bluuebunny/crossref_metadata_2025 huggingface dataset:
Updating the sulcal landscape of the human lateral parieto-occipital junction provides anatomical, functional, and cognitive insights
Authors: Willbrand Ethan H. , Tsai Yi-Heng , Gagnant Thomas , Weiner Kevin S.
Published: June 2023

Recent work has uncovered relationships between evolutionarily new small and shallow cerebral indentations, or sulci, and human behavior. Yet, this relationship remains unexplored in the lateral parietal cortex (LPC) and the lateral parieto-occipital junction (LPOJ). After defining thousands of sulci in a young adult cohort, we revised the previous LPC/LPOJ sulcal landscape to include four previously overlooked, small, shallow, and variable sulci. One of these sulci (ventral supralateral occipital sulcus, slocs-v) is present in nearly every hemisphere and is morphologically, architecturally, and functionally dissociable from neighboring sulci. A data-driven, model-based approach, relating sulcal depth to behavior further revealed that the morphology of only a subset of LPC/LPOJ sulci, including the slocs-v, is related to performance on a spatial orientation task. Our findings build on classic neuroanatomical theories and identify new neuroanatomical targets for future “precision imaging” studies exploring the relationship among brain structure, brain function, and cognitive abilities in individual participants.
How many variables does Wordclim have, really? Generative A.I. unravels the intrinsic dimension of bioclimatic variables
Authors: Dinnage Russell
Published: June 2023

The 19 standard bioclimatic variables available from the Worldclim dataset are some of the most used data in ecology and organismal biology. It is well know that many of the variables are correlated with each other, suggesting there is less than 19 independent dimensions of information in them. But how much information is there? Here I explore the 19 Worldclim bioclimatic variables from the perspective of the manifold hypothesis: that many high dimensional datasets are actually confined to a lower dimensional manifold embedded in an ambient space. Using a state of the art generative probabilistic model (variational autoencoder) to model the data on a non-linear manifold reveals that only 5 uncorrelated dimensions are adequate to capture the full range of variation in the bioclimatic variables. I show that these 5 variables have meaningful structure and are sufficient to produce species distribution models (SDMs) nearly as good and in some ways better than SDMs using the original 19 bioclimatic variables. I have made the 5 synthetic variables available as a raster dataset at 2.5 minute resolution in an R package that also includes functions to convert back and forth between the 5 variables and the original 19 (https://github.com/rdinnager/biocman).
Tracking SARS-CoV-2 seropositivity in rural communities using blood-fed mosquitoes
Authors: Krajacich Benjamin J. , Samaké Djibril , Dao Adama , Diallo Moussa , Sanogo Zana Lamissa , Yaro Alpha Seydou , Ziguimé Amatigué , Poudiougo Josué , Cissé Kadiatou , Traoré Mamadou , Assitoun Alassane dit , Faiman Roy , Zaidi Irfan , John Woodford , Duffy Patrick , Lehmann Tovi
Published: June 2023

The spread of SARS-CoV-2 cannot be well monitored and understood in areas without capacity for effective disease surveillance. Countries with a young population will have disproportionately large numbers of asymptomatic or pauci-symptomatic infections, further hindering detection of infection in the population. Sero-surveillance on a country-wide scale by trained medical professionals may be limited in scope in resource limited setting such as Mali. Novel ways of broadly sampling the human population in a non-invasive method would allow for large-scale surveillance at a reduced cost. Here we evaluate the collection of naturally bloodfed mosquitoes to test for human anti-SARS-CoV-2 antibodies in the laboratory and at five field locations in Mali. Immunoglobulin-G antibodies were found to be readily detectable within the mosquito bloodmeals by a bead-based immunoassay at least through 10 hours post-feeding with high sensitivity (0.900 ± 0.059) and specificity (0.924 ± 0.080), respectively, indicating that most blood-fed mosquitoes collected indoors during early morning hours (and thus, have likely fed the previous night) are viable samples for analysis. We find that reactivity to four SARS-CoV-2 antigens rose during the pandemic from pre-pandemic levels. Consistent with other sero-surveillance studies in Mali, crude seropositivity of blood sampled via mosquitoes was 6.3% in October/November 2020 over all sites, and increased to 25.1% overall, with the town closest to Bamako reaching 46.7% in February of 2021. Mosquito bloodmeals a viable target for conventional immunoassays, and therefore country-wide sero-surveillance of human diseases (both vector-borne and non-vector-borne) is attainable in areas where human-biting mosquitoes are common, and is an informative, cost-effective, non-invasive sampling option.
The Impact of Digital Technology in Care Homes on Unplanned Secondary Care Usage and Associated Costs
Authors: Garner Alex , Lewis Jen , Dixon Simon , Preston Nancy Jean , Caiado Camila C.C.S , Hanratty Barbara , Jones Monica , Knight Jo , Mason Suzanne M
Published: June 2023

Background

A substantial number of emergency department (ED) attendances from care homes could be classed as avoidable. HealthCall is a technology that aims to streamline residents’ care by recording their observations electronically. Observations are fed to remote clinical staff to triage referrals. This study assessed the effectiveness of the HealthCall technology to safely reduce unplanned secondary care usage and associated costs.

