bluuebunny/crossref_metadata_2025 huggingface dataset:
A Discard-and-Restart MD algorithm for the sampling of realistic protein transition states and enhance structure-based drug discovery
Authors: Ianeselli Alan , Howard Jonathon , Gerstein Mark B.
Published: June 2024

We introduce a Discard-and-Restart molecular dynamics (MD) algorithm tailored for the sampling of realistic protein transition states. It aids computational structure-based drug discovery by reducing the simulation times to compute transition pathways by up to 2000x. The algorithm iteratively performs short MD simulations and measures their proximity to a target state via a collective variable (CV) loss, which can be defined in a flexible fashion, locally or globally. Using the loss, if the trajectory proceeds toward the target, the MD simulation continues. Otherwise, it is discarded and a new MD simulation is restarted, with new initial velocities randomly drawn from a Boltzmann distribution. The discard-and-restart algorithm demonstrates efficacy and atomistic accuracy in capturing the folding pathways in several contexts: (1) fast-folding small protein domains; (2) the folding intermediate of the prion protein PrP; and (3) the spontaneous partial unfolding of α-Tubulin, a crucial event for microtubule severing. During each iteration of the algorithm, we are able to perform AI-based analysis of the transitory conformations to find binding pockets, which could potentially represent druggable sites. Overall, our algorithm enables systematic and computationally efficient exploration of conformational landscapes, enhancing the design of ligands targeting dynamic protein states.
The role of alternative splicing in marine-freshwater divergence in threespine stickleback
Authors: Rodríguez-Ramírez Carlos E. , Peichel Catherine L.
Published: June 2024

Alternative splicing (AS) regulates which parts of a gene are kept in the messenger RNA and has long been appreciated as a mechanism to increase the diversity of the proteome within eukaryotic species. There is a growing body of evidence that AS might also play an important role in adaptive evolution. However, the overall contribution of AS to phenotypic evolution and adaptation is still unknown. In this study we asked whether AS played a role in adaptation to divergent marine and freshwater habitats in threespine stickleback (Gasterosteus aculeatus). Using two published gill RNAseq datasets, we identified differentially expressed and differentially spliced genes (DEGs and DSGs) between population pairs of marine-freshwater stickleback in the Northeast Pacific and tested whether they are preferentially found in regions of the genome involved in freshwater-marine divergence. We found over one hundred DSGs, and they were found more often than expected by chance in peaks of genetic divergence and quantitative trait loci (QTL) that underlie phenotypic divergence between ecotypes. The enrichment of DSGs in these regions is similar to the enrichment of DEGs. Furthermore, we find that among the different types of AS, mutually exclusive exon splicing is the most strongly correlated with genetic divergence between ecotypes. Taken together, our results suggests that AS might have played a role in the adaptive divergence of marine and freshwater sticklebacks and that some types of AS might contribute more than others to adaptation.
Identification of novel H2A histone variants across diverse clades of algae
Authors: Rousselot Ellyn , Nehr Zofia , Aury Jean-Marc , Denoeud France , Cock Mark , Tirichine Leila , Duc Celine
Published: June 2024

Histones are recognized as one of the most conserved proteins across eukaryotes. They not only ensure DNA compaction in the nucleus but also participate in epigenetic regulation of genome expression. These key epigenetic players are divided into canonical histones, expressed during the S-phase, and variants, expressed throughout the cell cycle. Compared with other core histones, H2A proteins exhibit a high level of variability but the characterization of algal H2A variants remains very limited. In this study, we exploited genome data from 21 species to perform a phylogenetic analysis of brown seaweeds. We identified new H2A variants that are specific to the Phaeophyceae and closely-related sister group species. For each identified H2A protein, we characterized motifs present in the histone fold domain as well as in the N- and C-terminal tails. This approach enabled us to classify the different isoforms and to identify three new variants (H2A.N, H2A.O and H2A.E). Based on mass spectrometry and RNA-Seq data, we identified distinct epigenetics marks and specific expression patterns of the H2A variants in both vegetative and reproductive tissues as well as in response to various environmental conditions. These analyses identified sperm-specific variants and inferred putative roles for the newly discovered variants.
Polarization gratings aided common-path Hilbert holotomography for high-throughput lipid droplets content assay
Authors: Zdańkowski Piotr , Winnik Julianna , Rogalski Mikołaj , Marzejon Marcin J. , Wdowiak Emilia , Dudka Wioleta , Józwik Michał , Trusiak Maciej
Published: June 2024

