with micronuclei and causes chromothripsis, a mutagenic process where hundreds to thousands of mutations occur in a chromosome.

category: cancer biology


title: Absolute Winding Number Differentiates Spatial Navigation Strategies with Genetic Risk for Alzheimer's Disease

abstract: Spatial navigation and orientation are emerging as promising markers for altered cognition in prodromal Alzheimers disease, and even in cognitively normal individuals at risk for Alzheimers disease. The different APOE gene alleles confer various degrees of risk. The APOE2 allele is considered protective, APOE3 is seen as control, while APOE4 carriage is the major known genetic risk for Alzheimers disease. We have used mouse models carrying the three humanized APOE alleles and tested them in a spatial memory task in the Morris water maze. We introduce a new metric, the absolute winding number, to characterize the spatial search strategy, through the shape of the swim path. We show that this metric is robust to noise, and works for small group samples. Moreover, the absolute winding number better differentiated APOE3 carriers, through their straighter swim paths relative to both APOE2 and APOE4 genotypes. Finally, this novel metric was sensitive to sex differences, supporting increased vulnerability in females. We hypothesized differences in spatial memory and navigation strategies are linked to differences in brain networks, and showed that different genotypes have different reliance on the hippocampal and caudate putamen circuits, pointing to a role for white matter connections. Moreover, differences were most pronounced in females. This departure from a hippocampal centric to a brain network approach may open avenues for identifying regions linked to increased risk for Alzheimers disease, before overt disease manifestation. Further exploration of novel biomarkers based on spatial navigation strategies may enlarge the windows of opportunity for interventions. The proposed framework will be significant in dissecting vulnerable circuits associated with cognitive changes in prodromal Alzheimers disease.


title: Non-linearities and Timescales in Temporal Interference Deep Brain Stimulation

abstract:
ObjectiveIn temporal interference (TI) deep brain stimulation (DBS), the neurons of mice react to two interfering sinusoids with a slightly different frequency. This is called a temporal interference (TI) signal. It was previously seen that for the same input intensity, the neurons do not react to a purely sinusoidal signal. This study aims to get a better understanding into the mechanism for this, which is largely unknown.

MethodsThis study makes use of single compartment models to computationally simulate the response of neurons to the sinusoidal and TI-waveform. This study also compares different neuron models to get insight in which models are able to model the experimental behavior.

ResultsIt was found that integrate- and-fire models do not reflect the experimental behavior while the Hodgkin-Huxley and Frankenhaeuer-Huxley model do reflect this behavior. It was seen that changing the characteristics of the ion gates in the Frankenhaeuser-Huxley model alters the response to both sinusoidal and TI signal. It can even make sure that the firing threshold of the sinusoidal input becomes lower than that of the TI input.

ConclusionThe results show that the ion-gates have a big influence on the behavior and their characteristics can define the way the neuron reacts to sinusoidal and TI inputs.

SignificanceThis paper makes advances both in terms of biophysical insight of the neuron as well as the insight in computational modelling of TI-stimulation.


title: PELP: accounting for missing data in neural time series by Periodic Estimation of Lost Packets

abstract:
ObjectiveImplanted electrical stimulators with sensing capabilities have enabled the development of closed-loop neuromodulation therapies capable of responding to patient needs in real-time. Through a combination of rechargeable technologies and wireless data transmission, it is now possible for researchers to acquire extensive neural recordings from human participants in naturalistic settings using these bidirectional devices. However, data losses during wireless transmission hamper processing and the identification of neural signals of interest, driving the need for methodologies to properly estimate the impact of data loss.

ApproachTo accurately reconstruct the timing of data containing losses, we have developed a method called Periodic Estimation of Lost Packets (PELP) to precisely determine the number of samples lost from implanted recordings during active stimulation. PELP leverages a data-driven procedure for determining the period of stimulation and the knowledge that stimulation continues identically during periods where data are missing to accurately account for the number of samples lost.

Main resultsUsing simulated stimulation added to collected human EEG data, we show that PELP is robust to a range of stimulation waveforms and noise characteristics. Lastly, we successfully applied PELP to local field potential (LFP) recordings from an implanted, bidirectional device using data recorded in the clinic and the patients own home.