Methods

The study involved 118 care homes across the North East from 2018-2021. Routinely collected NHS secondary care data from County Durham and Darlington NHS Foundation Trust was linked with data from the HealthCall technology App. Four outcomes were modelled monthly using Generalised Linear Mixed Models: counts of emergency attendances, emergency admissions, emergency readmissions (28-days), and length of stay of emergency admissions. A similar approach was taken for costs. The impact ofHealthCall was tested on each outcome using the models.

Findings

Data from 8,702 residents was used in the analysis. Results show HealthCall reduces the number of emergency attendances by 11%[6%-15%], emergency admissions by 25% 20%-39%], readmissions reduced by 29%[24%-33%] and length of stay by 11%[3%-18%] (with an additional month-by-month decrease of 28%[24%-34%]). The cost analysis found a cost reduction of £57 per resident in 2018, increasing to £113 in 2021.

Interpretation

The introduction of a digital technology, such as HealthCall, significantly reduces contacts with and costs resulting from unplanned secondary care usage by care home residents.

Funding

This work was funded by Health Data Research UK, CFC0124.
Heterogeneity in Early Postpartum Metabolic Profiles Among Women with GDM Who Progressed to Type 2 Diabetes During 10-Year Follow-Up: The SWIFT Study
Authors: Khan Saifur R , Rost Hannes , Cox Brian , Razani Babak , Alexeeff Stacey , Wheeler Michael B. , Gunderson Erica P.
Published: June 2023

GDM is a strong risk factor for progression to T2D after pregnancy. Although both GDM and T2D exhibit heterogeneity, the link between the distinct heterogeneity of GDM and incident T2D has not been established. Herein, we evaluate early postpartum profiles of women with recent GDM who later developed incident T2D using a soft clustering method, followed by the integration of both clinical phenotypic variables and metabolomics to characterize these heterogeneous clusters/groups clinically and their molecular mechanisms. We identified three clusters based on two indices of glucose homeostasis at 6-9 weeks postpartum – HOMA-IR and HOMA-B among women who developed incident T2D during the 12-year follow-up. The clusters were classified as follows: pancreatic beta-cell dysfunction group (cluster-1), insulin resistant group (cluster-3), and a combination of both phenomena (cluster-2) comprising the majority of T2D. We also identified postnatal blood test parameters to distinguish the three clusters for clinical testing. Moreover, we compared these three clusters in their metabolomics profiles at the early stage of the disease to identify the mechanistic insights. A significantly higher concentration of a metabolite at the early stage of a T2D cluster than other clusters indicates its essentiality for the particular disease character. As such, the early-stage characters of T2D cluster-1 pathology include a higher concentration of sphingolipids, acyl-alkyl phosphatidylcholines, lysophosphatidylcholines, and glycine, indicating their essentiality for pancreatic beta-cell function. In contrast, the early-stage characteristics of T2D cluster-3 pathology include a higher concentration of diacyl phosphatidylcholines, acyl-carnitines, isoleucine, and glutamate, indicating their essentiality for insulin actions. Notably, all these biomolecules are found in the T2D cluster-2 with mediocre concentrations, indicating a true nature of a mixed group. In conclusion, we have deconstructed incident T2D heterogeneity and identified three clusters with their clinical testing procedures and molecular mechanisms. This information will aid in adopting proper interventions using a precision medicine approach.
Patterns of retention in care during clients’ first 12 months after HIV treatment initiation in South Africa: a retrospective cohort analysis using routinely collected data
Authors: Maskew Mhairi , Benade Mariet , Huber Amy , Pascoe Sophie , Sande Linda , Rosen Sydney
Published: June 2023

Background

Retention in HIV care during the early treatment period is one of the most serious challenges facing HIV programs, but the timing and patterns of early disengagement from care remain poorly understood. We describe patterns of engagement in HIV care during the first and second 6-month periods after initiation.

Methods

We analysed retrospective datasets of routinely collected EMR data from ≥18-year-old clients who initiated ART at public sector clinics in South Africa after 01/01/2018 and had ≥14 months potential follow up. Using scheduled visit dates, we classified observed visits into “as planned” or “late” and characterized engagement in care as continuous (all scheduled visits attended ≤28 days late), cyclical (at least one visit >28 days late with a return visit observed) or disengaged (visit not attended and no return visit to the same facility observed).

Results

33,821 client records were included (65% female, median age 33). By six months after ART initiation, 57% had remained continuously in care, 14% had engaged cyclically, 11% had transferred to another facility, 1% had died and 16% had disengaged from care at the initiating facility. Among disengagers in the first 6 months, 58% did not return after their initiation visit, 10% disengaged within the first three months, and the remaining 32% disengaged between 3-6 months. By 12 months after initiation, the overall proportion disengaged was 23%, and only 38% of the cohort had maintained continuous engagement for the full 12 -month period.. Patterns of engagement that were established during the first 6 months on ART demonstrated little change in months 7-12, with participants who were cyclically engaged in months 0-6 were nearly twice as likely to disengage in months 7-12 as continuous engagers in months 0-6 (relative risk 1.8, 95% CI: 1.70-1.99).

