bluuebunny/crossref_metadata_2025 huggingface dataset:
Serum and plasma protein biomarkers associated with frailty in patients with cirrhosis
Authors: Ha Nghiem B. , Seetharaman Srilakshmi , Kent Dorothea S. , Yao Frederick , Shui Amy M. , Huang Chiung-Yu , Walston Jeremy , Lai Jennifer C.
Published: March 2023

Frailty, a clinical phenotype of decreased physiological reserve, is a strong determinant of adverse health outcomes in patients with cirrhosis. The only cirrhosis-specific frailty metric is the Liver Frailty Index (LFI), which must be administered in person and may not be feasible for every clinical scenario. We sought to discover candidate serum/plasma protein biomarkers that could differentiate frail from robust patients with cirrhosis. A total of 140 adults with cirrhosis awaiting liver transplantation in the ambulatory setting with LFI assessments and available serum/plasma samples were included. We selected 70 pairs of patients on opposite ends of the frailty spectrum (LFI>4.4 for frail and LFI<3.2 for robust) who were matched by age, sex, etiology, HCC, and Model for End-Stage Liver Disease-Sodium. Twenty-five biomarkers with biologically plausible associations with frailty were analyzed using ELISA by a single laboratory. Conditional logistic regression was used to examine their association with frailty. Of the 25 biomarkers analyzed, we identified 7 proteins that were differentially expressed between frail and robust patients. We observed differences in 6 of the 7 proteins in the expected direction: (a) higher median values in frail versus robust with growth differentiation factor-15 (3682 vs. 2249 pg/mL), IL-6 (17.4 vs. 6.4 pg/mL), TNF-alpha receptor 1 (2062 vs. 1627 pg/mL), leucine-rich alpha-2 glycoprotein (44.0 vs. 38.6 μg/mL), and myostatin (4066 vs. 6006 ng/mL) and (b) lower median values in frail versus robust with alpha-2-Heremans-Schmid glycoprotein (0.11 vs. 0.13 mg/mL) and free total testosterone (1.2 vs. 2.4 ng/mL). These biomarkers represent inflammatory, musculoskeletal, and endocrine/metabolic systems, reflecting the multiple physiological derangements observed in frailty. These data lay the foundation for confirmatory work and development of a laboratory frailty index for patients with cirrhosis to improve diagnosis and prognostication.
Social Behavioral Impairments inSYNGAP1-Related Intellectual Disability
Authors: Naveed Hajera , McCormack Maria , Holder J. Lloyd
Published: March 2023

Synaptopathies are neurodevelopmental disorders caused by genetic mutations disrupting the development and function of neuronal synapses. We administered the validated Social Responsiveness Scale, Second Edition (SRS-2) to investigate the phenotypic presentation of social-behavioral impairments for the synaptopathy—SYNGAP1-related Intellectual Disability (SYNGAP1-ID) (n=32) compared with a phenotypically similar disorder Phelan-McDermid Syndrome (PMD) (n=27) and healthy controls (n=43). A short form SRS-2 analysis (n=85) was also conducted. BothSYNGAP1-ID and PMD had significantly elevated total and subcategory T-scores, with no significant score differences betweenSYNGAP1-ID and PMD, consistent between the full and short form. Mild to severe deficiencies in reciprocal social behavior were found in 100% of PMD individuals and 87.1% ofSYNGAP1-ID individuals. Additionally, the short form demonstrated greater utility forSYNGAP1-ID participants due to lower item-omission rates. In conclusion, significant impairment in reciprocal social behaviors is highly prevalent inSYNGAP1-ID.
Statistical Challenges when Analyzing SARS-CoV-2 RNA Measurements Below the Assay Limit of Quantification in COVID-19 Clinical Trials
Authors: Moser Carlee B , Chew Kara W , Giganti Mark J , Li Jonathan Z. , Aga Evgenia , Ritz Justin , Greninger Alex , Javan Arzhang Cyrus , Bender Ignacio Rachel A , Daar Eric S , Wohl David A , Currier Judith S , Eron Joseph J , Smith Davey M , Hughes Michael D
Published: March 2023

Most clinical trials evaluating COVID-19 therapeutics include assessments of antiviral activity. In recently completed outpatient trials, changes in nasal SARS-CoV-2 RNA levels from baseline were commonly assessed using analysis of covariance (ANCOVA) or mixed models for repeated measures (MMRM) with single-imputation for results below assay lower limits of quantification (LLoQ). Analyzing changes in viral RNA levels with singly-imputed values can lead to biased estimates of treatment effects. In this paper, using an illustrative example from the ACTIV-2 trial, we highlight potential pitfalls of imputation when using ANCOVA or MMRM methods, and illustrate how these methods can be used when considering values <LLoQ as censored measurements. Best practices when analyzing quantitative viral RNA data should include details about the assay and its LLoQ, completeness summaries of viral RNA data, and outcomes among participants with baseline viral RNA ≥LLoQ, as well as those with viral RNA <LLoQ.
Characterizing the limitations of using diagnosis codes in the context of machine learning for healthcare
Authors: Guo Lin Lawrence , Morse Keith E. , Aftandilian Catherine , Steinberg Ethan , Fries Jason , Posada Jose , Fleming Scott Lanyon , Lemmon Joshua , Jessa Karim , Shah Nigam , Sung Lillian
Published: March 2023

Importance

Diagnostic codes are commonly used as inputs for clinical prediction models, to create labels for prediction tasks, and to identify cohorts for multicenter network studies. However, the coverage rates of diagnostic codes and their variability across institutions are underexplored.

