bluuebunny/crossref_metadata_2025 huggingface dataset:
Intestinal helminth skews DC2 development towards regulatory phenotype to counter the anti-helminth immune response
Authors: Andrusaite Anna , Ridgewell Olivia , Ahlback Anna , Webster Holly , Yamaguchi Hiroki , Peel Molly , Frede Annika , Al-Khalidi Sarwah , Farthing Andrew , Heawood Anna , Smith Annabelle , Roberts Edward , Mowat Allan , Maizels Richard , Perona-Wright Georgia , Milling Simon
Published: September 2024

The intestinal immune system maintains a balance between active immunity needed for protection and tolerance towards harmless antigens. Dendritic cells (DCs) found in the intestinal mucosa are key to the adaptive arm of these immunoregulatory events. DCs sample antigens in the tissue and then migrate to the draining lymph nodes, where they prime the T cells that then migrate back to the tissue as effector or regulatory cells. Intestinal DC are highly heterogeneous, and it remains unclear exactly which subsets induces the different kinds of immune response, or what signalling molecules and cellular mechanisms are involved. Here, we have studied these issues usingHeligmosomoides polygyrus bakeri (Hpb)infection in mice, a model which is uniquely suited to dissecting this regulatory circuit in the gut, where it drives type 2 protective immunity at the same time as inhibiting other aspects of the immune response. Here, we characterise intestinal DC duringHpbinfection for the first time. We observed a dynamical change of intestinal DC populations throughout the course of infection that correlated with altered phenotype and function. In particular,Hpbinfection saw a rise in a population of CD103+DC2 that retained a potent ability to drive Tregs during the infection and unlike CD103-DC2, had a reduced ability to induce pro-inflammatory immune response. Furthermore, transcriptional analysis revealed that TGFβ signalling may be responsible for some of the changes observed. This was confirmedin vitro, where supplementation TGFβ orHpb-produced TGFβ mimic (TGM) replicated the immunomodulatory effects seen in DCsin vivo. Together, these results present a mechanistic explanation of how helminths such asHpbmay modulate host immune responses by altering the differentiation and function of local DCs. Furthermore, our work provides the basis for understanding immune homeostasis in the intestine at the molecular and cellular levels. Thus, this work fills out a crucial gap in our knowledge of basic biology underlining the DC decision between pro- and anti-inflammatory immune response in the central circuit of adaptive immune response.
Beneficial rhizobacteria and virus infection modulate the soybean metabolome and influence the feeding preferences of the virus vectorEpilachna varivestis
Authors: Pulido Hannier , Mauck Kerry E. , De Moraes Consuelo M. , Mescher Mark C.
Published: September 2024

There is growing evidence that microbial plant symbionts shape interactions between plants and other organisms by modulating gene expression and metabolism. However, the detailed mechanisms mediating such effects are not well understood, particularly in systems where plants interact simultaneously with multiple symbionts and antagonists. In this study, we employed a multi-factorial design to explore the individual and combined effects of two plant-beneficial rhizobacteria (Delftia acidovoransandBradyrhizobium japonicum) and a pathogen (Bean pod mottle virus: BPMV) on gene expression and metabolite production by soybean plants, as well as downstream effects on plant interactions with a beetle vector of BPMVEpilachna varivestis. Our results document microbial effects on basic metabolism and defense pathways, resulting in increased levels of primary metabolites and depletion of secondary metabolites. These changes are consistent with the observed feeding preferences of beetles for rhizobia-inoculated and virus-infected plants. Together, our results indicate that BPMV infection and rhizobacteria colonization cause dramatic changes in plant metabolites related to nutrition and defense, with significant consequences for an agriculturally important pathosystem.
Unveiling the hidden interactome of CRBN molecular glues with chemoproteomics
Authors: Baek Kheewoong , Metivier Rebecca J. , Burman Shourya S. Roy , Bushman Jonathan W. , Yoon Hojong , Lumpkin Ryan J. , Abeja Dinah M. , Lakshminarayan Megha , Yue Hong , Ojeda Samuel , Verano Alyssa L. , Gray Nathanael S. , Donovan Katherine A. , Fischer Eric S.
Published: September 2024

Targeted protein degradation and induced proximity refer to strategies that leverage the recruitment of proteins to facilitate their modification, regulation or degradation. As prospective design of glues remains challenging, unbiased discovery methods are needed to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of molecular glue targets. By mapping the targets of 20 CRBN-binding molecular glues, we identify 298 protein targets and demonstrate the utility of enrichment methods for identifying novel targets overlooked using established methods. We use a computational workflow to estimate target confidence and perform a biochemical screen to identify a lead compound for the new non-ZF target PPIL4. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.
53BP1 deficiency leads to hyperrecombination using break-induced replication (BIR)
Authors: Shah Sameer Bikram , Li Youhang , Li Shibo , Hu Qing , Wu Tong , Shi Yanmeng , Nguyen Tran , Ive Isaac , Shi Linda , Wang Hailong , Wu Xiaohua
Published: September 2024

