An ancestral genomic sequence that serves as a nucleation site for de novo gene birth

A short non-coding sequence present between the gamma-glutamyltransferase 1 (GGT1) and gamma-glutamyltransferase 5 (GGT5) genes, termed a spacer sequence has been detected in the genomes of Mus musculus, the house mouse and in Philippine tarsier, a primitive ancestral primate. It is highly conserved during primate evolution with certain sequences being totally invariant from mouse to humans. Evidence is presented to show this intergenic sequence serves as a nucleation site for the initiation of diverse genes. We also outline the birth of the human lincRNA gene BCRP3 (BCR activator of RhoGEF and GTPase 3 pseudogene) during primate evolution. The gene developmental process involves sequence initiation, addition of a complex of tandem transposable elements and addition of a segment of another gene. The sequence, initially formed in the Old World Monkeys such as the Rhesus monkey (Macaca mulatta) and the baboon (Papio anubis), develops into different primate genes before evolving into the human BCRP3 gene; it appears to also include trial and error during sequence/gene formation. The protein gene, GGT5 may have also formed by spacer sequence initiation in an ancient ancestor such as zebrafish, but spacer and GGT5 gene sequence drift during evolution produced a divergence that precludes further assessment.

Quantitative Isothermal Amplification on Paper Membranes using Amplification Nucleation Site Analysis

Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3,000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.

Effect of Dissolution of η′ Precipitates on Mechanical Properties of A7075-T6 Alloy

The effects of dissolution of the η′ phase by solution treatment on the mechanical properties of A7075-T6 alloy were investigated. Immediately after solution treatment of the T6 sheet at 450 oC or higher, elongation significantly increased and dissolution of the η′ phase occurred. η′ is the main hardening phase. After natural-aging, GPI, which is coherent with the aluminum matrix, was formed and strength increased. When bake hardening after natural-aging was performed, the yield strength slightly increased due to partial dissolution of the GPI and re-precipitation of the η′ phase. In contrast, after solution treatment at 400 oC, there was less elongation increase due to the precipitation of the coarse η phase at grain boundaries and low dissolution of the η′ phase. In addition, when bake hardening after natural-aging was performed, the yield strength decreased due to insufficient GPI, which is the nucleation site of the η′ phase. To promote reprecipitation of the η′ phase, the solution treatment temperature was set to a level that would increase solubility. As a result, the yield strength was significantly increased through re-precipitation of a large number of fine and uniform η′ phase. In addition, to increase the effect of dissolution, a pre-aging treatment was introduced and the bake hardenability can be improved after dissolution.

Mechanism of ice nucleation in liquid water on alkali feldspars

Crystallization of supercooled liquid water in most natural environments starts with heterogeneous nucleation of ice induced by a nucleation site. Mineral surfaces, which form the majority of aqueous interfaces in...

Sequences of seismic and aseismic slip on bimaterial faults show dominant rupture asymmetry and potential for elevated seismic hazard

We perform numerical simulations of sequences of earthquake and aseismic slip on planar rate and state faults separating dissimilar material within the 2-D plane strain approximation. We resolve all stages of the earthquake cycle from aseismic slip to fast ruptures while incorporating full inertia effects during seismic event propagation. We show that bimaterial coupling results in favorable nucleation site and subsequent asymmetric rupture propagation. We demonstrate that increasing the material contrast enhances this asymmetry leading to higher slip rates and normal stress drops in the preferred rupture propagation direction. The normal stress drop, induced by the bimaterial effect, leads to strong dynamic weakening of the fault and may destabilize the creeping region on a heterogeneous rate and state fault, resulting in extended rupture propagation. Such rupture penetration into creeping patches may lead to more frequent opening of earthquake gates, causing increased seismic hazard. Furthermore, bimaterial coupling may lead to irregular seismicity pattern in terms of event length, peak slip rates,and hypocenter location, depending on the properties of the creeping patches bordering the seismogenically active part of the fault . Our results highlight robust characteristics of bimaterial interfaces that persist over long sequence of events and suggest the need for further exploration of the role of material contrast in earthquake physics and models of seismic hazard.

CNN-based visual analysis to study local boiling characteristics

Visual analysis allows an estimate of different local boiling characteristics including bubble growth rate, departure diameters and frequencies of nucleation, nucleation site density and evolution of bubbles and dry spots in time. At the same time, visual determination of the presented characteristics in case of big amounts of data requires the development of the appropriate software which will allow not only determination of bubble location, but also an estimate of their sizes based on high-speed video. The presented problem can be solved by using the instance segmentation approach based on a convolutional neural network. In the presented work Mask R-CNN network architecture was used for estimation of the local boiling characteristics.

Substantial spatial variation in glacial erosion rates in the Dronning Maud Land Mountains, East Antarctica

The coast-parallel Dronning Maud Land (DML) mountains represent a key nucleation site for the protracted glaciation of Antarctica. Their evolution is therefore of special interest for understanding the formation and development of the Antarctic ice sheet. Extensive glacial erosion has clearly altered the landscape over the past 34 Myr. Yet, the total erosion still remains to be properly constrained. Here, we investigate the power of low-temperature thermochronology in quantifying glacial erosion in-situ. Our data document the differential erosion along the DML escarpment, with up to c. 1.5 and 2.4 km of erosion in western and central DML, respectively. Substantial erosion at the escarpment foothills, and limited erosion at high elevations and close to drainage divides, is consistent with an escarpment retreat model. Such differential erosion suggests major alterations of the landscape during 34 Myr of glaciation and should be implemented in future ice sheet models.

A review on the potential of filamentous fungi for microbial self-healing of concrete

Concrete is the most used construction material worldwide due to its abundant availability and inherent ease of manufacturing and application. However, the material bears several drawbacks such as the high susceptibility for crack formation, leading to reinforcement corrosion and structural degradation. Extensive research has therefore been performed on the use of microorganisms for biologically mediated self-healing of concrete by means of CaCO3 precipitation. Recently, filamentous fungi have been recognized as high-potential microorganisms for this application as their hyphae grow in an interwoven three-dimensional network which serves as nucleation site for CaCO3 precipitation to heal the crack. This potential is corroborated by the current state of the art on fungi-mediated self-healing concrete, which is not yet extensive but valuable to direct further research. In this review, we aim to broaden the perspectives on the use of fungi for concrete self-healing applications by first summarizing the major progress made in the field of microbial self-healing of concrete and then discussing pioneering work that has been done with fungi. Starting from insights and hypotheses on the types and principles of biomineralization that occur during microbial self-healing, novel potentially promising candidate species are proposed based on their abilities to promote CaCO3 formation or to survive in extreme conditions that are relevant for concrete. Additionally, an overview will be provided on the challenges, knowledge gaps and future perspectives in the field of fungi-mediated self-healing concrete.

Bubble dynamics and mechanistic boiling heat transfer prediction on a scored copper surface

In this study, pool boiling heat transfer of de-ionized water was experimentally studied on a scored copper surface at a heat-flux range of 0 - 60 W/cm2. Bubble dynamics in an isolated bubble region were carefully investigated, including bubble departure diameters, bubble departure frequencies, and active nucleation site densities. The bubble dynamics were compared with available models, indicating the suitable models regarding the present experimental results. Then, based on the bubble dynamics, a mechanistic heat transfer model, developed in our previous studies, was employed to predict the present boiling curve. In the mechanistic model, heat fluxes from natural convection, transient heat conduction, and microlayer evaporation were incorporated.