bluuebunny/crossref_metadata_2025 huggingface dataset:
Student and staff experiences of a novel curriculum-based peer support intervention (“study groups”) to support the mental health and wellbeing of postgraduate taught students
Authors: McCloud Tayla , James Tiffeny , Rowe Sarah , Huntley Jonathan , Lewis Gemma , Callender Claire , Johnson Sonia , Billings Jo
Published: February 2024

Background

In recent years there has been increasing concern for the wellbeing of higher education students, and institutions are under pressure to act. Loneliness and social isolation appear common among students, particularly postgraduate taught (PGT) students, and are linked to adverse outcomes such as depression and abandoning studies. We have in place a novel curriculum-based peer support intervention (“study groups”) that may help support the mental health and wellbeing of postgraduate taught students.

Aim

This study aimed to explore student and staff experiences of the study groups and their perceptions of how they may influence social cohesion, loneliness and wellbeing.

Methods

Qualitative semi-structured interviews were conducted with students and staff to explore their experiences and views of the study groups intervention. Transcripts of the interviews were analysed by the study authors following the principles of reflexive thematic analysis.

Results

We completed interviews with 20 students and five staff members. We found that students valued the study groups as a way to make friends, improve feelings of connectedness and cohesion, and receive emotional support. The shared experience of group members was key, although completing joint assignments could be a stressor for some.

Conclusions

This research suggests that this is a promising intervention to support the mental health and wellbeing of higher education students, and to reduce loneliness and improve social cohesion.
Factors associated with commuting stress among tertiary education employees in Georgetown, Guyana
Authors: Van-Veen Davon , Jamme Hue-Tam , Ross Heather , Chhetri Netra
Published: February 2024

The aim of this study was to identify factors associated with commuting stress using symptomatology among tertiary education employees in Georgetown Guyana. A cross sectional survey was conducted among 427 (100 male, 317 female) participants, with a mean age of 29.6(sd=8.7) years. Data about their demographic characteristics, psychosocial measures (perceived stress, coping and resilience), characteristics about their commute (length, mode, and satisfaction with commute infrastructure), and how often they experienced selected symptoms associated with stress on the daily commute was collected using a self administered questionnaire. A commuting stress score was calculated for each participant and this was followed by regression analysis. The results showed that after controlling for resiliency, coping, perception of job, total life stress, income levels and education all of which can contribute to how persons perceive hassles in their lives, the regression model demonstrated that females, persons who used public transportation, persons who have longer commute times and persons who are less satisfied with the commute infrastructure are more likely to report that they experience symptoms associated with stress while engaged in the daily commute compared to males, persons who use private transportation, persons who have shorter commute times and persons who are more satisfied with the commute infrastructure respectively. Once all controlled variables were accounted for, it appears that for this study population, age, where they live and whether or not they actively or passively commuted did not have any meaningful impact on whether they would report if they experienced stress associated symptoms while engaged in the daily commute. he results suggest the need for a multi-pronged approach to address commuting stress, involving individual healthcare, mental-health-centric urban transport design, improved commute infrastructure, and increased employer engagement. Future studies employing qualitative and experimental methods are recommended.
Identifying temporal patterns in the progression of neurodegenerative disease using unsupervised clustering
Authors: Giannoula Alexia , De Paepe Audrey E. , Sanz Ferran , Furlong Laura I. , Camara Estela
Published: February 2024

Objectives

One of the principal goals of Precision Medicine is to stratify patients by accounting for individual variability. However, extracting meaningful information from Real-World Data, such as Electronic Health Records, still remains challenging due to methodological and computational issues.

Materials & methods

A Dynamic Time Warping-based unsupervised-clustering methodology is presented in this paper for the clustering of patient trajectories of multi-modal health data on the basis of shared temporal characteristics. Building on an earlier methodology, a new dimension of time-varying numerical clinical and imaging features (six in total) is incorporated, through an adapted cost-minimization algorithm for clustering on different, possibly overlapping, feature subsets. A cluster evaluation process is also implemented, by admitting two user-defined parameters (granularity threshold and feature contribution). The model disease chosen is Huntington’s disease (HD), characterized by progressive neurodegeneration.

Results

From a wide range of examined user-defined parameters, four case examples are highlighted to exemplify the combined effects of feature weights and granularity threshold in the stratification of HD trajectories in homogeneous clusters. For each identified cluster, polynomial fits that describe the temporal behavior of the assessed features are provided for an informative comparison, together with their averaged values.

Discussion

The proposed data-mining methodology permits the stratification of distinct time patterns of multi-modal health data in individuals that share a diagnosis or future diagnosis, employing user-customized criteria beyond the current clinical practice.

Conclusions

This work bears implications for better analysis of individual variability in disease progression, opening doors to personalized preventative, diagnostic and therapeutic strategies.
Polygenic Prediction of Cellular Immune Responses to Mumps Vaccine
Authors: Coombes Brandon J. , Ovsyannikova Inna G. , Schaid Daniel J. , Warner Nathaniel D. , Poland Gregory A. , Kennedy Richard B.
Published: February 2024

In this report, we provide a follow-up analysis of a previously published genome-wide association study of host genetic variants associated with inter-individual variations in cellular immune responses to mumps vaccine. Here we report the results of a polygenic score (PGS) analysis showing how common variants can predict mumps vaccine response. We found higher PGS for IFNγ, IL-2, and TNFα were predictive of higher post-vaccine IFNγ (p-value = 2e-6), IL-2 (p = 2e-7), and TNFα (p = 0.004) levels, respectively. Control of immune responses after vaccination is complex and polygenic in nature. Our results suggest that the PGS-based approach enables better capture of the combined genetic effects that contribute to mumps vaccine-induced immunity, potentially offering a more comprehensive understanding than traditional single-variant GWAS. This approach will likely have broad utility in studying genetic control of immune responses to other vaccines and to infectious diseases.
FATAL: A Forensic AuTopsy Annotation tooL for digital recording of autopsy findings
Authors: Petersen Mikkel V. , Thomsen Asser H. , Hansen Kasper
Published: February 2024

The findings from forensic autopsies, where cause of death must be established and reported to legal authorities, are reported in paper-based formats. Practitioners are required to map 3D injury findings to 2D space. Here, we design and describe a digital Forensic AuTopsy Annotation tooL (FATAL), that can be used by practitioners to record systematically detailed autopsy findings onto an interactive 3D body model.

We employ a user-centred design process involving an expert forensic medicine team. We describe the iteration process and the final functionality determined, based on in-depth analyses of forensic clinical workflows, and feedback on the types of complex cases confronting practitioners.

FATAL functions include freehand drawing, a layer system for injury categorisation, trajectory plotting, surface area markings, and point-of-interest marking. Relevant external images, such as investigative report or autopsy photographs, can be loaded into the FATAL tool and assigned to individual annotations. The application streamlines workflows, supports template-driven documentation, and collates all forensic data into a single interface. Findings from the digital tool can be exported to a 2D report (PDF).

We highlight the advancements in accuracy, efficiency, and reproducibility afforded by a digital tool for forensic autopsy documentation. Potential applications in forensic medical examinations beyond autopsies are described, along with specific areas for extension, such as supporting touch screen and pen inputs, export for 3D printing models and extending the tool’s compatibility with custom 3D body models.

Highlights

FATAL is a digital platform for systematised detailed documentation of autopsy findings

The platform enables accurate annotation of injuries onto a 3D body model

Allows the forensic pathologist to move from traditional paper-based body diagrams to interactive 3D visualisations

The platform can export annotations to 2D body diagrams and embed them directly in custom PDF templates
Changes in injecting versus smoking heroin, fentanyl, and methamphetamine among people who inject drugs in San Diego, California, 2020 to 2023
Authors: Eger William H. , Abramovitz Daniela , Bazzi Angela R. , Bórquez Annick , Vera Carlos F. , Harvey-Vera Alicia , Friedman Joseph R. , Strathdee Steffanie A.
Published: February 2024

Background

Amidst a rapidly evolving drug supply in North America, people who inject drugs may be transitioning to smoking them. We aimed to assess changes in injecting and smoking heroin, fentanyl and methamphetamine among a cohort of people who injected drugs at baseline from San Diego, California.

Methods

Over five six-month periods spanning October 2020–April 2023, we assessed prevalence of injecting and smoking opioids or methamphetamine and whether participants used these drugs more frequently by smoking than injecting. Multivariable Poisson regression via Generalized Estimating Equations was used to examine time trends.

Results

Of 362 participants, median age was 40 years; most were male (72%), non-Hispanic (55%), and unhoused (67%). Among this cohort, of whom 100% injected (or injected and smoked) at baseline, by period five (two years later), 34% reported only smoking, while 59% injected and smoked, and 7% only injected. By period five, the adjusted relative risk (aRR) of injecting opioids was 0.41 (95% Confidence Interval [CI]: 0.33, 0.51) compared to period one, and the aRR for injecting methamphetamine was 0.50 (95% CI: 0.39, 0.63). Compared to period one, risks for smoking fentanyl rose significantly during period three (aRR=1.44, 95% CI: 1.06, 1.94), four (aRR=1.65, 95% CI: 1.24, 2.20) and five (aRR=1.90, 95% CI: 1.43, 2.53). Risks for smoking heroin and methamphetamine more frequently than injecting these drugs increased across all periods.

Conclusions

Opioid and methamphetamine injection declined precipitously, with notable increases in smoking these drugs. Research is urgently needed to understand the health consequences of these trends.
Mechanical confinement induces ferroptosis through mitochondrial dysfunction
Authors: Zhou Fang , Ju Robert J. , Kang Chenlu , Li Jiayi , Yang Ao , Libert Alexandre , Sun Yujie , Liang Ling , Hu Xiaoqing , Stehbens Samantha J. , Wu Congying
Published: February 2024

