bluuebunny/crossref_metadata_2025 huggingface dataset:
Community context influences the conjugation efficiency ofE. coli
Authors: Bustamante Misshelle , Koopman Floor , Martens Jesper , Brons Jolanda K. , DelaFuente Javier , Kuipers Oscar P. , van Doorn Sander , de Vos Marjon G.J.
Published: February 2024

In urinary tract infections different bacteria can live in a polymicrobial community, it is unknown how such community members affect the conjugation rate of uropathogenicEscherichia coli. We investigated the influence of the polymicrobial urinary tract infection (UTI) community context on the conjugation rate ofE. coliisolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donorE. colistrain containing pOXA-48 and six uropathogenicE. coliisolates in the presence and absence of five community members to elucidate their effect on the rate of conjugation. We found that the basal conjugation rates in the absence of community members are genotype dependent. Interestingly, bacterial interactions have an overall positive effect onE. coliconjugation rates. Particularly Gram-positive enterococcal species were found to enhance the conjugation rates of most uropathogenicE. coliisolates. We hypothesize that the nature and co-culture of the interactions is important for these increased conjugation rates in AUM.
Whole-Genome Analysis of Stress Resistance-Related Genes inListeria monocytogenes
Authors: Dou Xin , Liu Yangtai , Panagou Efstathios Z. , Zhu Huajian , Li Zhuosi , Dong Qingli
Published: February 2024

Listeria monocytogenesis a crucial foodborne pathogen with significant public health implications. This study analyzed whole-genome sequences (WGS) ofL. monocytogenesstrains from public databases, examining associations between resistance genes, lineage, strain type, isolation source, and geography. Results revealed that after eliminating duplicates and strains with incomplete WGS, a total of 316 strains were deemed suitable for subsequent analyses. Within these strains, lineages I and II were extensively distributed, predominantly isolated from clinical and food sources. 56.65% of these strains fell into seven major Clonal Complexes (CC), identified by Multilocus Sequence Typing (MLST), correlating significantly with isolation information. Analysis of 46 resistance-related genes showed a high consistency of resistance genes in the same type of strains, hinting at a potential causal chain of ‘habits-foods-environments evolutions’. Moreover, the standard strains exhibit similar gene carriage rates as the sample strains, with multiple variations observed in acid-resistance genes. In conclusion, through a comprehensive analysis of theL. monocytogenesgenome sequences, this study deepens our understanding of the differences and associations between its lineage, strain typing, isolation sources, geographical distribution, and resistance genes. It has also explored the potential impact of environmental noise on the expression of these genes, offering a scientific foundation for devising more effective prevention and control strategies againstL. monocytogenes. Future endeavors should further dissect the functions of stress resistance genes and the variations in their expression, with the aim of gaining a deeper insight into the risks posed byL. monocytogenesto public health safety.
KSHV genome harbors both constitutive and lytically induced enhancers
Authors: Chowdhury Nilabja Roy , Gurevich Vyacheslav , Shamay Meir
Published: February 2024

Kaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gamma-herpesvirus family and is a well-known human oncogenic virus. In infected cells, the viral genome of 165 kbp is circular DNA wrapped in chromatin. The tight control of gene expression is critical for latency, the transition into the lytic phase, and the development of viral-associated malignancies. Distal cis-regulatory elements (CRE), such as enhancers and silencers, can regulate gene expression in a position and orientation-independent manner. Open chromatin is another characteristic feature of enhancers. To systematically search for enhancers, we cloned all the open chromatin regions in the KSHV genome downstream to the luciferase gene and tested their enhancer activity in infected and uninfected cells. A silencer was detected upstream of the latency promoter (LANAp). Two constitutive enhancers were identified in the K12p-OriLyt-R and ORF29 Intron region, where ORF29 Intron is a tissue-specific enhancer. The following promoters: OriLyt-L, PANp, ALTp, and the Terminal Repeats (TRs) acted as lytically induced enhancers. Expression of the Replication and Transcription Activator (RTA), the master regulator of the lytic cycle, was sufficient to induce the activity of lytic enhancers in uninfected cells. We propose that the TRs that span about 24 kbp region serve as a “viral super-enhancer” that integrates the repressive effect of the latency protein LANA with the activating effect of RTA. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers and their regulated genes. The silencer and enhancers described here provide an additional layer to the complex gene regulation of herpesviruses.

