The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq.

BACKGROUND: Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome's limitations in describing higher functional phenotypes and protein events. Perhaps the most important shortfall with transcriptomic 'snapshots' of cell populations is that they risk being descriptive, only cataloging heterogeneity at one point in time, and without microenvironmental context. Studying the genetic ('nature') and environmental ('nurture') modifiers of heterogeneity, and how cell population dynamics unfold over time in response to these modifiers is key when studying highly plastic cells such as macrophages. RESULTS: We introduce the programmable Polaris™ microfluidic lab-on-chip for single-cell sequencing, which performs live-cell imaging while controlling for the culture microenvironment of each cell. Using gene-edited macrophages we demonstrate how previously unappreciated knockout effects of SAMHD1, such as an altered oxidative stress response, have a large paracrine signaling component. Furthermore, we demonstrate single-cell pathway enrichments for cell cycle arrest and APOBEC3G degradation, both associated with the oxidative stress response and altered proteostasis. Interestingly, SAMHD1 and APOBEC3G are both HIV-1 inhibitors ('restriction factors'), with no known co-regulation. CONCLUSION: As single-cell methods continue to mature, so will the ability to move beyond simple 'snapshots' of cell populations towards studying the determinants of population dynamics. By combining single-cell culture, live-cell imaging, and single-cell sequencing, we have demonstrated the ability to study cell phenotypes and microenvironmental influences. It's these microenvironmental components - ignored by standard single-cell workflows - that likely determine how macrophages, for example, react to inflammation and form treatment resistant HIV reservoirs.

Intramolecular oxonium ylide formation-[2,3] sigmatropic rearrangement of diazocarbonyl-substituted cyclic unsaturated acetals: a formal synthesis of hyperolactone C.

Rh(II)-catalyzed oxonium ylide formation-[2,3] sigmatropic rearrangement of α-diazo-ß-ketoesters possessing γ-cyclic unsaturated acetal substitution, followed by acid-catalyzed elimination-lactonization, provides a concise approach to 1,7-dioxaspiro[4.4]non-2-ene-4,6-diones. The process creates adjacent quaternary stereocenters with full control of the relative stereochemistry. An unsymmetrical monomethylated cyclic unsaturated acetal leads to hyperolactone C, where ylide formation-rearrangement proceeds with high selectivity between subtly nonequivalent acetal oxygen atoms.

Protection of HIV neutralizing aptamers against rectal and vaginal nucleases: implications for RNA-based therapeutics.

RNA-based drugs are an emerging class of therapeutics. They have the potential to regulate proteins, chromatin, as well as bind to specific proteins of interest in the form of aptamers. These aptamers are protected from nuclease attack by chemical modifications that enhance their stability for in vivo usage. However, nucleases are ubiquitous, and as we have yet to characterize the entire human microbiome it is likely that many nucleases are yet to be identified. Any novel, unusual enzymes present in vivo might reduce the efficacy of RNA-based therapeutics, even when they are chemically modified. We have previously identified an RNA-based aptamer capable of neutralizing a broad spectrum of clinical HIV-1 isolates and are developing it as a vaginal and rectal microbicide candidate. As a first step we addressed aptamer stability in the milieu of proteins present in these environments. Here we uncover a number of different nucleases that are able to rapidly degrade 2'-F-modified RNA. We demonstrate that the aptamer can be protected from the nuclease(s) present in the vaginal setting, without affecting its antiviral activity, by replacement of key positions with 2'-O-Me-modified nucleotides. Finally, we show that the aptamer can be protected from all nucleases present in both vaginal and rectal compartments using Zn(2+) cations. In conclusion we have derived a stable, antiviral RNA-based aptamer that could form the basis of a pre-exposure microbicide or be a valuable addition to the current tenofovir-based microbicide candidate undergoing clinical trials.

Two new species of Western Australian Abantiades Herrich-Schffer (Lepidoptera: Hepialidae) and a description of the female of Abantiades paradoxa (Tindale).

