bluuebunny/crossref_metadata_2025 huggingface dataset:
Socioeconomic status is not associated with survival in patients with brain metastases treated with stereotactic radiotherapy
Authors: Nagtegaal S.H.J. , Elias S.G. , Snijders T.J. , Verkooijen H.M. , Verhoeff J.J.C.
Published: October 2022

Background and purpose

In most cancer sites a low socioeconomic status (SES) is consistently associated with poorer survival. For brain metastasis, this relation is not well understood. Therefore, we studied the effect of SES on survival in Dutch brain metastasis patients treated with stereotactic radiosurgery in a tertiary radiotherapy facility.

Materials and methods

We retrospectively studied 404 consecutive patients treated with stereotactic radiosurgery for brain metastases in a tertiary referral centre between 2012 and 2017. Baseline prognostic factors for survival were collected. The SES score was based on education, income and employment. Cox proportional hazard models were made, corrected for the relevant variables identified from a directed acyclic graph (DAG). Adjustments were made in two ways in order to obtain comprehensive results: correcting for confounders (total effect), and correcting for confounders and mediating factors (direct effect).

Results

Unadjusted, estimation of the linear effect of SES on survival resulted in a HR of 0.92 (95%CI 0.82 – 1.04). The total effect of SES was achieved by correcting for age, resulting in a HR of 0.95, with a 95% CI of 0.84 – 1.07. The direct effect gave a HR of 0.96 (95%CI 0.84 – 1.10).

Conclusion

SES was not associated with survival in patients with brain metastases undergoing radiation therapy. When correcting for clinical variables, we found no significant relationship between SES and survival, with HRs suggesting limited clinical impact. The results suggest that patients’ survival outcomes after contemporary cancer treatment are unrelated to their employment status, education status and annual income.
A Mixed Methods Comparison of Artificial Intelligence-Powered Clinical Decision Support System Interfaces for Multiple Criteria Decision Making in Antidepressant Selection
Authors: Kleinerman Akiva , Benrimoh David , Golden Grace , Tanguay-Sela Myriam , Margolese Howard C. , Rosenfeld Ariel
Published: October 2022

BACKGROUND

Artificial intelligence-powered clinical decision support systems (AI-CDSS) have recently become foci of research. When clinicians face decisions about treatment selection, they must contemplate multiple criteria simultaneously. The relative importance of these criteria often depends on the clinical scenario, as well as clinician and patient preferences. It remains unclear how AI-CDSS can optimally assist clinicians in making these complex decisions. In this work we explore clinician reactions to different presentations of AI results in the context of multiple criteria decision-making during treatment selection for major depressive disorder.

METHODS

We developed an online platform for depression treatment selection to test three interfaces. In the probabilities alone (PA) interface, we presented probabilities of remission and three common side effects for five antidepressants. In the clinician-determined weights (CDW) interface, participants assigned weights to each of the outcomes and obtained a score for each treatment. In the expert-derived weights interface (EDW), outcomes were weighted based on expert opinion. Each participant completed three clinical scenarios, and each scenario was randomly paired with one interface. We collected participants’ impressions of the interfaces via questionnaires and written and verbal feedback.

RESULTS

Twenty-two physicians completed the study. Participants felt that the CDW interface was most clinically useful (H=10.29, p<0.01) and more frequently reported that it had an impact on their decision making (PA: in 55.5% of experienced scenarios, CDW: in 59.1%, EDW: in 36.6%). Clinicians most often chose a treatment different from their original choice after reading the clinical scenario in the CDW interface (PA: 26.3%, CDW: 33.3%, EDW: 15.8%).

CONCLUSION

Clinicians found a decision support interface where they could set the weights for different potential outcomes most useful for multi-criteria decision making. Allowing clinicians to weigh outcomes based on their expertise and the clinical scenario may be a key feature of a future clinically useful multi-criteria AI-CDSS.
Evaluation of primary allied healthcare in patients recovering from COVID-19: first results after six months follow-up in a Dutch nationwide prospective cohort study
Authors: Slotegraaf Anne I. , Gerards Marissa H.G. , Verburg Arie C. , de van der Schueren Marian A.E. , Kruizenga Hinke M. , Graff Maud J.L. , Cup Edith H.C. , Kalf Johanna G. , Lenssen Antoine F. , Meijer Willemijn M. , Kool Renée A. , de Bie Rob A. , van der Wees Philip J. , Hoogeboom Thomas J.
Published: October 2022

Objectives

To report the recovery of patients receiving primary allied healthcare after a COVID-19 infection at a six-month follow-up, and to explore which patient characteristics are associated with the changes in outcomes between the baseline and six-month follow-up.

Design

Prospective cohort study.

Setting

Allied healthcare in Dutch primary care.

Participants

1,451 adult patients recovering from COVID-19 and receiving treatment from one or more primary care allied health professional(s) (i.e., dietitian, exercise therapist, occupational therapist, physical therapist and/or speech and language therapist).