Objective

Primary objective was to describe lab- and diagnosis-based labels for 7 selected outcomes at three institutions. Secondary objectives were to describe agreement, sensitivity, and specificity of diagnosis-based labels against lab-based labels.

Methods

This study included three cohorts: SickKidsPedsfrom The Hospital for Sick Children, and StanfordPedsand StanfordAdultsfrom Stanford Medicine. We included seven clinical outcomes with lab-based definitions: acute kidney injury, hyperkalemia, hypoglycemia, hyponatremia, anemia, neutropenia and thrombocytopenia. For each outcome, we created four lab-based labels (abnormal, mild, moderate and severe) based on test result and one diagnosis-based label. Proportion of admissions with a positive label were presented for each outcome stratified by cohort. Using lab-based labels as the gold standard, agreement using Cohen’s Kappa, sensitivity and specificity were calculated for each lab-based severity level.

Results

The number of admissions included were: SickKidsPeds(n=59,298), StanfordPeds(n=24,639) and StanfordAdults(n=159,985). The proportion of admissions with a positive diagnosis-based label was significantly higher for StanfordPedscompared to SickKidsPedsacross all outcomes, with odds ratio (99.9% confidence interval) for abnormal diagnosis-based label ranging from 2.2 (1.7-2.7) for neutropenia to 18.4 (10.1-33.4) for hyperkalemia. Lab-based labels were more similar by institution. When using lab-based labels as the gold standard, Cohen’s Kappa and sensitivity were lower at SickKidsPedsfor all severity levels compared to StanfordPeds.

Conclusions

Across multiple outcomes, diagnosis codes were consistently different between the two pediatric institutions. This difference was not explained by differences in test results. These results may have implications for machine learning model development and deployment.
The First Insight into the Hereditary Fusion Gene Landscape of Amyotrophic Lateral Sclerosis
Authors: Yang Jinfeng , Yuan Fenghua , Palovcak Anna , Fei Ling , Zhuo Noah ,   NYGC ALS Consortium, Zhang Yanbin , Zhuo Degen
Published: March 2023

Amyotrophic lateral sclerosis (ALS) is a progressive nervous system disease that causes loss of muscle control. Over 30 mutated genes are associated with ASL. However, 90-95% of ASL cases have been found without a family history. Here, we have analyzed RNA-Seq data of NYGC ALS Consortium and identified fusion transcripts from ASL patients and non-neurologic controls (NNC). In this study, we combined previously-curated 1180 monozygotic (MZ) hereditary fusion genes (HFGs), and 204 HFGs discovered from NNC to analyze ASL fusion transcripts and identified 348 HFGs. Comparative analysis between ASL and GTEx shows that 139 HFGs are associated with ASL and ranged from 10.4% to 98.7% of 77 ASL patients. The most recurrent HFG isZNF528-ZNF880, detected in 98.7% of 77 ASL patients and 4.5% of 133 GTEx brain cortexes. Alignments of HFG transcripts from ASL with fusion transcripts from mesial temporal lobe epilepsy (MTLE) and Alzheimer’s disease (AD) showed that 43.9% and 11.6% of the ASL HFGs were present in MTLE and AD, respectively. The most recurrent and common HFG among ASL, MTLE, and AD wasADAMTSL3-SH3GL3, which behaves like ubiquitously-expressedSH3GL3-ADAMTSL3epigenetic fusion gene (EFG) and shows thatADAMTSL3-SH3GL3is a potential dormant or differentially-expressed HFG (dHFG), suggesting that they have common pathophysiological mechanisms. These HFGs associated with ASL have shown that HFGs are the missing genetic heritability and provide novel therapeutic targets for more efficient therapeutic drugs and methods to treat and cure many neurological diseases.
Prevalence of Elevated Blood Pressure and Left Ventricular Hypertrophy in Adolescents with Congenital Heart Disease
Authors: Walsh Aaron T. , Hor Kan N. , Eisner Mariah , Kallash Mahmoud , Spencer John David , Tran Andrew H.
Published: March 2023

Background

Left ventricular hypertrophy (LVH) associated with hypertension (HTN) is a predictor of cardiovascular (CV) events in adulthood. LVH is defined using left ventricular mass indexed to height2.7(LVMI-ht2.7) with current guidelines using the adult cutoff of 51 g/ht2.7; however, the pediatric cutoff is lower. Adults with congenital heart disease (CHD) have higher rates of HTN compared to the general adult population. Data on the prevalence of elevated blood pressure (SBP) in youths with CHD is limited. The aim of our study was to determine the prevalence of elevated BP and LVH in adolescents with CHD.

Methods

We retrospectively analyzed echocardiograms from patients with CHD from 2012-2019. Patients with biventricular CHD aged 13-17 years with documented BP, height, weight, and measurement of LVMI-ht2.7were included. We defined LVH using the pediatric cutoff of LVMI-ht2.7≥ 38.6 g/ht2.7. Patients were grouped by BP category into normotensive (NT, SBP < 120 mm Hg), Elevated BP (E-BP, 120 ≤ SBP < 130 mm Hg), Stage 1 HTN (HTN-1, 130 ≤ SBP < 140 mm Hg), and Stage 2 HTN (HTN-2, SBP ≥ 140 mm Hg). Prevalence of LVH was reported in each group defined as LVMI-HT2.7≥ 38.6 g/ht2.7.

