bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysing the effects of distance, taxon and biomass on vertebrate detections using bulk-collected carrion fly iDNA
Authors: Fernandes Kristen , Bateman Philip W. , Saunders Benjamin J. , Gibberd Mark , Bunce Michael , Bohmann Kristine , Nevill Paul
Published: April 2024

Invertebrate-derived DNA (iDNA) metabarcoding from carrion flies is a powerful, non-invasive tool that has value for assessing vertebrate diversity. However, unknowns exist around the factors that influence vertebrate detections, such as spatial limits to iDNA signals or if detections are influenced by taxonomic class or estimated biomass of the vertebrates of interest. Using a bulk-collection method, we captured flies from within a zoo and along transects extending 4 km away from this location. From 920 flies, we detected 28 vertebrate species. Of the 28 detected species, we identified 9 species kept at the zoo, 8 mammals and 1 bird, but no reptiles. iDNA detections were highly geographically localized, and only a few zoo animals were detected outside the zoo setting. However, due to the low number of detections in our dataset, we found no influence of the taxonomic group or the estimated biomass of animals on their detectability. Our data suggest that iDNA detections from bulk-collected carrion flies, at least in urban settings in Australia, are predominantly determined by geographic proximity to the sampling location. This study presents an important step in understanding how iDNA techniques can be used in biodiversity monitoring.
Ectopical expression of bacterial collagen-like protein supports its role as adhesin in host–parasite coevolution
Authors: Huessy Benjamin , Bumann Dirk , Ebert Dieter
Published: April 2024

For a profound understanding of antagonistic coevolution, it is necessary to identify the coevolving genes. The bacterium
Pasteuria
and its host, the microcrustacean
Daphnia
, are a well-characterized paradigm for co-evolution, but the underlying genes remain largely unknown. A genome-wide association study suggested a
Pasteuria
collagen-like protein 7 (Pcl7) as a candidate mediating parasite attachment and driving its coevolution with the host. Since
Pasteuria ramosa
cannot currently be genetically manipulated, we used
Bacillus thuringiensis
to express a fusion protein of a Pcl7 carboxy-terminus from
P. ramosa
and the amino-terminal domain of a
B. thuringiensis
collagen-like protein (CLP). Mutant
B. thuringiensis
(Pcl7-
Bt
) spores but not wild-type
B. thuringiensis
(WT-
Bt
) spores attached to the same site of susceptible hosts as
P. ramosa
. Furthermore, Pcl7-
Bt
spores attached readily to susceptible host genotypes, but only slightly to resistant host genotypes. These findings indicated that the fusion protein was properly expressed and folded and demonstrated that indeed the C-terminus of Pcl7 mediates attachment in a host genotype-specific manner. These results provide strong evidence for the involvement of a CLP in the coevolution of
Daphnia
and
P. ramosa
and open new avenues for genetic epidemiological studies of host–parasite interactions.
A robust algorithm for computational floating body dynamics
Authors: Roenby J. , Aliyar S. , Bredmose H.
Published: April 2024

We present a non-iterative algorithm, FloatStepper, for coupling the motion of a rigid body and an incompressible fluid in computational fluid dynamics (CFD) simulations. The purpose of the algorithm is to remove the so-called added mass instability problem, which may arise when a light, floating body interacts with a heavy fluid. The idea underlying the presented coupling method is to precede every computational time step by a series of prescribed probe body motions in which the fluid response is determined, thus revealing the decomposition of the net force and torque into two components: (i) an added mass contribution proportional to the instantaneous body acceleration and (ii) all other forces and torques. The algorithm is implemented and released as an open-source extension module to the widely used CFD toolbox, OpenFOAM, as an alternative to the existing body motion solvers. The accuracy of the algorithm is investigated with several single-phase and two-phase flow benchmark cases. The benchmarks demonstrate excellent stability properties, allowing simulations even with massless bodies. They also highlight aspects of the implementation, such as the mesh motion method, where it can be improved to further enhance the flexibility and predictive capabilities of the code.
Getting stuck in a rut as an emergent feature of a dynamic decision-making system
Authors: Warburton Matthew , Brookes Jack , Hasan Mohamed , Leonetti Matteo , Dogar Mehmet , Wang He , Cohn Anthony G. , Mushtaq Faisal , Mon-Williams Mark
Published: April 2024

Human sensorimotor decision making has a tendency to get ‘stuck in a rut’, being biased towards selecting a previously implemented action structure (hysteresis). Existing explanations propose this is the consequence of an agent efficiently modifying an existing plan, rather than creating a new plan from scratch. Instead, we propose that hysteresis is an emergent property of a system learning from the consequences of its actions. To examine this, 152 participants moved a cursor to a target on a tablet device while avoiding an obstacle. Hysteresis was observed when the obstacle moved sequentially across the screen between trials, whereby the participant continued moving around the same side of the obstacle despite it now requiring a larger movement than the alternative. Two further experiments (
n
= 20) showed an attenuation when time and resource constraints were eased. We created a simple computational model capturing probabilistic estimate updating that showed the same patterns of results. This provides, to our knowledge, the first computational demonstration of how sensorimotor decision making can get ‘stuck in a rut’ through the updating of the probability estimates associated with actions.
Comparative virulome analysis of four Staphylococcus epidermidis strains from human skin and platelet concentrates using whole genome sequencing
Authors: Yousuf Basit , Flint Annika , Weedmark Kelly , Pagotto Franco , Ramirez-Arcos Sandra
Published: April 2024

