Toward a uniform description of hydrogen bond and halogen bond: correlations of interaction energies with various geometric, electronic and topological parameters

Correlations between interaction energies and various structural parameters were established to reveal the differences between hydrogen bonds and halogen bonds.</p

SIRT1-mediated downregulation of p27(Kip1) is essential for overcoming contact inhibition of Kaposi's sarcoma-associated herpesvirus transformed cells

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic virus associated with Kaposi's sarcoma (KS), a malignancy commonly found in AIDS patients. Despite intensive studies in the last two decades, the mechanism of KSHV-induced cellular transformation and tumorigenesis remains unclear. In this study, we found that the expression of SIRT1, a metabolic sensor, was upregulated in a variety of KSHV-infected cells. In a model of KSHV-induced cellular transformation, SIRT1 knockdown with shRNAs or knockout by CRISPR/Cas9 gene editing dramatically suppressed cell proliferation and colony formation in soft agar of KSHV-transformed cells by inducing cell cycle arrest and contact inhibition. SIRT1 knockdown or knockout induced the expression of cyclin-dependent kinase inhibitor 1B (p27(Kip1)). Consequently, p27 knockdown rescued the inhibitory effect of SIRT1 knockdown or knockout on cell proliferation and colony formation. Furthermore, treatment of KSHV-transformed cells with a SIRT1 inhibitor, nicotinamide (NAM), had the same effect as SIRT1 knockdown and knockout. NAM significantly inhibited cell proliferation in culture and colony formation in soft agar, and induced cell cycle arrest. Significantly, NAM inhibited the progression of tumors and extended the survival of mice in a KSHV-induced tumor model. Collectively, these results demonstrate that SIRT1 suppression of p27 is required for KSHV-induced tumorigenesis and identify a potential therapeutic target for KS.

Quantitative Trait Locus Mapping of Soybean Maturity Gene E6

Soybean [ Glycine max (L.) Merr.] sensitivity to photoperiod determines adaptation to a specific range of latitudes for soybean cultivars. When temperate-adapted soybean cultivars are grown in low latitude under short day conditions, they flower early, resulting in low grain yield, and consequently limiting their utility in tropical areas. Most cultivars adapted to low-latitude environments have the trait of delayed flowering under short day conditions, and this trait is commonly called long juvenile (LJ). In this study, the E6 locus, the classical locus conditioning the LJ trait, was molecularly mapped on Gm04 near single-nucleotide polymorphism marker HRM101. Testcross, genetic mapping, and sequencing suggest that the E6 and J loci might be tightly linked. Genetic interaction evaluation between E6 and E1 suggests that E6 has a suppressive effect on E1 and that the function of E6 is dependent on E1. The tagging markers for E6 are very useful for molecular breeding for wide adaptation and stable productivity of soybean under lowlatitude environments. Molecular identification and functional characterization of the E6 gene will greatly facilitate the understanding of the genetic and molecular mechanisms underlying the LJ trait

The Ubiquitin/Proteasome System Mediates Entry and Endosomal Trafficking of Kaposi's Sarcoma-Associated Herpesvirus in Endothelial Cells

Ubiquitination, a post-translational modification, mediates diverse cellular functions including endocytic transport of molecules. Kaposi's sarcoma-associated herpesvirus (KSHV), an enveloped herpesvirus, enters endothelial cells primarily through clathrin-mediated endocytosis. Whether ubiquitination and proteasome activity regulates KSHV entry and endocytosis remains unknown. We showed that inhibition of proteasome activity reduced KSHV entry into endothelial cells and intracellular trafficking to nuclei, thus preventing KSHV infection of the cells. Three-dimensional (3-D) analyses revealed accumulation of KSHV particles in a cytoplasmic compartment identified as EEA1+ endosomal vesicles upon proteasome inhibition. KSHV particles are colocalized with ubiquitin-binding proteins epsin and eps15. Furthermore, ubiquitination mediates internalization of both KSHV and one of its receptors integrin β1. KSHV particles are colocalized with activated forms of the E3 ligase c-Cbl. Knock-down of c-Cbl or inhibition of its phosphorylation reduced viral entry and intracellular trafficking, resulting in decreased KSHV infectivity. These results demonstrate that ubiquitination mediates internalization of both KSHV and one of its cognate receptors integrin β1, and identify c-Cbl as a potential E3 ligase that facilitates this process

A global agenda for advancing freshwater biodiversity research

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.Peer reviewe

Open, Sharable, and Extensible Data Management for the Korea National Aquatic Ecological Monitoring and Assessment Program: A RESTful API-Based Approach

Implemented by a national law, the National Aquatic Ecological Monitoring Program (NAEMP) has been assessing the ecological health status of surface waters, focusing on streams and rivers, in Korea since 2007. The program involves ecological monitoring of multiple aquatic biota such as benthic diatoms, macroinvertebrates, fish, and plants as well as water quality and habitat parameters. Taking advantage of the national scale of long-term aquatic ecological monitoring and the standardization of protocols and methods, the datasets in NAEMP provide many opportunities for various advanced comparative and synthetic studies, policy-making, and ecological management. In order to realize these potentials and opportunities, we have developed a RESTful API-based data management system called OSAEM (the Open, Sharable and Extensible Data Management System for Aquatic Ecological Monitoring), which is designed to be open, sharable, and extensible. In this paper, we introduce the RESTful API-based data management approach, present the RESTful API for the OSAEM system, and discuss its applicability. An OSAEM prototype system is currently available on a commercial cloud service (Amazon EC2) but the system remains under active development

Theoretical analysis on the variation of value of travel time savings

This paper theoretically examines whether and how the value of travel time savings changes with the travel and individual socio-economic environments. A time allocation model for the general case of travel behavior is proposed following a review of basic theories of the value of time. Under some general assumptions, changes of value of travel time savings with travel time, travel cost, wage rate, and work time are examined by the comparative static analysis. Differences between the variation of the value of travel time savings and value of time as a resource are also discussed. The results provide the variation mechanisms of the value of time and verify some of the results of empirical studies.

Re-examination of the standards for transit oriented development influence zones in India

This is under the section Literature Review in Volume 12 (2019) of JTLU.Transit oriented development (TOD) is a land-use and transport integrated urban planning strategy that is highly acclaimed for promoting sustainable city development. This review aims to identify the problems regarding adoption of TOD standards or guidelines formulated by developed countries in developing countries, such as India, and the necessity of conducting adaptability studies on TOD influence areas. The existing studies show that the size of the influence area varies among different cities and travel modes. Accordingly, no single size influence zone is suitable for all cases. This review highlights the necessity of carefully considering the spatial extent of influence areas and modes other than walking as access or egress modes in the Indian context. Moreover, this review aims to provide insight on how to plan TOD in the context of developing countries, because the mobility patterns in these countries differ considerably from those in the developed world.Ann, Sangeetha; Jiang, Meilan; Yamamoto, Toshiyuki. (2019). Re-examination of the standards for transit oriented development influence zones in India. Retrieved from the University Digital Conservancy, 10.5198/jtlu.2019.1534