bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved classification of alcohol intake groups in the Intermittent-Access Two-Bottle choice rat model using a latent class linear mixed model
Authors: Angeles-Valdez Diego , López-Castro Alejandra , Rasgado-Toledo Jalil , Naranjo-Albarrán Lizbeth , Garza-Villarreal Eduardo A.
Published: September 2024

Alcohol use disorder (AUD) is a major public health problem in which preclinical models allow the study of AUD development, comorbidities and possible new treatments. The intermittent access two-bottle choice (IA2BC) model is a validated preclinical model for studying alcohol intake patterns similar to those present in AUD in human clinical studies. Typically, the mean/median of overall alcohol intake or the last drinking sessions is used as a threshold to divide groups of animals into high or low alcohol consumers. However, it would be more statistically valuable to stratify the groups using the full consumption data from all drinking sessions. In this study, we aimed to evaluate the effectiveness of using the time series data of all drinking sessions to stratify the population into high or low alcohol consumption groups, using a latent class linear mixed model (LCLMM). We compared LCLMM to traditional classification methods: percentiles, k-means clustering, and hierarchical clustering, and used simulations to compare accuracy between methods. Our results demonstrated that LCLMM outperforms other approaches, achieving superior accuracy (0.94) in identifying consumption patterns. By considering the entire trajectory of alcohol intake, LCLMM provides a more robust and nuanced characterization of high and low alcohol consumers. We advocate for the adoption of longitudinal statistical models in substance use disorder research, both in human studies and preclinical investigations, as they hold promise for enhancing population stratification and refining treatment strategies.
Structural proteomics defines a sequential priming mechanism for the progesterone receptor
Authors: Mann Matthew D. , Wang Min , Ferreon Josephine C. , Suess Michael P. , Jain Antrix , Malovannaya Anna , Alvarez Roberto Vera , Pascal Bruce D. , Kumar Raj , Edwards Dean P. , Griffin Patrick R.
Published: September 2024

The progesterone receptor (PR) is a steroid-responsive nuclear receptor with two isoforms: PR-A and PR-B. Disruption of PR-A:PR-B signaling is associated with breast cancer through interactions with oncogenic co-regulatory proteins (CoRs). However, molecular details of isoform-specific PR-CoR interactions remain poorly understood. Using structural mass spectrometry, we investigate the sequential binding mechanism of purified full-length PR and intact CoRs, steroid receptor coactivator 3 (SRC3) and p300, as complexes on target DNA. Our findings reveal selective CoR NR-box binding by PR and unique interaction surfaces between PR and CoRs during complex assembly, providing a structural basis for CoR sequential binding on PR. Antagonist-bound PR showed persistent CoR interactions, challenging the classical model of nuclear receptor activation and repression. Collectively, we offer a peptide-level perspective on the organization of the PR transcriptional complex and infer the mechanisms behind the interactions of these proteins, both in active and inactive conformations.
Target protein identification in live cells and organisms with a non-diffusive proximity tagging system
Authors: Sun Yingjie , Li Changheng , Deng Xiaofei , Li Wenjie , Deng Xiaoyi , Ge Weiqi , Shi Miaoyuan , Guo Ying , Yu Yanxun V , Zhou Hai-Bing , Jin Youngnam N
Published: September 2024

Identifying target proteins for bioactive molecules is essential for understanding their mechanisms, developing improved derivatives, and minimizing off-target effects. Despite advances in target identification (target-ID) technologies, significant challenges remain, impeding drug development. Most target-ID methods use cell lysates, but maintaining an intact cellular context is vital for capturing specific drug-protein interactions, such as those with transient protein complexes and membrane-associated proteins. To address these limitations, we developed POST-IT (Pup-On-target for Small molecule Target Identification Technology), a non-diffusive proximity tagging system for live cells, orthogonal to the eukaryotic system. POST-IT utilizes an engineered fusion of proteasomal accessory factor A (PafA) and HaloTag to transfer Pup to proximal proteins upon directly binding to the small molecule. After significant optimization to eliminate self-pupylation and polypupylation, minimize depupylation, and optimize chemical linkers, POST-IT successfully identified known targets and discovered a new binder, SEPHS2, for dasatinib, and VPS37C as a new target for hydroxychloroquine, enhancing our understanding these drugs’ mechanisms of action. Furthermore, we demonstrated the application of POST-IT in live zebrafish embryos, highlighting its potential for broad biological research and drug development.
Soil bacteria may be the natural reservoirs of drug resistance genes
Authors: Ahmad Salman , Awan Asad Bashir , Irfan Sofia , Haque Abdul
Published: September 2024

Soil bacteria are the main source of antibiotics because they produce them naturally to get territorial advantage. We collected deep soil samples and characterized cultivable microbes. We used morphological and cultural characters, biochemical reactions, 16s RNA PCR and DNA sequencing to identify the isolates. The isolates includedPseudomonasspp (12),Shigellaspp (2),E. coli(1),Klebsiella/Citrobacterspp (1),Micrococcus spp(2), unidentifiedBacillusspp.(18),Bacillus paramycoides(3),Paenibacillus lautus(2),Bacillus pacificus(2), andLysinibacillus pakistanensis(1). Out of these 44 isolates, 33 (75%) were multi-drug resistant. Clinically relevant and clinically irrelevant bacteria had similar drug resistance patterns (88.9% and 88.0%, 88.9% and 88.0%, 100 and 96.0%, 61.1% and 92%, 83.3% and 96%, 33.3% and 36%, 55.6% and 68.0%, and 83.3% and 60%) towards Ampicillin, Amoxicillin, Oxacillin, Azithromycin, Streptomycin, Gentamicin, Ceftriaxone and Sulfamethoxazole respectively. The observation that bacteria which cannot colonize humans/animals and therefore cannot enter the horizontal drug resistance gene transfer cycle in clinical settings also have a large and similar arsenal of drug resistance genes, may indicate that they are actually the natural reservoirs. Because they are more dynamic in their ability to survive in different conditions, they provide better fitness for maintenance of these reservoirs.