SignificanceBy effectively accounting for the timing of missing data, PELP enables the analysis of complex, naturalistic neural time series data from bidirectional implanted devices aiding in the development of novel therapeutic approaches. NCT04806516 (ClinicalTrials.gov).


title: The Heart's Pacemaker Mimics Brain Cytoarchitecture and Function: Autonomic innervation, a peripheral glial cell web, and a novel S100B expressing interstitial cell type impart structural and functional complexity to the sinoatrial node

abstract:
ObjectivesThis study sought to describe the 3D cytoarchitecture of sinoatrial node tissue, including autonomic innervation, peripheral glial cells, and pacemaker cells.

BackgroundThe sinoatrial node of the heart produces rhythmic action potentials (AP), generated via calcium signaling within and among pacemaker cells. Our previous work has described the SAN as composed of an HCN4-expressing pacemaker cell meshwork, which merges with a network of CX43+/F-actin+ cells. It is also known that sympathetic and parasympathetic innervation from epicardial ganglia create an autonomic plexus in the sinoatrial node, which modulates heart rate and rhythm. However, the anatomical details of the interaction of this plexus with the pacemaker cell meshwork have yet to be described.

Methods3D confocal laser-scanning microscopy of triple immunolabeled SAN whole mount preparations with combinations of antibodies for HCN4, S100B, GFAP, ChAT or VAChT, and TH, and transmission electron microscopy (TEM).

ResultsThe SAN exhibited heterogeneous autonomic innervation, which was accompanied by a web of peripheral glial cells (PGCs). Further, we identified a novel S100B+/GFAP- interstitial cell population, with unique morphology and distinct distribution pattern, creating complex interactions with other cell types in the node. TEM images showed a similar population of cells, here identified as telocytes, which appeared to secrete vesicles towards pacemaker cells. Application of S100B protein to SAN preparations induced distinct changes in rhythmogenic calcium signaling.

ConclusionsThe autonomic plexus and its associated peripheral glial cell web, a novel network of S100B expressing interstitial cells resembling telocytes, and a meshwork of HCN4+ cells interact to impart structural complexity to the sinoatrial node.

Summary Table
[Table 1][Table 1]

category: physiology


title: Summary statistics of memory-related fMRI activity reflect dissociable neuropsychological and anatomical signatures of neurocognitive aging

abstract: Memory-related functional magnetic resonance imaging (fMRI) activations show age-related differences across multiple brain regions that can be captured in summary statistics like single-value scores. Recently, we described two single-value scores reflecting deviations from prototypical whole-brain fMRI activity of young adults during successful encoding and novelty processing. Here, we investigate the construct validity of these scores for age-related neurocognitive changes in 153 healthy older adults. All scores correlated with episodic recall performance. The memory network scores, but not the novelty network scores, additionally correlated with medial temporal gray matter and a composite measure comprising pro-active inhibition, episodic memory, tonic alertness, flexibility, and working memory. Our results reveal that novelty-network-based fMRI scores have a high construct validity for episodic memory while encoding-network-based fMRI scores further capture individual differences in global cognition. These data motivate the further development of whole-brain fMRI single-value scores as biomarkers for network dysfunction in normal versus pathological aging.


title: Single-value scores of memory-related fMRI activity reflect dissociable neuropsychological and anatomical signatures of neurocognitive aging


title: Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age

abstract: The glacial cycles of the Pleistocene had a global impact on the evolution of species. Although the influence of genetic drift on population genetic dynamics is well understood, the role of selection in shaping patterns of genomic variation during these dramatic climatic changes is less clear. We used whole genome resequencing data to investigate the interplay between demography and natural selection and their influence on the genomic landscape of Downy and Hairy Woodpecker, species co-distributed in previously glaciated North America. Our results revealed a dynamic population history with repeated cycles of bottleneck and expansion, and genetic structure associated with glacial refugia. Levels of nucleotide diversity varied substantially along the genomes of Downy and Hairy Woodpecker, but this variation was highly correlated between the two species, suggesting the presence of conserved genomic features. Nucleotide diversity in both species was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity in regions of low recombination and high density of targets of selection. Despite strong temporal fluctuations in Ne, our demographic analyses indicate that Downy and Hairy Woodpecker were able to maintain relatively large effective population sizes during glaciations, which might have favored natural selection. The magnitude of the effect of linked selection seems to have been modulated by the individual demographic trajectory of populations and species, such that purifying selection has been more efficient in removing deleterious alleles in Hairy Woodpecker owing to its larger long-term Ne. These results highlight that while drift captures the expected signature of contracting and expanding populations during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.