Results

For participation (USER-P range 0 to 100), estimated mean differences of at least 2.3 points were observed after six months. For HRQoL (EQ-VAS range 0 to 100), the mean increase was 12.31 at six months. Furthermore, significant improvements were found for fatigue (FSS range 1 to 7): the mean decrease was –0.7 at six months. For physical functioning (PROMIS-PF range 13.8 to 61.3), the mean increase was 5.9 at six months. Mean differences of –0.8 for anxiety (HADS range 0 to 21), and –1.5 for depression (HADS range 0 to 21), were found after six months. Having a worse baseline score, hospital admission and male sex were associated with greater improvement between the baseline and six-month follow-up, whereas age, BMI, comorbidities and smoking status were not associated with mean changes in any outcome measure.

Conclusions

Patients recovering from COVID-19 who receive primary allied healthcare make progress in recovery, but still experience many limitations in their daily activities after six months. Our findings provide reference values to healthcare providers and healthcare policy-makers regarding what to expect from the recovery of patients who received health care from one or more primary care allied health professionals.

Trial registration

Clinicaltrials.govregistry (NCT04735744).
Experimenter familiarization is a crucial prerequisite for assessing behavioral outcomes and reduces stress in mice not only under chronic pain conditions
Authors: Segelcke Daniel , Talbot Steven R. , Palme Rupert , La Porta Carmen , Pogatzki-Zahn Esther , Bleich André , Tappe-Theodor Anke
Published: October 2022

ABSTARCT

Rodent behavior is affected by different environmental conditions. These do not only comprise experimental and housing conditions but also familiarization with the experimenter. However, specific effects on pain-related behavior and chronic pain conditions have not been examined. Therefore, we aimed to investigate the impact of different housing conditions, inverted day-night cycles, and experimenter familiarization on male mice following peripheral neuropathy using the spared nerve injury (SNI) model. Using a multimodal approach, we evaluated evoked pain-related-, anxiety- and depression-like behavior, corticosterone metabolite levels and utilized an integrative approach for relative-severity-assessment.

Different environmental conditions are represented by individually ventilated cages and standard open cages combined with a reversed day-night-light cycle and experimenter habituation, inducing differentially modulated multidimensional pain- and emotion-like phenotypes in SNI mice. In addition, familiarization reduced the stress level caused by behavioral tests. Although no environmental condition significantly modulated the severity in SNI mice, it influenced pain-affected phenotypes and is, therefore, crucial for designing and interpreting preclinical pain studies. Moreover, environmental conditions should be considered more in the reporting guidelines, described in more detail, and discussed as a potential influence on pain phenotypes.
Emerging variants of canine enteric coronavirus associated with seasonal outbreaks of severe canine gastroenteric disease
Authors: Cunningham-Oakes Edward , Pilgrim Jack , Darby Alistair C. , Appleton Charlotte , Jewell Chris , Rowlingson Barry , Cuartero Carmen Tamayo , Newton Richard , Sánchez-Vizcaíno Fernando , Fins Ivo Salgueiro , Brant Bethaney , Smith Shirley , Penrice-Randal Rebekah , Clegg Simon R. , Roberts Ashley P.E. , Millson Stefan H. , Pinchbeck Gina L. , Noble P-J. M. , Radford Alan D.
Published: October 2022

Canine enteric coronavirus (CECoV) variants have an emerging role in severe outbreaks of canine gastroenteritis. Here we used syndromic health data from a sentinel network of UK veterinary practices to identify an outbreak of severe canine gastroenteritis. Affected dogs frequently presented with vomiting, diarrhoea and inappetence. Data from sentinel diagnostic laboratories showed similar seasonal increases in CECoV diagnosis. Membrane glycoprotein (M) gene sequence analysis implied wide geographical circulation of a new CECoV variant. Whole genome sequencing suggested the main circulating 2022 variant was most closely related to one previously identified in 2020 with additional spike gene recombination; all variants were unrelated to CECoV-like viruses recently associated with human respiratory disease. Identifying factors that drive population-level evolution, and its implications for host protection and virulence, will be important to understand the emerging role of CECoV variants in canine and human health, and may act as a model for coronavirus population adaptation more widely.
Cell wall damage increases macromolecular crowding effects in the Escherichia coli cytoplasm
Authors: Pittas Theodoros , Zuo Weiyan , Boersma Arnold J.
Published: October 2022

The intracellular milieu is crowded with biomacromolecules. Macromolecular crowding changes the interactions, diffusion, and conformations of the biomacromolecules. Changes in intracellular crowding effects have been mostly ascribed to differences in biomacromolecule concentration. However, the spatial organization of these molecules should play a significant role in crowding effects. Here, we find that cell wall damage causes increased macromolecular crowding effects in the Escherichia coli cytoplasm. Using a genetically-encoded macromolecular crowding sensor, we see that crowding effects in E. coli spheroplasts and Penicillin G-treated cells well surpass crowding effects obtained using hyperosmotic stress. The crowding increase is not due to osmotic pressure, cell shape, crowder synthesis, or volume changes, and therefore not crowder concentration. Instead, a genetically-encoded nucleic acid stain and a small molecule DNA stain show nucleoid expansion and cytoplasmic mixing, which could cause these increased crowding effects. Our data demonstrate that cell stress from antibiotics or cell wall damage alters the biochemical organization in the cytoplasm and induces significant conformational changes in a probe protein.
Capsaicin-induced endocytosis of endogenous presynaptic CaV2.2 in DRG-spinal cord co-cultures inhibits presynaptic function
Authors: Ramgoolam Krishma H , Dolphin Annette C
Published: October 2022