Graphical Abstract

Virulome profile of four Staphylococcus epidermidis strains isolated from platelet concentrates and human skin.
CXCR2 perturbation promotes Staphylococcus aureus implant-associated infection
Authors: Akaraphanth Mike , Nordgren Tara M. , Gries Casey M.
Published: April 2024

Introduction.
Staphylococcus aureus is the leading cause of acute medical implant infections, representing a significant modern medical concern. The success of S. aureus as a pathogen in these cases resides in its arsenal of virulence factors, resistance to multiple antimicrobials, mechanisms of immune modulation, and ability to rapidly form biofilms associated with implant surfaces. S. aureus device-associated, biofilm-mediated infections are often persistent and notoriously difficult to treat, skewing innate immune responses to promote chronic reoccurring infections. While relatively little is known of the role neutrophils play in response to acute S. aureus biofilm infections, these effector cells must be efficiently recruited to sites of infection via directed chemotaxis. Here we investigate the effects of modulating CXC chemokine receptor 2 (CXCR2) activity, predominantly expressed on neutrophils, during S. aureus implant-associated infection.

Hypothesis. We hypothesize that modulation of CXCR2 expression and/or signalling activities during S. aureus infection, and thus neutrophil recruitment, extravasation and antimicrobial activity, will affect infection control and bacterial burdens in a mouse model of implant-associated infection.

Aim. This investigation aims to elucidate the impact of altered CXCR2 activity during S. aureus biofilm-mediated infection that may help develop a framework for an effective novel strategy to prevent morbidity and mortality associated with implant infections.

Methodology. To examine the role of CXCR2 during S. aureus implant infection, we employed a mouse model of indwelling subcutaneous catheter infection using a community-associated methicillin-resistant S. aureus (MRSA) strain. To assess the role of CXCR2 induction or inhibition during infection, treatment groups received daily intraperitoneal doses of either Lipocalin-2 (Lcn2) or AZD5069, respectively. At the end of the study, catheters and surrounding soft tissues were analysed for bacterial burdens and dissemination, and Cxcr2 transcription within the implant-associated tissues was quantified.

Results. Mice treated with Lcn2 developed higher bacterial burdens within the soft tissue surrounding the implant site, which was associated with increased Cxcr2 expression. AZD5069 treatment also resulted in increased implant- and tissues-associated bacterial titres, as well as enhanced Cxcr2 expression.

Conclusion. Our results demonstrate that CXCR2 plays an essential role in regulating the severity of S. aureus implant-associated infections. Interestingly, however, perturbation of CXCR2 expression or signalling both resulted in enhanced Cxcr2 transcription and elevated implant-associated bacterial burdens. Thus, CXCR2 appears finely tuned to efficiently recruit effector cells and mediate control of S. aureus biofilm-mediated infection.
Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain
Authors: Paoli-Iseppi Ricardo De , Joshi Shweta , Gleeson Josie , Joseph Prawer Yair David , You Yupei , Agarwal Ria , Li Anran , Hull Anthea , Whitehead Eloise Marie , Seo Yoonji , Kujawa Rhea , Chang Raphael , Dutt Mriga , McLean Catriona , Parker Benjamin Leo , Clark Michael Ben
Published: April 2024

Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or products (isoforms) made by risk genes. However, how these genes contribute to disease risk and onset through altered expression and RNA splicing is not well understood. Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profiled the RNA isoform repertoire of 31 high-confidence neuropsychiatric disorder risk genes in human brain. We show most risk genes are more complex than previously reported, identifying 363 novel isoforms and 28 novel exons, including isoforms which alter protein domains, and genes such asATG13andGATAD2Awhere most expression was from previously undiscovered isoforms. The greatest isoform diversity was present in the schizophrenia risk geneITIH4. Mass spectrometry of brain protein isolates confirmed translation of a novel exon skipping event in ITIH4, suggesting a new regulatory mechanism for this gene in brain. Our results emphasize the widespread presence of previously undetected RNA and protein isoforms in brain and provide an effective approach to address this knowledge gap. Uncovering the isoform repertoire of neuropsychiatric risk genes will underpin future analyses of the functional impact these isoforms have on neuropsychiatric disorders, enabling the translation of genomic findings into a pathophysiological understanding of disease.
Unlocking the mentally ill in Indonesia: An empirical study of the effectiveness of a “Bebas Pasung” program in Central Java
Authors: Tyas Tri H. , Good Mary-Jo D. , Pratikno Bambang , Subandi M.A. , Marchira Carla R. , Good Byron J.
Published: April 2024

Background

Locking or confinement of persons with severe mental illness has been common in Indonesia. In 2010, the Ministry of Health declared a policy that persons who were locked (pasung) should be unlocked or freed (bebas) from confinement and provided mental health services. This study is an empirical evaluation of the effectiveness of oneBebas Pasungprogram in Indonesia at two-year follow-up.

Methods

From medical records in Soerojo Mental Hospital, Magelang, Central Java, 114 persons with severe mental illness who had been unlocked, treated, and returned to the community from four districts served by the hospital were identified. At two-year follow-up, 62 caregivers were able to be contacted and willing to participate in a study. Data were collected from hospital records about condition of the patient at time of ‘unlocking’ and at discharge, and primary caregivers were interviewed about the previous locking and care of the patient since return, as well as experiences of caregiving.

