bluuebunny/crossref_metadata_2025 huggingface dataset:
Minimally invasive delivery of peptides to the spinal cord for behavior modulation
Authors: Gao Zhenghong , David Eric T. , Leong Tiffany W. , Li Xiaoqing , Cai Qi , Mwirigi Juliet , Giannotta Monica , Dejana Elisabetta , Wiggins John , Krishnagiri Sharada , Bachoo Robert M. , Price Theodore J. , Qin Zhengpeng
Published: May 2022

The blood-spinal cord barrier (BSCB) tightly regulates molecular transport from the blood to the spinal cord. Herein, we present a novel approach for transient modulation of BSCB permeability and localized delivery of peptides into the spinal cord for behavior modulation with high spatial resolution. This approach utilizes optical stimulation of vasculature-targeted nanoparticles and allows delivery of BSCB-nonpermeable molecules into the spinal cord without significant glial activation or impact on animal locomotor behavior. We demonstrate minimally invasive light delivery into the spinal cord using an optical fiber and BSCB permeability modulation in the lumbar region. Our method of BSCB modulation allows delivery of bombesin, a centrally-acting and itch-inducing peptide, into the spinal cord and induces a rapid and transient increase in itching behaviors in mice. This minimally invasive approach enables behavior modulation without genetic modifications and is promising for delivering a wide range of biologics into the spinal cord for behavior modulation and potentially therapy.

Significance Statement

Spinal cord diseases and disorders are common and cause significant disability, including chronic pain, paralysis, cognitive impairment, and mortality. The blood-spinal cord barrier is a considerable challenge for delivery by systemic therapeutic administration. We developed an optical approach for effectively and safely delivering molecules to the spinal cord to overcome this barrier. The fiberoptic method is minimally invasive and overcomes challenges that previous technologies face, including the complicated bone structure and standing waves that complicate BSCB opening using ultrasound. Optical stimulation offers unprecedented spatial resolution for the precise delivery in intricate spinal cord structures. Significantly, our approach modulates animal behavior (i.e., itch) without genetic modifications and demonstrates the potential for delivery of biologics such as peptides into the spinal cord.
Rudimentary Structure-Activity-Relationship study of the MMV Pathogen Box compound MMV675968 (2,4-diaminoquinazoline) unveils novel inhibitors of Trypanosoma brucei brucei DHFR enzyme
Authors: Dize Darline , Tata Rolland , Keumoe Rodrigue , Toghueo Rufin Marie Kouipou , Tchatat Mariscal Brice , Njanpa Cyrille Ngansop , Tchuenguia Vianey Claire , Yamthe Lauve Tchokouaha , Fokou Patrick Valere Tsouh , Laleu Benoît , Duffy James , Bishop Ozlem Tastan , Boyom Fabrice Fekam
Published: May 2022

New drugs are urgently needed for the treatment of human African trypanosomiasis (HAT). In line with our quest for dihydrofolate reductase (DHFR) inhibitors in trypanosomes, a small library of analogs of the antitrypanosomal hit (MMV675968) available at MMV as solid materials was screened for antitrypanosomal activity. In silico confirmation of two potent antitrypanosomal analogs as inhibitors of DHFR was achieved, together with elucidation of other antitrypanosomal modes of action. Overall, two analogs of the diaminoquinazoline derivative, MMV675968 reputed to inhibit the enzyme DHFR, displayed approximately 40-fold and 60-fold more potency and selectivity than the parent hit, respectively (MMV1578445 (10): IC50 = 0.045 µM, SI=1737; MMV1578467 (7): IC50 = 0.06 µM; SI=412). Analogs 7 and 10 were also strong binders of the DHFR enzyme, in all their accessible protonation states, and interacted with key DHFR ligand recognition residues Val32, Asp54, and Ile160. MMV1578445 (10) portrayed fast and irreversible trypanosomes growth arrest after 72 h and 4 h at IC99. Analogs 7 and 10 induced ferric iron reduction and DNA fragmentation or apoptosis induction, respectively. The two potent analogs endowed with suitable physicochemical properties are good candidates for further deciphering their potential as starting points for new drug development for HAT.

Author summary

African trypanosomiasis is a disease caused by parasites of the Trypanosoma brucei species which affect both humans and animals. We have adopted the fast-track drug repurposing approach to determine the antitrypanosomal activity of the open access MMV Pathogen Box compound library. The compound 2,4-diaminoquinazoline (MMV675998), known as a dihydrofolate reductase (DHFR) inhibitor was identified. Rudimentary structure-activity relationship investigation of this compound unveiled two highly active and selective derivatives MMV1578445 and MMV1578467 which were found to strongly inhibit the Trypanosoma brucei dihydrofolate reductase enzyme in silico. Besides, we demonstrated that analogues MMV1578445 and MMV1578467 could respectively reduce intrinsic ferric iron and induce apoptosis in trypanosomes. The two identified inhibitors of trypanosomes qualify as potential drug candidates that could be useful for future development as novel antitrypanosomal drugs.
Interplay between VSD, pore and membrane lipids in electromechanical coupling in HCN channels
Authors: Elbahnsi Ahmad , Cowgill John , Burtscher Verena , Wedemann Linda , Zeckey Luise , Chanda Baron , Delemotte Lucie
Published: May 2022

