bluuebunny/crossref_metadata_2025 huggingface dataset:
Systemic low-dose anti-fibrotic treatment attenuates ovarian aging in the mouse
Authors: Amargant Farners , Vieira Carol , Pritchard Michele T. , Duncan Francesca E.
Published: June 2024

The female reproductive system is one of the first to age in humans, resulting in infertility and endocrine disruptions. The aging ovary assumes a fibro-inflammatory milieu which negatively impacts gamete quantity and quality as well as ovulation. Here we tested whether the systemic delivery of anti-inflammatory (Etanercept) or anti-fibrotic (Pirfenidone) drugs attenuates ovarian aging in mice. We first evaluated the ability of these drugs to decrease the expression of fibro-inflammatory genes in primary ovarian stromal cells. Whereas Etanercept did not blockTnfexpression in ovarian stromal cells, Pirfenidone significantly reducedCol1a1expression. We then tested Pirfenidonein vivowhere the drug was delivered systemically via mini-osmotic pumps for 6-weeks. Pirfenidone mitigated the age-dependent increase in ovarian fibrosis without impacting overall health parameters. Ovarian function was improved in Pirfenidone-treated mice as evidenced by increased follicle and corpora lutea number, AMH levels, and improved estrous cyclicity. Transcriptomic analysis revealed that Pirfenidone treatment resulted in an upregulation of reproductive function-related genes at 8.5 months and a downregulation of inflammatory genes at 12 months of age. These findings demonstrate that reducing the fibroinflammatory ovarian microenvironment improves ovarian function, thereby supporting modulating the ovarian environment as a therapeutic avenue to extend reproductive longevity.
Total neuroelectric brain activity derived from resting-state MEG is invariable across the adult lifespan
Authors: Ustinin Mikhail , Boyko Anna , Rykunov Stanislav
Published: June 2024

Ageing of the human brain was studied using large array of experimental data. The magnetic encephalograms and magnetic resonance images of the head were obtained from the open archive CamCAN. Bad data were rejected, then functional tomograms were found - the spatial distribution of elementary spectral components. Physiological noise was eliminated by joint analysis of the functional tomograms and magnetic resonance images. By massively solving the inverse problem, multichannel spectra were transformed into time series of the power of elementary current dipoles. Age-related changes in the electrical power of various brain rhythms were examined. It was found that the summary electrical activity of the brain is constant throughout a person’s life. The electric power is redistributed during the lifetime: delta rhythm is diminishing, giving slow rise to all other rhythms.
Hyperspectral open source imaging system
Authors: Troscianko Jolyon
Published: June 2024

The spatial and spectral properties of the light environment underpin the appearance of scenes and objects. As such its measurement is crucial for understanding many aspects of animal behaviour, ecology and evolution, along with many more applications in fields ranging from optical physics, agriculture/plant sciences, human psychophysics, food science, architecture and materials sciences. The escalating threat of artificial light at night (ALAN) presents unique challenges for measuring the visual impact of light pollution, requiring measurement at low light levels across the human-visible and ultraviolet ranges, across all viewing angles, and often with high within-scene contrast.

Here I present a hyperspectral open-source imaging system (HOSI), an innovative and low-cost solution for collecting full-field hyperspectral data. The system uses a Hamamatsu C12880MA micro spectrometer to take single-point measurements, together with a motorised gimbal for spatial control. The hardware uses off-the-shelf components and 3D printed parts, costing around £350 in total. The system can run directly from a computer or smartphone with a graphical user interface, making it highly portable and user-friendly.

The HOSI system can take panoramic hyperspectral images that meet the difficult requirements of ALAN research, sensitive to low light around 0.001 cd.m-2, across 320-880nm range with spectral resolution of ∼9nm (FWHM) and spatial resolution of ∼0.2 degrees. The independent exposure of each pixel also allows for an extremely wide dynamic range that can encompass typical natural and artificially illuminated scenes, with sample night-time scans achieving peak-to-peak dynamic ranges of >50,000:1.

This system’s adaptability, cost-effectiveness, and open-source nature position it as a valuable tool for researchers investigating the complex relationships between light, environment, behaviour, ecology, and biodiversity, with further potential uses in many other fields.
TheDrosophilahematopoietic niche assembles through collective cell migration controlled by neighbor tissues and Slit-Robo signaling
Authors: Nelson Kara A. , Lenhart Kari F. , Anllo Lauren , DiNardo Stephen
Published: June 2024

Niches are often found in specific positions in tissues relative to the stem cells they support. Consistency of niche position suggests that placement is important for niche function. However, the complexity of most niches has precluded a thorough understanding of how their proper placement is established. To address this, we investigated the formation of a genetically tractable niche, theDrosophilaPosterior Signaling Center (PSC), the assembly of which had not been previously explored. This niche controls hematopoietic progenitors of the lymph gland (LG). PSC cells were previously shown to be specified laterally in the embryo, but ultimately reside dorsally, at the LG posterior. Here, using live-imaging, we show that PSC cells migrate as a tight collective and associate with multiple tissues during their trajectory to the LG posterior. We find that Slit emanating from two extrinsic sources, visceral mesoderm and cardioblasts, is required for the PSC to remain a collective, and for its attachment to cardioblasts during migration. Without proper Slit-Robo signaling, PSC cells disperse, form aberrant contacts, and ultimately fail to reach their stereotypical position near progenitors. Our work characterizes a novel example of niche formation and identifies an extrinsic signaling relay that controls precise niche positioning.