Results

We provide descriptive data concerning history of illness, reasons for locking, type of confinement, and care of the individual since return. 58% of those unlocked were men, 80% had diagnoses of schizophrenia, and mean age was 35. At follow-up, 24% of this sample had been re-locked; only 44% took medications regularly, including 33% of those re-locked and 47% of those not relocked. A majority cared for themselves, half were partially or fully productive, and the quality of life of family caregivers improved significantly since their family member was unlocked, treated, and returned home.

Conclusions

This program successfully unlocked, treated, and returned to their homes persons with severe mental illness living inpasungor restraints. Findings suggest such unlocking programs need to be linked more closely to community-based mental health and rehabilitation services, maintain care of the patient, and provide a path toward recovery.
Metabolomics Signatures of serotonin reuptake inhibitor (Escitalopram), serotonin norepinephrine reuptake inhibitor (Duloxetine) and Cognitive Behavior Therapy on Key Neurotransmitter Pathways in Major Depressive Disorder
Authors: Bhattacharyya Sudeepa , MahmoudianDehkordi Siamak , Sniatynski Matthew J , Belenky Marina , Marur Vasant R. , Rush A. John , Craighead W. Edward , Mayberg Helen S. , Dunlop Boadie W. , Kristal Bruce S , Kaddurah-Daouk Rima ,   Mood Disorder Precision Medicine Consortium
Published: April 2024

Metabolomics provides powerful tools that can inform about heterogeneity in disease and response to treatments. In this study, we employed an electrochemistry-based targeted metabolomics platform to assess the metabolic effects of three randomly-assigned treatments: escitalopram, duloxetine, and Cognitive Behavior Therapy (CBT) in 163 treatment-naïve outpatients with major depressive disorder. Serum samples from baseline and 12 weeks post-treatment were analyzed using targeted liquid chromatography-electrochemistry for metabolites related to tryptophan, tyrosine metabolism and related pathways. Changes in metabolite concentrations related to each treatment arm were identified and compared to define metabolic signatures of exposure. In addition, association between metabolites and depressive symptom severity (assessed with the 17-item Hamilton Rating Scale for Depression [HRSD17]) and anxiety symptom severity (assessed with the 14-item Hamilton Rating Scale for Anxiety [HRSA14]) were evaluated, both at baseline and after 12 weeks of treatment.

Significant reductions in serum serotonin level and increases in tryptophan-derived indoles that are gut bacterially derived were observed with escitalopram and duloxetine arms but not in CBT arm. These include indole-3-propionic acid (I3PA), indole-3-lactic acid (I3LA) and Indoxyl sulfate (IS), a uremic toxin. Purine-related metabolites were decreased across all arms. Different metabolites correlated with improved symptoms in the different treatment arms revealing potentially different mechanisms between response to antidepressant medications and to CBT.
Combined detrimental effect of male sex and GBA1 variants on cognitive decline in Parkinson’s Disease
Authors: Caminiti Silvia Paola , Avenali Micol , Galli Alice , Malito Rachele , Cuconato Giada , Pilotto Andrea , Padovani Alessandro , Blandini Fabio , Perani Daniela , Tassorelli Cristina , Valente Enza Maria ,   Parkinson’s Progression Markers Initiative (PPMI)
Published: April 2024

Background and Objective

Heterozygous variants in the glucocerebrosidase gene (GBA1) are the major genetic risk factor for Parkinson’s Disease (PD). GBA-PD has been associated with worse progression and higher risk of cognitive decline. Here we took advantage of the Parkinson’s Progression Markers Initiative (PPMI) to investigate whether sex could interact withGBA1carrier status in determining the clinical phenotype, with a special focus on cognitive decline.

Methods

We evaluated 118 PD subjects carryingGBA1variants (GBA-PD) and 450 with wild-type alleles (nonGBA-PD) included in the PPMI. Dopaminergic activity was assessed in a subset of 248 subjects (65%) with available123I-FP-CIT SPECT scans. Clinical features and dopaminergic activity were investigated in GBA-PD vs. nonGBA-PD groups, upon stratification by sex. PD subjects were followed for up to 6.5Dyears (median 6Dyears). Cox regression was used to model the hazard ratio (HR) of (1)GBA1genotype, (2) sex, (3) gene-by-sex interaction on cognitive decline at follow-up.

Results

Regardless of genotype, men suffering from PD exhibited higher motor disability while women showed more autonomic dysfunction. At baseline, GBA-PD showed more severe motor and non-motor features, and reduced dopamine uptake in the bilateral ventral putamen compared to nonGBA-PD. Within the GBA-PD group, males had higher occurrence of REM sleep behavior disorder and memory deficits. Of note, GBA-PD females showed a greater striatal dopaminergic deficit compared to males, despite presenting similar motor impairment. In longitudinal assessment, Cox Regression revealed that male sex (HR = 1.7),GBA1carrier status (HR =1.6) and, most importantly, GBA-by-male sex interaction (HR = 2.3) were significantly associated with a steeper cognitive decline. Upon stratification forGBA1variant class, both “severe” and “mild” variants were associated with increased risk of cognitive decline, again more relevant in males (HR = 2.3).