Hyperpolarized-activated and Cyclic Nucleotide-gated (HCN) channels are the only members of the voltage-gated ion channel superfamily in mammals that open upon hyperpolarization, conferring them pacemaker properties that are instrumental for rhythmic firing of cardiac and neuronal cells. Activation of their voltage-sensor domains (VSD) upon hyperpolarization occurs through a downward movement of the S4 helix bearing the gating charges, which triggers a break in the alpha-helical hydrogen bonding pattern at the level of a conserved Serine residue. Previous structural and molecular simulation studies had however failed to capture pore opening that should be triggered by VSD activation, presumably because of a low VSD/pore electromechanical coupling efficiency and the limited timescales accessible to such techniques. Here, we have used advanced modeling strategies, including enhanced sampling molecular dynamics simulations exploiting comparisons between non-domain swapped voltage-gated ion channel structures trapped in closed and open states to trigger pore gating and characterize electromechanical coupling in HCN1. We propose that the coupling mechanism involves the reorganization of the interfaces between the VSD helices, in particular S4, and the pore-forming helices S5 and S6, subtly shifting the balance between hydrophobic and hydrophilic interactions in a “domino effect” during activation and gating in this region. Remarkably, our simulations reveal state-dependent occupancy of lipid molecules at this emergent coupling interface, suggesting a key role of lipids in hyperpolarization-dependent gating. Our model provides a rationale for previous observations and a possible mechanism for regulation of HCN channels by the lipidic components of the membrane.
Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning
Authors: Yuan Qianmu , Chen Sheng , Wang Yu , Zhao Huiying , Yang Yuedong
Published: May 2022

More than one-third of the proteins contain metal ions in the Protein Data Bank. Correct identification of metal ion-binding residues is important for understanding protein functions and designing novel drugs. Due to the small size and high versatility of metal ions, it remains challenging to computationally predict their binding sites from protein sequence. Existing sequence-based methods are of low accuracy due to the lack of structural information, and time-consuming owing to the usage of multi-sequence alignment. Here, we propose LMetalSite, an alignment-free sequence-based predictor for binding sites of the four most frequently seen metal ions (Zn2+, Ca2+, Mg2+ and Mn2+). LMetalSite leverages the pretrained language model to rapidly generate informative sequence representations and employs transformer to capture long-range dependencies. Multi-task learning is adopted to compensate for the scarcity of training data and capture the intrinsic similarities between different metal ions. LMetalSite was shown to surpass state-of-the-art structure-based methods by more than 19.7%, 14.4%, 36.8%, and 12.6% in AUPR on the four independent tests, respectively. Further analyses indicated that the self-attention modules are effective to learn the structural contexts of residues from protein sequence.
Pangenome evolution in Escherichia coli is sequence type, not phylogroup, specific
Authors: Cummins Elizabeth A. , Hall Rebecca J. , Connor Chris , McInerney James O. , McNally Alan
Published: May 2022

The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that pangenome evolution is independent of phylogenetic signal at the phylogroup level, which may be a consequence of distinct sequence type-specific driving factors relating to ecology and pathogenic phenotype.

Data Summary

Supporting data and code have been provided within the article or through Supplementary Data files available at https://doi.org/10.6084/m9.figshare.19793758. Custom Python scripts used to perform analyses are available at github.com/lillycummins/InterPangenome unless otherwise stated in the text.
Correcting Modification-Mediated Errors in Nanopore Sequencing by Nucleotide Demodification and in silico Correction
Authors: Chiou Chien-Shun , Chen Bo-Han , Wang You-Wun , Kuo Nang-Ting , Chang Chih-Hsiang , Huang Yao-Ting
Published: May 2022

The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However, novel modifications untrained in the basecalling models can seriously reduce the quality. This paper reports a set of ONT-sequenced genomes with unexpected low quality (∼Q30) due to extensive new modifications. Demodification by whole-genome amplification (WGA) significantly improved the quality of all genomes (∼Q50-60) while losing the epigenome. We developed a computational method, Modpolish, for correcting modification-mediated errors without WGA. Modpolish produced high-quality genomes and uncovered the underlying modification motifs without loss of epigenome. Our results suggested that novel modifications are prone to ONT errors, which are correctable by WGA or Modpolish without additional short-read sequencing.
Omicron breakthrough infections in vaccinated or previously infected hamsters
Authors: Zhou Jie , Sukhova Ksenia , McKay Paul F. , Kurshan Ashwini , Yau Yeuk , Lechmere Thomas , Brown Jonathan C. , Moshe Maya , Kugasathan Ruthiran , Snell Luke B. , Edgeworth Jonathan D. , Shattock Robin J. , Doores Katie J. , Peacock Thomas P. , Barclay Wendy S.
Published: May 2022

