bluuebunny/crossref_metadata_2025 huggingface dataset:
Human iPSC 4R tauopathy model uncovers modifiers of tau propagation
Authors: Bravo Celeste Parra , Giani Alice Maria , Perez Jesus Madero , Zhao Zeping , Samelson Avi , Wong Man Ying , Evangelisti Alessandro , Fan Li , Pozner Tatyana , Mercedes Maria , Ye Pearly , Patel Tark , Yarahmady Allan , Carling Gillian , Lee Virginia M. Y. , Sharma Manu , Mok Sue-Ann , Luo Wenjie , Zhao Mingrui , Kampmann Martin , Gong Shiaoching , Gan Li
Published: June 2023

Tauopathies are age-associated neurodegenerative diseases whose mechanistic underpinnings remain elusive, partially due to lack of appropriate human models. Current human induced pluripotent stem cell (hiPSC)-derived neurons express very low levels of 4-repeat (4R)-tau isoforms that are normally expressed in adult brain. Here, we engineered new iPSC lines to express 4R-tau and 4R-tau carrying the P301SMAPTmutation when differentiated into neurons. 4R-P301S neurons display progressive Tau inclusions upon seeding with Tau fibrils and recapitulate features of tauopathy phenotypes, including shared transcriptomic signatures, autophagic body accumulation, and impaired neuronal activity. A CRISPRi screen of genes associated with Tau pathobiology identified over 500 genetic modifiers of Tau-seeding-induced Tau propagation, including retromer VPS29 and the UFMylation cascade as top modifiers. In AD brains, the UFMylation cascade is altered in neurofibrillary-tangle-bearing neurons. Inhibiting the UFMylation cascade suppressed seeding-induced Tau propagation. This model provides a powerful platform to identify novel therapeutic strategies for 4R tauopathy.
Why not both? A case study measuring cortisol and corticosterone in poison frogs
Authors: Westrick Sarah E. , Paitz Ryan T. , Fischer Eva K.
Published: June 2023

A general tenet in stress physiology is that the hypothalamic-pituitary-adrenal (HPA) axis predominantly produces one glucocorticoid (GC) in response to stressors. However, the two main glucocorticoids produced by vertebrates – cortisol and corticosterone – show variation across species in absolute levels, relative proportions, and stress responsivity. Therefore, focusing on a single GC may not tell the whole story. In this study, we measured both cortisol and corticosterone in water samples collected from five species of Dendrobatid poison frogs. Understanding the full picture of the physiological stress response in poison frogs is of special interest due to their susceptibility to environmental stressors and conservation status. Based on pioneering studies of steroidogenesis in a select few species of amphibians, corticosterone is thought to be dominant and more abundant in all amphibians. Counter to this idea, we found water-borne cortisol was more abundant than corticosterone in three of the five species.Dendrobates tinctoriusandPhyllobates terribilisreleased equal amounts of cortisol and corticosterone. When we stimulated the HPA axis inD. tinctorius, we found water-borne corticosterone was responsive to adrenocorticotropic hormone (ACTH), while cortisol did not change. Comparing plasma and water samples, we found water-borne cortisol was positively correlated with cortisol in plasma and the relationship between plasma and water-borne corticosterone was positive but not statistically significant. These results challenge the broadly accepted assumption that corticosterone is ‘dominant’ in amphibians and add to the growing literature highlighting the importance of measuring both GCs to understand (stress) physiology.
Identification of Natural Antiviral Drug Candidates Against Tilapia Lake Virus: Computational Drug Design Approaches
Authors: Sumon Md Afsar Ahmed , Asseri Amer H. , Molla Mohammad Habibur Rahman , Aljahdali Mohammed Othman , Hasan Md. Rifat , Rahman M. Aminur , Hasan Md. Tawheed , Sumon Tofael Ahmed , Gabr Mohamed Hosny , Islam Md. Shafiqul , Fakhurji Burhan , Moulay Mohammed , Larson Earl , Brown Christopher L.
Published: June 2023

Tilapia Lake Virus (TiLV) is a disease that affects tilapia fish, causing a high rate of sudden death at any stage of their growth. Unfortunately, there are currently no effective antiviral drugs or vaccines to control the progression of this disease. Researchers have discovered that the CRM1 protein plays a critical function in the development and spreading of animal viruses. By inhibiting CRM1, the virus’s spread in commercial fish farms can be suppressed. With this in mind, this study intended to identify potential antiviral drugs from two different tropical mangrove plants from tropical regions:Heritiera fomesandCeriops candolleana. To identify promising compounds that target the CRM1 protein, a computer-aided drug discovery approach is employed containing molecular docking, ADME (absorption, distribution, metabolism and excretion) analysis, toxicity assessment as well as molecular dynamics (MD) simulation. To estimate binding affinities of all phytochemicals, molecular docking is used and the top three candidate compounds with the highest docking scores were selected, which are CID107876 (-8.3), CID12795736 (-8.2), and CID12303662 (-7.9). We also evaluated the ADME and toxicity properties of these compounds. Finally, molecular dynamics simulation was conducted to analyze the stability of the protein-ligand complex structures and confirm the suitability of these compounds. The computational study demonstrated that the phytochemicals found inH. fomesandC. candolleanacould potentially serve as important inhibitors of TiLV, offering practical utility. However, furtherin vivoinvestigations are necessary to investigate the effectiveness of these compounds as antiviral drugs against the virus TiLV.
Exploring novel inflammation-related genetic and hematological predictors of response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer
Authors: Marinkovic Mladen , Stojanovic-Rundic Suzana , Stanojevic Aleksandra , Ostojic Marija , Gavrilovic Dusica , Jankovic Radmila , Maksimovic Natasa , Stroggilos Rafael , Zoidakis Jerome , Castellví-Bel Sergi , Fijneman Remond J.A. , Cavic Milena
Published: June 2023

Background

The standard initial treatment for locally advanced rectal cancer (LARC) is neoadjuvant chemoradiotherapy (nCRT). In order to select patients who would benefit the most from nCRT, there is a strong need for predictive biomarkers. The aim of this study was to evaluate the role of clinical, pathological, radiological, inflammation-related genetic, and hematological parameters in the prediction of response after nCRT.

Methods

In silicoanalysis of published transcriptomics datasets was conducted to identify the best candidate genes, whose expression will be measured using quantitative Real Time PCR (qRT-PCR) in pretreatment formaline-fixed paraffin-embedded (FFPE) samples. In this study, 75 patients with LARC, between June 2020 and January 2022, were prospectively included. Patients were assessed for tumor response in the 8th week after nCRT completion with pelvic MRI scan and rigid proctoscopy. For patients with a clinical complete response (cCR) and initially distant located tumor no immediate surgery was suggested (“watch and wait” approach). The response after surgery was assessed using histopathological tumor regression grading (TRG) categories from postoperative specimens by Mandard. Responders (R) were defined as patients with cCR without operative treatment, and those with TRG 1 and TRG 2 postoperative categories. Non-responders (NR) were patients classified as TRG 3-5.

Results

Responders group comprised 35 patients (46.6%) and NR group included 53.4% of patients. Analysis of published transcriptomics data identified genes that could predict response to treatment and their significance was assessed in our cohort by qRT-PCR. When comparison was made in the subgroup of patients who were operated (TRG1 vs. TRG4), the expression of IDO1 was significantly deregulated (p<0.05). Among hematological parameters between R and NR a significant difference in the response was detected for neutrophil-to-monocyte ratio (NMR), initial basophil, eosinophil and monocyte counts (p<0.01). According to MRI findings, non-responders were more often presented with extramural vascular invasion (p<0.05).

Conclusion

Based on logistic regression model, factors associated with favorable response to nCRT were found to be tumor morphology as well as hematological parameters which can be easily and routinely derived from initial laboratory results (NMR, eosinophil, basophil and monocyte counts) in a minimally invasive manner. Using various metrics, an aggregated score of the initial eosinophil, basophil, and monocyte counts demonstrated the best predictive performance.
Plaque characteristics derived from intravascular optical coherence tomography that predict major adverse cardiovascular events
Authors: Lee Juhwan , Gharaibeh Yazan , Zimin Vladislav N. , Kim Justin N. , Motairek Issam , Hassani Neda S. , Dallan Luis A. P. , Pereira Gabriel T. R. , Makhlouf Mohamed H. E. , Hoori Ammar , Al-Kindi Sadeer , Wilson David L.
Published: June 2023

Background

With its near histological resolution and its optical contrast, intravascular optical coherence tomography (IVOCT) is the only imaging modality that allows a unique assessment of microscopic plaque characteristics. This study aimed to investigate whether plaque characteristics derived from IVOCT could predict a long-term major adverse cardiovascular event (MACE).

Methods

This study was a single-center, retrospective study on 104 patients who had undergone IVOCT-guided percutaneous coronary intervention. Plaque characterization was performed using OCTOPUS software developed by our group. A total of 31 plaque features, including lesion length, lumen, calcium, fibrous cap (FC), and vulnerable plaque features (e.g., microchannel and cholesterol crystal), were computed from the baseline IVOCT images (obtained before stenting). For IVOCT plaque features, the discriminatory power for predicting MACE was determined using univariate/multivariate logistic regression as assessed by area under the receiver operating characteristic curve (AUC).

Results

Of 104 patients, MACE was identified in 24 patients (23.1%). Univariate logistic regression revealed that lesion length, maximum calcium angle, maximum calcium thickness, maximum FC angle, maximum FC area, and FC surface area were significantly associated with MACE (p<0.05). Additionally, cholesterol crystal and layered plaque showed a strong association with MACE (p<0.05). In the multivariate logistic analysis, only the FC surface area (OR 2.38, CI 0.98-5.83, p<0.05) was identified as a significant determinant for MACE, highlighting the importance of the 3D lesion analysis. The AUC of FC surface area for predicting MACE was 0.851 (95% CI 0.800-0.927, p<0.05). Luminal stenosis was not a strong predictor of the risk of MACE.