The N-type calcium channel, CaV2.2 is key to neurotransmission from the primary afferent terminals of dorsal root ganglion (DRG) neurons to their post-synaptic targets in the spinal cord. In this study we have utilized CaV2.2_HA knock-in mice, because the exofacial epitope tag in CaV2.2_HA enables accurate detection and localization of endogenous CaV2.2. CaV2.2_HA knock-in mice were used as a source of DRGs to exclusively study the presynaptic expression of N-type calcium channels in co-cultures between DRG neurons and wild-type spinal cord neurons. CaV2.2_HA is strongly expressed on the cell surface, particularly in TRPV1-positive small and medium DRG neurons. Super-resolution images of the presynaptic terminals revealed an increase in CaV2.2_HA expression and increased association with the post-synaptic marker Homer over time in vitro. Brief application of the TRPV1 agonist, capsaicin, resulted in a significant down-regulation of cell surface CaV2.2_HA expression in DRG neuron somata. At their presynaptic terminals, capsaicin caused a reduction in CaV2.2_HA proximity to and co-localization with the active zone marker RIM 1/2, as well as a lower contribution of N-type channels to single action potential-mediated Ca2+ influx. The mechanism of this down-regulation of CaV2.2_HA involves a Rab 11a-dependent trafficking process, since dominant-negative Rab11a(S25N) occludes the effect of capsaicin on presynaptic CaV2.2_HA expression, and also prevents the effect of capsaicin on action potential induced Ca2+ influx. Taken together, these data suggest that capsaicin causes a decrease in cell surface CaV2.2_HA expression in DRG terminals via a Rab11a-dependent endosomal trafficking pathway.
What moves when mice move a single whisker to touch? Individuality and stereotypy in behavior
Authors: Staab Marcel , Sehara Keisuke , Bahr Nora-Laurine , Dominiak Sina E. , Larkum Matthew E. , Sachdev Robert N. S.
Published: October 2022

A key function of the brain is to move the body through a rich, complex environment. When rodents engage their environment, they move their whiskers as they extract tactile information. Even though the study of whisking has a long history, the details of what mice move when they move a whisker actively to touch are still unknown. Here we trained head fixed mice in a simple go-cue task to move a whisker on one side of the face to touch a sensor and tracked facial movements. Our analysis shows that mice specifically control the movement of the whisker they use to touch and that as they move their whiskers, they move their nose and apply forces on the head-post in a manner that reflects the behavioral epoch. Importantly, mice controlled the setpoint, amplitude and frequency of movement of whiskers bilaterally and individually. Additionally, even though mice achieved the goal of the task -- to touch the sensor within 2 seconds -- how they did so, how they coordinated movement of the nose and forces on head post with movement of individual whiskers was stereotyped, specific and related to the distance they needed to move a whisker to touch the sensor. Our work shows how stereotyped mouse behavior can be, and it emphasizes both the level of fine motor control mice can exert over individual whiskers and the extent of facial movements in a goal directed whisking-to-touch task.
Rapid Cell Type-Specific Nascent Proteome Labeling in Drosophila
Authors: Villalobos-Cantor Stefanny , Barrett Ruth M. , Condon Alec F. , Arreola-Bustos Alicia , Rodriguez Kelsie M. , Cohen Michael S. , Martin Ian
Published: October 2022

Controlled protein synthesis is required to regulate gene expression and is often carried out in a cell type-specific manner. Protein synthesis is commonly measured by labeling the nascent proteome with amino acid analogs or isotope-containing amino acids. These methods have been difficult to implement in vivo as they require lengthy amino acid replacement procedures. O-propargyl-puromycin (OPP) is a puromycin analog that incorporates into nascent polypeptide chains. Through its terminal alkyne, OPP can be conjugated to a fluorophore-azide for directly visualizing nascent protein synthesis, or to a biotin-azide for capture and identification of newly-synthesized proteins. To achieve cell type-specific OPP incorporation, we developed phenylacetyl-OPP (PhAc-OPP), a puromycin analog harboring an enzyme-labile blocking group that can be removed by Penicillin G acylase (PGA). Here, we show that cell type-specific PGA expression in Drosophila can be used to achieve OPP labeling of newly-synthesized proteins in targeted cell populations within the brain. Following a brief 2-hour incubation of intact brains with PhAc-OPP, we observe robust imaging and affinity purification of OPP-labeled nascent proteins in PGA-targeted cell populations. We apply this method to show a pronounced age-related decline in neuronal protein synthesis in the fly brain, demonstrating the capability to quantitatively capture in vivo protein synthesis states using PhAc-OPP. This method, which we call POPPi (PGA-dependent OPP incorporation), should be applicable for rapidly visualizing protein synthesis and identifying nascent proteins synthesized under diverse physiological and pathological conditions with cellular specificity in vivo.
Host’s genetic background determines the outcome of reciprocal faecal transplantation on life-history traits and microbiome composition
Authors: Juottonen Heli , Moghadam Neda N. , Murphy Liam , Mappes Johanna , Galarza Juan A.
Published: October 2022

Background

Microbes play a role in fundamental ecological, chemical, and physiological processes of their host. Host life-history traits from defence to growth are therefore determined not only by abiotic environment and genotype but also by microbiota composition. However, the relative importance and interactive effects of these factors may vary between organisms. Such connections remain particularly elusive in Lepidoptera, which have been argued to lack a permanent microbiome and have microbiota primarily determined by their diet and environment.

