bluuebunny/crossref_metadata_2025 huggingface dataset:
NewSNCAmutation and structures of α-synuclein filaments from juvenile-onset synucleinopathy
Authors: Yang Yang , Garringer Holly J. , Shi Yang , Lövestam Sofia , Zhang Xianjun , Kotecha Abhay , Bacioglu Mehtap , Koto Atsuo , Takao Masaki , Spillantini Maria Grazia , Ghetti Bernardino , Vidal Ruben , Murzin Alexey G. , Scheres Sjors H.W. , Goedert Michel
Published: November 2022

A 21-nucleotide duplication in one allele ofSNCAwas identified in a previously described disease with abundant α-synuclein inclusions that we now call juvenile-onset synucleinopathy (JOS). Both wild-type α-synuclein and its insertion mutant containing seven additional residues (MAAAEKT) after residue 22 were present in sarkosyl-insoluble material that was extracted from frontal cortex of the individual with JOS and examined by electron cryo-microscopy. The structures of JOS filaments, comprising either a single protofilament, or a pair of protofilaments, revealed a new α-synuclein fold that differs from the folds of Lewy body diseases and multiple system atrophy (MSA). The JOS fold consists of a compact core, the sequence of which (residues 36-100 of wild-type α-synuclein) is unaffected by the mutation, and two disconnected density islands (A and B) of mixed sequences. There is a non-proteinaceous cofactor bound between the core and island A. The JOS fold resembles the common substructure of MSA type I and type II dimeric filaments, with its core segment approximating the C-terminal body of MSA protofilaments B and its islands mimicking the N-terminal arm of MSA protofilaments A. The partial similarity of JOS and MSA folds extends to the locations of their cofactor-binding sites. Our findings provide insight into a likely mechanism of JOS fibrillation in which mutant α-synuclein of 147 amino acids forms a nucleus with the JOS fold, around which wild-type and mutant proteins assemble during elongation.
Genetics and resource availability shape divergence in life history and behavior between locally-adapted populations of Atlantic mollies (Poecilia mexicana, Poeciliidae)
Authors: Coffin John L. , Williams Bethany L. , Tobler Michael
Published: November 2022

Phenotypic variation is common along environmental gradients, but it is often unknown to what extent it results from genetic differentiation between populations or phenotypic plasticity. We studied populations of a livebearing fish that have colonized streams rich in toxic hydrogen sulfide (H2S). In nature, there is strong phenotypic differentiation between adjacent sulfidic and nonsulfidic populations. In this study, we varied food availability to pregnant mothers from different populations to induce maternal effects, a form of plasticity, and repeatedly measured life-history and behavioral traits throughout the offspring’s ontogeny. Genetic differentiation affected most of the traits we measured, as sulfidic offspring tended to be born larger, mature later, have lower burst swimming performance, be more exploratory, and feed less accurately. In contrast, maternal effects impacted few traits and at a smaller magnitude, even though offspring from poorly provisioned mothers tended to be born larger and be more exploratory. Population differences and maternal effects (when both were present) acted synergistically, and there was no evidence for population differences in plasticity. Overall, our study suggests that phenotypic divergence between these populations in nature is primarily caused by genetic differentiation, and that plasticity mediated by maternal effects accentuates—but does not cause—differences between populations.
BiallelicSTAB1pathogenic variants cause hereditary hyperferritinemia
Authors: Monfrini Edoardo , Pelucchi Sara , Hollmén Maija , Viitala Miro , Mariani Raffaella , Bertola Francesca , Majore Silvia , Fonzo Alessio Di , Piperno Alberto
Published: November 2022

Serum ferritin measurement is a routine laboratory test to indirectly evaluate body iron content. However, many additional factors may elevate serum ferritin levels disproportionally to iron stores. Hyperferritinemia is a frequent finding in several conditions, both genetic and acquired. Despite the long history of clinical use, fundamental aspects of the biology of serum ferritin are still unclear. We studied eleven healthy subjects from eight different families presenting unexplained hyperferritinemia without iron overload. To detect the genetic cause of hyperferritinemia we carried out whole-exome sequencing. Immunohistochemistry and flow cytometry assays were performed on patient liver biopsies and monocyte-macrophages to confirm the pathogenic role of the identified candidate variants. Through a combined approach of whole-exome sequencing and homozygosity mapping, we found biallelic candidateSTAB1variants in ten subjects from seven families.STAB1encodes the multifunctional scavenger receptor stabilin-1. Immunohistochemical studies and flow cytometry analyses showed absent or markedly reduced stabilin-1 in patient liver samples, monocytes and monocyte-derived macrophages. We present biallelicSTAB1mutations as a new cause of inherited hyperferritinemia without iron overload suggesting the existence of new and unexpected function of stabilin-1 in ferritin metabolism.

