bluuebunny/crossref_metadata_2025 huggingface dataset:
Alcohol tolerance encoding in sleep regulatory circadian neurons in Drosophila
Authors: Lange Anthony P. , Wolf Fred W.
Published: February 2023

Alcohol tolerance is a simple form of behavioral and neural plasticity that occurs with the first drink. Neural plasticity in tolerance is likely a substrate for longer term adaptations that can lead to alcohol use disorder. Drosophila develop tolerance with characteristics similar to vertebrates, and it is useful model for determining the molecular and circuit encoding mechanisms in detail. Rapid tolerance, measured after the first alcohol exposure is completely metabolized, is localized to specific brain regions that are not interconnected in an obvious way. We used a forward neuroanatomical screen to identify three new neural sites for rapid tolerance encoding. One of these was comprised of two groups of neurons, the DN1a and DN1p glutamatergic neurons, that are part of the Drosophila circadian clock. We localized rapid tolerance to the two DN1a neurons that regulate arousal by light at night, temperature-dependent sleep timing, and night-time sleep. Two clock neurons that regulate evening activity, LNd6 and the 5th LNv, are postsynaptic to the DN1as and they promote rapid tolerance via the metabotropic glutamate receptor. Thus, rapid tolerance to alcohol overlaps with sleep regulatory neural circuitry, suggesting a mechanistic link.
Neural effects of TMS trains on the human prefrontal cortex
Authors: Ross Jessica M. , Cline Christopher C. , Sarkar Manjima , Truong Jade , Keller Corey J.
Published: February 2023

How does a train of TMS pulses modify neural activity in humans? Despite adoption of repetitive TMS (rTMS) for the treatment of neuropsychiatric disorders, we still do not understand how rTMS changes the human brain. This limited understanding stems in part from a lack of methods for noninvasively measuring the neural effects of a single TMS train — a fundamental building block of treatment — as well as the cumulative effects of consecutive TMS trains. Gaining this understanding would provide foundational knowledge to guide the next generation of treatments. Here, to overcome this limitation, we developed methods to noninvasively measure causal and acute changes in cortical excitability and evaluated this neural response to single and sequential TMS trains. In 16 healthy adults, standard 10 Hz trains were applied to the dorsolateral prefrontal cortex (dlPFC) in a randomized, sham-controlled, event-related design and changes were assessed based on the TMS-evoked potential (TEP), a measure of cortical excitability. We hypothesized that single TMS trains would induce changes in the local TEP amplitude and that those changes would accumulate across sequential trains, but primary analyses did not indicate evidence in support of either of these hypotheses. Exploratory analyses demonstrated non-local neural changes in sensor and source space and local neural changes in phase and source space. Together these results suggest that single and sequential TMS trains may not be sufficient to modulate local cortical excitability indexed by typical TEP amplitude metrics but may cause neural changes that can be detected outside the stimulation area or using phase or source space metrics. This work should be contextualized as methods development for the monitoring of transient noninvasive neural changes during rTMS and contributes to a growing understanding of the neural effects of rTMS.
A random forest model for predicting exosomal proteins using evolutionary information and motifs
Authors: Arora Akanksha , Patiyal Sumeet , Sharma Neelam , Devi Naorem Leimarembi , Kaur Dashleen , Raghava Gajendra P. S.
Published: February 2023

Identification of secretory proteins in body fluids is one of the key challenges in the development of non-invasive diagnostics. It has been shown in the part that a significant number of proteins are secreted by cells via exosomes called exosomal proteins. In this study, an attempt has been made to build a model that can predict exosomal proteins with high precision. All models are trained, tested, and evaluated on a non-redundant dataset comprising 2831 exosomal and 2831 non-exosomal proteins, where no two proteins have more than 40% similarity. Initially, the standard similarity-based method BLAST was used to predict exosomal proteins, which failed due to low-level similarity in the dataset. To overcome this challenge, machine learning based models have been developed using compositional features of proteins and achieved highest AUROC of 0.70. The performance of the ML-based models improved significantly to AUROC of 0.73 when evolutionary information in the form of PSSM profiles was used for building models. Our analysis indicates that exosomal proteins have wide range of motifs. In addition, it was observed that exosomal proteins contain different types of sequence-based motifs, which can be used for predicting exosomal proteins. Finally, a hybrid method has been developed that combines a motif-based approach and an ML-based model for predicting exosomal proteins, achieving a maximum AUROC 0.85 and MCC of 0.56 on an independent dataset. The hybrid model in this study performs better than the presently available methods when assessed on an independent dataset. A web server and a standalone software ExoProPred has been created for the scientific community to provide service, code, and data. (https://webs.iiitd.edu.in/raghava/exopropred/).

