bluuebunny/crossref_metadata_2025 huggingface dataset:
De novo genome assembly of four Andean potato weevil species (Premnotrypes, Rhigopsidius), the primary agricultural pest of the potato in South America
Authors: Jorgensen Kelsey C. , Garcia Obed A. , Alcázar Jesús , Walden Kimberly K.O. , Bigham Abigail W. , Morón Norma Mujica , Cobián Clorinda Vergara , Lesnik Julie J. , Fan Chuanzhu
Published: December 2023

The Andean potato weevil complex are the most widespread and serious insect pests to potato crops in the Andes. More broadly, genomic assemblies of insect pests are currently lacking in agricultural research, especially those from the order Coleoptera. These genome data are essential for identifying potential underlying mechanisms important to biological control strategies and food security in the highlands. Here, we present thede novogenome assemblies for four species of the Andean potato weevil complex:Premnotrypes vorax, P. suturicallus,P. latithorax, andRhigopsidius piercei. Genome assemblies exceeded the average size of those from the order Coleoptera and were highly repetitive: forP. vorax(1.33 Gb, 71.51% repetitive),P. latithorax(623 Mb, 59.03% repetitive),P. suturicallus(1.23 Gb, 70.19% repetitive), andR. piercei(1.55 Gb, 71.91% repetitive). We examined genomic regions related to metabolic potato plant detoxification and insecticide resistance using the available Colorado potato beetle (Leptinotarsa decemlineata) genome annotations as a guide. Our analysis of these weevil genomes identified chemosensory receptors and odorant binding proteins that could be related to detecting their hosts, the potato plant (Solanum tuberosum), as well as many genomic regions involved in subverting pesticide resistance. We have generated the first whole-genome assemblies of the Andean potato weevil complex that will be foundational for future agricultural pest management and entomological research in South America.

Author Summary

Within the South American Andean mountains the Andean potato weevil insects are the most widespread and serious pests to potatoes, destroying around 89% of potato harvests a year when insecticides are not used. Here, we collected and performed whole-genome sequencing for the first time for four Andean potato weevil species:Premnotrypes vorax, P. suturicallus,P. latithorax, andRhigopsidius piercei. After analysis of these genome assemblies, we found that they were large and highly repetitive compared to other published beetle genome data in the order Coleoptera. After further examination of these genome assemblies, we found regions related to metabolic potato plant detoxification, insecticide resistance, and chemosensory and odorant binding protein receptors that could be related to detecting potato plants. These genomic identifications provide novel molecular insight into regions associated with insecticide resistance, metabolic abilities, and environmental receptors, and can serve as a future valuable resource in classifying phylogenetic relationships as well as identifying regions of interest for improved pest management for potato farmers.
Inactivation of the Niemann Pick C1 cholesterol transporter 1 (NPC1) restricts SARS-CoV-2 infection
Authors: La Rosa Piergiorgio , Tiberi Jessica , Palermo Enrico , Tiano Sofia , Cortese Mirko , Hiscott John , Fiorenza Maria Teresa
Published: December 2023

The Niemann Pick C1 (NPC1) protein is an intracellular cholesterol transporter located in the late endosome/lysosome (LE/Ly) and is involved in cholesterol mobilization. Loss-of-function mutations of theNPC1gene lead to accumulation of cholesterol and sphingolipids in LE/Ly, resulting in severe fatal NPC1 disease. Cellular alterations associated with NPC1 inactivation affect both the integrity of lipid rafts and the endocytic pathway. Because the angiotensin-converting enzyme 2 (ACE2) and type 2 serine transmembrane protease (TMPRSS2) of the SARS-CoV-2 Spike (S) protein also localize to lipid rafts, we sought to investigate the hypothesis that NPC1 inactivation would generate an intrinsically unfavorable barrier to SARS-CoV-2 entry. In this study, we demonstrate that NPC1 pharmacological inactivation or CRISP/R-Cas mediated ablation of NPC1 dramatically reduced SARS-CoV-2 infectivity. More specifically, our findings demonstrate that pharmacological inactivation of NPC1 results in massive accumulation of ACE2 in the autophagosomal/lysosomal compartment. A >40-fold decrease in virus titer indicates that this effectively prevents VSV-Spike-GFP infection by impeding virus binding and entry. A similarly marked decrease in viral infectivity is observed in cells that had NPC1 expression genetically abrogated. These observations were further confirmed in ade novoSARS-CoV-2 infection paradigm, where cells were infected with the naturally pathogenic SARS-CoV-2. Overall, this work offers strong evidence that NPC1 function is essential for successful SARS-CoV-2 infection, thus implicating NPC1 as a potential therapeutic target in COVID-19 management.

Significance

A significant convergence exists between the cellular alterations associated with NPC1 inactivation and the mechanistic processes of SARS-CoV-2 infectivity. These alterations affect the integrity of lipid-enriched plasma membrane microdomains and the endocytic pathway. Furthermore, the cholesterol-regulated ACE2 receptor protein that facilitates SARS-Cov-2 viral binding and entry is targeted to the autophagolysosomal compartment upon NPC1 inactivation, thus hindering virus-host cell interaction. To our knowledge, this study provides the first evidence that NPC1 function represents a crucial factor for SARS-CoV-2 infection and suggests therapeutic opportunities.
Combining muscle-computer interface guided training with bihemispheric tDCS improves upper limb function in chronic stroke patients
Authors: Zhang Xue , Meesen Raf , Swinnen Stephan P. , Feys Hilde , Woolley Daniel G. , Cheng Hsiao-Ju , Wenderoth Nicole
Published: December 2023