In conclusion, our findings strongly support biallelicSTAB1mutations as a novel genetic cause of inherited hyperferritinemia without iron overload and suggest the existence of a new and unexpected function of stabilin-1 in ferritin metabolism.
Trends and predictors of unmet need for family planning among women living with HIV in Zambia: implications for elimination of Mother to Child Transmission of HIV
Authors: Lungu Edgar Arnold , Chewe Mwimba
Published: November 2022

Introduction

Prevention of Mother To Child Transmission (PMTCT) of HIV is one of the key strategies towards HIV epidemic control. Despite considerable progress in PMTCT of HIV over the past decade in Zambia, the country is yet to reach global and national target for elimination of Mother To Child Transmission of HIV. Avoidance of unintended pregnancy among women living with HIV provides is one of the cost-effective interventions in a comprehensive PMTCT of HIV approach. This study therefore aimed at ascertaining trends in and predictors of unmet need for family planning among women living with HIV in Zambia

Methods

The study employed a repeated cross sectional (RCS) study design, using data from the three (3) most recent consecutive rounds of the Zambia Demographic and Health Survey (ZDHS) conducted in 2007, 2013/2014 and 2018. The study used data from a total of 34,204 women aged 15-49 years from the three survey points, 2007, 2013/14 and 2018, among whom 4,985 were HIV positive, with a final sample size constituting 2,675 married women living with HIV. We used descriptive statistics and logistic regression analyses to respectively ascertain trends in and predictors of unmet need for family planning among married women living with HIV.

Results

Over the three survey points, unmet need for family planning among married women living with HIV has hardly declined, registering 22% in both the 2007 and 2018. Residence, age of women, household wealth, woman’s parity, employment, and age of spouse emerged as significant predictors of unmet need for family planning among women living with HIV in Zambia

Conclusion

Preventing one HIV infection in a child is averting lifetime costs of HIV treatment and associated healthcare costs. There is need to consider optimization of PMTCT interventions including shaping programming regarding prong 2 in a way that it responds to main causes of mother to child transmission of HIV in Zambia. Among other aspects, policy and practice needs to strengthen SRH/HIV integration and better target rural residents, younger women, those with high parity and consider positive male engagement to reduce unmet need for family planning among women living with HIV.
Women’s mortality following pregnancy affected by vaginal bleeding due to threatened miscarriage: a Danish cohort study
Authors: Dudukina Elena , Horváth-Puhó Erzsébet , Sørensen Henrik Toft , Ehrenstein Vera
Published: November 2022

Background

Women with only pregnancy terminations or only miscarriages have an increased mortality risk. We investigated the association between vaginal bleeding (VB) in pregnancy ending in childbirth and women’s mortality.

Methods

We conducted a cohort study in Denmark, which included 1,354,181 women and their 3,162,317 pregnancies (1979-2017) followed through 2018. We ascertained 70,835 VB-affected pregnancies and comparators: 2,236,359 VB-unaffected pregnancies ending in childbirth; 589,697 terminations; and 265,940 miscarriages. We computed all-cause and cause-specific mortality rates per 10,000 person-years (PY) and hazard ratios (HRs) with 95% confidence intervals (CIs) using Cox proportional hazards regression adjusted for age, calendar year, preexisting conditions, and socioeconomic factors.

Results

There were 2,320 deaths from any cause among women following VB-affected pregnancy (mortality rate: 15.2, 95% CI: 14.6-15.9 per 10,000 PY); 55,030 deaths following VB-unaffected pregnancy (12.7, 12.6-1.28); 27,500 deaths following a termination (21.9, 21.6-22.1), and 10,865 deaths following a miscarriage (19.2, 18.8-19.6).

For comparison of VB-affected vs VB-unaffected pregnancies, associations with all-cause (HR: 1.14, 95% CI: 1.09-1.19), natural-causes (HR: 1.15, 95% CI: 1.09-1.22) and non-natural causes (HR: 1.27, 95% CI: 1.08-1.48) mortality attenuated in a sensitivity analysis of pregnancies recorded in 1994-2017 (HR: 1.00, 95% CI: 0.90-1.12, HR: 0.98, 95% CI: 0.85-1.14, and HR: 1.04, 95% CI: 0.71-1.51, respectively). Contrasts with remaining comparators did not suggest increased risks of all-cause, natural, or non-natural mortality causes.

Conclusions

We found no evidence of an increased risk of mortality in women following VB-affected vs VB-unaffected pregnancy, termination, or miscarriage.

Key Messages

Previous studies mostly focused on short-term outcomes of the newborns and mothers following the vaginal bleeding-affected pregnancy. This study investigated the association between vaginal bleeding in pregnancy ending in childbirth and women’s mortality.

This registry-based cohort study found no evidence of an increased risk of all-cause or cause-specific mortality from natural or non-natural causes in women following vaginal bleeding-affected pregnancy compared with vaginal bleeding-unaffected pregnancy, termination, or miscarriage
Point-of-care prognostication in moderate Covid-19: analytical validation and diagnostic accuracy of a soluble urokinase plasminogen activator receptor (suPAR) rapid test
Authors: Chandna Arjun , Mahajan Raman , Gautam Priyanka , Mwandigha Lazaro , Dittrich Sabine , Kumar Vikash , Osborn Jennifer , Kumar Pragya , Koshiaris Constantinos , Varghese George M , Lubell Yoel , Burza Sakib
Published: November 2022

The soluble urokinase plasminogen activator receptor (suPAR) has been proposed as a biomarker for the risk stratification of patients presenting with acute infections. However, most studies evaluating suPAR have used platform-based assays, the diagnostic accuracy of which may differ from point-of-care tests capable of informing timely patient triage in settings without established laboratory capacity.

