bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial and Temporal Drug Usage Patterns in Wastewater Correlate with Socioeconomic and Demographic Indicators in Southern Nevada
Authors: Zhuang Xiaowei , Moshi Michael A. , Quinones Oscar , Trenholm Rebecca A. , Chang Ching-Lan , Cordes Dietmar , Vanderford Brett J. , Vo Van , Gerrity Daniel , Oh Edwin C.
Published: February 2024

Evaluating drug use within populations in the United States poses significant challenges due to various social, ethical, and legal constraints, often impeding the collection of accurate and timely data. Here, we aimed to overcome these barriers by conducting a comprehensive analysis of drug consumption trends and measuring their association with socioeconomic and demographic factors. From May 2022 to April 2023, we analyzed 208 wastewater samples from eight sampling locations across six wastewater treatment plants in Southern Nevada, covering a population of 2.4 million residents with 50 million annual tourists. Using bi-weekly influent wastewater samples, we employed mass spectrometry to detect 39 analytes, including pharmaceuticals and personal care products (PPCPs) and high risk substances (HRS). Our results revealed a significant increase over time in the level of stimulants such as cocaine (pFDR=1.40×10-10) and opioids, particularly norfentanyl (pFDR =1.66×10-12), while PPCPs exhibited seasonal variation such as peak usage of DEET, an active ingredient in insect repellents, during the summer (pFDR =0.05). Wastewater from socioeconomically disadvantaged or rural areas, as determined by Area Deprivation Index (ADI) and Rural-Urban Commuting Area Codes (RUCA) scores, demonstrated distinct overall usage patterns, such as higher usage/concentration of HRS, including cocaine (p=0.05) and norfentanyl (p=1.64×10-5). Our approach offers a near real-time, comprehensive tool to assess drug consumption and personal care product usage at a community level, linking wastewater patterns to socioeconomic and demographic factors. This approach has the potential to significantly enhance public health monitoring strategies in the United States.
Racial and Ethnic Differences in Obesity Treatment in the Veterans Affairs Healthcare System
Authors: Tisdale Rebecca L. , Beyene Tariku J. , Tang Wilson , Heidenreich Paul , Asch Steven , Yong Celina M.
Published: February 2024

Background

The burden of obesity in the United States and in the Veterans Affairs (VA) population disproportionately affects minoritized individuals. Major advances in the treatment of obesity have emerged in the last decade, including incretin-based injectables like semaglutide, but it is not clear that they are being distributed equitably. We examined the role that race and ethnicity play in the receipt of a lifestyle change program, medications, and surgical treatment for obesity.

Methods

We analyzed data from patients with BMI ≥27 in the national VA Healthcare System from 2018-2022. We used multivariate logistic regression to evaluate the association between race/ethnicity (American Indian/Alaska Native [AI/AN], Asian/Native Hawaiian/Pacific Islander [NHOPI], Non- Hispanic Black, Hispanic/Latino, Non-Hispanic White) and use of weight loss interventions (VA lifestyle change program, medication prescriptions, bariatric surgery), adjusting for age, gender, comorbidities, and diagnosis year.

Results

Among Veterans with BMI ≥27 (n=2,423,070), 38.8% had Class 1 obesity (BMI 30-34.9), 18.1% had Class 2 obesity (BMI 35-39.9), and 9.8% had Class 3 obesity (BMI>40), with significant differences by race/ethnicity (p<0.01). Across the cohort, 7.7% participated in the lifestyle change program, 7.9% received weight loss medications, and 0.1% underwent bariatric surgery. Compared to Non-Hispanic White patients, Veterans belonging to many racial/ethnic minority groups were more likely to participate in the lifestyle change program (Asian/NHOPI Veterans, 1.12 [95% CI 1.06-1.19]; Non-Hispanic Black Veterans, adj OR 1.24 [95% confidence interval [CI] 1.22-1.26]; Hispanic/Latino Veterans, adj OR 1.17 [95% CI 1.14-1.20]) and less likely to receive weight loss medications (AI/AN Veterans, adj OR 0.84 [95% CI 0.77-0.92]; Asian/NHOPI Veterans: adj OR 0.94 [95% CI 0.89-0.999]; Non-Hispanic Black Veterans, adj OR 0.75 [95% CI 0.74-0.76]; Hispanic/Latino Veterans, adj OR 0.94 [95% CI 0.91-0.97]). Black Veterans were also less likely to undergo bariatric surgery (adj OR 0.79 [95% CI 0.69-0.89]).

Conclusions

Among Veterans with obesity, rates of treatment across all modalities are low. Inequities in treatment approach by race/ethnicity suggest areas for focused intervention to close gaps in care.
Impact of Intravenous Iron Therapy on Hospitalizations and Mortality in Patients with Heart Failure and Iron Deficiency: A Systematic Review and Meta-Analysis
Authors: Wang Haiming , Li Yanhua , Zhou Jingjing , Wang Jing , Shao Junjie , Yue Shuai , Li Jiayue , Guo Xinhong , Zhang Ran
Published: February 2024

BACKGROUND

Intravenous iron therapy represents a promising potential treatment option for patients with heart failure (HF) and iron deficiency (ID), as it has been shown to improve clinical symptoms and enhance quality of life. To investigate the benefits of intravenous iron therapy on hard cardiovascular endpoints in HF and ID patients, we conducted a systematic review and meta-analysis of randomized controlled trials (RCTs).

