A transient apical extracellular matrix relays cytoskeletal patterns to shape permanent acellular ridges on the surface of adult C. elegans

Apical extracellular matrices can form protruding structures such as denticles, ridges, scales, or teeth on the surfaces of epithelia. The mechanisms that shape these structures remain poorly understood. Here, we show how the actin cytoskeleton and a provisional matrix work together to sculpt acellular longitudinal alae ridges in the cuticle of adult C. elegans. Transient actomyosin-dependent constriction of the underlying lateral epidermis accompanies deposition of the provisional matrix at the earliest stages of alae formation. Actin is required to pattern the provisional matrix into longitudinal bands that are initially offset from the pattern of longitudinal actin filaments. These bands appear ultrastructurally as alternating regions of adhesion and separation within laminated provisional matrix layers. The provisional matrix is required to establish these demarcated zones of adhesion and separation, which ultimately give rise to alae ridges and their intervening valleys, respectively. Provisional matrix proteins shape the alae ridges and valleys but are not present within the final structure. We propose a morphogenetic mechanism wherein cortical actin patterns are relayed mechanically to the laminated provisional matrix to set up distinct zones of matrix layer separation and accretion that shape a permanent and acellular matrix structure.

An interpretable protein localization prediction framework

Protein localization is related to many human diseases. Therefore, the prediction of protein localization is an essential task that has been extensively studied. Additionally, the study of the localization mechanism can provide more biological insights and testable hypotheses. In this thesis, we propose MULocDeep, a general deep learning-based localization prediction framework. We designed a matrix layer in its architecture to reflect the hierarchical relationships of localization in cells. This enables MULocDeep, to predict multiple localizations of a protein at both subcellular and suborganellar levels. We collected a dataset with 44 suborganellar localization annotations in 10 major subcellular compartments--the most comprehensive suborganelle localization dataset to date. Our collaborators also experimentally generated an independent dataset of mitochondrial proteins in Arabidopsis thaliana cell cultures, Solanum tuberosum tubers, and Vicia faba roots and made this dataset publicl using the above datasets show that overall, MULocDeep outperforms other major methods at both subcellular and suborganellar levels. We also applied Long short-term memory (LSTM) and the multi-head self-attention in MULocDeep to pursue a single amino acid level resolution when assessing their contributions to localization. This provides insights into the mechanism of protein sorting and localization motifs. Many of the candidate sites or motifs match the existing localization knowledge. A web server can be accessed at https://www.mu-loc.org/.

The Accessibility Analysis of COVID-19 Referral Hospitals to The Location of Fundamental Student

The Covid-19 pandemic that occurred in all parts of the world has had an impact on the various sectors. Not only in the economic sector but also in the educational sector. Until Month June Year 2020, the Indonesian government had carried out a new-normal policy. The purpose of the study was to analyze the affordability of the Covid-19 referral hospital to the position of students during the new-normal era. The affordability could be observed by the distance traveled by students to the nearest Covid-19 referral hospital. This study used the OD matrix layer from ArcMap 10.3. The sample used in this study was 87 students with 11 Covid-19 referral hospitals in East Nusa Tenggara Province. Based on the research results in the form of maps produced, showed that from 87 students observed, only 59 or 67.82% could reach the Covid-19 referral hospitals. Meanwhile, the other 28 students or 32.18% couldn’t be reached by the hospitals. The amount of students observed, located less than 15 km from the Covid-19 referral hospitals were 35 or 40.22% from the total of 87 students. The hospital which students refer to based on their location was the WZ. Yohanes hospital.

Extension of Pin-Based Point-Wise Energy Slowing-Down Method for VHTR Fuel with Double Heterogeneity

For the resonance treatment of a very high temperature reactors (VHTR) fuel with the double heterogeneity, an extension of the pin-based pointwise energy slowing-down method (PSM) was developed and implemented into DeCART. The proposed method, PSM-double heterogeneity (DH), has an improved spherical unit cell model with an explicit tri-structural isotropic (TRISO) model, a matrix layer, and a moderator for reflecting the moderation effect. The moderator volume was analytically derived using the relation of the Dancoff factor and the mean chord length. In the first step, the pointwise homogenized cross-sections for the compact was obtained after solving the slowing down equation for the spherical unit cell. Then, the shielded cross-section for the homogenized fuel compact was generated using the original PSM. The verification calculations were performed for the fuel pins with various packing fractions, compact sizes, TRISO sizes, and fuel temperatures. Additionally, two fuel block problems with very different sizes were examined and the depletion calculation was carried out for investigating the accuracy of the proposed method. They revealed that the PSM-DH has a good performance in the VHTR problems.