Cells exist in highly crowded environments where they are exposed to fluctuating mechanical forces arising from surrounding cells and the extracellular matrix microenvironment. In these settings, external forces are transmitted to intracellular organelles including the nucleus. While cells can survive confinement, extended duration of confinement or confinement in settings where cells are unable to escape, can result in cell death. How cells sense and respond to prolonged confinement to trigger cell death remains unclear. Here, we demonstrate that nuclear deformation generated by axial confinement triggers the programmed cell death pathway – ferroptosis. We show that axial confinement results in Drp1-dependent mitochondrial fragmentation and cPLA2 translocation to mitochondria, where Drp1 undergoes acute phase separation. Ensuing mitochondrial ROS accumulation and arachidonic acid production concertedly leads to lipid peroxidation evoking ferroptosis. Finally, of clinical relevance, we find that in human osteoarthritis tissue cPLA2 exhibits mitochondrial localization and high ROS levels. Together, our findings unveil a pivotal role for Drp1 and cPLA2 in linking mechanical confinement with mitochondrial dysfunction resulting in ferroptosis, which sheds new light on a mechanical mechanism of pathophysiology in osteoarthritis.
Thymidine Phosphorylase Mediates SARS-CoV-2 Spike Protein Enhanced Thrombosis in K18-hACE2TGMice
Authors: Roytenberg Renat , Yue Hong , DeHart Autumn , Kim Eugene , Bai Fang , Kim Yongick , Denning Krista , Kwei Alec , Zhang Quan , Liu Jiang , Zheng X. Long , Li Wei
Published: February 2024

COVID-19, caused by SARS-CoV-2, is associated with arterial and venous thrombosis, thereby increasing mortality. SARS-CoV-2 spike protein (SP), a viral envelope structural protein, is implicated in COVID-19-associated thrombosis. However, the underlying mechanisms remain unknown. Thymidine phosphorylase (TYMP), a newly identified prothrombotic protein, is upregulated in the plasma, platelets, and lungs of patients with COVID-19 but its role in COVID-19-associated thrombosis is not defined. In this study, we found that wild-type SARS-CoV-2 SP significantly promoted arterial thrombosis in K18-hACE2TGmice. SP-accelerated thrombosis was attenuated by inhibition or genetic ablation of TYMP. SP increased the expression of TYMP, resulting in the activation of signal transducer and activator of transcription 3 (STAT3) in BEAS-2B cells, a human bronchial epithelial cell line. A siRNA-mediated knockdown of TYMP inhibited SP-enhanced activation of STAT3. Platelets derived from SP-treated K18-hACE2TGmice also showed increased STAT3 activation, which was reduced by TYMP deficiency. Activated STAT3 is known to potentiate glycoprotein VI signaling in platelets. While SP did not influence ADP- or collagen-induced platelet aggregation, it significantly shortened activated partial thromboplastin time and this change was reversed by TYMP knockout. Additionally, platelet factor 4 (PF4) interacts with SP, which also complexes with TYMP. TYMP enhanced the formation of the SP/PF4 complex, which may potentially augment the prothrombotic and procoagulant effects of PF4. We conclude that SP upregulates TYMP expression, and TYMP inhibition or knockout mitigates SP-enhanced thrombosis. These findings indicate that inhibition of TYMP may be a novel therapeutic strategy for COVID-19-associated thrombosis.

Key Points

SARS-CoV-2 spike protein, thymidine phosphorylase, and platelet factor 4 form a complex that may promote clot formation.

Inhibiting thymidine phosphorylase attenuates SARS-CoV-2 spike protein-enhanced thrombosis, platelet activation, and coagulation.
Optimizing contrast in automated 4D-STEM cryo-tomography
Authors: Seifer Shahar , Kirchweger Peter , Edel Karlina Maria , Elbaum Michael
Published: February 2024

4D-STEM is an emerging approach to electron microscopy. While it has been developed principally for high resolution studies in materials science, the possibility to collect the entire transmitted flux makes it attractive for cryo-microscopy in application to life science and radiation-sensitive materials where dose efficiency is of utmost importance. We present a workflow to acquire tomographic tilt series of 4D-STEM datasets using a segmented diode and an ultra-fast pixelated detector, demonstrating the methods using a specimen of T4 bacteriophage. Full integration with the SerialEM platform conveniently provides all the tools for grid navigation and automation of the data collection. Scripts are provided to convert the raw data to mrc format files, and further to generate a variety of modes representing both scattering and phase contrast, including incoherent and annular bright field, integrated center of mass (iCOM), and parallax decomposition of a simulated integrated differential phase contrast (iDPC). Principal component analysis of virtual annular detectors proves particularly useful, and axial contrast is improved by 3D deconvolution with an optimized point spread function. Contrast optimization enables visualization of irregular features such as DNA strands and thin filaments of the phage tails, which would be lost upon averaging or imposition of an inappropriate symmetry.
Proteomics-based characterization of ribosome heterogeneity in adult mouse organs
Authors: Brunchault Marie R , Hesse Anne-Marie , Schaeffer Julia , Decourt Charlotte , Combes Florence , Nawabi Homaira , Couté Yohann , Belin Stephane
Published: February 2024