Transcranial direct current stimulation (tDCS) may facilitate neuroplasticity but with a limited effect when administered while stroke patients are at rest. Muscle-computer interface (MCI) training is a promising approach for training stroke patients even if they cannot produce overt movements. However, using tDCS to enhance MCI training has not been investigated. We combined bihemispheric tDCS with MCI training of the paretic wrist and examined the effectiveness of this intervention in chronic stroke patients. A crossover, double-blind, randomized trial was conducted. Twenty-six chronic stroke patients performed MCI wrist training for three consecutive days at home while receiving either real tDCS or sham tDCS in counterbalanced order and separated by at least 8 months. The primary outcome measure was the Fugl-Meyer Assessment Upper Extremity Scale (FMA-UE) which was measured one week before training, on the first training day, on the last training day, and one week after training. There was no significant difference in the baseline FMA-UE score between groups nor between intervention periods. Patients improved 3.850 ± 0.582 points in FMA-UE score when receiving real tDCS, and 0.963 ± 0.725 points when receiving sham tDCS (p=0.003). Additionally, patients also showed continuous improvement of their motor control of the MCI tasks over the training days. Our study showed that the training paradigm could lead to functional improvement in chronic stroke patients. We argue that an appropriate MCI training in combination with bihemispheric tDCS could be a useful adjuvant for neurorehabilitation in stroke patients.

NEW & NOTEWORTHY

Bihemispheric tDCS combined with a novel MCI training for motor control of wrist extensor can improve both proximal and distal arm function in chronic stroke patients. The training regimen can be personalized with adjustments made daily to accommodate the functional change throughout the intervention. This demonstrates that bihemispheric tDCS with MCI training could complement conventional post-stroke neurorehabilitation.
Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error
Authors: Challen Robert , Chatzilena Anastasia , Qian George , Oben Glenda , Kwiatkowska Rachel , Hyams Catherine , Finn Adam , Tsaneva-Atanasova Krasimira , Danon Leon
Published: December 2023

Multiplex panel tests identify many individual pathogens at once, using a set of component tests. In some panels the number of components can be large. If the panel is detecting causative pathogens for a single syndrome or disease then we might estimate the burden of that disease by combining the results of the panel, for example determining the prevalence of pneumococcal pneumonia as caused by many individual pneumococcal serotypes. When we are dealing with multiplex test panels with many components, test error in the individual components of a panel, even when present at very low levels, can cause significant overall error. Uncertainty in the sensitivity and specificity of the individual tests, and statistical fluctuations in the numbers of false positives and false negatives, will cause large uncertainty in the combined estimates of disease prevalence. In many cases this can be a source of significant bias. In this paper we develop a mathematical framework to characterise this issue, present novel statistical methods that adjust for this bias and quantify uncertainty, and use simulation to test these methods. As multiplex testing becomes more commonly used for screening in routine clinical practice, accumulation of test error due to the combination of large numbers of test results needs to be identified and corrected for.

Author summary

During analysis of pneumococcal incidence data obtained from serotype specific multiplex urine antigen testing, we identified that despite excellent test sensitivity and specificity, the small error rate in each individual serotype test has the potential to compound and cause large uncertainty in the resulting estimates of pneumococcal prevalence, obtained by combining individual results. This limits the accuracy of estimates of the burden of disease caused by vaccine preventable pneumococcal serotypes, and in certain situations can produce marked bias.
Small peptide fingerprint (peptidomics) of Amyotrophic Lateral Sclerosis in CSF
Authors: Lumi Rea , Petri Susanne , Siwy Justyna , Latosinska Agnieszka , Raad Julia , Zürbig Petra , Skripuletz Thomas , Mischak Harald , Beige Joachim
Published: December 2023

Background

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by abnormal protein aggregates in motor neurons. Present and earlier proteomic studies to characterize peptides in cerebrospinal fluid (CSF) associated with motoneuron pathology did not target the low molecular weight proteins and peptides. We generated the hypothesis that specific changes in CSF peptides or low molecular weight proteins are significantly changed in ALS, and that these changes may support deciphering molecular pathophysiology and even guide approaches towards therapeutic interventions.

Methods

Cerebrospinal fluid (CSF) from 50 ALS patients and 50 non-ALS controls was collected, centrifuged immediately after collection, aliquoted into polypropylene test tubes, frozen within 30–40 min after the puncture and stored at −80°C until use. Peptides were sequenced using capillary electrophoresis or liquid chromatography / mass spectrometry (CE-MS/MS or LC-MS/MS) analyses.

Findings

In cerebrospinal CSF from 50 patients and 50 non-ALS controls 33 peptides were found, of which 14 could be sequenced using a non-lytic single pot proteomic detection method, CE/MS. ALS deregulated peptides vs. controls included Integral membrane protein 2B, Neurosecretory protein VGF, Osteopontin, Neuroendocrine protein 7B2 (Secretogranin-V), EGF-containing fibulin-like extracellular matrix protein 1, Xylosyltransferase 1 XT-1, Chromogranin-A, Superoxide dismutase SOD-1, Secretogranin-1 (Chromogranin B), NR2F2 Nuclear Receptor Subfamily 2 Group F Member 2 and Collagen alpha-1(VII) chain.

Interpretation

Most striking deregulations in CSF from ALS patients were found in VGF, Osteopontin, SOD-1 and EFEMP1 peptides. No associations of disease severity, duration and region of onset with sequenced peptides were found.