Keypoints

Exosomal proteins or non-classical secretory proteins are secreted by via exosomes

A method has been developed for predicting exosomal proteins

Models have been trained, tested, and evaluated on non-redundant dataset

Wide range of sequence motifs have been discovered in exosomal proteins

A web server and standalone software have been developed
Induction of transmucosal protection by oral vaccination with an attenuatedChlamydia
Authors: Wang Yihui , He Rongze , Winner Halah , Gauduin Marie-Claire , Zhang Nu , He Cheng , Zhong Guangming
Published: February 2023

Chlamydia muridarumhas been used to study chlamydial pathogenesis since it induces mice to develop hydrosalpinx, a pathology observed inC. trachomatis-infected women. We identified aC. muridarummutant that is no longer able to induce hydrosalpinx. In the current study, we evaluated the mutant as an attenuated vaccine. Following an intravaginal immunization with the mutant, mice were protected from hydrosalpinx induced by wild typeC. muridarum. However, the mutant itself productively colonized the mouse genital tract and produced infectious organisms in vaginal swabs. Nevertheless, the mutant failed to produce infectious shedding in the rectal swabs following an oral inoculation. Importantly, mice orally inoculated with the mutant mounted transmucosal immunity against challenge infection of wild typeC. muridarumin the genital tract. The protection was detected as early as day 3 following the challenge infection and the immunized mice were protected from any significant pathology in the upper genital tract. However, the same orally immunized mice failed to prevent the colonization of wild typeC. muridarumin the gastrointestinal tract. The transmucosal immunity induced by the oral mutant was further validated in the airway. The orally vaccinated mice were protected from both lung infection and systemic toxicity caused by intranasally inoculated wild typeC. muridarumalthough the same mice still permitted the gastrointestinal colonization by the wild typeC. muridarum. These observations suggest that the mutantC. muridarummay be developed into anintracellularoralvaccine vector (or IntrOv) for selectively inducing transmucosal immunity in extra-gut tissues.
A rapid approach for sex assignment by RAD-seq using a reference genome
Authors: Peralta Diego M. , Túnez Juan I. , Rodríguez Cruz Ulises E. , Ceballos Santiago G.
Published: February 2023

Sex identification is a common objective in molecular ecology. While many vertebrates display sexual dimorphism, determining the sex can be challenging in certain situations, such as species lacking clear sex-related phenotypic characteristics or in studies using non-invasive methods. In these cases, DNA analyses serve as valuable tools not only for sex determination but also for validating sex assignment based on phenotypic traits. In this study, we developed a bioinformatic framework for sex assignment using genomic data obtained through GBS, and having an available closely related genome assembled at the chromosome level. Our method consists of twoad hocindexes that rely on the different properties of the mammalian heteromorphic sex chromosomes. For this purpose, we mapped RAD-seq loci to a reference genome and then obtained missingness and coverage depth values for the autosomes and X and Y chromosomes of each individual. Our methodology successfully determined the sex of 165 fur seals that had been phenotypically sexed in a previous study and 40 sea lions sampled in a non-invasive way. Additionally, we evaluated the accuracy of each index in sequences with varying average coverage depths, with Index Y proving greater reliability and robustness in assigning sex to individuals with low-depth coverage. We believe that the approach presented here can be extended to any animal taxa with known heteromorphic XY/ZW sex chromosome systems and that it can tolerate various qualities of GBS sequencing data.
Cohort profile: Virus Watch: Understanding community incidence, symptom profiles, and transmission of COVID-19 in relation to population movement and behaviour
Authors: Byrne Thomas , Kovar Jana , Beale Sarah , Braithwaite Isobel , Fragaszy Ellen , Fong Wing Lam Erica , Geismar Cyril , Hoskins Susan , Navaratnam Annalan M D , Nguyen Vincent , Patel Parth , Shrotri Madhumita , Yavlinsky Alexei , Hardelid Pia , Wijlaars Linda , Nastouli Eleni , Spyer Moira , Aryee Anna , Cox Ingemar , Lampos Vasileios , McKendry Rachel A , Cheng Tao , Johnson Anne M , Michie Susan , Gibbs Jo , Gilson Richard , Rodger Alison , Abubakar Ibrahim , Hayward Andrew , Aldridge Robert W
Published: February 2023

Key Features

Virus Watch is a national community cohort study of COVID-19 in households in England and Wales, established in June 2020. The study aims to provide evidence on which public health approaches are most effective in reducing transmission, and investigate community incidence, symptoms, and transmission of COVID-19 in relation to population movement and behaviours.

28,527 households and 58,628 participants of age (0-98 years, mean age 48), were recruited between June 2020 - July 2022

Data collected include demographics, details on occupation, co-morbidities, medications, and infection-prevention behaviours. Households are followed up weekly with illness surveys capturing symptoms and their severity, activities in the week prior to symptom onset and any COVID-19 test results. Monthly surveys capture household finance, employment, mental health, access to healthcare, vaccination uptake, activities and contacts. Data have been linked to Hospital Episode Statistics (HES), inpatient and critical care episodes, outpatient visits, emergency care contacts, mortality, virology testing and vaccination data held by NHS Digital.

Nested within Virus Watch are a serology & PCR cohort study (n=12,877) and a vaccine evaluation study (n=19,555).