Break-induced replication (BIR) is mutagenic, and thus its use requires tight regulation, yet the underlying mechanisms remain elusive. Here we uncover an important role of 53BP1 in suppressing BIR after end resection at double strand breaks (DSBs), distinct from its end protection activity, providing insight into the mechanisms governing BIR regulation and DSB repair pathway selection. We demonstrate that loss of 53BP1 induces BIR-like hyperrecombination, in a manner dependent on Polα-primase-mediated end fill-in DNA synthesis on single-stranded DNA (ssDNA) overhangs at DSBs, leading to PCNA ubiquitination and PIF1 recruitment to activate BIR. On broken replication forks, where BIR is required for repairing single-ended DSBs (seDSBs), SMARCAD1 displaces 53BP1 to facilitate the localization of ubiquitinated PCNA and PIF1 to DSBs for BIR activation. Hyper BIR associated with 53BP1 deficiency manifests template switching and large deletions, underscoring another aspect of 53BP1 in suppressing genome instability. The synthetic lethal interaction between the 53BP1 and BIR pathways provides opportunities for targeted cancer treatment.
Quantifying the influence of biophysical factors in shaping brain communication through remnant functional networks
Authors: Nakuci Johan , Garcia Javier , Bansal Kanika
Published: September 2024

Functional connectivity (FC) reflects brain-wide communication essential for cognition, yet the role of underlying biophysical factors in shaping FC remains unclear. We quantify the influence of physical factors - structural connectivity (SC) and Euclidean distance (DC), which capture anatomical wiring and regional distance - and molecular factors - gene expression similarity (GC) and neuroreceptor congruence (RC), representing neurobiological similarity - on resting-state FC. We assess how these factors impact graph-theoretic and gradient features, capturing pairwise and higher-order interactions. By generating remnant functional networks after selectively removing connections tied to specific factors, we show that molecular factors, particularly RC, dominate graph-theoretic features, while gradient features are shaped by a mix of molecular and physical factors, especially GC and DC. SC has a surprisingly minor role. We also link FC alterations to biophysical factors in schizophrenia, bipolar disorder, and ADHD, with physical factors differentiating these groups. These insights are key for understanding FC across various applications, including task performance, development, and clinical conditions.
A data-driven algorithm to determine1H-MRS basis set composition
Authors: Davies-Jenkins Christopher W. , Zöllner Helge J. , Simicic Dunja , Alcicek Seyma , Edden Richard A.E. , Oeltzschner Georg
Published: September 2024

Purpose

Metabolite amplitude estimates derived from linear combination modeling of MR spectra depend upon the precise list of constituent metabolite basis functions used (the “basis set”). The absence of clear consensus on the “ideal” composition or objective criteria to determine the suitability of a particular basis set contributes to the poor reproducibility of MRS. In this proof-of-concept study, we demonstrate a novel, data-driven approach for deciding the basis-set composition using Bayesian information criteria (BIC).

Methods

We have developed an algorithm that iteratively adds metabolites to the basis set using iterative modeling, informed by BIC scores. We investigated two quantitative “stopping conditions”, referred to as max-BIC and zero-amplitude, and whether to optimize the selection of basis set on a per-spectrum basis or at the group level. The algorithm was tested using two groups of synthetic in-vivo-like spectra representing healthy brain and tumor spectra, respectively, and the derived basis sets (and metabolite amplitude estimates) were compared to the ground truth.

Results

All derived basis sets correctly identified high-concentration metabolites and provided reasonable fits of the spectra. At the single-spectrum level, the two stopping conditions derived the underlying basis set with 77-87% accuracy. When optimizing across a group, basis set determination accuracy improved to 84-92%.

Conclusion

Data-driven determination of the basis set composition is feasible. With refinement, this approach could provide a valuable data-driven way to derive or refine basis sets, reducing the operator bias of MRS analyses, enhancing the objectivity of quantitative analyses, and increasing the clinical viability of MRS.
Decreased GABA levels during development result in increased connectivity in the larval zebrafish tectum
Authors: Liu Yang , Chen Yongkai , Duffy Carly R. , VanLeuven Ariel J , Byers John Branson , Schriever Hannah C. , Ball Rebecca E. , Carpenter Jessica M. , Gunderson Chelsea E. , Filipov Nikolay M. , Ma Ping , Kner Peter A. , Lauderdale James D.
Published: September 2024

γ-aminobutyric acid (GABA) is an abundant neurotransmitter that plays multiple roles in the vertebrate central nervous system (CNS). In the early developing CNS, GABAergic signaling acts to depolarize cells. It mediates several aspects of neural development, including cell proliferation, neuronal migration, neurite growth, and synapse formation, as well as the development of critical periods. Later in CNS development, GABAergic signaling acts in an inhibitory manner when it becomes the predominant inhibitory neurotransmitter in the brain. This behavior switch occurs due to changes in chloride/cation transporter expression. Abnormalities of GABAergic signaling appear to underlie several human neurological conditions, including seizure disorders. However, the impact of reduced GABAergic signaling on brain development has been challenging to study in mammals. Here we take advantage of zebrafish and light sheet imaging to assess the impact of reduced GABAergic signaling on the functional circuitry in the larval zebrafish optic tectum. Zebrafish have threegadgenes: twogad1paralogs known asgad1aandgad1b, andgad2.Thegad1bandgad2genes are expressed in the developing optic tectum. Null mutations ingad1bsignificantly reduce GABA levels in the brain and increase electrophysiological activity in the optic tectum. Fast light sheet imaging of genetically encoded calcium indicator (GCaMP)-expressinggab1bnull larval zebrafish revealed patterns of neural activity that were different than either gad1b-normal larvae orgad1b-normal larvae acutely exposed to pentylenetetrazole (PTZ). These results demonstrate that reduced GABAergic signaling during development increases functional connectivity and concomitantly hyper-synchronization of neuronal networks.

