Antithrombogenic polysaccharide coatings to improve hemocompatibility, protein-repellence, and endothelial cell response.

Polyester biomaterials play a crucial in vascular surgery, but suffer from unspecific protein adsorption, thrombogenicity, and inadequate endothelial cell response, which limit their success. To address these issues, we investigated the functionalization of polyester biomaterials with antithrombogenic polysaccharide coatings. A two-step and water-based method was used to coat cationized polycaprolactone with different sulfated polysaccharides (SPS), which resulted in long-term stability, tunable morphology, roughness, film thickness, chemical compositions, zeta potential, and water content. The coatings significantly increased the anticoagulant activity and reduced the thrombogenicity of polycaprolactone, particularly with highly sulfated heparin and cellulose sulfate. Less SPS, such as chondroitin sulfate, fucoidan, and carrageenan, despite showing reduced anticoagulant activity, also exhibited lower fibrinogen adsorption. The adhesion and viability of human primary endothelial cells cultured on modified polycaprolactone correlated with the type and sulfate content of the coatings.

Knowledge graphs facilitate prediction of drug response for acute myeloid leukemia.

Acute myeloid leukemia (AML) is a highly aggressive and heterogeneous disease, underscoring the need for improved therapeutic options and methods to optimally predict responses. With the wealth of available data resources, including clinical features, multiomics analysis, and ex vivo drug screening from AML patients, development of drug response prediction models has become feasible. Knowledge graphs (KGs) embed the relationships between different entities or features, allowing for explanation of a wide breadth of drug sensitivity and resistance mechanisms. We designed AML drug response prediction models guided by KGs. Our models included engineered features, relative gene expression between marker genes for each drug and regulators (e.g., transcription factors). We identified relative gene expression of FGD4-MIR4519, NPC2-GATA2, and BCL2-NFKB2 as predictive features for venetoclax ex vivo drug response. The KG-guided models provided high accuracy in independent test sets, overcame potential platform batch effects, and provided candidate drug sensitivity biomarkers for further validation.

Lipids from a snail host regulate the multicellular behavior of a predator of parasitic schistosomes.

Transmission of vector-borne diseases can be slowed by symbionts within the secondary hosts that spread disease. Snails spread schistosomiasis, and the snail symbiont Capsaspora owczarzaki kills schistosome larvae. In studying how Capsaspora colonizes its host snail, we discovered that Capsaspora responded to its host by forming multicellular aggregates. We elucidated the chemical cue for aggregation: hemolymph phosphatidylcholines (PCs). Furthermore, we uncovered that Capsaspora cells aggregate to different degrees in sera from different host snails-and these responses correlate with serum concentrations of PCs. Therefore, Capsaspora senses a host factor that can indicate the identity and physiological state of its host. Since cellular aggregation controls microbial motility, feeding, and immune evasion, this response within host tissue may be important for colonization. If so, snail serum PC and Capsaspora aggregation will be molecular and cellular markers to discern which conditions will favor the colonization of snails (and potential exclusion of schistosomes) by Capsaspora.

HSPB6: A lipid-dependent molecular chaperone inhibits α-synuclein aggregation.

The process of protein misfolding and aggregation is associated with various cytotoxic effects. Understanding how this phenomenon is regulated by the protein homeostasis system, however, is difficult, since it takes place through a complex non-linear network of coupled microscopic steps, including primary nucleation, fibril elongation, and secondary nucleation, which depend on environmental factors. To address this problem, we studied how the aggregation of α-synuclein, a protein associated with Parkinson's disease, is modulated by molecular chaperones and lipid membranes. We focused on small heat shock proteins (sHSPs/HSPBs), which interact with proteins and lipids and are upregulated during aging, a major risk factor for protein misfolding diseases. HSPBs act on different microscopic steps to prevent α-synuclein aggregation, with HSPB6 showing a lipid-dependent chaperone activity. Our findings provide an example of how HSPBs diversified their mechanisms of action to reach an efficient regulation of protein misfolding and aggregation within the complex cellular environment.

Widespread application of apomixis in agriculture requires further study of natural apomicts.