Impact Statement

A new example of niche formation is provided which reveals the mode of niche cell migration, implicates extrinsic sources that deliver positional information, and uncovers the signaling pathway required for the precise, stereotypical positioning of the niche.
A Novel Role of Hyaluronan and its Membrane Receptors, CD44 and RHAMM in Obesity-Related Glomerulopathy
Authors: Qi Bingxue , Musale Vishal , Weng Xiong , Banah Ayman K. , Murdoch Colin E. , Lay Abigail C. , Heesom Kate J. , Ju Wenjun , Bitzer Markus , Hills Claire , Coward Richard J.M. , Kang Li
Published: June 2024

Obesity-related glomerulopathy (ORG) contributes to diabetic nephropathy and kidney cancer, leading to chronic/end-stage kidney disease. To date, treatments for ORG are limited because of incomplete understanding of the disease pathogenesis. Here, we identified a novel role for hyaluronan (HA) and its membrane receptors, CD44 and RHAMM in obesity-associated renal inflammation, fibrosis, tubular injury, and kidney dysfunction. Pharmacological and genetic ablation of HA, CD44 or RHAMM reversed these renal disorders induced by high fat diet feeding in micein vivo. Increased HA content, and CD44 and RHAMM expression damaged the kidney via activation of TGF-β1/Smad2/3, P38/JNK MAPK and ROCK/ERK pathways. We further established a link between renal insulin resistance and ECM remodelling using human kidney cellsin vitro, shedding mechanistic insight into the role of HA, CD44 and RHAMM in the pathogenesis of ORG. Furthermore, in human kidney biopsies gene expression of CD44 and RHAMM was increased in chronic kidney disease and diabetic nephropathy, and their levels were correlated with markers of kidney (dys)function (GFR, serum creatinine, proteinuria). Our findings provide evidence for HA-CD44/RHAMM as a potential therapeutic target in ORG and consequent prevention of chronic kidney disease.
Adipogenic differentiation of hematopoietic lineage cells isolated from adipose tissue of humans
Authors: Gavin Kathleen M. , Conrad Bogdan , Sullivan Timothy , Vianzon Ruby , Acosta Alistaire S. , Kohrt Wendy M. , Klemm Dwight J.
Published: June 2024

We previously discovered some adipocytes in the major white fat depots of mice and humans arise from bone marrow-derived cells of hematopoietic lineage rather than conventional mesenchymal precursors, termed bone marrow-derived adipocytes (BMDA). Here we aimed to determine if hematopoietic lineage cells isolated from adipose tissue and circulation of humans could undergo adipogenic differentiationin vitro,thereby establishing anin vitromodel for studies of BMDA. We hypothesized that hematopoietic lineage cells isolated from adipose tissue, but not circulation, of humans would demonstrate adipogenic potential. Participants included younger (20-50 years) and older (>50-75 years) men and women, BMI 20-37 kg/m2. Subcutaneous abdominal adipose tissue biopsies were obtained and stromal cell populations identified by flow cytometry. Sorted cells underwentin vitrocultivation via traditional mesenchymal culture methodology (mesenchymal lineage) or a novel 3D-fibrin clot followed by traditional adherent culture (hematopoietic lineage) for assessment of proliferation and differentiation capacity. We found hematopoietic lineage cells isolated from the adipose tissue stroma, but not the circulation, were capable of proliferation and multilineage (adipogenic and osteogenic) differentiationin vitro. We provide a new investigative tool that can be used to perform translational studies of BMDAs and provide initial evidence that hematopoietic lineage cells isolated from the adipose tissue of humans can undergo hematopoietic-to-mesenchymal transition with multilineage differentiation potential in anin vitroenvironment.
In-silico studies on thermodynamics of ligand binding to Fluoride riboswitch aptamer
Authors: Das Soumi
Published: June 2024

Riboswitch is a non-coding messenger RNA (m-RNA) whose aptamer domain binds cognate ligands and subsequently undergoes conformational changes in the expression platform leading to the regulation of gene expression. Fluoride riboswitch has immense pharmacological potential due to its presence in some human bacterial pathogens. Several experimental studies shed light on the bacterial defense mechanism of Fluoride riboswitch upon binding of F-cognate ligand in the presence of Mg2+. However, the structural and thermodynamic basis of ligand binding with Fluoride riboswitch aptamer is not well known. This fascinates us for investigating the conformational stability of (i) the holo form of T. Petrophila fluoride riboswitch aptamer (RNA+F-+Mg2++K+) with respect to (ii) the apo form of fluoride riboswitch (RNA in the absence of F-+Mg2++K+). Conformational thermodynamics results derived from molecular dynamics simulation reveal that the holo form of the Fluoride riboswitch aptamer is stabilized by ion recognition site, pseudoknot, and stem1. However, Stem2, Loop1, Loop2, and most of the unpaired bases show significant disorder and destabilization. Molecular docking study validates the thermodynamically destabilized and disordered residues from Loop1 and Stem2 of the Fluoride riboswitch aptamer to serve as putative binding sites for non-cognate ligands. The global health system in the current century faces a serious crisis to counteract bacterial infection due to the severe emergence of bacterial resistance to antibiotics. Consequently, a need for a new generation of antibiotics against resistant bacteria is critically acclaimed. Our work hopefully improves the design of new ligands and aptamers which may be helpful in nucleic acid-targeted therapeutics.