In this contribution we present a novel polarization gratings aided common-path Hilbert holotomography (CP-HHT) for high-throughput 3D refractive index imaging. Addressing limitations in current holotomography methods, we leverage the extended space-bandwidth product (SBP) through robust phase demodulation using Hilbert spiral transform. Thanks to the application of polarization diffraction gratings our system enables fully tailored holographic settings such as fringe density and shear, thus allowing flexible hologram demodulation, while maintaining simplicity and robustness. The performance is tested on a 3D-printed (using two-photon polymerization) brain phantom and fixed HeLa cells supplemented with cholesterol and oleic acids. Reconstruction analysis using the brain phantom indicates that the Hilbert method provides comparable results and resolution to the Fourier transform method in a significantly expanded measurement throughput. Our CP-HHT approach demonstrates the unique (not possible by fluorescence) high-throughput (especially when compared to cryogenic electron microscopy) capability to differentiate between cholesterol esters vs. triacylglycerol (TAG) rich lipid droplets (LDs), thus has potential for label-free biological research at sub-cellular level. The quantitative analysis of LDs’ refractive index emphasizes the method’s sensitivity in distinguishing between LDs with different neutral lipid content, offering new insights into LD heterogeneity, thus reinforcing the versatility and applicability of our CP-HHT system in broader bioimaging applications.
ExploitingPseudomonas syringaeType 3 secretion to study effector contribution to disease in spinach
Authors: Mendel Melanie , Zuijdgeest Xander C. L. , Berg Femke van den , Meer Leroy van der , Elberse Joyce , Skiadas Petros , Seidl Michael F , Ackerveken Guido Van den , Jonge Ronnie de
Published: June 2024

Intensive cultivation practices of spinach create favourable conditions for the emergence and rapid evolution of pathogens, causing substantial economic damage. Research on host-pathogen interactions and host immunity in various leafy greens benefits from advanced biotechnological tools. The absence of specialised tools for spinach, however, constrains our understanding of spinach immunity. Here, we explored the potential of Type III Secretion System (T3SS)-mediated delivery to study the activity of pathogen effectors in spinach. We identified thePseudomonas syringaepv. tomatoDC3000 (DC3000) polymutant D36E, which lacks 36 known T3SS effectors (T3Es), as a promising T3SS-dependent effector delivery system in spinach. Unlike DC3000, which causes visual disease symptoms on spinach, D36E did not induce visible disease symptoms. Using D36E effector delivery, we screened 28 known DC3000 T3Es individually on spinach for effects on disease symptom development, bacterial proliferation reflecting bacterial virulence, and ROS bursts as a proxy for early immune responses. All three assays identified T3Es AvrE1 and HopM1 as crucial determinants of DC3000-like infection on spinach. Additionally, we observed that the T3E HopAD1 strongly suppressed ROS production in spinach. We present the first experimental evidence of plant pathogen effector activities in spinach. By establishing the D36E-effector delivery system in spinach, we pave the way for high-throughput effector studies on spinach. This system provides a critical link between genomics-based effector predictions in spinach pathogens and experimental validation, which is a crucial step for knowledge-driven resistance breeding in non-model crops like spinach.
Fitness advantage of sequential metabolic strategies emerges from community interactions in strongly fluctuating environments
Authors: Wang Zihan , Fu Yu , Goyal Akshit , Maslov Sergei
Published: June 2024

Microbes growing in fluctuating environments employ two key metabolic strategies: sequential (diauxic) utilization and co-utilization of nutrients. Most work has focused on understanding and comparing these strategies physiologically for the growth of single species, rather than ecologically for the assembly of complex natural communities. This is in part because of the lack of good metrics quantifying the fitness of different metabolic strategies in ecological contexts. Here, we present a new consumer-resource framework that incorporates dynamic proteome reallocation, and use it to compare the fitness of metabolic strategies during community assembly. We introduce two notions of fitness of a strategy in fluctuating environments: the time-averaged growth rate and the biomass-weighted prevalence of microbes using a given strategy. We find that sequential utilizers, although disadvantaged in pairwise competitions, gain a significant edge during community assembly — an advantage that becomes more pronounced with increasing community diversity and the size of the species pool from which they are assembled. Low diversity communities resemble pairwise competitions and are dominated by co-utilizers, whereas high diversity, mature communities are dominated by the sequential utilizers. This shift is driven by two factors: the difference in lag times and the increased structural stability conferred by sequential strategies. Overall, our work provides several testable predictions about the co-occurrence patterns of microbes using different metabolic strategies.
Coordinated function of paired NLRs confersYr84-mediated stripe rust resistance in wheat
Authors: Klymiuk Valentyna , Wiebe Krystalee , Chawla Harmeet Singh , Ens Jennifer , Subramaniam Rajagopal , Pozniak Curtis J.
Published: June 2024

Cloning of resistance genes expands our understanding of their function and facilitates their deployment in breeding. Here, we report the cloning of two genes from wild emmer wheat (Triticum turgidumssp.dicoccoides) underlyingYr84-mediated stripe rust resistance using a combination of fine mapping, long read-sequencing and mutation-induced functional validation. In contrast to all previously cloned stripe rust genes, the incompletely dominantYr84phenotype is conferred through the coordinated function of paired nucleotide-binding leucine-rich repeats (NLR) genesCNLandNL. We hypothesize that based on their genomic organization, annotation, expression profiles and predicted protein structure, CNL functions as a sensor NLR (sNLR) responsible for effector recognition, and NL acts as a helper NLR (hNLR) initiating downstream resistance cascades. The CNL and NL lack an integrated domain(s) previously implicated in effector recognition by paired NLRs, therefore these findings contribute new insights into plant paired NLRs structure and molecular mechanisms of function.
NaBC1 boron transporter enables myoblast response to substrate rigidity via fibronectin-binding integrins
Authors: Gonzalez-Valdivieso Juan , Ciccone Giuseppe , Barcelona-Estaje Eva , Rodrigo-Navarro Aleixandre , Castillo Rafael , Rico Patricia , Salmeron-Sanchez Manuel
Published: June 2024