METHODS

We implemented a systematical search of the PubMed, Embase and Cochrane Library databases for relevant RCTs of intravenous iron therapy in patients with HF and ID published from inception through January 20, 2024. Our primary endpoints of interest were HF hospitalizations, all-cause mortality, HF hospitalizations and cardiovascular death, cardiovascular hospitalizations and cardiovascular death. Sensitivity analyses and subgroup analyses were further performed to investigate additional clinical benefits in specific populations.

RESULTS

Eleven trials encompassing a collective cohort of 6511 participants met our predefined eligibility criteria and were included in our meta-analysis. The predominant form of intravenous iron utilized in the trials included in our analysis was ferric carboxymaltose. Intravenous iron therapy yielded a 40% relative reduction in HF hospitalization (OR 0.60, 95% CI 0.51-0.70;P= 0.00001), a 46% relative reduction in HF hospitalizations and cardiovascular death (OR 0.54, 95% CI 0.46-0.63;P<0.00001) and a 53% relative reduction in cardiovascular hospitalizations and cardiovascular death (OR 0.47, 95% CI 0.37-0.59;P<0.00001). Our analysis revealed no statistically significant differences in terms of all-cause mortality (OR 0.85, 95% CI 0.72-1.01;P=0.06) while this result was fragile (reverse fragility index of 2 and reverse fragility quotient of 0.0004). Subgroup analyses revealed more favorable effects of intravenous iron therapy in trials that had a follow-up duration of ≥ 24 weeks and a sample size of over 200 cases. Intravenous iron therapy had negligible effects on infection (OR 0.86, 95% CI 0.66-1.11;P=0.25), general disorders and administration site conditions (OR 1.35, 95% CI 0.93-1.94;P=0.11), injury, poisoning and procedural complications (OR 0.96, 95% CI 0.66-1.40;P=0.85).

CONCLUSION

Intravenous iron therapy in patients with HF and ID shows a significant reduction of rehospitalization for HF and cardiovascular death. The ferric carboxymaltose holds significant promise as a potential therapeutic agent for HF patients with ID.
Deep learning-based automatic classification of ischemic stroke subtype using diffusion-weighted images
Authors: Ryu Wi-Sun , Schellingerhout Dawid , Lee Hoyoun , Lee Keon-Joo , Kim Chi Kyung , Kim Beom Joon , Chung Jong-Won , Lim Jae-Sung , Kim Joon-Tae , Kim Dae-Hyun , Cha Jae-Kwan , Sunwoo Leonard , Kim Dongmin , Suh Sang-Il , Bang Oh Young , Bae Hee-Joon , Kim Dong-Eog
Published: February 2024

BACKGROUND

Accurate classification of ischemic stroke subtype is important for effective secondary prevention of stroke. We used diffusion-weighted imaging (DWI) and atrial fibrillation (AF) data to train a deep learning algorithm to classify stroke subtype.

METHODS

Model training, validation, and internal testing were done in 2,988 patients with acute ischemic stroke from three stroke centers by using U-net for infarct segmentation and EfficientNetV2 for stroke subtype classification. Experienced vascular neurologists (n=5) determined stroke subtypes for external test datasets, while establishing a consensus for clinical trial datasets using the TOAST classification. Infarcts on DW images were automatically segmented using an artificial intelligence solution that we recently developed, and their masks were fed as inputs to a deep learning algorithm (DWI-only algorithm). Subsequently, another model was trained, with the presence or absence of AF included in the training as a categorical variable (DWI+AF algorithm). These models were tested: a) internally against the opinion of the labeling experts, b) against fresh external DWI data, and also c) against clinical trial DWI data acquired at a later date.

RESULTS

In the training-and-validation datasets, the mean age was 68.0±12.5 (61.1% male). In internal testing, compared with the experts, the DWI-only algorithm and the DWI+AF algorithm respectively achieved moderate (65.3%) and near-strong (79.1%) agreement. In external testing, both algorithms again showed good agreements (59.3-60.7% and 73.7-74.0%, respectively). In the clinical trial dataset, compared with the expert consensus, percentage agreements and Cohen’s kappa were respectively 58.1% and 0.34 for the DWI-only algorithm vs. 72.9% and 0.57 for the DWI+AF algorithm. The corresponding values between experts were comparable (76.0% and 0.61) to the DWI+AF algorithm.

CONCLUSIONS

Our deep learning algorithm trained on a large dataset of DWI (both with or without AF information) was able to classify ischemic stroke subtypes as accurately as a consensus of stroke experts.
Jag1 represses Notch activation in lateral supporting cells and inhibits an outer hair cell fate in the medial compartment of the developing cochlea
Authors: de Haan Sandra , Corbat Agustin A. , Cederroth Christopher R. , Autrum Lisa G. , Hankeova Simona , Driver Elizabeth C. , Canlon Barbara , Kelley Matthew W. , Andersson Emma R.
Published: February 2024

