bluuebunny/crossref_metadata_2025 huggingface dataset:
GATA transcription factor in common bean: a comprehensive genome-wide functional characterization, identification, and abiotic stress response evaluation
Authors: Abdulla Mohamed Farah , Mostafa Karam , Aydin Abdullah , Kavas Musa
Published: April 2023

The GATA transcription factor has been extensively studied for its regulatory role in various biological processes in many plant species. The functional and molecular mechanism of GATA TFs in regulating tolerance to abiotic stress has not yet been studied in the common bean, a popular and commercially important crop affected by the intensifying climate change. This study analyzed the functional identity of the GATA gene family in the P. vulgaris genome under different abiotic and phytohormonal stress. TheGATAgene family was systematically investigated in theP. vulgarisgenome, and 31PvGATATFs were identified. The collinearity between the common bean, rice, andArabidopsiswas studied, and collinearity with Arabidopsis was higher than in rice. Among the 31PvGATAs, 18 showed duplicated events, which suggests the importance of gene duplication in contribution to GATA gene expansion. Furthermore, all thePvGATAgenes were classified into four major subfamilies, with eight, three, six, and 13 members in each subfamily (subfamilies I, II, III, and IV), respectively. A single GATA domain was also present in all PvGATA protein sequences, however, members of subfamily II contained additional domains like CCT and tify domains. The study also predicted and analyzed the promoter cis-regulatory elements (CREs). A total of 799 CREs was predicted in thePvGATAs, categorized into three categories, namely growth and development regulatory elements, stress-responsive elements, and phytohormone-responsive elements. The growth and development regulatory elements had the largest share of CREs in the promoter region ofPvGATAgenes. Additionally, we used qRT-PCR to investigate the expression profiles of fivePvGATAgenes in the common bean roots under abiotic and phytohormone treatments. The results suggest thatPvGATA1/10/25/28may play crucial roles in regulating plant resistance against salt and drought stress at 24 hours and may be involved in phytohormone-mediated stress signaling pathways. This study provides a comprehensive analysis of thePvGATAgene family, which can serve as a foundation for future research on the function ofGATATfs in abiotic stress tolerance in common bean plants.
Darapladib, an inhibitor of Lp-PLA2, sensitizes cancer cells to ferroptosis by remodeling lipid metabolism
Authors: Oh Mihee , Jang Seo Young , Lee Ji-Yoon , Kim Jong Woo , Jung Youngae , Seo Jinho , Han Tae-Su , Jang Eunji , Son Hye Young , Kim Dain , Kim Min Wook , Song Kwon-Ho , Oh Kyoung-Jin , Kim Won Kon , Bae Kwang-Hee , Huh Yong-Min , Han Baek-Soo , Lee Sang Chul , Hwang Geum-Sook , Lee Eun-Woo
Published: April 2023

Arachidonic and adrenic acids in the membrane play key roles in ferroptosis, but how these fatty acids are manipulated in cells is largely unknown. Here, we reveal that lipoprotein-associated phospholipase A2 (Lp-PLA2) controls intracellular phospholipid metabolism and contributes to ferroptosis resistance. A metabolic drug screen identified that darapladib (SB-480848), an inhibitor of Lp-PLA2, synergistically induced ferroptosis with GPX4 inhibitors. Notably, darapladib was able to enhance ferroptosis under lipoprotein-deficient or serum-free conditions. Furthermore, Lp-PLA2 was located in the membrane and cytoplasm and suppressed ferroptosis, suggesting the critical role of intracellular Lp-PLA2. Lipidomic analysis showed that phosphatidylethanolamine (PE) species were generally enriched, while lysophosphatidylethanolamine (lysoPE) and free fatty acid levels were reduced, upon darapladib treatment. Finally, combination treatment with darapladib and PACMA31, a GPX4 inhibitor, efficiently inhibited tumor growth in a xenograft model. Our study suggests that inhibition of Lp-PLA2 is a potential therapeutic strategy to enhance ferroptosis in cancer treatment.
The practice of breast self-examination and associated factors among female healthcare professionals working in selected hospitals in Kigali, Rwanda: A Cross Section Study
Authors: Wolde Mulugeta Tenna , Okova Rosemary , Habtu Michael , Wondafrash Mekitie , Bekele Abebe
Published: April 2023

Background

Breast self-examination is considered one of the main screening methods in detecting earlier stages of breast cancer. It is a useful technique if practiced every month by women above 20 years since globally breast cancer among women contributed to 685,000 deaths in 2020. However, the practice of breast self-examination among healthcare professionals is low in many developing countries. Therefore, this research was intended to measure the level of breast self-examination practice and determine associated factors among female healthcare professionals working in selected hospitals in Kigali, Rwanda.

Methods

A cross-sectional study was conducted among 221 randomly selected female healthcare professionals in four district hospitals in Kigali, Rwanda. A self-administered structured questionnaire was used as data collection instrument. The predictor variables were socio-demographic and obstetrics variables, knowledge on breast cancer and breast self-examination, attitude towards breast cancer and breast self-examination. Sample statistics such as frequencies, proportions and mean were used to recapitulate the findings in univariate analysis. Multiple logistic regression analysis was employed to identify statistically significant variables that predict breast self-examination practice. Adjusted odds ratio and 95% confidence level were reported. P-value < 0.05 was used to declare statistical significance.

