bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response
Authors: Rao Aakarsha , Ni Zijian , Suresh Dhruthi , Mohanty Chitrasen , Wang Albert R. , Lee Denis L , Nickel Kwangok P. , Varambally Sooryanarayana , Kimple Randall J. , Lambert Paul F. , Kendziorski Christina , Iyer Gopal
Published: October 2023

Integrated human papillomavirus (HPV-16) associated head and neck squamous cell carcinoma (HNSCC) tumors have worse survival outcomes compared to episomal HPV-16 HNSCC tumors. Therefore, there is a need to differentiate treatment for HPV-16 integrated HNSCC from other viral forms. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional coregulators. However, the mechanism of BET protein-mediated transcription of viral-cellular genes in the integrated viral-HNSCC genomes needs to be better understood. We show that BET inhibition downregulates E6 significantly independent of the viral transcription factor, E2, and there was overall heterogeneity in the downregulation of viral transcription in response to the effects of BET inhibition across HPV-associated cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4 and mirrored downregulation of viral E6 and E7 expression. Strikingly, there was heterogeneity in the reactivation of p53 levels despite E6 downregulation, while E7 downregulation did not alter Rb levels significantly. We identified that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A expression. Overall, our studies show that BET inhibition provokes a G1-cell cycle arrest with apoptotic activity and suggests that BET inhibition regulates both viral and cellular gene expression in HPV-associated HNSCC.
Uncovering the Roles ofMycobacterium tuberculosis melHin Redox and Bioenergetic Homeostasis: Implications for Antitubercular Therapy
Authors: Chen Yu-Ching , Yang Xinxin , Wang Nan , Sampson Nicole S.
Published: October 2023

Mycobacterium tuberculosis(Mtb), the pathogenic bacterium that causes tuberculosis, has evolved sophisticated defense mechanisms to counteract the cytotoxicity of reactive oxygen species (ROS) generated within host macrophages during infection. ThemelHgene inMtbandMycobacterium marinum(Mm) plays a crucial role in defense mechanisms against ROS generated during infection. We demonstrate thatmelHencodes an epoxide hydrolase and contributes to ROS detoxification. Deletion ofmelHinMmresulted in a mutant with increased sensitivity to oxidative stress, increased accumulation of aldehyde species, and decreased production of mycothiol and ergothioneine. This heightened vulnerability is attributed to the increased expression ofwhiB3, a universal stress sensor. The absence ofmelHalso resulted in reduced intracellular levels of NAD+, NADH, and ATP. Bacterial growth was impaired, even in the absence of external stressors, and the impairment was carbon-source-dependent. Initial MelH substrate specificity studies demonstrate a preference for epoxides with a single aromatic substituent. Taken together, these results highlight the role ofmelHin mycobacterial bioenergetic metabolism and provide new insights into the complex interplay between redox homeostasis and generation of reactive aldehyde species in mycobacteria.

Importance

This study unveils the pivotal role played by themelHgene inMycobacterium tuberculosisandMycobacterium marinumin combatting the detrimental impact of oxidative conditions during infection. This investigation revealed notable alterations in the level of cytokinin-associated aldehyde,para-hydroxybenzaldehyde, as well as the redox buffer ergothioneine, upon deletion ofmelH. Moreover, changes in crucial cofactors responsible for electron transfer highlightedmelH’s crucial function in maintaining a delicate equilibrium of redox and bioenergetic processes. MelH prefers epoxide small substrates with a phenyl substituted substrate. These findings collectively emphasize the potential ofmelHas an attractive target for the development of novel antitubercular therapies that sensitize mycobacteria to host stress, offering new avenues for combating tuberculosis.
Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance
Authors: Zhang Jason Z. , Ong Shao-En , Baker David , Maly Dustin J.
Published: October 2023

Recently developed covalent inhibitors for RasG12C provide the first pharmacological tools to target mutant Ras-driven cancers. However, the rapid development of resistance to current clinical Ras G12C inhibitors is common. Presumably, a subpopulation of RasG12C-expressing cells adapt their signaling to evade these inhibitors and the mechanisms for this phenomenon are unclear due to the lack of tools that can measure signaling with single-cell resolution. Here, we utilized recently developed Ras sensors to profile the environment of active Ras and to measure the activity of endogenous Ras in order to pair structure (Ras signalosome) to function (Ras activity), respectively, at a single-cell level. With this approach, we identified a subpopulation of KRasG12C cells treated with RasG12C-GDP inhibitors underwent oncogenic signaling and metabolic changes driven by WT Ras at the golgi and mutant Ras at the mitochondria, respectively. Our Ras sensors identified Major Vault Protein (MVP) as a mediator of Ras activation at both compartments by scaffolding Ras signaling pathway components and metabolite channels. We found that recently developed RasG12C-GTP inhibitors also led to MVP-mediated WT Ras signaling at the golgi, demonstrating that this a general mechanism RasG12C inhibitor resistance. Overall, single-cell analysis of structure-function relationships enabled the discovery of a RasG12C inhibitor-resistant subpopulation driven by MVP, providing insight into the complex and heterogenous rewiring occurring during drug resistance in cancer.
Precise cortical contributions to feedback sensorimotor control during reactive balance
Authors: Boebinger Scott , Payne Aiden , Martino Giovanni , Kerr Kennedy , Mirdamadi Jasmine , McKay J. Lucas , Borich Michael , Ting Lena
Published: October 2023