Conclusions

Patients with MACE had distinct plaque characteristics in IVOCT. In particular, large FC surface areas were a risk factor. Interestingly, cap thickness, a commonly highlighted feature for lesion vulnerability, was less predictive than cap area. Studies such as this one might someday lead to recommendations for pharmaceutical and interventional approaches.
Red flags for potential serious pathologies masquerading as musculoskeletal neck pain: a protocol for a systematic review of clinical practice guidelines
Authors: Feller Daniel , Chiarotto Alessandro , Koes Bart , Maselli Filippo , Mourad Firas
Published: June 2023

Background

Although benign most of the time, neck pain (NP) has been observed as the early manifestation of various serious cervical pathologies (e.g., malignancies, fractures). Red flags (RF) are signs and symptoms that raise suspicion of serious spinal pathology. Considering that it has been estimated that the incidence of delayed diagnosis of serious cervical pathologies ranges from 5% to 20%, investigating RFs for NP remains a priority for an informed practice and the patient’s safety. Therefore, the following systematic review will aim to identify red flags recommendations to triage serious pathologies in current clinical practice guidelines (CPGs) for patients with NP, to evaluate the consistency between different CPGs regarding RF recommendations, and to investigate on what study type the recommendation of CPGs are based.

Material and methods

We will search for CPGs for patients with specific or non – specific NP by searching MEDLINE (via PubMed), EMBASE, and PEDro electronic databases. Guidelines will also be searched through forward and backward citation tracking strategies (Web of Science), by consulting experts in the field, and by checking guideline organization databases. Also, we will screen the references of two recently published systematic reviews on CPGs for NP. For all the CPGs included, we will extract bibliographic information, the serious pathologies considered, the RF considered for all serious pathologies, the reference used to support all the RF cited in the guideline, and, if available, the diagnostic accuracy data for all the RF. Two authors will independently perform the study selection and data extraction processes.

Data synthesis

Results will be presented descriptively and using graphs and tables. We will evaluate the consistency among the guidelines in their endorsement of red flags using Fleiss’ kappa. Fleiss’ kappa will be presented separately for all serious pathologies the CPGs consider.
Predicting the impact of rare variants on RNA splicing in CAGI6
Authors: Lord Jenny , Oquendo Carolina Jaramillo , Wai Htoo A. , Douglas Andrew G.L , Bunyan David J. , Wang Yaqiong , Hu Zhiqiang , Zeng Zishuo , Danis Daniel , Katsonis Panagiotis , Williams Amanda , Lichtarge Olivier , Chang Yuchen , Bagnall Richard D. , Mount Stephen M. , Matthiasardottir Brynja , Lin Chiaofeng , van Overeem Hansen Thomas , Leman Raphael , Martins Alexandra , Houdayer Claude , Krieger Sophie , Bakolitsa Constantina , Peng Yisu , Kamandula Akash , Radivojac Predrag , Baralle Diana
Published: June 2023

Background

Variants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variant’s impact on splicing are needed to interpret the growing number of variants of unknown significance (VUS) identified by exome and genome sequencing. Here we present the results of the CAGI6 Splicing VUS challenge, which invited predictions of the splicing impact of 56 variants ascertained clinically and functionally validated to determine splicing impact.

Results

The performance of 12 prediction methods, along with SpliceAI and CADD, was compared on the 56 functionally validated variants. The maximum overall accuracy achieved was 82% from two different approaches, one weighting SpliceAI scores by minor allele frequency, and one applying the recently published Splicing Prediction Pipeline (SPiP). SPiP performed optimally in terms of sensitivity, while an ensemble method combining multiple prediction tools and information from databases exceeded all others for specificity.

Conclusions

Several challenge methods equalled or exceeded the performance of SpliceAI, with ultimate choice of prediction method likely to depend on experimental or clinical aims. One quarter of the variants were incorrectly predicted by at least 50% of the methods, highlighting the need for further improvements to splicing prediction methods for successful clinical application.
Evidence for glutamate excitotoxicity that occurs before the onset of striatal cell loss and motor symptoms in an ovine Huntington’s Disease model
Authors: Jiang Andrew , You Linya , Handley Renee R. , Hawkins Victoria , Reid Suzanne J. , Jacobsen Jessie C. , Patassini Stefano , Rudiger Skye R. , Mclaughlan Clive J. , Kelly Jennifer M. , Verma Paul J. , Bawden C. Simon , Gusella James F. , MacDonald Marcy E. , Waldvogel Henry J. , Faull Richard L.M. , Lehnert Klaus , Snell Russell G.
Published: June 2023

Background

Huntington’s disease (HD) is a neurodegenerative genetic disorder caused by an expansion in the CAG repeat tract of the huntingtin (HTT) gene resulting in a triad of behavioural, cognitive, and motor defects. Current knowledge of disease pathogenesis remains incomplete, and no disease course-modifying interventions are in clinical use. We have previously reported the development and characterisation of theOVT73transgenic sheep model of HD.OVT73captures an early prodromal phase of the disease with an absence of motor symptomatology even at 5-years of age and no detectable striatal cell loss.

Methods

To better understand the disease-initiating events we have undertaken a single nuclei transcriptome study of the striatum of an extensively studied cohort of 5-year-oldOVT73HD sheep and age matched wild-type controls.

