Chromatin jets define the properties of cohesin-driven in vivo loop extrusion.

Complex genomes show intricate organization in three-dimensional (3D) nuclear space. Current models posit that cohesin extrudes loops to form self-interacting domains delimited by the DNA binding protein CTCF. Here, we describe and quantitatively characterize cohesin-propelled, jet-like chromatin contacts as landmarks of loop extrusion in quiescent mammalian lymphocytes. Experimental observations and polymer simulations indicate that narrow origins of loop extrusion favor jet formation. Unless constrained by CTCF, jets propagate symmetrically for 1-2 Mb, providing an estimate for the range of in vivo loop extrusion. Asymmetric CTCF binding deflects the angle of jet propagation as experimental evidence that cohesin-mediated loop extrusion can switch from bi- to unidirectional and is controlled independently in both directions. These data offer new insights into the physiological behavior of in vivo cohesin-mediated loop extrusion and further our understanding of the principles that underlie genome organization.

Conserved non-coding elements: developmental gene regulation meets genome organization.

Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks-dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.

A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks.

The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data containing quantitative and qualitative information about genome architecture. Most conventional approaches to genome-wide chromosome conformation capture data are limited to the analysis of pre-defined features, and may therefore miss important biological information. One constraint is that biologically important features can be masked by high levels of technical noise in the data. Here we introduce a replicate-based method for deep learning from chromatin conformation contact maps. Using a Siamese network configuration our approach learns to distinguish technical noise from biological variation and outperforms image similarity metrics across a range of biological systems. The features extracted from Hi-C maps after perturbation of cohesin and CTCF reflect the distinct biological functions of cohesin and CTCF in the formation of domains and boundaries, respectively. The learnt distance metrics are biologically meaningful, as they mirror the density of cohesin and CTCF binding. These properties make our method a powerful tool for the exploration of chromosome conformation capture data, such as Hi-C capture Hi-C, and Micro-C.

Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes.

DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P < 1 × 10-7). We connect obesity-associated methylation variations to transcriptomic changes at >500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions.

Training to Improve Pro-Agility Performance: A Systematic Review.

Effective directional change in sport is imperative to success in key game situations. Change of direction (COD) ability is underpinned by various athletic qualities which can be developed through specific and non-specific training methods. This review examined the effect of specific and non-specific training methods on pro-agility performance, by analysing the intervention type and resulting magnitude of training effects on pro-agility shuttle performance. A total of 20 studies were included for review. Data from 638 subjects and 29 intervention groups involving seven different training methods were extracted and analysed in relation to training method classification and primary outcome measures. Interventions involving sprint training, plyometric training, resistance training, and combined resistance, plyometric, and sprint training were found to produce statistically significant positive change on pro-agility performance per session (p < 0.05). Sprint training (0.108 ES), plyometric training (0.092 ES), resistance training (0.087 ES), and combined resistance, plyometric, and sprint training (0.078 ES) methods were found to have the highest per session training effect. While total time is the typical unit of measure for this test, different types of training may lead to preferential improvements in either acceleration, deceleration, or COD phases of the pro-agility shuttle. Specifically, resisted or inclined sprinting may develop the linear acceleration phases, unilateral resistance training may promote increased strength to overcome the imposed forces during the deceleration and COD phases, multiplanar plyometrics can help enhance stretch-shortening cycle capabilities across different force vectors, and a combination of two or more of these methods may enable simultaneous development of each of these qualities.

Differential improvements in lipid profiles and Framingham recurrent risk score in patients with and without diabetes mellitus undergoing long-term cardiac rehabilitation.

OBJECTIVE: To determine whether lipid profiles and recurrent coronary heart disease (CHD) risk could be modified in patients with and without diabetes mellitus undergoing long-term cardiac rehabilitation (CR). DESIGN: Retrospective analysis of patient case records. SETTING: Community-based phase 4 CR program. PARTICIPANTS: Patients without diabetes (n=154; 89% men; mean ± SD age, 59.6 ± 8.5y; body mass index [BMI], 27.0 ± 3.5 kg/m²) and patients with diabetes (n=20; 81% men; mean age, 63.0 ± 8.7y; BMI, 28.7 ± 3.3 kg/m²) who completed 15 months of CR. INTERVENTIONS: Exercise testing and training, risk profiling, and risk-factor education. MAIN OUTCOME MEASURES: Cardiometabolic risk factors and 2- to 4-year Framingham recurrent CHD risk scores were assessed. RESULTS: At follow up, a significant main effect for time was evident for decreased body mass and waist circumference and improved low-density lipoprotein cholesterol (LDL-C) level and submaximal cardiorespiratory fitness (all P<.05), showing the benefits of CR in both groups. However, a significant group-by-time interaction effect was evident for high-density lipoprotein cholesterol (HDL-C) level and total cholesterol (TC)/HDL-C ratio (both P<.05). TC/HDL-C ratio improved (5.0 ± 1.5 to 4.4 ± 1.3) in patients without diabetes, but showed no improvement in patients with diabetes (4.8 ± 1.6 v 4.9 ± 1.6). CONCLUSIONS: We showed that numerous anthropometric, submaximal fitness, and cardiometabolic risk variables (especially LDL-C level) improved significantly after long-term CR. However, some aspects of cardiometabolic risk (measures incorporating TC and HDL-C) improved significantly in only the nondiabetic group.