While long thought to be invariable in all cellular organisms, evidence has emerged that the translation process,i.e.protein assembly from mRNA sequence decoding, is regulated by variable features of the translation machinery. Notably, ribosomes, the functional units of protein synthesis, display variations in their composition, depending on the developmental stage, cell type or physiopathological context, thus providing a new level of actionable regulation of gene expression. Yet, a comprehensive map of the heterogeneity of ribosome composition in ribosomal proteins (RPs) in different organs and tissues is not available. In this work, we explored tissue-specific ribosome heterogeneity using mass spectrometry-based quantitative proteomic characterization of ribosomal fractions purified from 14 adult mouse organs and tissues. We performed crossed clustering and statistical analyses of RP composition to highlight stable, variable and tissue-specific RPs across organs and tissues. Focusing on specific RPs, we validated their relative abundance with a targeted proteomic approach, which gave further insight into the tissue-specific ribosome RP signature. Finally, we investigated the origin of RP variations in ribosome fraction of the different tissues, by comparing RP relative abundances in our proteomic dataset and in three independent transcriptomic datasets. Interestingly, we found that, in some tissues, the RP abundance in purified ribosomes does not always correlate with the corresponding RP transcript level, arguing for a translational regulation of RP expression, and/or a regulated incorporation of RPs into ribosomes. Altogether, our data support the notion of a tissue-specific RP signature of ribosomes, which opens avenues to study how specific ribosomal composition provides an additional level of regulation to control gene expression in different tissues and organs.
Induction of expansion of ex vivo NK cells using a new feeder cell built in Brazil. An extended flow cytometry evaluation of K562.mbIL21.4BBL
Authors: Watanabe Caroline Mitiká , Ishihama Suzuki Caroline , Marins dos Santos Alessandro , Aloia Thiago Pinheiro Arrais , Lee Grace , Wald David , Okamoto Oswaldo Keith , Azevedo Julia T. Cottas de , Godoy Juliana Aparecida Preto de , Santos Fabio P. S. , Weinlich Ricardo , Kerbauy Lucila N. , Kutner Jose Mauro , Paiva Raquel de Melo Alves , Hamerschlak Nelson
Published: February 2024

Background

Natural killer (NK) cells are lymphocytes from the innate immune system capable of promoting an antitumor response through activation and inhibition receptors. NK cells can better mediate cell engraftment after hematopoietic stem cell transplantation (HSCT), decreasing relapse rates and preventing viral diseases after HSCT. These characteristics make NK cells eligible for application in cell therapy by increasing the frequency of NK cells in peripheral blood. Manufacturing and using feeder cells is necessary to expand NK cells while keeping their cytotoxic characteristics.

Aims

We aimed to develop feeder cells from a K562 leukemic cell line capable of promoting clonal expansion of NK cells ex vivo while preserving its antitumor potential.

Methods and results

Feeder cells, named K562.clone1, were produced by transduction of mbIL-21 and 4-1BBL proteins. Next, peripheral blood NK cells were co-cultivated with K562.clone1 and expanded more than 100 folds compared to NK cells co-cultivated with K562-WT (less than 10 folds). On the first day of cultivation, the average frequency of NK cells (CD3-CD56+CD16+/−) was 5.95% ± 3.92%, increasing to 83.97% ± 8.19% on the fourteenth day after co-cultivation with K562.Clone1, while the percentage of NK cells raised to 75.15% ± 7.57% when co-cultivated with control. In addition, NK cells expanded with the feeder K562.Clone1 were potentially cytotoxic against acute myeloid leukemia (AML) blast, tumor cell lines of leukemia and glial origin.

Conclusion

We successfully built a national feeder cell, named K562.Clone1. The co-culture with K562.Clone1 feeder cell, preserving their primordial functions such as missing-self, important to distinguish health and defective cell, and natural cytotoxicity against tumoral cells, and increasing the natural cytotoxicity.
Y chromosome sequencing data suggests dual paths of haplogroup N1a1 into Finland
Authors: Preussner Annina , Leinonen Jaakko , Riikonen Juha , Pirinen Matti , Tukiainen Taru
Published: February 2024

The paternally inherited Y chromosome is highly informative of genetic ancestry, therefore making it useful in studies of population history. In Finland, two Y- chromosomal haplogroups reveal the major substructure of the population: N1a1 (TAT) enriched in the northeast and I1a (M253) in the southwest, suggested to reflect eastern and western ancestry contributions to the population. Yet, beyond these major Y-chromosomal lineages, the distribution of finer-scale Y- chromosomal variation has not been assessed in Finland. Here we provide the most comprehensive Y-chromosomal study among the Finns up to date, exploiting full sequences for 1,802 geographically mapped Finnish Y chromosomes from the FINRISK project. We assessed the distribution of common Y-chromosomal haplogroups (frequency ≥ 1%) throughout 19 Finnish regions, and further compared the autosomal genetic backgrounds of the Y-chromosomal haplogroups. With such high-resolution data, we identified novel sublineages and geographical enrichment patterns among the major Finnish haplogroups N1a1 (64%), I1a (25%), R1a (4.3%), and R1b (4.8%). Most notably, we discovered that haplogroup N1a1 splits into three major lineages within the country. While two of the sublineages followed a northeastern enrichment pattern observed for N1a1 in general, the sublineage N1a1a1a1a1a (CTS2929) (22% of all samples) displayed an enrichment in the southwest. Further, the carriers of this haplogroup showed a high proportion of southwestern autosomal ancestry unlike the other N1a1 sublineages. Collectively, these results point to distinct demographics within haplogroup N1a1, possibly induced by two distinct arrival routes into Finland. Overall, our study suggests a more complex genetic population history for Finns than previously proposed.
Laboratory application of the Aquascope approach of automated imaging and classification for long-term plankton monitoring
Authors: Merkli Stefanie , Reyes Marta , Pomati Francesco
Published: February 2024