Cells are sensitive to the physical properties of their microenvironment and transduce them into biochemical cues that trigger gene expression and alter cell behavior. Numerous proteins, including integrins, are involved in these mechanotransductive events. Here, we identify a novel role for the boron transporter NaBC1 as a mechanotransducer. We demonstrate that soluble boron ions activate NaBC1 to enhance cell adhesion and intracellular tension in C2C12 myoblasts seeded on fibronectin-functionalised polyacrylamide (PAAm) hydrogels. Retrograde actin flow and traction forces exerted by these cells are significantly increasedin vitroin response to both increased boron concentration and hydrogel stiffness. These effects are fibronectin and NaBC1-mediated as they are abrogated in hydrogels coated with laminin-111 in place of fibronectin and in esiRNA NaBC1-silenced cells. Our findings thus demonstrate that NaBC1 controls boron homeostasis and also functions as a mechanosensor.
Highly Repeatable Tissue Proteomics for Kidney Transplant Pathology: Technical and Biological Validation of Protein Analysis using LC-MS/MS
Authors: Hofstraat Rianne , Marx Kristina , Blatnik Renata , Claessen Nike , Chojnacka Aleksandra , Peters-Sengers Hessel , Florquin Sandrine , Kers Jesper , Corthals Garry
Published: June 2024

Accurate pathological assessment of tissue samples is key for diagnosis and optimal treatment decisions. Traditional pathology techniques suffer from subjectivity resulting in inter-observer variability, and limitations in identifying subtle molecular changes. Omics approaches provide both molecular evidence and unbiased classification, which increases the quality and reliability of final tissue assessment. Here, we focus on mass spectrometry (MS)-based proteomics as a method to reveal biopsy tissue differences. For MS data to be useful, molecular information collected from formalin fixed paraffin embedding (FFPE) biopsy tissues needs to be consistent and quantitatively accurate and contain sufficient clinically relevant molecular information. Therefore, we developed an MS-based workflow and assessed the analytical repeatability on 36 kidney biopsies, ultimately analysing molecular differences and similarities of over 5000 proteins per biopsy. Additional 301 transplant biopsies were analysed to understand other physical parameters including effects of tissue size, standing time in autosampler, and the effect on clinical validation. MS data were acquired using Data-Independent Acquisition (DIA) which provides gigabytes of data per sample in the form of high proteome (and genome) representation, at exquisitely high quantitative accuracy. The FFPE-based method optimised here provides a coefficient of variation below 20%, analysing more than 5000 proteins per sample in parallel. We also observed that tissue thickness does affect the outcome of the data quality: 5 μm sections show more variation in the same sample than 10 μm sections. Notably, our data reveals an excellent agreement for the relative abundance of known protein biomarkers with kidney transplantation lesion scores used in clinical pathological diagnostics. The findings presented here demonstrate the ease, speed, and robustness of the MS-based method, where a wealth of molecular data from minute tissue sections can be used to assist and expand pathology, and possibly reduce the inter-observer variability.
Digital pathology assessment of kidney glomerular filtration barrier ultrastructure in an animal model of podocytopathy
Authors: Laudon Aksel , Wang Zhaoze , Zou Anqi , Sharma Richa , Ji Jiayi , Kim Connor , Qian Yingzhe , Ye Qin , Chen Hui , Henderson Joel M , Zhang Chao , Kolachalama Vijaya B , Lu Weining
Published: June 2024

Background

Transmission electron microscopy (TEM) images can visualize kidney glomerular filtration barrier ultrastructure, including the glomerular basement membrane (GBM) and podocyte foot processes (PFP). Podocytopathy is associated with glomerular filtration barrier morphological changes observed experimentally and clinically by measuring GBM or PFP width. However, these measurements are currently performed manually. This limits research on podocytopathy disease mechanisms and therapeutics due to labor intensiveness and inter-operator variability.

Methods

We developed a deep learning-based digital pathology computational method to measure GBM and PFP width in TEM images from the kidneys of Integrin-Linked Kinase (ILK) podocyte-specific conditional knockout (cKO) mouse, an animal model of podocytopathy, compared to wild-type (WT) control mouse. We obtained TEM images from WT and ILK cKO littermate mice at 4 weeks old. Our automated method was composed of two stages: a U-Net model for GBM segmentation, followed by an image processing algorithm for GBM and PFP width measurement. We evaluated its performance with a 4-fold cross-validation study on WT and ILK cKO mouse kidney pairs.

Results

Mean (95% confidence interval) GBM segmentation accuracy, calculated as Jaccard index, was 0.73 (0.70-0.76) for WT and 0.85 (0.83-0.87) for ILK cKO TEM images. Automated and manual GBM width measurements were similar for both WT (p=0.49) and ILK cKO (p=0.06) specimens. While automated and manual PFP width measurements were similar for WT (p=0.89), they differed for ILK cKO (p<0.05) specimens. WT and ILK cKO specimens were morphologically distinguishable by manual GBM (p<0.05) and PFP (p<0.05) width measurements. This phenotypic difference was reflected in the automated GBM (p<0.05) more than PFP (p=0.06) widths.