Study data are deposited in the Office of National Statistics (ONS) Secure Research Service (SRS). Survey data are available under restricted access upon request to ONS SRS.
Challenges in the distribution of antimicrobial medications in community dispensaries in Accra, Ghana
Authors: Greene Hannah Camille , Makovi Kinga , Abdul-Mumin Rafiatu , Bansal Akhil , Frimpong Jemima
Published: February 2023

Introduction

Community distribution of medications in low- and middle-income countries has been shown to accelerate the emergence of antimicrobial resistance. The distribution of medications is often carried out by private vendors operating under constrained conditions. Yet patterns in medicine distribution—and their consequences—are not well understood. The aim of this study was to illuminate the challenges reported by employees of chemical shops and pharmacies throughout Accra. Our objectives are twofold: to 1) assess obstacles and challenges faced by medicine vendors during their sales of antibiotic and antimalarial medications, and 2) identify opportunities for improving community-level stewardship of antimicrobials.

Methods

Responses to open-ended questions from a survey of 80 shopkeepers in pharmacies and chemical shops throughout Accra were analyzed using the socioecological model of public health.

Results

Overall, shopkeepers most often reported constraints at the interpersonal and community levels of the socioecological model of public health. These included the prohibitive costs of medicines, customer attitudes, and customers’ attempts at self-medication and uninformed antimicrobial use. Other challenges included a lack of diagnostic testing, supply chain issues, and the larger economic and healthcare situation of the community.

Discussion

The safe and effective distribution of medications was truncated by three main sources of obstacles: financial insecurity among customers, challenges directly in the treatment of illnesses, and broader issues with the fragmented healthcare infrastructure affecting shopkeepers’ roles as health educators and gatekeepers of medicines.

Conclusion

These context-specific findings identify tractable challenges faced by medicine vendors in Ghana, with relevance to antimicrobial stewardship across resource-poor settings globally. Addressing barriers faced by shopkeepers would provide an opportunity for significantly improving the provision of medications, and ultimately healthcare, at the community level. Such efforts will likely expand access to populations who may otherwise be unable to access services in formal institutions of care.
Relationship between cognition and frailty-A cross-sectional study among elders in the tribal areas of Mysuru
Authors: Vanmathi A , Kulkarni Praveen , Chauhan Dennis , Kumar D Sunil , Periera Prathiba , Kishor M , basheer Sayana
Published: February 2023

Background

Cognition declines as age advances. Frailty is a pre-disability state. cognitive impairment and frailty lower the quality of life of elders. studies done in this background were mostly in urban or rural areas. Hence the current study was conducted among elders in the tribal areas to find the relationship between cognition and frailty.

Materials and methods

It was a cross-sectional study done for a period of one year among 316 elders >60 years. Based on the reported prevalence of cognitive dysfunction among the elderly to be 25% (Rakesh M Patel et al), with 5% absolute allowable error,5% of alpha error, and 10% non-response rate) residing in the tribal areas of Mysuru. WHO-30 cluster sampling was used. MOCA-B was used for assessing cognition scale and the TFI scale was used for assessing frailty.

Results

The prevalence of cognitive impairment and frailty was 95.3 % and 61.4% respectively. Factors like Gender, education, type of family, physical, financial and emotional dependency, and preference of treatment were associated with cognition. There was also a significant association between cognition and frailty.

Conclusion

There was a higher prevalence of cognitive impairment among frail elders. Thus, early diagnosis and appropriate management are necessary for healthy ageing
A patient-centered comparative effectiveness research study of culturally appropriate options for diabetes self-management
Authors: Page-Reeves Janet , Murray-Krezan Cristina , Burge Mark R. , Mishra Shiraz I. , Regino Lidia , Bleecker Molly , Perez Daniel , McGrew Hannah Cole , Bearer Elaine L. , Erhardt Erik
Published: February 2023

This project compared the effectiveness of two evidence-based models of culturally competent diabetes health promotion:The Diabetes Self-Management Support Empowerment Model(DSMS), andThe Chronic Care Model(CCM). Our primary outcome was improvement in patient capacity for diabetes self-management as measured by the Diabetes Knowledge Questionnaire (DKQ) and the Patient Activation Measure (PAM). Our secondary outcome was patient success at diabetes self-management as measured by improvement in A1c, depression sores using the PHQ-9, and Body Mass Index (BMI). We also gathered data on the cultural competence of the program using the Consumer Assessment of HealthcareProviders and Systems Cultural Competence Set(CAHPS-CC). We compared patient outcomes in two existing sites in Albuquerque, New Mexico that serve a large population of Latino diabetes patients from low-income households. Participants were enrolled as dyads—a patient participant (n=226) and a social support participant (n=226). Outcomes over time and by program were analyzed using longitudinal linear mixed modeling, adjusted for patient participant demographic characteristics and other potential confounding covariates. Secondary outcomes were also adjusted for potential confounders. Interactions with both time and program helped to assess outcomes. This study did not find a difference between the two sites with respect to the primary outcome measures and only one of the three secondary outcomes showed differential results. The main difference between programs was that depression decreased more for CCM than for DSMS. An exploratory, subgroup analysis revealed that at CCM, patient participants with a very high A1c (>10) demonstrated a clinically meaningful decrease. However, given the higher cultural competence rating for the CCM, statistically significant improvement in depression, and the importance of social support to the patients, results suggest that a culturally and contextually situated diabetes self-management and education program design may deliver benefit for patients, especially for patients with higher A1c levels.
Clinico-microbiological profile and treatment outcomes in patients with isoniazid monoresistant tuberculosis in South India
Authors: Prasanna M Venkata , Muthuraj R , Raj R Vimal , Govindarajan S , Pajanivel R
Published: February 2023