Notch signaling regulates both inner and middle ear morphogenesis and establishes a strict pattern of sensory cells in the organ of Corti in the mammalian cochlea. Patients with Alagille syndrome have impaired Notch signaling (∼94% withJAG1mutations) resulting in sensorineural and conductive hearing loss. Here, we investigate the function of Jag1-mediated Notch activation in cochlear patterning and signaling using the Jag1 “Nodder” (Jag1Ndr/Ndr) mouse model of Alagille syndrome.Jag1Ndr/Ndrmice exhibited severe vestibular and auditory deficits and a dose-dependent increase in ectopic inner hair cells and a reduction in outer hair cells. Single cell RNA sequencing of the organ of Corti demonstrated a global dysregulation of genes associated with inner ear development and deafness. Analysis of individual cell types indicated a novel role for Jag1 in repressing Notch activation in lateral supporting cells and revealed a function for Jag1 in gene regulation and development of outer hair cells. Additionally, “outer hair cell-like” SLC26A5 (Prestin) positive cells were present in the medial compartment and pillar cell region ofJag1Ndr/Ndrmice and exhibited location-dependent expression of the inner hair cell fate-regulatorTbx2, revisiting the potency ofTbx2in driving inner hair cell commitment in “outer hair cell-like” cells in the Jag1-mutant IHC compartment. Our data reveals a novel role for Jag1 in repressing Notch activation in lateral supporting cells and highlights involvement for Notch signaling in inner versus outer hair cell specification and positioning.
Characterization of ribosome stalling and no-go mRNA decay stimulated by the Fragile X protein, FMRP
Authors: Scarpitti MaKenzie R. , Pastore Benjamin , Tang Wen , Kearse Michael G.
Published: February 2024

Loss of functional fragile X mental retardation protein (FMRP) causes fragile X syndrome (FXS) and is the leading monogenic cause of autism spectrum disorders and intellectual disability. FMRP is most notably a translational repressor and is thought to inhibit translation elongation by stalling ribosomes as FMRP-bound polyribosomes from brain tissue are resistant to puromycin and nuclease treatment. Here, we present data showing that the C-terminal non-canonical RNA-binding domain of FMRP is essential and sufficient to induce puromycin-resistant mRNA•ribosome complexes. Given that stalled ribosomes can stimulate ribosome collisions and no-go mRNA decay (NGD), we tested the ability of FMRP to drive NGD of its target transcripts in neuroblastoma cells. Indeed, FMRP and ribosomal proteins, but not PABPC1, were enriched in isolated nuclease-resistant disomes compared to controls. Using siRNA knockdown and RNA-seq, we identified 16 putative FMRP-mediated NGD substrates, many of which encode proteins involved in neuronal development and function. Increased mRNA stability of the putative substrates was also observed when either FMRP was depleted or NGD was prevented via RNAi. Taken together, these data support that FMRP stalls ribosomes and can stimulate NGD of a select set of transcripts in cells, revealing an unappreciated role of FMRP that would be misregulated in FXS.
Pia-FLOW: Deciphering hemodynamic maps of the pial vascular connectome and its response to arterial occlusion
Authors: Glück Chaim , Zhou Quanyu , Droux Jeanne , Chen Zhenyue , Glandorf Lukas , Wegener Susanne , Razansky Daniel , Weber Bruno , El Amki Mohamad
Published: February 2024

The pial vasculature is the sole source of blood supply to the neocortex. The brain is contained within the skull, a vascularized bone marrow with a unique anatomical connection to the brain. Recent developments in tissue clearing have enabled unprecedented mapping of the entire pial and calvarial vasculature. However, what are the absolute flow rates values of those vascular networks? This information cannot accurately be retrieved with the commonly used bioimaging methods. Here, we introduce Pia-FLOW, a new approach based on large-scale fluo-rescence localization microscopy, to attain hemodynamic imaging of the whole murine pial and calvarial vasculature at frame rates up to 1000 Hz and spatial resolution reaching 5.4 µm. Using Pia-FLOW, we provide detailed maps of flow velocity, direction and vascular diameters which can serve as ground-truth data for further studies, advancing our understanding of brain fluid dynamics. Furthermore, Pia-FLOW revealed that the pial vascular network functions as one unit for robust allocation of blood after stroke.
Npbwr1signaling mediates fast antidepressant action
Authors: Stein Gregor , Aly Janine S. , Lange Lisa , Manzolillo Annamaria , Riege Konstantin , Brancato Anna , Hübner Christian A. , Turecki Gustavo , Hoffmann Steve , Engmann Olivia
Published: February 2024

Chronic stress is a major risk factor for depression, a leading cause of disability and suicide. Because current antidepressants work slowly, have common side effects, and are only effective in a minority of patients, there is an unmet need to identify the underlying molecular mechanisms. Here, we reveal the receptor for neuropeptides B and W,Npbwr1, as a key regulator of depressive-like symptoms.Npbwr1is increased in the nucleus accumbens of chronically stressed mice and postmortem in patients diagnosed with depression. Using viral-mediated gene transfer, we demonstrate a causal link betweenNpbwr1, dendritic spine morphology, the biomarkerBdnf, and depressive-like behaviors. Importantly, microinjection of the synthetic antagonist ofNpbwr1, CYM50769, rapidly ameliorates depressive-like behavioral symptoms and altersBdnflevels. CYM50769 is selective, well tolerated, and shows effects up to 7 days after administration of a single dose. In summary, these findings drastically advance our understanding of mood and chronic stress and warrant further investigation of CYM50769 as a potential fast-acting antidepressant.
Functional Connectivity Differences in Distinct Dentato-Cortical Networks in Alzheimer’s Disease and Mild Cognitive Impairment
Authors: Herrejon Ivan A. , Jackson T. Bryan , Hicks Tracey H. , Bernard Jessica A. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: February 2024

