Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Aging and Exercise on Mitochondrial Quality Control in Skeletal Muscle

Mitochondria are characterized by its pivotal roles in managing energy production, reactive oxygen species, and calcium, whose aging-related structural and functional deteriorations are observed in aging muscle. Although it is still unclear how aging alters mitochondrial quality and quantity in skeletal muscle, dysregulation of mitochondrial biogenesis and dynamic controls has been suggested as key players for that. In this paper, we summarize current understandings on how aging regulates muscle mitochondrial biogenesis, while focusing on transcriptional regulations including PGC-1α, AMPK, p53, mtDNA, and Tfam. Further, we review current findings on the muscle mitochondrial dynamic systems in aging muscle: fusion/fission, autophagy/mitophagy, and protein import. Next, we also discuss how endurance and resistance exercises impact on the mitochondrial quality controls in aging muscle, suggesting possible effective exercise strategies to improve/maintain mitochondrial health.
Measuring magnetosomal pH of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 using pH-sensitive fluorescent proteins

Abstract Magnetotactic bacteria synthesize uniform-sized and regularly shaped magnetic nanoparticles in their organelles termed magnetosomes. Homeostasis of the magnetosome lumen must be maintained for its role accomplishment. Here, we developed a method to estimate the pH of a single living cell of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 using a pH-sensitive fluorescent protein E2GFP. Using the pH measurement, we estimated that the cytoplasmic pH was approximately 7.6 and periplasmic pH was approximately 7.2. Moreover, we estimated pH in the magnetosome lumen and cytoplasmic surface using fusion proteins of E2GFP and magnetosome-associated proteins. The pH in the magnetosome lumen increased during the exponential growth phase when magnetotactic bacteria actively synthesize magnetite crystals, whereas pH at the magnetosome surface was not affected by the growth stage. This live-cell pH measurement method will help for understanding magnetosome pH homeostasis to reveal molecular mechanisms of magnetite biomineralization in the bacterial organelle. We succeeded in measuring pH in the magnetosomes within living magnetotactic bacterium Magnetospirillum magneticum AMB-1 cells using the pH-sensitive fluorescent protein.
Unchanged Survival Rates of 14-3-3γ Knockout Mice after Inoculation with Pathological Prion Protein

ABSTRACT The diagnosis of sporadic Creutzfeldt-Jakob disease (CJD) is based on typical clinical findings and is supported by a positive 14-3-3 Western blot of cerebrospinal fluid. However, it is not clear whether 14-3-3 indicates general neuronal damage or is of pathophysiological relevance in CJD. The fact that the 14-3-3 isoform spectrum in cerebrospinal fluid does not correspond to that found in the brain points to a regulated process. To investigate a possible role of 14-3-3 proteins in transmissible spongiform diseases, we generated a 14-3-3γ-deficient mutant mouse line by using a classical knockout strategy. The anatomy and cage behavior of the mutant mice were normal. Western blot analyses of brain homogenates revealed no changes in the protein expression of other 14-3-3 isoforms (ε, β, ζ, and η). Proteomic analyses of mouse brains by two-dimensional differential gel electrophoresis showed that several proteins, including growth hormone, 1-Cys peroxiredoxin, CCT-zeta, glucose-6-phosphate isomerase, GRP170 precursor, and α-SNAP, were differentially expressed. Mutant and wild-type mice were inoculated either intracerebrally or intraperitoneally with the Rocky Mountain Laboratory strain of scrapie, but no differences were detected in the postinoculation survival rates. These results indicate that 14-3-3γ is unlikely to play a causal role in CJD and related diseases.
Special Protein Molecules Computational Identification

Computational identification of special protein molecules is a key issue in understanding protein function. It can guide molecular experiments and help to save costs. I assessed 18 papers published in the special issue of Int. J. Mol. Sci., and also discussed the related works. The computational methods employed in this special issue focused on machine learning, network analysis, and molecular docking. New methods and new topics were also proposed. There were in addition several wet experiments, with proven results showing promise. I hope our special issue will help in protein molecules identification researches.
Committing to quantum resistance: a slow defence for Bitcoin against a fast quantum computing attack