Conclusions

As recently as 2018, fewer than 60% and 45% of clients starting ART in South Africa were continuously engaged in care (no interruptions >28 days) at 6 and 12 months, respectively, at their initiating facilities. The needs of continuous and cyclical engagers and disengagers during the first 6 months after initiation may differ and require different interventions or models of care.
The respiratory enzyme complex Rnf is vital for metabolic adaptation and virulence inFusobacterium nucleatum
Authors: Britton Timmie A. , Wu Chenggang , Chen Yi-Wei , Franklin Dana , Chen Yimin , Camacho Martha I. , Luong Truc T. , Das Asis , Ton-That Hung
Published: June 2023

A prominent oral commensal and opportunistic pathogen,Fusobacterium nucleatumcan traverse to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains many metabolically changing environments enabling its virulence potential remains unclear. Informed by our genome-wide transposon mutagenesis, we report here that the highly conserved Rnf complex, encoded by thernfCDGEABgene cluster, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of the Rnf complex via non-polar, in-frame deletion ofrnfC(ΔrnfC) abrogates polymicrobial interaction (or coaggregation) associated with adhesin RadD and biofilm formation. The defect in coaggregation is not due to reduced cell surface of RadD, but rather an increased level of extracellular lysine, which binds RadD and inhibits coaggregation. Indeed, removal of extracellular lysine via washing ΔrnfCcells restores coaggregation, while addition of lysine inhibits this process. These phenotypes mirror that of a mutant (ΔkamA) that fails to metabolize extracellular lysine. Strikingly, the ΔrnfCmutant is defective in ATP production, cell growth, cell morphology, and expression of the enzyme MegL that produces hydrogen sulfide from cysteine. Targeted metabolic profiling demonstrated that catabolism of many amino acids, including histidine and lysine, is altered in ΔrnfCcells, thereby reducing production of ATP and metabolites including H2S and butyrate. Most importantly, we show that the ΔrnfCmutant is severely attenuated in a mouse model of preterm birth. The indispensable function of Rnf complex in fusobacterial pathogenesis via modulation of bacterial metabolism makes it an attractive target for developing therapeutic intervention.

IMPORTANCE

Although viewed as an oral commensal, the Gram-negativeF. nucleatumis an opportunistic pathogen that can spread to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains various metabolically changing environments enabling its virulence potential remains unclear. We demonstrate here that the highly conserved Rnf complex is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of this Rnf complex causes global defects in polymicrobial interaction, biofilm formation, cell growth and morphology, H2S production, and ATP synthesis. Targeted metabolomic profiling demonstrates that the loss of this respiratory enzyme significantly diminishes catabolism of numerous amino acids, which negatively impacts fusobacterial virulence as tested in a preterm birth model in mice.
Directed evolution of nanosensors for the detection of mycotoxins
Authors: Lambert Benjamin P. , Taheri Afsaneh , Wu Shang-Jung , Gillen Alice J. , Kashaninejad Mahdi , Boghossian Ardemis A.
Published: June 2023

In this study, we develop and apply a directed evolution approach to engineer the optical sensing properties of DNA-wrapped single-walled carbon nanotubes (DNA-SWCNTs) towards mycotoxins, a class of molecules critical to detect in the food industry. We successfully demonstrate the creation of sensors for the detection of both the aflatoxin B1 (AFB1) and fumonisin B1 (FB1) mycotoxins based on the specific response of the (9,4) and (7,5) SWCNT chirality fluorescence peaks, respectively. The resulting chirality-specific responsivity was used to demonstrate the multimodal detection of both mycotoxins at different wavelengths of light in the presence of complex food medium. Moreover, we show that directed evolution can be used not only to improve the chiral-dependent selectivity of our sensors to the mycotoxins, but also the sensor sensitivity and fluorescence intensity through multiple rounds of evolution. The approach demonstrated in this study is versatile and could be generalized to other SWCNT sensors as well as other nanosensors comprising a biological element.
H3.3-G34R Mutation-Mediated Epigenetic Reprogramming Leads to Enhanced Efficacy of Immune Stimulatory Gene Therapy in Diffuse Hemispheric Gliomas
Authors: Garcia-Fabiani Maria B. , Haase Santiago , Banerjee Kaushik , Zhu Ziwen , McClellan Brandon L. , Mujeeb Anzar A. , Li Yingxiang , Tronrud Claire E. , Varela Maria L. , West Molly E.J. , Yu Jin , Kadiyala Padma , Taher Ayman W. , Núñez Felipe J. , Alghamri Mahmoud S. , Comba Andrea , Mendez Flor M. , Nicola Candia Alejandro J. , Salazar Brittany , Nunez Fernando M. , Edwards Marta B. , Qin Tingting , Cartaxo Rodrigo T. , Niculcea Michael , Koschmann Carl , Venneti Sriram , Puigdelloses Vallcorba Montserrat , Nasajpour Emon , Pericoli Giulia , Vinci Maria , Kleinman Claudia L. , Jabado Nada , Chandler James P. , Sonabend Adam M. , DeCuypere Michael , Hambardzumyan Dolores , Prolo Laura M. , Mahaney Kelly B. , Grant Gerald A. , Petritsch Claudia K , Welch Joshua D. , Sartor Maureen A. , Lowenstein Pedro R. , Castro Maria G.
Published: June 2023

