High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic ...regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies.
We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test).
We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence.
Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
Single molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of programming ...expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for computational image analysis expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation in the expression of Cd4 by T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected with Trypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.
Lanthanum (La)-based materials have been recognized as promising adsorbents for aqueous phosphate removal. The incorporation of base metals into La (oxy)hydroxides represents an effective strategy ...to improve adsorption performance. Understanding how base metals affect phosphate adsorption is challenging but essential for the development of effective materials for phosphorus control. Herein, we demonstrated a high-performance LaFe (oxy)hydroxide and studied its mechanisms on phosphate adsorption. The P K edge X-ray absorption near edge structure (XANES) analysis showed that PO4 3– was preferentially bonded with La, and the lattice oxygen in LaFe (oxy)hydroxide was demonstrated to be the active site. The O K edge XANES suggested that Fe optimized the electron structure of La, and Fe/La metal orbital hybridization resulted in the shift of oxygen p character to unoccupied states, facilitating phosphate adsorption. Furthermore, surface analysis showed that the pore size and volume were increased due to the introduction of Fe, which enabled efficient utilization of the active sites and fast adsorption kinetics. The dual effects of Fe in LaFe (oxy)hydroxide greatly enhance the effectiveness of La and represent a new strategy for the development of future phosphorus-control materials.
•A commercial lithium-ion battery was integrated into a commercial micro-PV system.•Two alternative battery coupling architectures were developed and demonstrated.•The passive coupling uses a ...parallel electrical connection of the battery.•The active coupling uses a controlled converter with MPP charging algorithm.•The resulting 300 Wp/555 Wh systems successfully performed day-night energy shifts.
A balcony photovoltaic (PV) system, also known as a micro-PV system, is a small PV system consisting of one or two solar modules with an output of 100–600 Wp and a corresponding inverter that uses standard plugs to feed the renewable energy into the house grid. In the present study we demonstrate the integration of a commercial lithium-ion battery into a commercial micro-PV system. We firstly show simulations over one year with one second time resolution which we use to assess the influence of battery and PV size on self-consumption, self-sufficiency and the annual cost savings. We then develop and operate experimental setups using two different architectures for integrating the battery into the micro-PV system. In the passive hybrid architecture, the battery is in parallel electrical connection to the PV module. In the active hybrid architecture, an additional DC-DC converter is used. Both architectures include measures to avoid maximum power point tracking of the battery by the module inverter. Resulting PV/battery/inverter systems with 300 Wp PV and 555 Wh battery were tested in continuous operation over three days under real solar irradiance conditions. Both architectures were able to maintain stable operation and demonstrate the shift of PV energy from the day into the night. System efficiencies were observed comparable to a reference system without battery. This study therefore demonstrates the feasibility of both active and passive coupling architectures.
Species can be defined as populations that are diagnosably distinct, reproductively isolated, cohesive, or exclusive groups of organisms. Boundaries between species in sympatry are maintained by ...intrinsic barriers to gene exchange; these boundaries may not be uniform in space, in time, or across the genome. Here, we explore the nature of the species boundary, defined as the phenotypes/genes/genome regions that remain differentiated in the face of potential hybridization and introgression. We emphasize that species boundaries are semipermeable, with permeability (gene exchange) being a function of genome region. The early evidence for semipermeable species boundaries came from data on differential introgression in hybrid zones. This "genic view" of species was common in the hybrid zone literature even when few molecular markers were available to characterize genome-wide patterns of variation. Now, molecular tools allow detailed characterization of differentiation between diverging lineages and patterns of variation across natural hybrid zones, but the questions being asked by evolutionary biologists have remained much the same. Recent data (from DNA sequences and genotypes) reinforce earlier conclusions about the semipermeable nature of most species boundaries. However, debate persists over the nature and extent of genome divergence that accompanies speciation.
Van der Waals (vdW) heterostructures formed by two-dimensional atomic crystals provide a powerful approach towards designer condensed matter systems. Incommensurate heterobilayers with small twisting ...and/or lattice mismatch lead to the interesting concept of moiré superlattices, where the atomic registry is locally indistinguishable from commensurate bilayers but has local-to-local variation over long range. Here we show that such moiré superlattices can lead to periodic modulation of local topological order in vdW heterobilayers formed by two massive Dirac materials. By tuning the vdW heterojunction from normal to the inverted type-II regime via an interlayer bias, the commensurate heterobilayer can become a topological insulator (TI), depending on the interlayer hybridization controlled by the atomic registry between the vdW layers. This results in a mosaic pattern of TI regions and normal insulator (NI) regions in moiré superlattices, where topologically protected helical modes exist at the TI/NI phase boundaries. By using symmetry-based k dotp and tight-binding models, we predict that this topological phenomenon can be present in inverted transition metal dichalcogenides heterobilayers. Our work points to a new means of realizing programmable and electrically switchable topological superstructures from two-dimensional arrays of TI nano-dots to one-dimensional arrays of TI nano-stripes.
