bluuebunny/crossref_metadata_2025 huggingface dataset:
An economic evaluation ofWolbachiadeployments for dengue control in Vietnam
Authors: Turner Hugo C , Quyen Duong Le , Dias Reynold , Huong Phan Thi , Simmons Cameron P. , Anders Katherine L
Published: February 2023

Background

Dengue is a major public health challenge and a growing problem due to climate change. The release ofAedes aegyptimosquitoes infected with the intracellular bacteriumWolbachiais a novel form of vector control against dengue. However, there remains a need to evaluate the benefits of such an intervention at a large scale. In this paper, we evaluate the potential economic impact and cost-effectiveness of scaledWolbachiadeployments as a form of dengue control in Vietnam – targeted at the highest burden urban areas.

Methods

Ten settings within Vietnam were identified as priority locations for potential futureWolbachiadeployments (using a population replacement strategy). The effectiveness ofWolbachiadeployments in reducing the incidence of symptomatic dengue cases was assumed to be 75%. We assumed that the intervention would maintain this effectiveness for at least 20 years (but tested this assumption in the sensitivity analysis). A cost-utility analysis and cost-benefit analysis were conducted.

Results

From the health sector perspective, theWolbachiaintervention was projected to cost US$420 per disability-adjusted life year (DALY) averted. From the societal perspective, the overall cost-effectiveness ratio was negative, i.e. the economic benefits outweighed the costs. These results are contingent on the long-term effectiveness ofWolbachiareleases being sustained for 20 years. However, the intervention was still classed as cost-effective across the majority of the settings when assuming only 10 years of benefits.

Conclusion

Overall, we found that targeting high burden cities withWolbachiadeployments would be a cost-effective intervention in Vietnam and generate notable broader benefits besides health gains.
Adaptive metrics for an evolving pandemic A dynamic approach to area-level COVID-19 risk designations
Authors: Bilinski Alyssa M. , Salomon Joshua A. , Hatfield Laura A.
Published: February 2023

Throughout the COVID-19 pandemic, policymakers have proposed risk metrics, such as the CDC Community Levels, to guide local and state decision-making. However, risk metrics have not reliably predicted key outcomes and often lack transparency in terms of prioritization of false positive versus false negative signals. They have also struggled to maintain relevance over time due to slow and infrequent updates addressing new variants and shifts in vaccine- and infection-induced immunity. We make two contributions to address these weaknesses of risk metrics. We first present a framework to evaluate predictive accuracy based on policy targets related to severe disease and mortality, allowing for explicit preferences toward false negative versus false positive signals. This approach allows policymakers to optimize metrics for specific preferences and interventions. Second, we propose a novel method to update risk thresholds in real-time. We show that this adaptive approach to designating areas as “high risk” improves performance over static metrics in predicting 3-week-ahead mortality and intensive care usage at both state and county levels. We also demonstrate that with our approach, using only new hospital admissions to predict 3-week-ahead mortality and intensive care usage has performed consistently as well as metrics that also include cases and inpatient bed usage. Our results highlight that a key challenge for COVID-19 risk prediction is the changing relationship between indicators and outcomes of policy interest. Adaptive metrics therefore have a unique advantage in a rapidly evolving pandemic context.

Significance Statement

In the rapidly-evolving COVID-19 pandemic, public health risk metrics often become less relevant over time. Risk metrics are designed to predict future severe disease and mortality based on currently-available surveillance data, such as cases and hospitalizations. However, the relationship between cases, hospitalizations, and mortality has varied considerably over the course of the pandemic, in the context of new variants and shifts in vaccine- and infection-induced immunity. We propose an adaptive approach that regularly updates metrics based on the relationship between surveillance inputs and future outcomes of policy interest. Our method captures changing pandemic dynamics, requires only hospitalization input data, and outperforms static risk metrics in predicting high-risk states and counties.
Quantification of early nonpharmaceutical interventions aimed at slowing transmission of Coronavirus Disease 2019 in the Navajo Nation and surrounding states (Arizona, Colorado, New Mexico, and Utah)
Authors: Miller Ely F. , Neumann Jacob , Chen Ye , Mallela Abhishek , Lin Yen Ting , Hlavacek William S. , Posner Richard G.
Published: February 2023

During an early period of the Coronavirus Disease 2019 (COVID-19) pandemic, the Navajo Nation, much like New York City, experienced a relatively high rate of disease transmission. Yet, between January and October 2020, it experienced only a single period of growth in new COVID-19 cases, which ended when cases peaked in May 2020. The daily number of new cases slowly decayed in the summer of 2020 until late September 2020. In contrast, the surrounding states of Arizona, Colorado, New Mexico, and Utah all experienced at least two periods of growth in the same time frame, with second surges beginning in late May to early June. To investigate the causes of this difference, we used a compartmental model accounting for distinct periods of non-pharmaceutical interventions (NPIs) (e.g., behaviors that limit disease transmission) to analyze the epidemic in each of the five regions. We used Bayesian inference to estimate region-specific model parameters from regional surveillance data (daily reports of new COVID-19 cases) and to quantify uncertainty in parameter estimates and model predictions. Our results suggest that NPIs in the Navajo Nation were sustained over the period of interest, whereas in the surrounding states, NPIs were relaxed, which allowed for subsequent surges in cases. Our region-specific model parameterizations allow us to quantify the impacts of NPIs on disease incidence in the regions of interest.
The role of serum brain injury biomarkers in individuals with a mild-to-moderate COVID infection and Long-COVID - results from the prospective population-based COVI-GAPP study
Authors: Telser Julia , Grossmann Kirsten , Weideli Ornella C , Hillmann Dorothea , Aeschbacher Stefanie , Wohlwend Niklas , Velez Laura , Kuhle Jens , Maleska Aleksandra , Benkert Pascal , Risch Corina , Conen David , Risch Martin , Risch Lorenz
Published: February 2023