Impact Statement

We think this study has raised interesting questions and further probing at a larger scale and a greater depth will provide new insight that may be very helpful for understanding the phenomenon of spread of drug resistance among bacteria which is one of the paramount challenges for humanity.
Modular photostable fluorescent DNA blocks dissect the effects of pathogenic mutant kinesin on collective transport
Authors: Kita Tomoki , Sugie Ryota , Suzuki Yuki , Niwa Shinsuke
Published: September 2024

Intracellular transport is driven by teams of various motor proteins. Advances in DNA nanotechnology have enabled the programmable linkage of different types of motor proteins. In this study, we developed a modular, photostable, fluorescence-labeled tiny DNA origami block (FTOB) for extended observation of collective transport by selected motor combinations. The FTOB is designed as a 4-helix bundle (∼8.4 nm) with densely accumulated fluorescent dyes, minimizing blinking and photobleaching. By designing a pair of connector DNAs, FTOBs are heterodimerized following motor protein attachment using the ALFA-tag/nanobody system. Our system examined the impact of a pathogenic mutant kinesin on its collective movement with wild-type kinesin, clearly observing two distinct behaviors: the team’s velocity was generally governed by the slower mutant but occasionally surged to levels comparable to that of a single wild-type motor. Our photostable, robust, modular FTOB system could serve as a versatile tool for precisely dissecting cooperative cargo transport.
Single-nucleus multi-omics identifies shared and distinct pathways in Pick’s and Alzheimer’s disease
Authors: Shi Zechuan , Das Sudeshna , Morabito Samuel , Miyoshi Emily , Stocksdale Jennifer , Emerson Nora , Srinivasan Shushrruth Sai , Shahin Arshi , Rahimzadeh Negin , Cao Zhenkun , Silva Justine , Castaneda Andres Alonso , Head Elizabeth , Thompson Leslie , Swarup Vivek
Published: September 2024

The study of neurodegenerative diseases, particularly tauopathies like Pick’s disease (PiD) and Alzheimer’s disease (AD), offers insights into the underlying regulatory mechanisms. By investigating epigenomic variations in these conditions, we identified critical regulatory changes driving disease progression, revealing potential therapeutic targets. Our comparative analyses uncovered disease-enriched non-coding regions and genome-wide transcription factor (TF) binding differences, linking them to target genes. Notably, we identified a distal human-gained enhancer (HGE) associated with E3 ubiquitin ligase (UBE3A), highlighting disease-specific regulatory alterations. Additionally, fine-mapping of AD risk genes uncovered loci enriched in microglial enhancers and accessible in other cell types. Shared and distinct TF binding patterns were observed in neurons and glial cells across PiD and AD. We validated our findings using CRISPR to excise a predicted enhancer region in UBE3A and developed an interactive database (http://swaruplab.bio.uci.edu/scROAD) to visualize predicted single-cell TF occupancy and regulatory networks.
Cell-mechanical parameter estimation from 1D cell trajectories using simulation-based inference
Authors: Heyn Johannes C. J. , Atienza Juanatey Miguel , Falcke Martin , Rädler Joachim O.
Published: September 2024

Trajectories of motile cells represent a rich source of data that provide insights into the mechanisms of cell migration via mathematical modeling and statistical analysis. However, mechanistic models require cell type dependent parameter estimation, which in case of computational simulation is technically challenging due to the nonlinear and inherently stochastic nature of the models. Here, we employ simulation-based inference (SBI) to estimate cell specific model parameters from cell trajectories based on Bayesian inference. Using automated time-lapse image acquisition and image recognition large sets of 1D single cell trajectories are recorded from cells migrating on microfabricated lanes. A deep neural density estimator is trained via simulated trajectories generated from a previously published mechanical model of cell migration. The trained neural network in turn is used to infer the probability distribution of a limited number of model parameters that correspond to the experimental trajectories. Our results demonstrate the efficacy of SBI in discerning properties specific to non-cancerous breast epithelial cell line MCF-10A and cancerous breast epithelial cell line MDA-MB-231. Moreover, SBI is capable of unveiling the impact of inhibitors Latrunculin A and Y-27632 on the relevant elements in the model without prior knowledge of the effect of inhibitors. The proposed approach of SBI based data analysis combined with a standardized migration platform opens new avenues for the installation of cell motility libraries, including cytoskeleton drug efficacies,and may play a role in the evaluation of refined models.