Graphical Abstract

Highlights

Conformational stability of (i) the holo form of T. Petrophila fluoride riboswitch aptamer (RNA+F-+Mg2++K+) with respect to (ii) the apo form of fluoride riboswitch (RNA in the absence of F-+Mg2++K+) is studied.

Holo Fluoride riboswitch aptamer gets energetically and entropically stable at Pseudoknot, Stem1, and Ion recognition sites whereas Stem2, Loop1, Loop2, and most of the unpaired bases show significant disorder and destabilization.

The hydrogen bond network for Pseudoknot, Stem1, and Stem2 in apo Fluoride riboswitch is significantly weak.

Molecular Docking study confirms that the thermodynamically destabilized and disordered residues from Stem2 and Loop1 of the holo Fluoride riboswitch aptamer serve as putative binding sites for non-cognate ligands.
Decoding a cell’s fate: How Notch and Receptor Tyrosine Kinase Signals Specify the Drosophila R7 Photoreceptor
Authors: Arias Ronald A. , Tomlinson Andrew
Published: June 2024

The Drosophila R7 photoreceptor is a classic model for understanding how integration of signaling information can provide precise fate directives. It entails extensive interactions between the RTK and Notch signaling pathways, with Notch providing three distinct functions: it both opposes and promotes the general photoreceptor fate, and it determines the specific photoreceptor type. The RTK pathway promotes transcription ofphyl- a gene expression critical for photoreceptor specification. We show that Notch activity induces transcription ofyanwhich encodes a transcriptional repressor ofphyl. This defines the antagonism between the two pathways, with RTK promoting and Notch opposingphyltranscription. We previously showed that Notch provides Sevenless to the cell to allow RTK pathway hyperactivation to overcome the Notch repression, and we now identify the regulation of Yan activity as the integration site of the RTK and Notch functions. Once the cell is specified as a photoreceptor, the third Notch function then preventsseven-up(svp) transcription. The Svp transcription factor directs the R1/6 photoreceptor fate, and the prevention of its expression ensures the default R7 specification.

Summary Statement

This paper examines how the different signals received by the Drosophila R7 photoreceptor precursor are decoded and used to direct the cell’s appropriate differentiation pathway.
From many voices, one question: Community co-design of a population-based qualitative cancer research study
Authors: Ayre Susannah K. , Johnston Elizabeth A. , Bourdaniotis Xanthia E. , Zajdlewicz Leah , Beesley Vanessa L. , Pole Jason D. , Hansen Aaron , Gasper Harry , Cossio Danica , Lock Gemma , Goodwin Belinda C.
Published: June 2024

Purpose

This study formed the development stage of a population-based survey aiming to: (i) understand the needs and experiences of people affected by cancer in Queensland, Australia and (ii) recruit a pool of participants for ongoing cancer survivorship research. The current study aimed to co-design and test a single qualitative survey question and study invitation materials to maximise acceptability of, and participation in, the survey and future research.

Methods

Fifty-two community members participated across 15 co-design workshops and 20 pretest interviews. During workshops, participants generated and refined ideas for an open-ended survey question and provided feedback on a study invitation letter. The use of a single, open-ended question aims to minimise participant burden while collecting rich information about needs and experiences. The research team then shortlisted the question ideas and revised study invitation materials based on workshop feedback. Next, using interviews, community members were asked to respond to a shortlisted question to test its interpretability and relevance and to review revised invitation materials. Content analysis of participant feedback was used to identify principles for designing study materials.

Results

Ten principles for designing qualitative survey questions were identified from participant feedback. Key principles included:define the question timeframe and scope; provide reassurance that responses are valid and valued;anduse simple wording. For the study invitation materials, 11 principles were identified, including these key principles:communicate empathy and sensitivity; facilitate reciprocal benefit;andinclude a ‘human element’.The qualitative survey question and study invitation materials created using these principles were considered relevant and acceptable for use in a population-based survey.

Conclusions

Through community consultation and co-design, this study identified principles for designing qualitative data collection and invitation materials for use in cancer survivorship research. These principles can be applied by other researchers to develop study materials that are sensitive to the needs and preferences of community members.
Abnormal Blood Pressure Among Individuals Evaluated for Latent Tuberculosis Infection in a U.S. Public Health Tuberculosis Clinic
Authors: Stantliff Trevor M. , Salindri Argita D. , Egoavil-Espejo Rocio , Hall Ashton D. , Medina-Rodriguez Laura , Patel Kavya , Magee Matthew J. , Urbina Elaine M. , Huaman Moises A.
Published: June 2024