Background

During and after mild (no hospitalization) or moderate (hospitalization without ICU) SARS-CoV-2 infections, a wide range of symptoms, including neurological disorders have been reported. It is, however, unknown if these neurological symptoms are associated with brain injury and whether brain injury and related symptoms also emerge in patients suffering from Long-COVID. Neuronal biomarkers such as serum neurofilament light chain and glial fibrillary acidic protein can be used to elucidate neuro-axonal and astroglial injuries. We therefore investigated whether these biomarkers are associated with the COVID-19 infection status (mild-to-moderate), the associated symptoms and Long-COVID.

Methods

From 146 individuals of the general population with a post-acute, mild-to-moderate SARS-CoV-2 infection, serum neurofilament light chain (sNfL; marker of intra-axonal neuronal injury) and serum glial fibrillary acidic protein (sGFAP; marker of astrocytic activation/injury) were measured. Samples were taken before, during and after (five and ten months) a SARS-CoV-2 infection. Individual symptoms and Long-COVID status were assessed using questionnaires.

Results

Neurological symptoms were described for individuals after a mild and moderate COVID-19 infection, however, serum markers of brain injury (sNfL/sGFAP) did not change after an infection (sNfL:P= 0.74; sGFAP:P= 0.24) and were not associated with headache (P= 0.51), fatigue (P= 0.93), anosmia (P= 0.77) and ageusia (P= 0.47). In participants with Long-COVID, sGFAP (P= 0.038), but not sNfL (P= 0.58) significantly increased but was not associated with neurological symptoms.

Conclusion

Neurological symptoms in individuals after a mild-to-moderate SARS-CoV-2 infection with and without Long-COVID were not associated with brain injury, although there was some astroglial injury observed in Long-COVID patients.

Funding

The COVI-GAPP study received grants from the Innovative Medicines Initiative (IMI grant agreement number 101005177), the Princely House of Liechtenstein, the government of the Principality of Liechtenstein, and the Hanela Foundation (Switzerland). None of the funders played a role in the study design, data collection, data analysis, data interpretation, writing of the report, or decision to publish.
Accumulation of Tau in Extracellular Vesicles Disturbs the Astrocytic Mitochondrial System
Authors: Perbet Romain , Zufferey Valentin , Leroux Elodie , Parietti Enea , Espourteille Jeanne , Culebras Lucas , Perriot Sylvain , Pasquier Renaud Du , Bégard Séverine , Deramecourt Vincent , Déglon Nicole , Toni Nicolas , Buée Luc , Colin Morvane , Richetin Kevin
Published: February 2023

Tauopathies are neurodegenerative disorders involving the accumulation of tau isoforms in cell subpopulations such as astrocytes. The origins of the 3R and 4R isoforms of tau that accumulate in astrocytes remain unclear.

Extracellular vesicles (EVs) were isolated from primary neurons overexpressing 1N3R or 1N4R tau or from human brain extracts (progressive supranuclear palsy or Pick disease patients or controls) and characterized (electron microscopy, nanoparticle tracking analysis (NTA), proteomics). After the isolated EVs were added to primary astrocytes or human iPSC-derived astrocytes, tau transfer and mitochondrial system function were evaluated (ELISA, immunofluorescence, MitoTracker staining). We demonstrated that neurons in which 3R or 4R tau accumulated had the capacity to transfer tau to astrocytes and that EVs were essential for the propagation of both isoforms of tau. Treatment with tau-containing EVs disrupted the astrocytic mitochondrial system, altering mitochondrial morphology, dynamics and redox state. Although similar levels of 3R and 4R tau were transferred, 3R tau-containing EVs were significantly more damaging to astrocytes than 4R tau-containing EVs. Moreover, EVs isolated from the brain fluid of patients with different tauopathies affected mitochondrial function in astrocytes derived from human iPSCs. Our data highlight that tau pathology spreads to surrounding astrocytes via EVs-mediated transfer and modify their function.
Cytokinin response regulatorARR16regulates seed coat permeability in Arabidopsis natural accessions
Authors: Sano Naoto , Domergue Frédéric , North Helen M.
Published: February 2023