Significance Statement

Understanding the impact of reduced GABAergic signaling on vertebrate brain development and function will help elucidate the etiology of seizure initiation and propagation and other neurological disorders due to the altered formation of neural circuits. Here, we used fast light sheet imaging of larval zebrafish that neuronally expressed a genetically encoded calcium indicator (GCaMP) to assess the impact of reduced GABA levels through null mutation ofgad1bduring brain development. We show that reduced GABA levels during development result in increased functional connectivity in the brain.
Cryo-EM Structure of Phospholipase Cε Defines N-terminal Domains and their Roles in Activity
Authors: Samassekou Kadidia , Garland-Kuntz Elisabeth E. , Ohri Vaani , Fisher Isaac J. , Erramilli Satchal K. , Muralidharan Kaushik , Bogdan Livia M. , Gick Abigail M. , Kossiakoff Anthony A. , Lyon Angeline M.
Published: September 2024

Phospholipase Cε (PLCε) increases intracellular Ca2+and protein kinase C (PKC) activity in the cardiovascular system in response to stimulation of G protein coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). The ability of PLCε to respond to these diverse inputs is due, in part, to multiple, conformationally dynamic regulatory domains. However, this heterogeneity has also limited structural studies of the lipase to either individual domains or its catalytic core. Here, we report the 3.9 Å reconstruction of the largest fragment of PLCε to date in complex with an antigen binding fragment (Fab). The structure reveals that PLCε contains a pleckstrin homology (PH) domain and four tandem EF hands, including subfamily-specific insertions and intramolecular interactions with the catalytic core. The structure, together with a model of the holoenzyme, suggest that part of the N-terminus and PH domain form a continuous surface that could engage cytoplasmic leaflets of the plasma and perinuclear membranes, contributing to activity. Functional characterization of this surface confirm it is critical for maximum basal and G protein-stimulated activities. This study provides new insights into the autoinhibited, basal conformation of PLCε and the first mechanistic insights into how it engages cellular membranes for activity.
Fast Attentional Information Routing via High-Frequency Bursts in the Human Brain
Authors: Banaie Boroujeni Kianoush , Helfrich Randolph F. , Fiebelkorn Ian C. , Bentley Nicole , Lin Jack J. , Knight Robert T. , Kastner Sabine
Published: September 2024

Brain-wide communication supporting flexible behavior requires coordination between sensory and associative regions but how brain networks route sensory information at fast timescales to guide action remains unclear. Using spiking neural networks and human intracranial electrophysiology during spatial attention tasks, where participants detected targets at cued locations, we show that high-frequency activity bursts (HFAb) serve as information-carrying events, facilitating fast, long-range communications. HFAbs were evoked by sensory cues and targets, dynamically linked to low-frequency rhythms. Notably, both HFAb responses following cues and their decoupling from slow rhythms predicted performance accuracy. HFAbs were synchronized at the network-level, identifying distinct cue- and target-activated subnetworks. These subnetworks exhibited a temporal lead-lag organization following target onset, with cue-sactivated subnetworks preceding target-activated subnetworks when the cue provided relevant target information. Computational modeling indicated that HFAbs reflect transitions to coherent population spiking and are coordinated across networks through distinct mechanisms. Together, these findings establish HFAbs as neural mechanisms for fast, large-scale communication supporting attentional performance.
Direct measurement of PIP2 densities in biological membranes using a peptide-based sensor
Authors: Menon Vinay K , Wu Joy , Alonzo Alex , Rogers Kaitlyn , Scrudders Kevin L. , Selvarajan Suriya , Walke Andrew , Kundu Rajasree , Datta Ankona , Low-Nam Shalini Therese
Published: September 2024

Organization and composition of the plasma membrane are important modulators of many cellular programs. Phosphatidylinositol phosphate (PIP) lipids are low abundance membrane constituents with different arrangements of phosphate groups around an inositol head group that regulate a large number of signaling pathways. Many strategies have been developed to detect and track PIP species to monitor their clustering, mobility, and interaction with binding partners. We implement a peptide-based ratiometric sensor for the detection of PI(4,5)P2 lipids in reconstituted membrane systems that permit absolute quantification of PI(4,5)P2 densities down to physiological levels. The sensor is membrane permeable and easily applicable to measurements in living cells. Application of calibrated sensors to cells expressing common mutations in the small GTPase, Ras, showed a reshaping of surface PI(4,5)P2 levels and distributions in a mutation-specific manner. The rapid implementation of this quantitative sensing strategy to cellular studies of cellular signaling, membrane organization and dynamics should be broadly applicable.
Mobility patterns, activity locations, and tuberculosis in Nairobi, Kenya
Authors: Tram Khai Hoan , Ong’ang’o Jane , Kiplimo Richard , Hawn Thomas R. , Nduba Videlis , Horne David J. , Ross Jennifer M.
Published: September 2024

Background

Annually, over 3 million people develop TB but are not diagnosed and treated. We aimed to characterize the mobility patterns and activity locations of people with TB in an urban, high-burden setting to inform future active case finding (ACF) efforts.

