Klemen Bohinc

Bio: Klemen Bohinc is an academic researcher from University of Ljubljana. The author has contributed to research in topics: Adhesion & Surface charge. The author has an hindex of 29, co-authored 130 publications receiving 3038 citations. Previous affiliations of Klemen Bohinc include North Dakota State University & Jožef Stefan Institute.

Condensed DNA: condensing the concepts.

Abstract: DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The mechanistic details of DNA packing are essential for its functioning, as revealed by the recent developments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in the bulk of experimental and theoretical details. Here we try to condense some of these concepts and provide interconnections between the different fields. After a brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented. We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology.

Measurement of the neutron electric form-factor G(en) at 0.67-(GeV/c)**2 via He-3(pol.)(e(pol.),e' n)

Abstract: We have measured the neutron electric form factor ${G}_{\mathrm{en}}$ via ${}^{3}\stackrel{\ensuremath{\rightarrow}}{\mathrm{He}}(\stackrel{\ensuremath{\rightarrow}}{e}{,e}^{\ensuremath{'}}n)\mathrm{pp}$ at ${Q}^{2}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}0.67(\mathrm{GeV}/c{)}^{2}$ using the 3-spectrometer facility of the A1 Collaboration at the Mainz Microtron and a dedicated neutron detector. High pressure polarized ${}^{3}\stackrel{\ensuremath{\rightarrow}}{\mathrm{He}}$ gas was used as a target of polarized neutrons. ${G}_{\mathrm{en}}$ is determined from the ratio of the asymmetries ${A}_{\ensuremath{\perp}}{/A}_{\ensuremath{\parallel}}$ measured in quasifree kinematics with the target spin perpendicular and parallel to the momentum transfer. We find ${G}_{\mathrm{en}}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}0.052\ifmmode\pm\else\textpm\fi{}0.011\ifmmode\pm\else\textpm\fi{}0.005$.

Precise Neutron Magnetic Form Factors

Abstract: Precise data on the neutron magnetic form factor G_{mn} have been obtained with measurements of the ratio of cross sections of D(e,e'n) and D(e,e'p) up to momentum transfers of Q^2 = 0.9 (GeV/c)^2. Data with typical uncertainties of 1.5% are presented. These data allow for the first time to extract a precise value of the magnetic radius of the neutron.

Phd by thesis

Abstract: Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins

Abstract: Circulating microRNAs (miRNA) are relatively stable in plasma and are a new class of disease biomarkers. Here we present evidence that high-density lipoprotein (HDL) transports endogenous miRNAs and delivers them to recipient cells with functional targeting capabilities. Cellular export of miRNAs to HDL was demonstrated to be regulated by neutral sphingomyelinase. Reconstituted HDL injected into mice retrieved distinct miRNA profiles from normal and atherogenic models. HDL delivery of both exogenous and endogenous miRNAs resulted in the direct targeting of messenger RNA reporters. Furthermore, HDL-mediated delivery of miRNAs to recipient cells was demonstrated to be dependent on scavenger receptor class B type I. The human HDL-miRNA profile of normal subjects is significantly different from that of familial hypercholesterolemia subjects. Notably, HDL-miRNA from atherosclerotic subjects induced differential gene expression, with significant loss of conserved mRNA targets in cultured hepatocytes. Collectively, these observations indicate that HDL participates in a mechanism of intercellular communication involving the transport and delivery of miRNAs.

The Genomic Code for Nucleosome Positioning

Abstract: Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.