Two new species, Abantiades concordia sp. nov. and Abantiades malleus sp. nov., are described from Australia. Both species were collected in the Eastern Goldfields subregion of the Coolgardie bioregion in Western Australia. Abantiades concordia sp. nov. is shown to be closely related to A. paradoxa (Tindale, 1932) by sequence similarity of the mtDNA (COI) gene. The female of A. paradoxa is also described here for the first time. Abantiades paradoxa and the new species A. concordia sp. nov. are morphologically similar with respect to the structure of their genitalia, sternite VIII, wing patterning and their antennae with bi-forked rami. Abantiades malleus sp. nov. is quite distinct by sequence similarity of the mtDNA (COI) gene, but related in a clade with A. marcidus Tindale,1932, A. albofasciatus (Swinhoe, 1892), and A. furva (Tindale,1932), the latter species once placed in the synonymised Bordaia Tindale, 1932. Discussion of similar species once grouped under the genus Bordaia and under the genus Trictena Meyrick, 1890 (both junior synonyms of Abantiades Herrich-Schffer, 1855) is also included.

Delineation of the preferences and requirements of the human immunodeficiency virus type 1 dimerization initiation signal by using an in vivo cell-based selection approach.

HIV-1 packages two copies of RNA into one particle, and the dimerization initiation signal (DIS) in the viral RNA plays an important role in selecting the copackaged RNA partner. We analyzed the DIS sequences of the circulating HIV-1 isolates in the GenBank database and observed that, in addition to the prevalent GCGCGC, GTGCAC, and GTGCGC sequences, there are many other minor variants. To better understand the requirements for the DIS to carry out its function, we generated a plasmid library containing a subtype B HIV-1 genome with a randomized DIS, infected cells with viruses derived from the library, and monitored the emergence of variants at different time points until 100 days postinfection. We observed rapid loss of viral diversity and found that the selected variants contained palindromes in the DIS. The "wild-type" GCGCGC-containing virus was a major variant, whereas GTGCAC- and GTGCGC-containing viruses were present at low frequencies. Additionally, other 6-nucleotide (nt) palindromic sequences were selected; a major category of the selected variants contained two GC dyads in the center of the palindrome, flanked by a non-GC dyad. Surprisingly, variants with GC-rich 4-nt palindromes were sustained throughout the selection period at significant frequencies ( approximately 12 to 38%); of these, variants containing the CGCGC sequence were observed frequently, suggesting that this sequence has a selection advantage. These results revealed that multiple sequences can fulfill the function of the HIV-1 DIS. A common feature of the selected DIS sequence is a 4- or 6-nt GC-rich palindrome, although not all sequences with these characteristics were selected, suggesting the presence of other unidentified interactions.

Probing the HIV-1 genomic RNA trafficking pathway and dimerization by genetic recombination and single virion analyses.

Once transcribed, the nascent full-length RNA of HIV-1 must travel to the appropriate host cell sites to be translated or to find a partner RNA for copackaging to form newly generated viruses. In this report, we sought to delineate the location where HIV-1 RNA initiates dimerization and the influence of the RNA transport pathway used by the virus on downstream events essential to viral replication. Using a cell-fusion-dependent recombination assay, we demonstrate that the two RNAs destined for copackaging into the same virion select each other mostly within the cytoplasm. Moreover, by manipulating the RNA export element in the viral genome, we show that the export pathway taken is important for the ability of RNA molecules derived from two viruses to interact and be copackaged. These results further illustrate that at the point of dimerization the two main cellular export pathways are partially distinct. Lastly, by providing Gag in trans, we have demonstrated that Gag is able to package RNA from either export pathway, irrespective of the transport pathway used by the gag mRNA. These findings provide unique insights into the process of RNA export in general, and more specifically, of HIV-1 genomic RNA trafficking.

Two new endemic species of emAbantiades/em Herrich-Schäffer (Lepidoptera: Hepialidae) from Kangaroo Island, Australia.

Abantiades penneshawensis Moore Beaver sp. nov. and Abantiades rubrus Moore Beaver sp. nov. are described as new. Both species are endemic to Kangaroo Island, and although both are related to species that occur on the Australian mainland and other islands, they are distinguished from those sister and phenotypically similar species by morphology and mtDNA (COI) barcodes. These two new species raise the number of Abantiades species on Kangaroo Island to six, three being endemic, and 45 species in the genus for the whole of Australia. There are now 13 species of Hepialidae (one undescribed) known from Kangaroo Island and we discuss the potential effects of recent catastrophic fire on some distributions.

Structural interpretation in composite systems using powder X-ray diffraction: applications of error propagation to the pair distribution function.