Apomixis, or asexual reproduction through seeds, is frequent in nature but does not exist in any major crop species, yet the phenomenon has captivated researchers for decades given its potential for clonal seed production and plant breeding. A discussion on whether this field will benefit from the continued study of natural apomicts is warranted given the recent outstanding progress in engineering apomixis. Here, we summarize what is known about its genetic control and the status of applying synthetic apomixis in agriculture. We argue there is still much to be learned from natural apomicts, and learning from them is necessary to improve on current progress and guarantee the effective application of apomixis beyond the few genera it has shown promise in so far. Specifically, we stress the value of studying the repeated evolution of natural apomicts in a phylogenetic and comparative -omics context. Finally, we identify outstanding questions in the field and discuss how technological advancements can be used to help close these knowledge gaps. In particular, genomic resources are lacking for apomicts, and this must be remedied for widespread use of apomixis in agriculture.

Identification of XD23 as a potent inhibitor of osteosarcoma via downregulation of DKK1 and activation of the WNT/ß-catenin pathway.

Osteosarcoma, the most prevalent malignant bone tumor, is notorious for its aggressive growth and invasiveness. The highly mutable genome of osteosarcoma has made identifying a key oncogene challenging, hindering the development of targeted treatments. Our study validates the effectiveness of XD23, an anti-cancer agent we previously identified, in curbing osteosarcoma proliferation, metastasis, EMT differentiation, and bone destruction and promoting osteosarcoma apoptosis. It further elucidated that XD23 thwarts osteosarcoma by suppressing DKK1 expression, which in turn activates the WNT-ß/Catenin pathway. This research presents the concrete evidence of DKK1's involvement in osteosarcoma development, offering a foundation for the development of DKK1 inhibitors as novel treatments for this disease.

ZIKV induces P62-mediated autophagic degradation of TRAF6 through TRAF6-NS1 interaction.

Tumor necrosis factor receptor-associated factor 6 (TRAF6) is crucial in flavivirus infections, modulating the host immune response through interactions with viral proteins. Despite its importance, the relationship between TRAF6 and Zika virus (ZIKV) remains poorly understood. Our prior proteomics analysis revealed reduced TRAF6 protein levels in ZIKV-infected human trophoblast cells compared to non-infected controls. Subsequent studies in cell models and murine tissues confirmed a significant reduction in both TRAF6 mRNA and protein levels post-ZIKV infection. Further investigations unveiled that ZIKV induces P62-mediated degradation of TRAF6, with NS1 identified as the primary contributor. Co-localization and interaction studies demonstrated that NS1 promotes the association of P62, a key autophagy mediator, with TRAF6. Notably, our findings revealed TRAF6 enhances ZIKV infection, NS1 ubiquitination, NS1 expression, and the production of inflammatory cytokines and chemokines. These insights highlight the intricate TRAF6-ZIKV relationship, offering potential for drug targeting NS1-TRAF6 interactions to manage ZIKV infections effectively.

Development of a hepatic differentiation method in 2D culture from primary human hepatocyte-derived organoids for pharmaceutical research.

Human liver organoids derived from primary human hepatocytes (PHHs) are expected to be a hepatocyte source for preclinical in vitro studies of drug metabolism and disposition. Because hepatic functions of these organoids remain low, it is necessary to enhance the hepatic functions. Here, we develop a novel method for two dimensional (2D)-cultured hepatic differentiation from PHH-derived organoids by screening several compounds, cytokines, and growth factors. Hepatic gene expressions in the hepatocyte-like cells differentiated from PHH-derived organoids (Org-HEPs) were greatly increased, compared to those in PHH-derived organoids. The metabolic activities of cytochrome P450 (CYP) 1A2, CYP2C8, CYP2C19, CYP2E1, and CYP3A4 were at levels comparable to those in PHHs. The cell viability of Org-HEPs treated with hepatotoxic drugs was almost the same as that of PHHs. Thus, PHH-derived organoids could be differentiated into highly functional hepatocytes in 2D culture. Thus, Org-HEPs will be useful for pharmaceutical research, including hepatotoxicity tests.

Starving infecund widow spiders maintain sexual attractiveness and trade off safety for enhanced prey capture.