Results

Breast self-examination was practiced by 43.5% of female healthcare professionals. This prevalence is low compared to other studies. Attitude towards breast self-examination and breast cancer was the only predictor variable that was significantly associated with breast self-examination practice [AOR=1.032; 95% CI (1.001, 1.065), p-value=0.042]. However, number of pregnancy and number of children were not significantly associated with BSE practice in the multi-variate analysis. In addition, knowledge and attitude were linearly correlated with r=0.186, p=0.005.

Conclusions

The breast self-examination practice was found to be low. Attitude toward breast cancer and breast self-examination was positively associated with BSE practice. Moreover, attitude and knowledge were linearly associated. This suggests the need for continuous medical education on breast self-examination and breast cancer to increase the knowledge & BSE practice level of female healthcare professionals.
The analysis of risk factors associated with multimorbidity of anaemia, malaria, and malnutrition among children aged 6- 59 months in Nigeria
Authors: Obasohan Phillips Edomwonyi , Walters Stephen J. , Jacques Richard , Khatab Khaled
Published: April 2023

In the last ten years multimorbidity in children under the age of five years has becoming an emerging health issue in developing countries. The absence of a proper understanding of the causes, risk factors, and prevention of these new health disorders (multimorbidity) in children is a significant cause for concern, if the sustainable development goal 3 of ensuring healthy lives and the promotion of well-being for all especially in the associated aim of ending preventable deaths of new-borns and children must be achieved by 2030. In the past, most studies conducted in Nigeria and some other least developed nations of the world focused on these multiple diseases by employing conventional analytical techniques to examine them separately as distinct disease entities. But the study of multimorbidity of anaemia, malaria, and malnutrition has not been done, especially in children. This study aims to investigate the multiple overlaps in the impact of individual and contextual variables on the prevalence of multimorbidity among children aged 6 to 59 months in Nigeria. The study used two nationally representative cross-sectional surveys, the 2018 Nigeria Demographic and Health Survey and the 2018 National Human Development Report.

A series of multilevel mixed effect ordered logistic regression models were used to investigate the associations between child/parent/household variables (at level 1), community-related variables (at level 2) and area-related variables (at level 3), and the multimorbidity outcome (no disease, one disease only, two or more diseases). The interaction effects between child’s sex, age, and household wealth quintiles and the outcome while accounting for some covariates in the model were also investigated. The result shows that 48.3% (4,917/10,184) of the sample of children aged 6-59 months cohabit with two or more of the disease outcomes. Child’s sex, age, maternal education, mother’s anaemia status. household wealth quintiles, the proportion of community wealth status, states with high human development index, region, and place of residence, were among the significant predictors of MAMM (p<0.05). There was a significant interaction effect between a child’s age and wealth status when some other covariates were accounted for. The prevalence of MAMM observed in the sample is large, with almost half of the children living with two or more of the diseases at the time of the survey and several potentially modifiable risk factors have been identified. If suitable actions are not urgently taken, Nigeria’s ability to actualise the SDG 3 will be in grave danger. Therefore, possible actions to ameliorate this problem include developing and implementing a suitable policy that will pave the way for integrated care models to be developed.
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics
Authors: Makrodimitris Stavros , Pronk Bram , Abdelaal Tamim , Reinders Marcel
Published: April 2023

Multi-omic analyses contribute to understanding complex biological processes, but also to making reliable predictions about, for example, disease outcomes. Several linear joint dimensionality reduction methods exist, but recently neural networks are more commonly used to embed different-omics into the same non-linear manifold. We compared linear to non-linear joint embedding methods using bulk and single-cell data. For modality imputation, non-linear methods had a clear advantage. Comparisons in downstream supervised tasks lead to the following insights: First, concatenating the principal components of each modality is a competitive baseline for multi-modal prediction. If only one modality was available at test time, joint embeddings yielded significant performance improvements with respect to a unimodal predictor. Second, imputed omics profiles can be fed to classifiers trained on real data with limited performance drops. Overall, the product-of-experts architecture performed well in most tasks while a common encoder of concatenated modalities performed poorly.
Cellular Senescence is a Double-Edged Sword in Regulating Aged Immune Responses to Influenza
Authors: Torrance Blake L. , Panier Hunter A. , Cadar Andreia N. , Martin Dominique E. , Lorenzo Erica C. , Jellison Evan R. , Bartley Jenna M. , Haynes Laura
Published: April 2023

