International Journal of Molecular Science Best Paper Award 2014

International Journal of Molecular Science is instituting an annual award to recognize outstanding papers in the area of chemistry, molecular physics and molecular biology published in International Journal of Molecular Science. We are pleased to announce the third "International Journal of Molecular Science Best Paper Award" for 2014 [1,2]. Nominations were made by the Section Editors-in-Chief of International Journal of Molecular Science from all papers published in 2010

HMGN5 (High Mobility Group Nucleosome binding domain 5)

HMGN5 is a member of the high mobility group nucleosome binding domain (HMGN) protein family. HMGN proteins are ubiquitously expressed in vertebrate cells. They are nuclear proteins that bind specifically to nucleosomes without specificity for the DNA sequence and affect the structure and function of chromatin. HMGN5 sequences have been detected in all vertebrate tissues examines. HMGN5 differs from the other members of the HMGN family in that it is significantly larger and its amino acid sequence varies significantly between different vertebrate species

High mobility group proteins of amphibian oocytes: a large storage pool of a soluble high mobility group-1-like protein and involvement in transcriptional events

No abstract availabl

HMGN1 Modulates Nucleosome Occupancy and DNase I Hypersensitivity at the CpG Island Promoters of Embryonic Stem Cells

Chromatin structure plays a key role in regulating gene expression and embryonic differentiation; however, the factors that determine the organization of chromatin around regulatory sites are not fully known. Here we show that HMGN1, a nucleosome-binding protein ubiquitously expressed in vertebrate cells, preferentially binds to CpG island-containing promoters and affects the organization of nucleosomes, DNase I hypersensitivity, and the transcriptional profile of mouse embryonic stem cells and neural progenitors. Loss of HMGN1 alters the organization of an unstable nucleosome at transcription start sites, reduces the number of DNase I-hypersensitive sites genome wide, and decreases the number of nestin-positive neural progenitors in the subventricular zone (SVZ) region of mouse brain. Thus, architectural chromatin-binding proteins affect the transcription profile and chromatin structure during embryonic stem cell differentiation

A Java Program for LRE-Based Real-Time qPCR that Enables Large-Scale Absolute Quantification

Background: Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Findings: Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. Conclusions: The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples

Alkali extraction of archaeological and geological charcoal: evidence for diagenetic degradation and formation of humic acids

Charcoal forms a crucial source of archaeological and palaeoenvironmental data, providing a record of cultural activities, past climatic conditions and a means of chronological control via radiocarbon (<sup>14</sup>C) dating. Key to this is the perceived resistance of charcoal to post-depositional alteration, however recent research has highlighted the possibility for alteration and degradation of charcoal in the environment. An important aspect of such diagenesis is the potential for addition of exogenous 'humic acids' (HAs), to affect the accuracy of archaeological and palaeoenvironmental reconstructions based upon chemical analyses of HA-containing charcoal. However the release of significant quantities of HA from apparently pristine charcoals raises the question whether some HA could be derived via diagenetic alteration of charcoal itself. Here we address this question through comparison of freshly produced charcoal with samples from archaeological and geological sites exposed to environmental conditions for millennia using elemental (C/H/O) and isotopic (δ<sup>13</sup>C) measurements, Fourier Transform Infrared Spectroscopy (FTIR) and proton Liquid-State Nuclear Magnetic Resonance (<sup>1</sup>H NMR). The results of analyses show that the presence of highly carboxylated and aromatic alkali-extractable HA in charcoal from depositional environments can often be attributable to the effects of post-depositional processes, and that these substances can represent the products of post-depositional diagenetic alteration in charcoal

The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020

Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology