Miracle-dz/UniFAR-FTUs huggingface dataset:
Heat Shock Protein 90 kDa (Hsp90) Has a Second Functional Interaction Site with the Mitochondrial Import Receptor Tom70*

To accomplish its crucial role, mitochondria require proteins that are produced in the cytosol, delivered by cytosolic Hsp90, and translocated to its interior by the translocase outer membrane (TOM) complex. Hsp90 is a dimeric molecular chaperone and its function is modulated by its interaction with a large variety of co-chaperones expressed within the cell. An important family of co-chaperones is characterized by the presence of one TPR (tetratricopeptide repeat) domain, which binds to the C-terminal MEEVD motif of Hsp90. These include Tom70, an important component of the TOM complex. Despite a wealth of studies conducted on the relevance of Tom70·Hsp90 complex formation, there is a dearth of information regarding the exact molecular mode of interaction. To help fill this void, we have employed a combined experimental strategy consisting of cross-linking/mass spectrometry to investigate binding of the C-terminal Hsp90 domain to the cytosolic domain of Tom70. This approach has identified a novel region of contact between C-Hsp90 and Tom70, a finding that is confirmed by probing the corresponding peptides derived from cross-linking experiments via isothermal titration calorimetry and mitochondrial import assays. The data generated in this study are combined to input constraints for a molecular model of the Hsp90/Tom70 interaction, which has been validated by small angle x-ray scattering, hydrogen/deuterium exchange, and mass spectrometry. The resultant model suggests that only one of the MEEVD motifs within dimeric Hsp90 contacts Tom70. Collectively, our findings provide significant insight on the mechanisms by which preproteins interact with Hsp90 and are translocated via Tom70 to the mitochondria.
Cardiac Optogenetics and Optical Mapping – Overcoming Spectral Congestion in All-Optical Cardiac Electrophysiology

Optogenetic control of the heart is an emergent technology that offers unparalleled spatio-temporal control of cardiac dynamics via light-sensitive ion pumps and channels (opsins). This fast-evolving technique holds broad scope in both clinical and basic research setting. Combination of optogenetics with optical mapping of voltage or calcium fluorescent probes facilitates ‘all-optical’ electrophysiology, allowing precise optogenetic actuation of cardiac tissue with high spatio-temporal resolution imaging of action potential and calcium transient morphology and conduction patterns. In this review, we provide a synopsis of optogenetics and discuss in detail its use and compatibility with optical interrogation of cardiac electrophysiology. We briefly discuss the benefits of all-optical cardiac control and electrophysiological interrogation compared to traditional techniques, and describe mechanisms, unique features and limitations of optically induced cardiac control. In particular, we focus on state-of-the-art setup design, challenges in light delivery and filtering, and compatibility of opsins with fluorescent reporters used in optical mapping. The interaction of cardiac tissue with light, and physical and computational approaches to overcome the ‘spectral congestion’ that arises from the combination of optogenetics and optical mapping are discussed. Finally, we summarize recent preclinical work applications of combined cardiac optogenetics and optical mapping approach.
Attitude towards Knowledge Sharing Behavior

Based on the theory of reasoned action, this study is focused on an individual's behavior of knowledge sharing with respect to information systems/information technology (IS/IT) by investigating their attitude towards knowledge sharing. Three variables, namely extrinsic motivation, absorptive capacity and channel richness, were examined as influential factors affecting people's attitude towards knowledge sharing. A structural survey was conducted to test the relationships between attitude and the three variables. The results show that extrinsic motivation imposed no impact on an individual's attitude towards knowledge sharing while the other two factors played a significant part. The results are consistent with the psychological theories and we showed the applicability of the theories in the case of knowledge sharing.
A universal approach to the synthesis of noble metal nanodendrites and their catalytic properties.