Recent research has implicated the cerebellum in Alzheimer’s disease (AD), and cerebro-cerebellar network connectivity is emerging as a possible contributor to symptom severity. The cerebellar dentate nucleus (DN) has parallel motor and non-motor sub-regions that project to motor and frontal regions of the cerebral cortex, respectively. These distinct dentato-cortical networks have been delineated in the non-human primate and human brain. Importantly, cerebellar regions prone to atrophy in AD are functionally connected to atrophied regions of the cerebral cortex, suggesting that dysfunction perhaps occurs at a network level. Investigating functional connectivity (FC) alterations of the DN is a crucial step in understanding the cerebellum in AD and in mild cognitive impairment (MCI). Inclusion of this latter group stands to provide insights into cerebellar contributions prior to diagnosis of AD. The present study investigated FC differences in dorsal (dDN) and ventral (vDN) DN networks in MCI and AD relative to cognitively normal participants (CN) and relationships between FC and behavior. Our results showed patterns indicating both higher and lower functional connectivity in both dDN and vDN in AD compared to CN. However, connectivity in the AD group was lower when compared to MCI. We argue that these findings suggest that the patterns of higher FC in AD may act as a compensatory mechanism. Additionally, we found associations between the individual networks and behavior. There were significant interactions between dDN connectivity and motor symptoms. However, both DN seeds were associated with cognitive task performance. Together, these results indicate that cerebellar DN networks are impacted in AD, and this may impact behavior. In concert with the growing body of literature implicating the cerebellum in AD, our work further underscores the importance of investigations of this region. We speculate that much like in psychiatric diseases such as schizophrenia, cerebellar dysfunction results in negative impacts on thought and the organization therein. Further, this is consistent with recent arguments that the cerebellum provides crucial scaffolding for cognitive function in aging. Together, our findings stand to inform future clinical work in the diagnosis and understanding of this disease.
Identifying the factors governing internal state switches during nonstationary sensory decision-making
Authors: Mohammadi Zeinab , Ashwood Zoe C. ,   International Brain Laboratory, Pillow Jonathan W.
Published: February 2024

Recent work has revealed that mice do not rely on a stable strategy during perceptual decision-making, but switch between multiple strategies within a single session [1, 2]. However, this switching behavior has not yet been characterized in non-stationary environments, and the factors that govern switching remain unknown. Here we address these questions using an internal state model with input-driven transitions. Our approach relies on a hidden Markov model (HMM) with two sets of per-state generalized linear models (GLMs): a set of Bernoulli GLMs for modeling the animal state- and stimulus-dependent choice on each trial, and a multinomial GLM for modeling input-dependent transitions between states. We used this model to analyze a dataset from the International Brain Laboratory (IBL), in which mice performed a binary decision-making task with non-stationary stimulus statistics. We found that mouse behavior in this task was accurately described by a four-state model. This model contained two "engaged" states, in which performance was good despite slight left and right biases, and two "disengaged" states, where performance was low and exhibited with larger left and right biases, respectively. Our analyses revealed that mice preferentially used left-bias strategies during left-bias stimulus blocks, and right-bias strategies during right-bias stimulus blocks, meaning that they could achieve reasonably high performance even in disengaged states simply by biasing choice toward the side with greater prior probability. Our model showed that past choices and past stimuli predicted transitions between left- and right-bias states, while past rewards predicted transitions between engaged and disengaged states. In particular, greater past reward predicted transition to disengaged states, suggesting that disengagement may be associated with satiety.
Targeted Degradation of METTL3 Against Acute Myeloid Leukemia and Gastric Cancer
Authors: Hwang Kyubin , Bae Juhyeon , Jhe Yoo-Lim , Kim Jungmin , Cheong Jae-Ho , Sim Taebo
Published: February 2024

Accumulating evidence reveals the oncogenic role of methyltransferase-like 3 (METTL3) in a variety of cancer types, either dependent or independent of its m6A methyl transferase activity. We have designed proteolysis-targeting chimeras (PROTACs) targeting METTL3 and identifiedKH12as a potent METTL3 degrader. Treatment ofKH12on MOLM-13 cells causes more than 80% degradation of METTL3 with a half-maximal degradation concentration (DC50) of 220 nM in a dose-, time- and ubiquitin-dependent fashion. In addition,KH12reverses differentiation and possesses anti-proliferative effects surpassing the reported inhibitors in MOLM-13 cells. Furthermore,KH12significantly suppresses the growth of various gastric cancer (GC) cells, where the m6A-independent activity of METTL3 plays a crucial role in tumorigenesis. The anti-GC effect ofKH12was further confirmed in patient-derived organoids (PDOs). This study highlights the therapeutic potential of targeted degradation of epitranscriptomic writer METTL3 as an anti-cancer strategy.
PPARγ mediated enhanced lipid biogenesis fuelsMycobacterium tuberculosisgrowth in a drug-tolerant hepatocyte environment
Authors: Sarkar Binayak , Singh Jyotsna , Yadav Mohit , Sharma Priya , Sharma Raman Deep , Singh Shweta , Chandramouli Aakash , Mehdiratta Kritee , Kumar Ashwani , Kamat Siddhesh S. , Ghorpade Devram S. , Mohanty Debasisa , Kumar Dhiraj , Gokhale Rajesh S.
Published: February 2024