Results

We have identified transcriptional upregulation of genes encoding N-methyl-D-aspartate (NMDA), α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and kainate receptors inOVT73medium spiny neurons, the cell type preferentially lost early in HD. This observation supports the glutamate excitotoxicity hypothesis as an early neurodegeneration cascade-initiating process. Moreover, we also observed the downstream consequences of excitotoxic stress, including a downregulation of transcription of components for the oxidative phosphorylation complexes. We also found that pathways whose activity has been proposed to reduce excitotoxicity, including the CREB family of transcription factors (CREB1,ATF2, ATF4andATF7) were transcriptionally downregulated.

Conclusions

To our knowledge, theOVT73model is the first large mammalian HD model that exhibits transcriptomic signatures of an excitotoxic process in the absence of neuronal loss. Our results suggest that glutamate excitotoxicity is a disease-initiating process. Addressing this biochemical defect early may prevent neuronal loss and avoid the more complex secondary consequences precipitated by cell death.
Comprehensive analysis of network reconstruction approaches based on correlation in metagenomic data
Authors: Fuschi Alessandro , Merlotti Alessandra , Tran Thi Dong Binh , Nguyen Hoan , Weinstock George M. , Remondini Daniel
Published: June 2023

Microbiome analysis is transforming our understanding of biological processes related to human health, epidemiology (antimicrobial resistance, horizontal gene transfer) environmental and agricultural studies. At the core of microbiome analysis is the description of microbial communities based on quantification of microbial taxa and dynamics. In the study of bacterial abundances, it is becoming more relevant to consider their relationship, to embed these data in the framework of network theory, allowing characterization of features like node relevance, pathway and community structure. In this work we characterize the principal biases in reconstructing networks from correlation measures, associated with the compositional character of relative abundance data, the diversity of abundances and the presence of unobserved species within a single sample, that might lead to wrong correlation estimates. We show how most of these problems can be overcome by applying typical transformations for compositional data, that allow the application of simple measures such as Pearson’s correlation to correctly identify the positive and negative relationships between relative abundances, when data dimensionality is sufficiently high. Some issues remain, like the role of data sparsity, that if not properly addressed can lead to imbalances in correlation coefficient distribution.
A Systems Level Explanation for Gompertzian Mortality Patterns is provided by the “Multiple and Inter-dependent Component Cause Model”
Authors: Nielsen Pernille Yde , Jensen Majken K , Mitarai Namiko , Bhatt Samir
Published: June 2023

Understanding and facilitating healthy aging has become a major goal in medical research and it is becoming increasingly acknowledged that there is a need for understanding the aging phenotype as a whole rather than focusing on individual factors. Here, we provide a universal explanation for the emergence of Gompertzian mortality patterns using a systems approach to describe aging in complex organisms that consist of many inter-dependent subsystems. Our model relates to the Sufficient-Component Cause Model, widely used within the field of epidemiology, and we show that including inter-dependencies between subsystems and modeling the temporal evolution of subsystem failure results in Gompertizan mortality on the population level. Our model also provides temporal trajectories of mortality-risk for the individual. These results may give insight into understanding how biological age evolves stochastically within the individual, and how this in turn leads to a natural heterogeneity of biological age in a population.
High prevalence of haemosporidian parasites in Eurasian Jays
Authors: Schumm Yvonne R. , Lederer-Ponzer Naemi , Masello Juan F. , Quillfeldt Petra
Published: June 2023

Avian haemosporidians are vector-borne blood parasites, which infect a great variety of avian host species. The order Passeriformes has the highest average infection probability; nevertheless, some common species of this order have been rather poorly studied in terms of haemosporidian prevalence and diversity. In this study, we investigated the prevalence of haemosporidians in one of such species, the Eurasian JayGarrulus glandarius(Corvidae), from a forest population in Hesse, Central Germany. All individuals were infected with at least one haemosporidian genus, i.e. an overall prevalence of 100%. The most common infection pattern was a mixed infection withHaemoproteusandLeucocytozoon, whereas noPlasmodiuminfection was detected. Our results regarding lineage diversity combined with data from other studies indicate a rather pronounced host-specificity ofHaemoproteusandLeucocytozoonlineages infecting birds of the family Corvidae.
Metabolic transitions regulate global protein fatty acylation
Authors: Talwadekar Manasi , Khatri Subhash , Balaji Chinthapalli , Chakraborty Arnab , Basak Nandini-Pal , Kamat Siddhesh , Kolthur-Seetharam Ullas
Published: June 2023

Intermediary metabolites and flux through various pathways have emerged as key determinants of post-translational modifications. Independently, dynamic fluctuations in their concentrations are known to drive cellular energetics in a bi-directional manner. Notably, intracellular fatty acid pools that drastically change during fed and fasted states act as precursors for both ATP production and fatty acylation of proteins. Protein fatty acylation is well regarded for its role in regulating structure and functions of diverse proteins, however the effect of intracellular concentrations of fatty acids on protein modification is less understood. In this regard, we unequivocally demonstrate that metabolic contexts, viz. fed and fasted states, dictate the extent of global fatty acylation. Moreover, we show that presence or absence of glucose, that influences cellular and mitochondrial uptake/utilization of fatty acids, affects palmitoylation and oleoylation, which is consistent with their intracellular abundance in fed and fasted states. Employing complementary approaches including click-chemistry, lipidomics and imaging, we show the top-down control of cellular metabolic state. Importantly, our results establish the crucial role of mitochondria and retrograde signaling components like SIRT4, AMPK and mTOR in orchestrating protein fatty acylation at a whole cell level. Specifically, pharmacogenetic perturbations that alter either mitochondrial functions and/or retrograde signaling affect protein fatty acylation. Besides illustrating the cross-talk between carbohydrate and lipid metabolism in mediating bulk post-translational modification, our findings also highlight the involvement of mitochondrial energetics.
Epigenomic analysis of Formalin-Fixed Paraffin-Embedded samples by CUT&Tag
Authors: Henikoff Steven , Henikoff Jorja G. , Ahmad Kami , Paranal Ronald M. , Janssens Derek H. , Russell Zachary R. , Szulzewsky Frank , Kugel Sita , Holland Eric C.
Published: June 2023

