Accessible Region Conformation Capture (ARC-C) gives high resolution insights into genome architecture and regulation

Nuclear organization and chromatin interactions are important for genome function, yet determining chromatin connections at high-resolution remains a major challenge. To address this, we developed Accessible Region Conformation Capture (ARC-C), which profiles interactions between regulatory elements genome-wide without a capture step. Applied to C. elegans, we identify ~15,000 significant interactions between regulatory elements at 500bp resolution. Of 105 TFs or chromatin regulators tested, we find that the binding sites of 60 are enriched for interacting with each other, making them candidates for mediating interactions. These include cohesin and condensin II. Applying ARC-C to a mutant of transcription factor BLMP-1 detected changes in interactions between its targets. ARC-C simultaneously profiles domain level architecture, and we observe that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) which interact with A/B (active/inactive) compartment-like structure. Furthermore, we discovered that inactive compartment interactions are dependent on H3K9 methylation. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.

Mechanical And Thermodynamic Stabilities, Half-Metallic Property of Co2CrAl Heuslerene: A DFT Study

In the present study, the physical properties of the ground state in bulk and Co2CrAl Heuslerene compound are investigated by density functional theory (DFT). The effects of exchange-correlation potential on the calculations have been also investigated by GGA, GGA+U, and GGA+U+mBJ approximately. Here, three graphene-like structures with the thickness of about 8 Bohr have been labeled as α, β, and ϒ phases. The results demonstrate the mechanical stability of bulk Co2CrAl since it passes the elastic stability test. Having proved the static stability of the bulk and three Heuslerene shapes of Co2CrAl, it is essential to study dynamic stability as well. The accessible region in the thermodynamic phase diagrams confirms the thermodynamic stability of bulk Co2CrAl and all 2D phases of the compound. According to our electronic calculations, the bulk phase of Co2CrAl is a half-metal whose values of magnetic moment and spin polarization is 3 μB and 100% at the Fermi level, respectively. Besides, α and ϒ phases show the metal behavior for both spin directions in all imposed approximations. Finally, β phase exhibits different magnetic properties for different approximations. From 3eV to 2eV, GGA and GGA+U reveal the magnetic anisotropic and isotropic nature. Besides, an extremely anisotropic nature is observed at the Fermi level by GGA+U+mbJ.

The anomalies and criticality of liquid water

The origin of water’s anomalies has been a matter of long-standing debate. A two-state model, dating back to Röntgen, relies on the dynamical coexistence of two types of local structures—locally favored tetrahedral structure (LFTS) and disordered normal-liquid structure (DNLS)—in liquid water. Phenomenologically, this model not only explains water’s thermodynamic anomalies but also can rationalize the existence of a liquid–liquid critical point (LLCP) if there is a cooperative formation of LFTS. We recently found direct evidence for the coexistence of LFTS and DNLS in the experimental structure factor of liquid water. However, the existence of the LLCP and its impact on water’s properties has remained elusive, leaving the origin of water’s anomalies unclear. Here we propose a unique strategy to locate the LLCP of liquid water. First, we make a comprehensive analysis of a large set of experimental structural, thermodynamic, and dynamic data based on our hierarchical two-state model. This model predicts that the two thermodynamic and dynamical fluctuation maxima lines should cross at the LLCP if it exists, which we confirm by hundred-microsecond simulations for model waters. Based on recent experimental results of the compressibility and diffusivity measurements in the no man’s land, we reveal that the two lines cross around 184 K and 173 MPa for real water, suggesting the presence of the LLCP around there. Nevertheless, we find that the criticality is almost negligible in the experimentally accessible region of liquid water because it is too far from the LLCP. Our findings would provide a clue to settle the long-standing debate.

Jaringan Transportasi dan Pengembangan Destinasi Pariwisata di Kota Cirebon

Tourism development needs a good accessibility to support regional connectivity. This study aims to analyse the role of transportation network for tourism destination development in the Cirebon City. This research uses GIS-based network spatial analysis to obtain road network system components in each sub-district, thus transportation indices value which includes alpha index, beta index, Gama index, eta index and road density network. The results shows The Cirebon City has low-medium connectivity and accessibility with alpha index 0.1323, beta index 1.2608, Gama index, 0.4221, eta index 0.1576 and road network density reach 20.869 km / km2. On sub-district level, Pekalipan is the most accessible region based on all parameters of road network and create a suitable place for tourism development in the Cirebon City.

Prospects for the study of event-by-event fluctuations at MPD/NICA project

One of the main physics goals of the Multi Purpose Detector (MPD) is to investigate hot and dense baryonic matter in heavy ion collisions at NICA energies to search for the possible critical end point (CEP). Since the location of CEP is not clear the entire accessible region of the QCD phase diagram needs to be explored by scanning the full range of available beam energies. In case of CEP existence it can be observed by abnormal fluctuations of various quantities such as net-proton multiplicity. This task requires excellent particle identification (PID) capability over as large as possible phase space volume. The identification of charged hadrons is achieved at the momenta of 0:1 – 3 GeV/c. The results of hadron identification and preliminary possibility estimation of the study of event-by-event fluctuations at MPD will be presented.