Diffuse hemispheric glioma (DHG), H3 G34-mutant, representing 9-15% of cases, are aggressive Central Nervous System (CNS) tumors with poor prognosis. This study examines the role of epigenetic reprogramming of the immune microenvironment and the response to immune-mediated therapies in G34-mutant DHG. To this end, we utilized human G34-mutant DHG biopsies, primary G34-mutant DHG cultures, and genetically engineered G34-mutant mouse models (GEMMs). Our findings show that the G34 mutation alters histone marks’ deposition at promoter and enhancer regions, leading to the activation of the JAK/STAT pathway, which in turn results in an immune-permissive tumor microenvironment. The implementation of Ad-TK/Ad-Flt3L immunostimulatory gene therapy significantly improved median survival, and lead to over 50% long term survivors. Upon tumor rechallenge in the contralateral hemisphere without any additional treatment, the long-term survivors exhibited robust anti-tumor immunity and immunological memory. These results indicate that immune-mediated therapies hold significant potential for clinical translation in treating patients harboring H3.3-G34 mutant DHGs, offering a promising strategy for improving outcomes in this challenging cancer subtype affecting adolescents and young adults (AYA).

STATEMENT OF SIGNIFICANCE

This study uncovers the role of the H3.3-G34 mutation in reprogramming the tumor immune microenvironment in diffuse hemispheric gliomas. Our findings support the implementation of precision medicine informed immunotherapies, aiming at improving enhanced therapeutic outcomes in adolescents and young adults harboring H3.3-G34 mutant DHGs.
Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers
Authors: Kim Jee Min , Carcamo Claudia C. , Jazani Sina , Xie Zepei , Feng Xinyu A. , Yamadi Maryam , Poyton Matthew , Holland Katie L. , Grimm Jonathan B. , Lavis Luke D. , Ha Taekjip , Wu Carl
Published: June 2023

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ∼30 bp/sec on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data
Authors: Linse Johanna-Barbara , Hub Jochen S.
Published: June 2023

Biological macromolecules in solution are surrounded by a hydration shell, whose structure differs from the structure of bulk solvent. In crowded cellular environments, hydration shells constitute a large fraction of the overall solvent. While the importance of the hydration shell for numerous biological functions such as molecular recognition or enzymatic activity is widely acknowledged, it is poorly understood how the hydration shell is regulated by macromolecular shape and surface composition, mostly because a quantitative readout of the overall hydration shell structure has been missing. We show that small-angle scattering (SAS) in solution using X-rays (SAXS) or neutrons (SANS) provide a protein-specific footprint of the protein hydration shell that enables quantitative comparison with molecular dynamics (MD) simulations. By means of explicit-solvent SAS predictions, we derived the effect of the hydration shell contrast relative to bulk on the radii of gyrationRgof five proteins using 18 combinations of protein force field and water model. By comparing computedRgvalues from SAXS relative to SANS in D2O with consensus experimental data from a worldwide round-robin study, we found that several but not all force fields yield a hydration shell contrast in remarkable agreement with experimental data. The hydration shell contrast, as captured byRgvalues, strongly depends on the protein charge and geometric shape, thus providing a protein-specific footprint of protein–water interactions and a novel observable for scrutinizing atomistic hydration shell models against experimental data.
Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies
Authors: Schmidt Matthias , Lee Namil , Zhan Chunjun , Roberts Jacob B. , Nava Alberto A. , Keiser Leah , Vilchez Aaron , Chen Yan , Petzold Christopher J. , Haushalter Robert W. , Blank Lars M. , Keasling Jay D.
Published: June 2023

Type I polyketide synthases (T1PKSs) hold an enormous potential as a rational production platform for the biosynthesis of specialty chemicals. However, despite the great progress in this field, the heterologous expression of PKSs remains a major challenge. One of the first measures to improve heterologous gene expression can be codon optimization. Although controversial, choosing the wrong codon optimization strategy can have detrimental effects on protein and product levels. In this study, we analyzed 11 different codon variants of an engineered T1PKS and investigated in a systematic approach their influence on heterologous expression inCorynebacterium glutamicum,Escherichia coli, andPseudomonas putida. Our best performing codon variants exhibited a minimum 50-fold increase in PKS protein levels, which also enables the production of an unnatural polyketide in each of the hosts. Furthermore, we developed a free online tool (https://basebuddy.lbl.gov) that offers transparent and highly customizable codon optimization with up-to-date codon usage tables.

Here, we not only highlight the significance of codon optimization but also establish the groundwork for high-throughput assembly and characterization of PKS pathways in alternative hosts.
Sex disparities in age-related neuromuscular decline: unveiling female susceptibility from early to late elderly
Authors: Guo Yuxiao , Jones Eleanor J. , Smart Thomas F. , Altheyab Abdulmajeed , Gamage Nishadi , Stashuk Daniel W. , Piasecki Jessica , Phillips Bethan E. , Atherton Philip J. , Piasecki Mathew
Published: June 2023

Background

Females typically have a longer lifespan than males which is not matched by an improved healthspan, with older females having higher rates of frailty, characteristic of a sex specific degradation of the neuromuscular system. Several motor unit (MU) characteristics show sex-specific behaviour during mid-level contractions in healthy younger people, highlighting a potential influence of hormonal differences that may be augmented in older age. The purpose of this study was to investigate sex differences in physical performance and MU features of the aged human vastus lateralis (VL) from early to late elderly.