Discussion

We show, for the first time, that male sex andGBA1carrier status have an additive value in increasing the risk of cognitive decline in PD, despite the heightened dopaminergic vulnerability observed in GBA-PD females. The effect of sex onGBA1-related pathology warrants further examination and should be considered in future trials design and patients’ selection.
PersistentMycobacterium tuberculosisbioaerosol release in a tuberculosis-endemic setting
Authors: Dinkele Ryan , Gessner Sophia , Patterson Benjamin , McKerry Andrea , Hoosen Zeenat , Vazi Andiswa , Seldon Ronnett , Koch Anastasia , Warner Digby F. , Wood Robin
Published: April 2024

Pioneering studies linking symptomatic disease and cough-mediated release ofMycobacterium tuberculosis(Mtb) established the infectious origin of tuberculosis (TB), simultaneously informing the pervasive notion that pathology is a prerequisite forMtbtransmission. Our prior work has challenged this assumption: by sampling TB clinic attendees, we detected equivalent release ofMtb-containing bioaerosols by confirmed TB patients and individuals not receiving a TB diagnosis, and we demonstrated a time-dependent reduction inMtbbioaerosol positivity during six-months’ follow-up, irrespective of anti-TB chemotherapy. Now, by extending bioaerosol sampling to a randomly selected community cohort, we show thatMtbrelease is common in a TB-endemic setting: of 89 participants, 79.8% (71/89) producedMtbbioaerosols independently of QuantiFERON-TB Gold status, a standard test forMtbinfection; moreover, during two-months’ longitudinal sampling, only 2% (1/50) were seriallyMtbbioaerosol negative. These results necessitate a reframing of the prevailing paradigm ofMtbtransmission and infection, and may explain the current inability to elucidateMtbtransmission networks in TB-endemic regions.

Elucidating chains ofMycobacterium tuberculosistransmission is limited by a dependence on linking sputum-positive tuberculosis cases. Here, we report persistentM. tuberculosisbioaerosol release in the majority of a randomly selected community cohort. The contribution to tuberculosis transmission is unknown.
Elevating levels of the endocannabinoid 2-arachidonoylglycerol blunts opioid reward but not analgesia
Authors: Martínez-Rivera Arlene , Fetcho Robert N. , Birmingham Lizzie , Jiu Jin X , Yang Ruirong , Foord Careen , Scala-Chávez Diego , Mekawy Narmin , Pleil Kristen , Pickel Virginia M. , Liston Conor , Castorena Carlos M. , Levitz Joshua , Pan Ying-Xian , Briand Lisa A. , Rajadhyaksha Anjali M. , Lee Francis S.
Published: April 2024

Converging findings have established that the endocannabinoid (eCB) system serves as a possible target for the development of new treatments for pain as a complement to opioid-based treatments. Here we show in male and female mice that enhancing levels of the eCB, 2-arachidonoylglycerol (2-AG), through pharmacological inhibition of its catabolic enzyme, monoacylglycerol lipase (MAGL), either systemically or in the ventral tegmental area (VTA) with JZL184, leads to a substantial attenuation of the rewarding effects of opioids in male and female mice using conditioned place preference and self-administration paradigms, without altering their analgesic properties. These effects are driven by CB1 receptors (CB1Rs) within the VTA as VTA CB1R conditional knockout, counteracts JZL184’s effects. Conversely, pharmacologically enhancing the levels of the other eCB, anandamide (AEA), by inhibition of fatty acid amide hydrolase (FAAH) has no effect on opioid reward or analgesia. Using fiber photometry with fluorescent sensors for calcium and dopamine (DA), we find that enhancing 2-AG levels diminishes opioid reward-related nucleus accumbens (NAc) activity and DA neurotransmission. Together these findings reveal that 2-AG counteracts the rewarding properties of opioids and provides a potential adjunctive therapeutic strategy for opioid-related analgesic treatments.
Microbial ecology and site characteristics underlie differences in salinity-methane relationships in coastal wetlands
Authors: Bueno de Mesquita Clifton P. , Hartman Wyatt H. , Ardón Marcelo , Bernhardt Emily S. , Neubauer Scott C. , Weston Nathaniel B. , Tringe Susannah G.
Published: April 2024

Methane (CH4) is a potent greenhouse gas emitted by archaea in anaerobic environments such as wetland soils. Tidal freshwater wetlands are predicted to become increasingly saline as sea levels rise due to climate change. Previous work has shown that increases in salinity generally decrease CH4emissions, but with considerable variation, including instances where salinization increased CH4flux. We measured microbial community composition, biogeochemistry, and CH4flux from field samples and lab experiments from four different sites across a wide geographic range. We sought to assess how site differences and microbial ecology affect how CH4emissions are influenced by salinization. CH4flux was generally, but not always, positively correlated with CO2flux, soil carbon, ammonium, phosphate, and pH. Methanogen guilds were positively correlated with CH4flux across all sites, while methanotroph guilds were both positively and negatively correlated with CH4depending on site. There was mixed support for negative relationships between CH4fluxes and concentrations of alternative electron acceptors and abundances of taxa that reduce them. CH4/salinity relationships ranged from negative, to neutral, to positive and appeared to be influenced by site characteristics such as pH and plant composition, which also likely contributed to site differences in microbial communities. The activity of site-specific microbes that may respond differently to low-level salinity increases is likely an important driver of CH4/salinity relationships. Our results suggest several factors that make it difficult to generalize CH4/salinity relationships and highlight the need for paired microbial and flux measurements across a broader range of sites.
Single-cell analysis of lung epithelial cells reveals age and cell population-specific responses to SARS-CoV-2 infection in ciliated cells
Authors: Osborn Raven M. , Anderson Christopher S. , Leach Justin R. , Chu ChinYi , Dewhurst Stephen , Mariani Thomas J. , Thakar Juilee
Published: April 2024

