A high-resolution protein architecture of the budding yeast genome.

The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is not well defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP-exo/seq)1,2 to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex. Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI-SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs engaged with their cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.

What Makes a Beautiful Buttock Beautiful? A Case-Control Study Comparing Buttocks Models versus Normal Women by Magnetic Resonance Imaging, Photography and Anthropometry.

OBJECTIVES: To describe characteristics of women with aesthetically ideal buttocks and differentiate them from women with normal buttocks. METHODS: Case-control study comparing anatomy of women with ideal buttocks (buttocks models) to women with normal buttocks using magnetic resonance images, anthropometric measurements and photography. RESULTS: Comparing to normal women, buttocks models have a narrower waist, narrower iliac crest, wider C point, wider hips and bigger and thicker gluteus maximus muscle (GMM). A bigger GMM adds more projection to the C point, point of maximum projection in the lateral view is 2.7 cm higher than the pubic bone. The amount of subcutaneous fat was equal in models and controls. CONCLUSIONS: Our study provides new knowledge regarding the tridimensional aspects of the beauty of the buttocks area. A beautiful buttock is a conjunction of adequate bony shape, muscle development, subcutaneous fat layer, and tight skin. Comparing to normal women, buttocks models have a narrower waist, narrower iliac crest, wider C point, wider hips and bigger and thicker Gluteus Maximus Muscle. Accurate understanding of the aesthetic goals in a given patient can guide surgical technique. LEVEL OF EVIDENCE III: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation.

Differentiation from asexual blood stages to mature sexual gametocytes is required for the transmission of malaria parasites. Here, we report that the ApiAP2 transcription factor, PfAP2-G2 (PF3D7_1408200) plays a critical role in the maturation of Plasmodium falciparum gametocytes. PfAP2-G2 binds to the promoters of a wide array of genes that are expressed at many stages of the parasite life cycle. Interestingly, we also find binding of PfAP2-G2 within the gene body of almost 3,000 genes, which strongly correlates with the location of H3K36me3 and several other histone modifications as well as Heterochromatin Protein 1 (HP1), suggesting that occupancy of PfAP2-G2 in gene bodies may serve as an alternative regulatory mechanism. Disruption of pfap2-g2 does not impact asexual development, but the majority of sexual parasites are unable to mature beyond stage III gametocytes. The absence of pfap2-g2 leads to overexpression of 28% of the genes bound by PfAP2-G2 and none of the PfAP2-G2 bound genes are downregulated, suggesting that it is a repressor. We also find that PfAP2-G2 interacts with chromatin remodeling proteins, a microrchidia (MORC) protein, and another ApiAP2 protein (PF3D7_1139300). Overall our data demonstrate that PfAP2-G2 establishes an essential gametocyte maturation program in association with other chromatin-related proteins.

Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes.

The ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5' to 3' exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects crosslinking efficiencies. Therefore, the spatial organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between its subunits. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of coordinately bound regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. By producing consistent measurements of protein-DNA crosslinking strengths across multiple proteins, our approach enables characterization of relative spatial organization within a regulatory complex. Applying our approach to collections of ChIP-exo data, we demonstrate that it can recover aspects of regulatory complex spatial organization at yeast ribosomal protein genes and yeast tRNA genes. We also demonstrate the ability to quantify changes in protein-DNA complex organization across conditions by applying our approach to analyze Drosophila Pol II transcriptional components. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of spatial organization within protein-DNA complexes.

Machine-assisted foot stretching in the elderly: a comparison with self-stretching.

[Purpose] Self-stretching is the traditional at-home stretching method of choice. We developed an automatic foot-stretching machine to perform effective dorsiflexion stretching safely and easily at home. The effects of automatic stretching using our machine and self-stretching were investigated and compared. [Participants and Methods] Twelve healthy elderly people participated in the study. Automatic dorsiflexion static stretching was performed with the right foot, and self-stretching using a towel was performed with the left foot. Before and after each stretching, passive range of motion in dorsiflexion, maximal voluntary contraction strength in plantarflexion, passive resistive torque during passive dorsiflexion, and displacement of the muscle-tendon junction of the medial gastrocnemius muscle were measured. [Results] The range of motion in dorsiflexion had a significantly greater increase after automatic stretching than after self-stretching. The maximum strength in plantarflexion tended to decrease after automatic stretching but did not decrease after self-stretching. The passive resistive torque in both types of stretches decreased in some of the participants but increased in others. The displacement of the muscle-tendon junction of the medial gastrocnemius tended to shorten during automatic stretching as compared with self-stretching. [Conclusion] Foot stretching using a machine is as effective as self-stretching and tends to affect the tendon rather than the muscle.

Characterizing protein-DNA binding event subtypes in ChIP-exo data.