Tuberculosis infection (LTBI) has been associated with increased cardiovascular risks. We aimed to characterize abnormal blood pressure (BP) readings in individuals with LTBI. We conducted a retrospective study of adults with LTBI presenting for their initial medical visit at a large midwestern US public health clinic between 2019-2020. Abnormal BP was defined as having a systolic BP≥ 130mmHg and/or a diastolic BP≥ 80mmHg. Of 310 individuals with LTBI, median age was 36 years (interquartile range 27 – 48), 34% were male, 64% non-US-born; 58 (18.7%) were previously diagnosed with hypertension. The prevalence of any hypertension (i.e., had a history of hypertension and/or an abnormal BP reading) was 64.2% (95% confidence interval 58.7 – 69.4). Any hypertension was independently associated with older age, male sex, higher body mass index, and Black race. In conclusion, any hypertension was present in over half of adults evaluated for LTBI in our clinic. Established hypertension risk factors were also common among this group, suggesting that individuals with LTBI could benefit from clinical and public health interventions aiming to reduce the risk of future cardiovascular events.
Clinical Utility of the Molecular Microscope Diagnostic System in a Real-World Transplant Cohort: Moving Towards a New Paradigm
Authors: Fernandez Valledor Andrea , Moeller Cathrine M. , Rubinstein Gal , Rahman Salwa , Oren Daniel , Baranowska Julia , Lee Changhee , Salazar Ruben , Hennecken Carolyn , Rahman Afsana , Elad Boaz , Lotan Dor , DeFilippis Ersilia M. , Yunis Adil , Fried Justin , Raihkelkar Jayant , Oh Kyung T. , Bae David , Lin Edward , Lee Sun Hi. , Regan Matthew , Yuzelpolskaya Melana , Colombo Paolo , Majure David T. , Latif Farhana , Clerkin Kevin D. , Sayer Gabriel T. , Uriel Nir
Published: June 2024

Objectives

To evaluate the clinical implications of adjunctive molecular gene expression analysis (MMDx)of biopsy specimens in heart transplant (HT)recipients with suspected rejection.

Introduction

Histopathological evaluation remains the standard method for rejection diagnosis in HT. However, the wide interobserver variability combined with a relatively common incidence of “biopsy-negative” rejection has raised concerns about the likelihood of false-negative results. MMDx, which uses gene expression to detect early signs of rejection, is a promising test to further refine the assessment of HT rejection.

Methods

Single-center prospective study of 418 consecutivefor-causeendomyocardial biopsies performed between November 2022 and May 2024. Each biopsy was graded based on histology and assessed for rejection patterns using MMDx. MMDx results were deemed positive if borderline or definitive rejection was present. The impact of MMDx results on clinical management was evaluated. Primary outcomes were 1-year survival and graft dysfunction following MMDx-guided clinical management. Secondary outcomes included changes in donor-specific antibodies, MMDx gene transcripts, and donor-derived cell-free DNA (dd-cfDNA) levels.

Results

We analyzed 418 molecular samples from 237 unique patients. Histology identified rejection in 32 cases (7.7%), while MMDx identified rejection in 95 cases (22.7%). Notably, in 79 of the 95 cases where MMDx identified rejection, histology results were negative, with the majority of these cases being antibody-mediated rejection (62.1%). Samples with rejection on MMDx were more likely to show a combined elevation of dd-cfDNA and peripheral blood gene expression profiling than those with borderline or negative MMDx results (36.7% vs 28.0% vs 10.3%; p<0.001). MMDx results led to the implementation of specific antirejection protocols or changes in immunosuppression in 20.4% of cases, and in 73.4% of cases where histology was negative and MMDx showed rejection. 1-year survival was better in the positive MMDx group where clinical management was guided by MMDx results (87.0% vs 78.6%; log rank p=0.0017).

Conclusions

In our cohort, MMDx results more frequently indicated rejection than histology, often leading to the initiation of antirejection treatment. Intervention guided by positive MMDx results was associated with improved outcomes.

Graphical abstract
Social Determinants of Cardiovascular Disease in US Women with and without Breast Cancer
Authors: Wadden Elena , Yogeswaran Vidhushei , Ray Roberta M , Vasbinder Alexi , Shadyab Aladdin H , Xiao Qian , Richey Phyllis A , Saquib Nazmus , Sun Yangbo , Jung Su Yon , Pichardo Margaret S. , Manson JoAnn E , Anderson Garnet , Simon Michael , Stefanick Marcia , Reding Kerryn , Barac Ana , Cheng Richard K
Published: June 2024

Background

Social determinants of health (SDOH) may be related to CV risk in women with and without breast cancer (BC).

Methods

In 153,401 women without prevalent CV disease in the Women’s Health Initiative (WHI), SDOH factors included geographic region, rurality, insurance status, and household income. Cox proportional hazard models were used to assess associations between SDOH factors and a composite CV outcome (myocardial infarction, stroke, hospitalization for heart failure, or CV death). Effect modification by BC was assessed between BC status and SDOH.

Results

The final cohort included 10,954 (mean age 62±7 years) women who subsequently developed BC and 142,144 (mean age 63 ± 7) women without BC. During a median follow-up of 13 years, 18,148 women had an incident composite CV outcome. Rurality, low household income, and non-private insurance were associated with an increased risk of composite CV outcome and mortality in both women with and without BC. There was no effect modification by BC status for associations with rurality, insurance, or household income. By geographic region, there was no difference in composite CV outcome in women without BC. However, there was a significant interaction by BC status for geographic region and the composite endpoint (p=0.009). Women with BC in the South had a lower risk of the composite outcome (HR 0.68, 95% CI 0.54-0.87).