The ability of SARS-CoV-2 to evade antiviral immune signaling in the airway contributes to the severity of COVID-19 disease. Additionally, COVID-19 is influenced by age and has more severe presentations in older individuals. This raises questions about innate immune signaling as a function of lung development and age. Therefore, we investigated the transcriptome of different cell populations of the airway epithelium using pediatric and adult lung tissue samples from the LungMAP Human Tissue Core Biorepository. Specifically, lung lobes were digested and cultured into a biomimetic model of the airway epithelium on an air-liquid interface. Cells were then infected with SARS-CoV-2 and subjected to single-cell RNA sequencing. Transcriptional profiling and differential expression analysis were carried out using Seurat.

The clustering analysis identified several cell populations: club cells, proliferating epithelial cells, multiciliated precursor cells, ionocytes, and two biologically distinct clusters of ciliated cells (FOXJ1highand FOXJ1low). Interestingly, the two ciliated cell clusters showed different infection rates and enrichment of processes involved in ciliary biogenesis and function; we observed a cell-type-specific suppression of innate immunity in infected cells from the FOXJ1lowsubset. We also identified a significant number of genes that were differentially expressed in lung cells derived from children as compared to adults, suggesting the differential pathogenesis of SARS-CoV-2 infection in children versus adults. We discuss how this work can be used to identify drug targets to modulate molecular signaling cascades that mediate an innate immune response and begin to understand differences in COVID-19 outcomes for pediatric vs. adult populations.

Importance

Viral innate immune evasion leads to uncontrolled viral spread in infected tissues and increased pathogenicity in COVID-19. Understanding the dynamic of the antiviral signaling in lung tissues may help us to understand which molecular signals lead to more severe disease in different populations, particularly considering the enhanced vulnerability of older populations. This study provides foundational insight into the age-related differences in innate immune responses to SARS-CoV-2, identifying distinct patterns of infection and molecular signaling in different cell populations of airway epithelial cells from pediatric and adult lung tissues. The findings provide a deeper understanding of age-related differences in COVID-19 pathology and pave the way for developing targeted therapies.
Data-driven simple agent-based model of scratch assays on healthy and keloid fibroblasts
Authors: Urcun Stéphane , Rolin Gwenaël , Eftimie Raluca , Lozinski Alexei , Bordas Stéphane P.A.
Published: April 2024

In this study we propose a novel agent-based model to reproduce and propose new hypotheses on the biological mechanisms of cell-cell interactions and cell migration from data obtained during scratch assay with healthy and keloid fibroblasts. The advantage of the agent-based model we propose in this paper lies in its simplicity: only three governing parameters. We conducted a parametric sensitivity analysis and we incorporated the evaluation of contact inhibition of locomotion, aligning with the observed loss during malignant invasion. To study invasion modalities, we conductedin vitrowound healing assays using healthy and pseudo-tumoral (keloid) fibroblasts under diverse conditions: control, macrophage type 1 secretome, and macrophage type 2 secretome. Mitomycin inhibition of proliferation isolated the contribution of migration to wound filling. Our agent-based mathematical model describes configurations based on our microscopy imaging and statistical data, which enables quantitative comparisons between our experimental and numerical results. Calibration and evaluation were performed on the same experiments, enriched by external datasets. With only three governing parameters, our model not only demonstrated good agreement (8.78% to 18.75% error) with external evaluation datasets for all experimental configurations but also provided us with a nuanced understanding of keloid fibroblast behavior during wound healing, especially regarding contact inhibition dynamics.
Polar confinement of a macromolecular machine by an SRP-type GTPase
Authors: Dornes Anita , Schmidt Lisa Marie , Mais Christopher-Nils , Hook John C. , Pané-Farré Jan , Kressler Dieter , Thormann Kai , Bange Gert
Published: April 2024

The SRP-type GTPase FlhF, along with its regulator FlhG, orchestrates the localization and quantity of flagella in bacteria. Our study reveals that FlhF anchors developing flagellar structures to the polar landmark protein HubP/FimV, thereby restricting their formation to the cell pole. Specifically, the GTPase domain of FlhF interacts with HubP, while an as-yet-uncharacterized structured domain at the N-terminus of FlhF binds to FliG. This FlhF-bound FliG subsequently engages with the MS-ring protein FliF, but not with the C-ring proteins FliM/FliN. Consequently, FlhF’s interaction with HubP/FliG recruits a functional FliF/FliG complex to the pole, while FlhG’s modulation of FlhF controls FliG’s interaction with FliM/FliN, thereby regulating the progression of flagellar assembly at the pole.