MOTIVATION: Regulatory proteins associate with the genome either by directly binding cognate DNA motifs or via protein-protein interactions with other regulators. Each recruitment mechanism may be associated with distinct motifs and may also result in distinct characteristic patterns in high-resolution protein-DNA binding assays. For example, the ChIP-exo protocol precisely characterizes protein-DNA crosslinking patterns by combining chromatin immunoprecipitation (ChIP) with 5' → 3' exonuclease digestion. Since different regulatory complexes will result in different protein-DNA crosslinking signatures, analysis of ChIP-exo tag enrichment patterns should enable detection of multiple protein-DNA binding modes for a given regulatory protein. However, current ChIP-exo analysis methods either treat all binding events as being of a uniform type or rely on motifs to cluster binding events into subtypes. RESULTS: To systematically detect multiple protein-DNA interaction modes in a single ChIP-exo experiment, we introduce the ChIP-exo mixture model (ChExMix). ChExMix probabilistically models the genomic locations and subtype memberships of binding events using both ChIP-exo tag distribution patterns and DNA motifs. We demonstrate that ChExMix achieves accurate detection and classification of binding event subtypes using in silico mixed ChIP-exo data. We further demonstrate the unique analysis abilities of ChExMix using a collection of ChIP-exo experiments that profile the binding of key transcription factors in MCF-7 cells. In these data, ChExMix identifies possible recruitment mechanisms of FoxA1 and ERα, thus demonstrating that ChExMix can effectively stratify ChIP-exo binding events into biologically meaningful subtypes. AVAILABILITY AND IMPLEMENTATION: ChExMix is available from https://github.com/seqcode/chexmix. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Principal motion analysis of manual stretching techniques for the ankle joints.

[Purpose] Physical therapists frequently perform manual stretching of the ankle joints. Manual stretching procedures are challenging to define because they involve multidirectional joint motions and external forces. Therefore, in this paper, we propose a method for quantitatively and statistically analyzing the manual foot stretching techniques used by physical therapists. [Participants and Methods] The participants were four physical therapists, and three patients who have a spastic foot. We investigated the manual foot stretching techniques employed by the physical therapists using a three-dimensional analysis system and an instrumented brace with force sensors. Principal motion analysis was applied to the obtained data, and principal motions were determined. [Results] The first principal motion was the application of force for the dorsiflexion of the foot; second, the pushing/pulling of the heel; third, the eversion/inversion of the entire foot; and fourth, the eversion/inversion of the forefoot. Furthermore, the manual stretching techniques varied among the physical therapists, even for the same patient, and some techniques occurred only between particular pairs. [Conclusion] This study demonstrated the effectiveness of the principal motion analysis for the statistical assessment of manual stretching techniques and clarifying differences in stretching technique among physical therapists.

Combined conservative treatment and lymphatic venous anastomosis for severe lower limb lymphedema with recurrent cellulitis.

BACKGROUND: Lymphedema may be treated either conservatively or surgically. Although conservative therapy is the first-line treatment, some patients are refractory to it and repeat severe cellulitis. We usually perform lymphaticovenous anastomosis (LVA) for lymphedema patients, and LVA can reduce the frequency of cellulitis. CASE REPORT: A 67-year-old woman who had undergone a radical hysterectomy, pelvic lymphadenectomy, and postoperative radiotherapy for cervical cancer at the age 50 years. She developed lymphedema in both legs, and high-pressure compression stockings caused lymphorrhea in the groin and thigh, resulting in recurrent episodes of cellulitis. Lymphoscintigraphy revealed dilation of the lymphatic vessels in both legs. Results of an indocyanine green test revealed dermal backflow throughout the lower body. After wearing low-pressure stocking, we performed LVA to reduce cellulitis. After confirming the result of LVA, the patients started wearing high-pressure stocking. The patient underwent a subsequent LVA, 3 months after the first, to further improve edema. The lymphorrhea resolved, and cellulitis did not recur. CONCLUSIONS: The combination of surgical treatment and conservative treatment is important for severe lymphedema treatment. Although conservative treatment is usually said to be the first-line treatment, LVA can antecede in cases refractory to conservative treatment.

Effect of intradialytic exercise on geriatric issues in older patients undergoing hemodialysis: a single-center non-randomized controlled study.

PURPOSE: This study investigated the effect of 1 year of intradialytic exercise on older hemodialysis patients with geriatric issues. METHODS: Forty-six patients aged ≥ 70 years were non-randomly assigned to two groups (exercise group: 27, control group: 19). Intradialytic exercise consisted of 30 min of aerobic exercise using a cycle ergometer, and resistance training comprising four exercises using an elastic tube three times per week for 1 year. Handgrip strength, leg extremity muscle strength, 10-m walk speed, short physical performance battery, serum albumin, Geriatric Nutritional Risk Index (GNRI), geriatric depression scale, frailty, and mobility were each assessed before and after the intervention. RESULTS: The control group exhibited a significant reduction in handgrip strength, 10-m walking speed, serum albumin, and GNRI after intervention compared to baseline (p < 0.05). Conversely, no significant reductions were observed in the exercise group. The ΔGNRI (effect size, 0.69; 95% confidence interval [CI] - 5.21, - 0.1; p < 0.05) and Δserum albumin (effect size, 0.72; 95% CI - 0.31, - 0.02; p < 0.05) before and after the intervention declined significantly less in the exercise group than in the control group. Other between-group values were not significantly different. The number of frail patients and patients requiring walking assistance exhibited no significant intra-group or between-group differences before and after the intervention. CONCLUSION: Intradialytic exercise prevented the worsening of nutritional status and physical function in the exercise group compared to the control group. Exercise therapy during dialysis is an important aspect of patient care that helps prevent functional decline in older patients.