Subject Areas

Biological Physics / Interdisciplinary Physics
Cyanobacteria from marine oxygen deficient zones encode both form I and form II rubiscos
Authors: Jaffe Alexander L. , Harrison Kaitlin , Jain Navami , Taylor-Kearney Leah J. , Wang Renée Z. , Prywes Noam , Shih Patrick M. , Young Jodi , Rocap Gabrielle , Dekas Anne E.
Published: September 2024

Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon to biomass. To date, all studied Cyanobacterial lineages encode carbon fixation machinery hinged upon form I rubisco enzymes within a CO2-concentrating carboxysome. Here, we report that the AMZ IB lineage ofProchlorococcusfrom global oxygen deficient zones (ODZs) harbor both form I and form II rubisco enzymes, the latter of which are typically non-carboxysomal and possess biochemical properties tuned towards low oxygen environments. Our analyses reveal that these cyanobacterial form II enzymes are functionalin vitroand were likely acquired via lateral gene transfer from proteobacteria. Global metagenomic read recruitment demonstrates thatProchlorococcuswith form II rubisco are essentially restricted to ODZs in the Eastern Tropical Pacific, suggesting that acquisition may confer an advantage specifically under low-O2conditions. Populations of AMZ IBProchlorococcusexpress both forms of rubiscoin situ, with the highest form II rubisco expression at depths where both oxygen and light are particularly low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for the overall capacity of ODZs to sequester carbon.
3D modeling of thermostable xylanase from Thermotoga naphthophila a member of GH10 family: characterization studies of recombinant xylanase
Authors: Waris Asma , Awan Ali Raza , Wasim Muhammad , Hashmi Abu Seed , Rashid Naeem , Firyal Sehrish , khalid Aisha , Tayyab Muhammad
Published: September 2024

The current study was planned keeping in view the significance, industrial impact and import of xylanase to Pakistan. In this study, a thermostable recombinant xylanase fromThermotoga naphthophilawas produced and characterized. The PCR product (1.1 kb) was purified, ligated in the pTZ57R/T and was used for transformation of DH5α cells. The presence of the gene in the recombinant pTZ57R/T was confirmed by restriction analysis. The gene was sub-cloned in pET21a and expression was examined using BL21 CodonPlus (DE3) cells. The recombinant xylanase was expressed as an intracellular soluble protein. SDS-PAGE demonstrated the purified recombinant xylanase as 37 kDa protein. Xylanase showed its optimal activity at 90°C and pH 7. The enzyme was found thermostable and retained 67% activity after an incubation of 1.5h at 90°C in the presence of Mn2+. The xylanase activity was enhanced in the presence of Triton X-I00 while the presence of SDS, Tween 20 and Tween 80 showed a declined impact on the activity. Kinetics studies showed the VmaxandKmvalues of 2313 μmol/mg/min and 3.3 mg/ml respectively. The 3D structure analysis demonstrated the presence of a conserved active site comprised of two glutamate and substrate accommodate sites comprised of + 1, +2 and -1, -2 xylose binding sites in the structure of xylanase. The ability of this thermostable xylanase to work at a wide range of temperatures and pH makes it a suitable candidate for industrial applications.
Forecasting COVID-19, Influenza and RSV hospitalisations over winter 2023/24 in England
Authors: Mellor Jonathon , Tang Maria L. , Jones Owen ,   Infectious Disease Modelling Team, Ward Thomas , Riley Steven , Deeny Sarah R.
Published: September 2024

Seasonal respiratory viruses cause substantial pressure on healthcare systems, particularly over winter. System managers can mitigate the impact on patient care when they anticipate hospital admissions due to these viruses. Hospitalisation forecasts were used widely during the SARS-CoV-2 pandemic. Now, resurgent seasonal respiratory pathogens add complexity to system planning. We describe how a suite of forecasts for respiratory pathogens, embedded in national and regional decision-making structures, were used to mitigate the impact on hospital systems and patient care.

We developed forecasting models predicting hospital admissions and bed occupancy two weeks ahead for COVID-19, influenza, and RSV in England over winter 2023/24. Bed occupancy forecasts were informed by the ensemble admissions models. Forecasts were delivered in real-time at multiple scales. The use of sample-based forecasting allowed for effective reconciliation and trend interpretation.

Admission forecasts, particularly RSV and influenza, showed high skill at regional levels. Bed occupancy forecasts had well-calibrated coverage, owing to informative admissions forecasts and slower moving trends. National admissions forecasts had mean absolute percentage errors of 27.3%, 30.9% and 15.7% for COVID-19, influenza, and RSV respectively, with corresponding 90% coverages of 0.439, 0.807 and 0.779.

These real-time winter infectious disease forecasts produced by the UK Health Security Agency for healthcare system managers played an informative role in mitigating seasonal pressures. The models were delivered regularly and shared widely across the system to key users. This was achieved by producing reliable, fast, and epidemiologically informed ensembles of models. Though, a higher diversity of model approaches could have improved forecast accuracy.
Investigating Chemokine-Induced NF-κB Activation in Retinal Cells and Its Contribution to Age-Related Macular Degeneration Pathogenesis: A Systematic Review
Authors: Siddiqui Ifrah , Khan Nabeel Ahmad , Ahmad Fatima , Nawaz Maham , Naeem Almas , Khalid Muhammad Usaid , Mirza Usman Haroon , Danish Hamza Ali , Khalid Syed Saqib
Published: September 2024

Objective

To investigate the roles of chemokines in activating the NF-κB signaling pathway in retinal pigment epithelium (RPE) and photoreceptor cells, and their contribution to the pathogenesis of age-related macular degeneration (AMD).