Declarations of Interest

S. Petri received honoraria as speaker/consultant from Biogen GmbH, Roche, Novartis, Teva, Cytokinetics Inc., Desitin, Italfarmaco, Ferrer, Amylyx, and Zambon; and grants from DGM e.V, Federal Ministry of Education and Research, German Israeli Foundation for Scientific Research and Development, EU Joint Program for Neurodegenerative Disease Research. J. Beige received funding from GSK and German Federal Ministries of Research and Health.

Funding

There was no funding to the presented investigation

Ethical Approval

This study was approved by the ethics committee of Hannover Medical School. Written informed consent was obtained from all participants in accordance with the Declaration of Helsinki. Key words: ALS, CSF, proteomics, biomarker, peptidomics, peptide deregulation
A Qualitative Exploration of Patients’ Experiences of Living with Chronic Respiratory Diseases before and after Participating in a Pulmonary Rehabilitation Program at a Tertiary Hospital in Malawi, and Their Suggestions to Improve a Future Program
Authors: Bickton Fanuel M. , Mankhokwe Talumba , Chavula Beatrice , Chitedze Emily , Manda Martha , Fombe Cashon , Mitengo Martha , Mwahimba Langsfield , Isiagi Moses , van Zyl-Smit Richard N. , Hanekom Susan , Heine Martin , Shannon Harriet , Rylance Jamie , Chisati Enock , Gordon Stephen B. , Limbani Felix
Published: December 2023

Background

Community-based surveys suggest a substantial burden of chronic respiratory diseases (CRDs) in the Malawian population, causing significant morbidity and loss of economic productivity. Pulmonary rehabilitation (PR) is an effective non-pharmacological intervention for people with CRDs, but there is limited data on its feasibility and acceptability in Malawi.

Objectives

To explore the experiences of patients with CRDs before and after participating in a PR program at Queen Elizabeth Central Hospital (QECH), Blantyre, Malawi, and their suggestions to improve a future program.

Methods

Fourteen adult patients (eight females and six males) presenting with functionally limiting CRDs to QECH were invited to participate in a six-week PR program. Following program completion, face-to-face semi-structured in-depth interviews with the participants were conducted. Interviews were audio-recorded and transcribed verbatim. The transcripts were anonymised and thematically analysed using a deductive approach.

Results

Ten adults (five females and five males) participated in the PR program. Their documented CRD diagnoses included chronic obstructive pulmonary disease (COPD), asthma, post-tuberculosis lung disease, and bronchiectasis. Five key themes emerged: (1) experiences of living with a CRD before PR, (2) experiences of living with a CRD after PR, (3) feedback on the conduct of the completed PR program, (4) suggestions to improve a future PR program, and (5) program continuation/maintenance at home. Participants reported experiencing improvements in physical, psychological, and social health associated with PR program participation. The provision of transport was considered a key facilitator for PR program completion. Realising the gained PR benefits, participants were willing to continue exercising at their homes, albeit with potential barriers including a lack of equipment.

Conclusion

The PR program improved the participants’ perceived health status and was well-accepted. Addressing barriers related to transport facilitated immediate implementation while providing a challenge for the scaling and sustainability of PR beyond the project duration. These findings support the drive for shifting chronic care, including rehabilitation, towards primary care and community.

Trial Registration

Prospective; 27/08/2021; ISRCTN13836793
COVID-19 vaccine uptake and acceptability during the second phase of vaccine rollout: a community-based survey among household heads in Zamfara state, Nigeria, 2021
Authors: Idris Ahmad Suleiman , Aliyu Hafiz , Usman Rabi , Abubakar Ahmed Tijani , Maijawa Muhammad Abdullahi , Abdullahi Bello Suleiman , Balogun Muhammad Shakir , Olorukooba Abdulhakeem , Umeokonkwo Chukwuma , Maiyaki Abubakar , Sani Muhammad , Yisa Muhammad , Zubair Ismail Hadi , Chinedu Onu Hastings , Jatau Tenmuso David , Sabitu Kabir
Published: December 2023

Introduction

Vaccines have played an important role in the control of infectious diseases globally. COVID-19 vaccine was rolled out in Zamfara State for the public in August 2021. We aimed to determine the level of COVID-19 vaccine uptake, acceptance, and awareness in Zamfara state Nigeria, during the second phase of the COVID-19 roll-out in the community.

Methods

We executed a descriptive cross-sectional study in Zamfara state, Nigeria. We used multistage sampling technique to randomly select 910 household heads between October 12 to December 20, 2021. We used a semi-structured electronic questionnaire to collect data on sociodemographic characteristics, uptake, and acceptance of COVID-19 vaccine. We performed descriptive analysis; calculated frequencies, proportions, and produced tables and figures.

Results

Our 899 respondents had a median age of 48 years (interquartile range: 29.5-66.5). About 78.1% (711) were males. A majority of the respondents were within the age group 50-59 years. Of 897 respondents 47.2% (423) were educated up to the secondary school level.

Only 8.9% (81) had received COVID-19 vaccine. Of the 829 unvaccinated respondents, 10.1% (84) accepted to take the vaccine the current week of the interview, 38.4% (318) would it the following week, and 27.4% (227) the following month, while 12.2% (101) of the respondents rejected the vaccine,

Conclusion

COVID-19 vaccine had a poor uptake and acceptance rate in Zamfara State during the vaccine rollout. We recommended carefully designed and targeted sensitization campaigns to increase the demand of COVID-19 vaccine in the community.
Assessment of symptoms, quality of life and remnant gastric activity following gastric bypass using Gastric Alimetry®
Authors: Wang Tim Hsu-Han , Varghese Chris , Calder Stefan , Gharibans Armen , Evennett Nicholas , Beban Grant , Schamberg Gabriel , O’Grady Greg
Published: December 2023

Background

While most gastric bypass patients recover well, some experience long-term complications, including nausea, pain, stricture, and dumping. This study aimed to evaluate symptoms and quality of life (QoL) together with remnant stomach function using the novel Gastric Alimetry® system.