Methods

We conducted a population-based TB prevalence survey in Nairobi, Kenya, in 2022. Participants aged ≥15 years with TB symptoms or a suggestive chest x-ray submitted sputum for Xpert Ultra and culture. We collected data on individual activity locations and mobility and evaluated their association with the risk of pulmonary TB.

Results

The prevalence survey enrolled 6369 participants across nine clusters. There were significant differences in mobility patterns and activity locations between sexes and age groups. Mobility factors were not significantly associated with TB. In the adjusted analysis, age group 45–54 (OR 2.45), male sex (OR 2.95), and use of a social activity location (OR 1.96) were significantly associated with a higher risk of TB.

Conclusions

We did not find a significant association between mobility patterns and TB but found a positive association between reported ‘social’ activity locations and TB. Identification of ‘social’ activity locations, particularly bars, provides important insight into possible venues for spatially-targeted ACF activities.
Possible Mechanisms Of Action Of Light Inert Gases On Chemiluminescence Arising As A Result Of Lipid Peroxidation
Authors: Oliynyk Iryna
Published: September 2024

The use of inert gases in biology and medicine and their effect on biological objects both in vitro and in vivo remains an active area of research. It has been established that light noble gases affect antioxidant processes, free radical oxidation, and enhance chemiluminescence, but an explanation of the physical and chemical mechanisms of this effect is still lacking and is key to further theoretical and experimental studies, given the broad prospects for the use of noble gases in medicine. In this article, we present two of the possible mechanisms of light inert gases’ effect on chemiluminescence (CL), a phenomenon that occurs as a result of free radical recombination and chain breakage during lipid peroxidation. Since the effect on oxidation, in turn, precedes the effect on the antioxidant system and the body’s defense mechanisms.

One of the mechanisms of influence is based on the ability of inert gases to dissolve well in lipids and dissolve poorly in water. Their ability to dissolve in lipid bilayers and affect the conformation of lipid complexes can increase the surface area available for oxidation, the surface area that absorbs radiation and reduce the density of the environment, potentially increasing the availability of oxygen for oxidation reactions. This is the so-called spatial mechanism of inert gas influence on oxidation and chemiluminescence.

The second mechanism is based on the influence on the quantum chemical parameters of the reaction medium. The acceleration of VT relaxation processes, the impact on the components of the medium in quenching excited states, and the radiative decay time of the excited state.
Single-cell and spatiotemporal transcriptomic profiling of brain immune infiltration following Venezuelan equine encephalitis virus infection
Authors: Rangel Margarita V. , Sebastian Aimy , Leon Nicole F. , Phillips Ashlee M. , Gorman Bria M. , Hum Nicholas R. , Weilhammer Dina R.
Published: September 2024

Neurotropic alphaviruses such as Venezuelan equine encephalitis virus (VEEV) are critical human pathogens that continually expand to naïve populations and for which there are no licensed vaccines or therapeutics. VEEV is highly infectious via the aerosol route and is a recognized weaponizable biothreat that causes neurological disease in humans. The neuropathology of VEEV has been attributed to an inflammatory immune response in the brain yet the underlying mechanisms and specific immune cell populations involved are not fully elucidated. This study uses single-cell RNA sequencing to produce a comprehensive transcriptional profile of immune cells isolated from the brain over a time course of infection in a mouse model of VEEV. Analyses reveal differentially activated subpopulations of microglia, including a distinct type I interferon-expressing subpopulation. This is followed by the sequential infiltration of myeloid cells and cytotoxic lymphocytes, also comprising subpopulations with unique transcriptional signatures. We identify a subpopulation of myeloid cells that form a distinct localization pattern in the hippocampal region whereas lymphocytes are widely distributed, indicating differential modes of recruitment, including that to specific regions of the brain. Altogether, this study provides a high-resolution analysis of the immune response to VEEV in the brain and highlights potential avenues of investigation for therapeutics that target neuroinflammation in the brain.

Author Summary

Venezuelan equine encephalitis virus (VEEV) causes brain inflammation in both animals and humans when transmitted by mosquito bite or infectious aerosols. The mechanisms underlying disease caused by VEEV, including the role of the immune response in brain pathology, are not well understood. Here we performed a comprehensive assessment of the immune response to VEEV in the brain over time using two advanced sequencing techniques. Following infection, immune cells infiltrate the brain in a sequential fashion and display different activation profiles. Different types of immune cells also display strikingly different spatial patterns throughout the brain. This study provides the most comprehensive description of the immune response to VEEV in the brain performed to date and advances our understanding of immune-driven neuropathology and identification of therapeutic targets.
Abnormal mu rhythm state-related cortical and corticospinal responses in chronic stroke
Authors: Wischnewski Miles , Haigh Zachary J. , Berger Taylor A. , Rotteveel Jonna , van Oijen Tessa , Perera Nipun D. , Shirinpour Sina , Alekseichuk Ivan , Hawe Rachel L. , Opitz Alexander
Published: September 2024