Conclusions

SDOH are associated with an increased risk of CV events and mortality among women. There were no differential associations based on BC status, suggesting that women with BC face similar vulnerabilities related to SDOH.
CD11c-expressing microglia are transient, driven by interactions with apoptotic cells
Authors: Ghena Nathaniel , Anderson Sarah R , Roberts Jacqueline M , Irvin Emmalyn , Schwakopf Joon , Bosco Alejandra , Vetter Monica L
Published: June 2024

Microglia, the parenchymal macrophage of the central nervous system serve crucial remodeling functions throughout development. Microglia are transcriptionally heterogenous, suggesting that distinct microglial states confer discrete roles. Currently, little is known about how dynamic these states are, the cues that promote them, or how they impact microglial function. In the developing retina, we previously found a significant proportion of microglia express CD11c (Integrin αX, complement receptor 4,Itgax) which has also been reported in other developmental and disease contexts. Here, we sought to understand the regulation and function of CD11c+ microglia. We found that CD11c+ microglia track with prominent waves of neuronal apoptosis in postnatal retina. Using genetic fate mapping, we provide evidence that microglia transition out of the CD11c state to return to homeostasis. We show that CD11c+ microglia have elevated lysosomal content and contribute to the clearance of apoptotic neurons, and found that acquisition of CD11c expression is, in part, dependent upon the TAM receptor Axl. Using selective ablation, we found CD11c+ microglia are not uniquely critical for phagocytic clearance of apoptotic cells. Together, our data suggest CD11c+ microglia are a transient state induced by developmental apoptosis rather than a specialized subset mediating phagocytic elimination.
Developmental and age-related synapse elimination is mediated by glial Croquemort
Authors: Jay Taylor R , Kang Yunsik , Ouellet-Massicotte Victor , Micael Mariel Kristine B , Kacouros-Perkins Victoria L , Chen Jiakun , Sheehan Amy , Freeman Marc R
Published: June 2024

Neurons and glia work together to dynamically regulate neural circuit assembly and maintenance. In this study, we showDrosophilaexhibit large-scale synapse formation and elimination as part of normal CNS circuit maturation, and that glia use conserved molecules to regulate these processes. Using a high throughput ELISA-basedin vivoscreening assay, we identify new glial genes that regulate synapse numbers inDrosophila in vivo,including the scavenger receptor ortholog Croquemort (Crq). Crq acts as an essential regulator of glial-dependent synapse elimination during development, with glial Crq loss leading to excess CNS synapses and progressive seizure susceptibility in adults. Loss of Crq in glia also prevents age-related synaptic loss in the adult brain. This work provides new insights into the cellular and molecular mechanisms that underlie synapse development and maintenance across the lifespan, and identifies glial Crq as a key regulator of these processes.
DeePosit: an AI-based tool for detecting mouse urine and fecal depositions from thermal video clips of behavioral experiments
Authors: Peles David , Netser Shai , Ray Natalie , Suliman Taghreed , Wagner Shlomo
Published: June 2024

In many mammals, including rodents, social interactions are often accompanied by active urination (micturition), which is considered a mechanism for spatial scent marking. Urine and fecal deposits contain a variety of chemosensory signals that convey information about the individual’s identity, genetic strain, social rank, and physiological or hormonal state. Furthermore, scent marking has been shown to be influenced by the social context and by the individual’s internal state and experience. Therefore, analyzing scent-marking behavior during social interactions can provide valuable insight into the structure of mammalian social interactions in health and disease. However, conducting such analyses has been hindered by several technical challenges. For example, the widely used void spot assay lacks temporal resolution and is prone to artifacts, such as urine smearing. To solve these issues, recent studies employed thermal imaging for the spatio-temporal analysis of urination activity. However, this method involved manual analysis, which is time-consuming and susceptible to observer bias. Moreover, defecation activity was hardly analyzed by previous studies. In the present study, we integrate thermal imaging with an open-source algorithm based on a transformer-based video classifier for automatic detection and classification of urine and fecal deposits made by male and female mice during various social behavior assays. Our results reveal distinct dynamics of urination and defecation in a test-, strain- and sex-dependent manner, indicating two separate processes of scent marking in mice. We validate this algorithm, termed by us DeePosit, and show that its accuracy is comparable to that of a human annotator and that it is efficient in various setups and conditions. Thus, the method and tools introduced here enable efficient and unbiased automatic spatio-temporal analysis of scent marking behavior in the context of behavioral experiments in small rodents.
SubtiToolKit - a bioengineering kit forBacillus subtilisand Gram-positive bacteria
Authors: Caro-Astorga Joaquin , Rogan Matt , Malci Koray , Ming Hia , Debenedictis Erika , James Paul , Ellis Tom
Published: June 2024

Building DNA constructs of increasing complexity is key to synthetic biology. Golden Gate methods led to the creation of cloning toolkits - collections of modular standardized DNA parts hosted on hierarchic plasmids, developed for yeast, plants, Gram-negative bacteria, and human cells. However, Gram-positive bacteria have been neglected.Bacillus subtilisis a Gram-positive model organism and a workhorse in the bioindustry. Here, we present the SubtiToolKit, a high- efficiency cloning toolkit forB. subtilisand Gram-positive bacteria. Its design permits DNA constructs for transcriptional units, operons, knock-in and knock-out applications. It contains libraries of promoters, RBSs, fluorescent proteins, protein tags, terminators, genome integration parts, a no-leakage genetic device to control the expression of toxic products duringE. coliassembly, and a toolbox for industrially relevant strains ofGeobacillusandParageobacillusas an example of SubtiToolKit versatility for other Gram-positive bacteria and its future perspective as a reference toolkit.
Beyond Volume: Unraveling the Genetics of Human Brain Geometry
Authors: Primus Sabrina A. , Hoffstaedter Felix , Raimondo Federico , Eickhoff Simon B. , Winkelmann Juliane , Oexle Konrad , Patil Kaustubh R.
Published: June 2024

