Systematic review of Atractus schach (Serpentes: Dipsadidae) species complex from the Guiana Shield with description of three new species

The Guiana Shield harbours one of the best preserved and largest extents of tropical forest on Earth and an immense biodiversity. The herpetofauna of this region remains poorly known. The species-rich snake genus Atractus contains ～140 species, many with complicated taxonomic histories, including A. schach. Examination of specimens in museums and newly collected material from French Guiana has allowed the illustration of hemipenial morphology for the first time and an expanded diagnosis. Concatenated molecular phylogenetic (mitochondrial and nuclear genes) and phenotypic (morphometrics, external and hemipenial morphology) analyses confirm non-monophyly of the A. flammigerus group and indicate that A. schach is a species complex with three new species described here. The geographic distribution of A. schach sensu stricto is restricted to Guiana, Surinam, and French Guiana north of Tumucumaque massif. Populations tentatively assigned to A. schach from the east from French Guiana in the Roura lowlands to Almeirim, and from central Amazonia between the Negro and Trombetas rivers in Brazil are also recognized as new species. Our results suggest that populations from south of the Amazon River are not conspecific with those from the Guiana Shield.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:A7AE40BC-4716-4302-B3BE-1F43600B0A72     

Climate‐driven shifts in the distribution of koala‐browse species from the Last Interglacial to the near future

The koala's Phascolarctos cinereus distribution is currently restricted to eastern and south‐eastern Australia. However, fossil records dating from 70 ± 4 ka (ka = 10³ yr) from south‐western Australia and the Nullarbor Plain are evidence of subpopulation extinctions in the southwest at least after the Last Interglacial (~128–116 ka). We hypothesize that koala sub‐population extinctions resulted from the eastward retraction of the koala's main browse species in response to unsuitable climatic conditions. We further posit a general reduction in the distribution of main koala‐browse trees in the near future in response climate change. We modelled 60 koala‐browse species and constructed a set of correlative species distribution models for five time periods: Last Interglacial (~128–116 ka), Last Glacial Maximum (~23–19 ka), Mid‐Holocene (~7–5 ka), present (interpolations of observed data, representative of 1960–1990), and 2070. We based our projections on five hindcasts and one forecast of climatic variables extracted from WorldClim based on two general circulation models (considering the most pessimistic scenario of high greenhouse‐gas emissions) and topsoil clay fraction. We used 17 dates of koala fossil specimens identified as reliable from 70 (± 4) to 535 (± 49) ka, with the last appearance of koalas at 70 ka in the southwest. The main simulated koala‐browse species were at their greatest modelled extent of suitability during the Last Glacial Maximum, with the greatest loss of koala habitat occurring between the Mid‐Holocene and the present. We predict a similar habitat loss between the present and 2070. The spatial patterns of habitat change support our hypothesis that koala extinctions in the southwest, Nullarbor Plain and central South Australia resulted from the eastward retraction of the dominant koala‐browse species in response to long‐term climate changes. Future climate patterns will likely increase the extinction risk of koalas in their remaining eastern ranges.     

Genomic organization and primary structure of five homologous pairs of intron-less genes encoding secretory globins from the insect Chironomus thummi thummi

From a Chironomus thummi thummi genomic library we have isolated two distinct recombinant phages, CttG-1 and CttG-3, each carrying a cluster of five homologous globin genes. In addition to the previously reported nucleotide sequence of globin gene D (Antoine and Niessing, 1984) we present the chromosomal arrangement, primary structure and predicted amino acid sequence of nine globin genes. The divergently transcribed globin genes all lack introns, they encode secretory preglobins each containing a highly conserved signal peptide. The amino acid sequences deduced from the globin genes correspond to globin III and variants thereof, to globin IV, and to a novel globin, whose direct amino acid sequence has not yet been reported.     

Caspase-1 activation by Salmonella

Salmonella is an interesting example of how the selective pressure of host environments has led to the evolution of sophisticated bacterial virulence mechanisms. This microbe exploits the first-line of defence, the macrophage, as a crucial tool in the initiation of disease. After invasion of intestinal macrophages, a virulence protein secreted by Salmonella specifically induces apoptotic cell death by activating the cysteine protease caspase-1. The pro-apoptotic capability is necessary for successful pathogenesis. The study of mechanisms by which Salmonella induces programmed cell death offers new insights into how pathogens cause disease and into general mechanisms of activation of the innate immune system.     