Significance statement

Flagella serve as bacterial locomotion organelles, with their number and location, known as the flagellation pattern, being species-specific and among the earliest taxonomic criteria in microbiology. Bacteria replicate their flagellation pattern with each cell division. Flagella localization and abundance depends on the SRP-type GTPase FlhF, together with its regulator FlhG. Our study clarifies the mechanism through which FlhF coordinates the polar positioning of the flagellum, working in tandem with the polar landmark protein HubP and aiding in the assembly of flagellar MS-ring/C-ring components at the cellular pole.
Characterization and classification of fine-resolution soil profile for precision agriculture using random forest and self-organizing map
Authors: Elias Ani A. , Sharma Megha , Goel Shailendra
Published: April 2024

The availability of high throughput soil profile information is an important component in precision agriculture to perform efficient soil management for sustainable production. We collected 14 soil physiochemical features from Nagpur, Pune, and Haveri, representing target environments of safflower cultivation and also from our experiment station at Delhi, at fine resolution and created graphical maps to depict the variability. Additionally, we evaluated the predictive ability of two statistical learning models, random forest (RF) and self-organizing maps (SOM) against multinomial regression models for correctly classifying the soil profile. Clustering was performed around the medoids produced from the dissimilarity matrices of these models using partitioning around medoids (PAM) model. The robustness, versatility, and predictive ability of models in correctly classifying the soil profile to clusters were then tested using cross-validation which was repeated 100 times. This study was performed using training data with proportionate size varying from 60 to 95%, and increasing the unit area of observation up to nine times (or decreasing the total number of observations up to a ninth). RF model was found to be the best performing with average prediction accuracy above 85% in all settings which reached close to 100% in some settings. The predictive ability of all the models was maintained even when only the most influencing six variables were used for classification. The optimal training population size for prediction was found to be 70 – 80%. Based on our study, it is recommended to i) collect fine resolution edaphic features from a marginal farm before crop season, ii) use RF or SOM model to identify the most influencing features distinguishing the soil samples iii) expand the area of sample collection, find values for the most influencing features, and use RF model to correctly predict the class to which the new set of the soil belongs to.

Graphical abstract
Interaction between ciliary component proteins fromChlamydomonasrevealed by CRISPR/CAS9, cryo-electron tomography and mass spectrometry
Authors: Luo Leo , Zimmermann Noemi , Noga Akira , Leitner Alexander , Ishikawa Takashi
Published: April 2024

To understand molecular mechanism of ciliary beating motion, knowledge of location, interaction and dynamics of >400 component proteins are indispensable. While recent progress of structural biology revealed conformation and localization of >100 proteins, we still need to investigate their networking, art of their interaction and assembly mechanism. We applied CRISPR/CAS9 genome editing technique to the green algaeChlamydomonasto engineer a deletion mutant of a ciliary component, FAP263, located at the distal protrusion, and examined it structurally by cryo-electron tomography (cryo-ET) and mass spectrometry (MS). Cryo-ET and atomic model fitting demonstrated that the FAP263 deletion mutant lacks additional components, FAP78, and FAP184. Unassigned density near FAP263 in the cryo-ET map of WT cilia is likely FAP151, as suggested by cross-linking mass spectrometry. Based on the structure, we modeled how these four proteins might form a complex. Furthermore, it was shown that dynein f phosphorylation is inhibited in the FAP263 mutant, indicating an important role of this protein complex for dynein f phosphorylation. Our study demonstrates a novel approach to investigate protein networking inside cilia.
COA8 is a COX10-binding protein involved in the early biogenesis of cytochrome c oxidase
Authors: Brischigliaro Michele , Cunatova Kristyna , Cabrera-Orefice Alfredo , Pei Jimin , Franchin Cinzia , Roverso Marco , Povea-Cabello Suleva , Bogialli Sara , Arrigoni Giorgio , Arnold Susanne , Cong Qian , Zeviani Massimo , Viscomi Carlo , Fernandez-Vizarra Erika
Published: April 2024

Human cytochrome c oxidase (COX) is composed of fourteen subunits, only two of which are catalytic. The functions of a myriad of accessory factors are needed to put together the structural subunits, as well as for the formation of the active centers. The molecular roles of most of these factors are still unknown, even if they are essential for COX function since their defects cause severe mitochondrial disease. COA8 is exclusively found in metazoa and loss-of-function genetic variants cause mitochondrial encephalopathy and COX deficiency in humans. In this work, we have resolved the function of COA8, as a factor that specifically binds to COX10, the heme O synthase. This interaction is necessary not only for the stabilization of human COX10, but also to guarantee its catalytic activity as the first step for the synthesis of the heme A cofactor, which is a crucial component of the COX catalytic center.
Experience-induced drift in the neural coding of individual differences in perception
Authors: Maigler Kathleen C. , Crouse Ethan , Stone Bradly T. , Svedberg Daniel , Katz Donald B.
Published: April 2024

Like humans, no two rodents like precisely the same tastes. Here, we ask whether these individual differences determine cortical taste responses, late epochs of which “code” palatability. We show that rats’ individual preferences match late-epoch responses with a fidelity significantly higher than that expected on the basis of canonical palatability rankings. A single tasting session, however, induces “neural drift,” such that previously-assessed preferences are no longer reflected in cortical activity.
Modulation of endogenous opioid signaling by inhibitors of puromycin sensitive aminopeptidase
Authors: Singh Rohit , Jiang Rongrong , Williams Jessica , Dobariya Prakashkumar , Hanak Filip , Xie Jiashu , Rothwell Patrick E. , Vince Robert , More Swati S.
Published: April 2024