Mycobacterium tuberculosis(Mtb) infection of the lungs, besides producing prolonged cough with mucus, also causes progressive fatigue and cachexia with debilitating loss of muscle mass. While anti-tuberculosis (TB) drug therapy is directed toward eliminating bacilli, the treatment regimen ignores the systemic pathogenic derailments that probably dictate TB-associated mortality and morbidity. Presently, it is not understood whether Mtb spreads to metabolic organs and brings about these impairments. Here we show that Mtb creates a replication-conducive milieu of lipid droplets in hepatocytes by upregulating transcription factor PPARγ and scavenging lipids from the host cells. In hepatocytes, Mtb shields itself against the common anti-TB drugs by inducing drug-metabolizing enzymes. Infection of the hepatocytes in thein vivoaerosol mice model can be consistently observed post-week 4 along with enhanced expression of PPARγ and drug-metabolizing enzymes. Moreover, histopathological analysis indeed shows the presence of Mtb in hepatocytes along with granuloma-like structures in human biopsied liver sections. Hepatotropism of Mtb during the chronic infectious cycle results in immuno-metabolic dysregulation that could magnify local and systemic pathogenicity, altering clinical presentations.
Attentional guidance through object associations in visual cortex
Authors: Lerebourg Maëlle , de Lange Floris P. , Peelen Marius V.
Published: February 2024

Efficient behavior requires the rapid attentional selection of task-relevant objects. Preparatory activity of target-selective neurons in visual cortex is thought to support attentional selection, guiding spatial attention and favoring processing of target-matching input. However, naturalistic searches are often guided by non-targets, including target-associated “anchor” objects. For instance, when looking for a pen, we may direct our attention to the office desk on which we expect to find it. Here, using fMRI and eyetracking in a context-guided search task, we tested whether preparatory activity in visual cortex reflected the target, the guiding anchor object, or both. Participants learned associations between targets and anchors, reversing across two scene contexts, before searching for these targets. Participants’ first fixations were reliably guided by the associated anchor. Preparatory activity in lateral occipital cortex (LOC), and right intraparietal sulcus (IPS), represented the target-associated anchor rather than the target. These results shed light on the neural basis of context-guided search in structured environments.
Solaris: a panel of bright and sensitive hybrid voltage indicators for imaging membrane potential in cultured neurons
Authors: Yang Junqi , Zhu Siyan , Yang Luming , Peng Luxin , Han Yi , Hayward Rebecca Frank , Park Pojeong , Hu Dachao , Cohen Adam E. , Zou Peng
Published: February 2024

Dynamic changes in the membrane potential underlie neuronal activities. Fluorescent voltage indicators allow optical recording of electrical signaling across a neuronal population with cellular precision and at millisecond-level temporal resolution. Here we report the design and characterization of a chemigenetic hybrid voltage indicator, Solaris, in which a circularly permuted HaloTag is inserted into the first extracellular loop ofAcetabulariarhodopsin. Solaris is compatible with fluorogenic HaloTag ligands JF525, JF549, JF552, JF585, and JF635. The most sensitive conjugate, Solaris585, has more than 2-fold higher voltage sensitivity than the spectrally similar Voltron2585(ΔF/F0= -28.1 ± 1.3% versus -12.3 ± 0.7% per action potential in cultured neurons). Solaris585supports the measurement of optogenetically evoked spike activity or dual-color imaging in conjunction with green-emitting calcium or glutamate indicators. Solaris indicators are also applicable to fluorescence lifetime imaging, which probes the absolute membrane potential. This new hybrid voltage indicator is a valuable tool for imaging neuronal electrophysiological activities in cultured cells with substantially improved dynamic range compared to previous hybrid indicators.
Cell lipotypes localization in brain by mass spectrometry imaging
Authors: Martínez-Gardeazabal Jonatan , Moreno-Rodríguez Marta , Llorente-Ovejero Alberto , Gonález de San Román Estibaliz , Lombardero Laura , de Tena Iker Bengoetxea , Sustacha Juan , Matute Carlos , Manuel Iván , Bonifazi Paolo , Rodríguez-Puertas Rafael
Published: February 2024

The study investigates brain lipid super-specialisation by defining characteristic spectral lipotypic profiles for the five primary cerebral cell-types. Utilizing a computational approach, the research visualizes the anatomical distribution of these profiles with high spatial resolution in brain tissues. This method unveils cellular stereotypic lipidic signatures within the CNS, providing a new framework for exploring the physiological roles of lipids in diverse cell-types present in brain or in any other tissue.
Notch-signaling is required for mediating between two pattern forming processes during head regeneration inHydrapolyps
Authors: Steichele Mona , Sauermann Lara , Pan Qin , Moneer Jasmin , de la Porte Alexandra , Heß Martin , Mercker Moritz , Strube Catharina , Flaswinkel Heinrich , Jenewein Marcell , Böttger Angelika
Published: February 2024

Hydrapolyps regenerate lost body parts, including the head. In addition,Hydrahead tissue has organizer properties thus being able to recruit body column tissue from a host polyp to produce ectopic hydranths after transplantation. These pattern forming processes involve Notch- and Wnt/β-catenin-signaling.Hydrahead regeneration consists of two parts, hypostome/organizer and tentacle development. Previous work had shown that the Notch inhibitor DAPT blocks hypostome regeneration and organizer formation, but not the appearance of tentacle genes and tentacle tissue. Here we show that the β-catenin inhibitor iCRT14 blocks tentacle regeneration, but not regeneration of hypostome and organizer tissue. Using RT-qPCR gene expression analyzes during head regeneration we found that DAPT inhibitsHyWnt3- andHyBMP2/4expression and expression of transcriptional repressor genes includingCnGsc,Sp5andHyHes,while increasing expression ofHyBMP5/8band thec-fos-related geneHyKayak.ICRT14 blocks expression of the tentacle specification factorHyAlx,but not expression ofHyWnt3. Thus, in accordance with regeneration of two head structures we find two signaling and gene expression modules withHyWnt3andHyBMP4part of a hypostome/organizer module, andBMP5/8,HyAlxand β-catenin part of a tentacle module. We conclude that Notch functions as an inhibitor of tentacle production to allow regeneration of hypostome/head organizer. Furthermore, withHyKayakwe present a candidate target gene for HvNotch induced repressor genes. Using siRNA and the Fos/Jun-inhibitor T5224 we show that HyKayak attenuates the expression ofHyWnt3.Finally, Notch signaling was not required for head regeneration of fresh water polyps ofCraspedacusta. Polyps ofCraspedacustado not have tentacles and thus, after head removal only regenerate a hypostome with a crescent of nematocytes around the mouth opening. This corroborates the idea that Notch-signaling mediates between two pattern forming processes duringHydrahead regeneration.
Circadian regulation of endoplasmic reticulum calcium response in cultured mouse astrocytes
Authors: Ryu Ji Eun , Shim Kyu-Won , Roh Hyun Woong , Park Minsung , Lee Jae-Hyung , Kim Eun Young
Published: February 2024