The role of the cortex in shaping automatic whole-body motor behaviors such as walking and balance is poorly understood. Gait and balance are typically mediated through subcortical circuits, with the cortex becoming engaged as needed on an individual basis by task difficulty and complexity. However, we lack a mechanistic understanding of how increased cortical contribution to whole-body movements shapes motor output. Here we use reactive balance recovery as a paradigm to identify relationships between hierarchical control mechanisms and their engagement across balance tasks of increasing difficulty in young adults. We hypothesize that parallel sensorimotor feedback loops engaging subcortical and cortical circuits contribute to balance-correcting muscle activity, and that the involvement of cortical circuits increases with balance challenge. We decomposed balance-correcting muscle activity based on hypothesized subcortically- and cortically-mediated feedback components driven by similar sensory information, but with different loop delays. The initial balance-correcting muscle activity was engaged at all levels of balance difficulty. Its onset latency was consistent with subcortical sensorimotor loops observed in the lower limb. An even later, presumed, cortically-mediated burst of muscle activity became additionally engaged as balance task difficulty increased, at latencies consistent with longer transcortical sensorimotor loops. We further demonstrate that evoked cortical activity in central midline areas measured using electroencephalography (EEG) can be explained by a similar sensory transformation as muscle activity but at a delay consistent with its role in a transcortical loop driving later cortical contributions to balance-correcting muscle activity. These results demonstrate that a neuromechanical model of muscle activity can be used to infer cortical contributions to muscle activity without recording brain activity. Our model may provide a useful framework for evaluating changes in cortical contributions to balance that are associated with falls in older adults and in neurological disorders such as Parkinson’s disease.
The evolution of constitutively active humoral immune defenses inDrosophilapopulations under high parasite pressure
Authors: Zhou Shuyu Olivia , Arunkumar Ramesh , Ding Shuai Dominique , Leitão Alexandre B. , Jiggins Francis M.
Published: October 2023

Both constitutive and inducible immune mechanisms are employed by hosts for defense against infection. Constitutive immunity allows for a faster response, but it comes with an associated cost that is always present. This trade-off between speed and fitness costs leads to the theoretical prediction that constitutive immunity will be favored where parasite exposure is frequent. We selected populations ofDrosophila melanogasterunder high parasite pressure from the parasitoid waspLeptopilina boulardi.With RNA sequencing, we found the evolution of resistance in these populations was associated with them developing constitutively active humoral immunity, mediated by the larval fat body. Furthermore, these evolved populations were also able to induce gene expression in response to infection to a greater level, which indicates an overall more activated humoral immune response to parasitization. The anti-parasitoid immune response also relies on the JAK/STAT signaling pathway being activated in muscles following infection, and this induced response was only seen in populations that had evolved under high parasite pressure. We found that the cytokine Upd3, which induces this JAK/STAT response, is being expressed by immature lamellocytes. Furthermore, these immune cells became constitutively present when populations evolved resistance, potentially explaining why they gained the ability to activate JAK/STAT signaling. Thus, under intense parasitism, populations evolved resistance by increasing both constitutive and induced immune defenses, and there is likely an interplay between these two forms of immunity.

Author Summary

Immune defenses can be induced after infection or they may be constitutively active, even in uninfected individuals. As constitutive immunity is a more rapid response, theory predicts that it will be favored when animals frequently encounter parasites. When we subjected populations ofDrosophila melanogasterto high rates of parasitization from its natural parasite,Leptopilina boulardiparasitoid wasps, we indeed observed that the immune response became constitutively active. Uninfected insects had an activated humoral immune response and produced cytokine-secreting immune cells that were normally induced after infection. However, we also found that these populations evolved a greater induced response. This included a greatly increased cytokine response after infection, suggesting that the constitutive activation of some aspects of the immune system may allow a greater induced response in other tissues.
Very high frequencies of Familial Breast Cancer, low BRCA1/2 mutations and high Luminal molecular subtypes in Eastern Saudi Arabia necessitate the hunt for novel breast cancer hub genes
Authors: Al-Qurashi Tahani , Balghonaim Sarah , Albunyan Haya , Alduhailan Hattan , Almqhawi Latiffah , Zafar Irtaza Fatima , Abubaker Rehab , Malik Anees R , Mustafa Hani , Alanazi Nawaf , Iqbal Zafar
Published: October 2023