Method

Gastric bypass and conversion-to-bypass patients were recruited. The Gastric Alimetry system (Auckland, NZ) was employed, comprising a high-resolution electrode Array, and validated symptom logging App. The protocol comprised 30-minute fasting baseline, a 218kCal meal stimulus, and 4-hours of post-prandial recordings. Symptoms and QoL were evaluated using validated PAGI questionnaires. Remnant gastric electrophysiology evaluation included frequency, BMI-adjusted amplitude, and Gastric Alimetry Rhythm Index (GA-RI; reflecting pacemaker stability), with comparison to matched controls.

Results

38 participants were recruited with mean time from bypass 46.8 ± 28.6 months. One third of patients showed moderate to severe post-prandial symptoms, with patients PAGI-SYM 28 ± 19 vs controls 9 ± 17; PAGI-QoL 37 ± 31 vs 135 ± 22 (p<0.01). Remnant gastric function was markedly degraded shown by undetectable frequencies in 84% (vs 0% in controls), and low GA-RI (0.18 ± 0.08 vs 0.51 ± 0.22 in controls; p<0.0001). Impaired GA-RI and amplitude were correlated with worse PAGI-SYM and PAGI-QOL scores.

Conclusion

One third of post-bypass patients suffered significant upper GI symptoms with reduced QoL. The bypassed remnant stomach shows highly deranged electrophysiology, reflecting disuse degeneration. These derangements correlated with QoL, although causality was not addressed.
Extreme in Every Way: Exceedingly Low Genetic Diversity in Snow Leopards Due to Persistently Small Population Size
Authors: Solari Katherine A. , Morgan Simon , Poyarkov Andrey D. , Weckworth Byron , Samelius Gustaf , Sharma Koustubh , Ostrowski Stephane , Ramakrishnan Uma , Kubanychbekov Zairbek , Kachel Shannon , Johansson Örjan , Lkhagvajav Purevjav , Hemmingmoore Heather , Alexandrov Dmitry Y. , Bayaraa Munkhtsog , Grachev Alexey , Korablev Miroslav P. , Hernandez-Blanco Jose A. , Munkhtsog Bariushaa , Rosenbaum Barry , Rozhnov Viatcheslav V. , Rajabi Ali Madad , Noori Hafizullah , Suryawanshi Kulbhushansingh , Armstrong Ellie E. , Petrov Dmitri A.
Published: December 2023

Snow leopards (Panthera uncia) serve as an umbrella species whose conservation benefits their high-elevation Asian habitat. Their numbers are believed to be in decline due to numerous Anthropogenic threats; however, their conservation is hindered by numerous knowledge gaps. They are the least studied genetically of all big cat species with more to learn regarding their population structure, historical population size, and current levels of genetic diversity. Here, we use whole-genome sequencing data for 41 snow leopards (37 newly sequenced) to offer new insights into these unresolved questions. Among our samples, we find evidence of a primary genetic divide between the northern and southern part of the range around the Dzungarian Basin, as previously identified, and a secondary divide south of Kyrgyzstan around the Taklamakan Desert. Most noteworthy, we find that snow leopards have the lowest genetic diversity of any big cat species, due to a persistently small population size (relative to other big cat species) throughout their evolutionary history rather than recent inbreeding. Without a large population size or ample standing genetic variation to help buffer them from any forthcoming Anthropogenic challenges, snow leopard persistence may be more tenuous than currently appreciated.
Gene replacement therapy for Lafora disease in theEpm2a-/-mouse model
Authors: Zafra-Puerta Luis , Burgos Daniel F. , Iglesias-Cabeza Nerea , González-Fernández Juan , Sánchez-Martín Gema , Sánchez Marina P. , Serratosa José M.
Published: December 2023

Lafora disease is a rare and fatal form of progressive myoclonic epilepsy typically occurring early in adolescence. Common symptoms include seizures, dementia, and a progressive neurological decline leading to death within 5-15 years from onset. The disease results from mutations transmitted with autosomal recessive inheritance in theEPM2Agene, encoding laforin, a dual-specificity phosphatase, or theEPM2Bgene, encoding malin, an E3-ubiquitin ligase. Laforin has glucan phosphatase activity, is an adapter of enzymes involved in glycogen metabolism, is involved in endoplasmic reticulum-stress and protein clearance, and acts as a tumor suppressor protein. Laforin and malin work together in a complex to control glycogen synthesis and prevent the toxicity produced by misfolded proteins via the ubiquitin-proteasome system. Disruptions in either protein can lead to alterations in this complex, leading to the formation of Lafora bodies that contain abnormal, insoluble, and hyperphosphorylated forms of glycogen called polyglucosans.

We used theEpm2a-/-knock-out mouse model of Lafora disease to apply a gene replacement therapy by administering intracerebroventricular injections of a recombinant adeno-associated virus carrying the humanEPM2Agene. We evaluated the effects of this treatment by means of neuropathological studies, behavioral tests, video-electroencephalography recording, and proteomic/phosphoproteomic analysis.