Methods

This study included 21 healthy older males (mean ± SD, range: 67.2 ± 7.6, 56 – 81 yrs) and 17 healthy older females (69.5 ± 5.2, 60 – 78 yrs). Intramuscular electromyography data were collected from VL during standardised submaximal sustained contractions. Muscle size and physical performance characteristics were also measured. Multiple mixed-effects linear regression models with age considered were conducted and statistical significance was accepted when p<0.05.

Results

When compared to males, early to late elderly females had smaller cross-sectional area of VL (p<0.001), lower knee extensor torque (p<0.001) and poorer force steadiness (p=0.036), as well as higher MU firing rate (FR) (p=0.025) and greater MU FR variability (p=0.031). With progression from early to late elderly, both sexes showed decreased functional capacity at a similar rate.

Conclusion

Functional deterioration occurs to a similar extent in both sexes from early to late elderly. However, throughout the majority of the elderly period males demonstrate a greater muscle size, strength, and functional performance. Older females have greater MUFR variability and worse force steadiness than older males. These findings help to address the lack of MU data in older females, and suggest earlier interventions are needed in older females to prevent functional deterioration and reduce the health-sex paradox within ageing humans.
A large-scale study on the nocturnal behavior of African ungulates in zoos and its influencing factor
Authors: Gübert Jennifer , Hahn-Klimroth Max , Dierkes Paul W.
Published: June 2023

This study analyzed the nocturnal behavior of 196 individuals of 19 ungulate species in 20 zoos in Germany and the Netherlands. To the best of our knowledge, this is the first description of nocturnal behavior for some of the species. The importance of a wide range of possible factors influencing nocturnal behavior is discussed. Specifically, the behavioral states of standing and lying were analyzed, evaluating the proportion and number of phases in each behavior. The underlying data consists of 101,629 hours of video material from 9,239 nights. BOVIDS, a deep learning-based software package, was used to analyze the recordings. The analysis of the influencing factors was based on a random forest regression and a SHAP analysis. The results indicate that age, body size and feeding type are the most important factors influencing nocturnal behavior across all species. There are strong differences between the zebra species and the observed Cetartiodactyla as well as White Rhinos. The main difference is that zebras spend significantly less time in a lying position than Cetartiodactyla.
Can leafhoppers help us trace the impact of climate change on agriculture?
Authors: Plante Nicolas , Durivage Jeanne , Brochu Anne-Sophie , Dumonceaux Tim , Torres Dagoberto , Bahder Brian , Kits Joel , Dionne Antoine , Légaré Jean-Philippe , Tellier Stéphanie , Mcune Frédéric , Goulet Charles , Fournier Valérie , Pérez-López Edel
Published: June 2023

Climate change is reshaping agriculture and insect biodiversity worldwide. With rising temperatures, insect species with narrow thermal margins are expected to be pushed beyond their thermal limits, and losses related to herbivory and diseases transmitted by them will be experienced in new regions. Several previous studies have investigated this phenomenon in tropical and temperate regions, locally and globally; however, here, it is proposed that climate change’s impact on agriculture can be traced through the study of Nearctic migratory insects, specifically leafhoppers. To test this hypothesis, leafhoppers in strawberry fields located in the province of Québec, eastern Canada, were evaluated. The strawberry-leafhopper pathosystem offers a unique opportunity because leafhoppers can transmit, among other diseases, strawberry green petal disease (SbGP), which is associated with pathogenic phytoplasmas. Here, we found that in the last ten years, the number of leafhoppers has been increasing in correspondence with the number of SbGP cases detected in eastern Canada, reporting for the first time ten species new to eastern Canada and two to the country, although the leafhopper diversity has been seriously affected. Our model using more than 34 000 leafhoppers showed that their abundance is influenced by temperature, a factor that we found also influences the microbiome associated withMacrosteles quadrilineatus, which was one of the most abundant leafhoppers we observed. One of our most striking findings is that none of the insecticides used by strawberry growers can control leafhopper incidence, which could be linked to microbiome changes induced by changing temperatures. We suggest that Nearctic leafhoppers can be used as sentinels to trace the multilayered effects of climate change in agriculture.

GRAPHICAL ABSTRACT

IN BRIEF

The current climate crisis is reshaping insect biodiversity and abundance, but little is known about the direct effect of this phenomenon on agriculture. In this study, we explored leafhoppers, a group of agriculturally important insect pests and disease vectors, as sentinels of the effect of climate change on agriculture. Our findings indicate that this group of insects can help us to understand the effect of the current climate crisis on insect invasions, diversity, abundance, disease dynamics and insecticide resistance and to take quick action to ensure food security while achieving more sustainable agriculture.