Isoniazid (INH) is an important first-line medication for the treatment of tuberculosis. The impact that tuberculosis drug resistance has on treatment outcomes is a topic that is receiving a lot of attention these days because of the rising incidence of INH-resistant cases. Study involves a single group of patients who have been diagnosed with Isoniazid monoresistant tuberculosis. Treatment history and demographic data of the patients were obtained after informed consent. The mutation patterns of isoniazid were observed after multiplex PCR and Line Probe Assay (LPA). A total of 101 patient (M,F) records at the IRL, Puducherry were analyzed. The predominant gene responsible for TB was KATG (67.3%). The KATG Mut1 was a prime mutation observed in the present study population (58.41%). Study showed positive association with males (74%), occupation as coolie (88%), diabetes as comorbidity (33%), pulmonary tuberculosis as the TB site (98.01%), history of previous ATT intake in 43 patients (42.6%), katG mutation (67.3%), katG Mut 1 was the prime mutation (58.4%).The cure rate was high inINH high concentration resistancepatients which was statistically significant (p=0.0167). INH monoresistance mutations seen in 64.3% of the patients with katG, compared to inhA (34.65%). Similar to katG mutations, inhA mutations also have MUT1 as their most frequent gene pattern. There is a significant association between males, diabetes, smoking and alcohol addictions were associated with high risk of developing high dose INH monoresistance (katG). High prevalence of recurrent tuberculosis was seen in high dose INH monoresistance tuberculosis. Patients who are microbiologically confirmed pulmonary tuberculosis and diabetes with rifampicin sensitive status needs to be checked for LPA for isoniazid sensitivity status to prevent treatment failure and relapse. It is crucial to understand the gene pattern in each of these patients since these mutations are closely associated to high or low-degree resistance to INH
Correlates of symptomatic remission among individuals with post-COVID-19 condition
Authors: Perlis Roy H. , Santillana Mauricio , Ognyanova Katherine , Lazer David
Published: February 2023

Importance

Post-COVID-19 condition (PCC), or long COVID, has become prevalent. The course of this syndrome, and likelihood of remission, has not been characterized.

Objective

To quantify the rates of remission of PCC, and the sociodemographic features associated with remission.

Design

16 waves of a 50-state U.S. non-probability internet survey conducted between August 2020 and November 2022

Setting

Population-based

Participants

Survey respondents age 18 and older

Main Outcome and Measure

PCC remission, defined as reporting full recovery from COVID-19 symptoms among individuals who on a prior survey wave reported experiencing continued COVID-19 symptoms beyond 2 months after the initial month of symptoms.

Results

Among 423 survey respondents reporting continued symptoms more than 2 months after acute test-confirmed COVID-19 illness, who then completed at least 1 subsequent survey, mean age was 53.7 (SD 13.6) years; 293 (69%) identified as women, and 130 (31%) as men; 9 (2%) identified as Asian, 29 (7%) as Black, 13 (3%) as Hispanic, 15 (4%) as another category including Native American or Pacific Islander, and the remaining 357 (84%) as White. Overall, 131/423 (31%) of those who completed a subsequent survey reported no longer being symptomatic. In Cox regression models, male gender, younger age, lesser impact of PCC symptoms at initial visit, and infection when the Omicron strain predominated were all statistically significantly associated with greater likelihood of remission; presence of ‘brain fog’ or shortness of breath were associated with lesser likelihood of remission.

Conclusions and Relevance

A minority of individuals reported remission of PCC symptoms, highlighting the importance of efforts to identify treatments for this syndrome or means of preventing it.

Trial registration

N/A

Key Points

Question

How often do individuals with post-COVID-19 condition, or long COVID, recover fully, and what predicts this recovery?

Findings

Among 423 individuals who initially reported post-COVID-19 condition and completed at least one subsequent survey, 131 (31%) later described symptomatic remission. Younger age, male gender, lesser symptom severity at initial survey, and infection during Omicron-predominance were associated with greater likelihood of reporting recovery.

Meaning

A minority of people with post-COVID-19 condition report spontaneous remission of symptoms, highlighting the importance of developing treatments for this syndrome.
Research priorities for improving menstrual health across the life-course in low- and middle-income countries
Authors: Plesons Marina , Torondel Belen , Caruso Bethany A. , Hennegan Julie , Sommer Marni , Haver Jacqueline , Keiser Danielle , van Eijk Anna M , Zulaika Garazi , Mason Linda , Phillips-Howard Penelope A.
Published: February 2023

Background

Research on menstrual health is required to understand the needs of girls, women, and others who menstruate; and to strengthen programmes with evidence-based interventions to improve health, wellbeing, and productivity. The identification of research priorities is an important process to help researchers, policymakers, programmers, and funding agencies decide where to invest their efforts and resources.