For more than a century, Formalin Fixed Paraffin Embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our single-tube CUTAC protocol are sufficient to produce high-resolution maps of paused RNA Polymerase II (RNAPII) at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumor specimens and identify regulatory element markers with high confidence and precision. Our simple work-flow is suitable for automation, making possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
Mechanism of DNA origami folding elucidated by mesoscopic simulations
Authors: DeLuca Marcello , Ye Tao , Poirier Michael , Ke Yonggang , Castro Carlos , Arya Gaurav
Published: June 2023

DNA nanotechnology leverages the canonical base-pairing rules and geometry of DNA to create highly precise nanoscale structures with many potential applications. While the design and fabrication of DNA nanostructures is well-established, the self-assembly process that produces these structures is still poorly understood, especially for DNA origami that involve the assembly of hundreds of strands. Many experimental and computational efforts have sought to better understand DNA origami folding, but the small length and time scales of individual binding events and the long timescale over which folding occurs have posed significant challenges. Here, we present a new mesoscopic model that uses a switchable force field to capture the mechanical behavior of single- and double-stranded DNA motifs and transition between them at a coarseness level of up to 8 nucleotides per particle, allowing access to the long assembly timescales of DNA origami up to several kilobases in size. Brownian dynamics simulations of 4-helix bundle (4HB) structures using this model reveal a hierarchical folding process involving the zipping of structural domains into a partially folded precursor structure followed by gradual crystallization into the final structure. We elucidate the role of hybridization strength, scaffold routing, and staple design in the folding order and kinetics. Simulation of larger 32HB structures reveals heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to smaller, more accessible structures like the 4HB, which exhibit first-order kinetics and virtually defect-free folding. The development of this model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.
Transcriptional profiling of aging tissues from female and male African turquoise killifish
Authors: Xu Alan , Teefy Bryan B. , Lu Ryan J. , Nozownik Séverine , Tyers Alexandra M. , Valenzano Dario R. , Benayoun Bérénice A.
Published: June 2023

The African turquoise killifish is an emerging vertebrate model organism with great potential for aging research due to its naturally short lifespan. Thus far, turquoise killifish aging ‘omic’ studies using RNA-seq have examined a single organ, single sex and/or evaluated samples from non-reference strains. Here, we describe a resource dataset of ribosomal RNA depleted RNA-seq libraries generated from the brain, heart, muscle, and spleen from both sexes, as well as young and old animals, in the reference GRZ turquoise killifish strain. We provide basic quality control steps and demonstrate the utility of our dataset by performing differential gene expression and gene ontology analyses by age and sex. Importantly, we show that age has a greater impact than sex on transcriptional landscapes across probed tissues. Finally, we confirm transcription of transposable elements (TEs), which are highly abundant and increase in expression with age in brain tissue. This dataset will be a useful resource for exploring gene and TE expression as a function of both age and sex in a powerful naturally short-lived vertebrate model.
Co-occurrence of ST412Klebsiella pneumoniaeisolates with hypermucoviscous and no-mucoviscous phenotypes in a short-term hospitalized patient
Authors: Liang Qinghua , Zhang Biying , Wang Wei , Chen Nan , Luo Jingjing , Zhong Ying , Zhang Feiyang , Zhang Zhikun , Martín–Rodríguez Alberto J. , Wang Ying , Xiang Li , Zhuang Jiaru , Hu Renjing , Zhou Yingshun
Published: June 2023

Hypermucoviscosity(HMV) is a phenotype that is commonly associated with hypervirulence inKlebsiella pneumoniae. The factors that contribute to the emergence of HMV subpopulations remain unclear. In this study, eightK. pneumoniaestrains were recovered from an inpatient who were hospitalized for 20 days. Three of the isolates exhibited a non-HMV phenotype, which was concomitant with increased biofilm formation and higher siderophore secretion than the other five HMV isolates. All eight isolates were highly susceptible to serum killing, albeit HMV strains were remarkably more infective than non-HMV counterparts in a mouse model of infection. Whole genome sequencing(WGS) showed that the eight isolates belonged to the K57-ST412 lineage. Average nucleotide identity(ANI) analysis indicated that eight isolates share 99.96% to 99.99% similarity and were confirmed to be the same clone. Through comparative genomics analysis, 12 non-synonymous mutations were found among these isolates, seven of which in the non-HMV variants, includingrmpA(R96G) andwbap(S435R), which are assumed to be associated with the non-HMV phenotype. The mutationsmanB(G440L),dmsB(R193W) andtkt(A643N) occurred in HMV isolates only. RNA-Seq and RT-qPCR revealed transcripts of genes involved in transporter activity, carbohydrate metabolism and energy metabolism, includingcysK,paaF,vasD,celCandfruA, to be significantly dysregulated in the non-HMV strain K201060 compared to the HMV strain K201059, suggesting a participation in HMV phenotype development. This study suggests that co-occurrence of HMV and non-HMV phenotypes in the same clonal population may be mediated by mutational mechanisms as well as by certain genes involved in transport and central metabolism.