The seed coat that encases the embryo is constituted from multiple specialized-cell layers and their permeability significantly influences seed quality traits that have major agronomic impact. The regulatory mechanisms that modulate seed coat permeability are, however, not well understood. Here, we identified a novel regulatory gene for seed permeability through a genome wide association study (GWAS) in Arabidopsis based on image analysis of tetrazolium staining.Type-A ARABIDOPSIS RESPONSE REGULATOR 16(ARR16) is a component of the signal transduction pathway for the plant hormone cytokinins (CKs), and in addition to less permeable seed coats,arr16mutant seeds were larger, had a longer lifespan, and more suberin phenolics, the hydrophobic lipid biopolyester components of cell walls that act as a water-repellant. Moreover, double mutants in CK receptorARABIDOPSIS HISTIDINE KINASEgenes, notablyahk2 ahk4andahk3 ahk4, showed similar seed phenotypes to those ofarr16. Based on naturally-occurring variation in theARR16gene, eight haplotypes were detected and associated with permeable or impermeable phenotypes. Permeable haplotypes had significantly lower suberin autofluorescence compared to impermeable haplotypes. RT-qPCR analysis demonstrated thatARR16transcripts were highly abundant in developing seeds of representative accessions having permeable haplotypes but not in those of having impermeable haplotypes, indicating that these haplotypes were causal forARR16transcript abundance and thereby regulate seed coat permeability in natural accessions. Our findings demonstrate a new role for CKs signaling in seed coat differentiation and that this underlies natural variation for seed permeability through the modulation of suberin accumulation.

Significance Statement

Seed coat permeability affects key traits that impact seed quality, such as dormancy, longevity, and germination tolerance to abiotic stress. Little is currently known about how seed coat permeability is modulated. Here, we developed an original method for quantification of seed coat permeability through imaging and used this in a genome-wide association study with Arabidopsis accessions. The CKs response regulatorARR16was identified as a causal gene thereby establishing a novel function for this phytohormone in seed coat differentiation. Moreover, this was linked to the modulation of suberin accumulation byARR16and for the first time implicates CKs signal transduction in the control of suberin deposition in seeds.
Boldine modulates glial transcription and functional recovery in a murine model of contusion spinal cord injury
Authors: Toro Carlos A. , Johnson Kaitlin , Hansen Jens , Siddiq Mustafa M. , Vásquez Walter , Zhao Wei , Graham Zachary A. , Sáez Juan C. , Iyengar Ravi , Cardozo Christopher P.
Published: February 2023

Membrane channels such as connexins (Cx), pannexins (Panx) and P2X7receptors (P2X7R) are permeable to calcium ions and other small molecules such as ATP and glutamate. Release of ATP and glutamate through these channels is a key mechanism driving tissue response to traumas such as spinal cord injury (SCI). Boldine, an alkaloid isolated from the Chilean boldo tree, blocks both Cx hemichannels (HC) and Panx. To test if boldine could improve function after SCI, boldine or vehicle was administered to treat mice with a moderate severity contusion-induced SCI. Boldine led to greater spared white matter and increased locomotor function as determined by the Basso Mouse Scale and horizontal ladder rung walk tests. Boldine treatment reduced immunostaining for markers of activated microglia (Iba1) and astrocytic (GFAP) markers while increasing that for axon growth and neuroplasticity (GAP-43). Cell culture studies demonstrated that boldine blocked glial HC, specifically Cx26 and Cx30, in cultured astrocytes and blocked calcium entry through activated P2X7R. RT-qPCR studies showed that boldine treatment reduced expression of the chemokine Ccl2, cytokine IL-6 and microglial gene CD68, while increasing expression of the neurotransmission genes Snap25 and Grin2b, and Gap-43. Bulk RNA sequencing (of the spinal cord revealed that boldine modulated a large number of genes involved in neurotransmission in in spinal cord tissue just below the lesion epicenter at 14 days after SCI. Numbers of genes regulated by boldine was much lower at 28 days after injury. These results indicate that boldine treatment ameliorates injury and spares tissue to increase locomotor function.
Flow augmentation from off-channel storage improves salmonid habitat and survival
Authors: Rossi Gabriel J. , Obedzinski Mariska , Pneh Shelley , Pierce Sarah Nossaman , Boucher William T. , Slaughter Weston M. , Flynn Keane M. , Grantham Theodore E.
Published: February 2023

[A]

In the Western United States, juvenile salmon and steelhead are especially vulnerable to streamflow depletion in the dry season. Releasing water from off-channel storage is a method of streamflow augmentation increasingly used to offset impacts of anthropogenic flow alteration. However, to date, no studies have evaluated the effects of these small-scale flow augmentations on salmonids. Here we quantify the effects of one such augmentation project on habitat connectivity, water quality, invertebrate drift, juvenile salmonid movement and survival. Our study took place in a Northern California stream and included an unusually wet summer (2019) and a more typical dry summer (2020). We found that differences in ambient streamflows between the two years mediated the physical and ecological effects of a 13.9 L/s augmentation treatment. In the dry year, flow augmentation significantly improved dissolved oxygen and habitat connectivity at sites > 1.5 km downstream from the point of augmentation and had a marginal warming effect on stream temperature. During the wet year, both dissolved oxygen and water temperature effects were negligible. In both years, augmentation had a small but positive effect on invertebrate drift. Inter-pool movement of juvenile steelhead (Oncorhynchus mykiss) and stocked Coho Salmon (O. kisutch) increased due to augmentation during the dry summer. Flow augmentation also increased the survival probability for salmonids, with a larger effect during the dry summer (24% higher survival for Coho and 20% higher for steelhead), than during the wet summer (when no effect was observed for steelhead survival and Coho Salmon survival increased by 11%). This study indicates that appropriately designed and timed flow augmentations can improve conditions for rearing salmonids in small streams, particularly during dry years. More broadly it provides empirical evidence that efforts to restore summer streamflow in small, salmon-bearing streams can yield significant ecological benefits.
Coupled Biomechanical and Ionic Excitability in Developing Neural Cell Networks
Authors: Gates Sylvester J. , Alvarez Phillip , Cao Kan , O’Neill Kate , Losert Wolfgang
Published: February 2023

