Anti-CRISPR AcrIF9 functions by inducing the CRISPR–Cas complex to bind DNA non-specifically

Phages and other mobile genetic elements express anti-CRISPR proteins (Acrs) to protect their genomes from destruction by CRISPR–Cas systems. Acrs usually block the ability of CRISPR–Cas systems to bind or cleave their nucleic acid substrates. Here, we investigate an unusual Acr, AcrIF9, that induces a gain-of-function to a type I-F CRISPR–Cas (Csy) complex, causing it to bind strongly to DNA that lacks both a PAM sequence and sequence complementarity. We show that specific and non-specific dsDNA compete for the same site on the Csy:AcrIF9 complex with rapid exchange, but specific ssDNA appears to still bind through complementarity to the CRISPR RNA. Induction of non-specific DNA-binding is a shared property of diverse AcrIF9 homologues. Substitution of a conserved positively charged surface on AcrIF9 abrogated non-specific dsDNA-binding of the Csy:AcrIF9 complex, but specific dsDNA binding was maintained. AcrIF9 mutants with impaired non-specific dsDNA binding activity in vitro displayed a reduced ability to inhibit CRISPR–Cas activity in vivo. We conclude that misdirecting the CRISPR–Cas complex to bind non-specific DNA is a key component of the inhibitory mechanism of AcrIF9. This inhibitory mechanism is distinct from a previously characterized anti-CRISPR, AcrIF1, that sterically blocks DNA-binding, even though AcrIF1and AcrIF9 bind to the same site on the Csy complex.     

Genetic Population Structure Analysis in New Hampshire Reveals Eastern European Ancestry

Genetic structure due to ancestry has been well documented among many divergent human populations. However, the ability to associate ancestry with genetic substructure without using supervised clustering has not been explored in more presumably homogeneous and admixed US populations. The goal of this study was to determine if genetic structure could be detected in a United States population from a single state where the individuals have mixed European ancestry. Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups. We then correlated self-reported ancestry of the individuals with the Bayesian clustering results. Finnish and Russian/Polish/Lithuanian ancestries were most notably found to be associated with genetic substructure. The ancestral results were further explained and substantiated using New Hampshire census data from 1870 to 1930 when the largest waves of European immigrants came to the area. We also discerned distinct patterns of linkage disequilibrium (LD) between the genetic groups in the growth hormone receptor gene (GHR). To our knowledge, this is the first time such an investigation has uncovered a strong link between genetic structure and ancestry in what would otherwise be considered a homogenous US population.     

Construction and Characterization of a Bacterial Artificial Chromosome (BAC) Library of Pacific White Shrimp, Litopenaeus vannamei

The pacific white shrimp (Litopenaeus vannamei) is one of the most economically important marine aquaculture species in the world. To facilitate gene cloning and characterization, genome analysis, physical mapping, and molecular selection breeding of marine shrimp, we have developed the techniques to isolate high-quality megabase-sized DNA from hemocyte nuclear DNA of female shrimp and constructed a bacterial artificial chromosome (BAC) genomic library for the species. The library was constructed in the Hind III site of the vector pECBAC1, consisting of 101,760 clones arrayed in 265 384-well microtiter plates, with an average insert size of 101 kb, and covering the genome approximately fivefold. To characterize the library, 92,160 clones were spotted onto high-density nylon filters for hybridization screening. A set of 18 pairs of overgo probes designed from eight cDNA sequences of L. vannamei genes were used in hybridization screening, and 35 positive clones were identified. These results suggest that the shrimp BAC libraries will provide a useful resource for screening of genomic regions of interest candidate genes, gene families, or large-sized synthetic DNA region and promote future works on comparative genomics, physical mapping, and large-scale genome sequencing in the species.     

Construction and Characterization of Two Bacterial Artificial Chromosome Libraries of Zhikong Scallop, Chlamys farreri Jones et Preston, and Identification of BAC Clones Containing the Genes Involved in Its Innate Immune System

Large-insert bacterial artificial chromosome (BAC) libraries are necessary for advanced genetics and genomics research. To facilitate gene cloning and characterization, genome analysis, and physical mapping of scallop, two BAC libraries were constructed from nuclear DNA of Zhikong scallop, Chlamys farreri Jones et Preston. The libraries were constructed in the BamHI and MboI sites of the vector pECBAC1, respectively. The BamHI library consists of 73,728 clones, and approximately 99% of the clones contain scallop nuclear DNA inserts with an average size of 110 kb, covering 8.0x haploid genome equivalents. Similarly, the MboI library consists of 7680 clones, with an average insert of 145 kb and no insert-empty clones, thus providing a genome coverage of 1.1x. The combined libraries collectively contain a total of 81,408 BAC clones arrayed in 212 384-well microtiter plates, representing 9.1x haploid genome equivalents and having a probability of greater than 99% of discovering at least one positive clone with a single-copy sequence. High-density clone filters prepared from a subset of the two libraries were screened with nine pairs of Overgos designed from the cDNA or DNA sequences of six genes involved in the innate immune system of mollusks. Positive clones were identified for every gene, with an average of 5.3 BAC clones per gene probe. These results suggest that the two scallop BAC libraries provide useful tools for gene cloning, genome physical mapping, and large-scale sequencing in the species.     