The endogenous opioid system regulates pain through local release of neuropeptides and modulation of their action on opioid receptors. However, the effect of opioid peptides, the enkephalins, is short-lived due to their rapid hydrolysis by enkephalin-degrading enzymes. In turn, an innovative approach to the management of pain would be to increase the local concentration and prolong the stability of enkephalins by preventing their inactivation by neural enkephalinases such as puromycin sensitive aminopeptidase (PSA). Our previous structure-activity relationship studies offered the S-diphenylmethyl cysteinyl derivative of puromycin (20) as a nanomolar inhibitor of PSA. This chemical class, however, suffered from undesirable metabolism to nephrotoxic puromycin aminonucleoside (PAN). To prevent such toxicity, we designed and synthesized 5′-chloro substituted derivatives. The compounds retained the PSA inhibitory potency of the corresponding 5′-hydroxy analogs and had improved selectivity toward PSA. In vivo treatment with the lead compound19caused significantly reduced pain response in antinociception assays, alone and in combination with Met-enkephalin. The analgesic effect was reversed by the opioid antagonist naloxone, suggesting the involvement of opioid receptors. Further, PSA inhibition by compound19in brain slices caused local increase in endogenous enkephalin levels, corroborating our rationale. Pharmacokinetic assessment of compound19showed desirable plasma stability and identified the cysteinyl sulfur as the principal site of metabolic liability. We gained additional insight into inhibitor-PSA interactions by molecular modeling, which underscored the importance of bulky aromatic amino acid in puromycin scaffold. The results of this study strongly support our rationale for the development of PSA inhibitors for effective pain management.
Orbitofrontal high-gamma reflects spike-dissociable value and decision mechanisms
Authors: Sharma Dixit , Lupkin Shira M. , McGinty Vincent B.
Published: April 2024

The orbitofrontal cortex (OFC) plays a crucial role in value-based decision-making. While previous research has focused on spiking activity in OFC neurons, the role of OFC local field potentials (LFPs) in decision-making remains unclear. LFPs are important because they can reflect synaptic and subthreshold activity not directly coupled to spiking, and because they are potential targets for less invasive forms of brain-machine interface (BMI). We recorded LFPs and spiking activity using multi-channel vertical probes while monkeys performed a two-option value-based decision-making task. We compared the value- and decision-coding properties of high-gamma range LFPs (HG, 50-150 Hz) to the coding properties of spiking multi-unit activity (MUA) recorded concurrently on the same electrodes. Results show that HG and MUA both represent the values of decision targets, and that their representations have similar temporal profiles in a trial. However, we also identified value-coding properties of HG that were dissociable from the concurrently-measured MUA. On average across channels, HG amplitude increased monotonically with value, whereas the average value encoding in MUA was net neutral. HG also encoded a signal consistent with a comparison between the values of the two targets, a signal which was much weaker in MUA. In individual channels, HG was better able to predict choice outcomes than MUA; however, when simultaneously recorded channels were combined in population-based decoder, MUA provided more accurate predictions than HG. Interestingly, HG value representations were accentuated in channels in or near shallow cortical layers, suggesting a dissociation between neuronal sources of HG and MUA. In summary, we find that HG signals are dissociable from MUA with respect to cognitive variables encoded in prefrontal cortex, evident in the monotonic encoding of value, stronger encoding of value comparisons, and more accurate predictions about behavior. High-frequency LFPs may therefore be a viable – or even preferable – target for BMIs to assist cognitive function, opening the possibility for less invasive access to mental contents that would otherwise be observable only with spike-based measures.
Limb loss and specialized leg dynamics in tiny water-walking insects
Authors: O’Neil Johnathan N. , Yung Kai Lauren , Difini Gaetano , Rohilla Pankaj , Bhamla M. Saad
Published: April 2024

The air-water of the planet’s water bodies, such as ponds, lakes and streams, presents an uncertain ecological niche with predatory threats from above and below. AsMicroveliamove across the water surface in small ponds, they face potential injury from attacks by birds, fish, and underwater invertebrates. Thus, our study investigates the effects of losing individual or pairs of tarsi on theMicrovelia’sability to walk on water. Removal of both hind tarsi causesMicrovelia spp. to rock their bodies (yaw) while running across the water surface at ±19°, compared to ±7° in non-ablated specimens. This increase in yaw, resulting from the removal of hind tarsi, indicates thatMicroveliause their hind legs as ‘rudders’ to regulate yaw, originating from the contralateral middle legs’ strokes on the water’s surface through an alternating tripod gait. Ablation of the ipsilateral middle and hind tarsi disrupts directionality, makingMicroveliaturn in the direction of their intact limbs. This loss of directionality does not occur with the removal of contralateral middle and hind tarsi. However,Microvelialose their ability to use the alternating tripod gait to walk for water walking on the day of contralateral ablation. Remarkably, by the next dayMicroveliaadapt and regain the ability to walk on water using the alternating tripod gait. Our findings elucidate the specialized leg dynamics within the alternating tripod gait ofMicrovelia spp., and their adaptability to tarsal loss. This research could guide the development and design strategies of small, adaptive, and resilient micro-robots that can adapt to controller malfunction or actuator damage for walking on water and terrestrial surfaces.
Stored Elastic Bending Tension as a Mediator of Embryonic Body Folding
Authors: Zaher Mira , Yelin Ronit , Arraf Alaa A. , Jadon Julian , Asleh Manar Abboud , Goltzman Sivan , Shaulov Lihi , Reinhardt Dieter P. , Schultheiss Thomas M.
Published: April 2024