Results

855 patients were included. Mean (± standard deviation, SD) age was 15.5±1.5 years with 485/855 (56.7%) male, SBP 117±13.5 mmHg, and LVMI-ht2.734.2±10.5 g/ht2.7. 493/855 (57.7%) were in the NT group, 214/855 (25%) in E-BP, 99/855 (11.6%) in HTN-1, and 49/855 (5.7%) in HTN-2. Prevalence of LVH increased with higher SBP with 96/493 (19.5%) in NT, 80/214 (37.4%) in E-BP, 32/99 (32.3%) in HTN-1, and 20/49 (40.8%) in HTN-2. Of youths with LVH, 49/228 (21.5%) met adult criteria of ≥ 51 g/ht2.7. Age, male sex, and body mass index (BMI) percentile were significantly associated with increased LVMI-ht2.7.

Conclusions

Youths with CHD have a high prevalence of elevated BP, HTN, and LVH. BMI is a significant risk factor for the development of LVH in this population. These findings support early screening for HTN in this group because youths with CHD have baseline increased CV risk that may be compounded by obesity and long-term HTN.

Clinical Perspective

What is new?

The prevalence of abnormal blood pressure and LVH in adolescents with CHD is understudied and our data show that HTN and LVH are common in this population.

One-fifth of adolescents with biventricular congenital heart disease and left ventricular hypertrophy met adult criteria for left ventricular hypertrophy.

What are the clinical implications?

Left ventricular hypertrophy secondary to hypertension is linked to adverse cardiac events in adulthood.

Early screening and detection for abnormal blood pressure in the adolescent congenital heart disease population may lead to earlier initiation of lifestyle interventions or pharmacotherapy and mitigate long-term adverse clinical and financial outcomes in an already vulnerable population.
Bipartite invariance in mouse primary visual cortex
Authors: Ding Zhiwei , Tran Dat T. , Ponder Kayla , Cobos Erick , Ding Zhuokun , Fahey Paul G. , Wang Eric , Muhammad Taliah , Fu Jiakun , Cadena Santiago A. , Papadopoulos Stelios , Patel Saumil , Franke Katrin , Reimer Jacob , Sinz Fabian H. , Ecker Alexander S. , Pitkow Xaq , Tolias Andreas S.
Published: March 2023

A defining characteristic of intelligent systems, whether natural or artificial, is the ability to generalize and infer behaviorally relevant latent causes from high-dimensional sensory input, despite significant variations in the environment. To understand how brains achieve generalization, it is crucial to identify the features to which neurons respond selectively and invariantly. However, the high-dimensional nature of visual inputs, the non-linearity of information processing in the brain, and limited experimental time make it challenging to systematically characterize neuronal tuning and invariances, especially for natural stimuli. Here, we extended “inception loops” — a paradigm that iterates between large-scale recordings, neural predictive models, andin silicoexperiments followed byin vivoverification — to systematically characterize single neuron invariances in the mouse primary visual cortex. Using the predictive model we synthesized Diverse Exciting Inputs (DEIs), a set of inputs that differ substantially from each other while each driving a target neuron strongly, and verified these DEIs’ efficacyin vivo. We discovered a novel bipartite invariance: one portion of the receptive field encoded phase-invariant texturelike patterns, while the other portion encoded a fixed spatial pattern. Our analysis revealed that the division between the fixed and invariant portions of the receptive fields aligns with object boundaries defined by spatial frequency differences present in highly activating natural images. These findings suggest that bipartite invariance might play a role in segmentation by detecting texture-defined object boundaries, independent of the phase of the texture. We also replicated these bipartite DEIs in the functional connectomics MICrONs data set, which opens the way towards a circuit-level mechanistic understanding of this novel type of invariance. Our study demonstrates the power of using a data-driven deep learning approach to systematically characterize neuronal invariances. By applying this method across the visual hierarchy, cell types, and sensory modalities, we can decipher how latent variables are robustly extracted from natural scenes, leading to a deeper understanding of generalization.
Identifying keystone species in microbial communities using deep learning
Authors: Wang Xu-Wen , Sun Zheng , Jia Huijue , Michel-Mata Sebastian , Angulo Marco Tulio , Dai Lei , He Xuesong , Weiss Scott T. , Liu Yang-Yu
Published: March 2023

Previous studies suggested that microbial communities harbor keystone species whose removal can cause a dramatic shift in microbiome structure and functioning. Yet, an efficient method to systematically identify keystone species in microbial communities is still lacking. This is mainly due to our limited knowledge of microbial dynamics and the experimental and ethical difficulties of manipulating microbial communities. Here, we propose a Data-driven Keystone species Identification (DKI) framework based on deep learning to resolve this challenge. Our key idea is to implicitly learn the assembly rules of microbial communities from a particular habitat by training a deep learning model using microbiome samples collected from this habitat. The well-trained deep learning model enables us to quantify the community-specific keystoneness of each species in any microbiome sample from this habitat by conducting a thought experiment on species removal. We systematically validated this DKI framework using synthetic data generated from a classical population dynamics model in community ecology. We then applied DKI to analyze human gut, oral microbiome, soil, and coral microbiome data. We found that those taxa with high median keystoneness across different communities display strong community specificity, and many of them have been reported as keystone taxa in literature. The presented DKI framework demonstrates the power of machine learning in tackling a fundamental problem in community ecology, paving the way for the data-driven management of complex microbial communities.
Phage display uncovers a sequence motif that drives polypeptide binding to a conserved regulatory exosite of O-GlcNAc transferase
Authors: Alteen Matthew G. , Meek Richard W. , Kolappan Subramania , Busmann Jil A. , Cao Jessica , O’Gara Zoe , Derda Ratmir , Davies Gideon J. , Vocadlo David J.
Published: March 2023