The second and third years of the SARS-CoV-2 pandemic have been marked by the repeated emergence and replacement of ‘variants’ with genetic and phenotypic distance from the ancestral strains, the most recent examples being Delta and Omicron. Here we describe a hamster contact exposure challenge model to assess protection conferred by vaccination or prior infection against re-infection. We found that 2-doses of self-amplifying RNA vaccine based on the ancestral spike ameliorated weight loss following Delta infection and decreased viral loads, but had minimal effect on Omicron/BA.1 infection. Prior infection with ancestral or Alpha variant was partially protective against Omicron/BA.1 infection, whereas all animals previously infected with Delta and exposed to Omicron became infected, although shed less virus. We further tested whether prior infection with Omicron/BA.1 protected from re-infection with Delta or Omicron/BA.2. Omicron/BA.1 was protective against Omicron/BA.2, but not Delta reinfection, again showing Delta and Omicron have a very large antigenic distance. Indeed, cross-neutralisation assays with human antisera from otherwise immunonaïve individuals (unvaccinated and no known prior infection), confirmed a large antigenic distance between Delta and Omicron. Prior vaccination followed by Omicron or Delta breakthrough infection led to a higher degree of cross-reactivity to all tested variants. To conclude, cohorts whose only immune experience of COVID is Omicron/BA.1 infection may be particularly vulnerable to future circulation of Delta or Delta-like derivatives. In contrast, repeated exposure to antigenically distinct spikes, via infection and or vaccination drives a more cross-reactive immune response, both in hamsters and people.

One Sentence Summary

Infection with the Delta and Omicron SARS-CoV-2 variants do not provide cross-protective immunity against reinfection with one another in hamsters.
Histone H3K27 methyltransferase EZH2 interacts with MEG3-lncRNA to directly regulate integrin signaling and endothelial cell function
Authors: Dudnakova Tatiana , Dunn-Davies Hywel , Nogara Antonella , Rodor Julie , Thomas Anita , Parish Elisa , Gautier Philippe , Meynert Alison , Madeddu Paolo , Caporali Andrea , Baker Andrew , Tollervey David , Mitić Tijana
Published: May 2022

Enhancer of Zeste Homologue 2 (EZH2) modulates gene transcription during endothelial cell (EC) dysfunction, via interaction with non-coding RNAs (ncRNAs). Thus, EZH2 can act as a rheostat in deposition of histone H3K27 trimethylation (H3K27me3) to repress many genes. We profiled EZH2-RNA interactions using formaldehyde/UV assisted cross-linking ligation and sequencing of hybrids (FLASH-seq) in primary human ECs. Transcriptome-wide EZH2-associated ncRNAs and RNA–RNA interactome were obtained. This approach revealed EZH2 directly binding maternally expressed gene (MEG3) and MEG3:MEG3 hybrid structures. By chromatin immunoprecipitation with sequencing (ChIP-seq) following depletion of MEG3, we discovered that MEG3 targets and controls recruitment of EZH2/H3K27me3 onto a regulatory region of integrin subunit alpha 4 (ITGA4). MEG3 knockdown or pharmacological inhibition of EZH2 de-repressed ITGA4, whilst improving endothelial cell function in vitro, and increasing ITGA4 expression in vivo. Our study demonstrates new role for MEG3, as instrumental in epigenetic regulation of EC function by EZH2, through targeting of integrin-dependent signalling.
Geometric morphometric analysis reveals cranial shape divergence and asymmetry in extinct and extant species of big cats (Carnivora: Felidae)
Authors: Noga Aidan , Anyonge William , Powers Amanda K.
Published: May 2022

Felidae, a family of the order Carnivora, includes extinct and extant species of cats spread across a wide ecological and geographical landscape. Cats are well-suited for predation due to various physical and behavioral characteristics, such as optimized limb length, skull shape, as well as enhanced hearing and vision. Morphological changes across Felidae species, particularly changes in skull shape, are likely explained by differences in predatory and feeding behaviors. Toward that end, cranial shape was analyzed across six different extant and extinct Felidae species using two-dimensional geometric morphometrics. From the lateral cranial view, we discovered that the cheetah (Acinonyx jubatus) and the North American Sabretooth (Smilodon) had the most significant shape divergence, specifically at the frontal bone and post orbital regions of the skull. Specifically, we found that the Sabretooth had a significantly shorter coronoid process compared to other Felids. We also observed a significant difference in post orbital shape in the cheetah dorsal cranium. Interestingly, we found that both the cheetah and the extinct North American Lion demonstrate significant shape asymmetry in the postorbital region from a ventral view of the skull. Shape divergence and asymmetry in select Felid skulls may arise from decreased genetic diversity. Taken together, we reasoned that morphological changes in skull shape likely evolved to support differences in predatory behavior across Felidae.
Single cell analysis of the dorsal V-SVZ reveals differential quiescence of postnatal pallial and subpallial neural stem cells driven by TGFbeta/BMP-signalling
Authors: Marcy Guillaume , Foucault Louis , Babina Elodie , Texeraud Emeric , Zweifel Stefan , Heinrich Christophe , Hernandez-Vargas Hector , Parras Carlos , Jabaudon Denis , Raineteau Olivier
Published: May 2022