Waves and oscillations play a key role in the flow and processing of information in the brain. Recent work has demonstrated that in addition to electrical activity, biomechanical signaling can also be excitable and thus capable of self-sustaining oscillations and waves. Here we measured the biomechanical dynamics of actin polymerization in neural precursor cells throughout their differentiation into populations of neurons and astrocytes. Fluorescence-based live-cell imaging allowed us to analyze the dynamics of actin in conjunction with the dynamics of calcium signals. Actin dynamics throughout differentiation showed a rhythmic character, localized mostly in processes, with changes in scale associated with differentiation. Furthermore, actin dynamics impact ionic dynamics, with an increase in the frequency of calcium bursts accompanied by a decrease in cell-cell correlations when actin dynamics is inhibited. This impact of cytoskeletal dynamics on cell-cell coupling and ionic neural cell signaling suggests that information flow in the brain may be able to harness both biomechanical and electrical/ionic excitability.
Architecture and regulation of filamentous human cystathionine beta-synthase
Authors: McCorvie Thomas J. , Bailey Henry J. , Strain-Damerell Claire , Baslé Arnaud , Yue Wyatt W.
Published: February 2023

Cystathionine beta-synthase (CBS) is an essential metabolic enzyme across all domains of life involved in the production of glutathione, cysteine, and hydrogen sulphide1–4. Human CBS appends to its conserved catalytic domain a regulatory domain that modulates activity by S-adenosyl-L-methionine (SAM) and promotes oligomerization5–12, however the molecular basis is unknown. Here we show using cryo-electron microscopy that full-length human CBS in the basal and SAM-bound activated states polymerises as filaments mediated by a conserved regulatory domain loop. In the basal state, CBS regulatory domains sterically block the catalytic domain active site, resulting in a low activity filament with three CBS dimers per turn. This steric block is removed when in the activated state, one molecule of SAM binds to the regulatory domain, forming a high activity filament with two CBS dimers per turn. These large conformational changes result in a central filament of SAM stabilised regulatory domains at the core, decorated with highly flexible catalytic domains. Polymerization stabilises CBS and increases the cooperativity of allosteric activation by SAM. Together our findings elaborate our understanding of CBS enzyme regulation, and open new avenues for investigating the pathogenic mechanism and therapeutic opportunities for CBS-associated disorders3,13–17.
CBD can be combined with additional cannabinoids for optimal seizure reduction and requires GPR55 for its anticonvulsant effects
Authors: Kollipara Roshni , Langille Evan , Tobin Cameron , French Curtis R.
Published: February 2023

Background

Cannabis has demonstrated anticonvulsant properties, and cannabis-based medicines are approved to treat pediatric patients with severe pediatric epilepsies that are particularly refractive to approved anti-epileptic drugs (AEDs). About thirty percent of epileptic patients do not have satisfactory seizure management with AEDs and could potentially benefit from cannabis-based intervention. Here we report the use of single and combined cannabinoids to treat Pentylenetetrazol (PTZ) induced convulsions in a zebrafish model, their effect on gene expression, and a simple assay for assessing their uptake in zebrafish tissues. These data provide novel insights as to the potential of treating epilepsy with cannabinoids.

Methods

Zebrafish larvae were treated with cannabinoids and their seizures measured through an optimized behaviour tracking method. Cannabinoid uptake was measured with a novel HPLC-UV method. Gene expression changes were assessed using quantitative PCR (qPCR), and chemical inhibitors of potential cannabinoid receptors were used to block activity.

Results

Treatment with cannabinol (CBN), cannabichromene (CBC) and cannabigerol (CBG) decreased seizure intensity at lower doses than CBD when accounting for the amount of cannabinoid recovered from exposed larvae. Δ9-tetrahydrocannabinol (Δ9-THC), Δ8-tetrahydrocannabinol (Δ8-THC) were effective at higher doses. Synergistic effects were observed between CBD and other cannabinoids such as Δ9-THC, Δ8-THC, and CBG. The reduction of PTZ induced seizures via CBD is partially mediated by the G-protein coupled receptor GPR55, as pharmacological inhibition of the receptor reduced the therapeutic action of CBD. Changes in expression of endocannabinoid system (napepld, gde1, faah, ptgs2a) and neural (fosab, pyya) genes in response to phytocannabinoid treatment were observed and highlight novel mechanisms of phytocannabinoid action.