Conclusions

These results suggest that certain automated measurements enabled via deep learning-based digital pathology tools could distinguish healthy kidneys from those with podocytopathy. Our proposed method provides high-throughput, objective morphological analysis and could facilitate podocytopathy research and translate into clinical diagnosis.

Key points

We leveraged U-Net architecture in an algorithm to measure the widths of glomerular basement membrane and podocyte foot processes.

Deep learning-based automated measurement of glomerular filtration barrier morphology has promise in podocytopathy research and diagnosis.
De novo design of alpha-beta repeat proteins
Authors: Zorine Dmitri , Baker David
Published: June 2024

Proteins composed of a single structural unit tandemly repeated multiple times carry out a wide range of functions in biology. There has hence been considerable interest in designing such repeat proteins; previous approaches have employed strict constraints on secondary structure types and relative geometries, and most characterized designs either mimic a known natural topology, adhere closely to a parametric helical bundle architecture, or exploit very short repetitive sequences. Here, we describe Rosetta-based and deep learning hallucination methods for generating novel repeat protein architectures featuring mixed alpha-helix and beta-strand topologies, and 25 new highly stable alpha-beta proteins designed using these methods. We find that incorporation of terminal caps which prevent beta strand mediated intermolecular interactions increases the solubility and monomericity of individual designs as well as overall design success rate.
New mitochondrial gene order arrangements and evolutionary implications in the subclass Octocorallia
Authors: Poliseno Angelo , Quattrini Andrea M. , Lau Yee Wah , Pirro Stacy , Reimer James D. , McFadden Catherine S.
Published: June 2024

The complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length, and include 14 protein coding genes (PCGs), two ribosomal RNA genes and one tRNA. To date seven different gene orders (A-G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses and evolutionary reconstructions of mitochondrial genome evolution within the whole subclass Octocorallia have been often overlooked. Here we considered the complete mitochondrial genomes available for octocorals and explored their structure and gene order variability. Our results updated the actual number of mitochondrial gene order arrangements so far known for octocorals from seven to twelve, and allowed us to explore and preliminarily discuss the role of some of the structural and functional factors in the mitogenomes. We performed comparative mitogenomic analyses on the existing and novel octocoral gene orders, considering different mitogenomic structural features such as genome size, GC percentage, AT- and GC-skewness. The mitochondrial gene order history mapped on a recently published nuclear loci phylogeny showed that the most common rearrangement events in octocorals are inversions, and that the mitochondrial genome evolution in the subclass is discontinuous, with rearranged gene orders restricted only to some regions of the tree. We believe that different rearrangement events arose independently and most likely that new gene orders, instead of being derived from other rearranged orders, came from the ancestral and most common gene order. Finally, our data demonstrate how the study of mitochondrial gene orders can be used to explore the evolution of octocorals and in some cases can be used to assess the phylogenetic placement of certain taxa.
Probing the glioma micro-environment: analysis using biopsy in combination with ultra-fast cyclic immunolabeling
Authors: van Solinge Thomas S. , Oh Juhyun , Abels Erik , Koch Peter , Breakefield Xandra O. , Weissleder Ralph , Broekman Marike L.D.
Published: June 2024

The interaction between gliomas and the immune system is poorly understood and thus hindering development of effective immunotherapies for glioma patients. The immune response is highly variable during tumor development, and affected by therapies such as surgery, radiation, and chemotherapy. Currently, analysis of these local changes is difficult due to poor accessibility of the tumor and high-morbidity of sampling. In this study, we developed a model for repeat-biopsy in mice to study these local immunological changes over time. Using fine needle biopsy we were able to safely and repeatedly collect cells from intracranial tumors in mice. Ultra-fast cycling technology (FAST) was used for multi-cycle immunofluorescence of retrieved cells, and provided insights in the changing immune response over time. The combination of these techniques can be utilized to study changes in the immune response in glioma or other intracranial diseases over time, and in response to treatment within the same animal.

Teaser

Fine-needle biopsy and ultra-fast cycling technology techniques were developed to allow for repeat sampling and analysis of glial tumors in mice.
Directed Micro-Ecology Application System: On-site One-step Fermentation Facilitating Microbial Application Through Theoretical and Equipment Innovation
Authors: Ma Rui-qiang , Luo Yun-feng , Zhao Wei-min , Guo Jian-feng , Li Yanjie , Cui Wen-jing
Published: June 2024