Importance

In this study, we performed a systematic functional assay to identify cis-regulatory elements within the genome of the oncogenic herpesvirus, Kaposi sarcoma-associated herpesvirus (KSHV). Similar to other herpesviruses, KSHV presents both latent and lytic phases. Therefore, our assays were performed in uninfected cells, during latent infection, and under lytic conditions. We identified two constitutive enhancers, where one seems to be a tissue- specific enhancer. In addition, four lytically induced enhancers, which are all responsive to the Replication and Transcription Activator (RTA), were identified. Furthermore, a silencer was identified between the major latency promoter and lytic genes locus. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers with their regulated genes. The terminal repeats spanning a region of about 24 kbp, seem like a “viral super-enhancer” that integrates the repressive effect of the latency protein LANA with the activating effect of RTA to regulate latency to lytic transition.
Modeling metastatic progression from cross-sectional cancer genomics data
Authors: Rupp Kevin , Lösch Andreas , Hu Y. Linda , Nie Chenxi , Schill Rudolf , Klever Maren , Pfahler Simon , Grasedyck Lars , Wettig Tilo , Beerenwinkel Niko , Spang Rainer
Published: February 2024

Metastasis formation is a hallmark of cancer lethality. Yet, metastases are generally unobservable during their early stages of dissemination and spread to distant organs. Genomic datasets of matched primary tumors and metastases may offer insights into the underpinnings and the dynamics of metastasis formation. We present metMHN, a cancer progression model designed to deduce the joint progression of primary tumors and metastases using cross-sectional cancer genomics data. The model elucidates the statistical dependencies among genomic events, the formation of metastasis, and the clinical emergence of both primary tumors and their metastatic counterparts. metMHN enables the chronological reconstruction of mutational sequences and facilitates estimation of the timing of metastatic seeding. In a study of nearly 5000 lung adenocarcinomas, metMHN pinpointed TP53 and EGFR as mediators of metastasis formation. Furthermore, the study revealed that post-seeding adaptation is predominantly influenced by frequent copy number alterations. All datasets and code are available on GitHub athttps://github.com/cbg-ethz/metMHN.
Repression ofMRP51in cis does not contribute to the synthetic growth defect conferred by anhphMX4-marked deletion ofDBP1in aded1-tsmutant
Authors: Zhang Fan , Sen Neelam Dabas , Hinnebusch Alan G.
Published: February 2024

Powers et al. recently demonstrated that thehphMX6cassette used to deleteDPB1indbp1Δ::hphMX6yeast mutants leads to reduced expression incisof the adjacent geneMRP51, encoding the mitochondrial small subunit (SSU) ribosomal protein Mrp51. Here we provide evidence that elimination of Dbp1, not reducedMRP51expression, underlies the synthetic growth defect of adbp1Δ::hphMX6 ded1-tsmutant on glucose-containing medium, where respiration is dispensable, consistent with our previous conclusion that Dbp1 and Ded1 perform overlapping functions in stimulating translation initiation on mRNAs burdened with long or structured 5’UTRs in cells cultured with glucose.
Microbial community function increases host plant leaf growth in a pitcher plant experimental system
Authors: Bernardin Jessica R , Young Erica B , Gray Sarah M , Bittleston Leonora S
Published: February 2024

Across diverse ecosystems, bacteria and their host organisms engage in complex relationships having negative, neutral, or positive interactions. However, the specific effects of leaf-associated bacterial community functions on plant growth are poorly understood. To address this gap, we explored the relationships between bacterial community function and host plant growth in the purple pitcher plant (Sarracenia purpurea). The main aim of our research was to investigate how different bacterial community functions affect the growth and nutrient content in the plant. Previous research had suggested that microbial communities may aid in prey decomposition and subsequent nutrient acquisition in carnivorous plants, including S. purpurea. However, the specific functional roles of these bacterial communities in plant growth and nutrient uptake are not well known. In this study, sterile, freshly opened leaves (pitchers) were inoculated with three functionally distinct, pre-assembled bacterial communities and effects examined over 8 weeks. Bacterial community composition and function were measured using physiological assays, metagenomics, and metatranscriptomics. Distinct bacterial functions affected plant traits; a bacterial community enriched in decomposition and secondary metabolite production traits was associated with larger leaves with almost double the biomass of control pitchers. Physiological differences in bacterial communities were supported by metatranscriptomic analysis; for example, the bacterial community with the highest chitinase activity had greater expression of transcripts associated with chitinase enzymes. The relationship between bacterial community function and plant growth observed here indicates potential mechanisms for host-associated bacterial functions to support plant health and growth.
Investigate the causality and genetic association between migraine and Parkinson’s disease
Authors: Deng Ming-Gang , Zhou Xiuxiu , Liu Fang , Wang Kai , Luo Lingli , Zhang Min-Jie , Feng Qianqian , Liu Jiewei
Published: February 2024

Background

The relationship between migraine and Parkinson’s disease (PD) remains controversial. We intend to investigate the causal and genetic association between migraine and PD.

Methods

Data related to migraine [any migraine (AM), migraine without aura (MO), and migraine with aura (MA)] and PD were respectively obtained from the latest Genome-wide meta-analysis conducted by the International Headache Genetics Consortium and the International Parkinson’s Disease Genomics Consortium. Univariate Mendelian Randomization (UMR) and multivariate MR (MVMR) were conducted to estimate their bidirectional causality, and global/local genetic correlation and tissue expression analyses were utilized to assess their genetic associations.