The ventricular-subventricular zone (V-SVZ) is the largest neurogenic region of the postnatal forebrain, containing neural stem cells (NSCs) that emerge from both the embryonic pallium and subpallium. Despite of this dual origin, glutamatergic neurogenesis declines rapidly after birth, while gabaergic neurogenesis persists throughout life. Here, we performed single-cell RNA-sequencing (scRNA-Seq) of the postnatal dorsal V-SVZ for unravelling the mechanisms leading to pallial lineage germinal activity silencing. We identify cell lineage-specific NSCs primed for the generation of neurons or glial cells, as well as a large population of so far uncharacterized quiescent NSCs (qNSC). Pallial qNSCs enter a state of deep quiescence, characterized by persistent TGFbeta/BMP signalling, reduced transcriptional activity and Hopx expression, whilst in contrast, subpallial qNSCs remain transcriptionally primed for activation. Induction of deep pallial quiescence is paralleled by a rapid blockade of glutamatergic neuron production and differentiation. Finally, manipulation of the TGFbeta/BMP receptor Bmpr1a demonstrate its key role in mediating these effects at early postnatal times. Together, our results highlight a central role of TGFbeta/BMP-signalling in synchronizing quiescence induction and blockade of neuronal differentiation to rapidly silence pallial germinal activity after birth.
Structure of nucleosome-bound human PBAF complex
Authors: Wang Li , Yu Jiali , Yu Zishuo , Wang Qianmin , Li Wanjun , Ren Yulei , Chen Zhenguo , He Shuang , Xu Yanhui
Published: May 2022

BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite structural studies of nucleosome-bound human BAF and yeast SWI/SNF family complexes, it remains elusive how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides a framework to understand chromatin targeting of SWI/SNF family complexes.
Global predictions for the risk of establishment of Pierce’s disease of grapevines
Authors: Giménez-Romero Àlex , Galván Javier , Montesinos Marina , Bauzà Joan , Godefroid Martin , Fereres Alberto , Ramasco José J. , Matías Manuel A. , Moralejo Eduardo
Published: May 2022

The vector-borne bacterium Xylella fastidiosa is responsible for Pierce’s disease (PD), a lethal grapevine illness that originated in the Americas. The international plant trade is expanding the geographic range of this pathogen, posing a new threat to viticulture worldwide. To assess the potential incidence of PD, we have built a dynamic epidemiological model based on the response of 36-grapevine varieties to the pathogen in inoculation assays and on the vectors’ distribution when this information is available. Key temperature-driven epidemiological processes, such as PD symptom development and recovery, are mechanistically modelled. Integrating into the model highresolution spatiotemporal climatic data from 1981 onward and different infectivity (R0) scenarios, we show how the main wine-producing areas thrive mostly in non-risk, transient, or epidemic-risk zones with potentially low growth rates in PD incidence. Epidemic-risk zones with moderate to high growth rates are currently marginal outside the United States. However, a global expansion of epidemic-risk zones coupled with small increments in the disease growth rate is projected for 2050. Our study globally downscales the risk of PD establishment while highlighting the importance of considering climate variability, vector distribution and an invasive criterion in obtaining accurate risk maps to guide policy decision-making in plant health.
Ephemeral Resource Availability Makes Wild Guppies More Social
Authors: Snijders Lysanne , Krause Stefan , Tump Alan Novaes , Breuker Michael , Ramnarine Indar W. , Kurvers Ralf , Krause Jens
Published: May 2022

Resource availability and sociality are tightly coupled. Sociality facilitates resource access in a wide range of animal species. Simultaneously, resource availability may change sociality. However, experimental evidence for resource-driven social changes in the wild, beyond local aggregations at the resource, remains scarce. Moreover, it is largely unclear how potential changes in sociality relate to the social foraging benefits obtained by individual group members. Here, we recorded immediate and prolonged changes in social dynamics following ephemeral food availability in 18 mixed-sex Trinidadian guppies (Poecilia reticulata) groups in natural rainforest pools. Using a counter-balanced within-group design, the social associations within each group was observed before, between and after ephemeral patch availability for two consecutive days. We show that groups increased their time spent socially two-fold following ephemeral food patch, but not control (empty) patch, availability. Groups with stronger foraging motivation, measured as the average proportion of fish feeding, showed a stronger increase in sociality. This resource-induced increase in sociality was still detectable the next day. Increase in the time spent socially by a group also positively correlated with the more frequent arrival at detected food patches for individual members of motivated groups, which, in turn, correlated strongly with individual food consumption. Our study causally demonstrates that changes in ephemeral resource availability can induce rapid, substantial, and prolonged changes in the social dynamics of wild fish and that this change positively correlated with individual foraging success. Further research is needed to investigate whether this social change is a cause or consequence of individual foraging success and why some groups respond more strongly than others.
Recognition of BRAF by CDC37 and Re-Evaluation of the Activation Mechanism for the Class 2 BRAF-L597R Mutant
Authors: Bjorklund Dennis M. , Morgan R. Marc L. , Oberoi Jasmeen , Day Katie L. I. M. , Galliou Panagiota A. , Prodromou Chrisostomos
Published: May 2022