Clearance of senescent cells has demonstrated therapeutic potential in the context of chronic age-related diseases. Little is known, however, how clearing senescent cells affects the ability to respond to an acute infection and form quality immunological memory. We aimed to probe the effects of clearing senescent cells in aged mice on the immune response to influenza (flu) infection. We utilized a p16 trimodality reporter mouse model (p16-3MR) to allow for identification and selective deletion of p16-expressing senescent cells upon administration of ganciclovir (GCV). While p16-expressing senescent cells may exacerbate dysfunctional responses to a primary infection, our data suggest they may play a role in fostering memory cell generation. We demonstrate that although deletion of p16-expressing cells enhanced viral clearance, this also severely limited antibody production in the lungs of flu-infected aged mice. 30 days later, there were fewer flu-specific CD8 memory T cells and lower levels of flu-specific antibodies in the lungs of GCV treated mice. GCV treated mice were unable to mount an optimal memory response and demonstrated increased viral load following a heterosubtypic challenge. These results suggest that targeting senescent cells may potentiate primary responses while limiting the ability to form durable and protective immune memory with age.
Immunoproteasomal Processing of Isolevuglandin Adducts in Hypertension
Authors: de la Visitación Néstor , Chen Wei , Krishnan Jaya , Van Beusecum Justin P. , Amarnath Venkataraman , Hennen Elizabeth M. , Zhao Shilin , Saleem Mohammad , Ao Mingfang , Harrison David G. , Patrick David M.
Published: April 2023

Abstract Figure

Graphical Abstract

Isolevuglandins (isoLGs) are lipid aldehydes that form in the presence of reactive oxygen species (ROS) and drive immune activation. We found that isoLG-adducts are presented within the context of major histocompatibility complexes (MHC-I) by an immunoproteasome dependent mechanism.

Pharmacologic inhibition of LMP7, the chymotrypsin subunit of the immunoproteasome, attenuates hypertension and tissue inflammation in the angiotensin II (Ang II) model of hypertension. Genetic loss of function of all immunoproteasome subunits or conditional deletion of LMP7 in dendritic cell (DCs) or endothelial cells (ECs) attenuated hypertension, reduced aortic T cell infiltration, and reduced isoLG-adduct MHC-I interaction. Furthermore, isoLG adducts structurally resemble double-stranded DNA and contribute to the activation of STING in ECs. These studies define a critical role of the immunoproteasome in the processing and presentation of isoLG-adducts. Moreover they define a role of LMP7 as a regulator of T cell activation and tissue infiltration in hypertension.
Optogenetic stimulation reveals frequency-dependent resonance and encoding in V1 excitatory and inhibitory neurons
Authors: Broggini Ana Clara , Onorato Irene , Tzanou Athanasia , Sotomayor-Gómez Boris , Uran Cem , Vinck Martin
Published: April 2023

Cortical information processing is thought to be facilitated by the resonant properties of individual neurons and neuronal networks, which selectively amplify inputs at specific frequencies. We used optogenetics to test how different input frequencies are encoded by excitatory cells and parvalbumin-expressing (PV) interneurons in mouse V1. Spike phase-locking and power increased with frequency, reaching a broad peak around 80-100Hz. This effect was observed only for Chronos, a fast-kinetic opsin, but not for Channelrhodopsin-2. Surprisingly, neurons did not exhibit narrow-band resonance in specific frequency-ranges, and showed reliably phase-locking up to 140Hz. Strong phase-locking at high frequencies reflected non-linear input/output transformations, with neurons firing only in a narrow part of the cycle. By contrast, low-frequency inputs were encoded in a more continuous manner. Correspondingly, spectral coherence and firing rates showed little dependence on frequency and did not reflect transferred power. To investigate whether strong phase-locking facilitated the reliable encoding of inputs, we analyzed various spike-train distances and Fano factor. Interestingly, responses to lower rather than higher frequencies had more globally reliable spike-counts and timing structure. These findings have various practical implications for understanding the effects of optogenetic stimulation and choice of opsin. Furthermore, they show both PV and excitatory neurons respond with more local precision, i.e. phase-locking, to high-frequency inputs, but have more globally reliable responses to low-frequency inputs, suggesting differential coding regimes for these frequencies.
Quantifying the relationship between spreading depolarization and perivascular cerebrospinal fluid flow
Authors: Mukherjee Saikat , Mirzaee Mahsa , Tithof Jeffrey
Published: April 2023

Recent studies have linked spreading depolarization (SD, an electro-chemical wave in the brain following stroke, migraine, traumatic brain injury, and more) with increase in cerebrospinal fluid (CSF) flow through the perivascular spaces (PVSs, annular channels lining the brain vasculature). We develop a novel computational model that couples SD and CSF flow. We first use high order numerical simulations to solve a system of physiologically realistic reaction-diffusion equations which govern the spatiotemporal dynamics of ions in the extracellular and intracellular spaces of the brain cortex during SD. We then couple the SD wave with a 1D CSF flow model that captures the change in cross-sectional area, pressure, and volume flow rate through the PVSs. The coupling is modelled using an empirical relationship between the excess potassium ion concentration in the extracellular space following SD and the vessel radius. We find that the CSF volumetric flow rate depends intricately on the length and width of the PVS, as well as the vessel radius and the angle of incidence of the SD wave. We derive analytical expressions for pressure and volumetric flow rates of CSF through the PVS for a given SD wave and quantify CSF flow variations when two SD waves collide. Our numerical approach is very general and could be extended in the future to obtain novel, quantitative insights into how CSF flow in the brain couples with slow waves, functional hyperemia, seizures, or externally applied neural stimulations.
A comprehensive catalog with 100 million genes and 3,000 metagenome-assembled genomes from global cold seep sediments
Authors: Han Yingchun , Zhang Chuwen , Zhao Zhuoming , Peng Yongyi , Liao Jing , Jiang Qiuyun , Liu Qing , Shao Zongze , Dong Xiyang
Published: April 2023