Results

The UMR presented that AM (OR: 1.016, 95% CI: 0.908-1.135,p= 0.785), MO (OR: 0.944, 95% CI: 0.836-1.067,p= 0.358) and MA (OR: 1.006, 95% CI: 0.951, 1.064,p= 0.846) were unlikely to be associated with PD risk. Similarly, the reverse UMR analyses demonstrated that PD was unrelated to the risks of migraine and its subtypes. These null associations were supported by the MVMR when adjusted for coronary heart disease and hypertension. The global genetic correlation analyses presented that AM (rg= -0.061,p= 0.127), MA (rg= -0.047,p= 0.516), MO (rg= -0.063,p= 0.492) were generally not related to PD, and the local genetic correlation analyses shown they were also uncorrelated in any region. Additionally, the tissue expression analyses found they had no shared tissues.

Conclusion

This study suggested no causality or association between migraine and PD from the genetic perspective.
Unequal access to diagnosis of myalgic encephalomyelitis in England
Authors: Samms Gemma L. , Ponting Chris P.
Published: February 2024

Background

People with Myalgic Encephalomyelitis (ME/CFS; sometimes referred to as chronic fatigue syndrome) experience very poor health-related quality of life and only rarely recover. ME/CFS has no curative treatment and no single diagnostic test. Public health and policy decisions relevant to ME/CFS require knowledge of its prevalence and barriers to diagnosis. However, people with ME/CFS report lengthy diagnostic delays and widespread misunderstanding of their symptoms. Published prevalence estimates vary greatly by country, gender, age and ethnicity.

Methods

Hospital Episode Statistics data is routinely collected by the NHS in England together with patient age, gender and ethnicity. This data, downloaded from the Feasibility Self-Service of NHS DigiTrials, was used to stratify individuals with the ICD-10 code that best reflects ME/CFS symptoms (G93.3; “Postviral fatigue syndrome”) according to their age, self-reported gender and ethnicity, General Practice and NHS England Integrated Care Board (ICB).

Results

In all, 100,055 people in England had been diagnosed with ME/CFS (ICD-10:G93.3) between April 1 1989 and October 7 2023, 0.16% of all registered patients. Of these, 79,445 were females and 20,590 males, a female-to-male ratio of 3.88:1. Female relative to male prevalence peaked at about 6-to-1 in individuals’ fourth and fifth decades of life. Prevalence varied widely across the 42 ICBs: 0.086%-0.82% for females and 0.024%-0.21% for males. White individuals were approximately 5-fold more likely to be diagnosed with ME/CFS than others; black, Asian or Chinese ethnicities are associated with particularly low rates of ME/CFS diagnoses. This ethnicity bias is stronger than for other common diseases. Among active English GP practices, 176 (3%) had no registered ME/CFS patients. Eight ICBs (19%) each contained fewer than 8 other-than-white individuals with a G93.3 code despite their registers containing a total of 293,770 other-than-white patients.

Conclusion

Those who are disproportionately undiagnosed with ME/CFS are other-than-white ethnic groups, older females (>60y), older males (>80y), and people living in areas of multiple deprivation. The lifetime prevalence of ME/CFS for English females and males may be as high as 0.92% and 0.25%, respectively, or approximately 390,000 UK individuals overall. This improved estimate of ME/CFS prevalence allows more accurate assessment of the socioeconomic and disease burden imposed by ME/CFS.
Characteristics and completeness of reporting of systematic reviews of prevalence studies in adult populations: a meta-research study.
Authors: Buitrago-Garcia Diana , Robles-Rodriguez William Gildardo , Eslava-Schmalbach Javier H. , Salanti Georgia , Low Nicola
Published: February 2024

Objective: The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement, first published in 2009, has been widely endorsed and compliance is high in systematic reviews of intervention studies. Systematic reviews of prevalence studies are increasing in frequency, but their characteristics and reporting quality have not been examined in large studies. Our objectives were to describe the characteristics of systematic reviews of prevalence studies in adults, evaluate the completeness of reporting and explore study-level characteristics associated with the completeness of reporting. Study design and setting: We did a meta-epidemiological study. We searched 5 databases from January 2010 to December 2020 to identify systematic reviews of prevalence studies in adult populations. We used the PRISMA 2009 checklist to assess completeness of reporting and recorded additional characteristics. We conducted a descriptive analysis of review characteristics and linear regression to assess the relationship between compliance with PRISMA and publication characteristics. Results: We included 1172 systematic reviews of prevalence studies. The number of reviews increased from 25 in 2010 to 273 in 2020. The median PRISMA score for systematic reviews without meta-analysis was 17.5 out of a maximum of 23 and, for systematic reviews with meta-analysis, 22 out of a maximum of 25. Completeness of reporting, particularly for key items in the methods section was suboptimal. Systematic reviews that included a meta-analysis or reported using a reporting or conduct guideline were the factors most strongly associated with increased compliance with PRISMA 2009. Conclusion: Reporting of systematic reviews of prevalence was adequate for many PRISMA items. Nonetheless, this study highlights aspects for which special attention is needed. Development of a specific tool to assess the risk of bias in prevalence studies and an extension to the PRISMA statement could improve the conduct and reporting of systematic reviews of prevalence studies.
Political Economy Analysis of Health Taxes (Tobacco, Alcohol Drink, and Sugar Sweteened Beverage): Case Study of Three Provinces in Indonesia
Authors: Ahsan Abdillah , Amalia Nadira , Rahmayanti Krisna Puji , Adani Nadhila , Wiyono Nur Hadi , Endawansa Althof , Utami Maulida Gadis , Yuniar Adela Miranti , Anastasia Erika Valentina , Ayuning Pertiwi Yuyu Buono
Published: February 2024