Using samples and data collected during a prospective cohort study of 425 patients presenting with moderate Covid-19 to two hospitals in India, we evaluated the analytical performance and diagnostic accuracy of a commercially-available rapid diagnostic test (RDT) for suPAR, using an enzyme-linked immunoassay (ELISA) as the reference standard. Although agreement between the two tests was limited (bias = −2.46 ng/mL [95% CI = −2.65 to −2.27 ng/mL]), diagnostic accuracy to predict progression to supplemental oxygen requirement was comparable, whether suPAR was used alone (area under the receiver operating characteristic curve [AUC] of RDT = 0.73 [95% CI = 0.68 to 0.79] vs. AUC of ELISA = 0.70 [95% CI = 0.63 to 0.76]; p = 0.12) or as part of a previously published multivariable clinical prediction model (AUC of RDT-based model = 0.74 [95% CI = 0.66 to 0.83] vs. AUC of ELISA-based model = 0.72 [95% CI = 0.64 to 0.81]; p = 0.78).

Lack of agreement between the suPAR RDT and ELISA in our cohort warrants further investigation and highlights the importance of assessing candidate point-of-care tests to ensure management algorithms reflect the assay that will ultimately be used to inform patient care. The availability of a quantitative point-of-care test for suPAR opens the door to suPAR-guided risk stratification of patients with Covid-19 and other acute infections in settings with limited laboratory capacity.
Exploring the feasibility of integrating health, nutrition and stimulation interventions for children under three years in Nepal’s health system: a qualitative study
Authors: Dulal Sophiya , Saville Naomi M. , Merom Dafna , Giri Kalpana , Prost Audrey
Published: November 2022

Community-based primary care settings are a potential entry point for delivering Early Childhood Development (ECD) interventions in Nepal. Past studies have suggested that integrating stimulation with nutrition interventions is an effective way to deliver multiple benefits for children, but there is limited knowledge of how to do this in Nepal. We conducted a qualitative study in Nepal’s Dhanusha district to explore how stimulation interventions for early learning could be integrated into existing health and nutrition programmes within the public health system. Between March and April 2021, we completed semi-structured interviews with caregivers (n=18), health service providers (n=4), district (n=1) and national stakeholders (n=4), as well as policymakers (n=3). We also carried out focus group discussions with Female Community Health Volunteers (FCHVs) (n=2) and health facility operation and management committee members (n=2). We analysed data using the framework method. Respondents were positive about introducing stimulation interventions into maternal and child health and nutrition services. They thought that using health system structures would help in the implementation of integrated interventions. Respondents also highlighted that local governments play a lead role in decision-making but must be supported by provincial and national governments and external agencies. Key factors impeding the integration of stimulation into national programmes included a lack of intersectoral collaboration, poor health worker competency, increased workload for FCHVs, financial constraints, a lack of prioritisation of ECD and inadequate capacity in local governments. Key barriers influencing the uptake of intervention by community members included lack of knowledge about stimulation, caregivers’ limited time, lack of paternal engagement, poverty, religious or caste discrimination, and social restrictions for newlywed women and young mothers. There is an urgent need for an effective coordination mechanism between ministries and within all three tiers of government to support the integration and implementation of scalable ECD interventions in rural Nepal.
Investigating opportunities to prevent Type 2 Diabetes Mellitus after Gestational Diabetes Mellitus: the DIVINE-NSW study
Authors: Lee Vivian YJ , Beech Amanda , Makris Angela , Arnott Clare , Shanthosh Janani , Donges Katherine , Patel Anushka , Henry Amanda
Published: November 2022

Background

Gestational Diabetes Mellitus (GDM), once thought to be fully reversed after pregnancy, is now a firmly established independent risk factor for the subsequent development of Type 2 Diabetes Mellitus (T2DM), cardiovascular disease and other chronic conditions. This provides a strong rationale to identify preventive strategies in women with prior GDM, including intervention soon after childbirth. Currently, preventive strategies are mostly focused on modifying lifestyle, with an emphasis on diet and physical activity. However, evidence for the effectiveness of implementing and sustaining changes in behaviour through lifestyle programs is limited, and only a small proportion of women in Australia are thought to engage in lifestyle modification programs. Consideration of additional approaches, including pharmacotherapy, is therefore warranted. The current study aims to 1) measure the prevalence and identify the predictors (up to 4 years post-partum) of persisting dysglycaemia among a diverse population of urban Australian women with recent GDM, 2) understand women’s views and views of their healthcare providers on long-term risks of T2DM and barriers and facilitators to engaging in screening and preventive strategies (including pharmacotherapy) to mitigate these risks, and 3) examine the feasibility of a randomised controlled trial of preventive drug therapies in this population.

Methods

This is a retrospective cohort study with a qualitative sub-study. We will identify GDM-affected women who gave birth between January 2018 and December 2021 in at least three Sydney Hospitals (Liverpool Hospital, Royal Hospital for Women and St George Hospital) and invite them to participate in the study. Eligible participants will complete an online questionnaire and an oral glucose tolerance test to assess their current glycaemic status if they have not done so within 12 months of consent and are not currently pregnant. A subset of participants will be invited to participate in an interview to understand their perspectives of GDM, long-term risks and willingness to take preventive medications (including willingness to participate in trials of preventive medicines). Interviews with healthcare providers will also be conducted to understand their views of long-term diabetes risk, screening, and preventive strategies for women following GDM.

