GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data

Genome Architecture Mapping (GAM) is a recently developed method for mapping chromatin interactions genome-wide. GAM is based on sequencing genomic DNA extracted from thin cryosections of cell nuclei. As a new approach, GAM datasets require specialized analytical tools and approaches. Here we present GAMtools, a pipeline for analysing GAM datasets. GAMtools covers the automated mapping of raw next-generation sequencing data generated by GAM, detection of genomic regions present in each nuclear slice, calculation of quality control metrics, generation of inferred proximity matrices, plotting of heatmaps and detection of genomic features for which chromatin interactions are enriched/depleted

Self-Deploying Trusses Containing Shape-Memory Polymers

Composite truss structures are being developed that can be compacted for stowage and later deploy themselves to full size and shape. In the target applications, these smart structures will precisely self-deploy and support a large, lightweight space-based antenna. Self-deploying trusses offer a simple, light, and affordable alternative to articulated mechanisms or inflatable structures. The trusses may also be useful in such terrestrial applications as variable-geometry aircraft components or shelters that can be compacted, transported, and deployed quickly in hostile environments. The truss technology uses high-performance shape-memory-polymer (SMP) thermoset resin reinforced with fibers to form a helical composite structure. At normal operating temperatures, the truss material has the structural properties of a conventional composite. This enables truss designs with required torsion, bending, and compression stiffness. However, when heated to its designed glass transition temperature (Tg), the SMP matrix acquires the flexibility of an elastomer. In this state, the truss can be compressed telescopically to a configuration encompassing a fraction of its original volume. When cooled below Tg, the SMP reverts to a rigid state and holds the truss in the stowed configuration without external constraint. Heating the materials above Tg activates truss deployment as the composite material releases strain energy, driving the truss to its original memorized configuration without the need for further actuation. Laboratory prototype trusses have demonstrated repeatable self-deployment cycles following linear compaction exceeding an 11:1 ratio (see figure)

Flashing LEDs for microalgal production

Flashing lights are next-generation tools to mitigate light attenuation and increase the photosynthetic efficiency of microalgal cultivation systems illuminated by light-emitting diodes (LEDs). Optimal flashing light conditions depend on the reaction kinetics and properties of the linear electron transfer chain, energy dissipation, and storage mechanisms of a phototroph. In particular, extremely short and intense light flashes potentially mitigate light attenuation in photobioreactors without impairing photosynthesis. Intelligently controlling flashing light units and selecting electronic components can maximize light emission and energy efficiency. We discuss the biological, physical, and technical properties of flashing lights for algal production. We combine recent findings about photosynthetic pathways, self-shading in photobioreactors, and developments in solid-state technology towards the biotechnological application of LEDs to microalgal production.Foundation for Science and Technology (FCT, Portugal) [CCMAR/Multi/04326/2013]Nord UniversityNordland County Government (project Bioteknologi en framtidsrettet naering)INTERREG V-A Espana-Portugal project [0055 ALGARED + 5E]Portuguese Foundation for Science and Technology [SFRH/BD/105541/2014, SFRH/BD/115325/2016]info:eu-repo/semantics/publishedVersio

A Randomized Depression Prevention Trial Comparing Interpersonal Psychotherapy—Adolescent Skills Training To Group Counseling In Schools

Given the rise in depression disorders in adolescence, it is important to develop and study depression prevention programs for this age group. The current study examined the efficacy of Interpersonal Psychotherapy-Adolescent Skills Training (IPT-AST), a group prevention program for adolescent depression, in comparison to group programs that are typically delivered in school settings. In this indicated prevention trial, 186 adolescents with elevated depression symptoms were randomized to receive IPT-AST delivered by research staff or group counseling (GC) delivered by school counselors. Hierarchical linear modeling examined differences in rates of change in depressive symptoms and overall functioning from baseline to the 6-month follow-up assessment. Cox regression compared rates of depression diagnoses. Adolescents in IPT-AST showed significantly greater improvements in self-reported depressive symptoms and evaluator-rated overall functioning than GC adolescents from baseline to the 6-month follow-up. However, there were no significant differences between the two conditions in onset of depression diagnoses. Although both intervention conditions demonstrated significant improvements in depressive symptoms and overall functioning, results indicate that IPT-AST has modest benefits over groups run by school counselors which were matched on frequency and duration of sessions. In particular, IPT-AST outperformed GC in reduction of depressive symptoms and improvements in overall functioning. These findings point to the clinical utility of this depression prevention program, at least in the short-term. Additional follow-up is needed to determine the long-term effects of IPT-AST, relative to GC, particularly in preventing depression onset

High-resolution profiling of protein occupancy on polyadenylated RNA transcripts

A key prerequisite to understand how gene regulatory processes are controlled by the interplay of RNA-binding proteins (RBPs) and ribonucleoprotein complexes with RNAs is the generation of comprehensive high-resolution maps of protein-RNA interactions. Recent advances in next-generation sequencing technology accelerated the development of various crosslinking and immunoprecipitation (CLIP) approaches to broadly identify RNA regions contacted by RNA-binding proteins. However these methods only consider single RNA-binding proteins and their contact sites, irrespective of the overall cis-regulatory sequence space contacted by other RNA interacting factors. Here we describe the application of protein occupancy profiling, a novel approach that globally displays the RNA contact sites of the poly(A)+ RNA-bound proteome. Protein occupancy profiling enables the generation of transcriptome-wide maps of protein-RNA interactions on polyadenylated transcripts and narrows the sequence search space for transcript regions involved in cis-regulation of gene expression in response to internal or external stimuli, altered cellular programs or disease