The kinome specific co-chaperone, CDC37 (cell division cycle 37), is responsible for delivering BRAF (B-Rapidly Accelerated Fibrosarcoma) to the Hsp90 (heat shock protein 90) complex, where it is then translocated to the RAS (protooncogene product p21) complex at the plasma membrane for RAS mediated dimerization and subsequent activation. We identify a bipartite interaction between CDC37 and BRAF and delimitate the essential structural elements of CDC37 involved in BRAF recognition. We find an extended and conserved CDC37 motif, 20HPNID---SL--W31, responsible for recognizing the C-lobe of BRAF kinase domain, while the c-terminal domain of CDC37 is responsible for the second of the bipartite interaction with BRAF. We show that dimerization of BRAF, independent of nucleotide binding, can act as a potent signal that prevents CDC37 recognition and discuss the implications of mutations in BRAF and the consequences on signaling in a clinical setting, particularly for class 2 BRAF mutations.
Biomolecular solution X-ray scattering at n2STAR Beamline
Authors: Göcenler Oktay , Yenici Cansu M. , Kahraman Kerem , Büyükdağ Cengizhan , Dağ Çağdaş
Published: May 2022

Small angle X-ray Scattering (SAXS) is a method for determining basic structural characteristics such as size, shape, and surface of particles. SAXS can generate low resolution models of biomolecules faster than any other conventional structural biology tools. SAXS data is mostly collected in synchrotron facilities to obtain the best scattering data possible however home source SAXS devices can also generate valuable data when optimized properly. Here, we examined sample data collection and optimization at home source SAXS beamline in terms of concentration, purity, and the duration of data acquisition. We validated that high concentration, monodisperse and ultra pure protein samples obtained by size exclusion chromatography are necessary for generating viable SAXS data using home source beamline. Longer data collection time does not always generate higher resolutions but at least one hour is required for generating a feasible model from SAXS data. Furthermore, with small optimizations both during data collection and later data analysis SAXS can determine properties such as oligomerization, molecular mass, and overall shape of particles in solution under physiological conditions.
Temporal origin of mouse claustrum and development of its cortical projections
Authors: Hoerder-Suabedissen Anna , Ocana-Santero Gabriel , Draper Thomas H. , Scott Sophie A. , Kimani Jesse G. , Shelton Andrew M. , Butt Simon J.B. , Molnár Zoltán , Packer Adam M.
Published: May 2022

The claustrum is known for its extensive connectivity with many other forebrain regions, but its elongated shape and deep location have made further study difficult. We have sought to understand when mouse claustrum neurons are born, where they are located in developing brains and when they develop their widespread connections to cortex. We established that a well-characterised parvalbumin-plexus, which identifies the claustrum in adults, is only present from postnatal day (P)21. A myeloarchitectonic outline of the claustrum can be derived from a triangular fibre arrangement from P15. A dense patch of Nurr1+ cells is present at its core, and is already evident at birth. BrdU-birthdating of forebrain progenitors reveals that the majority of claustrum neurons are born during a narrow time window centred on embryonic day (E)12.5, which is later than the adjacent subplate and endopiriform nucleus. Retrograde tracing revealed that claustrum projections to anterior cingulate (ACA) and retrosplenial cortex (RSP) follow distinct developmental trajectories. Claustrum-ACA connectivity matures rapidly, and reaches adult-like innervation density by P10, whereas claustrum-RSP innervation emerges later over a protracted time window. This work establishes the timeline of claustrum development, and provides a framework for understanding how the claustrum is built and develops its unique connectivity.
From Data to Theory: Understanding the Role of Naive Learners in Cultural Change
Authors: Chimento Michael , Aplin Lucy M.
Published: May 2022

A change to a population’s social network is a change to the substrate of cultural transmission, affecting behavioral diversity and adaptive cultural evolution. While features of network structure such as population size and density have been well studied, less is understood about the influence of social processes such as population turnover— or the repeated replacement of individuals. Experimental data has led to the hypothesis that naive learners can drive cultural evolution by being better samplers, although this hypothesis has only been expressed verbally. We conduct a formal exploration of this hypothesis using a generative model that concurrently simulates its two key ingredients: social transmission and reinforcement learning. We explore how variation in turnover influences changes in the distributions of cultural behaviors over long and short time-scales. We simulate competition between a high and low reward behavior, while varying turnover magnitude and tempo. We find optimal turnover regimes that amplify the production of higher reward behaviors. We also find that these optimal regimes result in a new population composition, where fewer agents which know both behaviors, and more agents know only the high reward behavior. These two effects depend on network size, density, behavioral transmissibility, and characteristics of the learners. Our model provides formal theoretical support for, and predictions about, the hypothesis that naive learners can shape cultural change through their enhanced sampling ability, identified by previous experimental studies. By moving from experimental data to theory, we illuminate an under-discussed generative process arising from an interaction between social dynamics and learning that can lead to changes in cultural behavior.
Septin-Mediated RhoA Activation Engages the Exocyst Complex to Recruit the Cilium Transition Zone
Authors: Safavian Darya , Kim Moshe S. , Xie Hong , Dai Lu , Collins Richard F. , Froese Carol , Nagata Koh-ichi , Trimble William S.
Published: May 2022

Septins are filamentous GTPases that play important, but poorly characterized roles in ciliogenesis. Here, we show that SEPTIN9 regulates RhoA signaling at the base of cilia by binding and activating the RhoA guanine nucleotide exchange factor, ARHGEF18. GTP-RhoA is known to activate the membrane targeting exocyst complex, and suppression of SEPTIN9 causes disruption of ciliogenesis and mislocalization of an exocyst subunit, SEC8. Using basal body-targeted proteins we show that upregulating RhoA signaling at the cilium can rescue ciliary defects and mislocalization of SEC8 caused by global SEPTIN9 depletion. Moreover, we demonstrate that transition zone components, RPGRIP1L and TCTN2 fail to accumulate at the transition zone in cells lacking SEPTIN9 or depleted of the exocyst complex. Thus, SEPTIN9 regulates the recruitment of transition zone proteins on Golgi-derived vesicles by activating the exocyst via RhoA to allow the formation of primary cilia.
Cortical circuits modulate mouse social vocalizations
Authors: Gan-Or Benjamin , London Michael
Published: May 2022