Efforts to implement health tax policies to control the consumption of harmful commodities and enhance public health outcomes have garnered substantial recognition globally. However, their successful adoption remains a complex endeavour. This study takes a problem-driven political economy analysis (PEA) approach to investigate the challenges and opportunities surrounding health tax implementation, with a particular focus on sub-national government in Indonesia, where the decentralization context of health tax remains understudied. Employing a qualitative methodology by collecting data from a total of twelve focus group discussions (FGDs) conducted in three provinces—Lampung, Special Region of/Daerah Istimewa(DI) Yogyakarta, and Bali, each chosen to represent a specific commodity: tobacco, sugar-sweetened beverages (SSBs), and alcoholic beverages—we explore the multifaceted dynamics of health tax policies. These FGDs involved 117 participants, representing governmental institutions, non-governmental organizations (NGOs), and consumers. Our findings reveal that while health tax policies have the potential to contribute significantly to public health, challenges such as a lack of consumer awareness, bureaucratic complexities, and decentralized governance hinder implementation. Furthermore, this study underscores the importance of effective policy communication. It highlights the importance of earmarking health tax revenues for public health initiatives. It also reinforces the need to see health taxes as one intervention as part of a comprehensive public health approach including complementary non-fiscal measures like advertising restrictions and standardized packaging. Addressing these challenges is critical for realizing the full potential of health tax policies.
Factors Influencing the Uptake of Public Health Interventions Delivery by Community Pharmacists: A thematic literature review
Authors: Mumbi Audrey , Mugo Peter , Barasa Edwine , Abiiro Gilbert , Nzinga Jacinta
Published: February 2024

Background

Community pharmacies are the first point of contact for most people seeking treatment for minor illnesses in Low– and middle-income countries (LMICs). In recent years, the role of community pharmacists has evolved, and they play a significant role in the delivery of public health interventions (PHIs) aimed at health promotion and prevention such as smoking cessation services, weight management services, HIV prevention, and vaccination. This review aims to explore the evidence on the factors that influence community pharmacists to take up the role of delivery of these interventions.

Methods

Three electronic databases namely, Embase, Medline, and Scopus were searched for relevant literature from the inception of the database to December 2023. Reference lists of included articles were also searched for relevant articles. A total of 22 articles were included in the review based on our inclusion and exclusion criteria. The data were analyzed and synthesized using a thematic approach to identify the factors that influence the community pharmacist’s decision to take up the role of PHI delivery. Reporting of the findings was done according to the PRISMA checklist.

Findings

The search identified 10,927 articles of which 22 were included in the review. The main factors that drive the delivery of PHIs by community pharmacists were identified as; training and continuous education, remuneration and collaboration with other healthcare professionals. Other factors included structural and workflow adjustments and support from the government and regulatory bodies.

Conclusions

Evidence from this review indicates that the decision to expand the scope of practice of community pharmacists is influenced by various factors. Incorporating these factors into the design of policies and public health programs is critical for the successful integration of community pharmacists in the delivery of broader public health to meet the rising demand for health care across health systems.
Replicating enzymatic activity by positioning active sites with synthetic protein scaffolds
Authors: Ding Yujing , Zhang Shanshan , Hess Henry , Kong Xian , Zhang Yifei
Published: February 2024

Evolutionary constraints significantly limit the diversity of naturally occurring enzymes, thereby reducing the sequence repertoire available for enzyme discovery and engineering. Recent breakthroughs in protein structure prediction andde novodesign, powered by artificial intelligence, now enable us to create enzymes with desired functions without relying on traditional genome mining. Here, we demonstrate a computational strategy for creating new-to-nature PET hydrolases by leveraging the known catalytic mechanisms and implementing multiple deep learning algorithms and molecular computations. This strategy includes the extraction of functional motifs from a template enzyme (here we use leaf-branch compost cutinase, LCC), regeneration of new protein scaffolds, computational screening, experimental validation, and sequence refinement. We successfully replicate PET hydrolytic activity with designer enzymes that are at least 30% shorter in sequence length than LCC. Among them,RsPETase 1 stands out due to its robust expressibility. It exhibits comparable activity toIsPETase and considerable thermostability with a melting temperature of 56 °C, despite sharing only 34% sequence similarity with LCC. This work suggests that enzyme diversity can be expanded by recapitulating functional motifs with computationally built protein scaffolds, thus generating opportunities to acquire highly active and robust enzymes that do not exist in nature.
Coexistence of self-compatible and self-incompatible alleles in a plant metapopulation via spatial rock-paper-scissors dynamics
Authors: Daniel Sachit , Thattai Mukund
Published: February 2024