HIGHLIGHTS

Migratory leafhoppers benefit from temperature increases

Leafhopper-transmitted diseases have increased in the last decade

New non-migratory leafhoppers can be found now in Nearctic regions

Leafhopper insecticide resistance could be linked to the insect microbiome
Evidence for a chromosomal inversion maintaining divergent plumage phenotypes between extensively hybridizing yellowhammers (Emberiza citrinella) and pine buntings (E. leucocephalos)
Authors: Nikelski Ellen , Rubtsov Alexander S. , Irwin Darren
Published: June 2023

In an allopatric speciation model, populations of a species become isolated by a geographic barrier and develop reproductive isolation through genetic differentiation. When populations meet in secondary contact, the strength of evolved reproductive barriers determines the extent of hybridization and whether the populations will continue to diverge or merge back together. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are avian sister species that diverged in allopatry during the Pleistocene glaciations. Though they differ greatly in plumage and form distinct genetic clusters in allopatry, these taxa show negligible mitochondrial DNA differentiation and hybridize extensively in sympatry lending uncertainty to the state of reproductive isolation in the system. To assess the strength of reproductive barriers between taxa, we examined genomic differentiation across the yellowhammer and pine bunting system. We found that extensive admixture has occurred in sympatry, indicating that reproductive barriers between taxa are weak. We also identified a putative Z chromosome inversion that underlies plumage variation in the system, with the “pine bunting” inversion form showing dominance over the “yellowhammer” form. Our results suggest that yellowhammers and pine buntings are currently at a crossroads and that evolutionary forces may push this system towards either continued differentiation or population merging. However, even if these taxa merge, recombination suppression between chromosome Z inversion forms may maintain divergent plumage phenotypes within the system. In this way, our findings highlight the important role hybridization plays in increasing the genetic and phenotypic variation as well as the evolvability of a system.
Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids
Authors: Rudibaugh Thomas T. , Keung Albert J.
Published: June 2023

Dopamine signaling in the adult ventral forebrain regulates behavior, stress response, and memory formation and in neurodevelopment regulates neural differentiation and cell migration. Excessive dopamine levels including due to cocaine use both in utero and in adults could lead to long-term adverse consequences. The mechanisms underlying both homeostatic and pathological changes remain unclear, partly due to the diverse cellular responses elicited by dopamine and the reliance on animal models that exhibit species- specific differences in dopamine signaling. To address these limitations, 3-D cerebral organoids have emerged as human-derived models, recapitulating salient features of human cell signaling and neurodevelopment. Organoids have demonstrated responsiveness to external stimuli, including substances of abuse, making them valuable investigative models. In this study we utilize the Xiang-Tanaka ventral forebrain organoid model and characterize their response to acute and chronic dopamine or cocaine exposure. The findings revealed a robust immune response, novel response pathways, and a potential critical role for reactive oxygen species (ROS) in the developing ventral forebrain. These results highlight the potential of cerebral organoids asin vitrohuman models for studying complex biological processes in the brain.
Dectin-1/CARD9-induction of the TFEB and TFE3 gene network is dispensable for phagocyte anti-Aspergillusactivity in the lung
Authors: Aufiero Mariano A. , Shlezinger Neta , Gjonbalaj Mergim , Mills Kathleen A.M. , Ballabio Andrea , Hohl Tobias M.
Published: June 2023

Myeloid phagocytes of the respiratory immune system, such as neutrophils, monocytes, and alveolar macrophages, are essential for immunity toAspergillus fumigatus, the most common etiologic agent of mold pneumonia worldwide. Following engulfment ofA. fumigatusconidia, fusion of the phagosome with the lysosome, is a critical process for killing conidia. TFEB and TFE3 are transcription factors that regulate lysosomal biogenesis under stress and are activated by inflammatory stimuli in macrophages, but it is unknown whether TFEB and TFE3 contribute to anti-Aspergillusimmunity during infection. We found that lung neutrophils express TFEB and TFE3, and their target genes were upregulated duringA. fumigatuslung infection. Additionally,A. fumigatusinfection induced nuclear accumulation of TFEB and TFE3 in macrophages in a process regulated by Dectin-1 and CARD9 signaling. Genetic deletion ofTfebandTfe3impaired macrophage killing ofA. fumigatusconidia. However, in a murine immune competentAspergillusinfection model with genetic deficiency ofTfebandTfe3in hematopoietic cells, we surprisingly found that lung myeloid phagocytes had no defects in conidial phagocytosis or killing. Loss of TFEB and TFE3 did not impact murine survival or clearance ofA. fumigatusfrom the lungs. Our findings indicate that myeloid phagocytes activate TFEB and TFE3 in response toA. fumigatus, and while this pathway promotes macrophage fungicidal activityin vitro, genetic loss can be functionally compensated at the portal of infection in the lung, resulting in no measurable defect in fungal control and host survival.
Top-down modulation in canonical cortical circuits with short-term plasticity
Authors: Waitzmann Felix , Wu Yue Kris , Gjorgjieva Julijana
Published: June 2023