High‐Throughput DNA sequencing of ancient wood

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.     

A simple reverse genetics method to generate recombinant coronaviruses

Engineering recombinant viruses is a pre‐eminent tool for deciphering the biology of emerging viral pathogens such as the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). However, the large size of coronavirus genomes renders the current reverse genetics methods challenging. Here, we describe a simple method based on “infectious subgenomic amplicons” (ISA) technology to generate recombinant infectious coronaviruses with no need for reconstruction of the complete genomic cDNA and apply this method to SARS‐CoV‐2 and also to the feline enteric coronavirus. In both cases we rescue wild‐type viruses with biological characteristics similar to original strains. Specific mutations and fluorescent red reporter genes can be readily incorporated into the SARS‐CoV‐2 genome enabling the generation of a genomic variants and fluorescent reporter strains for in vivo experiments, serological diagnosis, and antiviral assays. The swiftness and simplicity of the ISA method has the potential to facilitate the advance of coronavirus reverse genetics studies, to explore the molecular biological properties of the SARS‐CoV‐2 variants, and to accelerate the development of effective therapeutic reagents.     

Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides (Figure 1). The growing product double-strand DNA (dsDNA) is extended with laminar flow and visualized by using an intercalating dye. Measuring the position of the growing DNA end in real time allows precise determination of replication rate (Figure 2). Furthermore, the length of completed DNA products reports on the processivity of replication. This experiment can be performed very easily and rapidly and requires only a fluorescence microscope with a reasonably sensitive camera.     

Elucidating the Role of a Tetrafluoroborate‐Based Ionic Liquid at the n‐Type Oxide/Perovskite Interface

Halide perovskites are currently one of the most heavily researched emerging photovoltaic materials. Despite achieving remarkable power conversion efficiencies, perovskite solar cells have not yet achieved their full potential, with the interfaces between the perovskite and the charge‐selective layers being where most recombination losses occur. In this study, a fluorinated ionic liquid (IL) is employed to modify the perovskite/SnO₂ interface. Using Kelvin probe and photoelectron spectroscopy measurements, it is shown that depositing the perovskite onto an IL‐treated substrate results in the crystallization of a perovskite film which has a more n‐type character, evidenced by a decrease of the work function and a shift of the Fermi level toward the conduction band. Photoluminescence spectroscopy and time‐resolved microwave conductivity are used to investigate the optoelectronic properties of the perovskite grown on neat and IL‐modified surfaces and it is found that the modified substrate yields a perovskite film which exhibits an order of magnitude lower trap density than the control. When incorporated into solar cells, this interface modification results in a reduction in the current–voltage hysteresis and an improvement in device performance, with the best performing devices achieving steady‐state PCEs exceeding 20%.     

Ultraviolet Photoemission Spectroscopy and Kelvin Probe Measurements on Metal Halide Perovskites: Advantages and Pitfalls

In this essay, a case study is presented on the electronic structure of several metal halide perovskites (MHP) using Kelvin probe (KP)‐based surface photovoltage (SPV) measurements and ultraviolet photoemission spectroscopy (UPS) to demonstrate the advantages, but also the pitfalls, of using these techniques to characterize the surfaces of these materials. The first part addresses the loss of halide species from perovskite surfaces upon supragap illumination in vacuum. This has the potential to cause both a long‐term alteration of the sample work function and a modification of the KP tip during SPV measurements. If undetected, this leads to a misinterpretation of the MHP surface potential. The second part illustrates the difficulties in determining the valence band maximum (VBM) of MHP surfaces with UPS and stresses the importance of taking into account the low density of states at the VBM edge. Given this circumstance, specific care must be taken to eliminate measurement artifacts in order to ascertain the presence or absence of low densities of electronic gap states above the VBM. This essay also highlights issues such as film degradation, nonequilibrium situations (e.g., SPV), and satellite emissions, which occur during photoemission spectroscopy.