Around 40% of flowering plants exhibit a preference for self-incompatibility systems (SI) on a macro-evolutionary scale. The dynamics of SI and self-compatible systems (SC) alleles can lead to the fixation of one genotype or coexistence, depending on factors like inbreeding depression and initial fractions. For the first time, we explore the dynamics of self-incompatible (SI) and self-compatible (SC) alleles in the presence of competitors, studying the relationship between population structure and SI frequency. Our numerical simulations consider non-instantaneous coupling between patches, focusing on a regime where the competitor’s fitness falls between inbred and outbred fitness. In this regime, SI, SC, and competitors exhibit repeating cycles of rock-paper-scissors dynamics both spatially and temporally. We find well-mixed environment leads to lower fractional population density of the focal species. Additionally in this regime, a paradoxical result emerges: in stress-free regions favorable to SI, the focal species may lose to the competitor.
An isothermal calorimetry assay for determining steady state kinetic and enzyme inhibition parameters for SARS-CoV-2 3CL-protease
Authors: Mazzei Luca , Ranieri Sofia , Greene-Cramer Rebecca , Cioffi Christopher , Montelione Gaetano T. , Ciurli Stefano
Published: February 2024

This manuscript describes the application of Isothermal Titration Calorimetry (ITC) to characterize the kinetics of 3CLprofrom the Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) and its inhibition by Ensitrelvir, a known non-covalent inhibitor. 3CLprois the main protease that plays a crucial role of producing the whole array of proteins necessary for the viral infection that caused the spread of COVID-19, responsible for millions of deaths worldwide as well as global economic and healthcare crises in recent years. The proposed calorimetric method proved to have several advantages over the two types of enzymatic assays so far applied to this system, namely Förster Resonance Energy Transfer (FRET) and Liquid Chromatography-Mass Spectrometry (LC-MS). The developed ITC-based assay provided a rapid response to 3CLproactivity, which was used to directly derive the kinetic enzymatic constantsKMandkcatreliably and reproducibly, as well as their temperature dependence, from which the activation energy of the reaction was obtained for the first time. The assay further revealed the existence of two modes of inhibition of 3CLproby Ensitrelvir, namely a competitive mode as previously inferred by crystallography as well as an unprecedented uncompetitive mode, further yielding the respective inhibition constants with high precision. The calorimetric method described in this paper is thus proposed to be generally and widely used in the discovery and development of drugs targeting 3CLpro.
Diversification of molecular pattern recognition in bacterial NLR-like proteins
Authors: Béchon Nathalie , Tal Nitzan , Stokar-Avihail Avigail , Melamed Sarah , Amitai Gil , Sorek Rotem
Published: February 2024

Antiviral STANDs (Avs) are bacterial anti-phage proteins that are evolutionarily related to immune pattern recognition receptors of the NLR family. Following recognition of a conserved phage protein, Avs proteins exhibit cellular toxicity and abort phage propagation by killing the infected cell. Type 2 Avs proteins (Avs2) were suggested to recognize the large terminase subunit of the phage as a signature of phage infection. Here, we show that while Avs2 fromKlebsiella pneumoniae(KpAvs2) can be activated when heterologously co-expressed with the terminase of phage SECphi18, during infectionin vivoKpAvs2 recognizes a different phage protein, named KpAvs2-stimulating protein 1 (Ksap1). We show that KpAvs2 directly binds Ksap1 to become activated, and that phages mutated in Ksap1 can escape KpAvs2 defense despite encoding an intact terminase. Our results exemplify the evolutionary diversification of molecular pattern recognition in bacterial Avs2 proteins, and highlight that pattern recognition during infection can differ from results obtained using heterologous co-expression assays.
Evolutionary innovation in conserved regulatory elements across the mammalian tree of life
Authors: Uebbing Severin , Kocher Acadia A. , Baumgartner Marybeth , Ji Yu , Bai Suxia , Xing Xiaojun , Nottoli Timothy , Noonan James P.
Published: February 2024

Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Evolution of enhancer sequences can alter target gene expression without causing detrimental misexpression in other contexts. It has long been thought that this modularity allows evolutionary changes in enhancers to escape pleiotropic constraints, which is especially important for evolutionary constrained developmental patterning genes. However, there is still little data supporting this hypothesis. Here we identified signatures of accelerated evolution in conserved enhancer elements across the mammalian phylogeny. We found that pleiotropic genes involved in gene regulatory and developmental processes were enriched for accelerated sequence evolution within their enhancer elements. These genes were associated with an excess number of enhancers compared to other genes, and due to this they exhibit a substantial degree of sequence acceleration over all their enhancers combined. We provide evidence that sequence acceleration is associated with turnover of regulatory function. We studied one acceleration event in depth and found that its sequence evolution led to the emergence of a new enhancer activity domain that may be involved in the evolution of digit reduction in hoofed mammals. Our results provide tangible evidence that enhancer evolution has been a frequent contributor to modifications involving constrained developmental signaling genes in mammals.
Surface versus volume synthesis governs growth-dependent efficacy of aβ-lactam antibiotic
Authors: Brouwers Rebecca , Mancini Leonardo , Tavaddod Sharareh , Biboy Jacob , Mauri Marco , Tatham Elizabeth , Enghardt Marie-Luise , Zander Ariane , Cicuta Pietro , Vollmer Waldemar , Allen Rosalind J.
Published: February 2024