Cortical dynamics and computations are strongly influenced by diverse GABAergic interneurons, including those expressing parvalbumin (PV), somatostatin (SST), and vasoactive intestinal peptide (VIP). Together with excitatory (E) neurons, they form a canonical microcircuit and exhibit counterintuitive nonlinear phenomena. One instance of such phenomena is response reversal, whereby SST neurons show opposite responses to top-down modulation via VIP depending on the presence of bottom-up sensory input, indicating that the network may function in different regimes under different stimulation conditions. Combining analytical and computational approaches, we demonstrate that model networks with multiple interneuron subtypes and experimentally identified short-term plasticity mechanisms can implement response reversal. Surprisingly, despite not directly affecting SST and VIP activity, PV-to-E short-term depression has a decisive impact on SST response reversal. We show how response reversal relates to inhibition stabilization and the paradoxical effect in the presence of several short-term plasticity mechanisms demonstrating that response reversal coincides with a change in the indispensability of SST for network stabilization. In summary, our work suggests a role of short-term plasticity mechanisms in generating nonlinear phenomena in networks with multiple interneuron subtypes and makes several experimentally testable predictions.
Entanglement in living systems
Authors: Day Thomas C. , Zamani-Dahaj S. Alireza , Bozdag G. Ozan , Burnetti Anthony J. , Bingham Emma P. , Conlin Peter L. , Ratcliff William C. , Yunker Peter J.
Published: June 2023

Many organisms exhibit branching morphologies that twist around each other and become entangled. Entanglement occurs when different objects interlock with each other, creating complex and often irreversible configurations. This physical phenomenon is well-studied in non-living materials, such as granular matter, polymers, and wires, where it has been shown that entanglement is highly sensitive to the geometry of the component parts. However, entanglement is not yet well understood in living systems, despite its presence in many organisms. In fact, recent work has shown that entanglement can evolve rapidly, and play a crucial role in the evolution of tough, macroscopic multicellular groups. Here, through a combination of experiments, simulations, and numerical analyses, we show that growth generically facilitates entanglement for a broad range of geometries. We find that experimentally grown entangled branches can be difficult or even impossible to disassemble through translation and rotation of rigid components, suggesting that there are many configurations of branches that growth can access that agitation cannot. We use simulations to show that branching trees readily grow into entangled configurations. In contrast to non-growing entangled materials, these trees entangle for a broad range of branch geometries. We thus propose that entanglement via growth is largely insensitive to the geometry of branched-trees, but instead will depend sensitively on time scales, ultimately achieving an entangled state once sufficient growth has occurred. We test this hypothesis in experiments with snowflake yeast, a model system of undifferentiated, branched multicellularity, showing that lengthening the time of growth leads to entanglement, and that entanglement via growth can occur for a wide range of geometries. Taken together, our work demonstrates that entanglement is more readily achieved in living systems than in their non-living counterparts, providing a widely-accessible and powerful mechanism for the evolution of novel biological material properties.
Dopamine D2 receptors in the bed nucleus of the stria terminalis modulate alcohol-related behaviors
Authors: Pati Dipanwita , Lee Sophia I. , Conley Sara Y. , Sides Tori , Boyt Kristen M. , Hunker Avery C. , Zweifel Larry S. , Kash Thomas L.
Published: June 2023

Dysregulation of the dopamine (DA) system is a hallmark of substance abuse disorders, including alcohol use disorder (AUD). Of the DA receptor subtypes, the DA D2 receptors (D2Rs) play a key role in the reinforcing effects of alcohol. D2Rs are expressed in numerous brain regions associated with the regulation of appetitive behaviors. One such region is the bed nucleus of the stria terminalis (BNST), which has been linked to the development and maintenance of AUD. Recently, we identified alcohol withdrawal-related neuroadaptations in the periaqueductal gray/dorsal raphe to BNST DA circuit in male mice. However, the role of D2R-expressing BNST neurons in voluntary alcohol consumption is not well characterized. In this study, we used a CRISPR-Cas9-based viral approach, to selectively reduce the expression of D2Rs in BNST VGAT neurons and interrogated the impact of BNST D2Rs in alcohol-related behaviors. In male mice, reduced D2R expression potentiated the stimulatory effects of alcohol and increased voluntary consumption of 20% w/v alcohol in a two-bottle choice intermittent access paradigm. This effect was not specific to alcohol, as D2R deletion also increased sucrose intake in male mice. Interestingly, cell-specific deletion of BNST D2Rs in female mice did not alter alcohol-related behaviors but lowered the threshold for mechanical pain sensitivity. Collectively, our findings suggest a role for postsynaptic BNST D2Rs in the modulation of sex-specific behavioral responses to alcohol and sucrose.
Lysinoalanine crosslinking is a conserved post-translational modification in the spirochete flagellar hook
Authors: Lynch Michael J. , Deshpande Maithili , Kyrniyati Kurni , Zhang Kai , James Milinda , Miller Michael , Zhang Sheng , Passalia Felipe J. , Wunder Elsio A. , Charon Nyles W. , Li Chunhao , Crane Brian R.
Published: June 2023