Cold seeps harbor abundant and diverse microbes that represent a tremendous potential for biological applications and also have a significant influence on biogeochemical cycles. Though recent metagenomic studies have expanded our understanding of the microbial community and function of seep microorganisms, the knowledge of diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic data from 16 cold seep sites across the globe to construct comprehensive gene and genome catalogs. The non-redundant gene catalog was comprised of 147 million genes (clustered at 95% amino acid identity), and 35.72% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) are obtained, most of which (94.31%) belong to novel species. Of them, 81 ANME species are identified covering all subclades except ANME-2d, and 23 syntrophic SRB species spanning Seep-SRB1a Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAGs catalogs are a valuable resource that enables expanded knowledge of the structure and functions of cold seep microbiomes.
Palmitoylethanolamide shows limited efficacy in controlling cerebral cryptococcosisin vivo
Authors: Munzen Melissa E. , Reguera-Gomez Marta , Hamed Mohamed F. , Enriquez Vanessa , Charles-Nino Claudia L. , Dores Michael R. , Alviña Karina , Martinez Luis R.
Published: April 2023

Cryptococcus neoformans(Cn) is an encapsulated neurotropic fungal pathogen and the causative agent of cryptococcal meningoencephalitis (CME) in humans. Recommended treatment for CME is Amphotericin B (AmpB) and 5-fluorocytosine (5-FC). Though effective, AmpB has displayed numerous adverse side effects due to its potency and nephrotoxicity, prompting investigation into alternative treatments. Palmitoylethanolamide (PEA) is an immunomodulatory compound capable of promoting neuroprotection and reducing inflammation. To investigate the efficacy of PEA as a therapeutic alternative for CME, we intracerebrally infected mice withCnand treated them with PEA or AmpB alone or in combination. Our results demonstrate that PEA alone does not significantly prolong survival nor reduce fungal burden, but when combined with AmpB, PEA exerts an additive effect and promotes both survivability and fungal clearance. However, we compared this combination to traditional AmpB and 5-FC treatment in a survivability study and observed lower efficacy. Overall, our study revealed that PEA alone is not effective as an antifungal agent in the treatment of CME. Importantly, we describe the therapeutic capability of PEA in the context ofCninfection and show that its immunomodulatory properties may confer limited protection when combined with an effective fungicidal agent.
Deletion of Neuroligins from Astrocytes Does Not Detectably Alter Synapse Numbers or Astrocyte Cytoarchitecture by Maturity
Authors: Golf Samantha R. , Trotter Justin H. , Wang Jinzhao , Nakahara George , Han Xiao , Wernig Marius , Südhof Thomas C.
Published: April 2023

Astrocytes perform multifarious roles in the formation, regulation, and function of synapses in the brain, but the mechanisms involved are incompletely understood. Interestingly, astrocytes abundantly express neuroligins, postsynaptic adhesion molecules that function as synaptic organizers by binding to presynaptic neurexins. Here we examined the function of neuroligins in astrocytes with a rigorous genetic approach that uses the conditional deletion of all major neuroligins (Nlgn1-3) in astrocytesin vivoand complemented this approach by a genetic deletion of neuroligins in glia cells that are co-cultured with human neurons. Our results show that early postnatal deletion of neuroligins from astrocytes in vivo has no detectable effect on cortical or hippocampal synapses and does not alter the cytoarchitecture of astrocytes when evaluated in young adult mice. Moreover, deletion of astrocytic neuroligins in co-cultures of human neurons produced no detectable consequences for the formation and function of synapses. Thus, astrocytic neuroligins are unlikely to fundamentally shape synapse formation or astrocyte morphogenesis but likely perform other important roles that remain to be discovered.
miR-125b-5p impacts extracellular vesicle biogenesis, trafficking, and EV subpopulation release in the porcine trophoblast by regulating ESCRT-dependent pathway
Authors: Guzewska Maria M. , Witek Krzysztof J. , Karnas Elżbieta , Rawski Michał , Zuba-Surma Ewa , Kaczmarek Monika M.
Published: April 2023

1.

Intercellular communication is a critical process that ensures cooperation between distinct cell types at the embryo–maternal interface. Extracellular vesicles (EVs) are considered to be potent mediators of this communication by transferring biological information in their cargo (e.g. miRNAs) to the recipient cells. miRNAs are small non-coding RNAs that affect the function and fate of neighboring and distant cells by regulating gene expression. Focusing on the maternal side of the dialog, we recently revealed the impact of embryonic signals, including miRNAs, on EV-mediated cell-to-cell communication. In this study, we show the regulatory mechanism of the miR-125b-5p ESCRT-mediated EV biogenesis pathway and the further secretion of EVs by trophoblasts at the time when the crucial steps of implantation are taking place.

To test the ability of miR-125b-5p to influence the expression of genes involved in the generation and release of EV subpopulations in porcine conceptuses, we used an ex vivo approach. Next, in silico and in vitro analyses were performed to confirm miRNA–mRNA interactions. Finally, EV trafficking and release were assessed using several imaging and particle analysis tools.