Functional microbial agents play a crucial role in various fields such as agriculture, feed fermentation, aquaculture, and environmental protection. However, traditional microbial agents were confronted with critical challenges such as limited shelf-life, reduced activity, and inconsistent efficacy. In this case, we innovatively proposed the concept of Directed Micro-Ecology (DME) and developed its application system, including a core module named DME intelligent fermentor (DME25). Over 40 functional strains, including bacterial strains and fungus strains, were successfully cultured to 10∼50 ×108CFU/mL within 20∼48 h and maintained a relatively low contamination rate (<2.5%). Finally, the stability and effectiveness of these DME-fermented strains were validated in different application areas, all of which exhibited perfect functional characteristics. Firstly, the bacillus strains inhibited the progression of wilt disease and significantly improved the growth of tomatoes. Secondly, all tested lactobacillus strains improved the nutrition and quality of fermented feed, complying with feed industry standards. Lastly, the ammonia nitrogen concentration, nitrite concentration of aquaculture water and phosphate concentration, COD of aquaculture tail water were significantly reduced within 1∼4 d. The successful application of the DME intelligent fermentor in different fields marks a pivotal breakthrough in technological innovation of microbial agents on-site one-step fermentation. This technological advancement opens new avenues for enhancing the stability and effectiveness of microbial agents, infusing powerful impetus to the development of microbial application.
Conditional frequency spectra as a tool for studying selection on complex traits in biobanks
Authors: Patel Roshni A. , Weiß Clemens L. , Zhu Huisheng , Mostafavi Hakhamanesh , Simons Yuval B. , Spence Jeffrey P. , Pritchard Jonathan K.
Published: June 2024

Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). The power to detect a trait-associated variant in GWAS is a function of frequency and effect size — but for traits under selection, the effect size of a variant determines the strength of selection against it, constraining its frequency. To account for GWAS ascertainment, we propose studying the joint distribution of allele frequencies across populations, conditional on the frequencies in the GWAS cohort. Before considering these conditional frequency spectra, we first characterized the impact of selection and non-equilibrium demography on allele frequency dynamics forwards and backwards in time. We then used these results to understand conditional frequency spectra under realistic human demography. Finally, we investigated empirical conditional frequency spectra for GWAS variants associated with 106 complex traits, finding compelling evidence for either stabilizing or purifying selection. Our results provide insight into polygenic score portability and other properties of variants ascertained with GWAS, highlighting the utility of conditional frequency spectra.
DR3E-Net: Drug Repurposing Network Framework Based on Deep Embedding, Differentially Expressed Genes, and Drug Side Effects
Authors: Bhak YoungMin , Park Joon Ho , Han Hyun Wook
Published: June 2024

In contrast to traditional de-novo drug discovery, which involves high costs and lengthy development times alongside a high failure rate, drug repurposing (DR) offers a potential solution to these challenges. This study introduces DR3E-Net, an in-silico DR framework that integrates embedded vectors of genetic expression influenced by drugs, differentially expressed genes (DEGs) associated with diseases, and information about drug side effects. The DR3E-Net utilized LINCS L1000 datasets, which comprised 680,909 samples, 3,820 drugs, and 977 genes after preprocessing. The deep-embedding model within DR3E-Net was trained on this dataset, facilitating the transformation of 977-dimensional vectors into 32-dimensional unit-hypersphere embeddings. Subsequently, cosine similarity (CS) was computed among them (Step 1). To further elaborate, agonistic drugs against DEG linked to a disease (Alzheimer’s disease (AD) in this study) were merged with outcomes from Step 1 (Step 2). Finally, the SIDER and SAEDR/DRIP databases were combined with the integrated results from Step 2 (Step 3).

The DR3E-Net was utilized to predict potential alternative drug candidates for three AD medications: donepezil, galantamine, and memantine. The drugs predicted by the deep-embedding model (Step 1) were combined with agonistic drugs against CRTAP gene, resulting in 111, 86, and 96 drugs, respectively (Step 2). Lastly, drug side effect information was incorporated with the aforementioned drug outcomes, yielding 21, 15, and 18 drugs (Step 3). DR3E-Net was developed to predict functionally similar drugs while considering disease-associated DEGs of patients and drug side effect information.
Bioprinting of aptamer-based programmable bioinks to modulate multiscale microvascular morphogenesis in 4D
Authors: Rana Deepti , Rangel Vincent R. , Padmanaban Prasanna , Trikalitis Vasileios D. , Kandar Ajoy , Kim Hae-Won , Rouwkema Jeroen
Published: June 2024

Dynamic growth factor presentation influences how individual endothelial cells assemble into complex vascular networks. Here, we developed programmable bioinks that facilitate dynamic VEGF presentation to guide vascular morphogenesis within 3D-bioprinted constructs. We leveraged aptamer’s high affinity for rapid VEGF sequestration in spatially confined regions and utilized aptamer-complementary sequence (CS) hybridization to tune VEGF release kinetics temporally, days after bioprinting. We show that spatial resolution of programmable bioink, combined with CS-triggered VEGF release, significantly influences alignment, organization, and morphogenesis of microvascular networks in bioprinted constructs. The presence of aptamer-tethered VEGF and the generation of instantaneous VEGF gradients upon CS-triggering restricted hierarchical network formation to the printed aptamer regions at all spatial resolutions. Network properties improved as the spatial resolution decreased, with low-resolution designs yielding the highest network properties. Specifically, CS-treated low-resolution designs exhibited significant vascular network remodeling, with increase in vessel density(1.35-fold), branching density(1.54-fold), and average vessel length(2.19-fold) compared to non-treated samples. Our results suggests that CS acts as an external trigger capable of inducing time-controlled changes in network organization and alignment on-demand within spatially localized regions of a bioprinted construct. We envision that these programmable bioinks will open new opportunities for bioengineering functional, hierarchically self-organized vascular networks within engineered tissues.
An ALK1-governed monocytic lineage shapes an immunosuppressive landscape in breast cancer metastases
Authors: Talkhoncheh Mehrnaz Safaee , Sjölund Jonas , Bolivar Paulina , Kurzejamska Ewa , Cordero Eugenia , Pagès Teia Vallès , Larsson Sara , Lehn Sophie , Frimannsson Gustav , Ingesson Viktor , Braun Sebastian , Pantaleo Jessica , Oudenaarden Clara , Lauss Martin , Pearsall R. Scott , Jönsson Göran B. , Rolny Charlotte , Bocci Matteo , Pietras Kristian
Published: June 2024