Vocalizations provide a means of communication with high fidelity and information rate for many species. Male mice emit ultrasonic vocalizations (USVs) during female courtship. Diencephalon and brainstem neural circuits have been shown to control the production of USVs, however, the role of cortical circuits in this process is debatable. We show that male mice produced USVs following intracortical microstimulation (ICMS) in a specific location of their anterior cingulate cortex (ACC). Moreover, ACC Ca2+-imaging showed an increase in Ca2+ dynamics preceding USV initiation. Optogenetically suppressing ACC activity caused mice to emit fewer USVs during courtship. Neuropixel electrophysiological recordings in head-restrained male mice indicated a differential increase in neural activity in response to female social exposure (SE). The firing rate in SE trials where USVs were emitted was significantly higher when compared to SE leading to silence. Taken together, these results indicate that the ACC is a key node in the neuronal circuits controlling USV production.
ExplaiNN: interpretable and transparent neural networks for genomics
Authors: Novakovsky Gherman , Fornes Oriol , Saraswat Manu , Mostafavi Sara , Wasserman Wyeth W.
Published: May 2022

Sequence-based deep learning models, particularly convolutional neural networks (CNNs), have shown superior performance on a wide range of genomic tasks. A key limitation of these models is the lack of interpretability, slowing down their adoption by the genomics community. Current approaches to model interpretation do not readily reveal how a model makes predictions, can be computationally intensive, and depend on the implemented architecture. Here, we introduce ExplaiNN, an adaptation of neural additive models[1] for genomic tasks wherein predictions are computed as a linear combination of multiple independent CNNs, each consisting of a single convolutional filter and fully connected layers. This approach brings together the expressiveness of CNNs with the interpretability of linear models, providing global (cell state level) as well as local (individual sequence level) biological insights into the data. We use ExplaiNN to predict transcription factor (TF) binding and chromatin accessibility states, demonstrating performance levels comparable to state-of-the-art methods, while providing a transparent view of the model’s predictions in a straightforward manner. Applied tode novomotif discovery, ExplaiNN identifies equivalent motifs to those obtained from specialized algorithms across a range of datasets. Finally, we present ExplaiNN as a plug-and-play platform in which pretrained TF binding models and annotated position weight matrices from reference databases can be easily combined. We expect that ExplaiNN will accelerate the adoption of deep learning by biological domain experts in their daily genomic sequence analyses.
Buforin II-Escherichia coli’s DNA interactome: Detailed biophysical characterization revealed nanoscale complexes likely formed by DNA supercoiling
Authors: Rubio-Olaya Daniela , Cifuentes Javier , Ruiz-Puentes Paola , Castañeda Octavio A. , Reyes Luis H. , Duitama Jorge , Muñoz Carolina , Cruz Juan C.
Published: May 2022

Antimicrobial peptides (AMPs) have emerged as exciting alternatives to the alarming increase of multiresistant bacteria due to their high activity against them through mechanisms that are thought to largely avoid resistance in the long term. Buforin II (BUFII) is an antibacterial peptide hypothesized to kill bacteria by crossing their membranes to interact with intracellular molecules and interrupt key processes for survival. In particular, interactions with DNA have been considered crucial for triggering cell death mechanisms. However, such interactions are still unknown, and thus far, no reports are available describing BUFII-DNA complexes. Here, we describe a complete biophysical study of the interaction between BUFII and Escherichia coli gDNA via spectrofluorimetric, spectroscopic, and microscopic techniques, complemented with whole-genome sequencing. The E. coli’s DNA-BUFII interactome was isolated by an in vitro pull-down method aided by BUFII-magnetite nanobioconjugates. Our results demonstrated that DNA-BUFII formed round-shape nanoscale complexes by strong electrostatic interactions, likely occurring nonspecifically throughout the entire bacterial genome. Further sequencing of the isolated DNA fragments corroborated this notion and led to hypothesize that BUFII is possibly responsible for inducing DNA’s supercoiling.

Other evidence for this idea was provided by the significant DNA conformational changes observed upon interaction with BUFII. Even though the evidence found fails to describe the complete action mechanism of BUFII in vivo, our findings pave the way to engineer DNA-peptide supramolecular complexes very precisely, which might find application in the field of gene therapy delivery.
Local synaptic inhibition mediates cerebellar granule cell pattern separation necessary for learned sensorimotor associations
Authors: Fleming Elizabeth A. , Field Greg D. , Tadross Michael R. , Hull Court
Published: May 2022