The circadian clock, an internal time-keeping system orchestrates 24-hour rhythms in physiology and behavior by regulating rhythmic transcription in cells. Astrocytes, the most abundant glial cells, play crucial roles in central nervous system (CNS) functions, but the impact of the circadian clock on astrocyte functions remains largely unexplored. In this study, we identified 412 circadian rhythmic transcripts in cultured mouse cortical astrocytes through RNA sequencing. Gene Ontology analysis indicated that genes involved in Ca2+homeostasis are under circadian control. Notably,Herpud1(Herp) exhibited robust circadian rhythmicity at both mRNA and protein levels, a rhythm disrupted in astrocytes lacking the circadian transcription factor, BMAL1. HERP regulated endoplasmic reticulum (ER) Ca2+release by modulating the degradation of inositol 1,4,5-trisphosphate receptors (ITPRs). ATP-stimulated ER Ca2+release varied with the circadian phase, being more pronounced at subjective night phase, likely due to the rhythmic expression of ITPR2. Correspondingly, ATP-stimulated cytosolic Ca2+increases were heightened at the subjective night phase. This rhythmic ER Ca2+response led to circadian phase-dependent variations in the phosphorylation of Connexin 43 (Ser368) and gap junctional communication. Given the role of gap junction channel (GJC) in propagating Ca2+signals, we suggest that this circadian regulation of ER Ca2+responses could affect astrocytic modulation of synaptic activity according to the time of day. Overall, our study enhances the understanding of how the circadian clock influences astrocyte function in the CNS, shedding light on their potential role in daily variations of brain activity and health.
Triplex real-time PCR ZKIR-T assay for simultaneous detection of theKlebsiella pneumoniaespecies complex and identification ofK. pneumoniaesensu stricto
Authors: Ligowska-Marzęta Małgorzata , Barbier Elodie , Rodrigues Carla , Piveteau Pascal , Schrøder Hansen Dennis , Hartmann Alain , Nielsen Eva Møller , Brisse Sylvain
Published: February 2024

Klebsiella pneumoniaespecies complex (KpSC) members, including the most important speciesK. pneumoniae(phylogroup Kp1 of the KpSC), are important opportunistic pathogens which display increasing rates of antimicrobial resistance worldwide. As they are widespread in food and the environment, there is a need for fast, sensitive and reliable methods to detect KpSC members in complex matrices. Previously, the ZKIR real-time PCR assay was developed to detect all KpSC members without distinction. Given that Kp1 is the clinically most significant phylogroup of the KpSC, here we aimed to simultaneously identify Kp1 while detecting all KpSC members. Three TaqMan probes were developed and used: thezkirP1 probe to detect phylogroups Kp1 to Kp5 and Kp7; thezkirP2 probe to detect phylogroup Kp6; and the Kp1 probe to specifically identify this phylogroup. The new assay was tested on a total of 95 KpSC and 19 non-KpSC strains from various sources, representing the different phylogroups as defined by whole genome sequencing. The results showed almost complete specificity, as the expected PCR results were obtained for 112 (98%) strains. The new triplex real-time PCR assay, called ZKIR-T, enables detection of all KpSC taxa while discriminating Kp1, which will be useful for rapid screening and to focus downstream analyses on chosen phylogroups of the KpSC.

Importance

The pathogens of theKlebsiella pneumoniaespecies complex are widespread in food and animals and are amongst the main pathogens responsible for multidrug resistant infections in humans. In this study, we developed a highly sensitive detection assay that enables detection of this group of bacteria, with the simultaneous identification of the most common and clinically important species. This triplex one-reaction assay was shown to be highly sensitive and precise, enabling fast screening of varied samples for the presence of KpSC andK. pneumoniae sensu stricto.
Aperiodic and Hurst EEG exponents across early human brain development: a systematic review
Authors: Stanyard R. A. , Mason D. , Ellis C. , Dickson H. , Short R. , Batalle D. , Arichi T.
Published: February 2024