Anthropogenic changes such as climate change and pollution have strong effects on plankton and its ecosystem services. In freshwater, phytoplankton forms the basis of the food web and plays a key role in water quality. It is therefore important to monitor the plankton community. In Switzerland, lake plankton has been monitored for decades by cantonal authorities. But in the future, there will be a limitation in the availability of trained taxonomists that are able to count plankton samples under the microscope as well as time and budget constraints. New technologies will be needed to fulfil the federal requirements on the monitoring of lakes in the future. Here we focus on two such instruments, both based on plankton automated imaging: the FlowCam and the Aquascope. The first is a commercially available instrument, the second is custom made. They are the only automated imaging instruments that can track freshwater plankton across the desired size range (phytoplankton and zooplankton). Their design makes them the state of the art technologies to make quantitative observations of plankton. While the FlowCam is a laboratory instrument, the Aquascope is originally designed for field deployment. In this report, we focus the empirical work on the laboratory application of the Aquascope approach of automated imaging and classification for long term plankton monitoring. We find that there are major advantages of the Aquascope approach but the application as a laboratory instrument still needs further development. The major advantages of the Aquascope approach compared to traditional, human-supervised, microscopy methods are the automation and the speed of the data processing, the availability of individual level traits and the management of the data generated. One of the major drawbacks is the lack of taxonomic resolution (mostly at the genus level). Nevertheless, we show that with a larger benchmarking project, it might be possible to continue the long term time series on a coarse taxonomic level as usually reported by cantonal authorities to the general public. We discuss advantages and limitations of Aquascope relative to traditional microscopy and FlowCam, and propose ways forward for future development and application of this approach.
Enterovirus A71 adaptation to heparan sulfate comes with capsid stability tradeoff
Authors: Tee Han Kang , Mathez Gregory , Cagno Valeria , Antanasijevic Aleksandar , Clément Sophie , Tapparel Caroline
Published: February 2024

Because of high mutation rates, viruses constantly adapt to new environments. When propagated in cell lines, certain viruses acquire positively charged amino acids on their surface proteins, enabling them to utilize negatively charged heparan sulfate (HS) as an attachment receptor. In this study, we used enterovirus A71 (EV-A71) as model and demonstrated that unlike the parental MP4 variant, the cell-adapted strong HS-binder MP4-97R/167G does not require acidification for uncoating and releases its genome in the neutral or weakly acidic environment of early endosomes. We experimentally confirmed that this pH-independent entry is not associated with the use of HS as an attachment receptor but rather with compromised capsid stability. We then extended these findings to another HS-dependent strain, suggesting that adaptation to HS generally modifies capsid stability and alters entry mechanism. Our data show EV-A71 pH-independent entry for the first time and, more importantly, highlight the intricate interplay between HS-binding, capsid stability, and viral fitness, wherein enhanced multiplication in cell lines leads to attenuation in hostilein vivoenvironments such as the gastrointestinal tract.
m6A landscape is more pervasive whenTrypanosoma bruceiexits the cell cycle
Authors: Serra Lúcia , Pereira Sara Silva , Viegas Idálio J. , Machado Henrique , López-Escobar Lara , Figueiredo Luisa M
Published: February 2024

N6-methyladenosine (m6A) is a mRNA modification with important roles in gene expression. In African trypanosomes, this post-transcriptional modification is detected in hundreds of transcripts and it affects the stability of the variant surface glycoprotein (VSG) transcript in the proliferating blood stream form. However, how m6A landscape varies across the life cycle remains poorly defined. Using full-length, non-fragmented RNA, we immunoprecipitated and sequenced m6A-modified transcripts across three life cycle stages ofTrypanosoma brucei– slender (proliferative), stumpy (quiescent), and procyclic forms (proliferative). We found that 1037 transcripts are methylated in at least one of these three life cycle stages. While 21% of methylated transcripts are common in the three stages of the life cycle, globally each stage has a distinct methylome. Interestingly, 47% of methylated transcripts are detected in the quiescent stumpy form only, suggesting a critical role for m6A when parasites exit the cell cycle and prepare for transmission by the Tsetse fly. In this stage, we found that a significant proportion of methylated transcripts encodes for proteins involved in RNA metabolism, which is consistent with their reduced transcription and translation. Moreover, we found that not all major surface proteins are regulated by m6A, as procyclins are not methylated, and that, within the VSG repertoire, not all VSG transcripts are demethylated upon parasite differentiation to procyclic form. This study reveals that the m6A regulatory landscape is specific to each life cycle stage, becoming more pervasive asT. bruceiexits the cell cycle.

African trypanosome parasites adapt to mammalian and insect hosts by adjusting gene expression, morphology, and metabolism. In this study, we focus on how N6-methyladenosine (m6A), a post-transcriptional modification, affects the parasite’s transcriptome throughout its differentiation from the mammalian host to the fly. We found that methylation is differentially regulated as the life cycle progresses, being particularly prevalent in the non-proliferative stumpy form, as more methylated transcripts are found at this insect-infective stage than in slender and procyclic forms. We further show that the not all parasite surface proteins are regulated by m6A and that the previously identified link between m6A methylation and the expression level of the major surface protein of bloodstream forms applies to the active variant surface glycoprotein, but not always to silent genes, suggesting two distinct regulatory mechanisms of (de)methylation.
A mitochondrial SET domain protein is essential inT. bruceiand required for mitochondrial morphology and function
Authors: Knight Emily W. , Ventura Rebeca Aquino , Mukala Niharikha , Morris Meredith T.
Published: February 2024