This study was carried out to find out incidence of familial breast cancer, frequencies of different histological and molecular subtypes of breast cancer, and proportion of breast cancer patient with BRCA1/2 mutations, to plan for its implementation in early cancer screening and personalized treatment in Eastern Saudi Arabia. The breast cancer incidence increased from 2009-2016 and peaked in 2012. Ductal carcinoma (80%) was the most common histological type and Luminal A/B the most common (74%) molecular types among all patients. The familial and non-familial breast cancer groups were compared based on their demographic and clinical characteristics. The mean age at diagnosis was 51.6±13.5 and 53.5±12.7 for familial and non-familial breast cancer patients respectively. A total of 10 (24.3%) of familial breast cancer patients were tested for BRCA gene mutations, and 5 (12.2%) were abnormal, making it 4.3% of total patients. In the familial group, significant correlation (p 0.04) was found between patients with age less than 50 and with more than one family member affected with breast or ovarian cancer. Significance was found between unilateral familial breast cancer and bone metastasis (p 0.004). In both familial and non-familial groups, significant correlation was found between unilateral breast cancer and liver metastasis (0.005 and 0.017 respectively). There was a significant association between unilateral non-familial breast cancer and luminal A molecular type (p 0.012). Analysis of TNM staging showed that (61%) of familial breast cancer patients were diagnosed at stage II. In conclusion, familial breast cancer incidence is increasingly high in Al-Ahsa region as compared to western populations which could be due to consanguineous marriage and social behaviors. It warrants further studies to explore familial breast cancer hub genes in Eastern Saudi Arabia and its implementation in early diagnosis and patient-tailored treatment of breast cancer.
Some principles for using epidemiologic study results to parameterize transmission models
Authors: Joshi Keya , Kahn Rebecca , Boyer Christopher , Lipsitch Marc
Published: October 2023

Background

Infectious disease models, including individual based models (IBMs), can be used to inform public health response. For these models to be effective, accurate estimates of key parameters describing the natural history of infection and disease are needed. However, obtaining these parameter estimates from epidemiological studies is not always straightforward. We aim to 1) outline challenges to parameter estimation that arise due to common biases found in epidemiologic studies and 2) describe the conditions under which careful consideration in the design and analysis of the study could allow us to obtain a causal estimate of the parameter of interest. In this discussion we do not focus on issues of generalizability and transportability.

Methods

Using examples from the COVID-19 pandemic, we first identify different ways of parameterizing IBMs and describe ideal study designs to estimate these parameters. Given real-world limitations, we describe challenges in parameter estimation due to confounding and conditioning on a post-exposure observation. We then describe ideal study designs that can lead to unbiased parameter estimates. We finally discuss additional challenges in estimating progression probabilities and the consequences of these challenges.

Results

Causal estimation can only occur if we are able to accurately measure and control for all confounding variables that create non-causal associations between the exposure and outcome of interest, which is sometimes challenging given the nature of the variables we need to measure. In the absence of perfect control, non-causal parameter estimates should still be used, as sometimes they are the best available information we have.

Conclusions

Identifying which estimates from epidemiologic studies correspond to the quantities needed to parameterize disease models, and determining whether these parameters have causal interpretations, can inform future study designs and improve inferences from infectious disease models. Understanding the way in which biases can arise in parameter estimation can inform sensitivity analyses or help with interpretation of results if the magnitude and direction of the bias is understood.
Research participants’ perception of ethical issues in stroke genomics and neurobiobanking research in Africa
Authors: Jegede Ayodele , Balogun Olubukola , Olorunsogbon Olorunyomi Felix , Nichols Michelle , Akinyemi Joshua , Jenkins Carolyn , Ogunronbi Mayowa , Singh Arti , Obiako Reginald , Wahab Kolawole , Bello Abiodun , Akpalu Albert , Sarfo Fred S. , Owolabi Lukman F. , Ojebuyi Babatunde , Adigun Muyiwa , Olujobi Dorcas , Musbahu Rabiu , Titiloye Musibau , Afolami Ibukun , Calys-Tagoe Benedict , Uvere Ezinne , Laryea Ruth , Fakunle Adekunle , Adeleye Osi , Adesina Deborah , Mensah Nathaniel , Oguike Wisdom , Coleman Nathaniel , Adeniyi Sunday , Omotoso Lanre , Asibey Shadrack , Melikam Lois , Yusuf Jibril , Gbenga Abdullateef , Mande Aliyu , Uthman Muhammed , Kalaria Rajesh N. , Owolabi Mayowa , Ovbiagele Bruce , Arulogun Oyedunni , Akinyemi Rufus O.
Published: October 2023

Background

There is a growing interest in stroke genomics and neurobiobanking research in Africa. These raise several ethical issues, such as consent, re-use, data sharing, storage, and incidental result of biological samples. Despite the availability of ethical guidelines developed for research in Africa, there is paucity of information on how the research participants’ perspectives could guide the research community on ethical issues in stroke genomics and neurobiobanking research. To explore African research participants’ perspectives on these issues, a study was conducted at existing Stroke Investigation Research and Education Network (SIREN) sites in Nigeria and Ghana.

Method

Using an exploratory design, twenty-eight Focus Group Discussions (FGDs) sessions were conducted with stroke survivors (n=7), caregivers(n=7), stroke - free controls(n=7), and Community Advisory Board members(n=7). Data were collected using an interview guide. Interviews were conducted in English and indigenous languages of the community, audio recorded, and transcribed verbatim. Data were analyzed using NVivo (March, 2020) Software.