title: The usefulness of sparse k-means in metabolomics data: Anexample from breast cancer data

abstract: In processing metabolomics data, multidimensional quantitative data from thousands of metabolites are often sparse, that is, only a small fraction of metabolites are relevant to the phenotype of interest. Clustering is therefore used to discover subtypes from omics data. Sparse processing, which selects important metabolites from the total omics data, is an effective clustering technique. This study investigated the effectiveness of sparse k-means for metabolomics data. Specifically, sparse k-means was used to cluster blood lipid metabolite data of breast cancer patients in two studies: (1) before and after menopause, and (2) pre- and postoperative chemotherapy. In both cases, sparse k-means showed comparable discrimination accuracy with fewer metabolites than k-means. Furthermore, when the L1 norm values were varied, no significant changes were observed. The mean silhouette coefficients of sparse k-means and k-means were (1) 0.38 {+/-} 0.14 (S.D.) and 0.17 {+/-} 0.01, (2) 0.38 {+/-} 0.07 and 0.17 {+/-} 0.01, indicating that feature selection using sparse k-means can improve clustering results. In addition, metabolite selection using sparse k-means was consistent regardless of the test data or the constrained value of the L1 norm, indicating robustness.


title: SpatialCorr: Identifying Gene Sets with Spatially Varying Correlation Structure

abstract: Recent advances in spatially resolved transcriptomics technologies enable both the measurement of genome-wide gene expression profiles and their mapping to spatial locations within a tissue. A first step in spatial transcriptomics data analysis is identifying genes with expression that varies spatially, and robust statistical methods exist to address this challenge. While useful, these methods do not detect spatial changes in the coordinated expression within a group of genes. To this end, we present SpatialCorr, a method for identifying sets of genes with spatially varying correlation structure. Given a collection of gene sets pre-defined by a user, SpatialCorr tests for spatially induced differences in the correlation of each gene set within tissue regions, as well as between and among regions. An application to cutaneous squamous cell carcinoma demonstrates the power of the approach for revealing biological insights not identified using existing methods.


title: Single-Droplet Surface-Enhanced Raman Scattering Decodes the Molecular Language of Liquid-Liquid Phase Separation

abstract: Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are involved in a myriad of critical cellular functions and debilitating neurodegenerative diseases. Elucidating the role of intrinsic disorder and conformational heterogeneity of intrinsically disordered proteins/regions (IDPs/IDRs) in these phase-separated membrane-less organelles is crucial to understanding the mechanism of formation and regulation of biomolecular condensates. Here we introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that utilizes surface-engineered, plasmonic, metal nanoparticles to unveil the inner workings of mesoscopic liquid droplets of Fused in Sarcoma (FUS) in the absence and presence of RNA. These highly sensitive measurements offer unprecedented sensitivity to capture the crucial interactions, conformational heterogeneity, and structural distributions within the condensed phase in a droplet-by-droplet manner. Such an ultra-sensitive single-droplet vibrational methodology can serve as a potent tool to decipher the key molecular drivers of biological phase transitions of a wide range of biomolecular condensates involved in physiology and disease.


title: AI-Generated Virtual Libraries Could Help Uncover RNA-Specific Regions of Chemical Space

abstract:
RNAs can recognize small-molecule ligands. However, the extent to which the molecules that they recognize differ from those recognized by proteins remains an open question. Cheminformatics analysis of experimentally validated RNA binders strongly suggests that RNA binders occupy a specific region of chemical space. However, less than 100 validated small molecule ligands are currently known. Here, we demonstrate how structure-based approaches could be used to navigate vast regions of the chemical space specific to ligand binding sites in five highly-structured RNAs. Our method involves using generative-AI to design target- and site-specific virtual libraries and then analyzing them using similar cheminformatics approaches as those used to assess experimentally validated RNA binders. Despite employing a completely orthogonal strategy, our results essentially reproduce the trends observed by analyzing the experimentally validated RNA binders. Large-scale generation of target and site-specific libraries may therefore prove to be helpful in simultaneously mapping the regions of chemical space unique to RNA and generating libraries that could be mined to identify novel RNA binders.

