Effects of disorder in location and size of fence barriers on molecular motion in cell membranes

The effect of disorder in the energetic heights and in the physical locations of fence barriers encountered by transmembrane molecules such as proteins and lipids in their motion in cell membranes is studied theoretically. The investigation takes as its starting point a recent analysis of a periodic system with constant distances between barriers and constant values of barrier heights, and employs effective medium theory to treat the disorder. The calculations make possible, in principle, the extraction of confinement parameters such as mean compartment sizes and mean intercompartmental transition rates from experimentally reported published observations. The analysis should be helpful both as an unusual application of effective medium theory and as an investigation of observed molecular movements in cell membranes.Comment: 9 pages, 5 figure

Switchgrass as a potential forage grass for Gümüşhane region and its biomass production

Dallı darı (Panicum virgatum L.) yüksek ot verimi, iyi düzeydeki yem değeri, biyoenerji kaynağı teşkil etmesi, derin kök sistemi geliştirmesi, toprağı iyileştirmesi, kurağa dayanıklı olması ve nispeten fakir yetişme ortamlarında gelişebilmesi gibi özellikleri nedeni ile önemli bir yem bitkisi türüdür. Dallı darının kökleri uygun yetişme ortamlarında 3.3 m. derine kadar inebilmektedir. Yıllık toprak üstü net biyokütle üretimi hektarda 17 ile 35 ton arasında değişmektedir. Ancak bu değer uygun olmayan yetişme ortamlarında 8-10 ton/ha’a kadar düşebilmektedir. Yıllık net toprak altı biyokütle üretimi yaklaşık 8 ton/ha cıvarında olabilmekte, bu değer kurak ve fakir yetişme ortamlarında 15 ton/ha’a kadar çıkabilmektedir. Dallı darı, uygun varyete ve orijinleri denenerek, Gümüşhane ve yöresi hayvancılığı için çok faydalı olabilecek bir tür niteliğindedir.Switchgrass is one of the important grass species with its deep root system, high annual above- and belowground production, good quality forage, potential to use for bioenergy, resistance to drought, ability to grow in poor soils and potential to improve soil quality. Switchgrass develops roots that penetrates up to 330 cm soil depth. Annual net aboveground production ranges from 17 to 35 tons/ha. However this value can decrease to 8 to 10 tons/ha in poor soil conditions. Annual net belowground production is generally around 8 tons/ha, but it can go up to 15 tons/ha in dry and poor soil conditions. Switchgrass could provide lots of benefits to livestock production in Gümüşhane if right varieties and cultivars have chose

Molecular motion in cell membranes: analytic study of fence-hindered random walks

A theoretical calculation is presented to describe the confined motion of transmembrane molecules in cell membranes. The study is analytic, based on Master equations for the probability of the molecules moving as random walkers, and leads to explicit usable solutions including expressions for the molecular mean square displacement and effective diffusion constants. One outcome is a detailed understanding of the dependence of the time variation of the mean square displacement on the initial placement of the molecule within the confined region. How to use the calculations is illustrated by extracting (confinement) compartment sizes from experimentally reported published observations from single particle tracking experiments on the diffusion of gold-tagged G-protein coupled mu-opioid receptors in the normal rat kidney cell membrane, and by further comparing the analytical results to observations on the diffusion of phospholipids, also in normal rat kidney cells.Comment: 10 pages, 5 figure

Çoruh vadisi fıstıkçamı orman ekosistemlerine ilişkin bitki örtüsü ve bazı fiziksel ve kimyasal toprak özelliklerinin incelenmesi

Bir Akdeniz bitki örtüsü olan fıstıkçamı Doğu Karadeniz Bölgesinde Trabzon- Söğütlü Deresi ve Artvin-Çoruh Vadisinde dar bir alanda yayılış göstermektedir. Koruma amaçlı ayrılması gereken bu alanlarda fıstıkçamının kalıcılığının sağlanmasında toprak etmenlerinin önemi büyüktür. Bu çalışmada Çoruh vadisi fıstıkçamı meşcerelerinden 8 adet toprak profili alınmıştır. Alınan toprak örneklerinin tekstür, pH, organik madde ve taşlılık oranları belirlenmiştir. Toprak pH’sı 6.3 ile 7.04, toprak organik maddesi ise 0.7 ile 8.1 arasında değişmiştir. Toprağın taşlılık oranı yüksek olup, horizonlaşma zayıftır. Meşcere kapalılığı zayıf olup yoğun diri örtü doğal gençleşme şansını azaltmıştır. Koruma altına alınmadığı takdirde buradaki fıstıkçamı meşcerelerinin yok olması kaçınılmaz görünmektedir.Stone pine (Pinus pinea L.), a mediterranian species, locally spreads in two locations of Eastern Blacksea Region: Tarbzon-Söğütlü Watershed and Artvin-Coruh Watershed. Understanding soil properties of these areas will be useful in preserving them. In this study 8 soil pits were dug in stone pine stands along Coruh Valley. Soil texture, soil organic matter content and soil pH were determined. Soil pH ranged from 6.3 to 7.04; soil organic matter content changed from 0.7 to 8.1. Coarse fragment content of soil were very high. Stand canopy was low and natural regeneration of stone pine were decreased by dense understory cover. It seems these stone pine stands will disappear if the necessary measures were not taken

Artvin-Hatilla Milli Parkı, doğu ladini meşçerelerinde görülen kurumaların ekolojik açıdan irdelenmesi