Result

Results revealed that stroke genomics and neurobiobanking research in Africa require researchers’ direct attention to ethical issues. Concerns were raised about understanding, disclosure and absence of coercion as components of true autonomous decision making in research participation. Participants argued that the risk and benefits attached to participation should be disclosed at the time of recruitment. Fears around data sharing were voiced as adherence to the principle of privacy and confidentiality were of paramount importance to participants. The preference was to receive the results of incidental findings with no stigma attached from society.

Conclusion

Research participants’ perspectives are a vital aspect of community engagement in stroke genomics and neurobiobanking research. Findings from this study suggest that research participants are interested in these fields of research in Africa if their concerns about ethical issues are appropriately addressed within the research framework.
Mapping geographic and demographic shifts in container breeding mosquito-borne disease transmission suitability in Central and South America in a warming world
Authors: Ryan Sadie J. , Lippi Catherine A. , Stewart-Ibarra Anna M
Published: October 2023

The recent Intergovernmental Panel on Climate Change Sixth Assessment Report (IPCC-AR6) report brought into sharp relief the potential health impacts of a changing climate across large geographic regions. It also highlighted the gaps in available evidence to support detailed quantitative assessments of health impacts for many regions. In an increasingly urbanizing world, there is a need for additional information about the risk of mosquito-borne diseases from vectors adapted to human water storage behavior. Specifically, a better understanding of the geographic distribution of disease risk under different scenarios of climate warming and human populations shifts. For the Central and South America chapter of the IPCC Working Group II report, regional extractions of published projections of dengue and Zika risk in a changing climate were generated by one of the authors of this study. In that process, the lack of a compendium of available published risk estimates became apparent. This paper responds to that need and extends the scope of the IPCC report results for Central and South America. We present novel geospatial descriptions of risk for transmission for five mosquito-borne disease systems under future projected climate and demographic scenarios, including the potential risk for malaria in the event of the introduction and establishment of a vector of high global concern,Anopheles stephensi. We then present country-level and IPCC geospatial sub-region risk descriptions under baseline and future projected scenarios. By including demographic projections using the shared socioeconomic pathway (SSP) scenarios, we capture potential future risk in a way that is transparent and straightforward to compare and replicate. The goal of this paper is to report on these model output data and their availability. From a sub-regional perspective, the largest proportional gains in risk will be seen in the Southwestern South America (SWS) sub-region, comprising much of the southwestern coastline, for which suitability forAedes aegyptitransmitted dengue and Zika risk will see massive increases with warming, putting a large number of people at risk under future scenarios. In contrast, at the country level, the largest projected population risk impacts will be seen in Brazil for both arboviral and potential introduced malaria risk, despite some risks projected to decrease as parts of the country are too hot to sustain transmission risk. This paper provides modeled outputs for future use, in addition to broad summary descriptions at regional and country levels.
Global distribution ofLeptospiraserovar isolations and detections from animal host species: a systematic review and online database
Authors: Hagedoorn Nienke N. , Maze Michael J. , Carugati Manuela , Cash-Goldwasser Shama , Allan Kathryn J. , Chen Kevin , Cossic Brieuc , Demeter Elena , Gallagher Sarah , German Richard , Galloway Renee L. , Habuš Josipa , Rubach Matthew P. , Shiokawa Kanae , Sulikhan Nadezhda , Crump John A.
Published: October 2023

Objectives

Leptospira,the spirochaete causing leptospirosis, can be classified into >250 antigenically distinct serovars. Although knowledge of the animal host species and geographic distribution ofLeptospiraserovars is critical to understand the human and animal epidemiology of leptospirosis, currently data are fragmented. We aimed to systematically review the literature on animal host species and geographic distribution ofLeptospiraserovars to examine associations between serovars with animal host species and regions, and to identify geographic regions in need of study.

Methods

Nine library databases were searched from inception through 9 March 2023 using keywords includingLeptospira, animal, and a list of serovars. We sought reports of detection ofLeptospira, from any animal, characterized by cross agglutinin absorption test, monoclonal antibody typing, serum factor analysis, or pulsed-field gel electrophoresis to identify the serovar.

Results

We included 409 reports, published from 1927 through 2022, yielding data on 154Leptospiraserovars. The reports included data from 66 (26.5%) of 249 countries. Detections were from 144 animal host species including 135 (93.8%) from the class Mammalia, 5 (3.5%) from Amphibia, 3 (2.1%) from Reptilia, and 1 (0.7%) from Arachnida. Across the animal host species,Leptospiraserovars that were detected in the largest number of animal species included Grippotyphosa (n=39), Icterohaemorrhagiae (n=29), Pomona (n=28), Australis (n=25), and Ballum (n=25). Of serovars, 76 were detected in a single animal host species. We created an online database to identify animal host species for each serovar by country.