Brain geometry impacts brain function. A quantitative encoding of form is provided by the Laplace-Beltrami operator’s spectrum of eigenvalues (LBS). We examined LBS genetics of 22 subcortical brain structures including cerebellum in 19,862 healthy White-British UK Biobank participants by multivariate GWAS (MOSTest) on the first 49 eigenvalues each. Controlling for surface and volume, we identified 80 unique variants (p<1/22*5E-8) influencing the shapes of one or several structures, with the highest yield (37 variants) for brain stem. The previously known influence of several of these loci on basic morphology, such as volume, is thus shown to also influence complex shape. Known associations of observed loci with blood pressure, neurodegeneration, alcohol consumption, and mental disorders hint at preclinical stages of these conditions potentially mediating the genetic effect on brain morphology. Significant correlations between LBS of several brain structures and the polygenic risks of hypertension, ischemic stroke and schizophrenia evince brain shapes as early biomarkers.
Antibiotic-free vaginal microbiota transplantation (VMT) changes vaginal microbiota and immune profile in women with asymptomatic dysbiosis – reporting of a randomized, placebo-controlled trial
Authors: Bosma Elleke F. , Mortensen Brynjulf , DeLong Kevin , Røpke Mads A. , Juel Helene Baek , Rich Randi , Axelsen Amalie M. , Scheeper Marouschka J. , Marvig Rasmus L. , Rasmussen Thomas Gundelund , Acosta Colleen , Binné Ulrich K. , Thomsen Anne Bloch , Ingerslev Hans-Christian , Zulfiqar Fareeha , Wrønding Tine , Cotter Paul D. , O’Brien Marcus , Patel Shriram , Dam Sarita A. , Nicholson Julia Albert , Nielsen Henriette Svarre , Dinan Timothy G. , McCarthy Fergus P. , van Hylckama Vlieg Johan E.T. , Ensign Laura M.
Published: June 2024

Here, we describe the first placebo-controlled trial of vaginal microbiota transplantation (VMT) in women with asymptomatic dysbiosis without the use of antibiotic pretreatment. Importantly, we also describe the implementation of a donor program and banking of donor cervicovaginal secretions (CVS) while retaining sample viability, which is crucial to allow for scale-up and confirmatory quality testing. By metagenome sequencing, we demonstrate that VMT provided a significant increase in combinedLactobacillusspecies in the active arm and strain-level genetic analysis confirmedLactobacillusengraftment. Moreover, VMT was well tolerated and showed a good safety profile. Furthermore, a shift toward increasedLactobacilluswas associated with a change in the expression profile of genes in the complement pathway to a more anti-inflammatory profile. Vaginal microbial and immune profile restoration using VMT may have a positive impact on a wide range of conditions in women’s health.
Transcriptomic and Metabolomic analyses in Monozygotic and Dizygotic twins
Authors: Hubers Nikki , Drouard Gabin , Jansen Rick , Pool René , Hottenga Jouke Jan , Ollikainen Miina , Wang Xiaoling , Willemsen Gonneke , Kaprio Jaakko , Boomsma Dorret I. , van Dongen Jenny
Published: June 2024

Monozygotic (MZ) and dizygotic (DZ) twins are studied to understand genetic and environmental influences on complex traits, however the mechanisms behind twinning are not completely understood. (Epi)genomic studies identified SNPs associated with DZ twinning and DNA methylation sites with MZ twinning. To find molecular biomarkers of twinning, we compared transcriptomics and metabolomics data from MZ and DZ twins. We analyzed 42,663 RNA transcripts in 1,453 MZ twins and 1,294 DZ twins from the Netherlands Twin Register (NTR), followed by sex-stratified analyses. The top 5% transcripts with lowest p-values were analyzed for replication in 217 MZ and 158 DZ twins from the older Finnish Twin cohort (FTC). In the NTR, one transcript (PURG)was significantly differentially expressed between MZ and DZ twins; but this did not replicate in FTC. Pathway analyses highlighted the WNT-pathway, previously associated with MZ twinning, and the TGF-B and SMAD pathway, previously associated with DZ twinning. Meta-analysis of 169 serum metabolites in 2,797 MZ and 2,040 DZ twins from the NTR, FTC and FinnTwin12, showed no metabolomic differences. Overall, we did not find replicable transcript-level expression differences in blood between MZ and DZ twins, but highlighted the TGF-B/SMAD pathway as a potential transcriptional biomarker for DZ twinning.
Development and validation of risk prediction models for childhood, teenage and young adult cancers: research protocol and statistical analysis plan
Authors: Saatci Defne , Harnden Anthony , Hippisley-Cox Julia
Published: June 2024

Background

Childhood, teenage and young adult (CTYA, 0-24 years) cancers are rare and diverse, making timely diagnosis challenging. Studies based on adult cancers suggest that the development and integration of clinical decision tools in primary care aid earlier cancer detection, yet, these have not been explored for CTYA cancers.

Aim

To develop and validate a primary care-based risk prediction tool to identify CTYA who are at increased risk of cancer.