Discussion

This study will help understand post-GDM care gaps and outcomes currently in Australia, as well as inform the design and conduct of future trials of preventive drug therapies in this population.

ANZCT Registration

ACTRN12621001618842
Buoyant-Antigen-Magnetic (BAM) ImmunoSeparation, isolation, and detection of Specific Pathogenic Bacterial Cells
Authors: McNaughton Brandon H. , Anker Jeffrey N. , Kinnunen Päivö K.
Published: November 2022

Separating, collecting, and detecting specific cells and molecules from complex and heterogeneous samples is key for many biomedical, environmental, and food safety applications. Antibodies are widely used to specifically bind cells and molecules to a solid support such as a column or suspended bead to separate, wash, and concentrate them. However, nonspecific binding of non-target cells and molecules to the support limits the specificity and resulting purity of traditional separation methods. Herein we describe a buoyant-antigen-magnetic (BAM) separation approach to increase specificity using two distinct separation processes with “AND” logic. Buoyant silica microbubbles and magnetic microbeads, each with their own antibody, bind to the target cell forming a BAM sandwich complex which can be separated from non-targeted cells (which are neither magnetic nor buoyant), as well as from cells bound to only single buoyant or magnetic microparticles but not both.Escherichia coliO157:H7, a pathogenic bacteria that can contaminate food products, was used as a model organism to establish a nearly 100-fold reduction in the non-specific carryover of non-targetEscherichia colibacteria in comparison to simple magnetic separation. Beads with no attached analyte were also removed. Furthermore, the BAM complexes could be visualized by eye (or camera) providing a rapid and sensitive method for pathogenic bacterial detection. Bacterial concentrations as low as 5 × 104CFU/ml were evident by eye and could easily be distinguished from non-targetS. aureusbacteria even at much higher concentrations (5x107cfu/mL). This approach enabled simple user-friendly measurement for on-site detection and isolation without expensive equipment.

HIGHLIGHTS
Optical measurement of glutamate release robustly reports short-term plasticity at a fast central synapse
Authors: Hain Paul Jakob Habakuk , Moser Tobias
Published: November 2022

Recently developed fluorescent neurotransmitter indicators have enabled direct measurements of neurotransmitter in the synaptic cleft. Precise optical measurements of neurotransmitter release may be used to make inferences about presynaptic function independent of electrophysiological measurement techniques. Here, we express iGluSnFR, a genetically encoded glutamate reporter in mouse spiral ganglion neurons to compare electrophysiological and optical readouts of presynaptic function and short-term synaptic plasticity at the endbulb of Held synapse. We conclude that iGluSnFR robustly and approximately linearly reports glutamate release from the endbulb of Held during synaptic transmission and allows assessment of short-term plasticity during high-frequency train stimuli. Furthermore, we show that iGluSnFR expression slightly alters the time course of spontaneous postsynaptic currents, but is unlikely to impact measurements of evoked synchronous release of many synaptic vesicles.
A 3D genome atlas of genetic variants and their pathological effects
Authors: Tang Li , Hill Matthew C. , He Mingxing , Chen Junhao , Ellinor Patrick T. , Li Min
Published: November 2022

The spatial architecture of the genome can be categorized into distinct layers. Each layer plays a critical role in transcriptional regulation and/or genomic integrity. Alterations at any level of the 3D genome can lead to an unwanted cascade of molecular events, which may ultimately drive the manifestation of disease. However, a comprehensive atlas of the mutations and structural genetic defects that affect genome organization has yet to be compiled. Moreover, we lack a centralized resource for interpretating the pathological effects of such genetic mutations. Therefore, we curated from the literature all the pathological alterations from the chromosome level on down to single nucleotide polymorphisms (SNPs) in order to investigate these diverse genetic mutations. Using a two-phase scoring algorithm, 3DFunc, we scored the transcriptomic causality of all variants in the context of 3D genome architecture from 20 cancer and 15 normal tissues. Further, 3DFunc can identify pathological variant-gene pairs in non-oncological diseases. Finally, we constructed a web-based database, 3DGeOD (https://www.csuligroup.com/3DGeOD/home), to provide all the curated variants, genomic disruptions, as well as the scoring results derived from 3DFunc. In summary, our study constructed a 3D genome atlas of genetic variants and will serve as a valuable resource for mining the putative pathological effects of any genetic mutation.
Automated decoding the mouse body postures in a whisker nuisance test
Authors: Chelini Gabriele , Fortunato-Asquini Tommaso , Ollari Ottavia , Pecchia Tommaso , Bozzi Yuri
Published: November 2022