Background

AMD is a leading cause of vision loss in older adults, driven by chronic inflammation and oxidative stress. The NF-κB transcription factor plays a key role in regulating these processes, with various chemokines, such as CCL2 and CX3CL1, influencing NF-κB activation. Despite advances in treatment, a deeper understanding of how chemokines affect NF-κB activation in RPE and photoreceptor cells remains critical for developing effective therapies. This study seeks to address this gap and improve AMD management.

Methods

A comprehensive search of databases, including PubMed, MEDLINE, and Google Scholar, was conducted to identify relevant studies on the roles of chemokines in activating NF-κB signaling in RPE and photoreceptor cells. The search covered chemokines such as CCL2 (MCP-1), CX3CL1 (Fractalkine), CCL3 (MIP-1α), CCL5 (RANTES), CXCL8 (IL-8), CXCL10 (IP-10), CXCL1 (GRO-α), CXCL12 (SDF-1), CCL11 (Eotaxin), CXCL16, CXCL9 (MIG), and CXCL11 (I-TAC). Studies were systematically reviewed following PRISMA guidelines to assess the involvement of these chemokines in NF-κB activation.

Results

The analysis revealed that chemokines, including CCL2, CX3CL1, CCL3, and CCL5, significantly activated NF-κB in RPE and photoreceptor cells, leading to increased inflammation and apoptosis through enhanced cytokine production and reactive oxygen species (ROS) generation. Additionally, CXCL8, CXCL10, CXCL1, and CXCL12 triggered NF-κB activation, contributing to oxidative stress and extracellular matrix (ECM) remodeling, which disrupts retinal structure and function. Other chemokines, such as CCL11, CXCL16, CXCL9, and CXCL11, sustained chronic inflammation and modulated matrix metalloproteinases (MMPs), further implicating them in AMD progression.

Conclusion

Chemokines, including CCL2, CX3CL1, CCL3, CCL5, CXCL8, CXCL10, CXCL1, CXCL12, CCL11, CXCL16, CXCL9, and CXCL11, activate the NF-κB pathway in RPE and photoreceptor cells, driving chronic inflammation, oxidative stress, and ECM remodeling in AMD. These findings highlight potential therapeutic targets to mitigate disease progression.
Discriminatory ability of adiposity phenotypes in identifying cardiometabolic disorders in indigenous and non-indigenous African populations
Authors: Kufe Clement Nyuyki , Mbanya Jean Claude
Published: September 2024

Background

Whether any of the anthropometric indices are associated with cardiometabolic outcomes in indigenous Fulani African populations is not known. This study evaluates anthropometric indices in Fulani and non-autochthonous populations in predicting cardiometabolic outcomes in indigenous and non-indigenous populations.

Methods

A population-based cross-sectional study recruited 1 921 participants of similar median aged 32 (24–45) years from Fulbe (settled Fulani), Mbororo (nomadic pastoral Fulani) and the general population. Body weight (BW), height, waist circumference (WC), and hip circumference (HC) were measured and body mass index (BMI), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR), Conicity Index (Cindex), body adiposity index (BAI), body roundness index (BRI) and body shape index (ABSI) were determined. The associations of anthropometric indices with cardiometabolic disorders were assessed by multivariable adjusted logistic regression and the area under the receiver-operating characteristic (ROC) curve compared the predictive abilities.

Results

Women had higher prevalence of MetS and the men had higher prevalence of hypertension and IFG/diabetes/hypertension while the prevalence of IFG/diabetes was similar in men and women. In women, the ROC and multivariable logistic regression analyses both showed consistent good performance of BW and BMI in identifying IFG/Diabetes in Fulbe and general population; BW, HC, BMI and BAI in Mbororo and BW, WC, HC, WHtR, and BRI in general population to predict hypertension and IFG/diabetes/hypertension. All the anthropometric indices showed good performance in all the groups to identify MetS. In men, WC, HC and BRI had good performance in all the groups while WC and BRI had good performance in all groups and HC in Fulbe and Mbororo to predict hypertension. The BW, WC, HC, BMI, WHtR, BAI and BRI showed consistent good performance in all the groups to predict MetS.

Conclusion

Anthropometric indices of adiposity are important risk assessing tools for cardiometabolic disorders in indigenous as well as non-autochthonous populations varying by ethnic group and sex.
Sex-Specific Skeletal Muscle Gene Expression Responses to Exercise Reveal Novel Direct Mediators of Insulin Sensitivity Change
Authors: Ma S , Morris MC , Hubal MJ , Ross LM , Huffman KM , Vann CG , Moore N , Hauser ER , Bareja A , Jiang R , Kummerfeld E , Barberio MD , Houmard JA , Bennett WB , Johnson JL , Timmons JA , Broderick G , Kraus VB , Aliferis CF , Kraus WE
Published: September 2024

BACKGROUND

Understanding the causal pathways, systems, and mechanisms through which exercise impacts human health is complex. This study explores molecular signaling related to whole-body insulin sensitivity (Si) by examining changes in skeletal muscle gene expression. The analysis considers differences by biological sex, exercise amount, and exercise intensity to identify potential molecular targets for developing pharmacologic agents that replicate the health benefits of exercise.

METHODS

The study involved 53 participants from the STRRIDE I and II trials who completed eight months of aerobic training. Skeletal muscle gene expression was measured using Affymetrix and Illumina technologies, while pre- and post-training Si was assessed via an intravenous glucose tolerance test. A novel gene discovery protocol, integrating three literature-derived and data-driven modeling strategies, was employed to identify causal pathways and direct causal factors based on differentially expressed transcripts associated with exercise intensity and amount.

