Abstract Objective Gastric cancer (GC) is a highly invasive malignancy with a propensity for lymph node metastasis. This study investigated how lactylation of TRIM29 contributes to the invasive behavior of GC and lymph node metastasis and the efficacy of chemotherapy for the disease. Methods We examined the expression levels of TRIM29 and its lactylation status in GC tissues and cell lines using quantitative reverse-transcription polymerase chain reaction, immunohistochemistry based on tissue microarrays and western blotting. Functional transwell migration, three-dimensional invasion assay and tube formation assays were performed to assess the role of TRIM29 in GC. The interaction between TRIM29 and heteronuclear ribonucleoprotein A1(hnRNPA1) was explored by co-immunoprecipitation and mass spectrometry. Results Expression of TRIM29 was significantly upregulated in GC tissues in comparison with adjacent non-tumor tissues. This upregulation was associated with lymph node metastasis, vascular tumors and a worse prognosis. Lactylation of TRIM29 in GC cells enhanced the migratory ability and invasiveness of these cells and lymph node metastasis. Mechanistically, TRIM29 formed a complex with hnRNPA1, which in turn activated the Wnt/β-catenin signaling pathway by stabilizing β-catenin in a ubiquitination-dependent manner. Targeting TRIM29 and lymphangiogenesis augmented the efficacy of 5-fluorouracil-based chemotherapy. Conclusion Lactylation of TRIM29 promotes invasive behavior and lymph node metastasis in GC cells by engaging the hnRNPA1-mediated Wnt/β-catenin pathway. Targeting TRIM29 and lymphangiogenesis may be a promising therapeutic strategy for patients with advanced GC.
Muhammad Danish Mujib, Nayab Mubashir, Ahmad Zahid Rao
et al.
<b>Background</b>: The global prevalence of Alzheimer’s disease (AD) has reached 55.2 million. AD is characterized by progressive deterioration in cognition and working memory (WM), which are essential for attention, reasoning, and learning. These impairments are associated with pathological changes in cortical and subcortical regions. Binaural beats (BBs), a non-invasive auditory neuromodulation technique, have demonstrated cognitive enhancement effects in healthy individuals; however, their impact on WM in patients with AD remains largely unexplored. <b>Methods</b>: This study investigated the effects of BB stimulation on WM and cognitive function in the temporal lobe of patients with AD using standardized Low-Resolution Electromagnetic Tomography (sLORETA). Twenty-five patients with AD were randomly assigned to either an experimental group (<i>n</i> = 15) that received BB stimulation or a control group (<i>n</i> = 10) that received standard auditory stimulation. EEG recordings were obtained before and after the intervention. <b>Results</b>: Paired <i>t</i>-tests conducted on timeframe and frequency-wise sLORETA images revealed significant increases (<i>p</i> < 0.05) in theta, alpha1, and alpha2 frequency bands in the experimental group. Activated regions included the inferior, middle, superior, and transverse temporal gyri; Brodmann areas (BA) 20, 21, 22, 40, and 42; as well as networks associated with working memory and cognition. <b>Conclusions</b>: These findings suggest that BB stimulation induces temporal lobe activation, thereby enhancing working memory and cognitive function in patients with AD.
Magdalena Jawor, Karol Tchorz, Marcin Ostoja-Helczynski
et al.
ABSTRACT The cohesin complex plays essential roles in chromosome organization and gene regulation, yet how cohesin dynamics are controlled during cell-state transitions remains poorly understood. Here, we examined how cohesin regulation is remodeled during the differentiation of mouse embryonic stem cells (mESCs) into the cardiomyocyte lineage using an in vitro differentiation system. We found that core cohesin subunits remain broadly stable at the protein level. In contrast, the levels of cohesin regulators, including the cohesin removal protein WAPL and the cohesin stabilizing protein ESCO1, decline sharply despite modest transcript-level changes. The cohesion maintenance factor Sororin was also reduced. To better understand the net effect of these changes on cohesin dynamics, we use live-cell FRAP of RAD21, which revealed increased cohesin mobility in differentiated cells without a change in recovery kinetics, consistent with reduced stable chromatin engagement or redistribution into a chromatin-unbound nuclear pool. To test functional consequences, we generated homozygous degron alleles for Wapl and Esco1 and induced acute degradation using a dTAG-based system. Loss of WAPL altered cell-cycle dynamics in stem cells and produced a characteristic “vermicelli” chromosome phenotype, consistent with abnormally high and lethal cohesin retention on chromatin. Surprisingly, depletion of ESCO1 had no clear impact on viability and cell cycle progression. Notably, despite loss of detectable WAPL protein in the differentiated cell population, we find that WAPL remains functionally required to maintain a viable interphase chromosome organization. Together, these findings identify cohesin regulators, rather than cohesin abundance, as central drivers of changes in cohesin dynamics during differentiation. They further show that even very low levels of WAPL continue to provide critical structural plasticity of chromosomes following cell cycle exit and lineage commitment.