The efficacy ofβ-lactam antibiotics depends strongly on bacterial growth rate. This can lead to poor correlation between in vivo action and in vitro assays, hindering effective prescribing – yet the mechanisms underlying growth-rate dependentβ-lactam action remain unclear. Here, we investigate growth-rate dependent action of mecillinam, aβ-lactam that targets the elongation-mediating PBP2 peptidoglycan transpeptidase enzyme, onEscherichia colicells. We show that mecillinam alters the balance between the rates of cell surface area and volume synthesis in a growth-rate dependent manner. Under mecillinam treatment, cell volume increases exponentially at a rate ﬁxed by the growth medium, but the cell’s ability to produce new surface area is compromised by the antibiotic. On rich medium, this imbalance leads to lysis, but on poor medium, slow-growing cells reach a new balance between surface area and volume synthesis, allowing sustained growth even at concentrations of mecillinam far above the EUCAST MIC value. A mathematical model based on surface area vs volume synthesis can quantitatively explain growth-medium dependent differences in mecillinam killing, as well as rescue from killing when cell morphology is perturbed in a microfluidic device.β-lactam antibiotic action is mechanistically complex, yet our work suggests that simple conceptual principles can help understand the interplay between molecular mechanism and cell physiology, potentially contributing to more effective use of these drugs.
Impacts of Self-Administered 3,4-Methylenedioxypyrovalerone (MDPV) Alone, and in Combination with Caffeine, on Recognition Memory and Striatal Monoamine Neurochemistry in Male Sprague-Dawley Rats: Comparisons with Methamphetamine and Cocaine
Authors: Seaman Robert W. , Lamon Kariann , Whitton Nicholas , Latimer Brian , Sulima Agnieszka , Rice Kenner C. , Murnane Kevin S. , Collins Gregory T.
Published: February 2024

Recent data suggest that 3,4-methylenedioxypyrovalerone (MDPV) has neurotoxic effects; however, the cognitive and neurochemical consequences of MDPV self-administration remain largely unexplored. Furthermore, despite the fact that drug preparations that contain MDPV often also contain caffeine, little is known regarding the toxic effects produced by the co-use of these two stimulants. The current study investigated the degree to which self-administered MDPV, or a mixture of MDPV+caffeine can produce deficits in recognition memory and alter neurochemistry relative to prototypical stimulants. Male Sprague-Dawley rats were provided 90-min or 12-h access to MDPV, MDPV+caffeine, methamphetamine, cocaine, or saline for 6 weeks. Novel object recognition (NOR) memory was evaluated prior to any drug self-administration history and 3 weeks after the final self-administration session. Rats that had 12-h access to methamphetamine and those that had 90-min or 12-h access to MDPV+caffeine exhibited significant deficits in NOR, whereas no significant deficits were observed in rats that self-administered cocaine or MDPV. Striatal mono-amine levels were not systematically affected. These data demonstrate synergism between MDPV and caffeine with regard to producing recognition memory deficits and lethality, highlighting the importance of recapitulating the manner in which drugs are used (e.g., in mixtures containing multiple stimulants, binge-like patterns of intake).
Building compositional tasks with shared neural subspaces
Authors: Tafazoli Sina , Bouchacourt Flora M. , Ardalan Adel , Markov Nikola T. , Uchimura Motoaki , Mattar Marcelo G. , Daw Nathaniel D. , Buschman Timothy J.
Published: February 2024

Cognition is remarkably flexible; we are able to rapidly learn and perform many different tasks1. Theoretical modeling has shown artificial neural networks trained to perform multiple tasks will re-use representations2and computational components3across tasks. By composing tasks from these sub-components, an agent can flexibly switch between tasks and rapidly learn new tasks4. Yet, whether such compositionality is found in the brain is unknown. Here, we show the same subspaces of neural activity represent task-relevant information across multiple tasks, with each task compositionally combining these subspaces in a task-specific manner. We trained monkeys to switch between three compositionally related tasks. Neural recordings found task-relevant information about stimulus features and motor actions were represented in subspaces of neural activity that were shared across tasks. When monkeys performed a task, neural representations in the relevant shared sensory subspace were transformed to the relevant shared motor subspace. Subspaces were flexibly engaged as monkeys discovered the task in effect; their internal belief about the current task predicted the strength of representations in task-relevant subspaces. In sum, our findings suggest that the brain can flexibly perform multiple tasks by compositionally combining task-relevant neural representations across tasks.
Sexually Dimorphic Influence of Circadian Pacemaker Neurons on Behavioral Rhythms
Authors: Iyer Aishwarya Ramakrishnan , Scholz-Carlson Eva , Bell Evardra , Biondi Grace , Richhariya Shlesha , Fernandez Maria P.
Published: February 2024