Gene therapy with recombinant adeno-associated virus containing theEPM2Agene ameliorated neurological and histopathological alterations, reduced epileptic activity and neuronal hyperexcitability, and decreased the formation of Lafora bodies. Differential quantitative proteomics and phosphoproteomics revealed beneficial changes in various molecular pathways altered in Lafora disease. Improvements were observed for up to nine months following a single intracerebroventricular injection. In conclusion, gene replacement therapy with humanEPM2Agene in theEpm2a-/-knock-out mice shows promise as a potential treatment for Lafora disease.
Dose, temperature and formulation shapeMetarhizium anisopliaevirulence against the oriental fruit fly: lessons for improving on-target control strategies
Authors: Chailleux Anaïs , Coulibaly Oumou Noumou , Diouf Babacar , Diop Samba , Sohel Ahmad , Brévault Thierry
Published: December 2023

Entomopathogenic fungi are a promising tool for the biological control of crop pests provided low or no impact on non-target organisms. Selection for host specificity as well as on-target applications open new avenues for more sustainable strategies for pest management. Isolates ofMetarhizium anisopliae(Metschn.) Sorokin have been identified as promising for developing innovative entomovectoring-based strategies for the control of the oriental fruit fly,Bactrocera dorsalis(Hendel) (Diptera: Tephritidae), in Africa. To be effective, this technology requires high strain virulence at a low number of spores, but sufficient incubation time to allow transmission to wild conspecifics. This depends on trophic interactions between the host and the pathogen, which are mediated by abiotic factors.

In the present study, we investigated the virulence of the Met69 strain against adult flies, depending on the inoculation dose, air temperature and formulation. High pathogenicity was observed at very low inoculation doses (LT50 of 4.85 days with 6100 spores per fly) independently of fly sex. Virulence increased with spore load in a tight range (5600 and 6100 spores per fly) and with air temperature observed in the field (20-28°C). Unexpectedly, corn starch used as an adjuvant to increase the carrying capacity of insects decreased the virulence of the pathogen.

The results will help improve area-wide control strategies based on the contamination of wild flies through auto-inoculation devices or interactions with released mass-reared sterile males coated with fungal spores. Furthermore, the study proposes an approach for calibrating area-wide control strategies, taking into account both the insect and pathogen bioecology and the environment in which they evolve.

Author roles

Anaïs Chailleux:Conceptualization, Funding acquisition, Methodology, Data curation, Writing – original draft.Oumou Noumou Coulibaly:Investigation, Writing – original draft.Babacar Diouf:Investigation, Visualization.Samba Diop:Investigation.Ahmad Sohel:Resources, Writing – review & editing.Thierry Brévault:Conceptualization, Funding acquisition, Project administration, Writing – review & editing.
Striatal dopamine reflects individual long-term learning trajectories
Authors: Liebana Garcia Samuel , Laffere Aeron , Toschi Chiara , Schilling Louisa , Podlaski Jacek , Fritsche Matthias , Zatka-Haas Peter , Li Yulong , Bogacz Rafal , Saxe Andrew , Lak Armin
Published: December 2023

Learning from naïve to expert occurs over long periods of time, accompanied by changes in the brain’s neuronal signals. The principles governing behavioural and neuronal dynamics during long-term learning remain unknown. We developed a psychophysical visual decision task for mice that allowed for studying learning trajectories from naïve to expert. Mice adopted sequences of strategies that became more stimulus-dependent over time, showing substantial diversity in the strategies they transitioned through and settled on. Remarkably, these transitions were systematic; the initial strategy of naïve mice predicted their strategy several weeks later. Longitudinal imaging of dopamine release in dorsal striatum demonstrated that dopamine signals evolved over learning, reflecting stimulus-choice associations linked to each individual’s strategy. A deep neural network model trained on the task with reinforcement learning captured behavioural and dopamine trajectories. The model’s learning dynamics accounted for the mice’s diverse and systematic learning trajectories through a hierarchy of saddle points. The model used prediction errors mirroring recorded dopamine signals to update its parameters, offering a concrete account of striatal dopamine’s role in long-term learning. Our results demonstrate that long-term learning is governed by diverse yet systematic transitions through behavioural strategies, and that dopamine signals exhibit key characteristics to support this learning.
Temporal Changes in Innate and Adaptive Immunity During Sepsis as Determined by ELISpot
Authors: Unsinger J , Osborne D , Walton AH , Han E , Sheets L , Mazer MB , Remy KE , Griffith TS , Rao M , Badovinac VP , Brackenridge SC , Turnbull I , Efron Philip A , Moldawer LL , Caldwell CC , Hotchkiss RS
Published: December 2023

Background

The inability to evaluate host immunity in a rapid quantitative manner in patients with sepsis has severely hampered development of novel immune therapies. The ELISpot assay is afunctionalbioassay that measures the number of cytokine-secreting cells and the relative amount of cytokine produced at the single-cell level. A key advantage of ELISpot is its excellent dynamic range enabling a more precise quantifiable assessment of host immunity. Herein, we tested the hypothesis on whether the ELISpot assay can detect dynamic changes in both innate and adaptive immunity as they often occur during sepsis. We also tested whether ELISpot could detect the effect of immune drug therapies to modulate innate and adaptive immunity.

Methods

Mice were made septic using sublethal cecal ligation and puncture (CLP). Blood and spleens were harvested serially andex vivoIFN-γ and TNF-α production were compared by ELISpot and ELISA. The capability of ELISpot to detect changes in innate and adaptive immunity due toin vivoimmune therapy with dexamethasone, IL-7, and arginine was also evaluated.