Abnormal response to sensory stimuli characterizes multiple neuropsychiatric conditions. However, not many tools are currently available to assess somatosensory abnormalities in rodent models of brain disorders, limiting the possibilities to study cellular and molecular correlates of this phenotypic trait. To this goal, previous studies relied on the whisker nuisance test (WNt), in which freely moving mice are constantly stimulated on their whiskers using a wood stick for a set time. The whisker-guided response is then deconstructed in behavioral categories indicative of either anxiety or curiosity. Thus far, WNt was shown to be a valuable tool to investigate sensory-driven abnormalities in mouse models of autism spectrum disorders (ASD), demonstrating a solid translational validity. Nevertheless, assessment of behavioral response in the WNt is currently limited by the lack of an objective quantification method. To overcome this limitation, we developed WNt3R (Whisker Nuisance Test in 3D for Rodents), a MATLAB toolbox that uses the output of the open-source software DeepLabCut to determine discrete body postures associated with multiple ethologically-relevant behaviors. Our results show that behavioral modules identified using WNt3R reliably decode mouse body postures, outperforming the manual user, thus offering a novel and unbiased approach to study altered somatosensory function in rodents.
Timescales of adaptation to context in horizontal sound localization
Authors: Andrejková Gabriela , Best Virginia , Kopčo Norbert
Published: November 2022

Psychophysical experiments explored how the repeated presentation of a context, consisting of an adaptor and a target, induces plasticity in the localization of an identical target presented alone on interleaved trials. The plasticity, and its time course, was examined both in a classroom and in an anechoic chamber. Adaptors and targets were 2-ms noise clicks and listeners were tasked with localizing the targets while ignoring the adaptors (when present). The context had either a fixed temporal structure, consisting of a single-click adaptor and a target, or its structure varied from trial to trial, either containing a single-click or an 8-click adaptor. The adaptor was presented either from a frontal or a lateral location, fixed within a run. The presence of context caused responses to the isolated targets to be displaced up to 14° away from the adaptor location. This effect was stronger and slower if the context was variable, growing over the 5-minute duration of the runs. Additionally, the fixed-context buildup had a slower onset in the classroom. Overall, the results illustrate that sound localization is subject to slow adaptive processes that depend on the spatial and temporal structure of the context and on the level of reverberation in the environment.
Assortative mating and mate-choice contributes to a developmental dimorphism inStreblospio benedicti
Authors: Ruskie Erika L. , Zakas Christina
Published: November 2022

Assortative mating, where individuals non-randomly mate with respect to phenotype or genotype, can occur when preferences between potential mates have evolved. When such mate preferences occur in a population it can drive evolutionary and phenotypic divergence. But the extent to which assortative mating, mate preference, and development are evolutionarily linked remains unclear. Here we useStreblospio benedicti, a marine annelid with a rare developmental dimorphism, to investigate if mate-choice could contribute to developmental evolution. ForS. benedictitwo types of ecologically and phenotypically similar adults persist in natural populations, but they give rise to distinctly different offspring with alternative lifehistories. This dimorphism persists despite the absence of post-zygotic reproductive barriers, where crosses between the developmental types can produce phenotypically intermediate offspring. How this life-history strategy evolved remains unknown, but assortative mating is a typical first step in evolutionary divergence. Here we investigate if female mate-choice is occurring in this species. We find that mate preferences could be contributing to the maintenance of alternative developmental and life-history strategies.
PTPN1 deficiency modulates BMPR2 signaling and induces endothelial dysfunction in Pulmonary Arterial Hypertension
Authors: Ali Md Khadem , Tian Xuefei , Zhao Lan , Schimmel Katharina , Rhodes Christopher J. , Wilkins Martin R. , Nicolls Mark R. , Spiekerkoetter Edda F.
Published: November 2022

Bone morphogenic protein receptor 2 (BMPR2) expression and signaling are impaired in pulmonary arterial hypertension (PAH). How BMPR2 signaling is decreased in PAH is poorly understood. Protein tyrosine phosphatases (PTPs) play important roles in vascular remodeling in PAH. To identify whether PTPs modify BMPR2 signaling we used a siRNA-mediated high throughput screening of 22,124 murine genes in mouse myoblastoma reporter cells using ID1 expression as read-out for BMPR2 signaling. We further experimentally validated the top hit, PTPN1 (PTP1B), in human healthy pulmonary arterial endothelial cells (PAECs) either silenced by siRNA or exposed to hypoxia and confirmed its relevance to PAH by measuring PTPN1 levels in blood and PAECs collected from PAH patients. We identified PTPN1 as a novel regulator of BMPR2 signaling in PAECs, which is downregulated in the blood of PAH patients and documented that downregulation of PTPN1 is linked to endothelial dysfunction in PAECs. These findings point to a potential involvement for PTPN1 in PAH and will aid in our understanding of the molecular mechanisms involved in the disease.
Intravital imaging-based genetic screen reveals the transcriptional network governingCandida albicansfilamentation during mammalian infection
Authors: Wakade Rohan S. , Ristow Laurie C. , Wellington Melanie , Krysan Damian J.
Published: November 2022