The Minor Matrix Protein VP24 from Ebola Virus Lacks Direct Lipid-Binding Properties

Viral protein 24 (VP24) from Ebola virus (EBOV) was first recognized as a minor matrix protein that associates with cellular membranes. However, more recent studies shed light on its roles in inhibiting viral genome transcription and replication, facilitating nucleocapsid assembly and transport, and interfering with immune responses in host cells through downregulation of interferon (IFN)-activated genes. Thus, whether VP24 is a peripheral protein with lipid-binding ability for matrix layer recruitment has not been explored. Here, we examined the lipid-binding ability of VP24 with a number of lipid-binding assays. The results indicated that VP24 lacked the ability to associate with lipids tested regardless of VP24 posttranslational modifications. We further demonstrate that the presence of the EBOV major matrix protein VP40 did not promote VP24 membrane association in vitro or in cells. Further, no protein–protein interactions between VP24 and VP40 were detected by co-immunoprecipitation. Confocal imaging and cellular membrane fractionation analyses in human cells suggested VP24 did not specifically localize at the plasma membrane inner leaflet. Overall, we provide evidence that EBOV VP24 is not a lipid-binding protein and its presence in the viral matrix layer is likely not dependent on direct lipid interactions.

The Minor Matrix Protein VP24 from Ebola Virus Lacks Direct Lipid-Binding Properties

Viral protein 24 (VP24) from Ebola virus (EBOV) was first recognized as a minor matrix protein that associates with cellular membranes. However, more recent studies shed light on its roles in inhibiting viral genome transcription and replication, facilitating nucleocapsid assembly and transport, and interfering with immune responses in host cells through downregulation of interferon (IFN)-activated genes. Thus, whether VP24 is a peripheral protein with lipid binding ability for matrix layer recruitment has not been explored. Here we examined the lipid binding ability of VP24 with a number of lipid binding assays. The results indicated that VP24 lacked the ability to associate with lipids tested regardless of VP24 posttranslational modifications. We further demonstrate that the presence of the EBOV major matrix protein VP40 did not promote VP24 membrane association in vitro or in cells. Further, no protein-protein interactions between VP24 and VP40 were detected by co-immunoprecipitation. Confocal imaging and cellular membrane fractionation analyses in human cells suggested VP24 did not specifically localize at the plasma membrane inner leaflet. Overall, we provide evidence that EBOV VP24 is not a lipid binding protein and its presence in the viral matrix layer is likely not dependent on direct lipid interactions.

Recellularization of bronchial extracellular matrix with primary bronchial smooth muscle cells

Severe asthma is associated with an increased airway smooth muscle (ASM) mass and an altered composition of the extracellular matrix (ECM). Studies have indicated that ECM-ASM cell interactions contribute to this remodeling and its limited reversibility with current therapy. Three-dimensional matrices allow the study of complex cellular responses to different stimuli in an almost natural environment. Our goal was to obtain acellular bronchial matrices and then develop a recellularization protocol with ASM cells. We studied equine bronchi as horses spontaneously develop a human asthma-like disease. The bronchi were decellularized using Triton/Sodium Deoxycholate. The obtained scaffolds retained their anatomical and histological properties. Using immunohistochemistry and a semi-quantitative score to compare native bronchi to scaffolds revealed no significant variation for matrixial proteins. A DNA quantification and electrophoresis indicated that most of DNA was 29.6 ng/mg of tissue ± 5.6 with remaining fragments of less than 100 bp. Primary ASM cells were seeded on the scaffolds. Histological analysis after recellularization showed that ASM cells migrated and proliferated primarily in the decellularized smooth muscle matrix, suggesting a chemotactic effect of the scaffolds. This is the first report of primary ASM cells preferentially repopulating the smooth muscle matrix layer in bronchial matrices. This protocol is now being used to study the molecular interactions occurring between the asthmatic ECMs and ASM to identify effectors of asthmatic bronchial remodeling.