A universal approach is presented for high-yield synthesis of Au, Pt, and Pd nanoflowers using the surfactant sodium N-(4-n-dodecyloxybenzoyl)-L-isoleucinate (SDBIL). The pH-dependent self-assembly using SDBIL is critical for nanoflower growth. The Pt and Pd nanoflowers show superior catalytic activity for Suzuki–Miyaura and Heck coupling reactions over spherical counterparts.
Immunolocalization of Adipocytes and Prostaglandin E2 and Its Four Receptor Proteins EP1, EP2, EP3, and EP4 in the Caprine Cervix During Spontaneous Term Labor1

ABSTRACT The mechanisms of cervical ripening and dilation in mammals remain obscure. Information is lacking about the localization of prostaglandin E2 (PGE2)-producing cells and PGE2 receptors (EP) in intrapartum cervix and whether cervical dilation at parturition is an active process. To reveal these mechanisms, immunolocalization of EP1–EP4 (official gene symbols PTGER1–PTGER4) and PGE2-producing cells in caprine cervix during nonpregnancy, pregnancy, and parturition was assayed by immunohistochemistry (IHC); the mRNA expression levels of PTGS2, PTGER2 (EP2), and PTGER4 (EP4) were determined using quantitative PCR; and the existence of adipocytes in the cervix at various stages was demonstrated with Oil Red O staining and IHC of perilipin A. The results suggested that in intrapartum caprine cervix staining of the PGE2 was observed in the overall tissues, for example, blood vessels, canal or glandular epithelia, serosa, circular and longitudinal muscles, and stroma in addition to adipocytes; EP2 was detectable in all the tissues other than glandular epithelia; EP4 was strongly expressed in all the tissues other than serosa; EP1 was detected mainly in arterioles and canal or glandular epithelia; and EP3 was poorly expressed only in stroma, canal epithelia, and circular muscles. Little or no expression of EP2, EP3, and EP4 as well as PGE2 in all cervical tissues was observed during nonpregnancy and pregnancy except for the strong expression of EP1 in canal or glandular epithelia during pregnancy. The mRNA expression levels of PTGS2, PTGER2, and PTGER4 were significantly higher in intrapartum than nonpregnant and midpregnant cervices (P < 0.01). Adipocytes appear only in the intrapartum cervix. These results support the concept that PGE2 modulates specific functions in various anatomical structures of the caprine cervix at labor and the appearance of adipocytes at labor is likely related to caprine cervical dilation.
Comparative Genome and Transcriptome Study of the Gene Expression Difference Between Pathogenic and Environmental Strains of Prototheca zopfii

Prototheca zopfii commonly exists in the environment, and causes invasive infections (protothecosis) in humans. The morbidity of protothecosis has increased rapidly in recent years, especially in systemic infections of patients with an impaired immune system. The infection in immunocompromised patients has a poor prognosis due to limited understanding of the pathogenesis of the disease, as most previous studies mainly focused on classification and recognition of pathogenic strains. In this study, we constructed the genome and transcriptome of two pathogenic strains and one environmental strain, by next generation sequencing methods. Based on our preliminary gene expression findings, genes in P. zopfii pathogenic strains are significantly up-regulated in metabolism in peroxisome, such as glyoxylate cycle, which may improve the organism’s resistance to the harsh environment in phagolysosome of macrophage and its ability to survive in an anaerobic environment. We also found some significant up-regulated genes, which are related to adherence and penetration in dermatophytes, and we speculate that this may enhance the virulence capacity of pathogenic strains. Finally, the genomes and transcriptomes of P. zopfii described here provide some base for further studies on the pathogenesis of this organism.
Molecular Actions of Thyroid Hormone on Breast Cancer Cell Migration and Invasion via Cortactin/N-WASP