TOC IMAGE O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: TNF signaling is required for castration-induced vascular damage preceding prostate cancer regression

abstract:
The mainstay treatment for locally advanced, recurrent, or metastatic prostate cancer (PrCa) is androgen deprivation therapy (ADT). ADT causes prostate cancers to shrink in volume, or regress, by inducing epithelial tumor cell apoptosis. In normal, non-neoplastic murine prostate, androgen deprivation via castration induces prostate gland regression that is dependent on TNF signaling. Besides this direct mechanism of action, castration has also been implicated in an indirect mechanism of prostate epithelial cell death which has been described as vascular regression. The initiating event is endothelial cell apoptosis and/or increased vascular permeability. This subsequently leads to reduced blood flow and perfusion, and then hypoxia, which may enhance epithelial cell apoptosis. Castration-induced vascular regression has been observed in both normal and neoplastic prostate. We used photoacoustic, power Doppler, and contrast-enhanced ultrasound imaging, and CD31 immunohistochemical staining of the microvasculature to assess vascular integrity in the period immediately following castration, enabling us to test the role of TNF signaling in vascular regression. In two mouse models of androgen-responsive prostate cancer, TNF signaling blockade using a soluble TNFR2 ligand trap reversed the functional aspects of vascular regression as well as structural changes in the microvasculature, including reduced vessel wall thickness, cross-sectional area and vessel perimeter length. These results demonstrate that TNF signaling is required for vascular regression, most likely inducing endothelial cell apoptosis and increasing vessel permeability. Since TNF is also the critical death receptor ligand for prostate epithelial cells, we propose that TNF is a multi-purpose, comprehensive signal within the prostate cancer micro-environment mediating prostate cancer regression following androgen deprivation.

SIGNIFICANCEThese studies define TNF as the mediator of androgen deprivation therapy-induced functional and structural vascular damage in prostate tumors.


title: Disentangling the molecular mechanisms underlying the retrieval and extinction of morphine withdrawal-associated memories in the basolateral amygdala and dentate gyrus.

abstract: Despite their indisputable efficacy for pain management, opiates prescription remains highly controversial due to their elevated addictive potential. Relapse in drug use is one of the principal problems for addiction treatment, being drug-associated memories among its main triggers. Consequently, the extinction of these memories has been proposed as a useful therapeutic tool. Hence, by using the conditioned place aversion (CPA) paradigm in rats we investigated some of the molecular mechanisms that occurred during the retrieval and extinction of morphine withdrawal memories in the basolateral amygdala (BLA) and the hippocampal dentate gyrus (DG), which control emotional and episodic memories, respectively. The retrieval of aversive memories associated with the abstinence syndrome paralleled with decreased mTOR activity and increased Arc and GluN1 expressions in the DG. Additionally, Arc mRNA levels in this nucleus very strongly correlated with the CPA score exhibited by the opiate-treated rats. On the other hand, despite the unaltered mTOR phosphorylation Arc augmented in the BLA. After the extinction test, Arc and GluN1 expressions raised in both the DG and BLA of control and morphine-treated animals. Remarkably, Homer1 expression in both areas correlated almost perfectly with the extinction showed by morphinedependent animals. Also, Arc expression in the DG correlated strongly with the extinction of the CPA manifested by the group treated with the opiate. Finally, our results support coordinated activity of some of these neuroplastic proteins for the extinction of morphine activity in a regional-dependent manner. Present data provide evidence of differential expression and activity of synaptic molecules during the retrieval and extinction of aversive memories of opiate withdrawal in amygdalar and hippocampal regions that will likely permit the development of therapeutic strategies able to minimize relapses induced by drug-associated aversive memories.