Our results indicated that conceptus development and implantation are accompanied by changes in the abundance of EV biogenesis and trafficking machinery. ESCRT-dependent EV biogenesis and the further secretion of EVs were modulated by miR-125b-5p, specifically impacting the ESCRT-II complex (via VPS36) and EV trafficking in primary porcine trophoblast cells. The identified miRNA–ESCRT interplay led to the generation and secretion of specific subpopulations of EVs.

miRNA present at the embryo–maternal interface governs EV-mediated communication between the mother and the developing conceptus, leading to the generation, trafficking, and release of characteristic subpopulations of EVs.
Myosin in autoinhibitedoffstate(s), stabilized by mavacamten, can be recruited via inotropic effectors
Authors: Ma Weikang , del Rio Carlos L. , Qi Lin , Prodanovic Momcilo , Mijailovich Srboljub , Zambataro Christopher , Gong Henry , Shimkunas Rafael , Gollapudi Sampath , Nag Suman , Irving Thomas C.
Published: April 2023

Mavacamten is a novel, FDA-approved, small molecule therapeutic designed to regulate cardiac function by selectively but reversibly inhibiting the enzymatic activity of myosin. It shifts myosin towards orderedoffstates close to the thick filament backbone. It remains unresolved whether mavacamten permanently sequesters these myosin heads in theoffstate(s) or whether these heads can be recruited in response to physiological stimuli when required to boost cardiac output. We show that cardiac myosins stabilized in theseoffstate(s) by mavacamten are recruitable by Ca2+, increased heart rate, stretch, and β-adrenergic (β-AR) stimulation, all known physiological inotropic effectors. At the molecular level, we show that, in presence of mavacamten, Ca2+increases myosin ATPase activity by shifting myosin heads from the reserve super-relaxed (SRX) state to the active disordered relaxed (DRX) state. At the myofilament level, both Ca2+and passive lengthening can shift orderedoffmyosin heads from positions close to the thick filament backbone to disorderedonstates closer to the thin filaments in the presence of mavacamten. In isolated rat cardiomyocytes, increased stimulation rates enhanced shortening fraction in mavacamten-treated cells. This observation was confirmedin vivoin telemetered rats, where left-ventricular dP/dtmax,an index of inotropy, increased with heart rate in mavacamten treated animals. Finally, we show that β-AR stimulationin vivoincreases left-ventricular function and stroke volume in the setting of mavacamten. Our data demonstrate that the mavacamten-promotedoffstates of myosin in the thick filament are activable, at least partially, thus leading to preservation of cardiac reserve mechanisms.

Significance statement

Mavacamten is the first myosin-targeted small molecule inhibitor approved by the FDA to treat obstructive hypertrophic cardiomyopathy by attenuating myocardial hyperdynamic contraction. The recruitment of cardiac contractility is, however, vital to ensure sufficient cardiac output during increased physiological demand. Here we show that major inotropic effectors are at least partially preserved in the setting of mavacamten, resulting in maintenance of cardiac reserve mechanisms. These results not only suggest an alternative mechanistic explanation, beyond mere LV outflow tract obstruction removal, for the clinically observed increase in peak oxygen uptake with exercise in HCM patients receiving mavacamten, but also lay the groundwork for a potential methodology to investigate the sarcomeric basis of chronotropic incompetence in disease states to motivate new therapeutic interventions.
Two Ascending Thermosensory Pathways from the Lateral Parabrachial Nucleus That Mediate Behavioral and Autonomous Thermoregulation
Authors: Yahiro Takaki , Kataoka Naoya , Nakamura Kazuhiro
Published: April 2023

Thermoregulatory behavior in homeothermic animals is an innate behavior to defend body core temperature from environmental thermal challenges in coordination with autonomous thermoregulatory responses. In contrast to the progress in understanding the central mechanisms of autonomous thermoregulation, those of behavioral thermoregulation remain poorly understood. We have previously shown that the lateral parabrachial nucleus (LPB) mediates cutaneous thermosensory afferent signaling for thermoregulation. To understand the thermosensory neural network for behavioral thermoregulation, in the present study, we investigated the roles of ascending thermosensory pathways from the LPB in avoidance behavior from innocuous heat and cold in rats. Neuronal tracing revealed two segregated groups of LPB neurons projecting to the median preoptic nucleus (MnPO), a thermoregulatory center (LPB→MnPO neurons), and those projecting to the central amygdaloid nucleus (CeA), a limbic emotion center (LPB→CeA neurons). While LPB→MnPO neurons include separate subgroups activated by heat or cold exposure of rats, LPB→CeA neurons were only activated by cold exposure. By selectively inhibiting LPB→MnPO or LPB→CeA neurons using tetanus toxin light chain or chemogenetic or optogenetic techniques, we found that LPB→MnPO transmission mediates heat avoidance, whereas LPB→CeA transmission contributes to cold avoidance.In vivoelectrophysiological experiments showed that skin cooling-evoked thermogenesis in brown adipose tissue requires not only LPB→MnPO neurons but also LPB→CeA neurons, providing a novel insight into the central mechanism of autonomous thermoregulation. Our findings reveal an important framework of central thermosensory afferent pathways to coordinate behavioral and autonomous thermoregulation and to generate the emotions of thermal comfort and discomfort that drive thermoregulatory behavior.
Interviewer Biases in Medical Survey Data: The Example of Blood Pressure Measurements
Authors: Geldsetzer Pascal , Chang Andrew Young , Meijer Erik , Sudharsanan Nikkil , Charu Vivek , Kramlinger Peter , Haarburger Richard
Published: April 2023