Methods and analysis

Using the QResearch Database, a nationally representative primary care database, we will generate an open cohort of children, teenagers and young adults (0-24 years) who were registered with a GP between 1stJanuary 1998 and 31stDecember 2019. CTYA will be followed up from the date at which the first cancer-relevant symptom is recorded in the records (index date) until the date of cancer diagnosis/6-months, whichever comes first. Candidate variables will include symptoms, signs, blood test results and demographic factors. Model derivation will include two approaches, Cox regression and logistic regression. Apparent performance of the derived model will be explored and subsequently internally-externally cross-validated to investigate performance heterogeneity and geographical transportability.
Development and verification of non-supervised smartphone-based methods for assessing pure-tone thresholds and loudness perception
Authors: Xu Chen , Schell-Majoor Lena , Kollmeier Birger
Published: June 2024

Objective

The benefit of using smartphones for hearing tests in a non-supervised, rapid, and contactless way has drawn a lot of interest, especially if supra-threshold measures are assessed that go beyond audiogram-based measures alone. It is unclear, nevertheless, how well these measures compare to more supervised and regulated manual audiometric assessments. The aim of this study is to validate such smartphone-based methods against standardized laboratory assessments.

Design

Pure-tone audiometry and categorical loudness scaling (CLS) were used. Three conditions with varying degrees of supervision were created and compared. In order to assess binaural and spectral loudness summation, both narrowband monaural and broadband binaural noise have been examined as CLS test stimuli.

Study sample

N = 21 individuals with normal hearing and N = 16 participants with mild-to-moderate hearing loss.

Results

The tests conducted here did not show any distinctions between smartphone-based and laboratory-based methods.

Conclusions

Non-supervised listening tests via smartphone may serve as a valid, reliable, and cost-effective approach, e.g., for pure-tone audiometry, CLS, and the evaluation of binaural and spectral loudness summation. In addition, the supra-threshold tests can be constructed to be invariant against missing calibration and external noise which makes them more robust for smartphone usage than audiogram measures.
Fingerprint method applied to data from a phase III clinical trial
Authors: Edenbrandt Lars
Published: June 2024

Researchers in the RECOMIA network have been developing AI tools for the automated analysis of PET/CT studies in lymphoma patients. To enhance these AI tools, the CALGB 50303 dataset from The Cancer Imaging Archive was identified for inclusion in their project. Ensuring the quality of databases used for AI training is crucial, and one quality control (QC) measure involves the AI-based Fingerprint method to verify correct de-identification of clinical trial images. The study applied the Fingerprint method to PET/CT studies from 130 patients, successfully detecting an incorrectly de-identified study and identifying its correct trial identification number. This demonstrates the feasibility of using AI for QC in clinical trials. AI-based methods offer significant opportunities for enhancing QC, providing automated, consistent, and objective analyses that reduce the workload on human annotators. Integrating AI into QC processes promises to improve accuracy, consistency, and efficiency, thereby enhancing data integrity and the reliability of clinical trial results. This study underscores the importance of further developing AI-based QC methods in clinical trials.
A mechanistic model of curative combination therapy explains lymphoma clinical trial results
Authors: Pomeroy Amy E. , Palmer Adam C.
Published: June 2024

Combinations of chemotherapies are used to treat many cancer types as they elicit higher cure rates and longer responses than single drugs. Several rationales contribute to the efficacy of combinations, including overcoming inter-patient and intra-tumor heterogeneity and improving efficacy through additive or synergistic pharmacological effects. We present a quantitative model that unifies these phenomena to simulate the clinical activity of curative combination therapies. This mechanistic simulation describes kinetics of tumor growth and death in response to treatment and outputs progression-free survival (PFS) distributions in patient populations. We applied this model to first-line combination therapy for Diffuse Large B-Cell Lymphoma, which is cured in most patients by the 5-drug combination RCHOP. This mechanistic model reproduced clinically observed PFS distributions, kinetics of tumor killing measured by circulating tumor DNA, and the adverse prognostic effect of tumor proliferation rate. The outcomes of nine phase 3 trials of new therapies combined with RCHOP were accurately predicted by the model, based on new therapies’ efficacies in trials in patients with relapsed or refractory disease. Finally, we used the model to explore how drug synergy and predictive biomarkers affect the chance of success of randomized trials. These findings show that curative combination therapies can be understood in quantitative and kinetic detail, and that predictive simulations can be used to aid the design of new treatment regimens and clinical trials in curative-intent settings.

SIGNIFICANCE

A novel model that incorporates pharmacological interactions in the presence of inter-patient and intra-tumor heterogeneity explains and predicts combination clinical trial outcomes of curative regimes used to treat Diffuse Large B-cell lymphoma. This model can be used to understand and inform optimal design of drug combinations and clinical trials.
Environmental Risk Factors Influence the Natural History of Familial Dilated Cardiomyopathy
Authors: Peters Stacey A. , Wright Leah , Yao Jess , McCall Lauren , Thompson Tina , Thompson Bryony , Johnson Renee , Huynh Quan , Santiago Celine F , Trainer Alison , Perrin Mark , James Paul , Zentner Dominica , Kalman Jon , Marwick Thomas H. , Fatkin Diane
Published: June 2024

Background

Familial dilated cardiomyopathy (DCM) is characterized by marked variability in phenotypic penetrance. The extent to which this is determined by patient-specific environmental factors is unknown.