Starving animals must balance their resources between immediate survival and future reproduction. False widow spiders, Steatoda grossa, inhabit indoor settings with scarce prey. Here, we investigated the effects of lengthy starvation on the physiology, web architecture, sexual signaling, and reproductive success of S. grossa females. Compared to well-fed females, starving females (1) lost body mass faster, (2) had lower survival, (3) produced more silk for prey capture than for safety, and (4) deposited less contact pheromone components on their webs but accelerated their hydrolysis to mate-attractant components. As starving females became infecund - but still attracted and copulated with males - they misguided males that would gain reproductive fitness by selecting fecund females. Whether starving females store sperm and potentially regain fecundity upon feeding is still unknown. Our study shows how prey shortage shapes sexual signaling, predation, and reproductive behavior of S. grossa females that seem to engage in deceptive signaling.

Positional information modulates transient regeneration-activated cell states during vertebrate appendage regeneration.

Injury is common in the life of organisms. Because the extent of damage cannot be predicted, injured organisms must determine how much tissue needs to be restored. Although it is known that amputation position affects the regeneration speed of appendages, mechanisms conveying positional information remain unclear. We investigated tissue dynamics in regenerating caudal fins of the African killifish (Nothobranchius furzeri) and found position-specific, differential spatial distribution modulation, persistence, and magnitude of proliferation. Single-cell RNA sequencing revealed a transient regeneration-activated cell state (TRACS) in the basal epidermis that is amplified to match a given amputation position and expresses components and modifiers of the extracellular matrix (ECM). Notably, CRISPR-Cas9-mediated deletion of the ECM modifier sequestosome 1 (sqstm1) increased the regenerative capacity of distal injuries, suggesting that regeneration growth rate can be uncoupled from amputation position. We propose that basal epidermis TRACS transduce positional information to the regenerating blastema by remodeling the ECM.

Follistatin controls the number of murine teeth by limiting TGF-ß signaling.

Supernumerary teeth are common developmental anomalies of dentition. However, the factors and mechanisms driving their formation remain largely unknown. Here, we report that conditional knockout of Fst, encoding an antagonist for the transforming growth factor ß (TGF-ß) signaling pathway, in both oral epithelium and mesenchyme of mice (Fst CKO ) led to supernumerary upper incisor teeth, arising from the lingual dental epithelium of the native teeth and preceded by an enlarged and split lingual cervical loop. Fst-deficiency greatly activated TGF-ß signaling in developing maxillary incisor teeth, associated with increased epithelium cell proliferation. Moreover, Fst CKO teeth exhibited increased expression of Tbx1, Sp6, and Sox2, which were identified as direct targets of TGF-ß/SMAD2 signaling. Finally, we show that upregulation of Tbx1 in response to Fst-deficiency was largely responsible for the formation of extra teeth in Fst CKO mice. Taken together, our investigation indicates a novel role for Fst in controlling murine tooth number by restricting TGF-ß signaling.

Branch-specific clustered parallel fiber input controls dendritic computation in Purkinje cells.

Most central neurons have intricately branched dendritic trees that integrate massive numbers of synaptic inputs. Intrinsic active mechanisms in dendrites can be heterogeneous and be modulated in a branch-specific way. However, it remains poorly understood how heterogeneous intrinsic properties contribute to processing of synaptic input. We propose the first computational model of the cerebellar Purkinje cell with dendritic heterogeneity, in which each branch is an individual unit and is characterized by its own set of ion channel conductance densities. When simultaneously activating a cluster of parallel fiber synapses, we measure the peak amplitude of a response and observe how changes in P-type calcium channel conductance density shift the dendritic responses from a linear one to a bimodal one including dendritic calcium spikes and vice-versa. These changes relate to the morphology of each branch. We show how dendritic calcium spikes propagate and how Kv4.3 channels block spreading depolarization to nearby branches.

The role of mitofusin 2 in regulating endothelial cell senescence: Implications for vascular aging.