Conclusions

We found that many countries have few or noLeptospiraserovars detected from animal host species and that many serovars were detected from a single animal species. Our study highlights the importance of efforts to identify animal host species of leptospirosis, especially in places with a high incidence of human leptospirosis. We provide an updated resource for leptospirosis researchers.
Source of data for artificial intelligence applications in vascular surgery - a scoping review
Authors: Powezka Katarzyna , Slater Luke , Wall Michael , Gkoutos Georgios , Juszczak Maciej
Published: October 2023

Background

Applications of Artificial Intelligence (AI) are gaining traction in healthcare, including vascular surgery. While most healthcare data is in the form of narrative text or audio recordings, natural language processing (NLP) offers the ability to extract structured information from unstructured medical records. This can be used to develop more accurate risk prediction models, and to identify patients for trials to improve recruitment. The goals of this scoping review were to determine the source of data used to develop AI-based algorithms with emphasis on natural language processing, establish their application in different areas of vascular surgery and identify a target audience of published journals.

Methods

A literature search was carried out using PubMed, EMBASE, and Google Scholar database from January 1996 to March 2023. Following screening, 342 peer-reviewed articles met the eligibility criteria.

Findings

Among the 342 articles meeting eligibility criteria, the majority (191) were published after 2020. NLP algorithms were described in 34 papers, while 115 and 193 papers focused on machine learning (ML) and deep learning (DL), respectively. Two-thirds (67.25%) were published in non-clinical journals. The AI-based algorithms found widest application in research related to aorta and its branches (126 articles), followed by carotid disease (85), and peripheral arterial disease (65). Image-based data were utilised in 216 articles, while 153 and 85 papers relied on medical records, and clinical parameters. The AI algorithms were used for predictive modelling (123 papers), medical image segmentation (118), and to aid identification, detection, and diagnosis (103). Only 18 publications aimed to enhance the understanding of vascular disease pathophysiology.

Interpretation

Utilisation of different data sources and AI technologies depends on the purpose of the undertaken research. Despite the abundance of available of textual data, the NLP is disproportionally underutilised AI sub-domain.

Funding

None.
Distinctive and complementary roles of default mode network subsystems in semantic cognition
Authors: Shao Ximing , Krieger-Redwood Katya , Zhang Meichao , Hoffman Paul , Lanzoni Lucilla , Leech Robert , Smallwood Jonathan , Jefferies Elizabeth
Published: October 2023

The default mode network (DMN) typically deactivates to external tasks, yet supports semantic cognition. It comprises medial temporal (MT), core, and fronto-temporal (FT) subsystems, but its functional organisation is unclear: the requirement for perceptual coupling versus decoupling, input modality (visual/verbal), type of information (social/spatial) and control demands all potentially affect its recruitment. We examined the effect of these factors on activation and deactivation of DMN subsystems during semantic cognition, across four task-based functional magnetic resonance imaging (fMRI) datasets, and localised these responses in whole-brain state space defined by gradients of intrinsic connectivity. FT showed activation consistent with a central role across domains, tasks and modalities, although it was most responsive to abstract, verbal tasks; this subsystem uniquely showed more ‘tuned’ states characterised by increases in both activation and deactivation when semantic retrieval demands were higher. MT also activated to both perceptually-coupled (scenes) and decoupled (autobiographical memory) tasks, and showed stronger responses to picture associations, consistent with a role in scene construction. Core DMN consistently showed deactivation, especially to externally-oriented tasks. These diverse contributions of DMN subsystems to semantic cognition were related to their location on intrinsic connectivity gradients: activation was closer to sensory-motor cortex than deactivation, particularly for FT and MT, while activation for core DMN was distant from both visual cortex and cognitive control. These results reveal distinctive yet complementary DMN responses: MT and FT support different memory-based representations that are accessed externally and internally, while deactivation in core DMN is associated with demanding, external semantic tasks.

Significance Statement

We delineate the functional organisation of DMN in semantic cognition, examining effects of perceptual coupling versus decoupling, input modality (visual/verbal), domain (social/spatial) and control demands across DMN subsystems in four fMRI datasets. These subsystems played complementary roles in semantic cognition related to their locations on gradients of intrinsic connectivity. Medial temporal and frontotemporal subsystems supported visuospatial and abstract conceptual information respectively, across both internally and externally-focussed tasks, while deactivation in core DMN was associated with focussed and externally-oriented semantic states. We conclude that both content and process are relevant to the functional architecture of DMN in semantic cognition.
Diverse prey capture strategies in teleost larvae
Authors: Mearns Duncan S. , Hunt Sydney A. , Schneider Martin W. , Parker Ash V. , Stemmer Manuel , Baier Herwig
Published: October 2023