In electroencephalographic (EEG) data, power-frequency slope exponents (1/fβ) can provide non-invasive markers ofin vivoneural activity excitation-inhibition (E:I) balance. E:I balance may be altered in neurodevelopmental conditions; hence, understanding how 1/fβevolves across infancy/childhood has implications for developing early assessments/interventions. This systematic review (PROSPERO-ID: CRD42023363294) explored the early maturation (0-26yrs) of resting-state EEG 1/fmeasures (aperiodic [AE], power law [PLE] and Hurst [HE] exponents), including studies containing ≥1 1/fmeasures and ≥10 typically developing participants. Five databases (including Embase and Scopus) were searched during March 2023. Forty-two studies were identified (Nparticipants=3478). Risk of bias was assessed using the Quality Assessment with Diverse Studies tool. Narrative synthesis of HE data suggests non-stationary EEG activity occurs throughout development. Age-related trends were complex, with rapid decreases in AEs during infancy and heterogenous changes thereafter. Regionally, AE maxima shifted developmentally, potentially reflecting spatial trends in maturing brain connectivity. This work highlights the importance of further characterising the development of 1/fmeasures to better understand how E:I balance shapes brain and cognitive development.
Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in aDrosophilaknock-in tauopathy model
Authors: Bukhari Hassan , Nithianandam Vanitha , Battaglia Rachel A. , Cicalo Anthony , Sarkar Souvarish , Comjean Aram , Hu Yanhui , Leventhal Matthew J. , Dong Xianjun , Feany Mel B.
Published: February 2024

Missense mutations in the gene encoding the microtubule-associated protein tau cause autosomal dominant forms of frontotemporal dementia. Multiple models of frontotemporal dementia based on transgenic expression of human tau in experimental model organisms, includingDrosophila, have been described. These models replicate key features of the human disease, but do not faithfully recreate the genetic context of the human disorder. Here we use CRISPR-Cas mediated gene editing to model frontotemporal dementia caused by the tau P301L mutation by creating the orthologous mutation, P251L, in the endogenousDrosophila taugene. Flies heterozygous or homozygous for tau P251L display age-dependent neurodegeneration, metabolic defects and accumulate DNA damage in affected neurons. To understand the molecular events promoting neuronal dysfunction and death in knock-in flies we performed single-cell RNA sequencing on approximately 130,000 cells from brains of tau P251L mutant and control flies. We found that expression of disease-associated mutant tau altered gene expression cell autonomously in all neuronal cell types identified and non-cell autonomously in glial cells. Cell signaling pathways, including glial-neuronal signaling, were broadly dysregulated as were brain region and cell-type specific protein interaction networks and gene regulatory programs. In summary, we present here a genetic model of tauopathy, which faithfully recapitulates the genetic context and phenotypic features of the human disease and use the results of comprehensive single cell sequencing analysis to outline pathways of neurotoxicity and highlight the role of non-cell autonomous changes in glia.
Comprehensive analysis of the microbial consortium in the culture of flagellateMonocercomonoides exilis
Authors: Jiménez-González Alejandro , Treitli Sebastian Cristian , Peña-Diaz Priscila , Janovská Anna , Beneš Vladimír , Žáček Petr , Hampl Vladimír
Published: February 2024

Monocercomonoides exilisis the only known amitochondriate eukaryote, making it an excellent model for studying the implications of mitochondrial reduction from a cellular and evolutionary point of view. AlthoughM. exilisis an endobiotic heterotroph, it can growin vitro, albeit with an uncharacterized and complex prokaryotic community. All attempts to growM. exilisaxenically have been unsuccessful. Here, we use metagenomic sequencing at different time points during culture growth to describe the composition and dynamics of this community. We assembled genomes of 24 from at least the 30 different bacterial species within. Based on DNA read abundances,M. exilisrepresents less than 1.5%, and the representation of dominant bacterial members changes over time. Genome-scale metabolic reconstruction, differential expression analysis and measurements of metabolites in the media showed that the community depends on organic carbon oxidation, fermentation, and hydrogen production without methanogenesis. This is consistent with the rapid decline of amino acids, nucleotides, glyceraldehyde, lactate, fatty acids, and alcohols in the media. The community depends on recycling the external supply of amino acids since it has a limited capacity to fix nitrogen gas and lacks ammonia oxidizers to close the nitrogen cycle. With the senescence of the culture, we observe changes in the expression of several metabolic pathways inM. exilis, particularly those adapting to starvation. We do not reveal any clear metabolic link to explain the dependence ofM. exilison prokaryotes.
Expression of novel androgen receptors in three GnRH neuron subtypes in the cichlid brain
Authors: Dussenne Mélanie , Alward Beau A.
Published: February 2024

Within a social hierarchy, an individuals’ social status determines its physiology and behavior. InA. burtoni, subordinate males can rise in rank to become dominant, which is accompanied by the upregulation of the entire HPG axis, including activation of GnRH1 neurons, a rise in circulating androgen levels and the display of specific aggressive and reproductive behaviors. Cichlids possess two other GnRH subtypes, GnRH2 and GnRH3, the latter being implicated in the display of male specific behaviors. Interestingly, some studies showed that these GnRH neurons are responsive to fluctuations in circulating androgen levels, suggesting a link between GnRH neurons and androgen receptors (ARs). Due to a teleost-specific whole genome duplication,A. burtonipossess two AR paralogs (ARα and ARβ) that are encoded by two different genes,ar1andar2, respectively. Even though social status has been strongly linked to androgens, whether ARα and/or ARβ are present in GnRH neurons remains unclear. Here, we used immunohistochemistry andin situhybridization chain reaction (HCR) to investigatear1andar2expression specifically in GnRH neurons. We find that all GnRH1 neurons intensely expressar1but only a few of them expressar2, suggesting the presence of genetically-distinct GnRH1 subtypes. Very fewar1andar2transcripts were found in GnRH2 neurons. GnRH3 neurons were found to express bothargenes. The presence of distinctargenes within GnRH neuron subtypes, most clearly observed for GnRH1 neurons, suggests differential control of these neurons by androgenic signaling. These findings provide valuable insight for future studies aimed at disentangling the androgenic control of GnRH neuron plasticity and reproductive plasticity across teleosts.
Anox2/cybbzebrafish mutant with defective neutrophil ROS production displays normal initial neutrophil recruitment to sterile tail injuries
Authors: Isiaku Abdulsalam I. , Zhang Zuobing , Pazhakh Vahid , Lieschke Graham J.
Published: February 2024