Successful hybridisation and subsequent introgression lead to the transfer of genetic material across species boundaries. In this process, species relative abundance can play a significant role. If ...one species is less abundant than the other, its females will receive many heterospecific gametes, increasing mate-recognition errors and thus hybridisation rate. Moreover, first-generation hybrids will also more likely mate with the more abundant species, leading to asymmetric introgression. These predictions have important fundamental consequences, especially during biological invasions or when a rare species threatened by extinction is surrounded by individuals from a related species. However, experimental tests in nature of the importance of the relative abundance of each species on hybridisation dynamics remain scarce. We assess here the impact of species relative abundance on hybridisation dynamics among four species from the European white oak species complex. A total of 2107 oak trees were genotyped at 10 microsatellite markers and Bayesian clustering methods were used to identify reference trees of each species. We then used these reference trees to simulate purebred and hybrid genotypes to determine optimal threshold for genetic assignment. With this approach, we found widespread evidence of hybridisation between all studied oak species, with high occurrence of hybrids, varying from 11% to 31% according to stand and sampling strategies. This finding suggests that hybridisation is a common phenomenon that plays a significant role in evolution of this oak species complex. In addition, we demonstrate a strong impact of species abundance on both hybridisation rate and introgression directionality.
Hybridization is a key molecular process in biology and biotechnology, but so far there is no predictive model for accurately determining hybridization rate constants based on sequence information. ...Here, we report a weighted neighbour voting (WNV) prediction algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants. To construct this algorithm we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (36 nt sub-sequences of the CYCS and VEGF genes) at temperatures ranging from 28 to 55 °C. Automated feature selection and weighting optimization resulted in a final six-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 3 with ∼91% accuracy, based on leave-one-out cross-validation. Accurate prediction of hybridization kinetics allows the design of efficient probe sequences for genomics research.
Redox reactions of oxygen have been considered critical in controlling the electrochemical properties of lithium‐excessive layered‐oxide electrodes. However, conventional electrode materials without ...overlithiation remain the most practical. Typically, cationic redox reactions are believed to dominate the electrochemical processes in conventional electrodes. Herein, we show unambiguous evidence of reversible anionic redox reactions in LiNi1/3Co1/3Mn1/3O2. The typical involvement of oxygen through hybridization with transition metals is discussed, as well as the intrinsic oxygen redox process at high potentials, which is 75 % reversible during initial cycling and 63 % retained after 10 cycles. Our results clarify the reaction mechanism at high potentials in conventional layered electrodes involving both cationic and anionic reactions and indicate the potential of utilizing reversible oxygen redox reactions in conventional layered oxides for high‐capacity lithium‐ion batteries.
At high potentials, with high potential for the use of conventional layered oxides to create high‐capacity batteries, reversible anionic redox activity in LiNi1/3Co1/3Mn1/3O2 was proved experimentally by state‐of‐the‐art characterization techniques. The cationic and anionic redox activities of LiNi1/3Co1/3Mn1/3O2 were quantified by considering transition‐metal–oxygen hybridization separately from intrinsic lattice O redox reactions at high potentials (see picture).
Background
Prior studies have shown the presence of immunohistochemical staining for the SARS‐CoV‐2 spike protein (SP) in endothelial cells and eccrine epithelium of acral perniosis classified as ...“COVID toes.” Yet, other studies have been unable to detect SARS‐CoV‐2 RNA in skin biopsies of “COVID toes” by reverse‐transcriptase polymerase chain reaction testing.
Objective
In order to address these apparently conflicting findings, we compared detection of SARS‐CoV‐2 SP, through RNA in situ hybridization (ISH) vs immunohistochemistry (IHC), in skin biopsies of acral perniotic lesions presenting during the COVID‐19 pandemic.
Results
Three of six cases showed positive immunohistochemical labeling of endothelial cells, with one of three cases with sufficient depth also having labeling of eccrine glands, using an anti‐SP SARS‐CoV‐2 antibody. These three cases positive with IHC were negative for SP by RNA ISH.
Conclusion
While the gold standard for detection of SARS‐CoV‐2 in tissue sections has yet to be determined, the detection of SARS‐CoV‐2 SP alone without spike RNA suggests that cleaved SP may be present in cutaneous endothelial cells and eccrine epithelium, providing a potential pathogenetic mechanism of COVID‐19 endotheliitis.
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