During development, amniote vertebrate embryos transform from a flat, multi-layered sheet into a three-dimensional cylindrical form, through ventral folding of the lateral sides of the sheet (the lateral plate, LP) and their fusion in the ventral midline. Although this basic aspect of vertebrate body plan formation has long been described, it is not understood at the mechanistic level. Each side of the LP is comprised of two tissue layers: a dorsal somatopleure (Sop) of pseudostratified coelomic epithelium, extracellular matrix (ECM) and ectoderm, and a ventral splanchnopleure (Spl) of similar construction except with endoderm instead of ectoderm. Using a chick embryo slice system we find that the flat stage is actually a poised balance of opposing elastic bending tensions, with dorsal bending tension in the Sop opposing ventral bending tension in the Spl. An intact extracellular matrix is required for generating the bending tensions, as localized enzymatic digestion of Sop or Spl ECM dissipates tension, while removal of the endodermal or ectodermal layers has no effect. As development proceeds, the Sop undergoes Epithelial-Mesenchymal Transition, ECM fragmentation and dissipation of dorsal bending tension, while the Spl ECM and ventral bending tension remain intact, thus changing the balance of bending forces in the LP to promote ventral folding. Consistent with these findings, interference with the elastic ECM component fibrillin in the Splin vivoreduces stored bending tension and perturbs ventral body folding. A generalizable conceptual model is presented in which embryonic growth, in the context of specific embryonic geometrical constraints, leads to accumulation of bending tension in the LP ECM, which is harnessed to drive body folding.
Development of BODIPY-based fluorescent probes for highly selective amino acid identification
Authors: Hendrick Nathaniel , Martin Andrew , Chan Andrew , Lenihan Jason , Reiter Harrison , Clough Mitchell , Jiang Lian , Whaley Eddie , Huh Yoo Jeong , McNeely James , Chen Anderson , Emili Andrew , Beeler Aaron
Published: April 2024

Amino acid sensing is a powerful tool for intra- and extra-cellular assays. We report herein the generation and optimization of bioconjugatable fluorescent reporter for pan-amino acid sensing, the OMNI probe, that through inductive electronics produces a unique photophysical response upon coupling to the α-amino group of an amino acid depending on the identity of the adjacent side chain. Using an auto-photocatalyzed Meerwein arylation reaction, we created a library of bis-arylated 8-methylthio-BODIPY dye derivatives exhibiting improved spectral variation, brightness, dynamic range, robustness, water solubility, and reactivity. Aryl groups with optimal photophysical behaviors were combined to create asymmetric versions conferring high spectral range, brightness, and water solubility. Combining aryl group modifications yielded a set of engineered asymmetric probes that achieved complete spectral resolution in a multi-variable analysis (fluorescent emission, lifetime, brightness) for all twenty native amino acid-dye conjugates while increasing reactivity toward amino acids in aqueous buffer. With our robust OMNI probe design, pan-amino acid resolution and identification through high sensitivity fluorescence down to single molecules is now routinely possible for diverse potential applications including protein sequencing.
Opposing actions of JIP4 and RILPL1 provide antagonistic motor force to dynamically regulate membrane reformation during lysosomal tubulation/sorting driven by LRRK2
Authors: Bonet-Ponce Luis , Tegicho Tsion , Beilina Alexandra , Kluss Jillian H. , Li Yan , Cookson Mark R.
Published: April 2024

Lysosomes are dynamic cellular structures that adaptively remodel their membrane in response to stimuli, including membrane damage. We previously uncovered a process we term LYTL (LYsosomal Tubulation/sorting driven by Leucine-Rich Repeat Kinase 2 [LRRK2]), wherein damaged lysosomes generate tubules sorted into mobile vesicles. LYTL is orchestrated by the Parkinson’s disease-associated kinase LRRK2 that recruits the motor adaptor protein and RHD family member JIP4 to lysosomes via phosphorylated RAB proteins. To identify new players involved in LYTL, we performed unbiased proteomics on isolated lysosomes after LRRK2 kinase inhibition. Our results demonstrate that there is recruitment of RILPL1 to ruptured lysosomes via LRRK2 activity to promote phosphorylation of RAB proteins at the lysosomal surface. RILPL1, which is also a member of the RHD family, enhances the clustering of LRRK2-positive lysosomes in the perinuclear area and causes retraction of LYTL tubules, in contrast to JIP4 which promotes LYTL tubule extension. Mechanistically, RILPL1 binds to p150Glued, a dynactin subunit, facilitating the transport of lysosomes and tubules to the minus end of microtubules. Further characterization of the tubulation process revealed that LYTL tubules move along tyrosinated microtubules, with tubulin tyrosination proving essential for tubule elongation. In summary, our findings emphasize the dynamic regulation of LYTL tubules by two distinct RHD proteins and pRAB effectors, serving as opposing motor adaptor proteins: JIP4, promoting tubulation via kinesin, and RILPL1, facilitating tubule retraction through dynein/dynactin. We infer that the two opposing processes generate a metastable lysosomal membrane deformation that facilitates dynamic tubulation events.