The modification of nucleocytoplasmic proteins by O-linked N-acetylglucosamine (O-GlcNAc) is an important regulator of cell physiology.O-GlcNAc is installed on over a thousand proteins by just one enzyme,O-GlcNAc transferase (OGT). How OGT is therefore regulated is therefore a topic of interest. To gain insight into these questions, we used OGT to perform phage display selection from an unbiased library of ∼108peptides of 15 amino acids in length. Following rounds of selection and deep mutational panning we identified a high-fidelity peptide consensus sequence, [Y/F]-x-P-x-Y-x-[I/M/F], that drives peptide binding to OGT. Peptides containing this sequence bind to OGT in the high nanomolar to low micromolar range and inhibit OGT in a non-competitive manner with low micromolar potencies. X-ray structural analyses of OGT in complex with a peptide containing this motif surprisingly revealed binding to an exosite proximal to the active site of OGT. This structure defines the detailed molecular basis driving peptide binding and explains the need for specific residues within the sequence motif. Analysis of the human proteome revealed this motif within 52 nuclear and cytoplasmic proteins. Collectively, these data suggest an unprecedented mode of regulation of OGT by which polypeptides can bind to this exosite to cause allosteric inhibition of OGT through steric occlusion of its active site. We expect these insights will drive improved understanding of the regulation of OGT within cells and enable the development of new chemical tools to exert fine control over OGT activity.

SIGNIFICANCE STATEMENT

Thousands of proteins within humans are modified by the monosaccharide N-acetylglucosamine (O-GlcNAc). O-GlcNAc regulates cellular physiology and is being pursued to create therapeutics. Remarkably, only one enzyme, O-GlcNAc transferase (OGT), installs O-GlcNAc and its regulation is poorly understood. By affinity selection using a vast peptide library, we uncover an amino acid sequence motif that drives binding of polypeptides to OGT. An OGT-peptide complex shows how this motif binds to an allosteric site proximal to the active site and inhibits OGT in an unprecedented manner. Given the distribution of this sequence motif within the human proteome proteins containing this motif likely regulate the activity of OGT, outlining a new mode by which OGT is controlled and opening new avenues for research.
A qualitative exploration into the role of illness perceptions in endometriosis-related quality of life
Authors: Moore Chloe , Cogan Nicola , Williams Lynn
Published: March 2023

Objectives

Endometriosis is linked to adverse quality of life (QoL) outcomes. In the absence of effective treatment for endometriosis-related symptoms, supporting the QoL of those experiencing endometriosis is crucial. Illness perception (IP) interventions have prompted modest increases in QoL in several chronic conditions, yet IPs have not been comprehensively studied in relation to endometriosis. It is, therefore, necessary to examine the IPs held by individuals experiencing endometriosis to establish whether IP-based interventions might be useful in supporting QoL in this population. This research aims to gain an understanding of the IPs held by people experiencing endometriosis and their impact on QoL.

Design

Qualitative using one-to-one online semi-structured interviews.

Methods

Thirty individuals with endometriosis participated. Interviews sought to gain an understanding of participants’ experiences and perceptions in relation to living with endometriosis. Reflexive thematic analysis was used to develop themes.

Results

Three major themes were developed: (1) a life disrupted; (2) lost and fragmented sense of self; and (3) complex emotional responses. Largely negative IPs were held by individuals living with the condition which, along with endometriosis-specific symptoms and reduced functioning, fuelled fears for the future and reduced QoL.

Conclusions

Endometriosis-specific symptoms fuelled adverse QoL outcomes directly, and indirectly through moulding IPs. The disruption to the life trajectory associated with experiencing the condition as well as perceptions of control had a major impact on participants’ wellbeing, self-concept, and the varied emotional responses associated with experiencing endometriosis. IP-based interventions may support the wellbeing of those experiencing endometriosis whilst effective treatment is sought.
6mA-Sniper: Quantifying 6mA Sites in Eukaryotes at Single-Nucleotide Resolution
Authors: Zhang Jie , Peng Qi , Ma Chengchuan , Wang Jiaxin , Xiao Chunfu , Li Ting , Liu Xiaoge , Zhou Liankui , Zhou Wei-Zhen , Ding Wanqiu , An Ni A. , Zhang Li , Liu Ying , Li Chuan-Yun
Published: March 2023