Animal behavior is adapted to the sensory environment in which it evolved, while also being constrained by physical limits, evolutionary history, and developmental trajectories. The hunting behavior of larval zebrafish (Danio rerio), a cyprinid native to streams in Eastern India, has been well characterized. However, it is unknown if the complement and sequence of movements employed during prey capture by zebrafish is universal across freshwater teleosts. Here, we explore the syntax of prey capture behavior in larval fish belonging to the cladePercomorpha, whose last common ancestor with cyprinids lived ∼240 million years ago. We compared the behavior of four cichlid species from Lake Tanganyika endemic to deep benthic parts of the lake (Lepidiolamprologus attenuatus,Lamprologus ocellatus, andNeolamprologus multifasciatus) or inhabiting rivers (Astatotilapia burtoni) with that of medaka (Oryzias latipes), a fish found in rice paddies in East Asia. Using high speed videography and neural networks, we tracked eye movements and extracted swim kinematics during hunting from larvae of these five species. Notably, we found that the repertoire of hunting movements of cichlids is broader than that of zebrafish, but shares basic features, such as eye convergence, positioning of prey centrally in the binocular visual field, and discrete prey capture bouts, including two kinds of capture strikes. In contrast, medaka swim continuously, track the prey monocularly without eye convergence, and position prey laterally before capturing them with a side swing. This configuration of kinematic motifs suggests that medaka may judge distance to prey predominantly by motion parallax, while cichlids and zebrafish may mainly use binocular visual cues. Together, our study documents the diversification of locomotor and oculomotor adaptations among hunting teleost larvae.
Astrocyte aquaporin mediates a tonic water efflux maintaining brain homeostasis
Authors: Pham Cuong , Komaki Yuji , Deàs-Just Anna , Le Gac Benjamin , Mouffle Christine , Franco Clara , Chaperon Agnès , Vialou Vincent , Tsurugizawa Tomokazu , Cauli Bruno , Li Dongdong
Published: October 2023

Brain water homeostasis not only provides a physical protection, but also determines the diffusion of chemical molecules key for information processing and metabolic stability. As a major type of glia in brain parenchyma, astrocytes are the dominant cell type expressing aquaporin water channel. How astrocyte aquaporin contributes to brain water homeostasis in basal physiology remains to be understood. We report that astrocyte aquaporin 4 (AQP4) mediates a tonic water efflux in basal conditions. Acute inhibition of astrocyte AQP4 leads to intracellular water accumulation as optically resolved by fluorescence-translated imaging in acute brain slices, andin vivoby fiber photometry in mobile mice. We then show that aquaporin-mediated constant water efflux maintains astrocyte volume and osmotic equilibrium, astrocyte and neuron Ca2+signaling, and extracellular space remodeling during optogenetically induced cortical spreading depression. Using diffusion-weighted magnetic resonance imaging (DW-MRI), we observed thatin vivoinhibition of AQP4 water efflux heterogeneously disturbs brain water homeostasis in a region-dependent manner. Our data suggest that astrocyte aquaporin, though bidirectional in nature, mediates a tonic water outflow to sustain cellular and environmental equilibrium in brain parenchyma.

Significance statement

Our brain is immersed, thus protected, in a water environment. It ensures intra- and extracellular molecular diffusion, which is vital for brain function and health. Brain water homeostasis is maintained by dynamic water transport between different cell types. Astrocytes are a main type of glial cell widely distributed in brain parenchyma, expressing the bidirectional aquaporin water channel. Here we show that in basal conditions, aquaporin channel mediates a tonic water efflux from astrocytes. This mechanism maintains astrocyte volume stability, activity-gated brain parenchyma remodeling and brain water homeostasis. Our finding sheds light on how astrocytes regulate water states in the brain, and will help to understand brain allostasis in specific life contexts.
Identification of Determinants that Allow Maintenance of High-Level Fluoroquinolone Resistance inAcinetobacter baumannii
Authors: Hamami Efrat , Huo Wenwen , Hernandez-Bird Juan , Castaneda Arnold , Bai Jinna , Syal Sapna , Ortiz-Marquez Juan C. , van Opijnen Tim , Geisinger Edward , Isberg Ralph R.
Published: October 2023

Acinetobacter baumanniiis associated with multidrug resistant (MDR) infections in healthcare settings, with fluoroquinolones such as ciprofloxacin being currently ineffective. Clinical isolates largely harbor mutations in the GyrA and TopoIV fluoroquinolone targets, as well as mutations that increase expression of drug resistance-nodulation-division (RND) efflux pumps. Factors critical for maintaining fitness levels of pump overproducers are uncharacterized despite their prevalence in clinical isolates. We here identify proteins that contribute to the fitness of FQR strains overexpressing three known RND systems using high-density insertion mutagenesis. Overexpression of the AdeFGH efflux pump caused hypersensitization to defects in outer membrane homeostatic regulation, including lesions that reduced LOS biosynthesis and blocked production of the majorA. baumanniiporin. In contrast, AdeAB pump hyperexpression, in the absence of elevatedadeCexpression (the outer membrane component of the pump), was relatively tolerant to loss of these functions, consistent with the outer membrane protein being the primary disruptive component. Surprisingly, overexpression of proton-transporting efflux pumps had little impact on cytosolic pH, consistent with a compensatory response to pump activity. The most striking transcriptional changes were associated with AdeFGH pump overexpression, including the activation of the phenylacetate (PAA) degradation regulon. Disruption of the PAA pathway resulted in cytosolic acidification and defective expression of genes involved in protection from oxidative stress. These results indicate that RND efflux pump overproduction is compensated by maintenance of outer membrane integrity inA. baumanniito facilitate fitness of FQR isolates.