The thyroid hormone triiodothyronine (T3) plays a fundamental role in growth regulation, differentiation, metabolism and cellular movement. These processes are particularly important considering that deregulation of T3 levels could promote abnormal responsiveness of mammary epithelial cells, which may lead to the development and progression of breast cancer (BC). Once cells migrate and invade different tissues, BC metastasis is the main cause of cancer-related death because it is particularly difficult to revert this multistep process. Cell migration integrates several steps that induce changes in cell structure and morphology to promote BC cell invasion. These sequential steps include actin cytoskeleton remodeling, focal adhesion complex formation and, finally, the turnover of branched actin filament networks. In this article, we demonstrate that T3 has the ability to modify the Epithelial-Mesenchymal Transition process. In addition, we show that T3 induces actin cytoskeleton reorganization, triggers focal adhesion formation and, as a consequence, promotes actin nucleation via non-genomic pathway. These events are specifically modulated by T3 via integrin αvβ3 to FAK/paxillin/cortactin/N-WASP/Arp2/3 complex signaling pathway, increasing cell adhesion, migration and invasion of T-47D BC cells. We suggest that T3 influences the progression of tumor metastasis by controlling signaling pathways that converge in cell motility. This knowledge is crucial for the development of novel therapeutic strategies for BC treatment.
Clustering of XML Schemas for Information Integration

As a prerequisite for information integration, this paper presents an efficient method for clustering XML schemas. The proposed method first computes similarities among schemas. The similarity is defined by the size of the common structure between two schemas under the assumption that the schemas with less cost to be integrated are more similar. Specifically, we extract one-to-one matchings between paths with the largest number of corresponding elements. Finally, a hierarchical clustering method is applied to the values of similarity. Experimental results with many XML schemas show that the method has performed better compared with previous works in terms of the accuracy of clustering, the clustering rate, the quality of clustering, and the time complexity.
DNA Mismatch Repair Interacts with CAF-1- and ASF1A-H3-H4-dependent Histone (H3-H4)2 Tetramer Deposition*

DNA mismatch repair (MMR) is required for the maintenance of genome stability and protection of humans from several types of cancer. Human MMR occurs in the chromatin environment, but little is known about the interactions between MMR and the chromatin environment. Previous research has suggested that MMR coincides with replication-coupled assembly of the newly synthesized DNA into nucleosomes. The first step in replication-coupled nucleosome assembly is CAF-1-dependent histone (H3-H4)2 tetramer deposition, a process that involves ASF1A-H3-H4 complex. In this work we used reconstituted human systems to investigate interactions between MMR and CAF-1- and ASF1A-H3-H4-dependent histone (H3-H4)2 tetramer deposition. We have found that MutSα inhibits CAF-1- and ASF1A-H3-H4-dependent packaging of a DNA mismatch into a tetrasome. This finding supports the idea that MMR occurs before the DNA mismatch is packaged into the tetrasome. Our experiments have also revealed that CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers does not interfere with MMR reactions. In addition, we have established that unnecessary degradation of the discontinuous strand that takes place in both DNA polymerase δ (Pol δ)- and DNA polymerase ϵ (Pol ϵ)-dependent MMR reactions is suppressed by CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers. These data suggest that CAF-1- and ASF1A-H3-H4-dependent deposition of the histone (H3-H4)2 tetramers is compatible with MMR and protects the discontinuous daughter strand from unnecessary degradation by MMR machinery.
Frequency of Publication and Topical Emphasis of Knowledge Management Books versus Doctoral Dissertations: 1983–2005

Citation analysis was used to collect data on the annual frequency and topical emphasis of books and doctoral dissertations on Knowledge Management (KM) published during the period 1983–2005. Chi-Square was used to compare KM books versus KM dissertations on the basis of frequency of publication and topical emphasis. Cramer's Phi was used to interpret the derived Chi-Square values' effect levels. Regarding annual frequency of publication, there was no significant difference between books and dissertations. KM books and dissertations followed a pattern of annual publication frequency similar to patterns reported in the literature. Regarding topical emphasis, there was a significant difference between books and dissertations. The analysis also supported a taxonomy or categorization model for topical emphasis reported in the literature. Recommendations for further study included: (1) citation analysis comparing the annual publication frequencies and topical emphasis of KM books, dissertations, and journal articles; (2) a bibliographic study comparing the types of sources cited in KM books, dissertations, and journal articles; and (3) additional studies on the categorization of the topics covered in KM books, dissertations, and journal articles. The study findings reflect: (1) KM's recent emergence as a generally accepted field of study and (2) key topics or KM constructs that merit greater attention by theorists and practitioners.
Carbon Investment Required for the Mobilization of Inorganic and Organic Phosphorus Bound to Goethite by an Arbuscular Mycorrhiza (Solanum lycopersicum x Rhizophagus irregularis)