WhileN6-methyldeoxyadenine (6mA) modification has been linked to fundamental regulatory processes in prokaryotes, its prevalence and functional implications in eukaryotes are controversial. Here, we report 6mA-Sniper to quantify 6mA sites in eukaryotes at single-nucleotide resolution. With 6mA-Sniper, we delineated an accurate 6mA profile inC. eleganswith 2,034 sites, significantly enriched on sequences of [GC]GAG motif. Twenty-six of 39 6mA events with MnlI restriction endonuclease sites were experimentally verified, demonstrating the feasibility of this method. Notably, the enrichment of these 6mA sites on a specific sequence motif, their within-population conservation and the combinatorial patterns, and the selective constrains on them jointly support an active model for the shaping of the profile by some undiscovered methyltransferases. In a joint study (Cell Research, in revision), Maet al.reported METL-9 as a new methyltransferase in shaping the basal and stress-dependent 6mA profile inC. elegans. Notably, with the 6mA profile identified by 6mA-Sniper at single-nucleotide resolution, we found that the levels of 6mAs are significantly decreased in strains with the removal of METL-9 (METL-9 KO-OP50), while generally increased afterP. aeruginosainfection, further verified the efficiency of 6mA-Sniper in accurately pinpointing 6mA sites. Moreover, for the regions marked by 998 6mA sites emerged specifically after the infection, we identified an enrichment of the upregulated genes after the infection. The gene upregulations are likely mediated through a mutual exclusive crosstalk between 6mA and H3K27me3 modification, as supported by their co-occurrence, and the signal of increased H3K27me3 at regions marked by 6mAs depleted in METL-9 KO-OP50 strains. Notably, in differentC. elegansstrains, the cross-strain genetic variants removing 6mA sites are associated with the decreased expression of their host genes, and the removal of two randomly-selected 6mA events with genome editing directly decreased the expression of their host genes. We thus highlight 6mA regulation as a previously-neglected regulator of transcriptome in eukaryotes.
Single-cell RNA sequencing across isogenicFUSandTARDBPALS lines reveals a shared early mitochondrial dysfunction unique to motor neurons
Authors: Schweingruber Christoph , Nijssen Jik , Mechtersheimer Jonas , Reber Stefan , Leboeuf Melanie , O’Brien Niamh , Mei Irene , Hedges Erin , Keuper Michaela , Aguila Benitez Julio , Radoi Vlad , Jastroch Martin , Ruepp Marc-David , Hedlund Eva
Published: March 2023

Mutations in the RNA/DNA-binding proteins FUS and TDP-43 cause the fatal disease amyotrophic lateral sclerosis (ALS). The precise mechanisms behind the selective motor neuron degeneration remain unclear and it is uncertain if ALS-causative mutations trigger motor neuron death through shared or distinct pathogenic pathways. To address these two questions, we performed single-cell RNA sequencing across neuron types derived from isogenic induced pluripotent stem cell lines, harbouring FUS P525L, FUS R495X, TARDBP M337V mutations or FUS knockout. The mutations elicited 5- to 15-fold greater transcriptional responses in motor neurons than interneurons. Approximately 20% of transcripts uniquely dysregulated in motor neurons were shared across FUS mutations, with half being driven by FUS gain-of-function. Among these, a majority pointed towards mitochondrial impairments, with attenuated pathways shared with the TARDBP M337V mutation. Meta-analysis demonstrated convergence on mitochondrial dysfunction withC9orf72-ALS patient-derived motor neurons. We observed impaired mitochondrial motility across ALS motor axons, even in isogenic FUS R244C motor neurons, which retain FUS in the nucleus, demonstrating shared toxic gain-of-function mechanisms acrossFUS- andTARDBP-ALS, uncoupled from protein mislocalization. These early signs of mitochondrial dysfunction unique to motor neurons could have profound implications for their survival and represent promising therapeutic targets across multiple ALS forms.
Single-residue mutation in protein kinase C toggles between cancer and neurodegeneration
Authors: Jones Alexander C. , Kornev Alexandr P. , Weng Jui-Hung , Manning Gerard , Taylor Susan S. , Newton Alexandra C.
Published: March 2023

Conventional protein kinase C (PKC) isozymes tune the signaling output of cells, with loss-of-function somatic mutations associated with cancer and gain-of-function germline mutations identified in neurodegeneration. PKC with impaired autoinhibition is removed from the cell by quality-control mechanisms to prevent accumulation of aberrantly active enzyme. Here, we examine how a single residue in the C1A domain of PKCβ, arginine 42 (R42), permits quality-control degradation when mutated to histidine in cancer (R42H) and blocks downregulation when mutated to proline in the neurodegenerative disease spinocerebellar ataxia (R42P). Using FRET-based biosensors, we determined that mutation of R42 to any residue, including lysine, resulted in reduced autoinhibition as indicated by higher basal activity and faster agonist-induced plasma membrane translocation. R42 is predicted to form a stabilizing salt bridge with E655 in the C-tail and mutation of E655, but not neighboring E657, also reduced autoinhibition. Western blot analysis revealed that whereas R42H had reduced stability, the R42P mutant was stable and insensitive to activator-induced ubiquitination and downregulation, an effect previously observed by deletion of the entire C1A domain. Molecular dynamics (MD) simulations and analysis of stable regions of the domain using local spatial pattern (LSP) alignment suggested that P42 interacts with Q66 to impair mobility and conformation of one of the ligand-binding loops. Additional mutation of Q66 to the smaller asparagine (R42P/Q66N), to remove conformational constraints, restored degradation sensitivity to that of WT. Our results unveil how disease-associated mutations of the same residue in the C1A domain can toggle between gain- or loss-of-function of PKC.
A prebiotic genetic alphabet as an early Darwinian ancestor for pre-RNA evolution
Authors: Sawant Anupam A. , Tripathi Sneha , Galande Sanjeev , Rajamani Sudha
Published: March 2023