We tested the microbiome specificity and its influence on life-history traits of two colour genotypes of the wood tiger moth (Arctia plantaginis) that differ in several traits, including growth. All individuals were grown in the laboratory for several generations with standardised conditions. We analysed the bacterial community of the genotypes before and after a reciprocal frass (i.e., larval faeces) transplantation and followed growth rate, pupal mass, and the production of defensive secretion.

Results

After transplantation, the fast-growing genotype grew at a significantly slower rate compared to the controls, but the slow-growing genotype did not change its growth rate. The frass transplant also increased the volume of defensive secretions in the fast-growing genotype but did not affect pupal mass. Overall, the fast-growing genotype appeared more susceptible to the transplantation than the slow-growing genotype.

Microbiome differences between the genotypes strongly suggest genotype-based selective filtering of bacteria from the diet and environment. A novel cluster of insect-associated Erysipelotrichaceae was exclusive to the fast-growing genotype, and specific Enterococcaceae were characteristic to the slow-growing genotype. These Enterococcaceae became more prevalent in the fast-growing genotype after the transplant, which suggests that the slower growth rate was potentially related to their presence.

Conclusions

We show that some genotype-specific life-history traits in a lepidopteran host can be reversed by a reciprocal frass transplantation. The results indicate that genotype-specific selective filtering can fine-tune the bacterial community at specific life stages, particularly the larval gut, even against a background of a highly variable community with stochastic assembly. Altogether, our findings suggest that the genotype of the host can influence its susceptibility to be colonized by microbiota with impact on key life-history traits.
Proteomics analysis of autophagy cargos reveals distinct adaptations in PINK1 and LRRK2 models of Parkinson disease
Authors: Goldsmith Juliet , Ordureau Alban , Boecker CA C Alexander , Arany Madeleine , Harper J Wade , Holzbaur Erika LF
Published: October 2022

Autophagy is essential for neuronal homeostasis, while defects in autophagy are implicated in Parkinson disease (PD), a prevalent and progressive neurodegenerative disorder. We used unbiased proteomics to compare cargos degraded by basal autophagy in the brain from two mouse models of PD, PINK1-/-and LRRK2G2019Smice. We find evidence for the upregulation of adaptive pathways to support homeostasis in both PD models. In PINK1-/-mice, we observed increased expression of the selective receptor BNIP3 along with evidence of engagement of other alternative pathways for mitophagy. Despite these changes, we find the rate of autophagic flux in PINK1-/-neurons is decreased. In LRRK2G2019Smice, hyperactive kinase activity known to impair autophagosomal and lysosomal function results in increased secretion of extracellular vesicles and autophagy cargo. In support of this observation, we find reduced levels of PIKFYVE, a negative regulator of extracellular vesicle secretion, in both brain and cortical neurons from LRRK2G2019Smice. Thus, distinct adaptive pathways are activated to compensate for perturbations induced by either loss of PINK1 or hyperactivation of LRRK2. Our findings highlight the engagement of compensatory pathways to maintain homeostasis in the brain, and provide insights into the vulnerabilities these compensatory changes may introduce that may further contribute to PD progression.
A scoping review of regulatory T cell dynamics in convalescent COVID-19 patients – Implications for Long COVID?
Authors: Haunhorst Simon , Bloch Wilhelm , Javelle Florian , Krüger Karsten , Baumgart Sabine , Drube Sebastian , Lemhöfer Christina , Reuken Philipp , Stallmach Andreas , Müller Michael , Zielinski Christina E. , Pletz Mathias W. , Gabriel Holger H.W. , Puta Christian
Published: October 2022

Background

Recovery from coronavirus disease 2019 (COVID-19) can be impaired by the persistence of symptoms or new-onset health complications, commonly referred to as Long COVID. In a subset of patients, Long COVID is associated with immune system perturbations of unknown etiology, which could be related to compromised immunoregulatory mechanisms.

Objective

The aim of this scoping review was to investigate if regulatory T cell (Treg) dysregulation is observable beyond the acute illness and if it might be involved in Long COVID immunopathology.

Design

A systematic search of studies investigating Tregs during COVID-19 convalescence was conducted on MEDLINE (via Pubmed) and Web of Science.

Results

The literature search yielded 17 relevant studies, of which three included a distinct cohort of patients with Long COVID. The reviewed studies suggest that the Treg population of COVID-19 patients can reconstitute quantitatively and functionally during recovery. However, the comparison between recovered and seronegative controls revealed that an infection-induced dysregulation of the Treg compartment can be sustained for at least several months. The small number of studies investigating Tregs in Long COVID allowed no firm conclusions to be drawn about their involvement in the syndrome’s etiology. Yet, even almost one year post-infection Long COVID patients exhibit significantly altered proportions of Tregs within the CD4+ T cell population.

