The middle region of an HP1-binding protein, HP1-BP74, associates with linker DNA at the entry/exit site of nucleosomal DNA

Kayoko Hayashihara, Susumu Uchiyama, Shigeru Shimamoto, Shouhei Kobayashi, Miroslav Tomschik, Hidekazu Wakamatsu, Daisuke No, Hiroki Sugahara, Naoto Hori, Masanori Noda, Tadayasu Ohkubo, Jordanka Zlatanova, Sachihiro Matsunaga, Kiichi Fukui. The Middle Region of an HP1-binding Protein, HP1-BP74, Associates with Linker DNA at the Entry/Exit Site of Nucleosomal DNA. Journal of Biological Chemistry, Volume 285, Issue 9, 2010, Pages 6498-6507. https://doi.org/10.1074/jbc.M109.092833

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Basis set limits of the second order M\uc3\ub8ller-Plesset correlation energies of water, methane, acetylene, ethylene, and benzene

We report second order M\uc3\ub8ller-Plesset (MP2) and MP2-F12 total energies on He, Ne, Ar, H2 O, C H4, C2 H2, C2 H4, and C6 H6, using the correlation consistent basis sets, aug-cc-pVXZ (X=D-7). Basis set extrapolation techniques are applied to the MP2 and MP2-F12/B methods. The performance of the methods is tested in the calculations of the atoms, He, Ne, and Ar. It is indicated that the two-point extrapolation of MP2-F12/B with the basis sets (X=5,6) is the most reliable. Similar accuracy is obtained using two-point extrapolated conventional MP2 with the basis sets (X=6,7). For the molecules investigated the valence MP2 correlation energy is estimated within 1 m Eh. \uc2\ua9 2007 American Institute of Physics

Cold-induced muscle atrophy in zebrafish: Insights from swimming activity and gene expression analysis

The investigation into the effects of cold acclimation on fish skeletal muscle function and its potential implications for muscle atrophy is of great interest to us. This study examines how rearing zebrafish at low temperatures affects their locomotor activity and the expression of genes associated with muscle atrophy. Zebrafish were exposed to temperatures ranging from 10 °C to 25 °C, and their swimming distance was measured. The expression levels of important muscle atrophy genes, Atrogin-1 and MuRF1, were also evaluated. Our findings show that swimming activity significantly decreases when the water temperature ranges from 10 °C to 15 °C, indicating a decrease in voluntary movement. Additionally, gene expression analysis shows a significant increase in the expression of Atrogin-1 and MuRF1 at 10 °C. This up-regulation could lead to muscle atrophy caused by decreased activity in cold temperatures. To investigate the effects of exercise on reducing muscle atrophy, we subjected zebrafish to forced swimming at a temperature of 8 °C for ten days. This treatment significantly reduced the expression of Atrogin-1 and MuRF1, emphasizing the importance of muscle stimulation in preventing muscle atrophy in zebrafish. These findings suggest that zebrafish can serve as a valuable model organism for studying muscle atrophy and can be utilized in drug screening for muscle atrophy-related disorders. Cold-reared zebrafish provide a practical and ethical approach to inducing disuse muscle atrophy, providing valuable insights into potential therapeutic strategies for addressing skeletal muscle atrophy

Lampreys Have a Single Gene Cluster for the Fast Skeletal Myosin Heavy Chain Gene Family

<div><p>Muscle tissues contain the most classic sarcomeric myosin, called myosin II, which consists of 2 heavy chains (MYHs) and 4 light chains. In the case of humans (tetrapod), a total of 6 fast skeletal-type MYH genes (<i>MYH</i>s) are clustered on a single chromosome. In contrast, torafugu (teleost) contains at least 13 fast skeletal <i>MYH</i>s, which are distributed in 5 genomic regions; the <i>MYH</i>s are clustered in 3 of these regions. In the present study, the evolutionary relationship among fast skeletal <i>MYH</i>s is elucidated by comparing the <i>MYH</i>s of teleosts and tetrapods with those of cyclostome lampreys, one of two groups of extant jawless vertebrates (agnathans). We found that lampreys contain at least 3 fast skeletal <i>MYH</i>s, which are clustered in a head-to-tail manner in a single genomic region. Although there was apparent synteny in the corresponding <i>MYH</i> cluster regions between lampreys and tetrapods, phylogenetic analysis indicated that lamprey and tetrapod <i>MYH</i>s have independently duplicated and diversified. Subsequent transgenic approaches showed that the 5′-flanking sequences of Japanese lamprey fast skeletal <i>MYH</i>s function as a regulatory sequence to drive specific reporter gene expression in the fast skeletal muscle of zebrafish embryos. Although zebrafish <i>MYH</i> promoters showed apparent activity to direct reporter gene expression in myogenic cells derived from mice, promoters from Japanese lamprey <i>MYH</i>s had no activity. These results suggest that the muscle-specific regulatory mechanisms are partially conserved between teleosts and tetrapods but not between cyclostomes and tetrapods, despite the conserved synteny.</p> </div