The cerebellar cortex plays a key role in generating predictive sensorimotor associations. To do so, the granule cell layer is thought to establish unique sensorimotor representations for learning. However, how this is achieved and how granule cell population responses contribute to behavior have remained unclear. To address these questions, we have used in vivo calcium imaging and granule cell-specific pharmacological manipulation of synaptic inhibition in awake, behaving mice. We find that inhibition sparsens and thresholds sensory responses, limiting overlap between sensory ensembles and preventing spiking in many granule cells that receive excitatory input. Moreover, we find that inhibition can be recruited in a stimulus-specific manner to powerfully decorrelate multisensory ensembles. Consistent with these results, we find that granule cell inhibition is required for sensory discrimination in a cerebellum-dependent behavior. These data thus reveal new mechanisms for granule cell layer pattern separation beyond those envisioned by classical models.
Actin filaments couple the protrusive tips to the nucleus through the I-BAR domain protein IRSp53 for migration of elongated cells on 1D fibers
Authors: Mukherjee Apratim , Ron Jonathan E. , Hu Hooi Ting , Nishimura Tamako , Hanawa-Suetsugu Kyoko , Behkam Bahareh , Gov Nir S. , Suetsugu Shiro , Nain Amrinder S.
Published: May 2022

The cell migration cycle proceeds with shaping the membrane to form new protrusive structures and redistribution of contractile machinery. The molecular mechanisms of cell migration are well-studied in 2D, but membrane shape-driven molecular migratory landscape in 3D fibrous matrices remains poorly described. 1D fibers recapitulate 3D migration, and here, we examined the role of membrane curvature regulator IRSp53 as a coupler between actin filaments and plasma membrane during cell migration on suspended 1D fibers. Cells attached, elongated, and migrated on the 1D fibers with the coiling of their leading-edge protrusions. IRSp53 depletion reduced cell-length spanning actin stress fibers, reduced protrusive activity, and contractility, leading to uncoupling of the nucleus from cellular movements. Using a theoretical model, the observed transition of IRSp53 depleted cells from rapid stick-slip migration to smooth, and slower migration was predicted to arise from reduced actin polymerization at the cell edges, which was verified by direct measurements of retrograde actin flow using speckle microscopy. Overall, we trace the effects of IRSp53 deep inside the cell from its actin-related activity at the cellular tips, thus demonstrating a unique role of IRSp53 in controlling cell migration in 3D.
Surveying non-visual arrestins reveals allosteric interactions between functional sites
Authors: Seckler James M. , Robinson Emily N. , Lewis Stephen J. , Grossfield Alan
Published: May 2022

1.

Arrestins are important scaffolding proteins that are expressed in all vertebrate animals. They regulate cell signaling events upon binding to active G-protein coupled receptors (GPCR) and trigger endocytosis of active GPCRs. While many of the functional sites on arrestins have been characterized, the question of how these sites interact is unanswered. We used anisotropic network modelling (ANM) together with our covariance compliment techniques to survey all of the available structures of the non-visual arrestins to map how structural changes and protein-binding affect their structural dynamics. We found that activation and clathrin binding have a marked effect on arrestin dynamics, and that these dynamics changes are localized to a small number of distant functional sites. These sites include α-helix 1, the lariat loop, nuclear localization domain, and the C-domain β-sheets on the C-loop side. Our techniques suggest that clathrin binding and/or GPCR activation of arrestin perturb the dynamics of these sites independent of structural changes.
A GATA factor radiation in Caenorhabditis rewired the endoderm specification network
Authors: Darragh Antonia C. , Rifkin Scott A.
Published: May 2022

Although similar developmental regulatory networks can produce diverse phenotypes, different networks can also produce the same phenotype. In theory, as long as development can produce an acceptable end phenotype, the details of the process could be shielded from selection, leading to the possibility of developmental system drift, where the developmental mechanisms underlying a stable phenotype continue to evolve. Many examples exist of divergent developmental genetics underlying conserved traits. However, studies that elucidate how these differences arose and how other features of development accommodated them are rarer. In Caenorhabditis elegans, six GATA-type transcription factors (GATA factors) comprise the zygotic part of the endoderm specification network. Here we show that the core of this network - five of the genes - originated within the genus during a brief but explosive radiation of this gene family and that at least three of them evolved from a single ancestral gene with at least two different spatio-temporal expression patterns. Based on analyses of their evolutionary history, gene structure, expression, and sequence, we explain how these GATA factors were integrated into this network. Our results show how gene duplication fueled the developmental system drift of the endoderm network in a phylogenetically brief period in developmentally canalized worms.
Acute Vaping of a golden Syrian Hamster is Feasible and Leads to Nicotine-Dependent Respiratory Tract Inflammation
Authors: Hinds Daniel M. , Nick Heidi J. , Vallin Tessa M. , Bloomquist Leslie A. , Christeson Sarah , Bratcher Preston E. , Cooper Emily H. , Brinton John T. , Bosco-Lauth Angela , White Carl W.
Published: May 2022

Introduction

E-cigarette vaping has become a major portion of nicotine consumption, especially for children and young adults. Although it is branded as a safer alternative to cigarette smoking, murine and rat models of sub-acute and chronic e-cigarette vaping exposure have shown many pro-inflammatory changes in the respiratory tract. An acute vaping exposure paradigm has not been demonstrated in the golden Syrian hamster, and the hamster is a readily available small animal model that has the unique benefit of becoming infected with and transmitting SARS-CoV-2 without genetic alteration to the animal or virus.