RNA-based genetic code is thought to be central to life’s emergence due to its dual ability for information transfer and catalysis. Nonetheless, the genetic code of early life was potentially not restricted to canonical genetic alphabets alone. The presence of an extensive repertoire of modified nucleobases in extant biology as ‘signatures of the past’, highlights the relevance of non-canonical alphabets, ably strengthened by experiments demonstrating their ready conversion into nucleosides and nucleotides. All these strongly support a pre-RNA World, wherein informational molecules are posited to have contained alternate genetic alphabets. Nevertheless, understanding pre-RNA molecules’ capacity to acquire emergent function has remained less prevalent. Further, the steps involved in their transition to a canonical RNA World has not been systematically studied in the origins of life framework. In this study, we report the synthesis of a prebiotically relevant genetic alphabet containing the non-canonical nucleobase, barbituric acid. We demonstrate for the first instance the enzymatic incorporation of this prebiotically plausible alphabet (BaTP) into an RNA, using proteinaceous T7 RNA polymerase. Pertinently, the incorporation of this genetic alphabet into a baby spinach aptamer did not affect its overall secondary structure, while also allowing it to retain its aptameric function. Furthermore, we demonstrate the faithful transfer of genetic information from pre-RNA-containing barbitudine nucleotides to DNA, using a high-fidelity RNA-dependent DNA polymerase. These findings allude to a putative pathway for the early molecular evolution of the genetic code of extant life.
Adaptive host responses to infection can resemble parasitic manipulation
Authors: Håkonsrud Jensen Camilla , Weidner Jacqueline , Giske Jarl , Jørgensen Christian , Eliassen Sigrunn , Mennerat Adèle
Published: March 2023

Using a dynamic optimisation model for juvenile fish in stochastic food environments, we investigate optimal hormonal regulation, energy allocation and foraging behaviour of a growing host infected by a parasite that only incurs an energetic cost. We find it optimal for the infected host to have higher levels of orexin, growth- and thyroid hormones, resulting in higher activity levels, increased foraging, and faster growth. This growth strategy thus displays several of the fingerprints often associated with parasite manipulation: higher levels of metabolic hormones, faster growth, higher allocation to reserves (i.e. parasite-induced gigantism), higher risk taking and eventually higher predation rate. However, there is no route for manipulation in our model, so these changes reflect adaptive host compensatory responses. Interestingly, several of these changes also increase the fitness of the parasite. Our results call for caution when interpreting observations of gigantism or risky host behaviours as parasite manipulation without further testing.
Upfront Menin-inhibitor resistance in multiply pretreated leukemias
Authors: Mahdavi Leila , Goodrow Haley , Alikarami Fatemeh , Lenard Alexandra , Riedel Simone S. , Libbrecht Clara , Bowser Isabel , Tasian Sarah K. , Falkenstein Catherine D. , Manning Bryan , Skuli Sarah , Carroll Martin P. , Wertheim Gerald , Cai Sheng F. , McGeehan Gerard , Xie Hongbo M. , Bernt Kathrin M.
Published: March 2023

Inhibitors of the Menin-KMT2A interaction are promising agents for the treatment ofKMT2A-rearranged (KMT2A-r) leukemias. We evaluated Menin inhibition in patient derived xenografts ofKMT2A-rleukemias with high-risk features. Three AMLs with high-risk fusion partners (MLLT10, MLLT4) and two infant ALL samples were sensitive to Menin inhibition. We also evaluated serial samples from two patients with multiply relapsed ALL. We found that highly pretreatedKMT2A-AFF1ALL samples were much less sensitive compared to cells obtained earlier in the same patients’ disease course. Since none of the patients had been treated with a Menin inhibitor, resistance in these highly pretreated samples was acquired in the absence to Menin inhibitor exposure. Transcriptomic analysis documented sustained on-target efficacy towards the canonical targets in the Menin-inhibitor in resistant cells. Targeted genomic analysis documented the emergence of multiple co-mutations, including RAS pathway andTP53mutations, although neither was sufficient to induce Menin-inhibitor resistance in vitro. Downregulation of KMT3D may account for resistance in one patients; inactivation of KMT2C/D had previously been reported to result in Menin inhibitor resistance. Future studies will need to clarify more broadly which genomic/epigenomic alterations drive upfront resistance. Regardless of mechanism, our data supports using Menin-inhibitors upfront or in early lines of therapy before substantial genomic or epigenomic evolution has occurred.
DnaJC7 specifically regulates tau seeding
Authors: Perez Valerie A. , Sanders David W. , Mendoza-Oliva Ayde , Stopschinski Barbara E. , Mullapudi Vishruth , White Charles L , Joachimiak Lukasz A. , Diamond Marc I.
Published: March 2023

Neurodegenerative tauopathies are caused by accumulation of toxic tau protein assemblies. This appears to involve template-based seeding events, whereby tau monomer changes conformation and is recruited to a growing aggregate. Several large families of chaperone proteins, including Hsp70s and J domain proteins (JDPs) cooperate to regulate the folding of intracellular proteins such as tau, but the factors that coordinate this activity are not well known. The JDP DnaJC7 binds tau and reduces its intracellular aggregation. However, it is unknown whether this is specific to DnaJC7 or if other JDPs might be similarly involved. We used proteomics within a cell model to determine that DnaJC7 co-purified with insoluble tau and colocalized with intracellular aggregates. We individually knocked out every possible JDP and tested the effect on intracellular aggregation and seeding. DnaJC7 knockout decreased aggregate clearance and increased intracellular tau seeding. This depended on the ability of the J domain (JD) of DnaJC7 to bind to Hsp70, as JD mutations that block binding to Hsp70 abrogated the protective activity. Disease-associated mutations in the JD and substrate binding site of DnaJC7 also abrogated its protective activity. DnaJC7 thus specifically regulates tau aggregation in cooperation with Hsp70.
A general computational design strategy for stabilizing viral class I fusion proteins
Authors: Gonzalez Karen J. , Huang Jiachen , Criado Miria F. , Banerjee Avik , Tompkins Stephen , Mousa Jarrod J. , Strauch Eva-Maria
Published: March 2023

