Locus-Specific Decoupling of Base Composition Evolution at Synonymous Sites and Introns along the Drosophila melanogaster and Drosophila sechellia Lineages

Selection is thought to be partially responsible for patterns of molecular evolution at synonymous sites within numerous Drosophila species. Recently, “per-site” and likelihood methods have been developed to detect loci for which positive selection is a major component of synonymous site evolution. An underlying assumption of these methods, however, is a homogeneous mutation process. To address this potential shortcoming, we perform a complementary analysis making gene-by-gene comparisons of paired synonymous site and intron substitution rates toward and away from the nucleotides G and C because preferred codons are G or C ending in Drosophila. This comparison may reduce both the false-positive rate (due to broadscale heterogeneity in mutation) and false-negative rate (due to lack of power comparing small numbers of sites) of the per-site and likelihood methods. We detect loci with patterns of evolution suggestive of synonymous site selection pressures predominately favoring unpreferred and preferred codons along the Drosophila melanogaster and Drosophila sechellia lineages, respectively. Intron selection pressures do not appear sufficient to explain all these results as the magnitude of the difference in synonymous and intron evolution is dependent on recombination environment and chromosomal location in a direction supporting the hypothesis of selectively driven synonymous fixations. This comparison identifies 101 loci with an apparent switch in codon preference between D. melanogaster and D. sechellia, a pattern previously only observed at the Notch locus

Employing an open-source tool to assess astrocyte tridimensional structure

Astrocytes display important features that allow them to maintain a close dialog with neurons, ultimately impacting brain function. The complex morphological structure of astrocytes is crucial to the role of astrocytes in brain networks. Therefore, assessing morphologic features of astrocytes will help provide insights into their physiological relevance in healthy and pathological conditions. Currently available tools that allow the tridimensional reconstruction of astrocytes present a number of disadvantages, including the need for advanced computational skills and powerful hardware, and are either time-consuming or costly. In this study, we optimized and validated the FIJI-ImageJ, Simple Neurite Tracer (SNT) plugin, an open-source software that aids in the reconstruction of GFAP-stained structure of astrocytes. We describe (1) the loading of confocal microscopy Z-stacks, (2) the selection criteria, (3) the reconstruction process, and (4) the post-reconstruction analysis of morphological features (process length, number, thickness, and arbor complexity). SNT allows the quantification of astrocyte morphometric parameters in a simple, efficient, and semi-automated manner. While SNT is simple to learn, and does not require advanced computational skills, it provides reproducible results, in different brain regions or pathophysiological states.The authors acknowledge funding from national funds through the FCT—Foundation for Science and Technology—project (PTDC/SAU-NSC/118194/2010) to G.T., V.M.S., S.G.G. and J.F.O., and fellowships (SFRH/BD/89714/2012 to V.M.S., SFRH/BPD/97281/2013 to J.F.O., SFRH/BD/101298/2014 to S.G.G., PD/BD/114120/2015 to S.P.N, and PD/BD/127822/2016 to G.T.); Marie Curie Fellowship FP7-PEOPLE-2010-IEF 273936 and BIAL Foundation Grants and 207/14 to J.F.O.; QREN and FEDER funds through Operational program for competitiveness factors—COMPETE, “ON.2 SR&TD Integrated Program—NORTE-07-0124-FEDER-000021”; National and European funds through FCT, and FEDER through COMPETE (PEst-C/SAU/LA0026/2011 and FCOMP-01-0124-FEDER-022724; PEst-C/SAU/LA0026/2013 and FCOMP-01-0124-FEDER-037298, respectively)info:eu-repo/semantics/publishedVersio

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Chlorine in PbCl₂‑Derived Hybrid-Perovskite Solar Absorbers

Chlorine in PbCl₂‑Derived Hybrid-Perovskite Solar Absorber

Radiative Thermal Annealing/in Situ X‑ray Diffraction Study of Methylammonium Lead Triiodide: Effect of Antisolvent, Humidity, Annealing Temperature Profile, and Film Substrates