The biology centered around the TGF-β type I receptor ALK1 (encoded byACVRL1)has been almost exclusively based on its reported endothelial expression pattern since its first functional characterization more than two decades ago. Here, in efforts to better define the therapeutic context in which to use ALK1 inhibitors, we uncover a population of tumor-associated macrophages (TAMs) that, by virtue of their unanticipatedAcvrl1expression, are effector targets for adjuvant anti-angiogenic immunotherapy in mouse models of metastatic breast cancer. The combinatorial benefit depended on ALK1-mediated modulation of the differentiation potential of bone marrow-derived granulocyte-macrophage progenitors, the release of CD14+monocytes into circulation, and their eventual extravasation. Notably,ACVRL1+TAMs coincided with an immunosuppressive phenotype, and were over-represented in human cancers progressing on therapy. Accordingly, breast cancer patients with a prominentACVRL1hiTAM signature exhibited a significantly shorter survival. In conclusion, we shed light on an unexpected multimodal regulation of tumorigenic phenotypes by ALK1 and demonstrate its utility as a target for anti-angiogenic immunotherapy.

Graphical abstract

See submitted file
Unveiling the Virulence Mechanism ofLeptosphaeria maculansin theBrassica napusInteraction: The Key Role of Sirodesmin PL in Cell Death Induction
Authors: Pombo Marina A. , Rosli Hernan G. , Maiale Santiago , Elliott Candace , Stieben Micaela E. , Romero Fernando M. , Garriz Andrés , Ruiz Oscar A. , Idnurm Alexander , Rossi Franco R.
Published: June 2024

Leptosphaeria maculansis the causal agent of blackleg disease inBrassica napus, leading to substantial yield losses. Sirodesmin PL, the principal toxin produced byL. maculans, has been implicated in the infective process in plants. However, the precise molecular and physiological mechanisms governing its effects remain elusive. This study investigates the changes induced by Sirodesmin PL at the transcriptomic, physiological, and morphological levels inB. napuscotyledons. Sirodesmin PL treatment upregulates genes associated with plant defense processes, including response to chitin, sulfur compound biosynthesis, toxin metabolism, oxidative stress response, and jasmonic acid/ethylene synthesis and signaling. Validation of these transcriptomic changes is evidenced by several typical defense response processes, such as the accumulation of reactive oxygen species (ROS) and callose deposition. Concomitantly, oxidized Sirodesmin PL induces concentration- and exposure duration-dependent cell death. This cellular death is likely attributed to diminished activity of photosystem II and a reduction in the number of chloroplasts per cell. In agreement, a down-regulation of genes associated with the photosynthesis process is observed following Sirodesmin PL treatment. Thus, it is plausible thatL. maculansexploits Sirodesmin PL as a virulence factor to instigate cell death inB. napusduring its necrotrophic stage, favoring the infective process.

Highlight

Sirodesmin PL, the principal toxin produced by Leptosphaeria maculans, induces cell death and defense mechanisms inBrassica napus, disrupting photosynthesis and facilitating the infective process
TEMR: Trans-ethnic Mendelian Randomization Method using Large-scale GWAS Summary Datasets
Authors: Hou Lei , Wu Sijia , Yuan Zhongshang , Li Hongkai , Xue Fuzhong
Published: June 2024

Available large-scale GWAS summary datasets predominantly stem from European populations, while sample sizes for other ethnicities, notably Central/South Asian, East Asian, African, Hispanic, etc. remain comparatively limited, which induces the low precision of causal effect estimation within these ethnicities using Mendelian Randomization (MR). In this paper, we propose a Trans-ethnic MR method called TEMR to improve statistical power and estimation precision of MR in the target population using trans-ethnic large-scale GWAS summary datasets. TEMR incorporates trans-ethnic genetic correlation coefficients through a conditional likelihood-based inference framework, producing calibrated p-values with substantially improved MR power. In the simulation study, TEMR exhibited superior precision and statistical power in the causal effects estimation within the target populations than other existing MR methods. Finally, we applied TEMR to infer causal relationships from 17 blood biomarkers to four diseases (hypertension, ischemic stroke, type 2 diabetes and schizophrenia) in East Asian, African and Hispanic/Latino populations leveraging the biobank-scale GWAS summary data from European. We found that causal biomarkers were mostly validated by previous MR methods, and we also discovered 13 new causal relationships that were not identified using previously published MR methods.
Protocol for a randomized cross-over study measuring the effect of reduced protein intake on autophagic flux in healthy adults
Authors: Fourrier Célia , Heilbronn Leonie K. , Teong Xiao Tong , Gore Jemima R. , Sargeant Timothy J. , Bensalem Julien
Published: June 2024