Conclusions

CBD can be combined with additional cannabinoids for optimal reduction of seizure activity and requires the activity of GPR55. Changes infosabregulation of gene expression and endocannabinoid signalling may influence the anticonvulsant effects of cannabis, however further investigation is required.
Spatio-temporal coherence of circadian clocks and gating of differentiation inAnabaenafilaments
Authors: Arbel-Goren Rinat , Dassa Bareket , Zhitnitsky Anna , Valladares Ana , Herrero Antonia , Flores Enrique , Stavans Joel
Published: February 2023

Circadian clock arrays in multicellular filaments of the heterocyst-forming cyanobacteriumAnabaenasp. strain PCC 7120 display remarkable spatio-temporal coherence under nitrogen-replete conditions. To shed light on the interplay between circadian clocks and the formation of developmental patterns, we followed the expression of a clock-controlled gene under nitrogen deprivation, at the level of individual cells. Our experiments showed that differentiation into heterocysts took place preferentially within a limited interval of the circadian clock cycle; that gene expression in different vegetative intervals along a developed filament was discoordinated; and that the circadian clock was active in individual heterocysts. Furthermore,Anabaenamutants lacking thekaiABCgenes encoding the circadian clock core components produced heterocysts but failed in diazotrophy. Therefore, genes related to some aspect of nitrogen fixation, rather than early or mid-heterocyst differentiation genes, are likely affected by the absence of the clock. A bioinformatics analysis supports the notion that RpaA may play a role as master regulator of clock outputs inAnabaena, the gating of differentiation by the circadian clock and the involvement of the clock in proper diazotrophic growth. Together, these results suggest that under nitrogen deficient conditions, the functional unit inAnabaenais reduced from a full filament under nitrogen-rich conditions, to the vegetative cell interval between heterocysts.
The thermostability of a Vaccine Delivery system X-Protein (VADEX-Pro) based protein nanoparticle
Authors: Liou Gunn-Guang , Kan Ming-Chung
Published: February 2023

We have adapted split GFP technology into the protein nanoparticle platform, Vaccine Delivery system X (VADEX), created in previous study. To evaluate the capability of this new platform, a model protein, maltose binding protein (MBP), was fused to the β-strand 11 of sfGFP and co-expressed with VADEX-10 which was composed of LYRRLE peptide and N-terminal part up to β-strand 10 of sfGFP. When these two fusion proteins were expressed in a cell, they were assembled into PNP spontaneously with a dynamic light scattering (DLS) particle size of 26 nm. This nanoparticle platform was renamed as VADEX-Pro for its capacity of expressing large protein on PNP. The thermostability of the assembled PNP was verified by both SDS-PAGE and DLS analysis following treatment. This PNP was stable at 25 °C and at temperatures as high as 40 °C for at least two months. Mutations that replaced cysteine residue of the LYRRLE peptide with serine or alanine destabilized and induced degradation of the VADEX-based PNP. The results in this study showed that the non-covalent complementation of split sfGFP became irreversible when reconstituted sfGFP was assembled in a VADEX-Pro PNP. This platform may be applied in developing thermostable vaccines.
Water hardness variously influences tissue physiology of freshwater fish -Cyprinus carpiovarkoi: A report on glucose, oxidative stress and antioxidant biomarkers
Authors: Dasgupta Proteek
Published: February 2023

Fishes endemic to freshwater habitat are strongly influenced by water hardness with physiological consequences. The present study aimed to understand the effects of four-fold sequential increase from soft to hard waters, on selected tissues of Koi carp, a popular ornamental freshwater fish. Secondary stress markers - Glucose, Oxidative stress (Malondialdehyde – Lipid Peroxidation damage) and Antioxidants (Catalase, Glutathione-S-Transferase and Glutathione) were quantified in gills and white muscle after 14 days of exposure to hardness of 75 (Soft - TS), 150 (Moderate - TM), 225 (Hard - TH) to 300 (Very Hard - TV) mg CaCO3/L. Both the examined tissues were distinctly affected by soft and moderate waters. Glucose in gills (p< 0.05) was proportional to the rise in hardness concentration. Soft, moderate and very hard waters (75, 150 and 300 mg CaCO3/L) affected gills and muscle due to elevated MDA concentrations (p< 0.05). CAT and GST provided antioxidative protection to the tissues. The study results showed tissue-specific differential responses and more importantly, concentrations below 225 mg CaCO3/L elicited strong oxidative impairment in both gill and muscle.
Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox
Authors: Middelkamp Sjors , Manders Freek , Peci Flavia , van Roosmalen Markus J. , González Diego Montiel , Bertrums Eline J.M. , van der Werf Inge , Derks Lucca L.M. , Groenen Niels M. , Verheul Mark , Trabut Laurianne , Brandsma Arianne M. , Antoniou Evangelia , Reinhardt Dirk , Bierings Marc , Belderbos Mirjam E. , van Boxtel Ruben
Published: February 2023

Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole genome sequencing (WGS), but still generate hundreds of artefacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolkit (PTATO), to accurately detect single base substitutions, small insertions and deletions (indels) and structural variants in PTA-based WGS data. PTATO includes a machine learning approach to distinguish PTA-artefacts from true mutations with high sensitivity (up to 90% for base substitution and 95% for indels), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that many hematopoietic stem and progenitor cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS technologies, have normal somatic single base substitution burdens, but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.
Pervasive, conserved secondary structure in highly charged protein regions
Authors: Triandafillou Catherine G. , Pan Rosalind Wenshan , Dinner Aaron R. , Drummond D. Allan
Published: February 2023