Health agencies rely upon survey-based physical measures to estimate the prevalence of key global health indicators such as hypertension. Such measures are usually collected by non-healthcare worker personnel and are potentially subject to measurement error due to variations in interviewer technique and setting, termed “interviewer effects”. In the context of physical measurements, particularly in low- and middle-income countries, interviewer-induced biases have not yet been examined. Using blood pressure as a case study, we aimed to determine the relative contribution of interviewer effects on the total variance of blood pressure measurements in three large nationally-representative health surveys from the Global South.

We utilized 169,681 observations between 2008 and 2019 from three health surveys (Indonesia Family Life Survey, National Income Dynamics Study of South Africa, and Longitudinal Aging Study in India). In a linear mixed model, we modeled systolic blood pressure as a continuous dependent variable and interviewer effects as random effects alongside individual factors as covariates. To quantify the interviewer effect-induced uncertainty in hypertension prevalence, we utilized a bootstrap approach comparing sub-samples of observed blood pressure measurements to their adjusted counterparts. Our analysis revealed that the proportion of variation contributed by interviewers to blood pressure measurements was statistically significant but small: approximately 0.24-2.2% depending on the cohort. Thus, hypertension prevalence estimates were not substantially impacted at national scales. However, individual extreme interviewers could account for measurement divergences as high as 12%. Thus, highly biased interviewers could have important impacts on hypertension estimates at the sub-district level.

Significance Statement

Physical measurements such as blood pressure are important indicators of countries’ health system performance. These measures are usually obtained in household surveys by study-specific interviewers, who are not clinical healthcare workers. Thus, there is a concern that they may contribute substantial measurement error. We used three large, nationally-representative health surveys from India, Indonesia, and South Africa to model the magnitude of the interviewer effect on blood pressure measurements, then projected their impact on estimations of country-level hypertension prevalence. At smaller geographic units, “extreme” interviewers could substantially bias hypertension estimates. Overall, however, the magnitude of the interviewer effects was small and, thus, unlikely to substantially bias hypertension prevalence estimates at the national level.
The TriScan: fast and sensitive 3D confocal fluorescence imaging using a simple optical design
Authors: Van den Eynde Robin , Verheyen Jon , Miclea Paul , Lazar Josef , Vandenberg Wim , Dedecker Peter
Published: April 2023

We present the TriScan, a compact and inexpensive fluorescence microscope that can combine the speed of widefield microscopy with the 3D-sectioning capabilities of confocal microscopy. The optical layout is based on a module that combines line-scan confocal imaging with a sensitive camera detector, realized using a simple optical layout that permits the use of arbitrarily fast scanning mirrors. The resulting design is theoretically capable of full field-of-view acquisition rates in the kilohertz regime combined with a diffraction-limited resolution and single-molecule sensitivity. In doing so, the system provides the ease-of- use and speed of widefield imaging combined with the optical sectioning of one-photon confocal imaging. The simple and inexpensive design is suitable for a broad variety of settings ranging from research to diagnostics and screening.
Computationally Engineered CRISPR-SpyCas9 High-Fidelity Variants with Improved Specificity and Reduced Non-specific DNA Damage
Authors: Rabinowitz Roy , Shor Oded , Zerbib Johanna , Herman Shay , Zelikson Natalie , Madiwale Shreyas , Yom-Tov Nataly , Ben-David Uri , Benninger Felix , Offen Daniel
Published: April 2023

The CRISPR-Cas system holds great promise in the treatment of diseases caused by genetic variations. As wildtype SpyCas9 is known to generate many off-target effects, its use in the clinic remains controversial due to safety concerns. Several high-fidelity Cas9 variants with greater specificity have been developed using rational design and directed evolution. However, the enhancement of specificity by these methods is limited by factors like selection pressure and library diversity. Thus,in-silicoprotein engineering may provide a more efficient route for enhancing specificity, although computationally testing these proteins remains challenging. We recently demonstrated the advantage of normal mode analysis to simulate and predict the enzymatic function of SpyCas9 in the presence of mismatches. Here, we report several mathematical models describing the entropy and functionality relationships in the CRISPR-Cas9 system. We demonstrate the invariant characteristics of these models across different conformational structures. Based on these invariant models, we developed ComPE, a novel computational protein engineering method to modify the protein and measure the vibrational entropy of wildtype or variant SpyCas9 in complex with its sgRNA and target DNA. Using this platform, we discovered novel high-fidelity Cas9 variants with improved specificity. We functionally validated the improved specificity of four variants, and the intact on-target activity in one of them. Lastly, we demonstrate their reduced off-target editing and non-specific gRNA-independent DNA damage, highlighting their advantages for clinical applications. The described method could be applied to a wide range of proteins, from CRISPR-Cas orthologs to distinct proteins in any field where engineered proteins can improve biological processes.
A benchmark of optimization solvers for genome-scale metabolic modeling
Authors: Machado Daniel
Published: April 2023