The motor cortex’s activity is state-dependent. Specifically, the sensorimotor mu rhythm phase relates to fluctuating levels of primary motor cortex (M1) excitability, previously demonstrated in young and healthy volunteers. However, it is unknown whether this observation is generalizable to individuals with brain lesions after a stroke. We investigated the phase relationship between the mu rhythm and cortical excitability by combining real-time processing of electroencephalography (EEG) signals and transcranial magnetic stimulation (TMS) of M1. In 11 chronic subcortical stroke survivors and 12 similar-aged healthy volunteers, we applied TMS to M1 at the peak, falling, trough, and rising phase of the sensorimotor mu oscillation. As outcome measures, we investigated the M1-to-muscle excitability by measuring motor-evoked potentials (MEPs) and local cortical activation by measuring TMS-evoked potentials (TEPs). We found that M1-to-muscle excitability in stroke survivors and older volunteers shows a phase-dependency similar to that in young healthy adults. That is, MEPs were increased and decreased at the trough and peak of the mu rhythm, respectively. However, individuals with stronger stroke-related motor symptoms showed a decreased phase preference. Further, phase-dependency was abolished in the local cortical activity, as measured with EEG, in the stroke-affected hemisphere, in contrast to the non-affected hemisphere as well as either hemisphere in healthy volunteers. Altogether, these results shed light on the state-dependency of motor cortex excitability after stroke. Our results indicate that the strength of phase preference of TMS motor responses could indicate the severity of motor impairment. These results could enable the development of improved TMS paradigms for recovery of motor impairment after stroke.
SARS-CoV-2 protein ORF3a induces Atg8ylation of lysosomal membranes
Authors: Ajnar Deepa , Sarkar Ananya , Riyaz Seema , Menon Poornima , Dutta Dipranil , Asati Pulkit , Sharma Priyanka , Pydi Sai P. , Kumar Suresh
Published: September 2024

Autophagy Conjugation machinery forms a center piece of autophagy and is essential for sequestration of a broad range of cargo destined for degradation. Apart from its role in canonical autophagy, recent evidence suggests an unconventional role of conjugation machinery. Membrane Atg8ylation is one of the manifestations of autophagy, wherein ATG8 conjugation machinery recruit mammalian ATG8s (mATG8s) to the damaged membranes for repair or removal. Herein, we show that SARS-CoV-2 factor ORF3a induces membrane Atg8ylation and selectively inflicts lysophagy, a cellular response to evade apoptotic cell death. mATG8s and SNARE protein syntaxin 17 (STX17) interact with ORF3a and are required for Atg8ylation induced by ORF3a. ORF3a displaces mTOR from the lysosomes and affects nuclear translocation of TFEB, which is dependent on mATG8s and STX17. Despite mTOR inhibition, its conventional target ULK1 is dispensable for ORF3a induced Atg8ylation. In addition, mATG8s and STX17 protected against the cell death induced by ORF3a. Overall, our findings demonstrate ORF3a induced lysosomal membrane Atg8ylation while identifying the unexpected role of STX17 in Atg8ylation.
Decoding Transcriptional Memory in Yeast Heat Shock and the Functional Implication of the RNA Binding Protein Mip6
Authors: Tejada-Colón Ana , Serrano-Quílez Joan , Nuño-Cabanes Carme , Rodríguez-Navarro Susana
Published: September 2024

Cells not only adapt to environmental changes, but they also “remember” specific signals, allowing them to respond more rapidly to future stressors. This phenomenon, known as transcriptional memory, is orchestrated by a complex interplay of epigenetics, transcription regulators and RNA metabolism factors. Although transcriptional memory has been well-studied in various contexts, its role in the heat shock (HS) response of yeast remains largely unexplored. In our study, we delve into the dynamics of HS memory in wild-type yeast and amip6Δ mutant, which lacks the RNA-binding protein Mip6. Notably, Mip6 has been shown to influence the expression of key stress-related genes and maintain low Msn2/4-dependent transcript levels under standard conditions. Our transcriptomic analysis offers novel insights into how yeast cells remember HS exposure. We uncover striking differences in gene expression patterns depending on whether genes are induced or repressed during HS memory. Furthermore, we find that an initial 15-minute heat shock triggers a response that becomes attenuated with just 5 additional minutes of stress. While the response kinetics between memory and non-memory conditions are similar, we report a subtle but important role for Mip6 in fine-tuning transcriptional memory and adaptation to heat stress. Biochemical and genetic evidence also suggests that Mip6 cooperates with alternative survival pathways independent of MSN2/4, and functionally interacts with the Rpd3 histone deacetylase complex, a key player in transcriptional memory and the HS response. These findings open up new avenues for understanding the molecular mechanisms behind heat stress adaptation in eukaryotes.
Sequential design of single-cell experiments to identify discrete stochastic models for gene expression.
Authors: Cook Joshua , Ron Eric , Svetlov Dmitri , Aguiulera Luis , Munsky Brian
Published: September 2024