Understanding how protein sequences confer function remains a defining challenge in molecular biology. Two approaches have yielded enormous insight yet are often pursued separately: structure-based, where sequence-encoded structures mediate function, and disorder-based, where sequences dictate physicochemical and dynamical properties which determine function in the absence of stable structure. Here we study highly charged protein regions (>40% charged residues), which are routinely presumed to be disordered. Using recent advances in structure prediction and experimental structures, we show that roughly 40% of these regions form well-structured helices. Features often used to predict disorder—high charge density, low hydrophobicity, low sequence complexity, and evolutionarily varying length—are also compatible with solvated, variable-length helices. We show that a simple composition classifier predicts the existence of structure far better than well-established heuristics based on charge and hydropathy. We show that helical structure is more prevalent than previously appreciated in highly charged regions of diverse proteomes and characterize the conservation of highly charged regions. Our results underscore the importance of integrating, rather than choosing between, structure- and disorder-based approaches.
Structural and biochemical characterization establishes a detailed understanding of KEAP1-CUL3 complex assembly
Authors: Adamson Roslin J , Payne N Connor , Bartual Sergio G. , Mazitschek Ralph , Bullock Alex N
Published: February 2023

KEAP1 promotes the ubiquitin-dependent degradation of NRF2 by assembling into a CUL3-dependent ubiquitin ligase complex. Oxidative and electrophilic stress inhibit KEAP1 allowing NRF2 to accumulate for transactivation of stress response genes. To date there are no structures of the KEAP1-CUL3 interaction nor binding data to show the contributions of different domains to their binding affinity. We determined a crystal structure of the BTB and 3-box domains of human KEAP1 in complex with the CUL3 N-terminal domain that showed a heterotetrameric assembly with 2:2 stoichiometry. To support the structural data, we developed a versatile TR-FRET-based assay system to profile the binding of BTB-domain-containing proteins to CUL3 and determine the contribution of distinct protein features, revealing the importance of the CUL3 N-terminal extension for high affinity binding. We further provide direct evidence that the investigational drug CDDO does not disrupt the KEAP1-CUL3 interaction, even at high concentrations, but reduces the affinity of KEAP1-CUL3 binding. The TR-FRET-based assay system offers a generalizable platform for profiling this protein class and may form a suitable screening platform for ligands that disrupt these interactions by targeting the BTB or 3-box domains to block E3 ligase function.

Graphical abstract

Highlights

A new crystal structure defines KEAP1 BTB and 3-box domain interactions with CUL3

KEAP1 and CUL3 form a heteromeric 2:2 complex with aKDvalue of 0.2 µM

A generalizable TR-FRET platform enables multimodal profiling of BTB proteins

The investigational drug CDDO is a partial antagonist of the KEAP1-CUL3 interaction
Characterization of microsatellite markers for the duckweedSpirodela polyrhizaandLemna minortested on samples from Europe or the United States of America
Authors: Kerstetter Jae E. , Reid Andrea L. , Armstrong Joshua T. , Zallek Taylor A. , Hobble Trapper T. , Turcotte Martin M.
Published: February 2023

Microsatellite primers are a valuable tool to use for both observational and experimental studies in numerous taxa. Here, we develop 18 and 16 microsatellite markers for the widespread duckweedsLemna minorandSpirodela polyrhiza, respectively. All 18L. minorprimers and 12 of the 16S. polyrhizaprimers amplified polymorphic loci when tested on samples from Europe or Western Pennsylvania, USA.
Loss of the benthic life stage in Medusozoa and colonization of the open ocean
Authors: Boosten Manon , Sant Camille , Da Silva Ophélie , Chaffron Samuel , Guidi Lionel , Leclère Lucas
Published: February 2023

In marine environments, life cycle strategies strongly impact species dispersal and their ability to colonize new habitats. Pelagic medusozoans (jellyfish and siphonophores) exhibit various reproductive strategies, variations of meroplanktonic and holoplanktonic life cycles. In the ancestral meroplanktonic life cycle, a benthic polyp stage alternates with a pelagic medusa stage. During the course of evolution, some medusozoans lost their benthic stage, leading to a holoplanktonic life cycle. The ecological consequences of these losses have not been addressed at global scale. Here, integrating metabarcoding and environmental data fromTara Oceansinto a phylogenetic framework, we show that each convergent transition toward a holoplanktonic life cycle is associated with a more offshore distribution compared to meroplanktonic medusozoans. Our analyses showed that holoplanktonic medusozoans are more globally distributed and relatively more abundant than meroplanktonic medusozoans, although they are less diversified and occupy a more peripheral position in a global plankton community interactome. This suggests that holoplanktonic medusozoans have acquired a greater tolerance to biotic and abiotic conditions. Overall, our results demonstrate the relationship between medusozoan life cycles, distribution, and biotic interactions, suggesting that the loss of the benthic stage promoted colonization of the open ocean.
Amygdala AVPR1A mediates susceptibility to chronic social isolation in females
Authors: François Marie , Delgado Isabella Canal , Lafond Alexandre , Lewis Eastman M. , Kuromaru Mia , Hassouna Rim , Deng Shuliang , Thaker Vidhu V. , Dölen Gül , Zeltser Lori M.
Published: February 2023