RESULTS

In women, the transcription factor targets identified were primarily influenced by exercise amount and were generally inhibitory. In contrast, in men, these targets were driven by exercise intensity and were generally activating. Transcription factors such as ATF1, CEBPA, BACH2, and STAT1 were commonly activating in both sexes. Specific transcriptional targets related to exercise-induced Si improvements included TACR3 and TMC7 for intensity-driven effects, and GRIN3B and EIF3B for amount-driven effects. Two key signaling pathways mediating aerobic exercise-induced Si improvements were identified: one centered on estrogen signaling and the other on phorbol ester (PKC) signaling, both converging on the epidermal growth factor receptor (EGFR) and other relevant targets.

CONCLUSIONS

The signaling pathways mediating Si improvements from aerobic exercise differed by sex and were further distinguished by exercise intensity and amount. Transcriptional adaptations in skeletal muscle related to Si improvements appear to be causally linked to estrogen and PKC signaling, with EGFR and other identified targets emerging as potential skeletal muscle-specific drug targets to mimic the beneficial effects of exercise on Si.
Sex-Specific Roles of Hypocretin Receptor Signaling in CRF Neurons on Alcohol Drinking, Anxiety, and BNST Neuronal Excitability
Authors: Ma Yihe , Sardar Haniyyah , Benabou Max E. , Yu Angeline C. , Morningstar Allison R. , Fajardo R. Nicolas , Kandil Isaac F. , Rogers Ethan T. , Vassalli Anne , Kauer Julie A. , Giardino William J.
Published: September 2024

Alcohol use disorder (AUD) is characterized by compulsive alcohol consumption and negative emotional states during withdrawal, often perpetuating a cycle of addiction through arousal dysfunction. The hypocretin/orexin (Hcrt) neuropeptide system, a key regulator of arousal, has been implicated in these processes, particularly in its interactions with corticotropin-releasing factor (CRF) neurons within the bed nucleus of the stria terminalis (BNST). We investigated the role of Hcrt receptor signaling in CRF neurons in modulating alcohol intake, anxiety behaviors, and BNST excitability, with a focus on sex-specific differences. Using CRF-specific genetic deletion of HcrtR1 and/or HcrtR2 receptors in mice, we found that deletion of HcrtR1 significantly reduced alcohol intake, with sex-specific effects on BNST excitability. CRF-specific HcrtR2 deletion, while not affecting alcohol consumption, decreased baseline anxiety-like behaviors in males relative to females. Moreover, the double deletion of both Hcrt receptors from CRF neurons led to reduced alcohol drinking in males and dampened anxiety behaviors and BNST excitability in both sexes during protracted withdrawal. These findings suggest that Hcrt signaling in CRF neurons plays a critical role in the persistence of excessive alcohol consumption and the development of negative affective states, with distinct contributions from HcrtR1 and HcrtR2. The observed sex-specific differences underscore the need for tailored therapeutic approaches targeting the Hcrt system in the treatment of AUD.
Switchable Conformation in Protein Subunits: Unveiling Assembly Dynamics of Icosahedral Viruses
Authors: Li Siyu , Tresset Guillaume , Zandi Roya
Published: September 2024

The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the genome to form highly symmetrical structures remains an unresolved puzzle. In this paper, we design novel subunits and develop a model that enables us to explore the assembly pathways and genome packaging mechanism of icosahedral viruses, which were previously inaccessible. Using molecular dynamics (MD) simulations, we observe capsid fragments, varying in protein number and morphology, assembling at different locations along the genome. Initially, these fragments create a disordered structure that later merges to form a perfect symmetric capsid. The model demonstrates remarkable strength in addressing numerous unresolved issues surrounding virus assembly. For instance, it enables us to explore the advantages of RNA packaging by capsid proteins over linear polymers. Our MD simulations are in excellent agreement with our experimental findings from small-angle X-ray scattering and cryo-transmission electron microscopy, carefully analyzing the assembly products of viral capsid proteins around RNAs with distinct topologies.
Swarming rate and timing of unmanaged honeybee colonies (Apis mellifera carnica) in a forest environment
Authors: Rutschmann Benjamin , Kohl Patrick L. , Steffan-Dewenter Ingolf
Published: September 2024

Investigating the life history of social insect colonies and the demography of their populations are important for their conservation, but data collection is challenging. There is a growing interest in understanding the population status of wild-living honeybee colonies across Europe, for which it is critical to collect data on survival and natality rates. Although survival rates can be investigated through regular inspections of wild nests, the accurate quantification of natality rates (i.e., the number of swarms produced per colony per year) remains a significant challenge. Using digital weight scales, we remotely monitored the natural swarming behavior of ten unmanagedApis mellifera carnicacolonies housed in static-volume hives (45L) in a forest region of southern Germany. During the 2019 season, between mid-May and late June, we recorded 17 swarming events, averaging 1.7 swarms per colony. Our observations offer a reference point for the timing, frequency, and size of honeybee swarms that helps us understand the natural reproductive patterns of wild-living honeybees in a temperate forest environment.
Integrating Phenomic Selection Using Single-Kernel Near-Infrared Spectroscopy and Genomic Selection for Corn Breeding Improvement
Authors: Graciano Rafaela P. , Peixoto Marco Antônio , Leach Kristen A. , Suzuki Noriko , Gustin Jeff , Settles A. Mark , Armstrong Paul R. , Resende Márcio F. R.
Published: September 2024