The immunological and chemical detection of N-(hexanoyl)phosphatidylethanolamine and N-(hexanoyl)phosphatidylserine in an oxidative model induced by carbon tetrachloride.

Lipid peroxidation products have a high reactivity against the primary amino groups of biomolecules such as aminophospholipids, proteins, and DNA. Until now, many papers have reported about the modification of biomolecules derived from lipid peroxides. Our group has also reported that aminophospholipids, such as phosphatidylethanolamine (PE), can be modified by lipid peroxidation including 13-hydroperoxyoctadecadienoic acid (13-HPODE). The aim of this study was to examine the oxidative stress in vivo by detecting the formation of N-(hexanoyl)phosphatidylethanolamine (HEPE) and N-(hexanoyl)phosphatidylserine (HEPS), a novel hexanoyl adduct, using a liquid chromatography/tandem mass spectrometry (LC/MS/MS) and a monoclonal antibody. Consequently, we observed that the formation of HEPE and HEPS occurred in the red blood cell (RBC) ghosts modified by 13-HPODE and the oxidative stress model induced by carbon tetrachloride (CCl(4)) using LC/MS/MS monitoring hexanoyl ethanolamine (HEEA), a head group of HEPE, and hexanoyl serine (HESE) as a part of HEPS. Furthermore, we obtained a novel type of monoclonal antibody against HEPE. This antibody could recognize HEPE in the liver of rats with oxidative stress in vivo.

ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes.

Regulatory proteins can employ multiple direct and indirect modes of interaction with the genome. The ChIP-exo mixture model (ChExMix) provides a principled approach to detecting multiple protein-DNA interaction modes in a single ChIP-exo experiment. ChExMix discovers and characterizes binding event subtypes in ChIP-exo data by leveraging both protein-DNA cross-linking signatures and DNA motifs. In this study, we present a summary of the major features and applications of ChExMix. We demonstrate that ChExMix does not require high-resolution protein-DNA binding assay data to detect binding event subtypes. Specifically, we apply ChExMix to analyze 393 ChIP-seq data profiles in K562 cells. Similar binding event subtypes are discovered across multiple proteins, suggesting the existence of colocalized regulatory protein modules that are recruited to DNA through a particular sequence-specific transcription factor. Our results thus suggest that ChExMix can characterize protein-DNA binding interaction modes using data from multiple types of protein-DNA interaction assays.

Replacing 40% of dietary animal fat with vegetable oil is associated with lower HDL cholesterol and higher cholesterol ester transfer protein in cynomolgus monkeys fed sufficient linoleic acid.

This study was designed to evaluate whether replacing approximately 40 g/100 g dietary animal fat with vegetable oil would improve plasma lipids and lipoproteins when diets contained prudent levels of total saturated acid (SFA), monounsaturated acid (MUFA) and PUFA. Using a cross-over design, male Cynomolgus monkeys (n = 10) were fed purified diets containing a mixture of fats. For the diet based on animal fat (AF-diet), approximately 85 g/100 g of the total fat was derived from pork fat, and approximately 40 g/100 g of this was replaced with olive oil for the vegetable oil-based diet (VO-diet). Thus, the fat content of the VO diet comprised 50% pork fat and 35% olive oil. The remaining 15% of the total fat (for both diets) was safflower oil. Both diets provided approximately 30% of total energy (%en) from fat, <10%en SFA and approximately 6-7%en from PUFA. Monkeys were rotated through two 7-wk feeding periods, during which time plasma lipids and lipoproteins were evaluated. Compared with the AF diet, plasma total cholesterol (TC) concentrations tended to be lower ( approximately 10%) after monkeys consumed the VO diet (3.18 +/- 0.83 vs. 3.52 +/- 0.93 mmol/L, P = 0.099), and this was due entirely to a significant 12% reduction in HDL cholesterol (1.53 +/- 0.41 vs. 1.73 +/- 0.47, mmol/L, P = 0.0009). Although plasma lipoprotein compositional analyses revealed no significant differences in either lipoprotein composition or the estimated particle diameters, the measurement of cholesterol ester transfer protein (CETP) using (3)H-cholesterol ester-labeled HDL revealed that the lower HDL cholesterol (HDL-C) when monkeys consumed the VO diet was associated with a 31% increase in transfer (P = 0.04). However, despite the changes in HDL-C, the TC/HDL-C ratio did not differ between monkeys after the two diet treatments. Regression analyses of data from these monkeys revealed a significant correlation between the dietary 16:0/18:2 ratio and plasma HDL-C. These data suggest that within the context of currently recommended prudent diets, it may be possible to manipulate HDL-C beneficially. Whether a similar effect would occur in humans warrants investigation.