Conclusions

Persistent alterations in cell frequency in Long COVID patients indicate that Treg dysregulation might be linked to immune system-associated sequelae. Future studies should aim to address the association of Treg adaptations with different symptom clusters and blood parameters beyond the sole quantification of cell frequencies while adhering to consensualized phenotyping strategies.
Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis regulatory elements
Authors: Anderson A. G. , Rogers B. B. , Loupe J. M. , Rodriguez-Nunez I. , Roberts S. C. , White L. M. , Brazell J. N. , Bunney W. E. , Bunney B. G. , Watson S. J. , Cochran J. N. , Myers R. M. , Rizzardi L. F.
Published: October 2022

Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer’s disease (AD) and unaffected controls have been well-documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq+snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell type-specific transposase accessible regions enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as candidate transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglial links were globally enriched for heritability of AD risk and previously identified active regulatory regions.
Artificial neural network language models predict human brain responses to language even after a developmentally realistic amount of training
Authors: Hosseini Eghbal A. , Schrimpf Martin , Zhang Yian , Bowman Samuel , Zaslavsky Noga , Fedorenko Evelina
Published: October 2022

Artificial neural networks have emerged as computationally plausible models of human language processing. A major criticism of these models is that the amount of training data they receive far exceeds that of humans during language learning. Here, we use two complementary approaches to ask how the models’ ability to capture human fMRI responses to sentences is affected by the amount of training data. First, we evaluate GPT-2 models trained on 1 million, 10 million, 100 million, or 1 billion words against an fMRI benchmark. We consider the 100-million-word model to be developmentally plausible in terms of the amount of training data given that this amount is similar to what children are estimated to be exposed to during the first 10 years of life. Second, we test the performance of a GPT-2 model trained on a 9-billion-token dataset to reach state-of-the-art next-word prediction performance on the human benchmark at different stages during training. Across both approaches, we find that (i) the models trained on a developmentally plausible amount of data already achieve near-maximal performance in capturing fMRI responses to sentences. Further, (ii) lower perplexity—a measure of next-word prediction performance—is associated with stronger alignment with human data, suggesting that models that have received enough training to achieve sufficiently high next-word prediction performance also acquire representations of sentences that are predictive of human fMRI responses. In tandem, these findings establish that althoughsometraining is necessary for the models’ predictive ability, a developmentally realistic amount of training (∼100 million words) may suffice.
The genome-wide mutational consequences of DNA hypomethylation
Authors: Besselink Nicolle , Keijer Janneke , Vermeulen Carlo , Boymans Sander , de Ridder Jeroen , van Hoeck Arne , Cuppen Edwin , Kuijk Ewart
Published: October 2022

DNA methylation is important for establishing and maintaining cell identity and for genomic stability. This is achieved by regulating the accessibility of regulatory and transcriptional elements and the compaction of subtelomeric, centromeric, and other inactive genomic regions. Carcinogenesis is accompanied by a global loss in DNA methylation, which facilitates the transformation of cells. Cancer hypomethylation may also cause genomic instability, for example through interference with the protective function of telomeres and centromeres. However, understanding the role(s) of hypomethylation in tumor evolution is incomplete because the precise mutational consequences of global hypomethylation have thus far not been systematically assessed. Here we made genome-wide inventories of all possible genetic variation that accumulates in single cells upon the long-term global hypomethylation by CRISPR/CAS9-mediated conditional knockdown of DNMT1. Depletion of DNMT1 results in a genomewide reduction in DNA methylation levels. Hypomethylated cells show reduced proliferation rates, reactivation of the inactive X-chromosome and abnormal nuclear morphologies. Prolonged hypomethylation is accompanied by increased chromosomal instability. However, there is no increase in mutational burden, enrichment for certain mutational signatures or structural changes to the genome. We conclude that the primary consequence of global hypomethylation is chromosomal instability and does not necessarily lead to other small-scale or structural mutational effects.
Pseudomonas apudapuassp. nov.,Pseudomonas fontissp. nov.,Pseudomonas idahonensissp. nov., andPseudomonas rubrasp. nov. isolated from in, and around, a rainbow trout farm
Authors: Testerman Todd , Varga Jackie , Donohue Hailey , Da Silva Caroline Vieira , Graf Joerg
Published: October 2022

During a large-scale bacterial culturing effort of biofilms in the vicinity of a rainbow trout aquaculture facility in Idaho, USA, ten isolates were identified as having pathogen inhibiting activity and were characterized further. These isolates were shown to be Gram negative, rod-shaped bacteria belonging to the genusPseudomonas. Whole genome comparisons and multi-locus sequence analysis using four housekeeping genes (16S rDNA,gyrA, rpoB, rpoD) showed that these 10 isolates clustered into four distinct species groups. These comparisons also indicated that these isolates were below the established species cutoffs for the genusPseudomonas. Further phenotypic characterization using API 20NE, API ZYM, and BioLog GENIII assays and chemotaxonomic analysis of cellular fatty acids were carried out. Based on the genomic, physiological, and chemotaxonomic properties of these isolates, we concluded that these strains composed four novel species ofPseudomonas. The proposed names are:Pseudomonas apudapuassp. nov. consisting of strains ID233, ID386T, and ID387 with ID386T(DSM 114641) as the type strain;Pseudomonas rubrasp. nov. consisting of strains ID291T, ID609, and ID1025 with ID291T(DSM 114640) as the type strain;Pseudomonas idahonensissp. nov. consisting of strains ID357Tand ID1048 with ID357T(DSM 114609) as the type strain; andPseudomonas fontissp. nov. consisting of strains ID656Tand ID681 with ID656T(DSM 114610) as the type strain.
Particle fusion of Single Molecule Localization Microscopy data reveals dimer structure of Nup96 in Nuclear Pore Complex
Authors: Wang Wenxiu , Jakobi Arjen , Wu Yu-Le , Ries Jonas , Stallinga Sjoerd , Rieger Bernd
Published: October 2022