Phenomic Selection (PS) is a cost-effective method proposed for predicting complex traits and enhancing genetic gain in breeding programs. The statistical procedures are similar to those utilized in genomic selection (GS) models, but molecular markers data are replaced with phenomic data, such as near-infrared spectroscopy (NIRS). However, the use of NIRS applied to PS typically utilized destructive sampling or collected data after the establishment of selection experiments in the field. Here, we explored the application of PS using non-destructive, single-kernel NIRS in a sweet corn breeding program, focusing on predicting future, unobserved field-based traits of economic importance, including ear and vegetative traits. Three models were employed on a diversity panel: G-BLUP and P-BLUP models, which used relationship matrices based on SNP and NIRS data, and a combined model. The genomic relationship matrices were evaluated with varying numbers of SNPs. Additionally, the P-BLUP model trained on the diversity panel was used to select doubled haploid (DH) lines for germination before planting, with predictions validated using observed data. The findings indicate that PS generated good predictive ability (e.g., 0.46 for plant height) and effectively distinguished between high and low germination rates in untested DH lines. Although GS generally outperformed PS, the model combining both information yielded the highest predictive ability, with considerably higher accuracies than GS when low marker densities were used. This study highlights the potential of NIRS both to achieve genetic gain where GS may not be feasible and to maintain/improve accuracy with SNP-based information while reducing genotyping costs.

Key message

Phenomic selection using whole seeds is a promising alternative to improve genetic gain and complement genomic selection in corn breeding. Models that combine genomic and phenomic data maximize the predictive ability.
Pcbp1 constrains Oct4 expression in the context of pluripotency
Authors: Bakhmet E. I. , Zinovyeva A. S. , Kuzmin A. A. , Smirnova D. V. , Gordeev M. N. , Petrenko E. E. , Aksenov N. D. , Tomilin A. N.
Published: September 2024

Oct4 is a commonly known marker of pluripotent stem cells as well as one of the key factors required for pluripotency induction. Its gene (Pou5f1) is subject to complicated regulation through distal and proximal enhancers. Noteworthy, this protein also plays an important role in primitive endoderm (PrE) specification, though the mechanisms driving its expression during this process are still unknown. Here we show that KH-domain protein Pcbp1 occupies poly(C)-sites of thePou5f1enhancers, butPcbp1knockout does not affect the Oct4 expression level in ESCs. On the contrary, Pcbp1 is essential for timely Oct4 downregulation upon differentiation signals. Residual Oct4 expression in turn leads to PrE specification, and this phenotype is reminiscent of that in ESCs constitutively expressing Oct4. Overall, our results point to Pcbp1 is a transcriptional regulator ofPou5f1,purported to synchronize Oct4 expression decline with the pluripotency network shutdown during differentiation. Oct4 being outside of this network loss its functions as factor of pluripotency and acts as PrE specifier.
Modeling Cortical Versus Hippocampal Network Dysfunction in a Human Brain Assembloid Model of Epilepsy and Intellectual Disability
Authors: McCrimmon Colin M. , Toker Daniel , Pahos Marie , Lozano Kevin , Lin Jack J. , Parent Jack , Tidball Andrew , Zheng Jie , Molnár László , Mody Istvan , Novitch Bennett G. , Samarasinghe Ranmal A.
Published: September 2024

Neurodevelopmental disorders often impair multiple cognitive domains. For instance, a genetic epilepsy syndrome might cause seizures due to cortical hyperexcitability and present with memory impairments arising from hippocampal dysfunction. This study examines how a single disorder differentially affects distinct brain regions by using human patient iPSC-derived cortical- and hippocampal-ganglionic eminence assembloids to model Developmental and Epileptic Encephalopathy 13 (DEE-13), a condition arising from gain-of-function mutations in theSCN8Agene. While cortical assembloids showed network hyperexcitability akin to epileptogenic tissue, hippocampal assembloids did not, and instead displayed network dysregulation patterns similar to in vivo hippocampal recordings from epilepsy patients. Predictive computational modeling, immunohistochemistry, and single-nucleus RNA sequencing revealed changes in excitatory and inhibitory neuron organization that were specific to hippocampal assembloids. These findings highlight the unique impacts of a single pathogenic variant across brain regions and establish hippocampal assembloids as a platform for studying neurodevelopmental disorders.
Spillover of managed bumble bees from Mediterranean orchards during mass flowering causes minor short-term ecological impacts
Authors: Catalan Nitsan Nachtom , Keasar Tamar , Keasar Chen , Nagari Moshe
Published: September 2024

Commercial bumble bee colonies are routinely used for crop pollination in greenhouses, and are increasingly introduced into orchards as well. Bumble bee spillover to natural habitats neighboring the orchards may interfere with local wild bees and impact the pollination of non-crop plants. Concurrently, foraging in natural habitats may diversify the bumble bees’ diets and improve colony development. To evaluate these potential effects, we placed commercialBombus terrestriscolonies in blooming Rosaceae orchards, 25-125 m away from the margins. We recorded the colonies’ mass gain, population sizes, composition of stored pollen, and temperature regulation. We monitored bee activity, and seed sets of the non-crop plantEruca sativa, along transects in a semi-natural shrubland up to 100 m away from the orchards, with managed bumble bees either present or absent. Rosaceae pollen comprised ∼1/3 of the colonies’ pollen stores at all distances from the orchard margins. Colonies placed closest to the margins showed prolonged development, produced fewer reproductive individuals, and had poorer thermoregulation than colonies closer to the orchards’ center. Possibly, abiotic stressors inhibited the bumble bees’ development near orchard borders. Wild bees were as active during the colonies’ deployment as after their removal.E. sativa’s seed sets decreased after bumble bee removal, but similar declines also occurred near a control orchard without managed bumble bees. Altogether, we found no short-term spillover effects of managed bumble bees on nearby plant-bee communities during the orchards’ two-week flowering. The colonies’ prompt removal after blooming can reduce longer-term ecological risks associated with managed bumble bees.
C7-substituted Quinolines as Potent Inhibitors of AdeG Efflux Pumps inAcinetobacter baumannii
Authors: Zhu Yiling , Hind Charlotte K , Al-Adhami Taha , Wand Matthew E. , Clifford Melanie , Sutton J. Mark , Rahman Khondaker Miraz
Published: September 2024