Many pathogenic viruses, including influenza virus, Ebola virus, coronaviruses, and Pneumoviruses, rely on class I fusion proteins to fuse viral and cellular membranes. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more favorable and stable postfusion state. An increasing amount of evidence exists highlighting that antibodies targeting the prefusion conformation are the most potent. However, many mutations have to be evaluated before identifying prefusion-stabilizing substitutions. We therefore established a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. As a proof of concept, we applied this principle to the fusion protein of the RSV, hMPV, and SARS-CoV-2 viruses. For each protein, we tested less than a handful of designs to identify stable versions. Solved structures of designed proteins from the three different viruses evidenced the atomic accuracy of our approach. Furthermore, the immunological response of the RSV F design compared to a current clinical candidate in a mouse model. While the parallel design of two conformations allows identifying and selectively modifying energetically less optimized positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. We recaptured many approaches previously introduced manually for the stabilization of viral surface proteins, such as cavity-filling, optimization of polar interactions, as well as postfusion-disruptive strategies. Using our approach, it is possible to focus on the most impacting mutations and potentially preserve the immunogen as closely as possible to its native version. The latter is important as sequence re-design can cause perturbations to B and T cell epitopes. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.
LIPUS attenuates knee joint capsule fibrosis and athrogenic contracture through the TGF-β1/Smad signaling pathway
Authors: Zhou Ting , Wang Feng , Zhou Yun , Zhou Chen Xu , Zhang Quan Bing
Published: March 2023

As one of main causes of athrogenic contracture, joint capsule fibrosis which is described as a condition with excessive deposition of collagen components and extracellular matrix (ECM) in joint capsule, is a response to long-time immobilization. The purpose of this study was to explore the effect and the underlying mechanism of low-intensity pulsed ultrasound (LIPUS) in treating knee joint capsule fibrosis. A rabbit model of knee joint capsule fibrosis induced by 6w-immobilization was employed in this study. The degree of knee joint capsule fibrosis was assessed by measurement of arthrogenic contracture and Masson-staining. Furthermore, malondialdehyde (MDA) and superoxide dismutase (SOD) were measured to assess the level of reactive oxygen species (ROS). Apart from these, the activation of TGF-β1/Smad signaling pathway was determined through western blot analysis contained TGF-β1, Smad2, p-Smad2, Smad3, p-Smad3 and Smad4, and immunohistochemical staining for p-Smad2/3 positive cells. After 6 wk-immobilization, the degree of arthrogenic contracture and the collagen density were increased. Moreover, the activity of MDA was upregulated and the content of SOD was downregulated. Correspondingly, the TGF-β1/Smad signaling pathway was significantly activated. After 2 wk-LIPUS treatment, the degree of arthrogenic contracture and the collagen density were lower than 2 wk-remobilizaiton. Relatively, the activity of MDA was decresed and the content of SOD was increased compared with 2 wk-remobilizaiton. Importantly,the TGF-β1/Smad signaling pathway was significantly inhibited compared with 2 wk-remobilizaiton. Our findings thus conclude that high level ROS and hyperactive TGF-β1/Smad signaling pathway might be one of the causes of knee joint capsule fibrosis induced by immobilization and LIPUS attenuated the severity of immobilization-induced knee joint capsule fibrosis through inhibition of the production of ROS and the activation of TGF-β1/Smad signaling pathway. Our findings might provide a theoretical basis for knee joint capsule fibrosis after immobilization and provide the potential therapeutic target.
The role of airborne particles in the epidemiology of clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus in commercial poultry production units
Authors: James Joe , Warren Caroline J. , De Silva Dilhani , Lewis Thomas , Grace Katherine , Reid Scott M. , Falchieri Marco , Brown Ian H. , Banyard Ashley C
Published: March 2023

Since October 2021, Europe has experienced the largest avian influenza virus (AIV) epizootic, caused by clade 2.3.4.4b H5N1 high pathogenicity AIV (HPAIV), with over 320 poultry and captive bird infected premises (IPs) and 2480 dead H5N1 positive wild birds detected in Great Britain alone. Many IPs have been detected as geographical clusters, raising questions around potential lateral spread between premises by airborne particles. Airborne transmission over short distances has been reported for some AIVs strains. However, the risk of airborne spread of this strain remains to be elucidated. We conducted extensive sampling from IPs where clade 2.3.4.4b H5N1 HPAIVs was confirmed during the 2022/23 epizootic, each representing a major poultry species (ducks, turkeys, and chickens). A range of environmental samples were collected inside and outside houses, including deposited dust, feathers, and other potential fomites. Viral RNA (vRNA) and infectious virus were detected in air samples collected from inside and outside, but in close proximity, of infected houses, with vRNA alone being detected greater distances (>10m) outside. Some dust samples collected outside of the affected houses contained infectious virus, while feathers from the affected houses, located up to 60m away, only contained vRNA. Together, these data suggest that airborne particles harbouring infectious HPAIV can be translocated short distances (<10m) through the air, while particles containing vRNA might travel further (<50m). Therefore, the potential for airborne transmission of clade 2.3.4.4b H5N1 HPAIV between premises is considered low. Other factors, including indirect contact with wild birds, fomite spread and the efficiency of biosecurity represent greater importance in disease incursion.