Candida albicansis one of the most common human fungal pathogens.C. albicanspathogenesis is tightly linked to its ability to under a morphogenetic transition from typically budding yeast to filamentous forms of hyphae and pseudohyphae. Filamentous morphogenesis is the most intensively studiedC. albicansvirulence traits; however, nearly all of these studies have been based on in vitro induction of filamentation. Using an intravital imaging assay of filamentation during mammalian infection, we have screened a library of transcription factor mutants to identify those that modulate both the initiation and maintenance of filamentation in vivo. We coupled this initial screen with genetic interaction analysis and in vivo transcription profiling to characterize the transcription factor network governing filamentation in infected mammalian tissue. Three core positive (Efg1, Brg1, and Rob1) and two core negative regulators (Nrg1 and Tup1) of filament initiation were identified. No previous systematic analysis of genes affecting the elongation step has been reported and we found that large set of transcription factors affect filament elongation in vivo including four (Hms1, Lys14, War1, Dal81) with no effect on in vitro elongation. We also show that the gene targets of initiation and elongation regulators are distinct. Genetic interaction analysis of the core positive and negative regulators revealed that the master regulator Efg1 primarily functions to mediate relief of Nrg1 repression and is dispensable for expression of hypha-associated genes in vitro and in vivo. Thus, our analysis not only provide the first characterization of the transcriptional network governingC. albicansfilamentation in vivo but also revealed a fundamentally new mode of function for Efg1, one of the most widely studiedC. albicanstranscription factors.
Astrocyte MCT1 expression does not contribute to the axonal degenerative phenotype observed with ubiquitous MCT1 depletion
Authors: Philips Thomas , Thompson Emily G. , Vijayakumar Balaji G. , Kent Erica R. , Miller Sean J. , Vidensky Svetlana , Farah Mohamed Hassan , Rothstein Jeffrey D.
Published: November 2022

We recently reported that loss of oligodendrocyte metabolic support through the lactate and pyruvate transporter Monocarboxylate Transporter 1 (MCT1) is well tolerated into adulthood. Only with advanced aging did we observe axonal degeneration and hypomyelination due to loss of MCT1 from oligodendroglia lineage cells. MCT1 is also expressed by other glial subtypes, such as astrocytes and endothelial cells where it has been suggested to be essential for learning and memory tasks. However, the importance of MCT1 in these cell types for long-term axonal metabolic support is still unknown. We therefore addressed whether conditional loss of MCT1 from either of these cell types would lead to widespread axonal degeneration with aging. Using a conditional null approach, similar to what was used for oligodendrocyte MCT1 depletion, we observed that conditional knockout of MCT1 from either astrocytes or endothelial cells did not cause neuronal injury. On the other hand, inducible ubiquitous depletion of MCT1 causes late-onset axonal degeneration, comparable with what was observed in our previous study using the oligodendrocyte lineage MCT1 null mice. In summary, we conclude that unlike oligodendrocyte MCT1, astrocyte MCT1 is not an essential driver of astrocyte mediated axonal energy homeostasis with aging.
β-Lapachone Regulates Mammalian Inositol Pyrophosphate Levels in an NQO1- and Oxygen-dependent Manner
Authors: Eisenbeis Verena B. , Qiu Danye , Strotmann Lisa , Liu Guizhen , Prucker Isabel , Ritter Kevin , Loenarz Christoph , Saiardi Adolfo , Jessen Henning J.
Published: November 2022

1

Inositol pyrophosphates (PP-InsPs) are energetic signalling molecules with important functions in mammals. As their biosynthesis depends on ATP concentration, PP-InsPs are tightly connected to cellular energy homeostasis. Consequently, an increasing number of studies involves PP-InsPs in metabolic disorders, such as type 2 diabetes, aspects of tumorigenesis, and hyperphosphatemia. Research conducted in yeast suggests that the PP-InsP pathway is activated in response to reactive oxygen species (ROS). However, the precise modulation of PP-InsPs during cellular ROS signalling is unknown. Here, we report how mammalian PP-InsP levels are changing during exposure to exogenous (H2O2) and endogenous ROS. Using capillary electrophoresis electrospray ionization mass spectrometry (CE-ESI-MS), we found that PP-InsP levels decrease upon exposure to oxidative stressors in HCT116 cells. Application of quinone drugs, particularly β-lapachone (β-lap), under normoxic and hypoxic conditions enabled us to produce ROSin celluloand to show that β-lap treatment caused PP-InsP changes that are oxygen dependent. Experiments in MDA-MB-231 breast cancer cells deficient of NAD(P)H:quinone oxidoreductase-1 (NQO1) demonstrated that β-lap requires NQO1-bioactivation to regulate the cellular metabolism of PP-InsPs. Critically, significant reductions in cellular ATP concentrations were not directly mirrored in reduced PP-InsP levels as shown in NQO1-deficient MDA-MB-231 cells treated with β-lap. The data presented here unveil new aspects of β-lap pharmacology and its impact on PP-InsP levels. Our identification of different quinone drugs as modulators of PP-InsP synthesis will allow to better appreciate their overall impact on cellular function.

2

Significance Statement

Inositol pyrophosphates (PP-InsPs) are messenger molecules regulating various functions in mammals. They are associated with the oxidative stress response, but the underlying mechanism is unclear. We investigate PP-InsP signalling in mammalian cells subjected to reactive oxygen species (ROS). Applying the quinone β-lapachone (β-lap) generated intracellular ROS resulting in decreased PP-InsP levels. This indicates a key role of PP-InsPs in cellular signalling under oxidative stress. Moreover, β-lap mediated PP-InsP signalling required oxygen and the enzyme NAD(P)H:quinone oxidoreductase-1 (NQO1). Since quinone drugs are cytotoxic, our data provide a basis for further investigations into the role of PP-InsPs during quinone-dependent chemotherapies. This is of special relevance since a phase II clinical trial demonstrated β-lap efficacy in a combination chemotherapy against pancreatic cancer.
Reconceptualizing beta diversity: a hypervolume geometric approach
Authors: Song Chuliang , Lu Muyang , Bennett Joseph R. , Gilbert Benjamin , Fortin Marie-Josée , Gonzalez Andrew
Published: November 2022