Importance

K. pneumoniaewith a hypermucoviscosity(HMV) phenotype is a community-acquired pathogen that associated with increased invasiveness and pathogenicity, and underlying diseases are the most common comorbid risk factors inducing metastatic complications. HMV was earlier attributed to the overproduction of capsular polysaccharide, and more data point to the possibility of several causes contribute to this bacterial phenotype. Here, we describe a unique event in which the same clonal population showed both HMV and non-HMV characteristics. Studies have demonstrated that this process is influenced by mutational processes and genes related to transport and central metabolism. These finding provide fresh insight into the mechanisms between behind co-occurrence of HMV and non-HMV phenotypes in monoclonal populations as well as potentially being critical in developing strategies to control the further spread of HMVK. pneumoniae.
Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modelling and Clustering
Authors: Tsangaris Thomas E. , Smyth Spencer , Gomes Gregory-Neal W. , Liu Zi Hao , Milchberg Moses , Bah Alaji , Wasney Gregory A. , Forman-Kay Julie D. , Gradinaru Claudiu C.
Published: June 2023

The intrinsically disordered 4E-BP2 protein regulates mRNA cap-dependent translation through the interaction with the predominantly folded eukaryotic initiation factor 4E (eIF4E). Phosphorylation of 4E-BP2 dramatically reduces eIF4E binding, in part by stabilizing a binding- incompatible folded domain (REF). Here, we used a Rosetta-based sampling algorithm optimized for IDRs to generate initial ensembles for two phospho forms of 4E-BP2, non- and five-fold phosphorylated (NP and 5P, respectively), with the 5P folded domain flanked by N- and C-terminal IDRs (N-IDR and C-IDR, respectively). We then applied an integrative Bayesian approach to obtain NP and 5P conformational ensembles that agree with experimental data from nuclear magnetic resonance, small-angle X-ray scattering and single-molecule Förster resonance energy transfer (smFRET). For the NP state, inter-residue distance scaling and 2D maps revealed the role of charge segregation and pi interactions in driving contacts between distal regions of the chain (∼70 residues apart). The 5P ensemble shows prominent contacts of the N-IDR region with the two phosphosites in the folded domain, pT37 and pT46, and, to a lesser extent, delocalized interactions with the C-IDR region. Agglomerative hierarchical clustering led to partitioning of each of the two ensembles into four clusters, with different global dimensions and contact maps. This helped delineate an NP cluster that, based on our smFRET data, is compatible with the eIF4E-bound state. 5P clusters were differentiated by interactions of C-IDR with the folded domain and of the N-IDR with the two phosphosites in the folded domain. Our study provides both a better visualization of fundamental structural poses of 4E-BP2 and a set of falsifiable insights on intrachain interactions that bias folding and binding of this protein.
Do native and introduced cover crops differ in their ability to suppress weeds and reduce seedbanks? A Case study in a Table Grape Vineyard
Authors: Fernando Margaret R. , Hale Lauren , Shrestha Anil
Published: June 2023

Cover cropping is considered a valuable tool for integrated weed management. However, weed suppression by cover crops can be inconsistent. We hypothesized that a native cover crop species may have greater capacity to suppress weeds than an introduced species owing to adaptive advantages. A study was conducted from 2020 to 2022 in a newly-established Autumn King tablegrape vineyard in Parlier, CA. Two cover crop treatments, a native plant species, phacelia (Phacelia tanacetifolia), or an introduced species, rye (Secale cerealeL. ‘Merced’), were compared to a no cover crop, herbicide-managed control for impacts on weed control. Cover crops were sown in 2019 in the center 1.8 m of the 3.6 m space between the grapevine rows. The experimental design was a randomized complete block with four replications. Percent cover, weed density, and weed biomass in different seasons were assessed in the inter-row spaces and the vine rows. Soil samples were collected in 2021 from the grape row and interrow spaces to assess the weed seedbank. After the cover crops were terminated, percent weed cover was lower in the interrow of the phacelia compared to the no cover crop plots at two sampling times. When cover crops were actively growing (winter/spring), phacelia plots had a 7-fold higher cover crop to weed biomass ratio compared to that of the rye plots, thus indicating greater weed suppression. However, weed seedling emergence from the seedbank samples of the cover crop plots were 2- to 4-fold greater (in the phacelia and rye, respectively) than from the no cover crop plots. In summary, phacelia suppressed weeds more than rye; however, they both resulted in a bigger weed seedbank size compared to the herbicide-managed no cover crop plots, so additional management practices will be needed for long term weed management with cover crops in vineyards.
A Gene Therapy for Hereditary Nonpolyposis Colorectal Cancer using CRISPR-Cas9 Nickase
Authors: Kannan Shravan , Man Joshua J
Published: June 2023