Genome-scale metabolic modeling is a powerful framework for predicting metabolic phenotypes of any organism with an annotated genome. For two decades, this framework has been used for rational design of microbial cell factories. In the last decade, the range of applications has exploded, and new frontiers have emerged, including the study of the gut microbiome and its health implications, and the role of microbial communities in global ecosystems. However, all the critical steps in this framework, from model construction to simulation, require the use of powerful linear optimization solvers, with the choice often relying on commercial solvers for their well-known computational efficiency. In this work, I benchmark a total of six solvers (two commercial and four open-source) and measure their performance to solve linear and mixed-integer linear problems of increasing complexity. Although commercial solvers are still the fastest, at least two open-source solvers show comparable performance. These results show that genome-scale metabolic modeling does not need to be hindered by commercial licensing schemes and can become a truly open science framework for solving urgent societal challenges.
Bill color is dynamic across the breeding season but not condition-dependent in Atlantic puffins
Authors: Kochvar Katja Helgeson , Wilson Amy Catherine , Bitton Pierre-Paul
Published: April 2023

Sexually monomorphic species have been historically overlooked in the sexual/social selection literature, but there is growing evidence that mutual ornamentation can be driven by selective forces such as mutual sexual selection or selection for individual recognition. Examining the properties of a trait may elucidate which forces most likely play a role, especially when comparing the characteristics of quality and identity traits. Atlantic puffins(Fratercula arctica)are an example of a mutually ornamented monomorphic species, where both males and females display a bright orange-red bill and orange gape rosette during the breeding season and are ornamented to similar degrees. In this study, we investigate whether the properties of the colorful bill and rosette, specifically lability across the breeding season and condition-dependence, more closely align with signals of quality or identity. Our findings support prior work that the bill is sexually monochromatic from an avian visual perspective. We also determined that the bill changes in a discriminable way within individuals and is especially dynamic in the fleshy cere and rosette. However, no metric of color on any region of the bill or rosette were significantly related to current body condition. Ultimately, we argue that bill color likely functions as a quality signal, although further study is needed to determine which aspect of quality coloration signals, if not condition. These results provide a basis for experimentally testing the signal value of the colorful bill in Atlantic puffins, and more broadly, a framework for investigating the properties of mutual ornamentation in avian species.

Lay summary

The properties of a colorful trait inform its potential function as a signal. We investigated whether the Atlantic puffin’s colorful bill could reflect an individual’s identity or quality. Because bill color changes within the breeding season, this feature is not stable enough to reliably signal identity. Bill color is also not related to a common proxy of quality (body condition) but may communicate another aspect of quality such as foraging or parenting ability.
Contribution of cortical layers to human dynamic functional connectivity
Authors: Pais-Roldán Patricia , Yun Seong Dae , Ramkiran Shukti , Veselinović Tanja , Neuner Irene , Zimmermann Markus , Felder Jörg , Shah N. Jon
Published: April 2023

Transitory states of the brain, sometimes linked to particular mental disorders, can be identified by conducting a dynamic analysis of connectivity in functional magnetic resonance imaging (fMRI) data. Here, we investigated whether the connectivity between corticallaminae(in contrast to between corticalareas), can vary during the course of a resting-state scan and whether this could impact the identification of brain states in the healthy brain.

We performed a sliding-window connectivity analysis of high-resolution fMRI data and found that the differential participation of the cortical layers in the overall cortical connectivity constitutes a more dynamic feature of the brain compared to region-to-region connectivity, with two main states (superficial vs. deep-laminae connectivity) fluctuating over time. Laminar connectivity restricted to the default mode network appeared relatively stable (superficial connectivity preferred), while the central executive and salience networks showed a fluctuating laminar preference. We anticipate that the dynamic analysis of connectivity focused on the different depths of the cerebral cortex could play an important role in characterizing healthy brain states as well as in identifying novel targets of psychiatric diseases.
A proximity proteomics pipeline with improved reproducibility and throughput
Authors: Zhong Xiaofang , Li Qiongyu , Polacco Benjamin J. , Patil Trupti , Marley Aaron , Foussard Helene , Khare Prachi , Vartak Rasika , Xu Jiewei , DiBerto Jeffrey F. , Roth Bryan L. , Eckhardt Manon , Zastrow Mark Von , Krogan Nevan J. , Hüttenhain Ruth
Published: April 2023