Quantum computers are expected to have a dramatic impact on numerous fields due to their anticipated ability to solve classes of mathematical problems much more efficiently than their classical counterparts. This particularly applies to domains involving integer factorization and discrete logarithms, such as public key cryptography. In this paper, we consider the threats a quantum-capable adversary could impose on Bitcoin, which currently uses the Elliptic Curve Digital Signature Algorithm (ECDSA) to sign transactions. We then propose a simple but slow commit–delay–reveal protocol, which allows users to securely move their funds from old (non-quantum-resistant) outputs to those adhering to a quantum-resistant digital signature scheme. The transition protocol functions even if ECDSA has already been compromised. While our scheme requires modifications to the Bitcoin protocol, these can be implemented as a soft fork.
Bottom-Up and Top-Down Effects Influence Bruchid Beetle Individual Performance but Not Population Densities in the Field

Plant quality (bottom-up) and natural enemies (top-down) can influence the individual performance of herbivorous insects on their host plants, but few studies measured at the same time the influence on population densities in the field. We investigated if plant quality of different wild common bean populations, Phaseolus vulgaris L. (Fabaceae), affects the performance of the bean weevil, Acanthoscelides obtectus (Say) (Coleoptera: Bruchidae), and one of its enemies, the ectoparasitoid Dinarmus basalis (Rondani) (Hymenoptera: Pteromalidae), in controlled laboratory experiments. Additionally, we examined if parasitoids influence the beetles' development and if increased individual beetle and parasitoid fitness lead to higher field population densities. We show that bean quality and parasitoids affected individual bean weevil performance under laboratory and field conditions. In the presence of parasitoids, fewer and smaller beetles emerged. However, beetle and parasitoid performance were not correlated. Increased individual performance was not leading to higher population densities; we found no correlations between measured performance components and beetle field infestation levels or parasitism rates. We conclude that bottom-up or top-down effects measured at the individual level do not always translate into population effects; therefore it is important to discriminate between effects acting on individual insects and those acting on populations.
Discrete Potts Model for Generating Superpixels on Noisy Images

Many computer vision applications, such as object recognition and segmentation, increasingly build on superpixels. However, there have been so far few superpixel algorithms that systematically deal with noisy images. We propose to first decompose the image into equal-sized rectangular patches, which also sets the maximum superpixel size. Within each patch, a Potts model for simultaneous segmentation and denoising is applied, that guarantees connected and non-overlapping superpixels and also produces a denoised image. The corresponding optimization problem is formulated as a mixed integer linear program (MILP), and solved by a commercial solver. Extensive experiments on the BSDS500 dataset images with noises are compared with other state-of-the-art superpixel methods. Our method achieves the best result in terms of a combined score (OP) composed of the under-segmentation error, boundary recall and compactness.
Invariant-Based Automatic Testing of Modern Web Applications

Ajax-based Web 2.0 applications rely on stateful asynchronous client/server communication, and client-side runtime manipulation of the DOM tree. This not only makes them fundamentally different from traditional web applications, but also more error-prone and harder to test. We propose a method for testing Ajax applications automatically, based on a crawler to infer a state-flow graph for all (client-side) user interface states. We identify Ajax-specific faults that can occur in such states (related to, e.g., DOM validity, error messages, discoverability, back-button compatibility) as well as DOM-tree invariants that can serve as oracles to detect such faults. Our approach, called Atusa, is implemented in a tool offering generic invariant checking components, a plugin-mechanism to add application-specific state validators, and generation of a test suite covering the paths obtained during crawling. We describe three case studies, consisting of six subjects, evaluating the type of invariants that can be obtained for Ajax applications as well as the fault revealing capabilities, scalability, required manual effort, and level of automation of our testing approach.
Research on Algorithm Recommended by Online Education for Big Data