Endothelial cell dysfunction contributes to age-related vascular diseases. Analyzing public databases and mouse tissues, we found decreased MFN2 expression in senescent endothelial cells and angiotensin II-treated mouse aortas. In human endothelial cells, Ang II reduced MFN2 expression while increasing senescence markers P21 and P53. siMFN2 treatment worsened Ang II-induced senescence, while MFN2 overexpression alleviated it. siMFN2 or Ang II treatment caused mitochondrial dysfunction and morphological abnormalities, including increased ROS production and reduced respiration, mitigated by ovMFN2 treatment. Further study revealed that BCL6, a negative regulator of MFN2, significantly contributes to Ang II-induced endothelial senescence. In vivo, Ang II infusion decreased MFN2 expression and increased BCL6, P21, and P53 expression in vascular endothelial cells. The shMfn2+Ang II group showed elevated senescence markers in vascular tissues. These findings highlight MFN2's regulatory role in endothelial cell senescence, emphasizing its importance in maintaining endothelial homeostasis and preventing age-related vascular diseases.

Advances in human pluripotent stem cell reporter systems.

The capability of human pluripotent stem cells (hPSCs) to self-renew and differentiate into any cell type has greatly contributed to the advancement of biomedicine. Reporter lines derived from hPSCs have played a crucial role in elucidating the mechanisms underlying human development and diseases by acting as an alternative reporter system that cannot be used in living humans. To bring hPSCs closer to clinical application in transplantation, scientists have generated reporter lines for isolating the desired cell populations, as well as improving graft quality and treatment outcomes. This review presents an overview of the applications of hPSC reporter lines and the important variables in designing a reporter system, including options for gene delivery and editing tools, design of reporter constructs, and selection of reporter genes. It also provides insights into the prospects of hPSC reporter lines and the challenges that must be overcome to maximize the potential of hPSC reporter lines.

Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.

Caveolin is a monotopic integral membrane protein, widely expressed in metazoa and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim of this disc are highly hydrophobic, suggesting that the complex incorporates into membranes by displacing hundreds of lipids from one leaflet. The feasibility of this unique molecular architecture and its biophysical and functional consequences are currently unknown. Using Langmuir film balance measurements, we find that CAV1-8S is highly surface active and intercalates into lipid monolayers. Molecular simulations of biomimetic bilayers support this 'leaflet replacement' model and reveal that while CAV1-8S effectively displaces phospholipids from one bilayer leaflet, it accumulates 40-70 cholesterol molecules into a disordered monolayer between the complex and its distal lipid leaflet. We find that CAV1-8S preferentially associates with positively curved membrane surfaces due to its influence on the conformations of distal leaflet lipids, and that these effects laterally sort lipids of the distal leaflet. Large-scale simulations of multiple caveolin assemblies confirmed their association with large, positively curved membrane morphologies, consistent with the shape of caveolae. Further, association with curved membranes regulates the exposure of caveolin residues implicated in protein-protein interactions. Altogether, the unique structure of CAV1-8S imparts unusual modes of membrane interaction with implications for membrane organization, morphology, and physiology.

Distinct functions of PAXX and MRI during chromosomal end joining.

A key step of Canonical Nonhomologous End Joining (C-NHEJ) is synapsis of DNA double strand break (DSB) ends for ligation. The DNA-PKcs dimer mediates synapsis in a long-range complex with DSB ends remaining apart, whereas the XLF homodimer can mediate synapsis in both long-range and short-range complexes. Recent structural studies found the PAXX homodimer may also facilitate synapsis in long-range complexes with DNA-PKcs via its interactions with Ku70. Thus, we examined the influence of PAXX in C-NHEJ of chromosomal DSBs, which we compared to another Ku-binding factor, MRI. Using EJ of blunt DSBs with Cas9 reporters as a readout for C-NHEJ, we found that PAXX and/or MRI are dispensable. However, when combined with disruption of DNA-PKcs, particularly with DNA-PKcs kinase inhibition, PAXX becomes important for blunt DSB EJ. In contrast, while DNA-PKcs is also important to suppress short deletion mutations with microhomology, this effect is not magnified with PAXX loss. MRI loss had no effect combined with DNA-PKcs disruption, but becomes important for blunt DSB EJ when combined with disruption of XLF, as is PAXX. Finally, XLF loss causes an increase in larger deletions compared to DNA-PKcs inhibition, which is magnified with combined loss of MRI. Altogether, we suggest that PAXX promotes DSB end synapsis during C-NHEJ in a manner that is partially redundant with DNA-PKcs and XLF, whereas MRI appears to be mainly important in the context of XLF disruption.