Efflux, mediated by a series of multidrug efflux pumps, is a major contributor to antibiotic resistance in Gram-negative bacteria. Efflux pump inhibitors (EPIs), which can block efflux, have the potential to be used as adjuvant therapies to re-sensitize bacteria to existing antibiotics. In this study, 36 quinoline-based compounds were synthesized as potential EPIs targeting Resistance Nodulation Division (RND) family pumps in the multidrug-resistant pathogenAcinetobacter baumannii. InA. baumanniistrains with overexpressed AdeFGH (chloramphenicol-adapted) and AdeABC (AYE, Ab5075-UW), these compounds enhanced Hoechst dye accumulation, indicating general efflux inhibition, and potentiated chloramphenicol which is an AdeG substrate. The research focused on two generations of quinoline compounds, with modifications at the C-7 position of first-generation compounds to improve hydrophobic interactions with the Phe loop in the AdeG efflux pump, to generate second-generation compounds. The modified quinolines showed strong pump inhibition and significant chloramphenicol potentiation, with MIC reductions of 4- to 64-fold. Notably, compounds1.8and3.8exhibited the highest inhibitory activity, while compounds1.3and3.3showed up to 64-fold potentiation, highlighting the importance of specific structural features at the C-7 position for efflux pump inhibition. The study also revealed selective inhibition of AdeFGH over AdeABC, with no potentiation observed for gentamicin, showing the specificity of these quinoline- based inhibitors. Importantly, the compounds showed no toxicity in a Galleria mellonella model at a 50 mg/kg dose level, highlighting their suitability as potential antibiotic adjuvants for combating bacterial resistance.
Molecular glues that inhibit deubiquitylase activity and inflammatory signalling
Authors: Chandler Francesca , Reddy Poli Adi Narayana , Bhutda Smita , Ross Rebecca L. , Datta Arindam , Walden Miriam , Walker Kieran , Di Donato Stefano , Cassel Joel A. , Prakesch Michael A. , Aman Ahmed , Datti Alessandro , Campbell Lisa J. , Foglizzo Martina , Bell Lillie , Stein Daniel N. , Ault James R. , Al-awar Rima S. , Calabrese Antonio N. , Sicheri Frank , Del Galdo Francesco , Salvino Joseph M. , Greenberg Roger A. , Zeqiraj Elton
Published: September 2024

Deubiquitylases (DUBs) are crucial in cell signalling and are often regulated by interactions within protein complexes. The BRCC36 isopeptidase complex (BRISC) regulates inflammatory signalling by cleaving K63-linked polyubiquitin chains on Type I interferon receptors (IFNAR1). As a Zn2+-dependent JAMM/MPN DUB, BRCC36 is challenging to target with selective inhibitors. We discovered first-in-class inhibitors, termedBRISC molecular glues(BLUEs), which stabilise a 16-subunit BRISC dimer in an autoinhibited conformation, blocking active sites and interactions with the targeting subunit SHMT2. This unique mode of action results in selective inhibition of BRISC over related complexes with the same catalytic subunit, splice variants and other JAMM/MPN DUBs. BLUE treatment reduced interferon-stimulated gene expression in cells containing wild type BRISC, and this effect was absent when using structure-guided, inhibitor-resistant BRISC mutants. Additionally, BLUEs increase IFNAR1 ubiquitylation and decrease IFNAR1 surface levels, offering a potential new strategy to mitigate Type I interferon-mediated diseases. Our approach also provides a template for designing selective inhibitors of large protein complexes by promoting, rather than blocking, protein-protein interactions.
Rational selection of TbpB variants elucidates a bivalent vaccine formulation with broad spectrum coverage againstNeisseria gonorrhoeae
Authors: Fegan Jamie E. , Islam Epshita A. , Curran David M. , Ng Dixon , Au Natalie , Currie Elissa G. , Zeppa Joseph , Lam Jessica , Schryvers Anthony B. , Moraes Trevor F. , Gray-Owen Scott D.
Published: September 2024