Reactive oxygen species (ROS) are important effectors and modifiers of the acute inflammatory response, recruiting neutrophils to sites of tissue injury. In turn, neutrophils are both consumers and producers of reactive oxygen species. Stimulated neutrophils generate reactive oxygen species in an oxidative burst through the activity of a multimeric phagocytic NADPH oxidase complex. Mutations in theNOX2/CYBB(previously gp91phox) NADPH oxidase subunit are the commonest cause of chronic granulomatous disease, a disease characterized by infection susceptibility and an inflammatory phenotype. To model chronic granulomatous disease, we made anox2/cybbzebrafish (Danio rerio) mutant and demonstrated it to have severely impaired neutrophil ROS production. Reduced early survival ofnox2mutant embryos indicated an essential requirement fornox2during early development. Innox2/cybbzebrafish mutants, the dynamics of initial neutrophil recruitment to both mild and severe surgical tailfin wounds was normal, suggesting that excessive neutrophil recruitment at the initiation of inflammation is not the primary cause of the “sterile” inflammatory phenotype of chronic granulomatous disease patients. Thisnox2zebrafish mutant adds to existing in vivo models for studying neutrophil reactive oxygen species function in development and disease.
Tryptanthrin Analogs Substoichiometrically Inhibit Seeded and Unseeded Tau4RD Aggregation
Authors: James Ellie I. , Baggett David W. , Chang Edcon , Schachter Joel , Nixey Thomas , Choi Karoline , Guttman Miklos , Nath Abhinav
Published: February 2024

Microtubule-associated protein tau is an intrinsically disordered protein (IDP) that forms characteristic fibrillar aggregates in several diseases, the most well-known of which is Alzheimer’s disease (AD). Despite keen interest in disrupting or inhibiting tau aggregation to treat AD and related dementias, there are currently no FDA-approved tau-targeting drugs. This is due, in part, to the fact that tau and other IDPs do not exhibit a single well-defined conformation but instead populate a fluctuating conformational ensemble that precludes finding a stable “druggable” pocket. Despite this challenge, we previously reported the discovery of two novel families of tau ligands, including a class of aggregation inhibitors, identified through a protocol that combines molecular dynamics, structural analysis, and machine learning. Here we extend our exploration of tau druggability with the identification of tryptanthrin and its analogs as potent, substoichiometric aggregation inhibitors, with the best compounds showing potencies in the low nanomolar range even at a ∼100-fold molar excess of tau4RD. Moreover, conservative changes in small molecule structure can have large impacts on inhibitory potency, demonstrating that similar structure-activity relationship (SAR) principles as used for traditional drug development also apply to tau and potentially to other IDPs.
Dynamic regulation of CeA gene expression during acute and protracted abstinence from chronic binge drinking of male and female C57BL/6J mice
Authors: Méndez Hernán G. , Neira Sofia , Flanigan Meghan E. , Haun Harold L. , Boyt Kristen M. , Thiele Todd E. , Kash Thomas L.
Published: February 2024

Binge alcohol consumption is a major risk factor for developing Alcohol Use Disorder (AUD) and is associated with alcohol-related problems like accidental injury, acute alcohol poisoning, and black-outs. While there are numerous brain regions that have been shown to play a role in this AUD in humans and animal models, the central nucleus of the amygdala (CeA) has emerged as a critically important locus mediating binge alcohol consumption. In this study, we sought to understand how relative gene expression of key signaling molecules in the CeA changes during different periods of abstinence following bouts of binge drinking. To test this, we performed drinking in the dark (DID) on two separate cohorts of C57BL/6J mice and collected CeA brain tissue at one day (acute) and 7 days (protracted) abstinence after DID. We used qRTPCR to evaluate relative gene expression changes of 25 distinct genes of interest related to G protein-coupled receptors (GPCRs), neuropeptides, ion channel subunits, and enzymes that have been previously implicated in AUD. Our findings show that during acute abstinence CeA punches collected from female mice had upregulated relative mRNA expression of the gamma-aminobutyric acid receptor subunit alpha 2 (Gabra2), and the peptidase, angiotensinase c (Prcp). CeA punches from male mice at the same time point in abstinence had upregulated relative mRNA encoding for neuropeptide-related molecules, neuropeptide Y (Npy) and somatostatin (Sst), as well as the neuropeptide Y receptor Y2 (Npyr2) but downregulated, Glutamate ionotropic receptor NMDA type subunit 1 (Grin1). After protracted abstinence CeA punches collected from female mice had increased mRNA expression of corticotropin releasing hormone (Crh) and Npy. While CeA punches collected from male mice at the same timepoint had upregulated relative mRNA expression of Npy2r and downregulated mRNA expression of Gabra2, Grin1 and opioid receptor kappa 1 (Oprk1). Our findings support that there are differences in how the CeA of male and female respond to binge-alcohol exposure, highlighting the need to understand the implications of such differences in the context of AUD and binge drinking behavior.