Evgeniya Melnik, Daria Akimova, Tatiana Markova
et al.
Arthrogryposis multiplex congenita (AMC) is a large group of congenital conditions characterized by joint contractures affecting two or more body areas. A part of AMC type is caused by heterozygous pathogenic variants in genes encoding sarcomeric components of skeletal muscle fibers. Here we report a 7-year-old boy with a phenotype including AMC with dysmorphic facial features, short stature, congenital malformations of brain, colon and lacrimal canal. Trio whole-genome sequencing identified compound heterozygosity in the UTRN gene, consisting of a splicing variant in intron 57 (c.8434 + 1G>A) and a large heterozygous deletion spanning exons 3–51 (NM_007124.3). It is known that utrophin, the product of the UTRN gene, is an autosomal homologue and a fetal form of a protein of skeletal muscles - dystrophin. The presence of multiple malformations in the patient’s phenotype is consistent with ubiquitous expression of utrophin in the embryonic period. The RNA-seq analysis revealed that the splicing variant introduces a premature termination codon, which is predicted to result in a truncated protein shorter by 615 amino acids (p.Val2786Argfs*34), and the deletion leads to transcription of a shortened RNA isoform. We suggest that these variants are hypomorphic and partially retain protein function, which explains the clinical picture in the patient. In aggregate, our findings provide evidence that rare biallelic recessive variants in UTRN cause a novel autosomal recessive multiple congenital arthrogryposis.
Sebastião V. T. F. de Almeida, Kilian Neves, Carla C. C. R. de Carvalho
Methylamines are present in numerous organisms and microorganisms capable of de novo trimethylamine (TMA) production are widely distributed, including microalgae. However, such compounds may hamper the application of microalgae biomass in commercially interesting products, such as food and feed products, due to the strong fishy smell. In the present study, several bacteria able to degrade TMA were isolated. Among them, a <i>Staphylococcus saprophyticus</i> strain was found particularly suitable to degrade TMA. After finding the best culture conditions, a bioprocess system was developed allowing the degradation of TMA from microalgae in a reactor by <i>S. saprophyticus</i> cells present in a second reactor without direct contact with media from both reactors. The system was found to be limited by TMA transfer through the gas phase, with the cells being able to degrade all available TMA.
Summary: Inhibition of the ceramide synthetic pathway with myriocin or an antisense oligonucleotide (ASO) targeting dihydroceramide desaturase (DES1) both improved hepatic insulin sensitivity in rats fed either a saturated or unsaturated fat diet and was associated with reductions in both hepatic ceramide and plasma membrane (PM)-sn-1,2-diacylglycerol (DAG) content. The insulin sensitizing effects of myriocin and Des1 ASO were abrogated by acute treatment with an ASO against DGAT2, which increased hepatic PM-sn-1,2-DAG but not hepatic C16 ceramide content. Increased PM-sn-1,2-DAG content was associated with protein kinase C (PKC)ε activation, increased insulin receptor (INSR)T1150 phosphorylation leading to reduced insulin-stimulated INSRY1152/AktS473 phosphorylation, and impaired insulin-mediated suppression of endogenous glucose production. These results demonstrate that inhibition of de novo ceramide synthesis by either myriocin treatment or DES1 knockdown protects against lipid-induced hepatic insulin resistance through a C16 ceramide-independent mechanism and that they mediate their effects to protect from lipid-induced hepatic insulin resistance via the PM-sn-1,2-DAG-PKCε-INSRT1150 phosphorylation pathway.