Females are more sensitive to social exclusion, which could contribute to their heightened susceptibility to anxiety disorders. Chronic social isolation stress (CSIS) for at least 7 weeks after puberty induces anxiety-related behavioral adaptations in female mice. Here, we show thatArginine vasopressin receptor 1a(Avpr1a)-expressing neurons in the central nucleus of the amygdala (CeA) mediate these sex-specific effects, in part, via projections to the caudate putamen. Loss of function studies demonstrate that AVPR1A signaling in the CeA is required for effects of CSIS on anxiety-related behaviors in females but has no effect in males or group housed females. This sex-specificity is mediated by AVP produced by a subpopulation of neurons in the posterodorsal medial nucleus of the amygdala that project to the CeA. Estrogen receptor alpha signaling in these neurons also contributes to preferential sensitivity of females to CSIS. These data support new therapeutic applications for AVPR1A antagonists in women.
Resolvin E1 improves efferocytosis and rescues severe aplastic anemia in mice
Authors: Grazda Rachel , Seyfried Allison N. , Maddipatti Krishna Rao , Fredman Gabrielle , MacNamara Katherine C.
Published: February 2023

Current treatments for severe aplastic anemia (SAA) rely on hematopoietic stem cell (HSC) transplantation and immunosuppressive therapies, however these treatments are not always effective. While immune-mediated destruction and inflammation are known drivers of SAA, the underlying mechanisms that lead to persistent inflammation are unknown. Using an established mouse model of SAA, we observed a significant increase in apoptotic cells within the bone marrow (BM) and demonstrate impaired efferocytosis in SAA mice, as compared to radiation controls. Single-cell transcriptomic analysis revealed heterogeneity among BM monocytes and unique populations emerged during SAA characterized by increased inflammatory signatures and significantly increased expression ofSirpaandCd47. CD47, a “don’t eat me” signal, was increased on both live and apoptotic BM cells, concurrent with markedly increased expression of signal regulatory protein alpha (SIRPα) on monocytes. Functionally, SIRPα blockade improved cell clearance and reduced accumulation of CD47-positive apoptotic cells. Lipidomic analysis revealed a reduction in the precursors of specialized pro-resolving lipid mediators (SPMs) and increased prostaglandins in the BM during SAA, indicative of impaired inflammation resolution. Specifically, 18-HEPE, a precursor of E-series resolvins, was significantly reduced in SAA-induced mice relative to radiation controls. Treatment of SAA mice with Resolvin E1 (RvE1) improved efferocytic function, BM cellularity, platelet output, and survival. Our data suggest that impaired efferocytosis and inflammation resolution contributes to SAA progression and demonstrate that SPMs, such as RvE1, offer new and/or complementary treatments for SAA that do not rely on immune suppression.

Key Points

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IFNγ impairs efferocytosis in SAA, correlating with increased SIRPahimonocytes and increased CD47 expression

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Pro-inflammatory and pro-resolving lipid mediators are imbalanced in SAA, and RvE1 treatment improved efferocytosis and disease outcomes
Prolongedin-vivotracking of vitreous fluid and its early diagnostic imaging biomarkers for cancer growth
Authors: Goswami Mayank , Shakya Snehlata , Zhang Pengfei
Published: February 2023

Purpose

Estimation of a correlation between cells in vitreous humour and growth in glioblastoma xenografts.

Methods

Streams of cells in vitreous humor are observed in optical coherence tomography (OCT) imaging data of animal (NSGS and Athymic Nude-Foxn1nu) eyes (34 in total) subjected to xenograft growth study, in-vivo. The cancer disease model is studied with and without nanodrug-based treatment protocols.

Results

The presence of CD8+ and CD4+ is reported inside the tumor using the same data earlier. The transition of these cells is shown to take place from the optic nerve via the vitreous into the nerve fiber layer (NFL) at tumor locations and xenograft -related injuries. Functional analysis of dense temporal imaging series (varying from 28 to more than 100 days) reveals a mild correlation between the volumetric growth of the tumor with the density of these cells, quantitatively and qualitatively.

The cross-correlation analysis indicates imaging assisted photodynamic treatment protocol perform relatively better if started with certain delay. Doxorubicin treatment to Nu/Nu Male and NSGS female transforms mild weak negative correlation into mild weak positive correlation.

Conclusions

The plots indicate that the mix of the cells in vitreous humor are effectively dominated by immunosuppressor cytotoxic component.

Translational Relevance

We propose that the vitreous cell density can be used as imaging biomarker helpful for clinicians in early diagnosis and treatment planning of similar disease models. The limitation of this work is that high resolution OCT systems and data-dependent image segmentation methods are required.
Identifying Promising Sequences For Protein Engineering Using A Deep Transformer Protein Language Model
Authors: Frisby Trevor S. , Langmead Christopher James
Published: February 2023

Protein engineers aim to discover and design novel sequences with targeted, desirable properties. Given the near limitless size of the protein sequence landscape, it is no surprise that these desirable sequences are often a relative rarity. This makes identifying such sequences a costly and time-consuming endeavor. In this work, we show how to use a deep Transformer Protein Language Model to identify sequences that have the mostpromise. Specifically, we use the model’s self-attention map to calculate a PROMISE SCORE that weights the relative importance of a given sequence according to predicted interactions with a specified binding partner. This PROMISE SCORE can then be used to identify strong binders worthy of further study and experimentation. We use the PROMISE SCORE within two protein engineering contexts— Nanobody (Nb) discovery and protein optimization. With Nb discovery, we show how the PROMISE SCORE provides an effective way to select lead sequences from Nb repertoires. With protein optimization, we show how to use the PROMISE SCORE to select site-specific mutagenesis experiments that identify a high percentage of improved sequences. In both cases, we also show how the self-attention map used to calculate the PROMISE SCORE can indicate which regions of a protein are involved in intermolecular interactions that drive the targeted property. Finally, we describe how to fine-tune the Transformer Protein Language Model to learn a predictive model for the targeted property, and discuss the capabilities and limitations of fine-tuning with and without knowledge transfer within the context of protein engineering.
Vacuum Insulated Probe Heated ElectroSpray Ionization source (VIP-HESI) enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer
Authors: Midha Mukul K. , Kapil Charu , Maes Michal , Baxter David H. , Morrone Seamus R. , Prokop Timothy J. , Moritz Robert L.
Published: February 2023