Methods

Using a two-day, whole-body vaping exposure protocol in male golden Syrian hamsters, we evaluated serum cotinine, bronchoalveolar lavage cells, lung and nasal histopathology, and gene expression in the nasopharynx and lung through RT-qPCR. Depending on the presence of nonnormality or outliers, statistical analysis was performed by ANOVA or Kruskal-Wallis tests. For tests that were statistically significant (p-value <0.05), post-hoc Tukey-Kramer and Dunn’s tests, respectively, were performed to make pairwise comparisons between groups.

Results

In nasal tissue, RT-qPCR analysis revealed nicotine-dependent increases in genes associated with type 1 inflammation (CCL-5 and CXCL-10), fibrosis (TGF-β), and a nicotine-independent decrease in the vasculogenesis/angiogenesis gene VEGF-A. In the lung, nicotine-dependent increases in the expression of genes involved in the renin-angiotensin pathway (ACE, ACE2), coagulation (tissue factor, Serpine-1), extracellular matrix remodeling (MMP-2, MMP-9), type 1 inflammation (IL-1β, TNF-α, and CXCL-10), fibrosis (TGF-β and Serpine-1), oxidative stress response (SOD-2), neutrophil extracellular traps release (ELANE), and vasculogenesis and angiogenesis (VEGF-A) were identified.

Conclusion

To our knowledge, this is the first demonstration that the Syrian hamster is a viable model of e-cig induced inhalational injury. In addition, this is the first report that e-cig vaping with nicotine can increase tissue factor gene expression in the lung. Our results show that even an acute exposure to e-cigarette vaping causes significant upregulation in the respiratory tract of pathways involving the renin-angiotensin system, coagulation, extracellular matrix remodeling, type 1 inflammation, fibrosis, oxidative stress response, NETosis, vasculogenesis, and angiogenesis.
Conformational Dynamics and Mechanisms of Client Protein Integration into the Hsp90 Chaperone Controlled by Allosteric Interactions of Regulatory Switches: Perturbation-Based Network Approach for Mutational Profiling of the Hsp90 Binding and Allostery
Authors: Verkhivker Gennady M.
Published: May 2022

Understanding allosteric mechanisms of the Hsp90 chaperone interactions with cochaperones and client protein clientele is fundamental to dissect activation and regulation of many proteins. In this work, atomistic simulations are combined with perturbation-based approaches and dynamic network modeling for a comparative mutational profiling of the Hsp90 binding and allosteric interaction networks in the three Hsp90 maturation complexes with FKBP51 and P23 cochaperones and the glucocorticoid receptor (GR) client. The conformational dynamics signatures of the Hsp90 complexes and dynamics fluctuation analysis revealed how the intrinsic plasticity of the Hsp90 dimer can be modulated by cochaperone and client protein to stabilize the closed dimer state required at the maturation stage of the ATPase cycle. In silico deep mutational scanning of the protein residues characterized the hotspots of protein stability and binding affinity in the Hsp90 complexes, showing that binding hotspots may often coincide with the regulatory centers that modulate dynamic allostery in the Hsp90 dimer. We introduce a perturbation-based network approach for mutational scanning of allosteric residue potentials and characterize allosteric switch clusters that control mechanism of cochaperone-dependent client recognition and remodeling by the Hsp90 chaperone. The results revealed a conserved network of allosteric switches in the Hsp90 complexes that allow cochaperones and GR protein become integrated into the Hsp90 system by anchoring to the conformational switch points in the functional Hsp90 regions. This study suggests that the Hsp90 binding and allostery may operate under a regulatory mechanism in which activation or repression of the Hsp90 activity can be pre-encoded in the allosterically regulated Hsp90 dimer motions. By binding directly to the conformational switch centers on the Hsp90, cochaperones and interacting proteins can efficiently modulate allosteric interactions and long-range communications required for client remodeling and activation.
Repurposed drugs and their combinations prevent morbidity-inducing dermonecrosis caused by diverse cytotoxic snake venoms
Authors: Hall Steven R. , Rasmussen Sean A. , Crittenden Edouard , Dawson Charlotte A. , Bartlett Keirah E. , Westhorpe Adam P. , Albulescu Laura-Oana , Kool Jeroen , María Gutiérrez José , Casewell Nicholas R.
Published: May 2022

Morbidity from snakebite envenoming affects approximately 400,000 people annually. Tissue damage at the bite-site often leaves victims with catastrophic life-long injuries and is largely untreatable by currently available antivenoms. Repurposing small molecule drugs that inhibit specific snake venom toxins offers a potential new treatment strategy for tackling this neglected tropical disease. Using human skin cell assays as an initial model for snakebite-induced dermonecrosis, we show that the repurposed drugs 2,3-dimercapto-1-propanesulfonic acid (DMPS), marimastat, and varespladib, alone or in combination, reduce the cytotoxic potency of a broad range of medically important snake venoms up to 5.7-fold. Thereafter, using a preclinical murine model of dermonecrosis, we demonstrate that the dual therapeutic combinations of DMPS or marimastat with varespladib potently inhibit the dermonecrotic activity of three geographically distinct and medically important snake venoms. These findings strongly support the future translation of repurposed drug combinations as broad-spectrum therapeutics for preventing morbidity caused by snakebite.