The circadian system regulates the timing of multiple molecular, physiological, metabolic, and behavioral phenomena. InDrosophila,as in other species, most of the research on how the timekeeping system in the brain controls the timing of behavioral outputs has been conducted in males, or sex has not been included as a biological variable. A critical set of circadian pacemaker neurons inDrosophilarelease the neuropeptide pigment-dispersing factor (PDF), which functions as a key output factor in the network with complex effects on other clock neurons. Lack ofPdfor its receptor,PdfR,results in most flies displaying arrhythmicity in activity–rest cycles under constant conditions. However, our results show that female circadian rhythms are less affected by mutations in bothPdfandPdfR. Crispr-Cas9-mediated mutagenesis ofPdf,specifically in ventral lateral neurons (LNvs), also has a greater effect on male rhythms. We tested the influence of M-cells on the circadian network and showed that speeding up the molecular clock specifically in M-cells led to sexually dimorphic phenotypes, with a more pronounced effect on male rhythmic behavior. Our results suggest that the female circadian system is more resilient to manipulations of M-cells and the PDF pathway, suggesting that circadian timekeeping is more distributed across the clock neuron network in females.
Dissociating endogenous and exogenous delta activity during natural speech comprehension
Authors: Chalas Nikos , Meyer Lars , Lo Chia-Wen , Park Hyojin , Kluger Daniel S. , Abbasi Omid , Kayser Christoph , Nitsch Robert , Gross Joachim
Published: February 2024

Decoding human speech requires the brain to segment the incoming acoustic signal into meaningful linguistic units, ranging from syllables and words to phrases. Integrating these linguistic constituents into a coherent percept sets the root of compositional meaning and hence understanding. One important cue for segmentation in natural speech are prosodic cues, such as pauses, but their interplay with higher-level linguistic processing is still unknown. Here we dissociate the neural tracking of prosodic pauses from the segmentation of multi-word chunks using magnetoencephalography (MEG). We find that manipulating the regularity of pauses disrupts slow speech-brain tracking bilaterally in auditory areas (below 2 Hz) and in turn increases left-lateralized coherence of higher frequency auditory activity at speech onsets (around 25 - 45 Hz). Critically, we also find that multi-word chunks—defined as short, coherent bundles of inter-word dependencies—are processed through the rhythmic fluctuations of low frequency activity (below 2 Hz) bilaterally and independently of prosodic cues. Importantly, low-frequency alignment at chunk onsets increases the accuracy of an encoding model in bilateral auditory and frontal areas, while controlling for the effect of acoustics. Our findings provide novel insights into the neural basis of speech perception, demonstrating that both acoustic features (prosodic cues) and abstract processing at the multi-word timescale are underpinned independently by low-frequency electrophysiological brain activity.
Using CRISPR–Cas9-Based Methods for Genome Editing inStaphylococcus aureus
Authors: Gründling Angelika , Ji Quanjiang , Salipante Stephen J.
Published: February 2024

Chromosomal mutations and targeted gene deletions and inactivations inStaphylococcus aureusare typically generated using the allelic exchange method. In recent years, however, more rapid methods have been developed, often using CRISPR–Cas9-based systems. Here, we describe recently developed CRISPR–Cas9-based plasmid systems for use inS. aureus,and discuss their use for targeted gene mutation and inactivation. First, we describe how a CRISPR–Cas9 counterselection strategy can be combined with a recombineering strategy to generate gene deletions inS. aureus. We then introduce dead Cas9 (dCas9) and Cas9 nickase (nCas9) enzymes, and discuss how the nCas9 enzyme fused to different nucleoside deaminases can be used to introduce specific base changes in target genes. We then discuss how the nCas9-deaminase fusion enzymes can be used for targeted gene inactivation via the introduction of premature stop codons or by mutating the start codon. Together, these tools highlight the power and potential of CRISPR–Cas9-based methods for genome editing inS. aureus.
A new modular framework for high-level application development at HEPS
Authors: Lu Xiaohan , Zhao Yaliang , Ji Hongfei , Jiao Yi , Li Jingyi , Li Nan , Meng Cai , Peng Yuemei , Ji Daheng , Wei Yuanyuan , Xu Haisheng , Pan Weimin , Xu Gang
Published: February 2024

As a representative of the fourth-generation light sources, the High Energy Photon Source (HEPS) in Beijing, China, utilizes a multi-bend achromat lattice to obtain an approximately 100 times emittance reduction compared with third-generation light sources. New technologies bring new challenges to operate the storage ring. In order to meet the beam commissioning requirements of HEPS, a new framework for the development of high-level applications (HLAs) has been created. The key part of the new framework is a dual-layer physical module to facilitate the seamless fusion of physical simulation models with the real machine, allowing for fast switching between different simulation models to accommodate the various simulation scenarios. As a framework designed for development of physical applications, all variables are based on physical quantities. This allows physicists to analytically assess measurement parameters and optimize machine parameters in a more intuitive manner. To enhance both extensibility and adaptability, a modular design strategy is utilized, partitioning the entire framework into discrete modules in alignment with the requirements of HLA development. This strategy not only facilitates the independent development of each module but also minimizes inter-module coupling, thereby simplifying the maintenance and expansion of the entire framework. To simplify the development complexity, the design of the new framework is implemented using Python and is called Python-based Accelerator Physics Application Set (Pyapas). Taking advantage of Python's flexibility and robust library support, we are able to develop and iterate quickly, while also allowing for seamless integration with other scientific computing applications. HLAs for both the HEPS linac and booster have been successfully developed. During the beam commissioning process at the linac, Pyapas's ease of use and reliability have significantly reduced the time required for the beam commissioning operators. As a development framework for HLA designed for the new-generation light sources, Pyapas has the versatility to be employed with HEPS, as well as with other comparable light sources, due to its adaptability.
Exploring the dynamics of innovation: patterns of growth and contraction in the local food industry
Authors: Rytkönen Paulina Ines , Skoglund Wilhelm , Oghazi Pejvak , Laven Daniel
Published: February 2024