Bu çalışmada Artvin-Hatilla Milli parkında görülen böcek kaynaklı kurumaların ekolojik nedenlerinin ortaya konması amaçlanmıştır. Bu amaçla alandaki sağlıklı ve kurumuş büklerden toprak ve artım örnekleri alınarak incelenmiştir. İnceleme sonucu, kuruyan ağaçların son 20 yılda artımları azalan ağaçlar olduğu belirlenmiştirIn this study, the ecelogical reasons behind the spruce-dying in Hatilla National Park were evaluated in Artvin, Turkey. Soil and ingrowth samples were taken from both healty and damaged stands. Our results showed that trees damaged by the spruce bark beetle were those having decreasing growth ring widths in last 20 years

Quantifying single nucleotide variant detection sensitivity in exome sequencing

BACKGROUND: The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to detect genuine polymorphisms. To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed. RESULTS: Using down-sampling of 30 deeply sequenced exomes and a set of gold-standard single nucleotide variant (SNV) genotype calls for each sample, we developed an empirical model relating the read depth at a polymorphic site to the probability of calling the correct genotype at that site. We find that measured sensitivity in SNV detection is substantially worse than that predicted from the naive expectation of sampling from a binomial. This calibrated model allows us to produce single nucleotide resolution SNV sensitivity estimates which can be merged to give summary sensitivity measures for any arbitrary partition of the target sequences (nucleotide, exon, gene, pathway, exome). These metrics are directly comparable between platforms and can be combined between samples to give “power estimates” for an entire study. We estimate a local read depth of 13X is required to detect the alleles and genotype of a heterozygous SNV 95% of the time, but only 3X for a homozygous SNV. At a mean on-target read depth of 20X, commonly used for rare disease exome sequencing studies, we predict 5–15% of heterozygous and 1–4% of homozygous SNVs in the targeted regions will be missed. CONCLUSIONS: Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the “missing heritability” of quantitative traits

The nonlinear time-dependent response of isotactic polypropylene

Tensile creep tests, tensile relaxation tests and a tensile test with a constant rate of strain are performed on injection-molded isotactic polypropylene at room temperature in the vicinity of the yield point. A constitutive model is derived for the time-dependent behavior of semi-crystalline polymers. A polymer is treated as an equivalent network of chains bridged by permanent junctions. The network is modelled as an ensemble of passive meso-regions (with affine nodes) and active meso-domains (where junctions slip with respect to their positions in the bulk medium with various rates). The distribution of activation energies for sliding in active meso-regions is described by a random energy model. Adjustable parameters in the stress--strain relations are found by fitting experimental data. It is demonstrated that the concentration of active meso-domains monotonically grows with strain, whereas the average potential energy for sliding of junctions and the standard deviation of activation energies suffer substantial drops at the yield point. With reference to the concept of dual population of crystalline lamellae, these changes in material parameters are attributed to transition from breakage of subsidiary (thin) lamellae in the sub-yield region to fragmentation of primary (thick) lamellae in the post-yield region of deformation.Comment: 29 pages, 12 figure

Ultrafast single-molecule imaging reveals focal adhesion nano-architecture and molecular dynamics

細胞膜上の分子がバレエの群舞のように見えてきた： 1蛍光分子の感度で、究極速度で撮像できるカメラを開発. 京都大学プレスリリース. 2023-06-06.Using our newly developed ultrafast camera described in the companion paper, we reduced the data acquisition periods required for photoactivation/photoconversion localization microscopy (PALM, using mEos3.2) and direct stochastic reconstruction microscopy (dSTORM, using HMSiR) by a factor of ≈30 compared with standard methods, for much greater view-fields, with localization precisions of 29 and 19 nm, respectively, thus opening up previously inaccessible spatiotemporal scales to cell biology research. Simultaneous two-color PALM-dSTORM and PALM-ultrafast (10 kHz) single fluorescent-molecule imaging-tracking has been realized. They revealed the dynamic nanoorganization of the focal adhesion (FA), leading to the compartmentalized archipelago FA model, consisting of FA-protein islands with broad diversities in size (13–100 nm; mean island diameter ≈30 nm), protein copy numbers, compositions, and stoichiometries, which dot the partitioned fluid membrane (74-nm compartments in the FA vs. 109-nm compartments outside the FA). Integrins are recruited to these islands by hop diffusion. The FA-protein islands form loose ≈320 nm clusters and function as units for recruiting FA proteins

Adaptable antigen matrix platforms for peptide vaccination strategies and T cell-mediated anti-tumor immunity

Injection of antigenic peptides has been widely used as a vaccine strategy to boost T cell immunity. However, the poor immunogenicity of single peptides can potentially be strengthened through modification of the tertiary structure and the selection of the accompanying adjuvant. Here, we generated antigenic peptides into non-linear trimers by solid phase peptide synthesis, thereby enhancing antigen presentation by dendritic cells to CD8+ T cells in vitro and in vivo. CD8+ T cells from mice vaccinated with trimers showed an KLRG1+ effector phenotype and were able to recognize and kill antigen-expressing tumor cells ex vivo. Importantly, trimers outperformed synthetic long peptide in terms of T cell response even when equal number of epitopes were used for immunization. To improve the synthesis of trimers containing difficult peptide sequences, we developed a novel small molecule that functions as conjugation platform for synthetic long peptides. This platform, termed Antigen MAtriX (AMAX) improved yield, purity and solubility of trimers over conventional solid phase synthesis strategies. AMAX outperformed synthetic long peptides in terms of both CD8+ and CD4+ T cell responses and allowed functionalization with DC-SIGN-binding carbohydrates for in vivo dendritic cell targeting strategies, boosting T cell responses even further. Moreover, we show that ag