Beta diversity—the variation among community compositions in a region—is a fundamental measure of biodiversity. Despite a diverse set of measures to quantify beta diversity, most measures have posited that beta diversity is maximized when each community has a single distinct species. However, this assumption overlooks the ecological significance of species interactions and non-additivity in ecological systems, where the function and behaviour of species depend on other species in a community. Here, we introduce a geometric approach to measure beta diversity as the hypervolume of the geometric embedding of a metacommunity. This approach explicitly accounts for non-additivity and captures the idea that introducing a unique, species-rich community composition to a metacommunity increases beta diversity. We show that our hypervolume measure is closely linked to and naturally extends previous information- and variation-based measures while providing a unifying geometric framework for widely adopted extensions of beta diversity. Applying our geometric measures to empirical data, we address two long-standing questions in beta diversity research—the latitudinal pattern of beta diversity and the effect of sampling effort—and present novel ecological insights that were previously obscured by the limitations of traditional approaches. In sum, our geometric approach reconceptualizes beta diversity, offering an alternative and complementary perspective to previous measures, with immediate applicability to existing data.
Proteomic analysis defines the interactome of telomerase in the protozoan parasite,Trypanosoma brucei
Authors: Davis Justin A. , Reyes Andres V. , Nitika  , Saha Arpita , Wolfgeher Donald J. , Xu Shou-Ling , Truman Andrew W. , Li Bibo , Chakrabarti Kausik
Published: November 2022

Telomerase is a ribonucleoprotein enzyme responsible for maintaining the telomeric end of the chromosome. The telomerase enzyme requires two main components to function: the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), which provides the template for telomeric DNA synthesis. TR is a long noncoding RNA, which forms the basis of a large structural scaffold upon which many accessory proteins can bind and form the complete telomerase holoenzyme. These accessory protein interactions are required for telomerase activity and regulation inside cells. The interacting partners of TERT have been well studied in yeast, human, andTetrahymenamodels, but not in lower eukaryotes, including clinically relevant human parasites. Here, using the protozoan parasite,Trypanosoma brucei(T. brucei) as a model, we have identified the interactome ofT. bruceiTERT (TbTERT) using a mass spectrometry-based approach. We identified previously known and unknown interacting factors ofTbTERT, highlighting unique features ofT. bruceitelomerase biology. These unique interactions withTbTERT, suggest mechanistic differences in telomere maintenance betweenT. bruceiand other eukaryotes.
Cholecystokinin exerts a major control on corticostriatal synapse and motor behavior
Authors: Guillaume Chloé , Sáez María , Castellano Blandine , Parnet Patricia , Reig Ramon , Paillé Vincent
Published: November 2022

Cholecystokinin (CCK) is a neuropeptide detected and produced at high concentrations in the brain. To date it was mainly used as a neuronal marker of neuronal subtypes and its role as a neuromodulator was poorly known. However, few studies showed that it could be an essential neuromodulator in various brain structures, playing a role on synaptic plasticity and memory consolidation. In order to better understand the processes by which CCK impacts plasticity, we focus our attention on the striatum, a nucleus involved in procedural learning and motor behavior, with a rich expression of CCK receptor type 2 (CCK2R). By usingin-vivoandex-vivoelectrophysiological approaches, we show that CCK is involved in the corticostriatal synaptic transmission and has a key role in its plasticity. Usingin-vivooptopatch-clamp of identified MSNs, we observe a decrease of corticostriatal synaptic transmission after an injection of CCK2R antagonist, leading to a reduction of evoked excitatory post synaptic potential recorded on both MSNs populations (direct and indirect pathways). In addition, we evaluate the impact of CCK2R antagonist on corticostriatal synaptic plasticity using Spike Timing Dependent Plasticity (STDP) protocols on MSNs of acute rat brain slices. Results demonstrate that the CCK2R antagonist is able to reverse the corticostriatal synaptic plasticity (i.e. LTP protocol leads to LTD). Finally, we evaluate the effect of CCK2R antagonist on the motor behavior of juvenile rats challenged with different locomotor tests and show a sex-dependent impairment of motor behavior. Overall, our results demonstrate that CCK and its receptor CCK2R are essential for inputs processing encoding in the corticostriatal network with consequences on motor activity.

Significant statement

Cholecystokinin (CCK) is considered to be one of the most abundant neuropeptides in the brain but its role as a neuromodulator is not well understood. In our study we investigate its role on the corticostriatal transmission which is a well characterized synapse highly involved in motor and cognitive functions. Here, we show that CCK2R is crucial for the corticostriatal synaptic transmission and plasticity. Indeed, CCK binding on CCK2R is essential for LTP induction by STDP. Finally, we demonstrate that the blockage of CCK2R affects corticostriatal synaptic transmission and motor ability in male rats.
Antimicrobial resistance gene lack in tick-borne pathogenic bacteria
Authors: Papp Márton , Tóth Adrienn Gréta , Valcz Gábor , Makrai László , Nagy Sára Ágnes , Farkas Róbert , Solymosi Norbert
Published: November 2022