Purpose

The purpose of this study is shed light on the underlying forces behind entrepreneurship within a regional innovation system (RIS) in a remote rural region. The authors examine the following questions: Which are the main underlying forces behind the entrepreneurial process in a rural RIS characterized by traditionally low-tech, small-scale businesses? How can the development of a low-tech regional innovation system be conceptualized?

Design/methodology/approach

The design of the study is based on entrepreneurship theory. Data analysis followed practices used in phenomenography, a research approach used to analyse and identify commonalities and variations in populations' perceptions of a certain phenomenon. Data are composed using semi-structured interviews and a database composed of company information of all firms in the population.

Findings

A proactive mobilization of regional stakeholders and resources can be an important driving force behind the entrepreneurial process and generation of a rural RIS. Innovation can be generated within low-tech industries turning the rural context into an asset. An RIS in a remote rural context can be initiated and orchestrated by regional authorities, but knowledge brokering and orchestration can also be managed by networks of small-scale businesses brought together by mutual benefit and common interests.

Research limitations/implications

Regional innovation systems theory is most often used to study high-tech industries. But by combining regional innovation systems with rural entrepreneurship and entrepreneurship context theory is a fruitful avenue to understand the role of rural entrepreneurship in regional development, even in remote and peripheral regions. Innovation does not need to entail high-tech international environments; it can appear as the result of efforts in low-tech industries in rural and remote environments. The authors’ findings need to be scrutinized; therefore, the authors call for more research on regional innovation systems in rural environments.

Practical implications

It is possible for regional authorities to orchestrate a development process through the actions of a strong regional agent but also by supporting the creation of networks of small businesses that are built on trust and common interests.

Originality/value

This study contributes to the literature with a new perspective to the study of entrepreneurship and of regional innovation systems. Entrepreneurship research with focus on rural contexts most often highlight limits to entrepreneurship and see entrepreneurship as “just running a business”. A perspective that starts from innovation and innovative behaviour, despite the rural context and embedded resources, helps to generate new knowledge that can enrich the understanding of entrepreneurship and also be the foundation for more precise business development policies in rural settings.
Exploring how YouTube videos demonstrating preparation of dried wood ear mushrooms could pose food safety risks: a case study
Authors: Archila-Godínez Juan Carlos , Chen Han , Cheng Gloria , Manjrekar Sanjana Sanjay , Feng Yaohua
Published: February 2024

Purpose

In 2020, an outbreak of Salmonella Stanley linked to imported dried wood ear mushrooms affected 55 individuals in the United States of America. These mushrooms, commonly used in Asian cuisine, require processing, like rehydration and cutting, before serving. The US Centres for Disease Control and Prevention advise food preparers to use boiling water for rehydration to inactivate vegetative bacterial pathogens. Little is known about how food handlers prepare this ethnic ingredient and which handling procedures could enable Salmonella proliferation.

Design/methodology/approach

This study used content analysis to investigate handling practices for dried wood ear mushrooms as demonstrated in YouTube recipe videos and to identify food safety implications during handling of the product. A total of 125 Chinese- and English-language YouTube videos were analysed.

Findings

Major steps in handling procedures were identified, including rehydration, cutting/tearing and blanching. Around 62% of the videos failed to specify the water temperature for rehydration. Only three videos specified a water temperature of 100 °C for rehydrating the mushrooms, and 36% of the videos did not specify the soaking duration. Only one video showed handwashing, cleaning and sanitising of surfaces when handling the dried wood ear mushrooms.

Practical implications

This study found that most YouTube videos provided vague and inconsistent descriptions of the rehydration procedure, including water temperature and soaking duration. Food preparers were advised to use boiling water for rehydration to inactivate vegetative bacterial pathogens. However, boiling water alone is insufficient to inactivate all bacterial spores. Extended periods of soaking and storage could be of concern for spore germination and bacterial growth. More validation studies need to be conducted to provide guidance on how to safely handle the mushrooms.

Originality/value

This study will make a distinctive contribution to the field of food safety by being the first to investigate the handling procedure of a unique ethnic food ingredient, dried wood ear mushrooms, which has been linked to a previous outbreak and multiple recalls in the United States of America. The valuable data collected from this study can help target food handling education as well as influence future microbial validation study design and risk assessment.