Autophagy is a cellular mechanism that degrades damaged or unwanted material from cells and is particularly important during ageing. Autophagy has been widely studied in pre-clinical models and is known to respond to nutrient availability and in particular amino acids. However, clinical data are limited. This protocol paper describes a randomized cross-over clinical study investigating the effect of a four-week long reduction of dietary protein intake on autophagic flux (autophagic degradative activity) measured via a blood test in healthy adults. Sixty-one healthy participants will be recruited. Study participants will be randomly assigned to one of two diets for four weeks, then cross over to the other diet with a four-week washout period between diets. The diets will be: 1) Average Protein Diet: a control comparator diet with a macronutrient profile of 20% of energy from protein, 35% from fat (<10% saturated) and 45% from carbohydrate, with >30 g of fiber/day; 2) Reduced Protein Diet: 10% protein, 35% fat (<10% saturated), 55% carbohydrate, >30 g of fiber/day. This diet will provide 0.7 g of protein per kg of body weight (the recommended minimum daily protein intake). The primary outcome will be the change in autophagic flux between each diet. This study aims to determine whether reducing dietary protein intake in healthy adults can increase autophagy in humans. If positive, it creates the possibility that nutritional strategies could be used to prevent or delay autophagy- related diseases such as Alzheimer disease or atherosclerosis.
A Formal Model of Mood Disorders Based on the Neural Circuit Dynamics of the Triple Network Model
Authors: Rubin Alan Lawrence , Walth Mark
Published: June 2024

Psychiatric diagnoses are based on consensus and are not related to pathophysiology, leading to confusion in treatment and in basic and clinical psychiatric research. The pathology of mood disorders arises from the intrinsic function and interactions between key neural circuits of the triple network. These circuits are the central executive network composed of the dorsolateral prefrontal cortex and posterior parietal cortex; the default mode network consisting of the dorsal medial prefrontal cortex, posterior cingulate/precuneus and angular gyrus and the salience network made up of the anterior insula, dorsal anterior cingulate cortex associated with subcortical limbic nodes including the amygdala. In this work, we develop a formal model using nonlinear dynamics and network theory, which captures the dynamic interactions of these three brain networks, allowing us to illustrate how various mood disorders can arise. Recurrent circuit dynamics are modeled on the physio-dynamics of a single neural component and is dependent on a balance of total input (feedforward and feedback) and the sensitivity of activation of its neural components. We use the average percentage of maximal firing rate frequency as a measure of network activity over long periods, which corresponds to fMRI activity.

While the circuits function at moderate rates in euthymia, depressive symptoms are due to hypoactivity of the CEN and SN and hyperactivity of the DMN. Mania arises from a hyperactive SN with hypofunction of the CEN and moderate to high activity of the DMN. Functional abnormalities arise from genetic or epigenetic changes, affecting either the weight of neural interconnections or the sensitivity of activation of neurons comprising the network. Decreased excitation in unipolar depressive states is caused by diminished dendritic branches and decreased density of AMPA and NMDA receptors or a decrease in glutamate released by presynaptic neurons. All bipolar states result from heightened neural sensitivity due to altered sodium, calcium, or potassium channel conductance. Our formal model of mood disorders is consistent with fMRI studies, genetic research, as well as preclinical and clinical studies.
Hyperintense Acute Reperfusion Marker Sign in Patients with Diffusion Weighted Image-negative Transient Ischemic Attack HARM Sign in DWI-negative TIA
Authors: Kim Taewoo , Kim Bum Joon , Woo Ho Geol , Lee Kyung Mi , Park Sangil , Chang Dae-il , Heo Sung Hyuk
Published: June 2024

Background

The hyperintense acute reperfusion marker (HARM) sign is a hyperintense signal observed on postcontrast fluid-attenuated recovery inversion images and is strongly associated with cerebral ischemic insults. The clinical significance of the HARM sign in transient ischemic attack (TIA) has rarely been studied, unlike that in stroke. This study investigated the association between the HARM sign and clinical factors of diffusion-weighted imaging (DWI)-negative TIA, and the relationship between the HARM sign and recurrence of TIA and ischemic stroke.

Methods

We included 329 consecutive patients with DWI-negative TIA and divided them into two groups according to the HARM sign: 299 patients in the HARM(-) group and 30 patients in the HARM(+) group. Clinical information, brain imaging and follow-up data were collected from medical records and phone calls, and compared using HARM sign.