“Big data” is becoming a hot topic in the Internet. The long tail problem of the massive online courses also becomes the biggest headache for operation team of online education. The manner in which the reader wants most courses show to be presented before the user is the key to improve the quality of online edu-cation. Personalized recommendation system is to discover the readers interests tendency based on the existing user data, project data, and interactive data, thus to provide personalized product recommendation for readers. This article is based on the two kinds of algorithms, namely the content and the collaborative filtering recommendation to propose an improved integration scheme, which can make good use of existing data to discover the useful knowledge for readers’ recommendation. The method firstly solves the sparsity problem in traditional collaborative filtering, and meanwhile we start from the global structure relation of course, to analyze the relationship between the reader and the course more comprehensively. The algorithm to improve the accuracy of recommendation from multiple angles, and provides a feasible method for precise recommendation of online educational video.
Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1

Significance The RNA lariat debranching enzyme Dbr1 cleaves the 2′,5′-phosphodiester linkages in intron lariats generated during pre-mRNA splicing. The enzyme is central to RNA metabolism because its activity is required for intron turnover and for the production of small nucleolar RNAs and microRNAs encoded in intronic RNA. Here, the kinetics of Dbr1-mediated debranching of a synthetic RNA substrate are measured by using apoenzyme reconstituted with various divalent cations. The results suggest Fe and Zn are preferred cofactors. Structures of a binuclear catalytic mutant in complex with bona fide branched RNAs reveal a metal-bridging hydroxide positioned to attack the scissile phosphate. The results clarify structure/function relationships in Dbr1 enzymes and are guiding the search for inhibitors that hold promise as therapies for retroviral infections and neurodegenerative disease. Intron lariats are circular, branched RNAs (bRNAs) produced during pre-mRNA splicing. Their unusual chemical and topological properties arise from branch-point nucleotides harboring vicinal 2′,5′- and 3′,5′-phosphodiester linkages. The 2′,5′-bonds must be hydrolyzed by the RNA debranching enzyme Dbr1 before spliced introns can be degraded or processed into small nucleolar RNA and microRNA derived from intronic RNA. Here, we measure the activity of Dbr1 from Entamoeba histolytica by using a synthetic, dark-quenched bRNA substrate that fluoresces upon hydrolysis. Purified enzyme contains nearly stoichiometric equivalents of Fe and Zn per polypeptide and demonstrates turnover rates of ∼3 s−1. Similar rates are observed when apo-Dbr1 is reconstituted with Fe(II)+Zn(II) under aerobic conditions. Under anaerobic conditions, a rate of ∼4.0 s−1 is observed when apoenzyme is reconstituted with Fe(II). In contrast, apo-Dbr1 reconstituted with Mn(II) or Fe(II) under aerobic conditions is inactive. Diffraction data from crystals of purified enzyme using X-rays tuned to the Fe absorption edge show Fe partitions primarily to the β-pocket and Zn to the α-pocket. Structures of the catalytic mutant H91A in complex with 7-mer and 16-mer synthetic bRNAs reveal bona fide RNA branchpoints in the Dbr1 active site. A bridging hydroxide is in optimal position for nucleophilic attack of the scissile phosphate. The results clarify uncertainties regarding structure/function relationships in Dbr1 enzymes, and the fluorogenic probe permits high-throughput screening for inhibitors that may hold promise as treatments for retroviral infections and neurodegenerative disease.
PupilNet, Measuring Task Evoked Pupillary Response using Commodity RGB Tablet Cameras

Pupillary diameter monitoring has been proven successful at objectively measuring cognitive load that might otherwise be unobservable. This paper compares three different algorithms for measuring cognitive load using commodity cameras. We compare the performance of modified starburst algorithm (from previous work) and propose two new algorithms: 2 Level Snakuscules and a convolutional neural network which we call PupilNet. In a user study with eleven participants, our comparisons show PupilNet outperforms other algorithms in measuring pupil dilation, is robust to various lighting conditions, and robust to different eye colors. We show that the difference between PupilNet and a gold standard head-mounted gaze tracker varies only from -2.6% to 2.8%. Finally, we also show that PupilNet gives similar conclusions about cognitive load during a longer duration typing task.
Single-Cell Analysis Reveals Early Manifestation of Cancerous Phenotype in Pre-Malignant Esophageal Cells