Tick-borne infections, including those of bacterial origin, are significant public health issues. Antimicrobial resistance (AMR), which is one of the most pressing health challenges of our time, is driven by specific genetic determinants, primarily by the antimicrobial resistance genes (ARGs) of bacteria. In our work, we investigated the occurrence of ARGs in the genomes of tick-borne bacterial species that can cause human infections. For this purpose, we processed short/long reads of 1550 bacterial isolates of the generaAnaplasma(n=20),Bartonella(n=131),Borrelia(n=311),Coxiella(n=73),Ehrlichia(n=13),Francisella(n=959) andRickettsia(n=43) generated by second/third generation sequencing that have been freely accessible at the NCBI SRA repository. FromFrancisella tularensis, 98.9% of the samples contained the FTU-1 gene, and 16.3% contained additional ARGs. Only 2.2% of isolates from other genera (Bartonella: 2,Coxiella: 8,Ehrlichia: 1,Rickettsia: 2) contained any ARG. We found that the odds of ARG occurrence inCoxiellasamples were significantly higher in isolates related to farm animals than from other sources. Our results describe a lack in ARGs in these bacteria and suggest that antibiotic susceptibility testing might be considered before the treatment of tick-borne infections in farm animals.
CommonNNClustering—A Python package for generic common-nearest-neighbour clustering
Authors: Kapp-Joswig Jan-Oliver , Keller Bettina G.
Published: November 2022

Density-based clustering procedures are widely used in a variety of data science applications. Their advantage lies in the capability to find arbitrarily shaped and sized clusters and robustness against outliers. In particular, they proved effective in the analysis of Molecular Dynamics simulations, where they serve to identify relevant, low energetic molecular conformations. As such, they can provide a convenient basis for the construction of kinetic (coreset) Markov-state models. Here we present the opensource Python project CommonNNClustering, which provides an easy-to-use and efficient re-implementation of the commonnearest-neighbour (CommonNN) method. The package provides functionalities for hierarchical clustering and an evaluation of the results. We put our emphasis on a generic API design to keep the implementation flexible and open for customisation.
A Dystroglycan–Laminin–Integrin axis controls cell basal geometry remodeling in the developingDrosophilaretina
Authors: Walther Rhian F. , Lancaster Courtney , Burden Jemima J. , Pichaud Franck
Published: November 2022

Cell shape remodeling is a principal driver of epithelial tissue morphogenesis. While progress continues to be made in our understanding of the pathways that control the apical (top) geometry of epithelial cells, we know comparatively little about those that control cell basal (bottom) geometry. To examine this issue, we used the fly ommatidium, which is the basic visual unit of the compound eye. The ommatidium is shaped as a hexagonal prism, and generating this three-dimensional structure requires ommatidial cells to adopt specific apical and basal polygonal geometries. Using this model system, we find that generating cell type-specific basal geometries starts with patterning of the basement membrane, whereby Laminin accumulates at discrete locations across the basal surface of the retina. We show that the Dystroglycan surface receptor promotes this localized Laminin accumulation. Moreover, our results reveal that localized accumulation of Laminin–Dystroglycan induces polarization of Integrin adhesion in ommatidial cells. This underpins cell basal geometry remodeling by anchoring the basal surface of cells to the basement membrane at specific, discrete locations. Altogether, our work shows that patterning of a basement membrane by generating discrete Laminin domains, can direct Integrin adhesion. In the retina, this pathway generates specific basal polygonal geometries to organize a complex multicellular structure in three-dimensions.
Kinetic and thermodynamic allostery in the Ras protein family
Authors: Manley Leigh J. , Lin Milo M.
Published: November 2022

Allostery, the tranfer of information between distant parts of a macromolecule, is a fundamental feature of protein function and regulation. However, allosteric mechanisms are usually not explained by protein structure, requiring information on correlated fluctuations uniquely accessible to molecular simulation. Existing work to extract allosteric pathways from molecular dynamics simulations has focused on thermodynamic correlations. Here we show how kinetic correlations (i.e. dynamical activity) encode complementary information essential to explain observed variations in allosteric regulation. We performed atomistic simulations, totalling 0.5 milliseconds, on H, K, and NRas isoforms in the apo, GTP, and GDP-bound states of Ras protein, with and without complexing to its downstream effector, Raf. We show that differences in experimentally measured intrinsic and Raf-dependent catalytic speed amongst the three isoforms can be explained by dynamical activity and entropy, respectively. We show that Switch I and Switch II are the primary components of thermodynamic and kinetic allosteric networks, consistent with the key roles of these two motifs. These communication networks are altered by the hydrolysis of the substrate gamma phosphate, leading to increased entropy in HRas loops involved in substrate release. We find that the putative allosteric region is not coupled in KRas, but is coupled to the hydrolysis arm switch II in NRas and HRas, and that the mechanism in the latter two isoforms are thermodynamic and kinetic, respectively. Binding of Raf-RBD further activates thermodynamic allostery in HRas and KRas but has limited effect on NRas. These results indicate that kinetic and thermodynamic correlations are both needed to explain protein function and allostery. These two distinct channels of allosteric regulation, and their combinatorial variability, may explain how subtle mutational differences can lead to diverse regulatory profiles among enzymatic proteins.