Control of gene regulation requires quantitatively accurate predictions of heterogeneous cellular responses. When inferred from single-cell experiments, discrete stochastic models can enable such predictions, but such experiments are highly adjustable, allowing for almost infinitely many potential designs (e.g., at different induction levels, for different measurement times, or considering different observed biological species). Not all experiments are equally informative, experiments are time-consuming or expensive to perform, and research begins with limited prior information with which to construct models. To address these concerns, we developed a sequential experiment design strategy that starts with simple preliminary experiments and then integrates chemical master equations to compute the likelihood of single-cell data, a Bayesian inference procedure to sample posterior parameter distributions, and a finite state projection based Fisher information matrix to estimate the expected information for different designs for subsequent experiments. Using simulated then real single-cell data, we determined practical working principles to reduce the overall number of experiments needed to achieve predictive, quantitative understanding of single-cell responses.
Sympathetic innervation of interscapular brown adipose tissue is not a predominant mediator of OT-elicited reductions of body weight gain and adiposity in male diet-induced obese rats
Authors: Edwards Melise M. , Nguyen Ha K. , Dodson Andrew D. , Herbertson Adam J. , Honeycutt Mackenzie K. , Slattery Jared D. , Rambousek June R. , Tsui Edison , Wolden-Hanson Tami , Wietecha Tomasz A. , Graham James L. , Tapia Geronimo P. , Sikkema Carl L. , O’Brien Kevin D. , Mundinger Thomas O. , Peskind Elaine R. , Ryu Vitaly , Havel Peter J. , Khan Arshad M. , Taborsky Gerald J. , Blevins James E.
Published: September 2024

Recent studies indicate that central administration of oxytocin (OT) reduces body weight (BW) in high fat diet-induced obese (DIO) rodents by reducing energy intake and increasing energy expenditure (EE). Previous studies in our lab have shown that administration of OT into the fourth ventricle (4V; hindbrain) elicits weight loss and stimulates interscapular brown adipose tissue temperature (TIBAT) in DIO rats. We hypothesized that OT-elicited stimulation of sympathetic nervous system (SNS) activation of IBAT contributes to its ability to activate BAT and reduce BW in DIO rats. To test this, we determined the effect of disrupting SNS activation of IBAT on OT-elicited stimulation of TIBATand reduction of BW in DIO rats. We first confirmed that bilateral surgical SNS denervation to IBAT was successful based on having achieved ≥ 60% reduction in IBAT norepinephrine (NE) content from DIO rats. NE content was selectively reduced in IBAT by 94.7 ± 2.7, 96.8 ± 1.8 and 85.9 ± 6.1% (P<0.05) at 1, 6 and 7-weeks post-denervation, respectively, and was unchanged in liver or inguinal white adipose tissue. We then measured the impact of bilateral surgical SNS denervation to IBAT on the ability of acute 4V OT (1, 5 µg) to stimulate TIBATin DIO rats. We found that the high dose of 4V OT (5 µg) stimulated TIBATsimilarly between sham and denervated rats (P=NS) and that the effects of 4V OT to stimulate TIBATdid not require beta-3 adrenergic receptor signaling. We subsequently measured the effect of bilateral surgical denervation of IBAT on the effect of chronic 4V OT (16 nmol/day) or vehicle infusion to reduce BW, adiposity, and energy intake in DIO rats. Chronic 4V OT reduced BW gain by –7.2 ± 9.6 g and –14.1 ± 8.8 g in sham and denervated rats (P<0.05 vs vehicle treatment), respectively, and this effect was similar between groups (P=NS). These effects were associated with reductions in adiposity and energy intake (P<0.05). Collectively, these findings support the hypothesis that sympathetic innervation of IBAT is not required for central OT to increase BAT thermogenesis and reduce BW gain and adiposity in male DIO rats.
Gene identification for ocular congenital cranial motor neuron disorders using human sequencing, zebrafish screening, and protein binding microarrays
Authors: Jurgens Julie A. , Ruiz Paola M. Matos , King Jessica , Foster Emma E. , Berube Lindsay , Chan Wai-Man , Barry Brenda J. , Jeong Raehoon , Rothman Elisabeth , Whitman Mary C. , MacKinnon Sarah , Rivera-Quiles Cristina , Pratt Brandon M. , Easterbrooks Teresa , Mensching Fiona M. , Di Gioia Silvio Alessandro , Pais Lynn , England Eleina M. , de Berardinis Teresa , Magli Adriano , Koc Feray , Asakawa Kazuhide , Kawakami Koichi , O’Donnell-Luria Anne , Hunter David G. , Robson Caroline D. , Bulyk Martha L. , Engle Elizabeth C.
Published: September 2024

Purpose

To functionally evaluate novel human sequence-derived candidate genes and variants for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs).

Methods

Through exome and genome sequencing of a genetically unsolved human oCCDD cohort, we previously identified variants in 80 strong candidate genes. Here, we further prioritized a subset of these (43 human genes, 57 zebrafish genes) using a G0 CRISPR/Cas9-based knockout assay in zebrafish and generated F2 germline mutants for seventeen. We tested the functionality of variants of uncertain significance in known and novel candidate transcription factor-encoding genes through protein binding microarrays.

Results

We first demonstrated the feasibility of the G0 screen by targeting known oCCDD genesphox2aandmafba. 70-90% of gene-targeted G0 zebrafish embryos recapitulated germline homozygous null-equivalent phenotypes. Using this approach, we then identified three novel candidate oCCDD genes (SEMA3F,OLIG2,andFRMD4B) with putative contributions to human and zebrafish cranial motor development. In addition, protein binding microarrays demonstrated reduced or abolished DNA binding of human variants of uncertain significance in known and novel sequence-derived transcription factorsPHOX2A(p.(Trp137Cys)),MAFB(p.(Glu223Lys)), andOLIG2(p.(Arg156Leu)).