Cellular heterogeneity plays a pivotal role in a variety of functional processes in vivo including carcinogenesis. However, our knowledge about cell-to-cell diversity and how differences in individual cells manifest in alterations at the population level remains very limited mainly due to the lack of appropriate tools enabling studies at the single-cell level. We present a study on changes in cellular heterogeneity in the context of pre-malignant progression in response to hypoxic stress. Utilizing pre-malignant progression of Barrett’s esophagus (BE) as a disease model system we studied molecular mechanisms underlying the progression from metaplastic to dysplastic (pre-cancerous) stage. We used newly developed methods enabling measurements of cell-to-cell differences in copy numbers of mitochondrial DNA, expression levels of a set of mitochondrial and nuclear genes involved in hypoxia response pathways, and mitochondrial membrane potential. In contrast to bulk cell studies reported earlier, our study shows significant differences between metaplastic and dysplastic BE cells in both average values and single-cell parameter distributions of mtDNA copy numbers, mitochondrial function, and mRNA expression levels of studied genes. Based on single-cell data analysis, we propose that mitochondria may be one of the key factors in pre-malignant progression in BE.
Downregulation of Cellular Protective Factors of Rumen Epithelium in Goats Fed High Energy Diet

Energy-rich diets can challenge metabolic and protective functions of the rumen epithelial cells, but the underlying factors are unclear. This study sought to evaluate proteomic changes of the rumen epithelium in goats fed a low, medium, or high energy diet. Expression of protein changes were compared by two-dimensional differential gel electrophoresis followed by protein identification with matrix assisted laser desorption ionisation tandem time-of-flight mass spectrometry. Of about 2,000 spots commonly detected in all gels, 64 spots were significantly regulated, which were traced back to 24 unique proteins. Interestingly, the expression profiles of several chaperone proteins with important cellular protective functions such as heat shock cognate 71 kDa protein, peroxiredoxin-6, serpin H1, protein disulfide-isomerase, and selenium-binding protein were collectively downregulated in response to high dietary energy supply. Similar regulation patterns were obtained for some other proteins involved in transport or metabolic functions. In contrast, metabolic enzymes like retinal dehydrogenase 1 and ATP synthase subunit beta, mitochondrial precursor were upregulated in response to high energy diet. Lower expressions of chaperone proteins in the rumen epithelial cells in response to high energy supply may suggest that these cells were less protected against the potentially harmful rumen toxic compounds, which might have consequences for rumen and systemic health. Our findings also suggest that energy-rich diets and the resulting acidotic insult may render rumen epithelial cells more vulnerable to cellular damage by attenuating their cell defense system, hence facilitating the impairment of rumen barrier function, typically observed in energy-rich fed ruminants.
Comparative Phenotypic, Molecular, and Virulence Characterization of Vibrio parahaemolyticus O3:K6 Isolates

ABSTRACT Historically, Vibrio parahaemolyticus infections have been characterized by sporadic cases caused by multiple, diverse serotypes. However, since 1996, V. parahaemolyticus serotype O3:K6 strains have been associated with several large-scale outbreaks of illness, suggesting the emergence of a “new” group of organisms with enhanced virulence. We have applied three different molecular subtyping techniques to identify an appropriate method for differentiating O3:K6 isolates from other serotypes. Pulsed-field gel electrophoresis (PFGE) following NotI digestion differentiated seven closely related subtypes among O3:K6 and related strains, which were distinct from PFGE patterns for non-O3:K6 isolates. Ribotyping and tdh sequencing were less discriminatory than PFGE, but further confirmed close genetic relationships among recent O3:K6 isolates. In vitro adherence and cytotoxicity studies with human epithelial cells showed that O3:K6 isolates exhibited statistically higher levels of adherence and cytotoxicity to host cells than non-O3:K6 isolates. Epithelial cell cytotoxicity patterns were determined with a lactate dehydrogenase release assay. At 3 h postinfection, high relative cytotoxicities (>50% maximum lactate dehydrogenase activity) were found among a greater proportion of recently isolated O3:K6 and closely related strains (75%) than among the non-O3:K6 isolates (23%). A statistically significant relationship between adherence and cytotoxicity suggests that the pathogenic potential of some isolates may be associated with increased adherence to epithelial cells. Our findings suggest that enhanced adherence and cytotoxicity may contribute to the apparent unique pathogenic potential of V. parahaemolyticus O3:K6 strains.
Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling

Malate dehydrogenase (MDH) and citrate synthase (CS) are two pacemaking enzymes involved in the tricarboxylic acid (TCA) cycle. Oxaloacetate (OAA) molecules are the intermediate substrates that are transferred from the MDH to CS to carry out sequential catalysis. It is known that, to achieve a high flux of intermediate transport and reduce the probability of substrate leaking, a MDH‐CS metabolon forms to enhance the OAA substrate channeling. In this study, we aim to understand the OAA channeling within possible MDH‐CS metabolons that have different structural orientations in their complexes. Three MDH‐CS metabolons from native bovine, wild‐type porcine, and recombinant sources, published in recent work, were selected to calculate OAA transfer efficiency by Brownian dynamics (BD) simulations and to study, through electrostatic potential calculations, a possible role of charges that drive the substrate channeling. Our results show that an electrostatic channel is formed in the metabolons of native bovine and recombinant porcine enzymes, which guides the oppositely charged OAA molecules passing through the channel and enhances the transfer efficiency. However, the channeling probability in a suggested wild‐type porcine metabolon conformation is reduced due to an extended diffusion length between the MDH and CS active sites, implying that the corresponding arrangements of MDH and CS result in the decrease of electrostatic steering between substrates and protein surface and then reduce the substrate transfer efficiency from one active site to another.
Anaplastic Lymphoma Kinase Mutation (ALK F1174C) in Small Cell Carcinoma of the Prostate and Molecular Response to Alectinib

Purpose: Small cell carcinoma of the prostate (SCCP) is an aggressive disease that can arise de novo or by transdifferentiation from prostate adenocarcinoma. Alterations in anaplastic lymphoma kinase (ALK) gene are involved in neuroblastoma, lung cancer, and other malignancies, but its role in SCCP has not been documented. We describe a patient with refractory de novo SCCP with ALK F1174C–activating mutation who obtained clinical benefit from treatment with ALK inhibitor. Experimental Design: Next-generation sequencing (NGS) was used to analyze primary and circulating tumor DNA (ctDNA). Prostate cancer databases were queried for alterations in ALK gene, mRNA, and its impact in clinical outcomes. In vitro prostate cell line/organoid models were generated by lentiviral-mediated expression of ALK and ALK F1174C and assessed for response to ALK inhibitors crizotinib and alectinib. Results: NGS analysis of the primary tumor and ctDNA of a 39-year-old patient with refractory SSCP identified ALK F1174C mutation. Treatment with second-generation ALK inhibitor alectinib resulted in radiographic stable disease for over 6 months, symptomatic improvement, and significant molecular response as reflected by declining ctDNA allele fraction. Analysis of prostate cancer datasets showed that ALK amplification was associated with poor outcome. In prostate cancer cells and organoids, ALK F1174C expression enhanced growth and induced expression of the neuroendocrine marker neuron-specific enolase. Alectinib was more effective than crizotinib in inhibiting ALK F1174C–expressing cell growth. Conclusions: These findings implicate ALK-activating mutations in SCCP pathogenesis and suggest the therapeutic potential of targeting ALK molecular alterations in some patients with SCCP. Clin Cancer Res; 24(12); 2732–9. ©2018 AACR.