Importance

Acinetobacter baumanniiis a pathogen that often causes multidrug resistant (MDR) infections in healthcare settings, presenting a threat to the efficacy of known therapeutic interventions. Fluoroquinolones such as ciprofloxacin are currently ineffective against a majority of clinicalA. baumanniiisolates, many of which express pumps that remove this antibiotic class from within the bacterium. Three of these pumps can be found in most clinical isolates, with one of the three often hyperproduced at all times. In this study we identify proteins that are necessary for the fitness of pump hyperproducers. The identified proteins are necessary to stabilize the outer membrane and allow the cytoplasm to tolerate the accumulation of ions as a consequence of excess pump activity. These results point to strategies for developing therapies that combine known antibiotics with drugs that target proteins important for survival of strains hyperexpressing efflux pumps.
A Method For Estimating The Cholesterol Affinity Of Integral Membrane Proteins From Experimental Data
Authors: Steck Theodore L. , Tabei S. M. Ali , Lange Yvonne
Published: October 2023

The cholesterol affinities of many integral plasma membrane proteins have been estimated by molecular computation. However, these values lack experimental confirmation. We therefore developed a simple mathematical model to extract sterol affinity constants and stoichiometries from published isotherms for the dependence of the activity of such proteins on membrane cholesterol concentration. The binding curves for these proteins are sigmoidal with strongly-lagged thresholds attributable to competition for the cholesterol by bilayer phospholipids. The model provided isotherms that matched the experimental data using published values for the sterol association constants and stoichiometries of the phospholipids. Three oligomeric transporters were found to bind cholesterol without cooperativity with dimensionless association constants of 35 for Kir3.4* and 100 for both Kir2 and a GAT transporter. (The corresponding ρG° values were -8.8, -11.4 and -11.4 KJ/mol, respectively.) These association constants are significantly lower than those for the phospholipids which range from ∼100 to 6,000. The BK channel, the nicotinic acetylcholine receptor and the M192I mutant of Kir3.4* appear to bind multiple cholesterol molecules cooperatively (n = 2 or 4) with subunit affinities of 563, 950 and 700, respectively. The model predicts that the three less avid transporters are approximately half-saturated in their native plasma membranes; hence, sensitive to variations in cholesterol in vivo. The more avid proteins would be nearly saturated in vivo. The method can be applied to any integral protein or other ligand in any bilayer for which there are reasonable estimates of the sterol affinities and stoichiometries of the phospholipids.
Regulation of BACH1 by hemin improves cardiac function in a mouse model of myocardial infarction
Authors: Alvino Valeria , Katare Rajesh , Fricker Annabell , Avolio Elisa , Caputo Massimo , Madeddu Paolo , Slater Sadie
Published: October 2023

Aims

The BTB and CNC homology 1 (BACH1) transcription factor is a repressor of heme oxygenase-1 (HMOX1), a pivotal enzyme involved in antioxidant response and iron recycling. Here we investigated whether pharmacological modulation of the BACH1 by hemin impacts on antioxidant responses and reparative angiogenesis in a mouse model of myocardial infarction (MI).

Methods and results

In vitrostudies on vascular cells showed hemin treatment downregulates BACH1 gene and protein expression and upregulates HMOX1. This axis was confirmed to be modulated in the murine infarcted heart, with BACH1 being upregulated, and HMOX1 downregulated compared to sham. Treatment with hemin every 3 days for 28 days post-MI significantly decreased BACH1 and increased HMOX1 protein expression, though no decrease in oxidative stress markers was detected. Hemin treated mice showed increases in both capillary and arteriole density, and reduced iron accumulation compared with controls. Furthermore, echocardiology measurements showed hemin treatment induced significant improvements in left ventricular wall thickness, and cardiac function as indicated by increased ejection fraction, fractional shortening, and stroke volume measurements.

Conclusion

Hemin has therapeutic potential to improve revascularisation and cardiac function in the heart post-MI.
NMR structure of the Orf63 pro-lytic protein from lambda bacteriophage
Authors: Khan Naushaba , Graham Tavawn , Franciszkiewicz Katarzyna , Bloch Sylwia , Nejman-Faleńczyk Bożena , Wegrzyn Alicja , Donaldson Logan W
Published: October 2023

Theorf63gene resides in a region of the lambda bacteriophage genome between theexoandxisgenes and is among the earliest genes transcribed during infection. In lambda phage and Shiga toxin (Stx) producing phages found in enterohemorrhagicE. coli(EHEC) associated with food poisoning, Orf63 expression reduces the host survival and hastens the period between infection and lysis thereby giving it pro-lysogenic qualities. The NMR structure of dimeric Orf63 reveals a fold consisting of two helices and one strand that all make extensive intermolecular contacts. Structure-based data mining failed to identify any Orf63 homolog beyond the family of temperate bacteriophages. A machine learning approach was used to design an amphipathic helical ligand that bound a hydrophobic cleft on Orf63. This approach may open a new path towards designing therapeutics that antagonize the contributions of Stx phages in EHEC outbreaks.
Structure-guided mutagenesis of OSCAs reveals differential activation to mechanical stimuli
Authors: Jojoa-Cruz Sebastian , Dubin Adrienne E. , Lee Wen-Hsin , Ward Andrew
Published: October 2023