IMPORTANCE

Understanding the routes of avian influenza virus incursion into poultry premises is critical to ensure the implementation of effective preventative measures, reducing the risk of spread of the virus. Extensive environmental sampling across three infected premises, representing the major global commercial poultry species, detected viral RNA and infectious virus in air samples, dust, and other fomites inside of the houses containing infected poultry, as well as within the immediate proximity of infected houses. This suggests that particles harbouring infectious virus may travel short distances outside of affected houses, which may potentially contribute to house-to-house transmission on the same premises, but not at distances likely to contribute to the transmission to another poultry premises. Consequently, control efforts should be focused on traditional, robust biosecurity measures at key barriers on poultry houses. Human behaviour in and around poultry houses as factors contributing to biosecurity risks should be considered.
Drift of neural ensembles driven by slow fluctuations of intrinsic excitability
Authors: Delamare Geoffroy , Zaki Yosif , Cai Denise J , Clopath Claudia
Published: March 2023

Representational drift refers to the dynamic nature of neural representations in the brain despite the behavior being seemingly stable. Although drift has been observed in many different brain regions, the mechanisms underlying it are not known. Since intrinsic neural excitability is suggested to play a key role in regulating memory allocation, fluctuations of excitability could bias the reactivation of previously stored memory ensembles and therefore act as a motor for drift. Here, we propose a rate-based plastic recurrent neural network with slow fluctuations of intrinsic excitability. We first show that subsequent reactivations of a neural ensemble can lead to drift of this ensemble. The model predicts that drift is induced by co-activation of previously active neurons along with neurons with high excitability which leads to remodeling of the recurrent weights. Consistent with previous experimental works, the drifting ensemble is informative about its temporal history. Crucially, we show that the gradual nature of the drift is necessary for decoding temporal information from the activity of the ensemble. Finally, we show that the memory is preserved and can be decoded by an output neuron having plastic synapses with the main region.
A Machine Learning approach to study plant functional trait divergence
Authors: Majumder Sambadi , Mason Chase M.
Published: March 2023

Premise of the study

Plant functional traits are often used to describe spectra of ecological strategies among species. Here we demonstrate a machine learning approach for identifying the traits that contribute most to interspecific phenotypic divergence in multivariate trait space.

Methods

Descriptive and predictive machine learning approaches were applied to trait data for the genusHelianthus, including Random Forest and Gradient Boosting Machine classifiers, Recursive Feature Elimination, and the Boruta algorithm. These approaches were applied at the genus level as well as within each of the three major clades within the genus to examine the variability in major axes of trait divergence in three independent species radiations.

Key Results

Machine learning models were able to predict species identity from functional traits with high accuracy, and differences in functional trait importance were observed between the genus level and clade levels indicating different axes of phenotypic divergence.

Conclusions

Applying machine-learning approaches to identify divergent traits can provide insights into the predictability or repeatability of evolution through comparison of parallel diversification of clades within a genus. These approaches can be implemented in a range of contexts across basic and applied plant science from interspecific divergence to intraspecific variation across time, space, and environmental conditions.
compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes
Authors: Paril Jefferson , Zare Tannaz , Fournier-Level Alexandre
Published: March 2023

The dawn of cost-effective genome assembly is enabling deep comparative genomics to address fundamental evolutionary questions by comparing the genomes of multiple species. However, comparative genomics analyses often deploy multiple, often purpose-built frameworks, limiting their transferability and replicability. Here, we developed compare_genomes, a transferable and extensible comparative genomics workflow package which streamlines the identification of orthologous families within and across genomes and tests for the presence of several mechanisms of evolution (gene family expansion or contraction and substitution rates within protein-coding sequences).
Proximity interaction analysis of thePlasmodium falciparumputative ubiquitin ligasePfRNF1 reveals a role in RNA regulation
Authors: Farrukh Afia , Musabyimana Jean Pierre , Distler Ute , Tenzer Stefan , Pradel Gabriele , Ngwa Che Julius
Published: March 2023

Some proteins have acquired both ubiquitin ligase activity and RNA-binding properties and are therefore known as RNA-binding Ubiquitin ligases (RBULs). These proteins provide a link between the RNA metabolism and the ubiquitin proteasome system (UPS). The UPS is a crucial protein surveillance system of eukaryotes primarily involved in the selective proteolysis of proteins which are covalently marked with ubiquitin through a series of steps involving ubiquitin E1 activating, E2 conjugating and E3 ligating enzymes. The UPS also regulates other key cellular processes such as cell cycle, proliferation, cell differentiation, transcription and signal transduction. While RBULs have been characterized in other organisms, little is known about their role inPlasmodium falciparum, the causative agent of the deadliest human malaria, malaria tropica. In this study, we characterized a previously identified putativeP. falciparumRING finger E3 ligasePfRNF1. We show that the protein is highly expressed in sexual stage parasites and mainly present in immature male gametocytes. Using proximity interaction studies with parasite lines expressingPfRNF1 tagged with the Biotin ligase BirA, we identified an interaction network ofPfRNF1 in both the asexual blood stages and gametocytes composed mainly of ribosomal proteins, RNA-binding proteins including translational repressors such DOZI, CITH, PUF1 and members of the CCR4-NOT complex, as well as proteins of the UPS such as RPN11, RPT1 and RPT6. Our interaction network analysis revealsPfRNF1 as a potential RNA-binding E3 ligase which links RNA dependent processes with protein ubiquitination to regulate gene expression.

Importance

RBULs provide a link between RNA-mediated processes with the ubiquitin system. Only a few RBULs have been identified and none has been characterized in the malaria parasiteP. falciparum. In this study, we unveiled the interactome of the putativeP. falciparumE3 ligasePfRNF1. We show thatPfRNF1 interacts with both proteins of the ubiquitin system as well as RNA-binding proteins therefore indicating that it is a putative RBUL which links RNA regulation with the ubiquitin system inP. falciparum.