Conclusions

This study nominates three strong novel candidate oCCDD genes (SEMA3F,OLIG2,andFRMD4B) and supports the functionality and putative pathogenicity of transcription factor candidate variantsPHOX2Ap.(Trp137Cys),MAFBp.(Glu223Lys), andOLIG2p.(Arg156Leu). Our findings support that G0 loss-of-function screening in zebrafish can be coupled with human sequence analysis and protein binding microarrays to aid in prioritizing oCCDD candidate genes/variants.
A modulator of cognitive function: Cerebellum modifies human cortical network dynamics via integration
Authors: Bansal Kanika , Cattaneo Zaira , Oldrati Viola , Ferrari Chiara , Grossman Emily D. , Garcia Javier O.
Published: September 2024

The cerebellum, with distinctive architecture and extensive cortical connections, has long been associated with motor control; however, evidence suggests its role extends beyond motor functions, playing a crucial role in cognitive processes. Despite these insights, how cerebellar computations modulate cortical networks remains elusive. Here, we evaluate dynamic network reconfigurations in the cerebral cortex connectivity following noninvasive inhibitory repetitive transcranial magnetic stimulation (rTMS) targeting the right cerebellum. Using dynamic community detection, we uncover the dynamic network properties by which cerebellar stimulation spreads through the cortex, inspecting the evolution of modular network structures prior to and after cerebellar stimulation. Our results indicate that: (1)flexibility, or the likelihood of network nodes to change module allegiances, increases post stimulation; (2) dynamic patterns in which module allegiances emerge and evolve are individualistic and do not follow a single functional prototype; and (3) cerebellar nodes play the role of integrators for distinct network modules. These results suggest that the cerebellum plays a pivotal role in modulating distributed cortical activity, seamlessly integrating and segregating information beyond motor control. This integrative capacity may underlie the cerebellum’s contributions to high-level cognitive functions and, more broadly, to the foundation of human intelligence.
Outside your shell: how temperature shapes genetic variation in two species of congeneric marine snails
Authors: Wuitchik Daniel M , Fifer James E , Huzar Alexa K , Pechenick Jan A , Uricchio Lawrence , Davies Sarah W.
Published: September 2024

Intertidal organisms withstand extreme temperature fluctuations, and their ability to cope with this variation may affect their distributions across the seascape. Genetic variation and local environments likely interact to determine variation in thermal performance across intertidal species ranges, so characterizing the relationship between temperature variation and population structure is key to understanding the biology of marine invertebrates. Here, we use 2bRAD-sequencing to examine population genetic structure in two congeneric intertidal marine gastropods (Crepidula fornicata, C. plana), sampled from locations along a natural temperature gradient on the Northeast shores of the United States. These two species share similar life histories, yet C. plana exhibits a narrower distribution than C. fornicata. Our results demonstrate that both species show patterns of genetic divergence consistent with isolation by distance, though this pattern was only significant in C. fornicata. Both putatively selected and neutral loci displayed significant spatial structuring in C. fornicata; however, only putatively selected loci showed significant clustering in C. plana. When exploring whether temperature differences explained genetic differentiation, we found that 9-12% of genetic differentiation was explained by temperature variation in each species even when controlling for latitude and neutral population structure. Our results suggest that temperature shapes adaptive variation across the seascape in both Crepidula species and encourages further research to differentiate our results from models of neutral evolutionary drift.
Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs
Authors: Dzwigonska Monika , Rosa Patrycja , Kaza Beata , Lipiec Szymon , Cyranowski Salwador , Ellert-Miklaszewska Aleksandra , Kominek Agata , Obrebski Tomasz , Malik Anna R. , Piwocka Katarzyna , Mieczkowski Jakub , Kaminska Bozena , Leszczynska Katarzyna B.
Published: September 2024

Hypoxia rapidly alters gene expression to allow cellular adaptation to challenging conditions and support tumour growth. Hypoxia also affects the chromatin structure by modifications of histones and DNA methylation. Glioblastoma (GBM) is an aggressive, deadly primary brain tumour for which there is no effective treatment. The tumour microenvironment of GBM is highly heterogeneous, with infiltration of glioma-associated microglia and macrophages (GAMs) and the presence of necrotic, hypoxic regions which significantly impair effectiveness of therapies. The mechanisms through which hypoxia alters the tumour microenvironment and regulates functions of infiltrating immune cells remain poorly understood.

Here, we show that hypoxia modulates the expression of myeloid markers in distinct ways: upregulates the expression of monocytic markerLgals3and downregulates the microglial markersP2ry12andTmem119in microglial and monocytic GAMsin vitroandin vivo. Underlying genome-wide hypoxia-dependent transcriptomic changes in microglial cells were identified using microglia-glioma co-cultures and validated in human and mouse GBM single- cell transcriptomics datasets. Numerous GAM subtype markers are dysregulated in response to hypoxic stress due to associated changes in chromatin accessibility, as determined using ATACseq. While hypoxia alone drives a decrease of the overall chromatin accessibility at gene promoters, the exposure to glioma cells under hypoxic conditions leads to both increases and decreases of chromatin accessibility at promoter regions in microglial cells. Hypoxia downregulates the chromatin accessibility at the regions enriched in motifs for transcription factors known as master regulators of microglial cell identity and function, includingSPI1orIRF8. Overall, our results highlight the importance of hypoxic stress as a strong intratumoral regulator of myeloid cell functions, which adds a new dimension to the characterisation of particular GAM subpopulations.
Protonation effects in protein-ligand complexes - a case study of endothiapepsin and pepstatin A with computational and experimental methods
Authors: Vatheuer Helge , Palomino-Hernández Oscar , Müller Janis , Galonska Phillip , Glinca Serghei , Czodrowski Paul
Published: September 2024