Toxicity and bioaccumulation of iron in soil microalgae

Microalgae are extensively used in the remediation of heavy metals like iron. However, factors like toxicity, bioavailability and iron speciation play a major role in its removal by microalgae. Thus, in this study, toxicity of three different iron salts (FeSO₄, FeCl₃ and Fe(NO₃)₃) was evaluated towards three soil microalgal isolates, Chlorella sp. MM3, Chlamydomonas sp. MM7 and Chlorococcum sp. MM11. Interestingly, all the three iron salts gave different EC50 concentrations; however, ferric nitrate was found to be significantly more toxic followed by ferrous sulphate and ferric chloride. The EC₅₀ analysis revealed that Chlorella sp. was significantly resistant to iron compared to other microalgae. However, almost 900 μg g^?1 iron was accumulated by Chlamydomonas sp. grown with 12 mg L^?1 ferric nitrate as an iron source when compared to other algae and iron salts. The time-course bioaccumulation confirmed that all the three microalgae adsorb the ferric salts such as ferric nitrate and ferric chloride more rapidly than ferrous salt, whereas intracellular accumulation was found to be rapid for ferrous salts. However, the amount of iron accumulated or adsorbed by algae, irrespective of species, from ferrous sulphate medium is comparatively lower than ferric chloride and ferric nitrate medium. The Fourier transform infrared spectroscopy (FTIR) analysis shows that the oxygen atom and P?=?O group of polysaccharides present in the cell wall of algae played a major role in the bioaccumulation of iron ions by algae.     

Reproduction in a carnivorous sponge: the significance of the absence of an aquiferous system to the sponge body plan

Sponges usually produce, release, and capture gametes via the aquiferous system, and so the absence of both choanocytes and an aquiferous system in the carnivorous sponge Asbestopluma occidentalis has led to unusual characteristics of development for this Phylum. Sperm are highly specialized elongate cells tightly packed into spermatic cysts in the peripheral tissue of the sponge. Mature spermatozoa have proacrosomal vesicles at the anterior end and a ciliary pit surrounding the flagellum. Clusters of four to five oocytes are in synchronous stages of cleavage, suggesting that fertilization is synchronous. All stages of embryos occur in the same individual. Early cleavage was holoblastic and equal; blastomeres in two-, four- and eight-cell embryos were compact and 16-cell stage embryos were bi-layered. Late-stage embryos show three cellular regions along the anterior-posterior axis: the anterior hemisphere with heterogeneous cells, a mid-region with cells lying perpendicular to the A-P axis in a collagenous matrix, and small cells at the posterior pole. Unusually for Porifera, multiciliated cells cover all but the posterior pole. It is inferred that fertilization occurs by capture of intact spermatic cysts whose surrounding forceps spicules become trapped in the anisochelae of neighboring sponges. The elongate shape of sperm may be designed to penetrate the loose collagenous mesohyl, such that the arrival of a packet of sperm would lead to simultaneous fertilization of oocytes in a cluster. Loss of the water canal system in carnivorous sponges has allowed the evolution of features that are highly specialized for the habitat of this animal, but such modifications were not necessarily a prerequisite for the subsequent evolution of metazoans. Given the extremely versatile mechanisms of gametogenesis, embryogenesis, and tissue/body structure in sponges, generalizations regarding basal metazoan reproduction, development, and structure must be approached with caution.     

A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence.

Sequencing of the rice genome has provided a platform for functional genomics research of rice and other cereal species. However, multiple approaches are needed to determine the functions of its genes and sequences and to use the genome sequencing results for genetic improvement of cereal crops. Here, we report a plant-transformation-competent, binary bacterial artificial chromosome (BIBAC) and bacterial artificial chromosome (BAC) based map of rice to facilitate these studies. The map was constructed from 20 835 BIBAC and BAC clones, and consisted of 579 overlapping BIBAC/BAC contigs. To facilitate functional analysis of chromosome 8 genomic sequence and cloning of the genes and QTLs mapped to the chromosome, we anchored the chromosomal contigs to the existing rice genetic maps. The chromosomal map consists of 11 contigs, 59 genetic markers, and 36 sequence tagged sites, spanning a total of ca. 38 Mb in physical length. Comparative analysis between the genetic and physical maps of chromosome 8 showed that there are 3 "hot" and 2 "cold" spots of genetic recombination along the chromosomal arms in addition to the "cold spot" in the centromeric region, suggesting that the sequence component contents of a chromosome may affect its local genetic recombination frequencies. Because of its plant transformability, the BIBAC/BAC map could provide a platform for functional analysis of the rice genome sequence and effective use of the sequencing results for gene and QTL cloning and molecular breeding.     