title: Time-Optimal Adaptation in Metabolic Network Models

abstract: Analysis of metabolic models using constraint-based optimization has emerged as an important computational technique to elucidate and eventually predict cellular metabolism and growth. In this work, we introduce time-optimal adaptation (TOA), a new constraint-based modeling approach that allows us to evaluate the fastest possible adaptation to a pre-defined cellular state while fulfilling a given set of dynamic and static constraints. TOA falls into the mathematical problem class of time-optimal control problems, and, in its general form, can be applied in a broad sense and thereby extends most existing constraint-based modeling frameworks. Specifically, We introduce a general mathematical framework that captures many existing constraint-based methods and define TOA within this framework. We then exemplify TOA using a coarse-grained self-replicator model and demonstrate that TOA allows us to explain several well known experimental phenomena that are difficult to explore using existing constraint-based analysis methods. We show that TOA can explain accumulation of storage compounds in constant environments, as well as overshoot uptake metabolism after a period of nutrient scarcity. TOA reveals that organisms with internal temporal degrees of freedom, such as storage, can in most environments outperform organisms with a static intracellular composition. Furthermore, TOA shows that organisms adapted to better growth conditions than present in the environment ("optimists") typically outperform organisms adapted to poorer growth conditions ("pessimists").

category: systems biology


title: Expression analysis of Huntington disease mouse models reveals robust striatum disease signatures

abstract:
Huntingtons disease is caused by expanded trinucleotide repeats in the huntingtin gene (HTT), and a higher number of repeats is associated with an earlier age of disease onset. Although the causative gene has been identified, its connections to the observed disease phenotypes is still unclear. Mouse models engineered to contain increasing numbers of trinucleotide repeats were sacrificed at different ages to detect RNA-level and protein-level changes specific to each repeat length and age in order to examine the transcriptional and translational characteristics of the disease. RNA-seq and quantitative proteomics data were collected on 14 types of tissues at up to 8 repeat lengths and in up to 3 different ages, and differential gene and protein expression were examined. A modified method of imputing missing proteomics data was employed and is described here. The most dysregulated tissue at both the RNA and protein levels was the striatum, and a strong gender effect was observed in all of the liver experiments. The full differential expression results are available to the research community on the HDinHD.org website. The results of multiple expression tests in the striatum were combined to generate an RNA disease signature and a protein disease signature, and the signatures were validated in external data sets. These signatures represent molecular readouts of disease progression in HD mice, which further characterizes their HD-related phenotype and can be useful in the preclinical evaluation of candidate therapeutic interventions.

Author SummaryMouse models of Huntingtons disease were engineered to allow a detailed examination of how the disease causes changes in gene activity in a variety of tissues. Among the 14 tissues studied, the one most affected by the disease in our experiments was the striatum, a brain region involved in voluntary movement. The liver results showed large differences in gene activity between the male and female mice. In our analysis, we propose a minor change in how proteomics data is typically analyzed in order to improve the ranking of significant results. Using the striatum data in this study and in others, we identified robust genetic signatures of disease at both the RNA and protein levels.


title: Accelerated cognitive decline in obese mouse model of Alzheimer's disease is linked to sialic acid-driven immune deregulation

abstract: Systemic immunity supports healthy brain homeostasis. Accordingly, conditions causing systemic immune deregulation may accelerate onset of neurodegeneration in predisposed individuals. Here we show that, in the 5xFAD mouse model of Alzheimers disease (AD), high-fat diet-induced obesity accelerated cognitive decline, which was associated with immune deviations comprising increased splenic frequencies of exhausted CD4+ T effector memory cells and CD4+FOXP3+ regulatory T cells (Tregs). Non-targeted plasma metabolomics identified N-acetylneuraminic acid (NANA), the predominant sialic acid, as the major obesity-induced metabolite in 5xFAD mice, the levels of which directly correlated with Tregs abundance and inversely correlated with cognitive performance. Visceral adipose tissue macrophages were identified by sNuc-Seq as one potential source of NANA. Exposure to NANA led to immune deregulation in middle-aged wild-type mice, and ex vivo in human T cells. Our study identified diet-induced immune deregulation, potentially via sialic acid, as a previously unrecognized link between obesity and AD.


title: Category-specific fMRI Correlates of Picture Naming: a study with Arabs and Filipinos

abstract:
Cross cultural neuroimaging work has demonstrated differences in neural correlates of some cognitive processes between individuals from different cultures, often comparing American and Chinese subjects. In contrast, a limited number of studies examined Arab and/or Filipino participants. This fMRI study aimed to demonstrate neural activations during animal and tool picture naming by 18 healthy Arabs and 18 healthy Filipino participants. In animal naming contrasted with tool naming, Arabs preferentially activated regions in the right lateral occipital and fusiform cortices, whereas Filipinos recruited bilateral visual areas. Cross-group comparisons of animal naming revealed that Arabs recruited right visual areas more than Filipinos, who in turn recruited the cerebellum more than Arabs. In tool naming, Arabs preferentially activated a predominantly left frontoparietal network, whereas no regions were identified in Filipinos, and no differences in activation between groups were found. Using a low-demand picture-naming task, this study revealed category-specific neural activations during picture naming by Arabs and Filipinos, as well as between-group differences in animal naming. The results suggest that Arabs and Filipinos may have culture-specific differences in processing animate and inanimate pictures, and caution against generalizing findings from the more commonly studied populations, especially in verbal tasks such as picture naming.