Neisseria gonorrhoeaeis the causative agent of gonorrhea, an on-going public health problem due in part to the lack of success with efforts to develop an efficacious vaccine to prevent this sexually transmitted infection. An attractive candidate vaccine antigen because of its essential function and surface exposure, the gonococcal transferrin binding protein B (TbpB) exhibits high levels of antigenic variability which poses a significant obstacle in evoking a broadly protective vaccine composition. Here, we utilize phylogenetic information to rationally select TbpB variants for inclusion into a potential gonococcal vaccine and identify two TbpB variants that when formulated together elicit a highly cross-reactive antibody response in both rabbits and mice against a diverse panel of TbpB variants and clinically relevant gonococcal strains. Further, this formulation performed well in experimental proxies of real-world usage, including eliciting bactericidal activity against 8 diverse gonococcal strains and decreasing the median duration of colonization after vaginal infection in female mice by two heterologous strains ofN. gonorrhoeae. Together, these data support the use of a combination of TbpB variants for a broadly protective gonococcal vaccine.
Optimizing Digital PCR Assays for Multiplexed Microbial Source Tracking in Surface Waters
Authors: Ghosh Shimul , Bivins Aaron
Published: September 2024

Digital PCR (dPCR) shows great promise for precise, sensitive, and inhibition-resilient measurement of nucleic acids in surface water, providing an advantage for applications such as microbial source tracking (MST). Herein, we describe our empirical optimization of two triplex format dPCR reactions (Triplex 1 - Cow M2, Rum2Bac, Cow M3; Triplex 2 - HF183/BacR287, Pig2Bac, Entero1a) on the QIAcuity One system for MST. Each triplex produced gene copy measurements similar to single-plex format assays for a standard reference material (SRM 2917) at a fixed concentration and along a concentration gradient. For achieved water samples previously tested by single-plex assays, each triplex also produced MST marker measurements comparable to the single-plex results. The triplexes described here can be directly adopted for MST on the QIAcuity, or the optimization protocol we demonstrate can be used to develop additional multiplex assays on the QIAcuity system.
Endophilin A1 facilitates organization of the GABAergic postsynaptic machinery to maintain excitation-inhibition balance
Authors: Chen Xue , Pan Deng , Liu Jia-Jia , Yang Yanrui
Published: September 2024

The assembly and operation of neural circuits in the brain rely on the coordination and balance of excitatory and inhibitory activities. Inhibitory synapses are key regulators of the functional balance of neural circuits. However, due to the diversity of inhibitory presynaptic neurons, the complex composition of postsynaptic receptor subunits and the lack of typical postsynaptic dense structure, there are relatively few studies on the regulatory mechanisms for inhibitory synaptic structure and function, and insufficient understanding of the cellular and molecular abnormalities of inhibitory synapses in neurological and neuropsychiatric disorders. Here, we report a crucial role for endophilin A1 in inhibitory synapses. We show that endophilin A1 directly interacts with the inhibitory postsynaptic scaffold protein gephyrin in excitatory neurons, and promotes organization of the inhibitory postsynaptic density and synaptic recruitment/stabilization of the γ-aminobutyric acid type A receptors via its plasma membrane association and actin polymerization promoting activities. Loss of endophilin A1 by gene knockout in mouse hippocampal CA1 pyramidal cells weakens inhibitory synaptic transmission and causes imbalance in the excitatory/inhibitory function of neural circuits, leading to increased susceptibility to epilepsy. Our findings identify endophilin A1 as an iPSD component and provide new insights into the organization and stabilization of inhibitory postsynapses to maintain E/I balance as well as the pathogenesis of epilepsy.
Human transferrin and lactoferrin cooperatively supportNeisseria meningitidiscolonization in the murine nasopharynx
Authors: Lee Isaac S. , Fegan Jamie E. , Currie Elissa G. , Bojagora Anna , Leung Nelly Y. , Rancourt Derrick , Taha Muhamed-Kheir , Schryvers Anthony B. , Gray-Owen Scott D.
Published: September 2024

Neisseria meningitidisis a human-restricted bacteria that is a normal nasopharyngeal resident, yet it can also disseminate, causing invasive meningococcal disease. Meningococci are highly adapted to life in humans, with human-specific virulence factors contributing to bacterial adhesion, nutrient acquisition and immune evasion. While these factors have been explored in isolation, their relative contribution during infection has not been considered due to their absence in small animal models and their expression by different human cell types not readily combined in eitherin vitroorex vivosystems. Herein, we show that transgenic expression of the iron-binding glycoproteins human transferrin and lactoferrin can each facilitateN. meningitidisreplication in mouse serum but that transferrin was required to support infection-induced sepsis. While these host proteins are insufficient to allow nasopharyngeal colonization alone, mice co-expressing these and human CEACAM1 support robust colonization. In this case, meningococcal colonization elicits an acute elevation in both transferrin and lactoferrin levels within the upper respiratory mucosa, with transferrin levels remaining elevated while lactoferrin returns to basal levels after establishment of infection. Competitive infection of triple transgenic animals with transferrin- and lactoferrin- binding protein mutants selects for bacteria expressing the transferrin receptor, implicating the critical contribution of transferrin-based iron acquisition to support colonization. These transgenic animals have thus allowed us to disentangle the relative contribution of three virulence factors during colonization and invasive disease, and provides a novelin vivomodel that can support extended meningococcal colonization, opening a new avenue to explore the meningococcal lifestyle within its primary niche.
Vps4 substrate binding and coupled mechanisms of Vps4p substrate recruitment and release from autoinhibition
Authors: Wienkers HJ , Han H , Whitby FG , Hill CP
Published: September 2024

The ESCRT pathway’s AAA+ ATPase, Vps4p, remodels ESCRT-III complexes to drive membrane fission. Here, we use peptide binding assays to further the understanding of substrate specificity and the mechanism of autoinhibition. Our results reveal unexpected sequence preference to the substrate binding groove and an elegant mechanism of regulation that couples localization to substrate with release from autoinhibition.