Nutrient supply in phosphorus (P)-limited ecosystems, with most P being associated with secondary minerals, has to rely on efficient nutrient allocation strategies, such as those involving mycorrhizal symbioses. Yet, little is known about the extent of photo-assimilate transfer to the fungal partner, who in turn mobilizes mineral-bound P sources required by the plant. This study aims to explore the carbon (C)–P trade between an arbuscular mycorrhizal (AM) plant and its ability to incorporate P from differently accessible P sources. We compared P uptake rates of AM plants for orthophosphate (OP) and phytic acid (PA), applied to mesocosms in either dissolved form or bound to goethite (α-FeOOH). The design of the mesocosms allowed the plant to only access the P in the fungal compartment via the AM hyphae. We hypothesized the AM plant to invest more C into the symbiosis, if P is present in the less accessible form. To estimate the C budget of the symbiosis, we determined total organic carbon (OC), 16:1ω5c phospholipid fatty acid (PLFA; AM fungi extraradical mycelium), 16:1ω5c neutral lipid fatty acid (NLFA; AM fungi energy storage), and CO2 cumulative respiration in the fungal compartment. A ratio to the total C mobilized into the fungal compartment (OC+CO2 cumulative respiration) and the P incorporated into the AM plant (Total C/P) was calculated to estimate the C investment made by the AM plant into its symbiotic partner. AM plants incorporated P derived from all four P sources exclusively via the mycorrhizal pathway in different amounts and kinetics. The Total C/P ratio was significantly larger for those AM plants accessing the goethite-bound P compounds. They also transferred significantly larger amounts of PLFA and NLFA to their fungal partner, both indicating a larger plant C investment per P taken up. Our data provide first evidence about the ability of an AM plant to incorporate P from an organic source bound to a secondary mineral. The different C investments of AM plants into P allocation from variably available sources suggests a broad nexus between P mining strategies, resource partitioning in soil, and the amounts of C accumulated in terrestrial soils.
Drosophila mRNA Localization During Later Development: Past, Present, and Future

Multiple mechanisms tightly regulate mRNAs during their transcription, translation, and degradation. Of these, the physical localization of mRNAs to specific cytoplasmic regions is relatively easy to detect; however, linking localization to functional regulatory roles has been more difficult to establish. Historically, Drosophila melanogaster is a highly effective model to identify localized mRNAs and has helped identify roles for this process by regulating various cell activities. The majority of the well-characterized functional roles for localizing mRNAs to sub-regions of the cytoplasm have come from the Drosophila oocyte and early syncytial embryo. At present, relatively few functional roles have been established for mRNA localization within the relatively smaller, differentiated somatic cell lineages characteristic of later development, beginning with the cellular blastoderm, and the multiple cell lineages that make up the gastrulating embryo, larva, and adult. This review is divided into three parts—the first outlines past evidence for cytoplasmic mRNA localization affecting aspects of cellular activity post-blastoderm development in Drosophila. The majority of these known examples come from highly polarized cell lineages such as differentiating neurons. The second part considers the present state of affairs where we now know that many, if not most mRNAs are localized to discrete cytoplasmic regions in one or more somatic cell lineages of cellularized embryos, larvae or adults. Assuming that the phenomenon of cytoplasmic mRNA localization represents an underlying functional activity, and correlation with the encoded proteins suggests that mRNA localization is involved in far more than neuronal differentiation. Thus, it seems highly likely that past-identified examples represent only a small fraction of localization-based mRNA regulation in somatic cells. The last part highlights recent technological advances that now provide an opportunity for probing the role of mRNA localization in Drosophila, moving beyond cataloging the diversity of localized mRNAs to a similar understanding of how localization affects mRNA activity.
A Missing Connection: A Review of the Macrostructural Anatomy and Tractography of the Acoustic Radiation