Results

The HARM(+) patients were older and had higher systolic blood pressure, shorter symptom duration, and more frequent history of recent TIA or stroke and symptomatic artery stenosis or occlusion. Multivariate logistic regression revealed that recent TIA or stroke within 12 months (OR 6.623), symptom duration under 1 hour (OR 2.735), and relevant artery stenosis or occlusion (OR 2.761) were independently associated with the HARM sign. Cortical symptoms including aphasia were more prevalent in the HARM(+) group. During follow-up, HARM(+) patients showed higher recurrence rates of ischemic stroke (13.3% vs. 3.0%, p = 0.023). However, multivariate Cox analysis indicated that symptomatic stenosis or occlusion, rather than the HARM sign, was independently associated with stroke recurrence.

Conclusion

The HARM sign in DWI-negative TIA patients is linked to older age, recent cerebrovascular events, shorter symptom duration, and large artery stenosis or occlusion. While the HARM sign correlates with higher recurrence of ischemic stroke, large artery stenosis or occlusion is the primary independent predictor.
Prevalence and Detection of Obstructive Sleep Apnea Early after Stroke
Authors: Klingman Karen J. , Billinger Sandra A. , Britton-Carpenter Amanda , Bartsch Bria , Duncan Pamela W. , Fulk George D.
Published: June 2024

Background

Obstructive sleep apnea (OSA) negatively impacts post-stroke recovery. This study’s purpose: examine the prevalence of undiagnosed OSA and describe a simple tool to identify those at-risk for OSA in the early phase of stroke recovery.

Methods

This was a cross-sectional descriptive study of people ∼15 days post-stroke. Adults with stroke diagnosis admitted to inpatient rehabilitation over a 3-year period were included if they were alert/arousable, able to consent/assent to participation, and excluded if they had a pre-existing OSA diagnosis, other neurologic health conditions, recent craniectomy, global aphasia, inability to ambulate 150 feet independently pre-stroke, pregnant, or inability to understand English. OSA was deemed present if oxygen desaturation index (ODI) of >=15 resulted from overnight oximetry measures. Prevalence of OSA was determined accordingly. Four participant characteristics comprised the “BASH” tool (body mass index >=35, age>=50, sex=male, hypertension=yes). A receiver operator characteristics (ROC) curve analysis was performed with BASH as test variable and OSA presence as state variable.

Results

Participants (n=123) were 50.4% male, averaged 64.12 years old (sd 14.08), and self-identified race as 75.6% White, 20.3% Black/African American, 2.4%>1 race, and 1.6% other; 22% had OSA. ROC analysis indicated BASH score >=3 predicts presence of OSA (sensitivity=0.778, specificity=0.656, area under the curve =0.746, p<0.001).

Conclusions

Prevalence of undiagnosed OSA in the early stroke recovery phase is high. With detection of OSA post-stroke, it may be possible to offset untreated OSA’s deleterious impact on post-stroke recovery of function. The BASH tool is an effective OSA screener for this application.
Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction
Authors: Dahlberg Simon K. , Bonet David Fernández , Franzén Lovisa , Ståhl Patrik L. , Hoffecker Ian T.
Published: June 2024

We reanalyzed data from the Slide-tags method developed by Russellet al. and discovered a hidden, spatially informative network formed during the transfer of spatial tags to nuclei. The structure of this network conveys sufficient information to infer cell locations entirely without ground truth from spatial indexing, placing Slide-tags among a new generation of optics-free, network-based imaging-by-sequencing approaches, a fundamental departure from classical spatial sequencing technologies based on pre-indexed arrays.
Triadic Dynamics of Gastric Bacterial Microbiome, Phageome, and Host Genotype, with Implications for Disease Associations
Authors: Szymczak Aleksander , Gembara Katarzyna , Majewska Joanna , Miernikiewicz Paulina , Ferenc Stanisław , Gnus Jan , Kłak Marlena , Jędruchniewicz Natalia , Witkiewicz Wojciech , Dąbrowska Krystyna
Published: June 2024

The microbiota plays a key role for human health, and microbiome composition has been linked to specific health disorders many times. Different fractions of the microbiome enter dynamic interactions, particularly bacteria and bacteriophages (phages) – viruses preying on bacteria. Since the microbiome exists inside the human body, the body strongly affects the microbes, although not in a uniform way, but shaped by the extreme diversity of human genetic variants. These triadic dynamics of the bacterial microbiome, phageome, and human host genotype remain poorly understood; hence our goal in this study was to comprehend them as a holistic and interdependent system.

Gastric biopsies were the source of the stomach microbiome (bacteria and phages). Genotyping of patients was conducted on blood samples. They were analyzed by next generation sequencing followed by multiway statistical comparisons of identified bacterial and phage taxa, human genetic variants, and medical data from the patients, including gastric disorder diagnostics.

Commonly expected associations between presence of bacteriophages and their specific hosts were not found to be a universal principle. With comparable SNP correlations, the strongest associations betweenStaphylococcusand some staphylococcal phages orEnterobacteriaand some enterobacteria phages were discovered. However, many more phage groups were not found to be clearly associated with their bacterial hosts, though often associated with SNPs, particularly those linked to immunological functions and body responses to bacteria and viruses. Thus, in addition to the expected effect on phage communities by shaping the communities of their bacterial hosts, the human body seems to affect phages directly, selecting for phages that survive its specific selective pressure, which can be defined by detection of particular genetic variants.