A gradient-forming MipZ protein mediating the control of cell division in the magnetotactic bacterium Magnetospirillum gryphiswaldense

Cell division needs to be tightly regulated and closely coordinated with other cellular processes to ensure the generation of fully viable offspring. Here, we investigate division site placement by the cell division regulator MipZ in the alphaproteobacterium Magnetospirillum gryphiswaldense, a species that forms linear chains of magnetosomes to navigate within the geomagnetic field. We show that M. gryphiswaldense contains two MipZ homologs, termed MipZ1 and MipZ2. MipZ2 localizes to the division site, but its absence does not cause any obvious phenotype. MipZ1, by contrast, forms a dynamic bipolar gradient, and its deletion or overproduction cause cell filamentation, suggesting an important role in cell division. The monomeric form of MipZ1 interacts with the chromosome partitioning protein ParB, whereas its ATP-dependent dimeric form shows non-specific DNA-binding activity. Notably, both the dimeric and, to a lesser extent, the monomeric form inhibit FtsZ polymerization in vitro. MipZ1 thus represents a canonical gradient-forming MipZ homolog that critically contributes to the spatiotemporal control of FtsZ ring formation. Collectively, our findings add to the view that the regulatory role of MipZ proteins in cell division is conserved among many alphaproteobacteria. However, their number and biochemical properties may have adapted to the specific needs of the host organism

The association among diet, dietary fiber, and bowel preparation at colonoscopy

BACKGROUND AND AIMS: Pre-colonoscopy dietary restrictions vary widely and lack evidence-based guidance. We investigated whether fiber and various other foods/macronutrients consumed during the 3 days before colonoscopy are associated with bowel preparation quality. METHODS: This was a prospective observational study among patients scheduled for outpatient colonoscopy. Patients received instructions including split-dose polyethylene glycol, avoidance of vegetables/beans 2 days before colonoscopy, and a clear liquid diet the day before colonoscopy. Two 24-hour dietary recall interviews and 1 patient-recorded food log measured dietary intake on the 3 days before colonoscopy. The Nutrition Data System for Research was used to estimate dietary exposures. Our primary outcome was the quality of bowel preparation measured by the Boston Bowel Preparation Scale (BBPS). RESULTS: We enrolled 201 patients from November 2015 to September 2016 with complete data for 168. The mean age was 59 years (standard deviation, 7 years), and 90% of colonoscopies were conducted for screening/surveillance. Only 17% and 77% of patients complied with diet restrictions 2 and 1 day(s) before colonoscopy, respectively. We found no association between foods consumed 2 and 3 days before colonoscopy and BBPS scores. However, BPPS was positively associated with intake of gelatin, and inversely associated with intake of red meat, poultry, and vegetables on the day before colonoscopy. CONCLUSIONS: Our findings support recent guidelines encouraging unrestricted diets >1 day before colonoscopy if using a split-dose bowel regimen. Furthermore, we found no evidence to restrict dietary fiber 1 day before colonoscopy. We also found evidence to promote consumption of gelatin and avoidance of red meat, poultry, and vegetables 1 day before colonoscopy.Dr Jacobson has acted as a consultant for MOTUS GI and Remedy Partners. All other authors disclosed no financial relationships relevant to this publication. Supported by NIH/NIDDK R21DK105476. (R21DK105476 - NIH/NIDDK)Accepted manuscrip

Ultrafast nonequilibrium evolution of excitonic modes in semiconductors

We study the time evolution of excitonic states after photoexcitation in the one-dimensional spinless extended Falicov-Kimball model. Several numerical methods are employed and benchmarked against each other: time-dependent mean-field simulations, the second-Born approximation (2BA) within the Kadanoff-Baym formalism, the generalized Kadanoff-Baym ansatz (GKBA) implemented with the 2BA, and the infinite time-evolving block decimation (iTEBD) method. It is found that the GKBA gives the best agreement with iTEBD and captures the relevant physics. Excitations to the particle-hole continuum and resonant excitations of the equilibrium exciton result in a qualitatively different dynamics. In the former case, the exciton binding energy remains positive and the frequency of the corresponding coherent oscillations is smaller than the band gap. On the other hand, resonant excitations trigger a collective mode whose frequency is larger than the band gap. We discuss the origin of these different behaviors by evaluating the nonequilibrium susceptibility using the nonthermal distribution and a random phase approximation. The peculiar mode with frequency larger than the band gap is associated with a partial population inversion with a sharp energy cutoff. We also discuss the effects of the cooling by a phonon bath. We demonstrate the real-time development of coherence in the polarization, which indicates excitonic condensation out of equilibrium

Dynamics of Srf, p300 and histone modifications during cardiac maturation in mouse

The adaptation of the cellular network to functional changes, timing and patterning of gene expression is regulated by binding of transcription factors to gene regulatory elements, which in turn depends on co-occurring histone modifications. These two layers influence each other, enabling a further level of regulatory fine-tuning. We analyzed the interdependencies between histone 3 acetylation, histone 3 lysine 4 dimethylation, the transcription factor Srf and the histone acetyltransferase p300 in an in vivo model using chromatin immunoprecipitation in a time-series during cardiac maturation in mouse. We found a strong correlation between the presence of the two histone modifications and binding of Srf and p300. Using linear modeling techniques we could show that each factor contributes individually as well as conjointly to histone 3 acetylation and gene expression, probably aided by accompanying histone 3 lysine 4 dimethylation. We further demonstrate that changes in gene expression during cardiac maturation are attended by changes of the analyzed regulators while revealing a high variability of combinatorial regulation. Finally, we propose a model of Srf-driven gene expression in cardiomyocytes