The auditory system of mammals is dedicated to encoding, elaborating and transporting acoustic information from the auditory nerve to the auditory cortex. The acoustic radiation (AR) constitutes the thalamo-cortical projection of this system, conveying the auditory signals from the medial geniculate nucleus (MGN) of the thalamus to the transverse temporal gyrus on the superior temporal lobe. While representing one of the major sensory pathways of the primate brain, the currently available anatomical information of this white matter bundle is quite limited in humans, thus constituting a notable omission in clinical and general studies on auditory processing and language perception. Tracing procedures in humans have restricted applications, and the in vivo reconstruction of this bundle using diffusion tractography techniques remains challenging. Hence, a more accurate and reliable reconstruction of the AR is necessary for understanding the neurobiological substrates supporting audition and language processing mechanisms in both health and disease. This review aims to unite available information on the macroscopic anatomy and topography of the AR in humans and non-human primates. Particular attention is brought to the anatomical characteristics that make this bundle difficult to reconstruct using non-invasive techniques, such as diffusion-based tractography. Open questions in the field and possible future research directions are discussed.
Regulation of Gap-Junctional Communication Between Cumulus Cells During In Vitro Maturation in Swine, a Gap-FRAP Study1

ABSTRACT Intercellular gap-junctional communication (GJC) plays an important role in ovarian cell physiology. Closure of GJC has been proposed to be involved in oocyte maturation, particularly in the resumption of meiosis, both in vivo and in vitro, by controlling the flow of meiosis inhibitors, such as cAMP and cGMP. Understanding how GJC dynamics are regulated during in vitro maturation (IVM) could provide a powerful tool for controlling meiotic resumption and oocyte maturation in vitro. Since little is known about the GJC dynamic regulation between cumulus cells, we have developed an assay based on recovery of calcein fluorescence in photobleached cumulus cells, a gap-FRAP assay. The GJC profile has been characterized during the first hours of porcine IVM. We showed that equine chorionic gonadotropin (eCG) and epidermal growth factor (EGF) down-regulated GJC effectiveness between cumulus cells. However, human chorionic gonadotropin was not down-regulating GJC effectiveness. We also showed that the GJC network expanded during this period and that this effect was not regulated by gonadotropins. Porcine follicular fluid present in the maturation medium also had an impact on GJC regulation, increasing GJC network establishment and the effectiveness of calcein transfer rate between cumulus cells. These results show that both eCG and EGF are regulating the decrease in GJC effectiveness after 4.5 h of IVM, while the network extension is gonadotropin independent. Regulation of GJC between cumulus cells would then be specifically regulated during in vitro IVM.
Development of Quantitative Microscopy-Based Assays for Evaluating Dynamics of Living Cultures of Mouse Spermatogonial Stem/Progenitor Cells1

ABSTRACT Spermatogonial stem cell (SSC) self-renewal and differentiation are required for continuous production of spermatozoa and long-term fertility. Studying SSCs in vivo remains challenging because SSCs are rare cells and definitive molecular markers for their identification are lacking. The development of a method for propagating SSCs in vitro greatly facilitated analysis of SSCs. The cultured cells grow as clusters of a dynamic mixture of “true” stem cells and differentiating progenitor cells. Cells in the stem/progenitor culture system share many properties with spermatogonia in vivo; however, to fully exploit it as a model for spermatogonial development, new assays are needed that account for the dynamic heterogeneity inherent in the culture system. Here, assays were developed for quantifying dynamics of cultures of stem/progenitor cells that expressed histone-green fluorescent protein (GFP). First, we built on published results showing that cluster formation in vitro reliably predicts the relative number of SSCs. The GFP-based in vitro cluster assay allows quantification of SSCs with significantly fewer resources than a transplantation assay. Second, we compared the dynamics of differentiation in two experimental paradigms by imaging over a 17-day time frame. Finally, we performed short-term live imaging and observed cell migration, coordinated cell proliferation, and cell death resembling that of spermatogonia in the testes. The methods that we present provide a foundation for the use of fluorescent reporters in future microscopy-based high-throughput screens by using living spermatogonial stem/progenitor cultures applicable to toxicology, contraceptive discovery, and identification of regulators of self-renewal and differentiation.