Colin L. Welsh, Abigail E. Conklin, Lalima K. Madan
Cyclic-AMP-dependent protein kinase A (PKA) is a critical enzyme involved in various signaling pathways that plays a crucial role in regulating cellular processes including metabolism, gene transcription, cell proliferation, and differentiation. In this study, the mechanisms of allostery in PKA were investigated by analyzing the vast repertoire of crystal structures available in the RCSB database. From existing structures of murine and human PKA, we elucidated the conformational ensembles and protein dynamics that are altered in a ligand-dependent manner. Distance metrics to analyze conformations of the G-loop were proposed to delineate different states of PKA and were compared to existing structural metrics. Furthermore, ligand-dependent flexibility was investigated through normalized B′-factors to better understand the inherent dynamics in PKA. The presented study provides a contemporary approach to traditional methods in engaging the use of crystal structures for understanding protein dynamics. Importantly, our studies provide a deeper understanding into the conformational ensemble of PKA as the enzyme progresses through its catalytic cycle. These studies provide insights into kinase regulation that can be applied to both PKA individually and protein kinases as a class.
Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.
Patrick F. Smallhorn-West, Philippa J. Cohen, Renato A. Morais
et al.
Partially protected areas are now the dominant global form of spatial management aimed at preserving ecosystem integrity and managing human use. However, most evaluations of their efficacy use only a narrow set of conservation indicators that reflect a fraction of ways in which protection can succeed or fail. In this paper, we examine three case studies of partially protected coral reef fishery systems to evaluate benefits and risks of their use as a management tool. We use data from community-based management arrangements in three Pacific Island countries to demonstrate three vignettes of how partial protection can boost fisheries production, enhance the ease with which fishers catch their prey, and alter the composition of fisheries yields. These changes in fisheries productivity, catchability, and vulnerability under partial protection carry substantial benefits for fishers. However, they also carry significant risks for ecosystems and fisheries livelihoods unless adaptively managed so as to confer the short to medium term benefits in resource performance without risking longer term sustainability.
Ivan S. Zhidkov, Ernst Z. Kurmaev, Marcello Condorelli
et al.
The results of X-ray photoelectron spectra (XPS) characterization of the surface of Ag-Au colloidal nanoparticles (Ag-Au NPs), prepared by laser ablation in water before and after interaction with linear carbon chains (LCC), are presented. No additional features appear in high-energy resolved XPS core level spectra of Ag-Au NPs which indicates that surface is not oxidized. The measurements of XPS Ag 3d-spectrum of (Ag-Au)@LCC manifests the additional low-energy structure that is associated with the formation of Ag–C bonds. The charge transfer between Au atoms on the NPs surface and LCC was established. Additionally, some oxidation of the Ag atoms on the surface of (Ag-Au)@LCC is observed which arises during laser ablation in water. We assume that oxidative species will preferably interact with the areas outside the LCC instead of oxidizing the carbon chains which was confirmed by XPS C 1s spectra.
Abstract Background Canine prostate cancer represents a unique model for human prostate cancer. In vitro systems offer various possibilities but Xenograft in vivo imaging allows studying complex tasks as tumor progression and drug intervention longitudinal. Herein, we established three canine prostate carcinoma cell lines stably expressing fluorescent proteins allowing deep tissue in vivo imaging. Methods Three canine prostate carcinoma (cPC) cell lines were stably transfected with fluorescent proteins in red, far-red and near infra-red spectrum, followed by G418 selection. Fluorescent protein expression was demonstrated by microscopy, flow cytometry and a NightOWL LB 983 in vivo imaging system. Cellular and molecular characteristics of the generated cell lines were compared to the parental cell line CT1258. Cell proliferation, metabolic activity and sphere formation capacity were analyzed. Stem cell marker expression was examined by qPCR and genomic copy number variation by genomic DNA whole genome sequencing. Results Three stably fluorescent protein transfected cPC cell lines were established and characterized. Compared to the parental cell line, no significant difference in cell proliferation and metabolic activity were detected. Genomic copy number variation analyses and stem cell marker gene expression revealed in general no significant changes. However, the generated cell line CT1258-mKate2C showed uniquely no distal CFA16 deletion and an elevated metabolic activity. The introduced fluorescencent proteins allowed highly sensitive detection in an in vivo imaging system starting at cell numbers of 0.156 × 106. Furthermore, we demonstrated a similar sphere formation capacity in the fluorescent cell lines. Interestingly, the clone selected CT1258-mKate2C, showed increased sphere formation ability. Discussion Starting from a well characterized cPC cell line three novel fluorescent cell lines were established showing high cellular and molecular similarity to the parental cell line. The introduction of the fluorescent proteins did not alter the established cell lines significantly. The red fluorescence allows deep tissue imaging, which conventional GFP labeling is not able to realize. Conclusion As no significant differences were detected between the established cell lines and the very well characterized parental CT1258 the new fluorescent cell lines allow deep tissue in vivo imaging for perspective in vivo evaluation of novel therapeutic regimens.