Protein lysine methylation is a ubiquitous post-translational modification. First identified in histone tails, many non-histone proteins are methylated at lysine residues. SET domain proteins catalyze the transfer of a methyl group from a donor such as S-adenosyl-L-methionine (SAM) to lysine residues. In this work, we identify a novel SET domain protein, TbSETD, in the African trypanosome,Trypanosoma brucei, and demonstrate that it is essential in both insect stage procyclic form and bloodstream form parasites. Epitope-tagged TbSETD localizes to the mitochondrion and TbSETD-deficient parasites exhibit growth defects, altered mitochondrial morphology, increased ROS levels, and increased sensitivity to apoptotic triggers. TbSETD binding proteins identified in immunoprecipitation experiments were enriched in mitoribosomal proteins. We also demonstrate that TbSETD immunoprecipitated from parasites has methyltransferase activityin vitroand methyllysine western blots reveal that TbSETD-deficient parasites have reduced levels of a 37 kDa mitochondrial protein. OrthoMCL DB indicates TbSETD is conserved only in kinetoplastids, suggesting a unique role in the biology of these parasites, and highlighting its potential as a drug target.

Significance

Kinetoplastid parasites include several medically important organisms for which current treatments are insufficient. SET domain protein lysine methyltransferases (PKMTs) are highly druggable and have predominately been studied in the context of chromatin remodeling and gene expression. This work provides the first example of a SET domain PKMT that localizes to the mitochondria in any protozoan parasite and the first implication that protein lysine methylation may be important to mitoribosomal biogenesis.
ErbB inhibition rescues nigral dopamine neuron hyperactivity and repetitive behaviors in a mouse model of fragile X syndrome
Authors: D’Addario Sebastian Luca , Rosina Eleonora , Massaro Cenere Mariangela , Bagni Claudia , Mercuri Nicola Biagio , Ledonne Ada
Published: February 2024

Repetitive behaviors are core symptoms of autism spectrum disorders (ASD) and fragile X syndrome (FXS), the prevalent genetic cause of intellectual disability and autism. The nigrostriatal dopamine (DA) circuit rules movement and habit formation; therefore, its dysregulation stands as a leading substrate for repetitive behaviors. However, beyond indirect evidence, specific assessment of nigral DA neuron activity in ASD and FXS models is lacking. Here, we show that hyperactivity of substantia nigra pars compacta (SNpc) DA neurons is an early feature of FXS. The underlying mechanisms rely on mGluR1 and ErbB receptors. Up-regulation of ErbB4 and ErbB2 in nigral DA neurons drives neuronal hyperactivity and repetitive behaviors of the FXS mouse, simultaneously rescued by ErbB inhibition. In conclusion, beyond providing the first evidence of dysregulation of the SNpc DA nucleus in FXS, we identify novel targets - ErbB receptors - whose inhibition proficiently attenuates repetitive behaviors, thus opening an avenue toward innovative therapies for ASD and FXS.
FLIPs: Novel Genetically Encoded Biosensors for Functional Imaging of Cell Signaling by Polarization Microscopy
Authors: Miclea Paul , Nagy-Marková Vendula , Van den Eynde Robin , Vandenberg Wim , Sakhi Alina , Bondar Alexey , Myšková Jitka , Dedecker Peter , Lazar Josef
Published: February 2024

Genetically encoded fluorescent biosensors convert specific biomolecular events into optically detectable signals. By revealing biochemical processesin situ, they have revolutionized cell biology. However, imaging molecular processes often requires modifying the proteins involved, and many molecular processes are still to be imaged. Here we present a novel, widely applicable design of genetically encoded biosensors that notably expand the observation possibilities, by taking advantage of a hitherto overlooked detection principle: directionality of optical properties of fluorescent proteins. The probes, which we term FLIPs, offer an extremely simple design, high sensitivity, multiplexing capability, ratiometric readout and resilience to bleaching artifacts, without requiring any modifications to the probe targets. We demonstrate their performance on real-time single-cell imaging of activation of G protein-coupled receptors (GPCRs), G proteins, arrestins, small GTPases, as well as receptor tyrosine kinases, even at endogenous expression levels. We also identify a new, pronounced, endocytosis-associated conformational change in a GPCR–β-arrestin complex. By demonstrating a novel detection principle and allowing many more cellular processes to be visualized, FLIPs are likely to inspire numerous future developments and insights.
An age-specific platelet differentiation path from hematopoietic stem cells contributes to exacerbated thrombosis
Authors: Poscablo DM , Worthington AK , Smith-Berdan S , Manso BA , Adili R , Cool T , Reggiardo RE , Dahmen S , Beaudin AE , Boyer SW , Holinstat M , Forsberg EC
Published: February 2024

Platelet dysregulation is drastically increased with advanced age and contributes to making cardiovascular disorders the leading cause of death of elderly humans. Hematopoietic stem and progenitor cells continuously give rise to platelets, but their contributions to variable platelet production and activity throughout life remain unclear. Here we reveal a direct differentiation pathway from hematopoietic stem cells into platelets that is unique to aging. An unequivocal genetic lineage tracing mouse model demonstrated that this age-specific pathway is progressively propagated over time. Remarkably, the age-specific platelet path is decoupled from all other hematopoietic lineages, including erythropoiesis, and operates as an additional layer in parallel with canonical platelet production. This results in two molecularly and functionally distinct populations of megakaryocyte progenitor cells that that operate in parallel. The age-specific megakaryocyte progenitor population has profoundly enhanced capacity to engraft, expand, and reconstitute platelets, and produces an additional platelet population that exists only in old mice. Consistent with increased thrombotic incidence upon aging, the two pools of co-existing platelets contribute to age-related thrombocytosis and dramatically increased thrombosisin vivo. Upon acute, platelet-specific stress, the age-specific MkPs endowed old mice with superior capacity to rapidly restore platelet counts. These findings reveal stem cell-based aging as a mechanism for platelet dysregulation and identify an aging-induced population of functionally enhanced MkPs as a unique source of age-specific platelets.