High-resolution mapping of regulatory element interactions and genome architecture using ARC-C

Interactions between cis-regulatory elements such as promoters and enhancers are important for transcription but global identification of these interactions remains a major challenge. Leveraging the chromatin accessiblity of regulatory elements, we developed ARC-C (accessible region chromosome conformation capture), which profiles chromatin regulatory interactions genome-wide at high resolution. Applying ARC-C to C. elegans, we identify ~15,000 significant interactions at 500bp resolution. Regions bound by transcription factors and chromatin regulators such as cohesin and condensin II are enriched for interactions, and we use ARC-C to show that the BLMP-1 transcription factor mediates interactions between its targets. Investigating domain level architecture, we find that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) and that these domains interact to form A/B (active/inactive) compartment structure. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.

An examination of the Devonian fishes of Michigan

We surveyed the taxa, ecosystems, and localities of the Devonian fishes of Michigan to provide a framework for renewed study, to learn about the diversity and number of these fishes, and to investigate their connection to other North American faunas. Nineteen genera of fishes have been found in the Middle and Late Devonian deposits of Michigan, of which thirteen are ‘placoderms’ represented by material ranging from articulated head shields to ichthyoliths. As expected from the marine nature of these deposits, ‘placoderms’ are overwhelmingly arthrodire in nature, but two genera of ptyctodonts have been reported along with less common petalichthyid material. The remaining fish fauna consists of fin-spines attributed to ‘acanthodians’, two genera of potential crown chondrichthyans, an isolated dipnoan, and onychodont teeth/jaw material. There was an apparent drop in fish diversity and fossil abundance between Middle and Late Devonian sediments. This pattern may be attributed to a paucity of Late Devonian sites, along with a relative lack of recent collection efforts at existing outcrops. It may also be due to a shift towards open water pelagic environments at Late Devonian localities, as opposed to the nearshore reef fauna preserved in the more numerous Middle Devonian localities. The Middle Devonian vertebrate fauna in Michigan shows strong connections with same-age assemblages from Ohio and New York. Finally, we document the presence of partially articulated vertebrate remains associated with benthic invertebrates, an uncommon occurrence in Devonian strata outside of North America. We anticipate this new survey will guide future field work efforts in an undersampled yet highly accessible region that preserves an abundance of fishes from a critical interval in marine vertebrate evolution.

NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

ABSTRACTFaithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription preinitiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results establish NF-Y as a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation.

On the asymptotic analysis of the JWKB method via change of dependent variable in the first-order Bessel’s equation

The first-order Jeffreys–Wentzel–Kramers–Brillouin method (called (JWKB)1) is a conventional semi-classical approximation method used in quantum mechanical systems for accurate solutions. It is known to give accurate energy and wave-function in the classically accessible region of the related quantum mechanical system defined by Schroedinger’s equation whereas the solutions in the classically inaccessible region require special treatment, conventionally known as the asymptotic matching rules. In this work, (JWKB)1 solution of the Bessel differential equation of the first order (called (BDE)1), chosen as a mathematical model, is studied by being transformed into the normal form via the change of dependent variable. General JWKB solution of the initial value problem where appropriately chosen initial values are applied is studied in both normal and standard form representations to be analyzed by the generalized JWKB asymptotic matching rules regarding the Sij matrix elements defined in the literature. Consequently, regions requiring first-order and zeroth-order JWKB approximations are determined successfully.

Estimation of a Moving Heat Source due to a Micromilling Process Using the Modified TFBGF Technique

Moving heat sources are present in numerous engineering problems as welding and machining processes, heat treatment, or biological heating. In all these cases, the heat input identification represents an important factor in the optimization of the process. The aim of this study is to investigate the heat flux delivered to a workpiece during a micromilling process. The temperature measurements were obtained using a thermocouple at an accessible region of the workpiece surface while micromilling a small channel. The analytical solution is calculated from a 3D transient heat conduction model with a moving heat source, called direct problem. The estimation of the moving heat source uses the Transfer Function Based on Green’s Function Method. This method is based on Green’s function and the equivalence between thermal and dynamic systems. The technique is simple without iterative processes and extremely fast. From the temperature on accessible regions it is possible to estimate the heat flux by an inverse procedure of the Fast Fourier Transform. A test of micromilling of 6365 aluminium alloy was made and the heat delivered to the workpiece was estimated. The estimation of the heat without use of optimization technique is the great advantage of the technique proposed.