Hereditary non-polyposis colorectal cancer (HNPCC) is an inherited disorder characterized by an increased risk of developing colorectal cancer before age 50. HNPCC is predominantly caused by genetic mutations in MLH1 and MSH2, which are involved in DNA mismatch repair. Current standard practice is to perform prophylactic colectomy, resulting in debilitating aftereffects for life. Though the genetic cause of HNPCC is well-known, there are currently no available treatments that target these mutations. Herein we describe a novel treatment protocol using a CRISPR-Cas9n-based genetic therapy to restore DNA mismatch repair. First, gRNA and template DNA targeting the most prevalent mutation clusters in MLH1 and MSH2 as well as CRISPR-Cas9n elements will be packaged into an integrase-deficient lentiviral vector. Then, the viral vector will be used to transduce human colonic tumor-derived organoids as well as administered systemically in mouse models of HNPCC. Mice will be monitored clinically and for signs of disease progression. At termination, colonic tissue will be harvested and analyzed for restoration of the wild-type MLH1 and MSH2 sequence and biochemical markers of HNPCC. This protocol offers an alternative strategy using CRISPR-Cas9n-based gene therapy to prevent tumor formation in patients, avoid morbid surgery, and significantly improve quality of life.
Evaluation ofApolipoprotein e4allele as susceptible factor for neurodegenerative diseases among Eastern Indians
Authors: Sadhukhan Dipanwita , Mishra Smriti , Mukherjee Priyanka , Biswas Atanu , Hui Subhra Prakash , Banerjee Tapas Kumar , Biswas Arindam
Published: June 2023

Introduction

Apolipoprotein E (ApoE) and age have been identified as the major risk factors for several neurodegenerative disorders. Among the three major isoforms (ApoE2, ApoE3 & ApoE4) ofAPOE, ApoE4often shows ethnicity dependent association with neurodegenerative diseases. In the present study, we aim to determine thee4allele/genotype frequency among the different neurodegenerative disorders and their correlation with several demographic and clinical parameters from eastern India.

Material & Methods

A total of 826 individuals were recruited for this study which includes 128 PD-MCI, 144 PDD, 90 DLB, 114 FTD, 94 AD and 256 unrelated neurologically controls from eastern India. Subjects were analysed forAPOEgenotype (E2, E3andE4) by PCR-RFLP techniques and Sanger sequencing.

Results

TheAPOE4allele was significantly associated with each of the disease subtypes, selected for the study (P = 0.016 to 0.000), whilee3allele was predominant among controls. Further stratification of subjects identified significant overrepresentation of (a) positive family history for FTD (P = 0.0414) & AD (P = 0.029) and (b) early age at onset of for PDD (P = 0.0316) and FTD (P = 0.0034) among thee4allele carriers. Furthermore, lowering of BMSE score was also observed among thee4allele carriers of AD subjects (P = 0.0324).

Conclusion

There is a significant association ofAPOE4allele with different neurodegenerative diseases influencing lowering of age at onset, BMSE score and positive family history among ethnic Bengali population of eastern India.
Tiny Earth CURE improves student persistence in science
Authors: Miller Sarah , Aldana Cristian Cervantes , Du Wenyi , Lee Hyewon , Maldonado Natalia , Sandoval Perla , Vong Janice , Young Gerald , Handelsman Jo , Broderick Nichole A. , Hernandez Paul R. , Estrada Mica
Published: June 2023

Course-based undergraduate research experiences (CUREs) enhance student retention in STEM, particularly among students who belong to historically excluded communities. Yet the mechanisms by which CUREs contribute to student integration and persistence are poorly understood. Utilizing the Tripartite Integration Model of Social Influence (TIMSI), this longitudinal study examines how Tiny Earth, an antibiotic-discovery CURE, impacts students’ scientific self-efficacy, scientific identity, endorsement of scientific community values, and intentions to persist in science. The study also explores how gains in TIMSI factors vary as a function of student demographics and course characteristics. Results of pre-and post-course measurements show that scientific self-efficacy and identity increased among students in Tiny Earth, and some student demographics and course characteristics moderated these gains. Gains in scientific self-efficacy, identity, and values correlated with gains in persistence intentions, whereas student demographics and course characteristics did not. Results of this study show that the Tiny Earth CURE enhanced students’ integration into the scientific community, which was linked to intentions of students of both historically underrepresented and majority groups to persist in STEM. We discuss how courses that provide opportunity to learn science skills in the context of a CURE can contribute toward enlarging and diversifying the STEM workforce.
Assembly processes of bacterial and fungal community differ between desert and oasis habitats in an arid inland river basin, northwest China
Authors: Wang Wen-Juan , Ding Yi-Ming , Ren Ming-Xun , Li Jing-Wen
Published: June 2023

Oasis habitat play a critical role in arid areas, yet little is known about microbial community assembly processes and its differences in oasis and desert habitat in arid inland river basin.

Herein, using 21 and 18 sample data respectively collected from oasis and desert habitats at the lower reaches of Heihe River, northwest China, we examined the assembly processes of soil bacterial and fungal communities and revealed the driving factors affecting the relative contributions of deterministic and stochastic processes.