Methods

A modified version of the Child Health and Nutrition Research Initiative (CHNRI) approach was utilized to reach consensus on a set of research priority questions. Multisector stakeholders with expertise in policy, programming, financial support, and/or research relating to menstrual health were identified through networks and the literature. Individuals were invited to submit priority questions through survey monkey online on i) understanding the problem; ii) designing and implementing interventions; iii) integrating and scaling up interventions. Responses were consolidated and individuals were then invited to rank these questions based on i) novelty; ii) potential for intervention; and iii) importance/impact. Research priority scores were calculated from these responses and analyzed to evaluate associations with social and occupational characteristics of participating respondents.

Results

Eighty-two participants, of whom 89% were female and 39.0% from low- and middle-income countries (LMIC), proposed a total of 1135 research questions: 45.9% on understanding the problem, 39.7% on designing and implementing interventions, 12.7% on integrating and scale-up, plus 1.5% on other aspects. Questions were consolidated into a final list of 91 unique research questions. Sixty-six participants, of whom 80.3% were women and 39.4% from LMIC, ranked these questions. Top ten-ranked research priority questions comprised four questions on ‘understanding the problem’, four on ‘designing and implementing interventions’, one on ‘integrating and scaling up’, and one on ‘measurement and research’. Academics gave higher prioritization to ‘designing and implementing interventions,’ and lower prioritization to questions on ‘understanding the problem,’ ‘integrating and scaling up,’ and ‘measurement and research.

Conclusions

Use of CHNRI generated unique research priority questions from expertise internationally. The top-ranking research priorities can be utilized by policymakers, programmers, researchers, and funders to guide future research in menstrual health.
Potentiated cholinergic and corticofugal inputs support reorganized sensory processing in the basolateral amygdala during auditory threat acquisition and retrieval
Authors: Asokan Meenakshi M. , Watanabe Yurika , Kimchi Eyal Y. , Polley Daniel B.
Published: February 2023

Reappraising neutral stimuli as environmental threats reflects rapid and discriminative changes in sensory processing within the basolateral amygdala (BLA). To understand how BLA inputs are also reorganized during discriminative threat learning, we performed multi-regional measurements of acetylcholine (ACh) release, single unit spiking, and functional coupling in the mouse BLA and higher-order auditory cortex (HO-AC). During threat memory recall, sounds paired with shock (CS+) elicited relatively higher firing rates in BLA units and optogenetically targeted corticoamygdalar (CAmy) units, though not in neighboring HO-AC units. Functional coupling was potentiated for descending CAmy projections prior to and during CS+ threat memory recall but ascending amygdalocortical coupling was unchanged. During threat acquisition, sound-evoked ACh release was selectively enhanced for the CS+ in BLA but not HO-AC. These findings suggest that phasic cholinergic inputs facilitate discriminative plasticity in the BLA during threat acquisition that is subsequently reinforced through potentiated auditory corticofugal inputs during memory recall.
Stable sound decoding despite modulated sound representation in the auditory cortex
Authors: Funamizu Akihiro , Marbach Fred , Zador Anthony M
Published: February 2023

The activity of neurons in the auditory cortex is driven by both sounds and non-sensory context. To investigate the neuronal correlates of non-sensory context, we trained head-fixed mice to perform a two-alternative choice auditory task in which either reward or stimulus expectation (prior) was manipulated in blocks. Using two-photon calcium imaging to record populations of single neurons in auditory cortex, we found that both stimulus and reward expectation modulated the activity of these neurons. A linear decoder trained on this population activity could decode stimuli as well or better than predicted by the animal’s performance. Interestingly, the optimal decoder was stable even in the face of variable sensory representations. Neither the context nor the mouse’s choice could be reliably decoded from the recorded neural activity. Our findings suggest that in spite of modulation of auditory cortical activity by task priors, auditory cortex does not represent sufficient information about these priors to exploit them optimally and that decisions in this task require that rapidly changing sensory information be combined with more slowly varying task information extracted and represented in brain regions other than auditory cortex.
Comprehensive mutagenesis maps the effect of all single codon mutations in the AAV2repgene on AAV production
Authors: Jain Nina K. , Ogden Pierce J. , Church George M.
Published: February 2023

Recombinant adeno-associated viruses (rAAVs) are the predominant gene therapy vector. Several rAAV vectored therapies have achieved regulatory approval, but production of sufficient rAAV quantities remains difficult. The AAV Rep proteins, which are essential for genome replication and packaging, represent a promising engineering target for improvement of rAAV production but remain underexplored. To gain a comprehensive understanding of the Rep proteins and their mutational landscape, we assayed the effects of all 39,297 possible single codon mutations to the AAV2repgene on AAV2 production. Most beneficial variants are not observed in nature, indicating that improved production may require synthetic mutations. Additionally, the effects of AAV2repmutations were largely consistent across capsid serotypes, suggesting that production benefits are capsid independent. Our results provide a detailed sequence-to-function map that enhances our understanding of Rep protein function and lays the groundwork for Rep engineering and enhancement of large-scale gene therapy production.
The biocide triclosan induces (p)ppGpp dependent antibiotic tolerance and alters SarA dependent biofilm structures inStaphylococcus aureus
Authors: Walsh Dean , Salzer Andrea , Wolz Christiane , Aylott Jonathan , Hardie Kim R
Published: February 2023