Results

ELISpot confirmed a decreased innate and adaptive immunity responsiveness during sepsis progression. More importantly, ELISpot was also able to detect changes in adaptive and innate immunity in response to immune-modulatory reagents, for example dexamethasone, arginine, and IL-7 in a readily quantifiable manner, as predicted by the reagents known mechanisms of action. ELISpot and ELISA results tended to parallel one another although some differences were noted.

Conclusion

ELISpot offers a unique capability to assess the functional status of both adaptive and innate immunity over time. The results presented herein demonstrate that ELISpot can also be used to detect and follow thein vivoeffects of drugs to ameliorate sepsis-induced immune dysfunction. This capability would be a major advance in guiding new immune therapies in sepsis.
Electro-Osmotic Flow Generation via a Sticky Ion Action
Authors: Mehrafrooz Behzad , Yu Luning , Siwy Zuzanna , Wanunu Meni , Aksimentiev Aleksei
Published: December 2023

Selective transport of ions through nanometer-sized pores is fundamental to cell biology and central to many technological processes such as water desalination and electrical energy storage. Conventional methods for generating ion selectivity include placement of fixed electrical charges at the inner surface of a nanopore through either point mutations in a protein pore or chemical treatment of a solid-state nanopore surface, with each nanopore type requiring a custom approach. Here, we describe a general method for transforming a nanoscale pore into a highly selective, anion-conducting channel capable of generating a giant electro-osmotic effect. Our molecular dynamics simulations and reverse potential measurements show that exposure of a biological nanopore to high concentrations of guanidinium chloride renders the nanopore surface positively charged due to transient binding of guanidinium cations to the protein surface. A comparison of four biological nanopores reveals the relationship between ion selectivity, nanopore shape, composition of the nanopore surface, and electro-osmotic flow. Remarkably, guanidinium ions are also found to produce anion selectivity and a giant electro-osmotic flow in solid-state nanopores via the same mechanism. Our sticky-ion approach to generate electro-osmotic flow can have numerous applications in controlling molecular transport at the nanoscale and for detection, identification, and sequencing of individual proteins.
Neuroanatomical changes observed over the course of a human pregnancy
Authors: Pritschet Laura , Taylor Caitlin M , Cossio Daniela , Santander Tyler , Grotzinger Hannah , Faskowitz Joshua , Handwerker Daniel A , Layher Evan , Chrastil Elizabeth R , Jacobs Emily G.
Published: December 2023

Pregnancy is a period of profound hormonal and physiological change experienced by millions of women annually, yet the neural changes unfolding in the maternal brain throughout gestation have not been studied in humans. Leveraging precision imaging, we mapped neuroanatomical changes in an individual from preconception through two years postpartum. Pronounced decreases in gray matter volume and cortical thickness were evident across the brain, which stand in contrast to increases in white matter microstructural integrity, ventricle volume, and cerebrospinal fluid, with few regions untouched by the transition to motherhood. This dataset serves as the first comprehensive map of the human brain across gestation, providing an open-access resource for the brain imaging community to stimulate further exploration and discovery.
Anti-Diffusion in an Algae-Bacteria Microcosm: Photosynthesis, Chemotaxis, and Expulsion
Authors: Prakash Praneet , Baig Yasa , Peaudecerf François J. , Goldstein Raymond E.
Published: December 2023

In Nature there are significant relationships known between microorganisms from two kingdoms of life, as in the supply of vitamin B12by bacteria to algae. Such interactions motivate general investigations into the spatio-temporal dynamics of metabolite exchanges. Here we study by experiment and theory a model system: a coculture of the bacteriumB. subtilis, an obligate aerobe that is chemotactic to oxygen, and a nonmotile mutant of the algaC. reinhardtii, which photosynthetically produces oxygen when illuminated. Strikingly, when a shaft of light illuminates a thin, initially uniform suspension of the two, the chemotactic influx of bacteria to the photosyn-thetically active region leads to expulsion of the algae from that area. This effect arises from algal transport due to spatially-varying collective behavior of bacteria, and is mathematically related to the “turbulent diamagnetism” associated with magnetic flux expulsion in stars.
Hidden hearing loss in a Charcot-Marie-Tooth type 1A mouse model
Authors: Cassinotti Luis R. , Ji Lingchao , Yuk M. Caroline , Desai Aditi S. , Cass Nathan D. , Amir Zahara A. , Corfas Gabriel
Published: December 2023

Hidden hearing loss (HHL), a recently described auditory neuropathy characterized by normal audiometric thresholds but reduced sound-evoked cochlear compound action potentials, has been proposed to contribute to hearing difficulty in noisy environments in people with normal hearing thresholds, a widespread complaint. While most studies on HHL pathogenesis have focused on inner hair cell (IHC) synaptopathy, we recently showed that transient auditory nerve (AN) demyelination also causes HHL in mice. To test the impact of myelinopathy on hearing in a clinically relevant model, we studied a mouse model of Charcot-Marie-Tooth type 1A (CMT1A), the most prevalent hereditary peripheral neuropathy in humans. CMT1A mice exhibited the functional hallmarks of HHL together with disorganization of AN heminodes near the IHCs with minor loss of AN fibers. These results support the hypothesis that mild disruptions of AN myelination can cause HHL, and that heminodal defects contribute to the alterations in the sound-evoked cochlear compound action potentials seen in this mouse model. Also, these findings suggest that patients with CMT1A or other mild peripheral neuropathies are likely to suffer from HHL. Furthermore, these results suggest that studies of hearing in CMT1A patients might help develop robust clinical tests for HHL, which are currently lacking.
Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America
Authors: Tomás Gonzalo , Marandino Ana , Panzera Yanina , Rodríguez Sirley , Wallau Gabriel Luz , Dezordi Filipe Zimmer , Pérez Ramiro , Bassetti Lucía , Negro Raúl , Williman Joaquín , Uriarte Valeria , Grazioli Fabiana , Leizagoyen Carmen , Riverón Sabrina , Coronel Jaime , Bello Soledad , Páez Enrique , Lima Martín , Méndez Virginia , Pérez Ruben
Published: December 2023