HIGHLIGHTS{blacksquare} The neural correlates of animal and tool picture naming in Arabs and Filipinos are category specific.
{blacksquare}Animal naming by Arabs tended to preferentially activate the nondominant ventral visual stream.
{blacksquare}Animal naming by Filipinos activated bilateral visual areas, and the cerebellum.
{blacksquare}Tool naming by Arabs activated dominant frontoparietal areas related to praxis.
{blacksquare}Results suggest that Arabs and Filipinos have culture-specific differences in visual processing.


title: Selective influence of dopamine on electrocortical signatures of error monitoring: a combined EEG and immersive virtual reality study in Parkinson's disease

abstract:
Detecting errors in ones own and others actions is likely linked to the discrepancy between intended or expected and produced or observed output. To detect and process the occurrence of salient events seems associated to the release of dopamine, the balance of which is profoundly altered in Parkinsons disease (PD). EEG studies in healthy participants indicate that the occurrence of errors in observed actions triggers a variety of electrocortical indices (like mid-frontal theta activity, error-related delta and the Error Positivity, oPe), that seem to map different aspects of error detection and performance monitoring. Whether these indices are differently modulated by dopamine in the same individual has never been investigated. To explore this issue, we recorded EEG markers of error detection by asking healthy controls (HCs) and PD patients to observe ecological reach-to-grasp a glass actions performed by a virtual arm seen in first person perspective. PD patients were tested under their dopaminergic medication ( on-condition), and after dopaminergic withdrawal ( off-condition). HCs showed a clear oPe and an increase of delta and theta power during the observation of erroneous vs. correct actions. In PD patients, oPe and delta responses were always preserved. Crucially, however, an error-related increase of theta power was found in  on but not in  off state PD patients. Thus, different EEG error signatures may index the activity of independent systems and error related theta power is selectively modulated by dopamine depletion. Our findings may pave the way to the discovery of dopamine-related biomarkers of higher-order motor cognition dysfunctions that may have crucial theoretical and clinical implications.

Significance StatementDopaminergic neurons respond to salient events during performance monitoring. Yet, the impact of dopamine depletion on the human reactivity to observed errors is still unclear. We recorded EEG in patients with Parkinsons Disease (PD) under dopaminergic treatment ( on-condition) and medication withdrawal ( off-condition) while they observed correct and erroneous goal-related actions performed by a virtual limb. Analysis of Error Positivity (oPe) and theta and delta power increase, markers of physiological error-monitoring, indicates that while the formers were intact, the latter was preserved in the  on and altered in the  off condition. Thus, different EEG markers of error monitoring likely rely on independent circuits. Moreover, mid-frontal theta activity alterations may represent a marker of dopamine-related neurophysiological impairments of higher-order cognition.


title: A wearable platform for closed-loop stimulation and recording of single- neuron and local field potential activity in freely-moving humans

abstract: Advances in technologies that can record and stimulate deep-brain activity in humans have led to impactful discoveries within the field of neuroscience and contributed to the development of novel therapies for neurological and psychiatric disorders. Further progress, however, has been hindered by device limitations in that recording of single-neuron activity during freely-moving behaviors in humans has not been possible. Additionally, implantable neurostimulation devices, currently approved for human use, have limited stimulation programmability and lack full-duplex bi-directional capability. Here, we developed a wearable bi-directional closed-loop neuromodulation system (Neuro-stack) and used it to record single-neuron and local field potential activity during stationary and ambulatory behavior in humans. Together with a highly flexible and customizable stimulation capability, the Neuro-stack provides an opportunity to investigate the neurophysiological basis of disease, develop improved responsive neuromodulation therapies, explore brain function during naturalistic behaviors in humans, and consequently, bridge decades of neuroscientific findings across species.