>HIGHLIGHTS

Aging leads to two parallel platelet specification paths from HSCs

The shortcut platelet pathway is perpetuated by highly expansive MkPs unique to aging

The age-specific differentiation path contributes to thrombosis and platelet hyperreactivity

Age-specific MkPs serve as potent first responders to acute platelet loss
Synergistic and antagonistic drug interactions are prevalent but not conserved across acute myeloid leukemia cell lines
Authors: Kalkan Fatma Neslihan , Yildiz Muhammed Sadik , Wood N. Ezgi , Farid Michael , McCoy Melissa , Zhang Chengcheng , Lin Milo , Posner Bruce , Chung Stephen S. , Toprak Erdal
Published: February 2024

Acute myeloid leukemia (AML) is the most prevalent type of leukemia in adults. Despite advancements in medicine, the standard treatment that utilizes a combination of cytarabine and daunorubicin for AML has remained the same for decades. Combination drug therapies are proven to be an effective way to achieve targeted efficacy while minimizing drug dosage along with the unintended side effects. However, a systematic survey of synergistic potential of drug-drug interactions in the context of AML pathology is currently lacking. Here we examine the interactions between 15 frequently used cancer drugs across distinct AML cell lines and demonstrate that synergistic and antagonistic drug-drug interactions are widespread but not conserved across these cell lines. Notably, enasidenib (AG-221) and venetoclax (ABT-199), recently approved anticancer agents, exhibited the highest counts of synergistic interactions and the fewest antagonistic ones. In contrast, 6-Thioguanine (6-TG), a purine analog, was involved in the highest number of antagonistic interactions. The interactions we report here cannot be attributed solely to the inherent synergistic or antagonistic natures of these three drugs, as each drug we examined was involved in several synergistic or antagonistic interactions in the cell lines we tested. Moreover, we observed that these drug-drug interactions are not conserved across cell lines, suggesting that the success of combination therapies might vary depending on AML genotypes. For instance, we found that a single mutation in the TF1 cell line could dramatically alter drug-drug interactions, even turning synergistic interactions into antagonistic ones, as seen with AG-221 and cladribine A (2CdA). Our findings provide a preclinical survey of the potential synergistic effects revealing the complexity of the problemin vitro. However, the exploitable synergistic regimes in clinical scenarios remain to be explored. We anticipate these results to be an insightful guideline for future clinical studies, aiming to refine chemotherapy regimens and ultimately enhance patient outcomes.
Functional marker CAPS-799 of theTaPHT1;9-4Bgene is useful for screening phosphorus-efficient wheat cultivars
Authors: Wang Jinfeng , Chen Zedong , Shi Huanting , Lou Chuang , Fu Kaixia , Wang Yaxin , Yu Bo , Guo Tiancai , Wang Yonghua , Wang Pengfei , Kang Guozhang
Published: February 2024

Context

In our previous study,TaPHT1;9-4B, one key high-affinity Pi transporter, was found to greatly contribute to Pi acquisition and transportation, and its functional marker CAPS-799 was subsequently developed to identify its Pi-efficient elite haplotype.

Objective

The study aimed to screen a varieties of wheat cultivars by using the above CAPS-799, identify its Pi-efficient elite haplotype cultivars, and reveal its physiological mechanism.

Methods

Successive two-year field experiments without Pi fertilizer supply, and hydroponic experiment with low Pi (10 μM) were performed. P concentrations, biomasses, grain yields, yield components, root growth parameters, andTaPHT1;9-4Btranscript levels were measured. Total P accumulation and transport efficiency, and the relative growth rates were calculated.

Results

Eight Pi-efficient wheat cultivars (Hap3haplotype) were screened out by using the CAPS-799 from 80 modern major cultivars, and in successive two-year field experiments, their grain yields, spike numbers, P absorption and transport efficiencies were significantly higher than those ofNon-Hap3haplotypes (Hap1, 2and4) under no Pi fertilizer supply condition, and therefore, these eight cultivars belonged to Pi-efficient elite haplotype.TaPHT1;9-4Btranscript levels in roots at the early stage of grain filling period in field experiment, and the relative growth rates of total root surface areas, volumes and mean root diameters ofHap3cultivars in hydroponic experiment, were markedly higher than other haplotypes.

Conclusions

CAPS-799 was a useful functional marker for screening Pi-efficient wheat cultivars, and its Pi-efficient wheat cultivars were characterized with higherTaPHT1;9-4Btranscript levels and more roots.