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Cytology
The formation of the neocortex relies on intracellular and extracellular signaling molecules that are involved in the sequential steps of corticogenesis, ranging from the proliferation and differentiation of neural progenitor cells to the migration and dendrite formation of neocortical neurons. Abnormalities in these steps lead to disruption of the cortical structure and circuit, and underly various neurodevelopmental diseases, including dyslexia and autism spectrum disorder (ASD). In this review, we focus on the axon guidance signaling Slit-Robo, and address the multifaceted roles of Slit-Robo signaling in neocortical development. Recent studies have clarified the roles of Slit-Robo signaling not only in axon guidance but also in progenitor cell proliferation and migration, and the maturation of neocortical neurons. We further discuss the etiology of neurodevelopmental diseases, which are caused by defects in Slit-Robo signaling during neocortical formation.
Human knee joints move smoothly under high load conditions due to articular cartilage and synovial fluid. Much attention is paid to the role of proteoglycans. It is suggested that a part of proteoglycan forms aggregate on the cartilage surface, making a polymer brush, which has an important role in lubrication. In order to examine the lubrication mechanism in detail, we constructed a full atom model of a polymer brush system, and carried out a series of molecular dynamics simulations to analyze its frictional properties under constant shear. We use chondroitin 6-sulfate molecules grafted on resilient surface as the polymer brush and water with sodium ions as the synovial liquid. In the steady state, polymers have large deformation and the flow of synovial fluid becomes deviate from the Coutette flow, leading to a drastic reduction of friction. Longer chains have larger reduction.
Farinaz Khosravian, Fatemeh Ketabchi, Nasrin Hadi
et al.
Background: Prostate cancer is the second most prevalent cancer among men all over the world. Over the past 10 years, prostate cancer prevalence has increased in Iran. Growth factors have an important role in the regulation and growth of malignant and normal prostate cells. Therefore, the purpose of this investigation is to examine the association of the expression profile of IGF1, EGF, and FGF2 with prostate cancer in an Iranian male population.
Materials and methods: In this investigation, the quantitative real-time RT-PCR technique was applied to evaluate the expression profiles of IGF, EGF, and FGF2 in the peripheral blood samples of 40 patients with prostate cancer and 40 healthy individuals. Moreover, the relative expressions of IGF1, EGF, and FGF2 in various stages of disease were evaluated.
Results: Our obtained data indicated a significant increase in the expression of EGF and FGF2 in patients with prostate cancer compared with the healthy subjects (P = 0.02 and P = 0.009, respectively). In contrast, the expression level of IGF1 was not significantly different between the patients and controls (P = 0.052), but the expression level of IGF1 was lower in the patients' group. Additionally, it has been observed that IGF1, EGF, and FGF2 expression were directly associated with the stage of disease.
Conclusions: Our results suggest that EGF and FGF2 probably have important role in prostate cancer and were consistent with what had previously been reported. On the other hand, our data revealed no association between the expression of IGF1 and prostate cancer in the population studied.
Big lighting data are required for evaluation of lighting performance and impacts on human beings, environment, and ecology for smart urban lighting. However, traditional approaches of measuring road lighting cannot achieve this aim. We propose a rule-of-thumb model approach based on some feature points to reconstruct road lighting in urban areas. We validated the reconstructed illuminance with both software simulated and real road lighting scenes, and the average error is between 6 and 19%. This precision is acceptable in practical applications. Using this approach, we reconstructed the illuminance of three real road lighting environments in a block and further estimated the mesopic luminance and melanopic illuminance performance. In the future, by virtue of Geographic Information System technology, the approach may provide big lighting data for evaluation and analysis, and help build smarter urban lighting.