The dimeric two-pore OSCA/TMEM63 family has recently been identified as mechanically activated ion channels. Previously, based on the unique features of the structure of OSCA1.2, we postulated the potential involvement of several structural elements in sensing membrane tension1. Interestingly, while OSCA1, 2, and 3 clades are activated by membrane stretch in cell-attached patches (i.e., they are stretch-activated channels), they differ in their ability to transduce membrane deformation induced by a blunt probe (poking). In an effort to understand the domains contributing to mechanical signal transduction, we used cryo-electron microscopy to solve the structure ofArabidopsis thaliana(At) OSCA3.1, which, unlike AtOSCA1.2, only produced stretch- but not poke-activated currents in our initial characterization2. Mutagenesis and electrophysiological assessment of conserved and divergent putative mechanosensitive features of OSCA1.2 reveal a selective disruption of the macroscopic currents elicited by poking without considerable effects on stretch-activated currents (SAC). Our results support the involvement of the amphipathic helix and lipid-interacting residues in the membrane fenestration in the response to poking. Our findings position these two structural elements as potential sources of functional diversity within the family.
Separation of sticker-spacer energetics governs the coalescence of metastable condensates
Authors: Chattaraj Aniruddha , Shakhnovich Eugene I.
Published: October 2023

Biological condensates often emerge as a multi-droplet state and never coalesce into one large droplet within the experimental timespan. Previous work revealed that the sticker-spacer architecture of biopolymers may dynamically stabilize the multi-droplet state. Here, we simulate the condensate coalescence using metadynamics approach and reveal two distinct physical mechanisms underlying the fusion of droplets. Condensates made of sticker-spacer polymers readily undergo a kinetic arrest when stickers exhibit slow exchange while fast exchanging stickers at similar levels of saturation allow merger to equilibrium states. On the other hand, condensates composed of homopolymers fuse readily until they reach a threshold density. Increase in entropy upon inter-condensate mixing of chains drives the fusion of sticker-spacer chains. We map the range of mechanisms of kinetic arrest from slow sticker exchange dynamics to density mediated in terms of energetic separation of stickers and spacers. Our predictions appear to be in qualitative agreement with recent experiments probing dynamic nature of protein-RNA condensates.

Statement of significance

A key conundrum of biological condensates is the coexistence of multiple droplets, in direct variance with classical predictions of mean-field theories of polymer solutions. Our current study uncovers that the merging of sticker-spacer condensate is an entropy driven process, as opposed to the surface energy driven fusion that are observed for canonical liquid droplets. This entropy, stemming from the inter-condensate polymer exchange, makes the droplet merging process dependent on inter-sticker dissociation kinetics. Stronger inter-sticker interaction triggers a kinetic arrest, preventing the condensate merger even at a low density. Our prediction starkly correlates with recent experimental findings on protein-RNA condensates in vitro and in vivo, highlighting the biological relevance of the interplay of kinetics and thermodynamics.
Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma
Authors: Kamayirese Seraphine , Maity Sibaprasad , Dieckman Lynne M. , Hansen Laura A. , Lovas Sándor
Published: October 2023

14-3-3ε is involved in various types of malignancies by increasing cell proliferation, promoting cell invasion or inhibiting apoptosis. In cutaneous squamous cell carcinoma (cSCC), 14-3-3ε is over expressed and mislocalized from the nucleus to the cytoplasm where it interacts with the cell division cycle 25 A (CDC25A) and suppresses apoptosis. Hence inhibition of the 14-3-3ε - CDC25A interaction is an attractive target for promoting apoptosis in cSCC. In this work, we optimized the structure of our previously designed inhibitor of 14-3-3ε – CDC25A interaction, pT, a phosphopeptide fragment corresponding to one of the two binding regions of CDC25A to 14-3-3ε. Starting from pT, we developed peptide analogs that bind 14-3-3ε with nanomolar affinities. Peptide analogs were designed by shortening the pT peptide, and introducing modifications at position 510 of the pT(502-510) analog. Both molecular dynamics (MD) simulations and biophysical methods were used to determine peptides binding to 14-3-3ε. Shortening the pT peptide from 14 to 9 amino acid residues resulted in a peptide (pT(502-510)) that binds 14-3-3ε with a KDvalue of 45.2 nM. Gly to Phe substitution in position 510 of pT(502-510) led to further improvement in affinity (KD: 22.0 nM) of the peptide for 14-3-3ε. Our results suggest that the designed peptide analogs are potential candidates for inhibiting 14-3-3ε -CDC25A interactions in cSCC cells; thus, inducing their apoptosis.