We found that deterministic processes, especially variable selection, dominated bacterial community assembly in oasis habitat, while stochastic processes were more important in desert habitat. By contrast, stochastic processes dominated fungal community assembly both in oasis and desert habitats, in which dispersal limitation played a more important role. Environmental (e.g. EC) and biotic factors (microbial species associations) significantly mediated the bacterial community assembly. However, both environmental and biotic factors had little/no effects on fungal community assembly.

This study highlights the soil microbial community assembly is habitat- and taxon-dependent, and environmental (EC) and biotic factors play an important role in regulating these assembly processes in arid inland river basin.
Probing the dissociation pathway of a kinetically labile transthyretin mutant
Authors: Sun Xun , Ferguson James A. , Leach Benjamin I. , Stanfield Robyn L. , Dyson H. Jane , Wright Peter E.
Published: June 2023

Aggregation of transthyretin (TTR) is associated with devastating TTR amyloid disease. Amyloidosis begins with dissociation of the native tetramer to form a monomeric intermediate that assembles into pathogenic aggregates. This process is accelerated in vitro at low pH, but the dissociation and reassembly of TTR at neutral pH remains poorly understood, due to the low population of intermediates. We use NMR studies with a highly sensitive19F probe that allows deconvolution of relative populations of a destabilized A25T mutant at concentrations as low as 2 µM. The A25T mutation, located at the weak dimer interface, perturbs both the weak and strong dimer interfaces. A tetramer-dimer-monomer (TDM) equilibrium model is proposed to account for concentration- and temperature-dependent population changes. All thermodynamic and kinetic parameters and activation energetics for dissociation of the native A25T tetramer, as well as a destabilized alternative tetramer (T*) with a mispacked F87 side chain, were extracted by van’t Hoff and19F NMR line-shape analysis. The conversion from T to T*, the slowest first-order kinetic step, shows anti-Arrhenius behavior. The19F and methyl chemical shifts of probes close to the strong dimer interface in the dimer and T* species are degenerate, implicating interfacial perturbation as a common structural feature of these intermediate species. Molecular dynamics (MD) simulations further suggest more frequent F87 ring flipping on the nanoscale timescale in the A25T dimer than in the tetramer. Our integrated approach offers quantitative insights into the energy landscape of the dissociation pathway of TTR at neutral pH.
IRE1-mediated degradation ofpre-miR-301apromotes apoptosis through upregulation ofGADD45A
Authors: Gebert Magdalena , Bartoszewska Sylwia , Opalinski Lukasz , Collawn James F. , Bartoszewski Rafał
Published: June 2023

The unfolded protein response is a survival signaling pathway that is induced during various types of ER stress. Here we focus on the IRE1 pathway to determine IRE1’s role in miRNA regulation during ER stress. During induction of ER stress in human bronchial epithelial cells, we utilized next generation sequencing to demonstrate thatpre-miR-301aandpre-miR-106b, were significantly increased in the presence of an IRE1 inhibitor. Conversely, using nuclear-cytosolic fractionation on ER stressed cells, we found that these three pre-miRNAs were decreased in the nuclear fractions without the IRE1 inhibitor. We also found thatmiR-301a-3ptargets the proapoptotic UPR factor, growth arrest and DNA-damage-inducible alpha (GADD45A). InhibitingmiR-301a-3plevels or blocking its predicted miRNA binding site inGADD45A’s 3’ UTR with a target protector increasedGADD45AmRNA expression. An elevation ofXBP1sexpression had no effect onGADD45AmRNA expression. We also demonstrated that the introduction of a target protector for themiR-301a-3pbinding site inGADD45AmRNA during ER stress promoted cell death in the airway epithelial cells. These results indicated that IRE1’s endonuclease activity is a two-edged sword that splicesXBP1mRNA for survival and degradespre-miR-301ato elevate the mRNA expression of a pro-apoptotic gene, GADD45A.
Aberrant type 2 dopamine receptor availability in criminal psychopathy
Authors: Lukkarinen Lasse , Tuisku Jouni , Sun Lihua , Helin Semi , Karlsson Henry K. , Venetjoki Niina , Salomaa Marja , Rautio Päivi , Hirvonen Jussi , Lauerma Hannu , Tiihonen Jari , Nummenmaa Lauri
Published: June 2023

Background

Psychopathy is characterized by antisocial behavior, poor behavioral control and lacking empathy, and structural alterations in the corresponding neural circuits. Molecular brain basis of psychopathy remains poorly characterized.

Methods

Here we studied type 2 dopamine receptor (D2R) and mu-opioid receptor (MOR) availability in convicted violent offenders with high psychopathic traits (n=11) and healthy matched controls (n=19) using positron emission tomography (PET). D2R were measured with radioligand [11C]raclopride and MORs with radioligand [11C]carfentanil.

Results

Psychopathic subjects had lowered D2R availability in caudate and putamen, and D2R striatal availability was also associated with degree of psychopathic traits in this prisoner sample. No group differences were found in MOR availability, although in the prisoner sample, psychopathic traits were negatively correlated with MOR availability amygdala and nucleus accumbens.

Conclusions

We conclude that D2R signaling could be the putative neuromolecular pathway for psychopathy, whereas evidence for the aberrant MOR system is more limited.