Implications

CAPS-799 will be used to screen or develop Pi-efficient wheat cultivars.
Short communications of a new circulating Dengue genotype III American II lineage in Mexico: outbreak 2022-2023
Authors: Madera-Sandoval RL , Rodríguez-Maldonado AP , Rivero-Arredondo SV , Quiroz-Mercado J , Molina-Gomez IE , Hernandez-Rivas L , Lopez-Martinez I , Vazquez-Pichardo M , Correa-Morales F , Wong-Arámbula C
Published: February 2024

We report for the first time the circulation of American II lineage of Dengue virus serotype 3 genotype III in Mexico uncovered by the genomic surveillance in charge of the Instituto de Diagnóstico y Referencia Epidemiológicos through sequencing the whole genome using Illumina platform. The importance of the characterization of a new lineage circulating in Mexico impacts public health and the actions to be taken to mitigate new outbreaks and in the future associate them with clinical responses that the new lineage may cause.
Syndemic Geographic Patterns of Cancer Types in a Health Deprived Area of England: a new Paradigm for Public Health Cancer Interventions?
Authors: Jones Catherine , Keegan Tom , Knox Andy , Birtle Alison , Mendes Jessica A. , Heys Kelly , Atkinson Peter , Sedda Luigi
Published: February 2024

Cancer poses a significant public health challenge, and accurate tools are crucial for effective intervention, especially in high-risk areas. The North West of England, historically identified as a region with high cancer incidence, has become a focus for public health initiatives. This study aims to analyse cancer risk factors, demographic trends and spatial patterns in this region by employing a novel spatial joint modelling framework designed to account for large frequencies of left-censored data.

Cancer diagnoses were collected at the postcode sector level. The dataset was left-censored due to confidentiality issues, and categorised as interval censored. Demographic and behavioural factors, alongside socio-economic variables, both at individual and geographic unit levels, were obtained from the linkage of primary and secondary health data and various open source datasets. An ecological investigation was conducted using joint spatial modelling on nine cancer types (breast, colorectal, gynaecology, haematology, head and neck, lung, skin, upper GI, urology), for which explanatory factors were selected by employing an accelerated failure model with lognormal distribution. Post-processing included principal components analysis and hierarchical clustering to delineate geographic areas with similar spatial patterns of different cancer types.

The study included 15,506 cancer diagnoses from 2017 to 2022, with the highest incidence in skin, breast and urology cancers. Preliminary censoring adjustments reduced censored records from 86% to 60%. Factors such as age, ethnicity, frailty and comorbidities were associated with cancer risk. The analysis identified 22 relevant variables, with comorbidities and ethnicity being prominent. The spatial distribution of the risk and cumulative risk of the cancer types revealed regional variations, with five clusters identified. Rural areas were the least affected by cancer and Barrow-in-Furness was the area with the highest cancer risk.

This study emphasizes the need for targeted interventions addressing health inequalities in different geographical regions. The findings suggest the need for tailored public health interventions, considering specific risk factors and socio-economic disparities. Policymakers can utilize the spatial patterns identified to allocate resources effectively and implement targeted cancer prevention programmes.
A missense mutation in theXan-hgene encoding the Mg-chelatase subunit I leads to a viable pale green line with phenotypic features of potential interest for barley breeding programs
Authors: Persello Andrea , Tadini Luca , Rotasperti Lisa , Ballabio Federico , Tagliani Andrea , Torricella Viola , Jahns Peter , Dalal Ahan , Moshelion Menachem , Camilloni Carlo , Rosignoli Serena , Hansson Mats , Cattivelli Luigi , Horner David , Rossini Laura , Tondelli Alessandro , Salvi Silvio , Pesaresi Paolo
Published: February 2024

The pale green trait, i.e. reduced chlorophyll content, has been shown to increase the efficiency of photosynthesis and biomass accumulation when photosynthetic microorganisms and tobacco plants are cultivated at high densities. Thus, thehus1barley mutant is defective in photosystem antenna biogenesis, and exhibits a 50% reduction in leaf chlorophyll content. Nevertheless, its agronomical performance under standard field conditions is comparable to that of the wild-type. This supports the notion that crops can decrease their investment in antenna proteins and chlorophyll biosynthesis without detrimental effects on productivity. Here, we assess the effects of reducing leaf chlorophyll content in barley by altering the chlorophyll biosynthesis pathway (CBP). To this end, we have isolated and characterised the pale green barley mutantxan-h.chli-1, which carries a missense mutation in theXan-hgene for subunit I of Mg-chelatase (HvCHLI), the first enzyme in the CBP. Intriguingly,xan-h.chli-1is the only known viable homozygous mutant at theXan-hlocus in barley. The Arg298Lys amino-acid substitution in the ATP-binding cleft causes a slight decrease inHvCHLI protein abundance, and a marked reduction in Mg-chelatase activity. Under controlled growth conditions, mutant plants display reduced accumulation of antenna and photosystem core subunits, together with reduced photosystem II yield relative to wild type under moderate illumination, and consistently higher than wild-type levels at high light intensities. Moreover, the reduced content of leaf chlorophyll is associated with a stable reduction in daily transpiration rate, and slight decreases in total biomass accumulation and water-use efficiency. These traits are reminiscent of phenotypic features of wild barley accessions and landraces that thrive under arid climatic conditions. Overall, our findings make thexan-h.chli-1allelic variant of potential interest for tailoring barley, and other crop plants, for growth in harsh environments.