The biocide triclosan is used extensively in both household and hospital settings. The chronic exposure to the biocide occurring in individuals that use triclosan-containing products results in low levels of triclosan present in the human body that has been linked to induction of antibiotic tolerance and altered biofilm formation. Here we aimed to unravel the molecular mechanisms involved in triclosan induced antibiotic tolerance and biofilm formation inStaphylococcus aureus. Triclosan treatment prior to planktonic exposure to bactericidal antibiotics resulted in 1,000 fold higher viable cell counts compared to non-pretreated cultures. Triclosan pretreatment also protectedS. aureusbiofilms against otherwise lethal doses of antibiotics as shown by live/dead cell staining and viable cell counting. Triclosan mediated antibiotic tolerance in planktonic and biofilm cultures required an active stringent response because a pppGpp0strain was not protected from antibiotic killing. Incubation ofS. aureuswith triclosan also altered biofilm structure due to SarA-mediated overproduction of the polysaccharide intercellular adhesin (PIA) in the biofilm matrix. Thus, physiologically relevant concentrations of triclosan can trigger (p)ppGpp dependent antibiotic tolerance as well as SarA dependent biofilm formation.

Importance

The prevalent bacteriumStaphylococcus aureusinfects skin lesions and indwelling devices, and this can cause sepsis with 33% mortality. Intrinsic to this is the formation of co-ordinated communities (biofilms) protected by a polysaccharide coat.S. aureusis increasingly difficult to eradicate due to its antibiotic resistance. Protection against Methicillin ResistantS. aureus(MRSA) includes pre-hospital admission washing with products containing biocides. The biocide triclosan is the predominant antibacterial compound in sewage in Ontario due to its use in household and hospital settings. Levels of triclosan accumulate with exposure in humans. The significance of our research is in identifying the mechanisms triggered by exposure ofS. aureusto physiological levels of triclosan that go on to raise the tolerance ofS. aureusto antibiotics and promote the formation of biofilms. This understanding will inform future criteria used to determine effective antimicrobial treatments.
Imaging dendritic spines in the hippocampus of a living mouse by 3D-STED microscopy
Authors: Bancelin Stéphane , Mercier Luc , Roos Johannes , Belkadi Mohamed , Pfeiffer Thomas , Kim Sun Kwang , Nägerl U. Valentin
Published: February 2023

STED microscopy has been used to address a wide range of neurobiological questions in optically well-accessible samples like cell culture or brain slices. However, the application of STED to deeply embedded structures in the brain of living animals remains technically challenging. In previous work, we established chronic STED imaging in the hippocampusin vivobut the gain in spatial resolution was restricted to the lateral plane. In this study, we report on extending the gain in STED resolution into the optical axis to visualize dendritic spines in the hippocampusin vivo. The approach is based on a spatial light modulator to shape the focal STED light intensity in all three dimensions and a conically shaped window that is compatible with an objective that has a long working distance and a high numerical aperture. Moreover, we corrected distortions of the laser wavefront to optimize the shape of the bottle beam of the STED laser, which is required for 3D-STED microscopy. In summary, we present a methodology to improve the axial resolution for STED microscopy in the deeply embedded hippocampusin vivo, facilitating longitudinal studies of neuroanatomical plasticity at the nanoscale in a wide range of (patho-)physiological contexts.
“Distinct inhibitory neurons differently shape neuronal codes for sound intensity in the auditory cortex”
Authors: Tobin Melanie , Sheth Janaki , Wood Katherine C. , Michel Erin K. , Geffen Maria N.
Published: February 2023

Cortical circuits contain multiple types of inhibitory neurons which shape how information is processed within neuronal networks. Here, we asked whether somatostatin-expressing (SST) and vasoactive intestinal peptide-expressing (VIP) inhibitory neurons have distinct effects on population neuronal responses to noise bursts of varying intensities. We optogenetically stimulated SST or VIP neurons while simultaneously measuring the calcium responses of populations of hundreds of neurons in the auditory cortex of male and female awake, head-fixed mice to sounds. Upon SST neuronal activation, noise bursts representations became more discrete for different intensity levels, relying on cell identity rather than strength. By contrast, upon VIP neuronal activation, noise bursts of different intensity level activated overlapping neuronal populations, albeit at different response strengths. At the single-cell level, SST and VIP neuronal activation differentially modulated the response-level curves of monotonic and nonmonotonic neurons. SST neuronal activation effects were consistent with a shift of the neuronal population responses toward a more localist code with different cells responding to sounds of different intensity. By contrast, VIP neuronal activation shifted responses towards a more distributed code, in which sounds of different intensity level are encoded in the relative response of similar populations of cells. These results delineate how distinct inhibitory neurons in the auditory cortex dynamically control cortical population codes. Different inhibitory neuronal populations may be recruited under different behavioral demands, depending on whether categorical or invariant representations are advantageous for the task.