The highly pathogenic avian influenza viruses of the clade 2.3.4.4b have caused unprecedented deaths in South American wild birds, poultry, and marine mammals. In September 2023, pinnipeds and seabirds appeared dead on the Uruguayan Atlantic coast. Sixteen influenza virus strains were characterized by real-time reverse transcription PCR and genome sequencing in samples from sea lions (Otaria flavescens), fur seals (Arctocephalus australis), and terns (Sterna hirundinacea). Phylogenetic and ancestral reconstruction analysis showed that these strains have pinnipeds as the most likely ancestral host, representing a recent introduction of the clade 2.3.4.4b in Uruguay. The Uruguayan and closely related strains from Peru (sea lions) and Chile (sea lions and a human case) carry mammalian adaptative residues 591K and 701N in the viral polymerase basic protein 2 (PB2). Our findings suggest that the clade 2.3.4.4b strains in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route.
Choice anticipation as gated accumulation of sensory predictions
Authors: Caie Brandon , Endres Dominik , Khan Aarlenne Z. , Blohm Gunnar
Published: December 2023

Predictions are combined with sensory information when making choices. Accumulator models have conceptualized predictions as trial-by-trial updates to a baseline evidence level. These models have been successful in explaining the influence of choice history across-trials, however they do not account for how sensory information is transformed into choice evidence within-trials. Here, we derive a gated accumulator that models the onset of evidence accumulation as a combination of delayed sensory information and a prediction of sensory timing. To test how the delays interact with across-trial predictions, we designed a free choice saccade task where participants directed eye movements to either of two targets that appeared with variable delays and asynchronies. Despite instructions not to anticipate, participants responded prior to target onset on some trials. We reasoned that anticipatory responses may reflect a trade-off between inhibiting and facilitating the onset of evidence accumulation via a gating mechanism as target appearance became more likely. Using a choice history analysis, we found that anticipatory responses were more likely following repeated choices, despite task randomization, suggesting that the balance between anticipatory and sensory responses was driven by a prediction of sensory timing. By fitting the gated accumulator model to the data, we found that variance in within-trial fluctuations in baseline evidence best explained the joint increase of anticipatory responses and faster sensory-guided responses with longer delays. Thus, we conclude that a prediction of sensory timing is involved in balancing the costs of anticipation with lowering the amount of accumulated evidence required to trigger saccadic choice, which could be explained by history-dependence in the baseline dynamics of a gated accumulator.

New and Noteworthy

Evidence accumulation models are used to study how recent history impacts the processes underlying how we make choices. Biophysical evidence suggests that the accumulation of evidence is gated, however classic accumulator models do not account for this, so little is known about how recent history may influence the gating process. In this work, computational modeling and experimental data from a free choice saccade task argue that predictions of the timing of sensory information are important in controlling how evidence accumulation is gated, and that signatures of these predictions can be detected even in randomized task environments where history effects may not be expected.
Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome
Authors: López-Alfonzo Erika M. , Saurabh Ayush , Zarafshan Sahar , Pressé Steve , Martin Andreas
Published: December 2023

The 26S proteasome is the major eukaryotic protease responsible for protein quality control, proteostasis, and the modulation of numerous vital processes through the degradation of regulatory proteins. Commitment to degradation occurs when conserved pore loops in the proteasomal heterohexameric ATPase motor engage the flexible initiation region of a polyubiquitinated protein substrate for subsequent mechanical unfolding and translocation into a proteolytic chamber. Here, we usedin vitrobiochemical and single-molecule FRET-based assays with mutant reconstituted 26S proteasomes from yeast to characterize how the pore-1 loops of individual ATPase subunits in the AAA+ motor contribute to the different steps of substrate degradation and affect the proteasome conformational dynamics. We found that the pore-1 loop of the Rpt6 ATPase subunit plays particularly important roles in substrate capture, engagement, and unfolding, while the pore-1 loop of the Rpt4 ATPase is critical for providing sufficient grip for substrate unraveling and maintaining a processing-competent state of the proteasome. Interestingly, these pore-1-loop contributions correlate with their positions in the spiral-staircase arrangements of ATPase subunits in the substrate-free and substrate-degrading proteasome, providing new insights into the mechanisms of substrate processing by the 26S proteasome and related hexameric ATPase motors.
Targeting HLA-E Positive Cancers with a Novel NKG2A/C Switch Receptor
Authors: Sætersmoen Michelle , Kotchetkov Ivan S. , Torralba-Raga Lamberto , Mansilla-Soto Jorge , Sohlberg Ebba , Krokeide Silje Zandstra , Hammer Quirin , Sadelain Michel , Malmberg Karl-Johan
Published: December 2023