BAC library development for allotetraploid Leymus (Triticeae) wildryes enable comparative genetic analysis of lax-barrenstalk1 orthogene sequences and growth habit QTLs

Tall-caespitose basin wildrye (Leymus cinereus) and rhizomatous creeping wildrye (Leymus triticoides) are perennial Triticeae relatives of wheat and barley. Quantitative trait loci (QTLs) controlling rhizome proliferation were previously detected on homoeologous regions of LG3a and LG3b in two full-sib families derived from allotetraploid hybrids. Triticeae homoeologous group 3 aligns to rice chromosome 1, which contains the rice lax panicle and maize barrenstalk1 orthogene responsible for induction of axillary branch meristems, but this gene has not been mapped or sequenced in Triticeae. We developed bacterial artificial chromosome (BAC) libraries representing 6.1 haploid equivalents of the tetraploid Leymus genome (10.7 Mb). Overgo probes designed from the lax-barrenstalk1 orthogene hybridized to 12 Leymus BAC clones. Deduced amino-acid sequences from seven BAC clones were highly conserved with the rice, maize, and sorghum lax-barrenstalk1orthogenes. Gene specific primers designed from two of the most divergent BAC clones map to homoeologous regions of Leymus LG3a and LG3b and align with the lax-barrenstalk1 orthogene on rice 1L. Comparisons of genomic DNA sequences revealed two other conserved regions surrounding the Leymus LG3a, rice, and sorghum lax-barrenstalk1 ortholoci, and one of these regions was also present in maize and Leymus LG3b sequences. Comparisons of Leymus LG3a and LG3b lax-barrenstalk1 coding sequences and flanking genomic regions elucidate molecular differences between subgenomes.     

A distribution model for Glossina brevipalpis and Glossina austeni in Southern Mozambique,Eswatini and South Africa for enhanced area-wide integrated pest management approaches

BackgroundGlossina austeni and Glossina brevipalpis (Diptera: Glossinidae) are the sole cyclical vectors of African trypanosomes in South Africa, Eswatini and southern Mozambique. These populations represent the southernmost distribution of tsetse flies on the African continent. Accurate knowledge of infested areas is a prerequisite to develop and implement efficient and cost-effective control strategies, and distribution models may reduce large-scale, extensive entomological surveys that are time consuming and expensive. The objective was to develop a MaxEnt species distribution model and habitat suitability maps for the southern tsetse belt of South Africa, Eswatini and southern Mozambique.Methodology/Principal findingsThe present study used existing entomological survey data of G. austeni and G. brevipalpis to develop a MaxEnt species distribution model and habitat suitability maps. Distribution models and a checkerboard analysis indicated an overlapping presence of the two species and the most suitable habitat for both species were protected areas and the coastal strip in KwaZulu-Natal Province, South Africa and Maputo Province, Mozambique. The predicted presence extents, to a small degree, into communal farming areas adjacent to the protected areas and coastline, especially in the Matutuíne District of Mozambique. The quality of the MaxEnt model was assessed using an independent data set and indicated good performance with high predictive power (AUC > 0.80 for both species).Conclusions/SignificanceThe models indicated that cattle density, land surface temperature and protected areas, in relation with vegetation are the main factors contributing to the distribution of the two tsetse species in the area. Changes in the climate, agricultural practices and land-use have had a significant and rapid impact on tsetse abundance in the area. The model predicted low habitat suitability in the Gaza and Inhambane Provinces of Mozambique, i.e., the area north of the Matutuíne District. This might indicate that the southern tsetse population is isolated from the main tsetse belt in the north of Mozambique. The updated distribution models will be useful for planning tsetse and trypanosomosis interventions in the area.     

Initial Effects of Wildfire on Freshwater Turtle Nesting Habitat

Natural wildfire regimes are important for ecosystem succession but can have negative ecological effects depending on fire characteristics. A portion of a granite rock barrens landscape that extends along the eastern shoreline of Georgian Bay, Lake Huron to eastern Ontario, Canada, burned in 2018 during a wildfire that affected >11,000 ha. This landscape is a biodiversity hotspot providing habitat for many species at risk where freshwater turtles nest in soil deposits in cracks and crevices in the bedrock dominated by moss (Polytrichum spp.) and lichen (Cladonia spp.) cover. To assess the initial effect of wildfire on freshwater turtle nesting habitat, we measured soil depths and estimated moss, lichen, and vascular plant cover at 2 morphology types (crevice, flat) in burned and unburned areas of the landscape. The probability that burned flat plots supported soil was near zero; the burned flat plots had 98% less soil volume compared to unburned flat plots. Although crevices were more resistant to soil loss, burned crevices still had a 15% lower probability of having soil and 35% less soil volume compared to unburned crevice plots. We estimated nest site availability by calculating the number of locations with shallow (5–10 cm), intermediate (10–20 cm), and deep (>20 cm) soils required for a small (5 cm × 5 cm) or medium (10 cm × 10 cm) nest chamber. Overall, the burned open rock barrens had 71–73% fewer sites with suitable soil depth and volume for a nest chamber of either size. Furthermore, burned plots had almost no lichen and moss cover but were dominated by bare soil, forbs, and jack pine (Pinus banksiana) seedlings. Although the loss of tree cover in previously forested areas may increase nest site availability for freshwater turtles in newly open areas, we suggest that organic soil combustion and soil erosion may require restoration activities in the post-fire landscape to support successful nesting of at-risk turtles. © 2020 The Wildlife Society.