Organic–inorganic hybrid halide perovskites are one of the most promising emerging photovoltaic materials due to their high efficiency and potentially low processing cost. Here, we present a well-controlled, manufacturing relevant annealing method, radiative thermal annealing, for the methylammonium lead triiodide (MAPbI₃) films formed by a solvent engineering process, with dimethylformamide (DMF) and dimethyl sulfoxide (DMSO) as solvent and diethyl ether as the antisolvent. Radiative thermal annealing can produce high quality perovskite films, evidenced by high efficiency solar cell devices (∼18% power conversion efficiency), in a shorter time than the widely used hot plate annealing. Using in situ X-ray diffraction during the radiative annealing, we show that the role of the antisolvent is not to form an important intermediate compound (a PbI₂-MAI-DMSO complex) by washing of the main solvent (DMF), but to achieve a pinhole free, uniform film of MAPbI₃ with minimal intermediate compound. Importantly, we show that having a PbI₂-MAI-DMSO intermediate compound does not guarantee a high quality (pinhole free) perovskite film. We directly show that humidity induces MAPbI₃ to decompose into PbI₂ more rapidly and, as such, negatively impacts the reproducibility of the device performance. The study is extended to reveal the effect of annealing temperature profile and deposition substrate to demonstrate the complexity of perovskite processing parameters. This coupled experimental approach allows a better understanding of the effect of processing protocols, including antisolvent, humidity, and annealing profile, on MAPbI₃ film quality and the resultant solar cell performance

Transformation from crystalline precursor to perovskite in PbCl2-derived MAPbI3

Understanding the formation chemistry of metal halide perovskites is key to optimizing processing conditions and realizing enhanced optoelectronic properties. Here, we reveal the structure of the crystalline precursor in the formation of methylammonium lead iodide (MAPbI3) from the single-step deposition of lead chloride and three equivalents of methylammonium iodide (PbCl2 + 3MAI) (MA = CH3NH3). The as-spun film consists of crystalline MA2PbI3Cl, which is composed of one-dimensional chains of lead halide octahedra, coexisting with disordered MACl. We show that the transformation of precursor into perovskite is not favored in the presence of MACl, and thus the gradual evaporation of MACl acts as a self-regulating mechanism to slow the conversion. We propose the stable precursor phase enables dense film coverage and the slow transformation may lead to improved crystal quality. This enhanced chemical understanding is paramount for the rational control of film deposition and the fabrication of superior optoelectronic devices

Formation of Nanoscale Composites of Compound Semiconductors Driven by Charge Transfer

Composites are a class of materials that are formed by mixing two or more components. These materials often have new functional properties compared to their constituent materials. Traditionally composites are formed by self-assembly due to structural dissimilarities or by engineering different layers or structures in the material. Here we report the synthesis of a uniform and stoichiometric composite of CdO and SnTe with a novel nanocomposite structure stabilized by the dissimilarity of the electronic band structure of the constituent materials. The composite has interesting electronic properties which range from highly n-type in CdO to semi-insulating in the intermediate composition range to highly p-type in SnTe. This can be explained by the overlap of the conduction and valence band of the constituent compounds. Ultimately, our work identifies a new class of composite semiconductors in which nanoscale self-organization is driven and stabilized by charge transfer between constituent materials

Chemical Bath Deposition of p-Type Transparent, Highly Conducting (CuS)x:(ZnS)1-x Nanocomposite Thin Films and Fabrication of Si Heterojunction Solar Cells.

P-type transparent conducting films of nanocrystalline (CuS)x:(ZnS)1-x were synthesized by facile and low-cost chemical bath deposition. Wide angle X-ray scattering (WAXS) and high resolution transmission electron microscopy (HRTEM) were used to evaluate the nanocomposite structure, which consists of sub-5 nm crystallites of sphalerite ZnS and covellite CuS. Film transparency can be controlled by tuning the size of the nanocrystallites, which is achieved by adjusting the concentration of the complexing agent during growth; optimal films have optical transmission above 70% in the visible range of the spectrum. The hole conductivity increases with the fraction of the covellite phase and can be as high as 1000 S cm(-1), which is higher than most reported p-type transparent materials and approaches that of n-type transparent materials such as indium tin oxide (ITO) and aluminum doped zinc oxide (AZO) synthesized at a similar temperature. Heterojunction p-(CuS)x:(ZnS)1-x/n-Si solar cells were fabricated with the nanocomposite film serving as a hole-selective contact. Under 1 sun illumination, an open circuit voltage of 535 mV was observed. This value compares favorably to other emerging heterojunction Si solar cells which use a low temperature process to fabricate the contact, such as single-walled carbon nanotube/Si (370-530 mV) and graphene/Si (360-552 mV)