Proximity labeling (PL) through biotinylation coupled with mass spectrometry (MS) has emerged as a powerful technique for capturing spatial proteomes within living cells. Large-scale sample processing for proximity proteomics requires a workflow that minimizes hands-on time while enhancing quantitative reproducibility. Here, we present a scalable PL pipeline integrating automated enrichment of biotinylated proteins in a 96-well plate format. By combining this pipeline with an optimized quantitative MS acquisition method based on data-independent acquisition (DIA), we not only significantly increased sample throughput but also improved the reproducibility of protein identification and quantification. We applied this pipeline to delineate subcellular proteomes across various cellular compartments, including endosomes, late endosomes/lysosomes, the Golgi apparatus, and the plasma membrane. Moreover, employing 5HT2Aserotonin receptor as a model, we investigated temporal changes of proximal interaction networks induced by the receptor’s activation with serotonin. Finally, to demonstrate the applicability of our PL pipeline across multiple experimental conditions, we further modified the PL pipeline for reduced sample input amounts to accommodate CRISPR-based gene knockout, and assessed the dynamics of the 5HT2Anetwork in response to the perturbation of selected proximal interactors. Importantly, the presented PL approach is universally applicable to PL proteomics using biotinylation-based PL enzymes, increasing both throughput and reproducibility of standard protocols.
DiscoGen: Learning to Discover Gene Regulatory Networks
Authors: Ke Nan Rosemary , Dunn Sara-Jane , Bornschein Jorg , Chiappa Silvia , Rey Melanie , Lespiau Jean-Baptiste , Cassirer Albin , Wang Jane , Weber Theophane , Barrett David , Botvinick Matthew , Goyal Anirudh , Mozer Mike , Rezende Danilo
Published: April 2023

Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in biology. GRNs model the activatory and inhibitory interactions between genes and are inherently causal in nature. To accurately identify GRNs, perturbational data is required. However, most GRN discovery methods only operate on observational data. Recent advances in neural network-based causal discovery methods have significantly improved causal discovery, including handling interventional data, improvements in performance and scalability. However, applying state-of-the-art (SOTA) causal discovery methods in biology poses challenges, such as noisy data and a large number of samples. Thus, adapting the causal discovery methods is necessary to handle these challenges. In this paper, we introduce DiscoGen, a neural network-based GRN discovery method that can denoise gene expression measurements and handle interventional data. We demonstrate that our model outperforms SOTA neural network-based causal discovery methods.
The RNA binding proteins LARP4A and LARP4B promote sarcoma and carcinoma growth and metastasis
Authors: Coleman Jennifer C. , Tattersall Luke , Yianni Val , Knight Laura , Yu Hongqiang , Hallett Sadie , Johnson Philip , Caetano Ana , Cosstick Charlie , Ridley Anne , Gartland Alison , Conte Maria R , Grigoriadis Agamemnon E.
Published: April 2023

RNA-binding proteins (RBPs) are emerging as important regulators of pathogenesis, including cancer. Here we reveal that the recently characterised RBPs LARP4A and LARP4B are differentially overexpressed in primary osteosarcoma and osteosarcoma lung metastases, as well as in prostate cancer. Depletion of LARP4A and LARP4B inhibited primary tumour growth and metastatic spread in xenograft studies, as well as inhibiting cell proliferation, motility and migration. Transcriptomic profiling combined with high content multiparametric cell cycle analysis unveiled a central role for LARP4B, but not LARP4A, in regulating cell cycle progression in osteosarcoma and prostate cancer cell lines, potentially through modulating the post-transcriptional regulation of RNA targets that include key cell cycle proteins such as Cyclins B1 and E2, Aurora B and E2F1. Our work assigns new functions to LARP4A and LARP4B as pro-tumorigenic proteins in bone and prostate cancer, highlights their similarities while indicating distinct functional aspects, and adds significantly to the rapidly increasing roles of RBPs in different cancer models. Uncovering clear biological roles for these paralogous proteins provides new avenues for identifying novel tissue-specific targets and potential druggable intervention.
Rewiring of master transcription factor cistromes during high-grade serous ovarian cancer development
Authors: Nameki Robbin A. , Chang Heidi , Yu Pak , Abbasi Forough , Lin Xianzhi , Reddy Jessica , Haro Marcela , Fonseca Marcos AS , Freedman Matthew L. , Drapkin Ronny , Corona Rosario I. , Lawrenson Kate
Published: April 2023

The transcription factors MECOM, PAX8, SOX17 and WT1 are candidate master regulators of high-grade serous ‘ovarian’ cancer (HGSC), yet their cooperative role in the hypothesized tissue of origin, the fallopian tube secretory epithelium (FTSEC) is unknown. We generated 26 epigenome (CUT&TAG, CUT&RUN, ATAC-seq and HiC) data sets and 24 profiles of RNA-seq transcription factor knock-down followed by RNA sequencing in FTSEC and HGSC models to define binding sites and gene sets regulated by these factors incisandtrans. This revealed that MECOM, PAX8, SOX17 and WT1 are lineage-enriched, super-enhancer associated master regulators whose cooperative DNA-binding patterns and target genes are re-wired during tumor development. All four TFs were indispensable for HGSC clonogenicity and survival but only depletion of PAX8 and WT1 impaired FTSEC cell survival. These four TFs were pharmacologically inhibited by transcriptional inhibitors only in HGSCs but not in FTSECs. Collectively, our data highlights that tumor-specific epigenetic remodeling is tightly related to MECOM, PAX8, SOX17 and WT1 activity and these transcription factors are targetable in a tumor-specific manner through transcriptional inhibitors.