Evolutionary adaptation under climate change: Aedes sp. demonstrates potential to adapt to warming.

Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, facilitating expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their warm edges through evolutionary adaptation remains unknown. Here, we investigate the potential for thermal adaptation in Aedes sierrensis, a congener of the major disease vector species that experiences large thermal gradients in its native range, by assaying tolerance to prolonged and acute heat exposure, and its genetic basis in a diverse, field-derived population. We found pervasive evidence of heritable genetic variation in acute heat tolerance, which phenotypically trades off with tolerance to prolonged heat exposure. A simple evolutionary model based on our data shows that the estimated maximum rate of evolutionary adaptation in mosquito heat tolerance typically exceeds that of projected climate warming under idealized conditions. Our findings indicate that natural mosquito populations may have the potential to track projected warming via genetic adaptation. Prior climate-based projections may thus underestimate the range of mosquito and mosquito-borne disease distributions under future climate conditions.

Co-zorbs: Motile, multispecies biofilms aid transport of diverse bacterial species.

Biofilms are three-dimensional structures containing one or more bacterial species embedded in extracellular polymeric substances. Although most biofilms are stationary, Flavobacterium johnsoniae forms a motile spherical biofilm called a zorb, which is propelled by its base cells and contains a polysaccharide core. Here, we report formation of spatially organized, motile, multispecies biofilms, designated "co-zorbs," that are distinguished by a core-shell structure. F. johnsoniae forms zorbs whose cells collect other bacterial species and transport them to the zorb core, forming a co-zorb. Live imaging revealed that co-zorbs also form in zebrafish, thereby demonstrating a new type of bacterial movement in vivo. This discovery opens new avenues for understanding community behaviors, the role of biofilms in bulk bacterial transport, and collective strategies for microbial success in various environments.

An ensemble deep learning model for predicting minimum inhibitory concentrations of antimicrobial peptides against pathogenic bacteria.

The rise of antibiotic resistance necessitates effective alternative therapies. Antimicrobial peptides (AMPs) are promising due to their broad inhibitory effects. This study focuses on predicting the minimum inhibitory concentration (MIC) of AMPs against whom-priority pathogens: Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa ATCC 27853. We developed a comprehensive regression model integrating AMP sequence-based and genomic features. Using eight AI-based architectures, including deep learning with protein language model embeddings, we created an ensemble model combining bi-directional long short-term memory (BiLSTM), convolutional neural network (CNN), and multi-branch model (MBM). The ensemble model showed superior performance with Pearson correlation coefficients of 0.756, 0.781, and 0.802 for the bacterial strains, demonstrating its accuracy in predicting MIC values. This work sets a foundation for future studies to enhance model performance and advance AMP applications in combating antibiotic resistance.

FNIP1 suppresses colorectal cancer progression through inhibiting STAT3 phosphorylation and nuclear translocation.

Folliculin interacting protein 1 (FNIP1) primarily participates in regulating cellular energy metabolism and is associated with Birt-Hogg-Dubé (BHD) syndrome. Although FNIP1 has been demonstrated to function as both a tumor suppressor and promoter, its role in colorectal cancer (CRC) remains unclear. Our study demonstrated a significant downregulation of FNIP1 in CRC, correlating with shorter overall and disease-specific survival. FNIP1 may potentially serve as an independent prognostic factor in CRC. Moreover, FNIP1 inhibited CRC progression in vitro and in vivo. Mechanistically, FNIP1 bound to phosphorylated signal transducer and activator of transcription-3 (p-STAT3) and downregulated its expression. FNIP1 deletion increased STAT3 phosphorylation and nuclear localization, thereby promoting CRC progression. The use of p-STAT3-specific chemical inhibitors successfully mitigated excessive tumorigenesis resulting from FNIP1 absence. Thus, our results suggest that FNIP1 hinders CRC progression by suppressing STAT3 phosphorylation and nuclear translocation. FNIP1 may be a candidate prognostic indicator and a therapeutic target for intervention in CRC.