SIGNIFICANCE

Information about sounds is represented in the auditory cortex by neuronal population activity that has a characteristic sparse structure. Cortical neuronal populations comprise multiple types of excitatory and inhibitory neurons. Here, we find that activating different types of inhibitory neurons differentially controls population neuronal representations, with one type of inhibitory neurons increasing the differences in the identity of the cells recruited to represent the different sounds, and another inhibitory neuron type changing the relative activity level of overlapping neuronal populations. Such transformations may be beneficial for different types of auditory behaviors, suggesting that these different types of inhibitory neurons may be recruited under different behavioral constraints in optimizing neuronal representations of sounds.
Design approaches to expand the toolkit for building cotranscriptionally encoded RNA strand displacement circuits
Authors: Schaffter Samuel W. , Wintenberg Molly E. , Murphy Terence M. , Strychalski Elizabeth A.
Published: February 2023

Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation with potential applications spanningin vitrodiagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced togetherviatranscription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize 220 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components,i.e., a toolkit, enabling circuits with up to four-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.
tRNA m1G9 modification depends on substrate-specific RNA conformational changes induced by the methyltransferase Trm10
Authors: Strassler Sarah E. , Bowles Isobel E. , Krishnamohan Aiswarya , Kim Hyejeong , Edgington Catherine B. , Kuiper Emily G. , Hancock Clio J. , Comstock Lindsay R. , Jackman Jane E. , Conn Graeme L.
Published: February 2023

The methyltransferase Trm10 modifies a subset of tRNAs on the base N1 position of the 9th nucleotide in the tRNA core. Trm10 is conserved throughout Eukarya and Archaea, and mutations in the human gene (TRMT10A) have been linked to neurological disorders such as microcephaly and intellectual disability, as well as defects in glucose metabolism. Of the 26 tRNAs in yeast with guanosine at position 9, only 14 are substrates for Trm10. However, no common sequence or other posttranscriptional modifications have been identified among these substrates, suggesting the presence of some other tRNA feature(s) which allow Trm10 to distinguish substrate from nonsubstrate tRNAs. Here, we show that substrate recognition bySaccharomyces cerevisiaeTrm10 is dependent on both intrinsic tRNA flexibility and the ability of the enzyme to induce specific tRNA conformational changes upon binding. Using the sensitive RNA structure-probing method SHAPE, conformational changes upon binding to Trm10 in tRNA substrates, but not nonsubstrates, were identified and mapped onto a model of Trm10-bound tRNA. These changes may play an important role in substrate recognition by allowing Trm10 to gain access to the target nucleotide. Our results highlight a novel mechanism of substrate recognition by a conserved tRNA modifying enzyme. Further, these studies reveal a strategy for substrate recognition that may be broadly employed by tRNA-modifying enzymes which must distinguish between structurally similar tRNA species.
Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation
Authors: Martinez M. , Petit J. , Leyva A. , Sogues A. , Megrian D. , Rodriguez A. , Gaday Q. , Ben Assaya M. , Portela M. , Haouz A. , Ducret A. , Grangeasse C. , Alzari P. M. , Durán R. , Wehenkel A.
Published: February 2023

The orderCorynebacterialesincludes major industrial and pathogenic actinobacteria such asCorynebacterium glutamicumorMycobacterium tuberculosis. Their elaborate multi-layered cell wall, composed primarily of the mycolyl-arabinogalactan-peptidoglycan complex, and their polar growth mode impose a stringent coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the tropomyosin-like protein Wag31. Here, we report the identification of two new divisome members, a gephyrin-like repurposed molybdotransferase (GLP) and its membrane receptor (GLPR). We show that the interplay between the GLPR/GLP module, FtsZ and Wag31 is crucial for orchestrating cell cycle progression. Our results provide a detailed molecular understanding of the crosstalk between two essential machineries, the divisome and elongasome, and reveal thatCorynebacterialeshave evolved a protein scaffold to control cell division and morphogenesis similar to the gephyrin/GlyR system that in higher eukaryotes mediates synaptic signaling through network organization of membrane receptors and the microtubule cytoskeleton.
Host-microbiome transplants of the schistosome snail hostBiomphalaria glabratareflect species-specific associations
Authors: Schols Ruben , Vanoverberghe Isabel , Huyse Tine , Decaestecker Ellen
Published: February 2023