1

Protonation states serve as an essential molecular recognition motif for biological processes. Their correct consideration is key to successful drug design campaigns, since chemoinformatic tools usually deal with default protonation states of ligands and proteins and miss atypical protonation states. The protonation pattern for the Endothiapepsin/PepstatinA (EP/pepA) complex is investigated using different dry lab and wet lab techniques. ITC experiments revealed an uptake of more than one mole of protons upon pepA binding to EP. Since these experiments were performed at physiological conditions (and not at pH=4 at which a large variety of crystal structures is available), a novel crystal structure at pH=7.6 was determined. This crystal structure showed that only modest structural changes occur upon increasing the pH value. This lead to computational studies to reveal the exact location of the protonation event. Both computational studies could reveal a significant pKa shift resulting in non-default protonation state and that the catalytic dyad is responsible for the uptake of protons. This study shows that assessing protonation states for two separate systems (protein and ligand) might result in the incorrect assignment of protonation states and hence incorrect calculation of binding energy.
Cross-Sectional Analysis of the Association Between Abnormal Immune Responses in the Pathogenesis of Postpartum Cardiomyopathy in Ethiopian Women: A Hospital-based Study at Saint Paul Hospital
Authors: Paulos Azarreia , Mulu Leul , Metiku Kalab
Published: September 2024

1.0

Background

Postpartum cardiomyopathy (PPCM) is a condition that is characterized by the weakening of heart muscles which is known as left ventricular dysfunction and occurs during the later stages of pregnancy or during the early stages of postpartum.

Objective

To evaluate the role of abnormal immune responses and risk factors such as advanced age, high parity, and presence of gestational diabetes in the pathogenesis of PPCM in Ethiopia.

Method

A cross-sectional hospital-based study was conducted at Saint Paul Millennium Medical College (SPMCC) between January 2021 and January 2023. All female pregnant patients who were attending the Maternal Care Fetal Unit, Antenatal Unit, and High-Risk Unit at SPMMC were included in this study. However, among those patients, those mothers younger than 20 years old and older than 40 years old were excluded from the study. The total sample size collected from this facility was 250 patients.

Results

Oxidative stress and inflammation were primarily correlated with pre-eclampsia and gestational diabetes. These risk factors were particularly prevalent within patients diagnosed with PPCM, 52.8% and 40% respectively. Prolactin Cleavage and Microvascular Dysfunction was associated with higher BMI and advanced age. With a general increasing trend observed in PPCM incidence and advancing age. As well as a high prevalence rate of PPCM in patients with Obesity Class I (at 33.0%). Another notable risk factor was high parity ( 45.0% with 4+ prior pregnancies). The most common symptom presented was dyspnea at 35.0%. The mortality rate was 14% whilst recurrence and the fully recovered ratio were at 13.1% and 34.0%, respectively.

Conclusion

Results aligned with those conducted in other African countries (e.g. Zambia and South Africa) however mitigating high mortality as well as low full recovery rate will need to be done by earlier diagnosis, effective treatment, and intervention mechanisms. A different study design will need to be conducted (over a longer time period) to support and make findings more holistic.
Prediction of the ectasia screening index from raw Casia2 volume data for keratoconus identification by using convolutional neural networks
Authors: Mirsalehi Maziar , Fassbind Benjamin , Streich Andreas , Langenbucher Achim
Published: September 2024

Purpose

Prediction of Ectasia Screening Index (ESI), an estimator provided by the Casia2 for identifying keratoconus, from raw Optical Coherence Tomography (OCT) data with Convolutional Neural Networks (CNN).

Methods

Three CNN architectures (ResNet18, DenseNet121 and EfficientNetB0) were employed to predict the ESI. Mean Absolute Error (MAE) was used as the performance metric for predicting the ESI by the adapted CNN models on the test set. Scans with an ESI value higher than a certain threshold were classified asKeratoconus, while the remaining scans were classified asNot Keratoconus. The models’ performance was evaluated using metrics such as accuracy, sensitivity, specificity, Positive Predictive Value (PPV) and F1 score on data collected from patients examined at the eye clinic of the Homburg University Hospital. The raw data from the Casia2 device, in 3dv format, was converted into 16 images per examination of one eye. For the training, validation and testing phases, 3689, 1050 and 1078 scans (3dv files) were selected, respectively.

Results

In the prediction of the ESI, the MAE values for the adapted ResNet18, DenseNet121 and EfficientNetB0, rounded to two decimal places, were 7.15, 6.64 and 5.86, respectively. In the classification task, the three networks yielded an accuracy of 94.80%, 95.27% and 95.83%, respectively; a sensitivity of 92.07%, 94.64% and 94.17%, respectively; a specificity of 96.61%, 95.69% and 96.92%, respectively; a PPV of 94.72%, 93.55% and 95.28%, respectively; and a F1 score of 93.38%, 94.09% and 94.72%, respectively.

Conclusions

Our results show that the prediction of keratokonus based on the ESI values estimated from raw data outperforms previous approaches using processed data. Adapted EfficientNetB0 outperformed both the other adapted models and those in state-of-the-art studies, with the highest accuracy and F1 score.