Single molecule localization microscopy offers nowadays resolution nearly down to the molecular level with specific molecular labelling, thereby being a promising tool for structural biology. In practice, however, the actual value to this field is limited primarily by incomplete fluorescent labeling of the structure. This missing information can be completed by merging information from many structurally identical particles equivalent to cryo-EM single-particle analysis. In this analysis, we present particle averaging of fluorescently labelled Nup96 in the Nuclear Pore Complex followed by data analysis to show that Nup96 occurs as a dimer with in total 32 copies per pore. We use Artificial Intelligence assisted modeling in Alphafold to extend the existing cryo-EM model of Nup96 to accurately pinpoint the positions of the fluorescent labels and show the accuracy of the match between fluorescent and cryo-EM data to be better than 3 nm in-plane and 5 nm out-of-plane.
Heterosynaptic Plasticity of the Visuo-auditory Projection Requires Cholecystokinin released from Entorhinal Cortex Afferents
Authors: Sun Wenjian , Wu Haohao , Peng Yujie , Tang Peng , Zhao Ming , Zheng Xuejiao , Feng Hemin , Li Hao , Liang Ye , Li Jing , Su Junfeng , Chen Xi , Hökfelt Tomas , He Jufang
Published: October 2022

The entorhinal cortex is involved in establishing enduring visuo-auditory associative memory in the neocortex. Here we explored the mechanisms underlying this synaptic plasticity related to projections from the visual and entorhinal cortices to the auditory cortex, using optogenetics of dual pathways. High-frequency laser stimulation (HFLS) of the visuo-auditory projection did not induce long-term potentiation (LTP). However, after pairing with sound stimulus, the visuo-auditory inputs were potentiated following either infusion of cholecystokinin (CCK) or HFLS of the entorhino-auditory CCK-expressing projection. Combining retrograde tracing and RNAscope in situ hybridization, we show that CCK expression is higher in entorhinal cortex neurons projecting to the auditory cortex than in those originating from the visual cortex. In the presence of CCK, potentiation in the neocortex occurred when the pre-synaptic input arrived 200 ms before post-synaptic firing, even after just five trials of pairing. Behaviorally, inhibition of CCK signaling blocked the generation of associative memory. Our results indicate that neocortical visuo-auditory association is formed through heterosynaptic plasticity, which depends on release of CCK in the neocortex mostly from entorhinal afferents.
Nuclear autophagy interactome unveils WSTF as a constitutive nuclear inhibitor of inflammation
Authors: Wang Yu , Eapen Vinay V. , Kournoutis Athanasios , Onorati Angelique , Li Xianting , Zhou Xiaoting , Cetinbas Murat , Wang Lu , Liu Jihe , Bretz Corey , Zhou Zhuo , Ho Sui Shannan J. , Saladi Srinivas Vinod , Sadreyev Ruslan I. , Adams Peter D. , Kingston Robert E. , Yue Zhenyu , Johansen Terje , Dou Zhixun
Published: October 2022

Macroautophagy (hereafter referred to as autophagy) degrades a variety of cellular components. A poorly understood area is autophagic degradation of nuclear substrates, or “nuclear autophagy”. It remains unclear what can be degraded by autophagy from the mammalian nuclei. We began our study by investigating the nuclear binding partners of ATG8 family proteins that play important roles in recognizing autophagy substrates. We systematically evaluated the ATG8 nuclear interactome in primary human cells and in mouse brain, identifying hundreds of novel interactions. We continued our study by evaluating the nuclear proteomes of cellular senescence, a stable form of cell cycle arrest program associated with inflammation, in which nuclear autophagy is involved. Combined with the ATG8 nuclear interactome data, we identified WSTF, a component of the ISWI chromatin remodeling complex, as a novel substrate of nuclear autophagy. The degradation of WSTF, mediated by a direct interaction with the GABARAP isoform of ATG8, promotes chromatin accessibility of inflammatory genes and induces senescence-associated inflammation. Furthermore, WSTF directly binds the p65 subunit of NF-κB and inhibits its acetylation, thus blocking inflammatory gene expression in the setting of senescence, cancer, and pathogen infection. In addition, we show that loss of WSTF is required for the immuno-surveillance of oncogenic Ras in mouse liver; forced expression of WSTF inhibited tumor-suppressive inflammation and led to the development of liver tumors. Taken together, our study provides a global view of mammalian nuclear autophagy and reveals a novel nuclear inhibitor of inflammation implicated in diverse pathological contexts. Targeting WSTF may be broadly valuable as therapeutic intervention of inflammatory diseases.
Structural Analysis of Phosphorylation Proteoforms in a Dynamic Heterogeneous System Using Flash Oxidation Coupled In-Line with Ion Exchange Chromatography
Authors: Cheng Zhi , Misra Sandeep K. , Shami Anter , Sharp Joshua S.
Published: October 2022