Snail-borne diseases affect more than a quarter of a billion people worldwide and pose a high burden in the livestock industry. A fundamental understanding of the drivers of the epidemiology of these diseases is crucial for the development of sustainable control measures. The microbiome is increasingly being recognized as an important player in the tripartite interaction between parasitic flatworms, snail intermediate hosts and the snail microbiome. In order to better understand these interactions, transplant experiments are needed, which rely on the development of a reliable and reproducible protocol to obtain microbiome-disturbed snails. Here we report on the first successful snail microbiome transplants, which indicate thatBiomphalaria glabratacan accrue novel bacterial assemblies depending on the available environmental bacteria obtained from donor snails. Moreover, the phylogenetic relatedness to the donor significantly affected the survival probability of the recipients, corroborating the phylosymbiosis pattern in freshwater snails. The transplant technique described here, complemented by field-based studies, could facilitate future research endeavors to investigate the role of specific bacteria or bacterial communities in parasitic flatworm resistance ofB. glabrataand might ultimately pave the way for microbiome-mediated control of snail-borne diseases.
Abemaciclib restricts HCMV replication by suppressing pUL97-mediated phosphorylation of SAMHD1
Authors: Syrigos Georgios Vavouras , Feige Maximilian , Dirlam Alicia , Businger Ramona , Gruska Iris , Wiebusch Lüder , Hamprecht Klaus , Schindler Michael
Published: February 2023

Human cytomegalovirus (HCMV) is a herpesvirus that causes life-threatening infections in newborns or immunosuppressed patients. For viral replication, HCMV establishes a network of cellular interactions, among others cyclin-dependent kinases (CDK). Furthermore, HCMV encodes pUL97, a viral kinase, which is a CDK-homologue. HCMV uses pUL97 in order to phosphorylate and thereby antagonize SAMHD1, an antiviral host cell factor. Since HCMV has several mechanisms to evade restriction by SAMHD1, we first analyzed the kinetics of SAMHD1-inactivation and found that phosphorylation of SAMHD1 by pUL97 occurs directly after infection of macrophages. We hence hypothesized that inhibition of this process qualifies as efficient antiviral target and FDA approved CDK-inhibitors (CDKIs) might be potent antivirals that prevent the inactivation of SAMHD1. Indeed, Abemaciclib, a 2ndgeneration CDKI exhibited superior IC50s against HCMV in infected macrophages and the antiviral activity largely relied on its ability to block pUL97-mediated SAMHD1-phosphorylation. Altogether, our study highlights the therapeutic potential of clinically-approved CDKIs as antivirals against HCMV, sheds light on their mode of action and establishes SAMHD1 as a valid and highly potent therapeutic target.
Segregational drift hinders the evolution of antibiotic resistance on polyploid replicons
Authors: Garoña Ana , Santer Mario , Hülter Nils F. , Uecker Hildegard , Dagan Tal
Published: February 2023

The emergence of antibiotic resistance under treatment depends on the availability of resistance alleles and their establishment in the population. Novel resistance alleles are encoded either in chromosomal or extrachromosomal genetic elements; both types may be present in multiple copies within the cell. However, the effect of polyploidy on the emergence of antibiotic resistance remains understudied. Here we show that the establishment of resistance alleles in microbial populations depends on the ploidy level. Evolving bacterial populations under selection for antibiotic resistance, we demonstrate that resistance alleles in polyploid elements are lost frequently in comparison to alleles in monoploid elements due to segregational drift. Integrating the experiments with a mathematical model, we find an agreement between the theoretical and empirical allele dynamics, confirming our understanding of the allele segregation process. Using the mathematical model, we further show that the effect of polyploidy on the establishment probability of beneficial alleles is strongest for low replicon copy numbers and plateaus for high replicon copy numbers. Our results suggest that the distribution of fitness effects for mutations that get fixed in a population depends on the replicon ploidy level. Our study indicates that strategies for drug treatment of bacterial infections should take into consideration the pathogen ploidy level.
Lianas in tropical dry forests have higher embolism resistance but similar hydraulic efficiency than lianas in rainforests
Authors: Gerolamo Caian S. , Pereira Luciano , Costa Flavia R. C. , Jansen Steven , Angyalossy Veronica , Nogueira Anselmo
Published: February 2023

Lianas are increasing in relative abundance and biomass, mainly in seasonally dry forests, but it is unclear if this is associated with their hydraulic strategy. Here, we ask whether liana of seasonally dry forests are safer and more efficient in water transport than those of rainforest, which could explain liana distribution patterns and their recent increases. We measured hydraulic traits on five pairs of congeneric liana species (tribe Bignonieae) on one seasonal dry Atlantic forest and one Amazon rainforest. The predawn and minimum water potential, and the water potential at which 50% of the maximum gas amount was discharged were, on average, more negative in the liana species of the seasonal forest. However, these patterns were not constant at the genus level. The positive hydraulic safety margins and hydraulic efficiency were similar among species congeners across sites. The Bignonieae lianas studied likely experience equally low levels of embolism during drought, and maintain a high conductive capacity with efficient use of xylem space, which may favor survival and growth across tropical forests. The likely evolutionary convergence of high hydraulic safety associated with the opportunistic strategy of rapid growth, especially in disturbed areas can favor the abundant liana species in seasonal forests.

Highlight

Tropical forest liana species have high hydraulic efficiency and high interspecific variability in hydraulic safety. Despite this variability, some seasonal forest liana species have greater hydraulic safety than rainforest lianas, indicating an evolutionary convergence across lineages.