By far the largest contribution to ion detectability in liquid chromatography-driven mass spectrometry-based proteomics is the efficient generation of peptide ions by the electrospray source. To maximize the transfer of peptides from liquid to a gaseous phase to allow molecular ions to enter the mass spectrometer at micro-spray flow rates, an efficient electrospray process is required. Here we describe superior performance of new Vacuum-Insulated-Probe-Heated-ElectroSpray-Ionization source (VIP-HESI) coupled with micro-spray flow rate chromatography and Bruker timsTOF PRO mass spectrometer. VIP-HESI significantly improves chromatography signals in comparison to nano-spray ionization using the CaptiveSpray source and provides increased protein detection with higher quantitative precision, enhancing reproducibility of sample injection amounts. Protein quantitation of human K562 lymphoblast samples displayed excellent chromatographic retention time reproducibility (<10% coefficient-of-variation (CV)) with no signal degradation over extended periods of time, and a mouse plasma proteome analysis identified 12% more plasma protein groups allowing large-scale analysis to proceed with confidence (1,267 proteins at 0.4% CV). We show that Slice-PASEF mode with VIP-HESI setup is sensitive in identifying low amounts of peptide without losing quantitative precision. We demonstrate that VIP-HESI coupled with micro-flow-rate chromatography achieves higher depth of coverage and run-to-run reproducibility for a broad range of proteomic applications.
Predicting Brain Amyloid Positivity from T1 weighted brain MRI and MRI-derived Gray Matter, White Matter and CSF maps using Transfer Learning on 3D CNNs*
Authors: Chattopadhyay Tamoghna , Ozarkar Saket S. , Buwa Ketaki , Thomopoulos Sophia I. , Thompson Paul M. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2023

Abnormal β-amyloid (Aβ) accumulation in the brain is an early indicator of Alzheimer’s disease and practical tests could help identify patients who could respond to treatment, now that promising anti-amyloid drugs are available. Even so, Aβ positivity (Aβ+) is assessed using PET or CSF assays, both highly invasive procedures. Here, we investigate how well Aβ+ can be predicted from T1 weighted brain MRI and gray matter, white matter and cerebrospinal fluid segmentations from T1-weighted brain MRI (T1w), a less invasive alternative. We used 3D convolutional neural networks to predict Aβ+ based on 3D brain MRI data, from 762 elderly subjects (mean age: 75.1 yrs. ±7.6SD; 394F/368M; 459 healthy controls, 67 with MCI and 236 with dementia) scanned as part of the Alzheimer’s Disease Neuroimaging Initiative. We also tested whether the accuracy increases when using transfer learning from the larger UK Biobank dataset. Overall, the 3D CNN predicted Aβ+ with 76% balanced accuracy from T1w scans. The closest performance to this was using white matter maps alone when the model was pre-trained on an age prediction in the UK Biobank. The performance of individual tissue maps was less than the T1w, but transfer learning helped increase the accuracy. Although tests on more diverse data are warranted, deep learned models from standard MRI show initial promise for Aβ+ estimation, before considering more invasive procedures.

Clinical Relevance

Early detection of Aβ positivity from less invasive MRI images, could offer a screening test prior to more invasive testing procedures.
Electroacupuncture prevents astrocyte atrophy to alleviate depression
Authors: Lin Si-Si , Zhou Bin , Chen Bin-Jie , Jiang Ruo-Tian , Li Baoman , Illes Peter , Semyanov Alexey , Tang Yong , Verkhratsky Alexei
Published: February 2023

Astrocyte atrophy is the main histopathological hallmark of the major depressive disorder (MDD) in humans and in animal models of depression. Here we show that electroacupuncture prevents astrocyte atrophy in the prefrontal cortex and alleviates depressive-like behaviour in mice subjected to the chronic unpredictable mild stress (CUMS). Treatment of mice with CUMS induced depressive-like phenotypes as confirmed by sucrose preference test, tail suspension test, and forced swim test. These behavioural changes were paralleled with morphological atrophy of astrocytes in the prefrontal cortex, revealed by analysis of 3D reconstructions of confocal Z-stack images of mCherry expressing astrocytes. This morphological atrophy was accompanied with a decrease in expression of cytoskeletal linker Ezrin, associated with formation of astrocytic leaflets, which form astroglial synaptic cradle. Electroacupuncture at the acupoint ST36 as well as treatment with anti-depressant fluoxetine prevented depressive-like behaviours, astrocytic atrophy and down-regulation of astrocytic ezrin. In conclusion, our data further strengthen the notion of a primary role of astrocytic atrophy in depression and reveal astrocytes as cellular target for electroacupuncture in treatment of depressive disorders.