Protein post-translational modifications (PTMs) are key modulators of protein structure and function that often change in a dynamic fashion in response to cellular stimuli. Dynamic post-translational modifications are very challenging to structurally characterize using modern techniques, including covalent labeling methods, due to the presence of multiple proteoforms and conformers together in solution. Here, we have coupled ion exchange HPLC with a flash oxidation system (IEX LC-FOX) to successfully elucidate structural changes among three phosphoproteoforms of ovalbumin (OVA) during dephosphorylation with alkaline phosphatase (AP). Real-time dosimetry indicates no difference in effective radical dose between peaks or across the peak, demonstrating both the lack of scavenging of the NaCl gradient and the lack of a concentration effect on radical dose between peaks of different intensities. The use of IEX LC-FOX allows us to structurally probe each phosphoproteoform as it elutes from the column, capturing structural data before the dynamics of the system reintroduce heterogeneity. We found significant differences in residue-level oxidation between the hydroxyl radical footprint of non-phosphorylated, mono-phosphorylated and di-phosphorylated ovalbumin. Not only were our data consistent with the previously reported stabilization of ovalbumin structure by phosphorylation, but local structural changes were also consistent with the measured order of dephosphorylation of Ser344 being removed first. These results demonstrate the utility of IEX LC-FOX for measuring the structural effects of PTMs, even in dynamic systems.
Three-dimensional genome re-wiring in loci with Human Accelerated Regions
Authors: Keough Kathleen C. , Whalen Sean , Inoue Fumitaka , Przytycki Pawel F. , Fair Tyler , Deng Chengyu , Steyert Marilyn , Ryu Hane , Lindblad-Toh Kerstin , Karlsson Elinor ,   Zoonomia Consortium, Nowakowski Tomasz , Ahituv Nadav , Pollen Alex , Pollard Katherine S.
Published: October 2022

Human Accelerated Regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with the largest alignment of mammalian genomes to date. To facilitate exploration of accelerated evolution in other lineages, we implemented an open-source Nextflow pipeline that runs on any computing platform. Combining deep-learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains (TADs) containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci in multiple cell types suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.

One-Sentence Summary

Human-specific changes to 3D genome organization may have contributed to rapid evolution of mammalian-conserved loci in the human genome.
The nuclear Argonaute HRDE-1 directs target gene re-localization and shuttles to nuage to promote small RNA mediated inherited silencing
Authors: Ding Yue-He , Ochoa Humberto , Ishidate Takao , Mello Craig C.
Published: October 2022

Argonaute small-RNA pathways engage heterochromatin-silencing co-factors to promote transgenerational inheritance in animals. However, little is known about how heterochromatin and small-RNA pathways interact to transmit silencing. Here we show that the induction of heterochromatin silencing in C. elegans by RNAi or by artificially tethering pathway components to target RNA correlates with the co-localization of the target alleles in pachytene nuclei. Tethering the nuclear Argonaute WAGO-9/HRDE-1 induces heterochromatin formation, but also functions independently to induce small-RNA amplification. We show that HRDE-1 shuttles to nuage domains called mutator foci where amplification is thought to occur. Tethering a heterochromatin-silencing factor, NRDE-2, induces heterochromatin silencing and also induces the de-novo synthesis of HRDE-1 guide RNAs, and through HRDE-1 acts to further amplify downstream small-RNA silencing. Our findings support a model in which HRDE-1 functions both upstream, to initiate heterochromatin silencing, and downstream, to stimulate small-RNA amplification, establishing a self-enforcing mechanism that propagates silencing to offspring.
Atypical NMDA Receptors Limit Synaptic Plasticity in the Adult Ventral Hippocampus
Authors: Hurley Emily P. , Mukherjee Bandhan , Fang Lisa , Barnes Jocelyn R. , Nafar Firoozeh , Hirasawa Michiru , Parsons Matthew P.
Published: October 2022

N-methyl-D-aspartate receptors (NMDARs) assemble as functionally diverse heterotetramers. Incorporation of the GluN3A subunit into NMDARs alters conventional NMDAR properties by reducing both magnesium sensitivity and calcium permeability. GluN1 together with GluN3A can also form functional receptors that lack a glutamate binding site and instead serve as excitatory glycine receptors (eGlyRs). GluN3A expression is high in early development but naturally declines to low levels in most brain regions by adulthood. Interestingly, GluN3A expression remains elevated in the CA1 of the adult ventral hippocampus (VH), but not in the dorsal hippocampus (DH). The DH and VH are now well-understood to play very different functional roles, with the DH being primarily involved in cognitive functions and the VH in emotional processing. Why GluN3A persists in the adult VH, and the impact its presence has on glutamatergic neurotransmission in the VH is currently unknown. Here, we show that GluN3A remains elevated both at synaptic and extrasynaptic locations in the adult VH, assembling as GluN1/GluN2/GluN3A NMDARs with reduced magnesium sensitivity, as well as GluN1/GluN3A eGlyRs. By comparing various synaptic properties in the DH and VH of wild-type (WT) and GluN3A knockout (KO) mice, we demonstrate that GluN3A persistence in the VH attenuates glutamate release, limits postsynaptic calcium influx through NMDARs, and reduces the magnitude of NMDAR-dependent long-term potentiation. In comparison, GluN3A KO had relatively little effect on these same properties in the DH. In all, our data demonstrate that GluN3A persistence in the VH represents a key modulator of VH excitability and therefore may play a central role in emotional processing.
Distinct effects of disease-associated TREM2 R47H/+ and T66M mutations on iPSC-derived microglia
Authors: Penney Jay , Ralvenius William T , Loon Anjanet , Cerit Oyku , Dileep Vishnu , Milo Blerta , Woolf Hannah , Tsai Li-Huei
Published: October 2022