Human rotavirus type 2: cultivation in vitro.

A strain of type 2 human rotavirus (Wa) was grown to relatively high titer through 14 passages in primary cultures of African green monkey kidney (AGMK) cells. This passage series was initiated with virus that had been passaged 11 times serially in newborn gnotobiotic piglets. In contrast, virus present in the stool of patient Wa as well as virus from the first, second, or third passage in piglets could not be propagated successfully in African green monkey kidney cells. Prior to each passage in cell culture, the virus was treated with trypsin and the inoculated cultures were centrifuged at low speed. Cultivation of a type 2 human rotavirus should aid attempts to characterize this virus and to develop a means of immunoprophylaxis for a serious diarrheal disease of human infants.

Safety and effectiveness of amoxicillin in the treatment of inflammatory acne.

Acne is a common skin disease that predominantly affects teenagers and young adults. Systemic antibiotic therapy, including tetracyclines, macrolides, and trimethoprim-sulfamethoxazole, is indicated in moderate-to-severe inflammatory disease. However, in certain cases, these antibiotics and other commonly prescribed treatments including oral contraceptives, spironolactone, and isotretinoin may be prohibited, especially in cases of pregnancy and drug intolerance. In this retrospective study, we assessed the safety and efficacy of systemic amoxicillin, which has a favorable tolerability profile and compatibility with pregnancy in the treatment of inflammatory acne.

Capecitabine induced inflammation of actinic keratoses.

Capecitabine, an oral prodrug of 5-fluorouracil, is a systemic chemotherapeutic agent used in the treatment of metastatic breast and colon cancer. Patients undergoing capecitabine therapy may experience inflammation and irritation of existing actinic keratoses. Oncologists and dermatologists alike should be aware of this side effect.

Spironolactone for the treatment of acne in women, a retrospective study of 110 patients.

BACKGROUND: There is limited evidence on the safety and efficacy of spironolactone in the treatment of women with acne. Thus, for many dermatologists spironolactone remains an alternative rather than a mainstay treatment for female patients with acne. METHODS: An electronic medical records search tool was used to select data from a group of women who received spironolactone to treat acne and were evaluated with the comprehensive acne severity scale (CASS) before treatment and at all follow-up visits. Data points were collected for CASS scores at each follow-up visit, concurrent and previous treatments, and side effects. These data points were used to draw conclusions about the safety and efficacy of spironolactone in this patient population. RESULTS: There were 110 patients that met all eligibility requirements. Of these, 94 patients saw an improvement in their CASS score and 61 patients completely cleared their score to 0. There were 16 patients who did not improve and six who relapsed after initial improvement. The women saw an average improvement in their acne by 73.1% for the face, 75.9% for the chest, and 77.6% for the back. Fifty-one women experienced side effects, but only six found them bothersome enough to stop taking spironolactone. CONCLUSION: A majority of women in this study saw a dramatic improvement in their acne while treated with spironolactone. There were low rates of relapse or discontinuation of the medication. To further promote the use of spironolactone as a first-line systemic treatment for women with acne, there must be more prospective controlled trials.

Clonality of basal cell carcinoma--molecular analysis of an interesting case.

Tumor cells represent a single clone of cells that have undergone a series of mutations in genomic DNA. This process, known as clonal evolution, is a distinguishing feature of cancer. The human androgen receptor gene (HUMARA; GenBank) contains a highly polymorphic cytosine-adenine-guanine trinucleotide repeat that can be used to determine clonality by depicting X chromosome inactivation patterns. Random X chromosome inactivation is consistent with polyclonality; nonrandom X chromosome inactivation indicates a clonal population of cells. Basal cell carcinoma (BCC) demonstrates an atypical growth pattern in that it grows slowly, rarely metastasizes, and is rarely lethal. Whether this tumor results from the accumulation of mutations in a single cell with subsequent clonal expansion or reflects a polyclonal response by a group of cells to a growth stimulus is unknown. To provide further insight into the molecular events characterizing BCCs, we determined the clonal origin of five modular BCCs from a female patient by analyzing X chromosome inactivation patterns at the HUMARA locus. All tumors demonstrated a nonrandom pattern of X chromosome inactivation, consistent with monoclonal proliferation. These findings provide strong genetic evidence that sporadic BCCs develop by clonal evolution and support the contention that a series of mutations in a single cell is responsible for the altered growth state seen in these transformed epithelial cells.