Spirochete bacteria cause Lyme disease, leptospirosis, syphilis and several other human illnesses. Unlike other bacteria, spirochete flagella are enclosed within the periplasmic space where the filaments distort and push the cell body by action of the flagellar motors. We previously demonstrated that the oral pathogenTreponema denticola(Td) catalyzes the formation of covalent lysinoalanine (Lal) crosslinks between conserved cysteine and lysine residues of the FlgE protein that composes the flagellar hook. Although not necessary for hook assembly, Lal is required for motility of Td, presumably due to the stabilizing effect of the crosslink. Herein, we extend these findings to other, representative spirochete species across the phylum. We confirm the presence of Lal crosslinked peptides in recombinant andin vivo-derived samples fromTreponemaspp.,Borreliellaspp.,Brachyspiraspp., andLeptospiraspp.. Like with Td, a mutant strain of the Lyme disease pathogenBorreliella burgdorferiunable to form the crosslink has impaired motility. FlgE fromLeptospiraspp. does not conserve the Lal-forming cysteine residue which is instead substituted by serine. Nevertheless,Leptospira interrogansalso forms Lal, with several different Lal isoforms being detected between Ser-179 and Lys-145, Lys-148, and Lys-166, thereby highlighting species or order-specific differences within the phylum. Our data reveals that the Lal crosslink is a conserved and necessary post-translational modification across the spirochete phylum and may thus represent an effective target for spirochete-specific antimicrobials.

Significance Statement

The phylum Spirochaetota contains bacterial pathogens responsible for a variety of diseases, including Lyme disease, syphilis, periodontal disease, and leptospirosis. Motility of these pathogens is a major virulence factor that contributes to infectivity and host colonization. The oral pathogenTreponema denticolaproduces a post-translational modification (PTM) in the form of a lysinoalanine (Lal) crosslink between neighboring subunits of the flagellar hook protein FlgE. Herein, we demonstrate that representative spirochetes species across the phylum all form Lal in their flagellar hooks.T. denticolaandB. burgdorfericells incapable of forming the crosslink are non-motile, thereby establishing the general role of the Lal PTM in the unusual type of flagellar motility evolved by spirochetes.
CRISPR screening by AAV episome-sequencing (CrAAVe-seq) is a highly scalable cell type-specificin vivoscreening platform
Authors: Ramani Biswarathan , Rose Indigo V.L. , Teyssier Noam , Pan Andrew , Danner-Bocks Spencer , Sanghal Tanya , Yadanar Lin , Tian Ruilin , Ma Keran , Palop Jorge J. , Kampmann Martin
Published: June 2023

There is a significant need for scalable CRISPR-based genetic screening methods that can be applied directly in mammalian tissuesin vivowhile enabling cell type-specific analysis. To address this, we developed an adeno-associated virus (AAV)-based CRISPR screening platform, CrAAVe- seq, that incorporates a Cre-sensitive sgRNA construct for pooled screening within targeted cell populations in mouse tissues. We demonstrate the utility of this approach by screening two distinct large sgRNA libraries, together targeting over 5,000 genes, in mouse brains to create a robust profile of neuron-essential genes. We validate two genes as strongly neuron-essential in both primary mouse neurons andin vivo, confirming the predictive power of our platform. By comparing results from individual mice and across different cell populations, we highlight the reproducibility and scalability of the platform and show that it is highly sensitive even for screening smaller neuronal subpopulations. We systematically characterize the impact of sgRNA library size, mouse cohort size, the size of the targeted cell population, viral titer, and multiplicity of infection on screen performance to establish general guidelines for large-scalein vivoscreens.
Profiling the neuroimmune cascade in 3xTg mice exposed to successive mild traumatic brain injuries
Authors: Pybus Alyssa F. , Bitarafan Sara , Brothers Rowan O. , Rohrer Alivia , Khaitan Arushi , Moctezuma Felix Rivera , Udeshi Kareena , Davies Brae , Triplett Sydney , Dammer Eric , Rangaraju Srikant , Buckley Erin M. , Wood Levi B.
Published: June 2023

Repetitive mild traumatic brain injuries (rmTBI) sustained within a window of vulnerability can result in long term cognitive deficits, depression, and eventual neurodegeneration associated with tau pathology, amyloid beta (Aβ) plaques, gliosis, and neuronal and functional loss. However, we have limited understanding of how successive injuries acutely affect the brain to result in these devastating long-term consequences. In the current study, we addressed the question of how repeated injuries affect the brain in the acute phase of injury (<24hr) by exposing the 3xTg-AD mouse model of tau and Aβ pathology to successive (1x, 3x, 5x) once-daily weight drop closed-head injuries and quantifying immune markers, pathological markers, and transcriptional profiles at 30min, 4hr, and 24hr after each injury. We used young adult mice (2-4 months old) to model the effects of rmTBI relevant to young adult athletes, and in the absence of significant tau and Aβ pathology. Importantly, we identified pronounced sexual dimorphism, with females eliciting more differentially expressed proteins after injury compared to males. Specifically, females showed: 1) a single injury caused a decrease in neuron-enriched genes inversely correlated with inflammatory protein expression as well as an increase in AD-related genes within 24hr, 2) each injury significantly increased expression of a group of cortical cytokines (IL-1α, IL-1β, IL-2, IL-9, IL-13, IL-17, KC) and MAPK phospho-proteins (phospho-Atf2, phospho-Mek1), several of which were co-labeled with neurons and correlated with phospho-tau, and 3) repetitive injury caused increased expression of genes associated with astrocyte reactivity and immune function. Collectively our data suggest that neurons respond to a single injury within 24h, while other cell types including astrocytes transition to inflammatory phenotypes within days of repetitive injury.