Genetic findings have highlighted key roles for microglia in the pathology of neurodegenerative conditions such as Alzheimer’s disease (AD). Distinct mutations in the microglial protein TREM2 (triggering receptor expressed on myeloid cells 2) are associated with different forms of neurodegeneration in humans; R47H/+ mutations increase AD risk, while loss-of-function mutations such as TREM2 T66M result in more severe forms of neurodegeneration. We employed gene editing and stem cell models to gain insight into the effects of these mutations on human iPSC-derived microglia. We found divergent effects of TREM2 R47H/+ and T66M mutations on gene expression, with R47H/+ cells exhibiting a pro-inflammatory gene expression signature. Both the TREM2 R47H/+ and T66M mutations caused similar impairments in microglial movement and the uptake of multiple substrates, while R47H/+ microglia were hyper-responsive to inflammatory stimuli, consistent with their gene expression signature. We developed an in vitro laser-induced injury model in neuron-microglia co-cultures, finding an impaired injury response by TREM2 R47H/+ microglia. Furthermore, in xenotransplantation experiments, mouse brains transplanted with TREM2 R47H/+ microglia exhibited reduced synaptic density. Consistently, we observed upregulation of multiple complement cascade components in TREM2 R47H/+ microglia, suggesting that inappropriate synaptic pruning may underlie the effect. Thus, these findings identify shared and distinct effects of these two TREM2 mutations on microglial gene expression and function. While the TREM2 T66M mutation impairs microglial movement and uptake processes, the TREM2 R47H/+ mutation additionally confers multiple potentially detrimental effects on human microglia, likely to underlie its association with AD.
X-ray diffraction with micrometre spatial resolution for highly absorbing samples
Authors: Chakrabarti Prerana , Wildeis Anna , Hartmann Markus , Brandt Robert , Döhrmann Ralph , Fevola Giovanni , Ossig Christina , Stuckelberger Michael Elias , Garrevoet Jan , Falch Ken Vidar , Galbierz Vanessa , Falkenberg Gerald , Modregger Peter
Published: October 2022

X-ray diffraction with high spatial resolution is commonly used to characterize (poly)crystalline samples with, for example, respect to local strain, residual stress, grain boundaries and texture. However, the investigation of highly absorbing samples or the simultaneous assessment of high-Z materials by X-ray fluorescence have been limited due to the utilization of low photon energies. Here, a goniometer-based setup implemented at the P06 beamline of PETRA III that allows for micrometre spatial resolution with a photon energy of 35 keV and above is reported. A highly focused beam was achieved by using compound refractive lenses, and high-precision sample manipulation was enabled by a goniometer that allows up to 5D scans (three rotations and two translations). As experimental examples, the determination of local strain variations in martensitic steel samples with micrometre spatial resolution, as well as the simultaneous elemental distribution for high-Z materials in a thin-film solar cell, are demonstrated. The proposed approach allows users from the materials-science community to determine micro-structural properties even in highly absorbing samples.
Employees' adoption of HR analytics – a theoretical framework based on career construction theory
Authors: Dhankhar Kiran , Singh Abhishek
Published: October 2022

Purpose

Drawing upon the career construction theory, the present study aims to propose and test a mediation model exploring the association among technology readiness, adoption of human resource (HR) analytics by HR professionals, and organizational career growth.

Design/methodology/approach

A survey has been conducted to collect data from HR professionals (N = 347) working in various industrial sectors in India. The data collected is analyzed for mediation using SPSS PROCESS Macro (Model 4).

Findings

The study provided evidence about the mediating role of individual adoption of HR analytics between technology readiness (motivators, inhibitors) and organization career growth (career goal progress, professional ability development, promotion speed and remuneration growth).

Research limitations/implications

Firstly, the results provide evidence in relation to the career construction theory with respect to adoption of human resource analytics by HR professionals. Secondly, the study findings validate the technology readiness model in the context of adopting HR analytics. Thirdly and most significantly, the study proposes a novel theoretical framework for adoption of HR analytics by HR professionals in organizations.

Practical implications

The findings imply that HR professionals' technology readiness (motivators and inhibitors) can facilitate better adoption of HR analytics in organizations. Moreover, the adoption of HR analytics shall promote better career growth for HR professionals.

Originality/value

The present study builds and tests a theoretical framework based on technology readiness, individual adoption of HR analytics, and organization career growth. The study is the first of its kind to the best of the authors' knowledge.