Newer skin signs of systemic disease.

The skin is a well-known reflection of internal disease states. It provides the astute clinician with clues that lead to the diagnosis of systemic illness. While skin disease is rarely life-threatening, serious morbidity and mortality may be avoided by early recognition of subtle cutaneous signs signaling internal problems. The recent literature was reviewed to glean new findings that either added new associations to older syndromes or described completely new diseases. While entire books are written regarding the "Skin Signs of Internal Disease", this article focuses only on the newest of such findings.

Dermatologic formularies in the managed care setting.

Formularies and formulary systems are not a new concept in medical practice. In this country, they have been used in selected settings since the Revolutionary War and formal guidelines were published in 1933. They are in essence a collection of prescribing policies of physicians in a particular practice setting. Formularies are administered by a system in which medical staff members working through a pharmacy and therapeutics (P&T) committee recommend, evaluate, appraise, and select drugs to be included in the medication list. The system also develops, maintains, and enforces policies regarding how restrictive the process will be and what methods will be used to ensure compliance and verify that educational and quality standards are met.

On the importance of the clinician-educator. Dermatology fellowship for academic clinician teachers.

Within each academic dermatology department there usually exists one clinician who is viewed as the "gold standard" against which diagnostic and therapeutic acumen are measured. As a patient with a puzzling disorder is discussed at rounds, it is to this master that the final word falls, whose recommendation for treatment gets the nod; it is to his or her words that people remain quiet and listen intently. They are commonly also the leading teachers in the medical centers, passing on to succeeding generations the factual knowledge, spiced with bits of philosophy, ethics, and anecdote, that helps to ensure the development of dermatology residents into superb practitioners. They are often the ones most responsible for generating medical student interest in our specialty. Such individuals in our current lingo are "clinician-educators," the rock residents depend on to provide role models to emulate in the diagnosis, care, and treatment of our patients and to whom the community looks to for help in caring for their patients with the most difficult diagnoses.

Cutaneous group B streptococcal infection.

A 20-year-old man had a penile ulceration from which a pure, heavy growth of group B streptococcus was cultured. Cutaneous infection with this organism is unusual, and it is most often reported in postpartum women, diabetic patients, and immunocompromised individuals. Vaginal colonization with group B streptococcus is common. Since traumatic erosions or ulcerations of the penis are not uncommon, it is likely that a certain number of unrecognized infections of this type occur.

Acquired dyskeratotic leukoplakia.

A 36-year-old woman developed progressive dyskeratotic leukoplakia of the palate, lips, attached gingiva, and labial surfaces of the genitalia. On microscopic examination, clusters of dyskeratotic cells were found throughout the epithelium, except in the basal cell layer. The clinical and histologic differential diagnosis included candidiasis, oral hairy leukoplakia, lichen planus, condyloma acuminatum, Darier's disease, hereditary benign intraepithelial dyskeratosis, and white sponge nevus. Her clinical and histologic findings do not permit classification into any of these well-recognized entities.

Staphylococcus aureus infection as a complication of isotretinoin therapy.

Eighteen patients developed Staphylococcus aureus infection during or shortly after a five-month course of therapy with isotretinoin. Staphylococcus aureus was recovered both from lesions and from the anterior nares. In a prospective study, 4% of control patients treated with isotretinoin alone developed S aureus infection, while none who applied topical antibiotic to the anterior nares developed infection. Control patients had a 64% prevalence of anterior nares colonization with S aureus, compared with 18% in the topical antibiotic group.

Graft-v-host disease.

Increasing numbers of persons are undergoing bone marrow transplantation for severe aplastic anemia and hematologic malignant neoplasms, and the proportion of those surviving has increased. Graft-v-host disease (GVHD) will, therefore, be seen with increasing frequency in the future. Graft-v-host disease occurs when immunocompetent donor lymphoid cells recognize and attack antigens of the immunocompromised host. We describe the clinical and histologic appearance of the different types of GVHD and discuss treatment, pathogenesis, and prevention of this entity.

The role of the myofibroblast in Dupuytren's contracture.

A case report of Dupuytren's contracture illustrates the functional and light and electron microscopic characteristics of the myofibroblast. The myofibroblast is now associated with an increasing number of diseases, and is believed to be a morphologic and functional variant of the fibroblast, which shows changes typical of smooth-muscle cells. Its presence may be suspected by light microscopy, but its ultrastructure is characteristic. Its distinctive electron microscopic features are a fibrillar system in the cytoplasm similar to that of a smooth muscle, nuclear deformations indicative of contraction, and surface membrane differentiations that provide attachment to neighboring cells and stroma.