Methods

A retrospective longitudinal cohort study was performed in families with DCM-causing genetic variants. Environmental factors were classified into two subsets based on evidence for a causal link to depressed myocardial contractility, termed (1) DCM-promoting factors and (2) heart failure (HF) comorbidities. These factors were correlated with DCM diagnosis, disease trajectory, and adverse events.

Results

105 probands and family members were recruited: 51 genotype-positive, phenotype-positive (G+P+), 24 genotype-positive, phenotype-negative (G+P-), and 30 genotype-negative, phenotype-negative (G-P-). Baseline characteristics were similar between the 3 genotype groups. DCM-promoting environmental factors (eg. alcohol excess) were enriched in G+P+ individuals compared to G+P-(P<0.001) and G-P-(P=0.003) and were significantly associated with age at DCM onset (HR 2.01,P=0.014). HF comorbidities (eg. Diabetes) had a similar prevalence in G+P+ and G-P-but were significantly reduced in the G+P-group. Fluctuations in left ventricular ejection fraction during follow-up were linked to changes in environmental factors in 35/45 (78%) of instances: 32 (91%) of these were DCM-promoting factors. HF comorbidities, but not DCM-promoting factors, were associated with adverse events in G+ individuals (OR 4.9,P=0.004).

Conclusion

We identified distinct subsets of environmental factors that affect DCM penetrance and adverse outcomes respectively. Our data highlight DCM-promoting environmental factors as key determinants of penetrance and disease trajectory. Collectively, these findings provide a new framework for risk factor assessment in familial DCM and have important implications for clinical management.
Nuclear assembly in giant unilamellar vesicles encapsulatingXenopusegg extract
Authors: Takamori Sho , Mimura Hisatoshi , Osaki Toshihisa , Kondo Tomo , Shintomi Miyuki , Shintomi Keishi , Ohsugi Miho , Takeuchi Shoji
Published: June 2024

The reconstitution of a cell nucleus in a lipid bilayer-enclosed synthetic cell makes great strides in bottom-up synthetic biology. In this study, we propose a method for assembling a nucleus in giant unilamellar vesicles (GUVs). To induce reconstitution of the nucleus, we utilize interphase egg extract of African clawed frogsXenopus laevis, known as a biochemically controllable cell-free system capable of transforming an added sperm chromatin into a nucleusin vitro. We enhanced GUV formation efficiency by the inverted emulsion method through incorporating prolonged waiting time and adding chloroform into lipid-dispersed oil, facilitating subsequent nuclear assembly reactions in the GUVs.Characterization of nucleus-like structures formed in the GUVs revealed the presence of dense DNA and accumulated GFP-NLS in the structure, indicative of functional nuclear import. Immunostaining further validated the presence of nuclear pore complexes on the surfaces of these nucleus-like structures. Our approach offers a versatile platform for constructing artificial cellular systems that closely mimic eukaryotic cells.

Teaser

A cell nucleus is reconstituted in lipid bilayer-enclosed confinements using egg extract from African clawed frogs.
Heteromeric amyloid filaments of ANXA11 and TDP-43 in FTLD-TDP Type C
Authors: Arseni Diana , Nonaka Takashi , Jacobsen Max H. , Murzin Alexey G. , Cracco Laura , Peak-Chew Sew Y. , Garringer Holly J. , Kawakami Ito , Suzuki Hisaomi , Onaya Misumoto , Saito Yuko , Murayama Shigeo , Geula Changiz , Vidal Ruben , Newell Kathy L. , Mesulam Marsel , Ghetti Bernardino , Hasegawa Masato , Ryskeldi-Falcon Benjamin
Published: June 2024

Neurodegenerative diseases are characterised by the abnormal filamentous assembly of specific proteins in the central nervous system1. Human genetic studies established a causal role for protein assembly in neurodegeneration2. However, the underlying molecular mechanisms remain largely unknown, which is limiting progress in developing clinical tools for these diseases. Recent advances in electron cryo-microscopy (cryo-EM) have enabled the structures of the protein filaments to be determined from patient brains1. All diseases studied to date have been characterised by the self-assembly of a single intracellular protein in homomeric amyloid filaments, including that of TAR DNA-binding protein 43 (TDP-43) in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) Types A and B3,4. Here, we used cryo-EM to determine filament structures from the brains of individuals with FTLD-TDP Type C, one of the most common forms of sporadic FTLD-TDP. Unexpectedly, the structures revealed that a second protein, annexin A11 (ANXA11), co-assembles with TDP-43 in heteromeric amyloid filaments. The ordered filament fold is formed by TDP-43 residues G282/284–N345 and ANXA11 residues L39–L74 from their respective low-complexity domains (LCDs). Regions of TDP-43 and ANXA11 previously implicated in protein-protein interactions form an extensive hydrophobic interface at the centre of the filament fold. Immunoblots of the filaments revealed that the majority of ANXA11 exists as a ∼22 kDa N-terminal fragment (NTF) lacking the annexin core domain. Immunohistochemistry of brain sections confirmed the co-localisation of ANXA11 and TDP-43 in inclusions, redefining the histopathology of FTLD-TDP Type C. This work establishes a central role for ANXA11 in FTLD-TDP Type C. The unprecedented formation of heteromeric amyloid filaments in human brain revises our understanding of amyloid assembly and may be of significance for the pathogenesis of neurodegenerative diseases.