HLA-E is overexpressed by approximately 80% of solid tumors, including malignant glioblastoma, and is emerging as a major checkpoint for NKG2A+CD8+T cells and NK cells in the tumor microenvironment and circulation. This axis operates side-by-side with PD-L1 to shut down effector responses by T and NK cells. Here, we engineered a novel chimeric A/C switch receptor, combining the strong HLA-E binding affinity of the NKG2A receptor ectodomain with the activating signaling of the NKG2C receptor endodomain. We found that A/C Switch-transduced NK and T cells displayed superior and specific cytotoxic function when challenged with tumor cells exhibiting medium to high HLA-E expression. Furthermore, A/C Switch-expressing human T cells demonstrated enhanced anti-tumor function in a xenograft model of glioblastoma. Importantly, the activity of the modified T cells was governed by an equilibrium between A/C Switch transduction level and HLA-E expression, creating a therapeutic window to safeguard against on-target off-tumor toxicities. Indeed, normal cells remained insensitive to A/C Switch engineered T cells even after pre-treatment with IFN-γ to induce HLA-E expression. We propose that this novel A/C switch receptor may operate alone to control tumor cells expressing high levels of HLA-E or in combination with other engineered specificities to overcome the suppressive NKG2A/HLA-E checkpoint.
Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
Authors: Olmedillas Eduardo , Rajamanickam Roshan R. , Avalos Ruben Diaz , Sosa Fernanda A. , Zandonatti Michelle A. , Harkins Stephanie S. , Shresta Sujan , Hastie Kathryn M. , Saphire Erica Ollmann
Published: December 2023

The 800 million human infections with SARS-CoV-2 and the likely emergence of new variants and additional coronaviruses necessitate a better understanding of the essential spike glycoprotein and the development of immunogens that foster broader and more durable immunity. The S2 fusion subunit is more conserved in sequence, is essential to function, and would be a desirable immunogen to boost broadly reactive antibodies. It is, however, unstable in structure and in its wild-type form, cannot be expressed alone without irreversible collapse into a six-helix bundle. In addition to the irreversible conformational changes of fusion, biophysical measurements indicate that spike also undergoes a reversible breathing action. However, spike in an open, “breathing” conformation has not yet been visualized at high resolution. Here we describe an S2-only antigen, engineered to remain in its relevant, pre-fusion viral surface conformation in the absence of S1. We also describe a panel of natural human antibodies specific for S2 from vaccinated and convalescent individuals. One of these mAbs, from a convalescent individual, afforded a high-resolution cryo-EM structure of the prefusion S2. The structure reveals a complex captured in an “open” conformation with greater stabilizing intermolecular interactions at the base and a repositioned fusion peptide. Together, this work provides an antigen for advancement of next-generation “booster” immunogens and illuminates the likely breathing adjustments of the coronavirus spike.
A Fluorogenic-Based Assay to Measure Chaperone-Mediated Autophagic Activity in Cells and Tissues
Authors: Jonnavithula Anila , Tandar Megan , Umar Mohammed , Orton Scott N. , Woodrum MacKenzie C , Mookherjee Sohom , Boudina Sihem , Symons J. David , Ghosh Rajeshwary
Published: December 2023

Objective

Pathologies including cardiovascular diseases, cancer, and neurological disorders are caused by the accumulation of misfolded / damaged proteins. Intracellular protein degradation mechanisms play a critical role in the clearance of these disease-causing proteins. Chaperone mediated autophagy (CMA) is a protein degradation pathway that employs chaperones to bind proteins, bearing a unique KFERQ-like motif, for delivery to a CMA-specific Lysosome Associated Membrane Protein 2a (LAMP2a) receptor for lysosomal degradation. To date, steady-state CMA function has been assessed by measuring LAMP2A protein expression. However, this does not provide information regarding CMA degradation activity. To fill this dearth of tools / assays to measure CMA activity, we generated a CMA-specific fluorogenic substrate assay.

Methods

A KFERQ-AMC [Lys-Phe-Asp-Arg-Gln-AMC(7-amino-4-methylcou-marin)] fluorogenic CMA substrate was synthesized from Solid-Phase Peptide Synthesis. KFERQ-AMC, when cleaved via lysosomal hydrolysis, causes AMC to release and fluoresce (Excitation:355 nm, Emission:460 nm). Using an inhibitor of lysosomal proteases, i.e., E64D [L-trans-Epoxy-succinyl-leucylamido(4-guanidino)butane)], responsible for cleaving CMA substrates, the actual CMA activity was determined. Essentially,CMA activity = (substrate)fluorescence- (substrate+E64D)fluorescence.To confirm specificity of the KFERQ sequence for CMA, negative control peptides were used.

Results

Heart, liver, and kidney lysates containing intact lysosomes were obtained from 4-month-old adult male mice. First, lysates incubated with KFERQ-AMC displayed a time dependent (0-5 hour) increase in AMC fluorescence vs. lysates incubated with negative control peptides. These data validate the specificity of KFERQ for CMA. Of note, liver exhibited the highest CMA (6-fold; p<0.05) > kidney (2.4-fold) > heart (0.4-fold) at 5-hours. Second, E64D prevented KFERQ-AMC degradation, substantiating that KFERQ-AMC is degraded via lysosomes. Third, cleavage of KFERQ-AMC and resulting AMC fluorescence was inhibited in Human embryonic kidney (HEK) cells and H9c2 cardiac cells transfected withLamp2avs. control siRNA. Further, enhancing CMA usingLamp2aadenovirus upregulated KFERQ degradation. These data suggest that LAMP2A is required for KFERQ degradation.Conclusion.We have generated a novel assay for measuring CMA activity in cells and tissues in a variety of experimental contexts.

Abstract Figure

Graphical Abstract

Proposed mechanism of KFERQ-AMC degradation via CMA