PURPOSE: To develop a method for drawing statistical inferences from differences between multiple experimental pair distribution function (PDF) transforms of powder X-ray diffraction (PXRD) data. METHODS: The appropriate treatment of initial PXRD error estimates using traditional error propagation algorithms was tested using Monte Carlo simulations on amorphous ketoconazole. An amorphous felodipine:polyvinyl pyrrolidone:vinyl acetate (PVPva) physical mixture was prepared to define an error threshold. Co-solidified products of felodipine:PVPva and terfenadine:PVPva were prepared using a melt-quench method and subsequently analyzed using PXRD and PDF. Differential scanning calorimetry (DSC) was used as an additional characterization method. RESULTS: The appropriate manipulation of initial PXRD error estimates through the PDF transform were confirmed using the Monte Carlo simulations for amorphous ketoconazole. The felodipine:PVPva physical mixture PDF analysis determined ±3σ to be an appropriate error threshold. Using the PDF and error propagation principles, the felodipine:PVPva co-solidified product was determined to be completely miscible, and the terfenadine:PVPva co-solidified product, although having appearances of an amorphous molecular solid dispersion by DSC, was determined to be phase-separated. CONCLUSIONS: Statistically based inferences were successfully drawn from PDF transforms of PXRD patterns obtained from composite systems. The principles applied herein may be universally adapted to many different systems and provide a fundamentally sound basis for drawing structural conclusions from PDF studies.

HIV-1 RNA dimerization: It takes two to tango.

Each viral particle of HIV-1, the infectious agent of AIDS, contains two copies of the full-length viral genomic RNA. Encapsidating two copies of genomic RNA is one of the characteristics of the retrovirus family. The two RNA molecules are both positive-sense and often identical; furthermore, each RNA encodes the full complement of genetic information required for viral replication. The two strands of RNA are intricately entwined within the core of the mature infectious virus as a ribonuclear complex with the viral proteins, including nucleocapsid. Multiple steps in the biogenesis of the genomic full-length RNA are involved in achieving this location and dimeric state. The viral sequences and proteins involved in the process of RNA dimerization, both for the initial interstrand contact and subsequent steps that result in the condensed, stable conformation of the genomic RNA, are outlined in this review. In addition, the impact of the dimeric state of HIV-1 viral RNA is discussed with respect to its importance in efficient viral replication and, consequently, the potential development of antiviral strategies designed to disrupt the formation of dimeric RNA.

Description of two new Australian species of Abantiades Herrich-Schäffer (Lepidoptera: Hepialidae) and females of two further species with notes on their biogeography.

Abantiades cephalocorvus sp. nov. and Abantiades tembyi sp. nov. are described, along with the previously undescribed females of A. macropusinsulariae Simonsen, 2018 and A. pallida Simonsen, 2018. All of these species belong to a triforked Abantiades Herrich-Schäffer clade that is loosely centred around the Nullarbor and other arid regions of Australia. We explore DNA barcodes (mtDNA COI gene) from these and other Abantiades and discuss their significance for species recognition. The species distributions are entirely or largely allopatric and we discuss their origins from a widespread common ancestor that was likely distributed over inland and coastal regions in the mid- to late-Mesozoic before the onset of desertification. Notes on new distributional data for all of the known species in this clade are included.

Four new tri-forked species of the Australian genus Abantiades Herrich-Schäffer (Lepidoptera: Hepialidae) from the "dark obscura clade".

A distinct group of Abantiades Herrich-Schäffer species is here confirmed as a valid clade that we refer to as the "dark obscura clade" supported by morphological and mtDNA evidence. The clade is the sister group of A. obscura Simonsen of north-western Australia and comprises four new species: Abantiades centralia sp. nov., A. kayi sp. nov., A. zonatriticum sp. nov., and A. hutchinsoni sp. nov. These species together with A. obscura, are reciprocally allopatric and have a combined distribution spanning much of the western half of Australia and this distribution is consistent with their each differentiating locally from a widespread ancestor. The four new species raise the diversity of Abantiades to 42 species. [Zoobank urn:lsid:zoobank.org:pub:C05458D1-0D34-4432-8EC4-D031ED6B7BEF].

Three new ghost moths of the genus Oxycanus Walker, 1856 from Australia (Lepidoptera: Hepialidae).

Three new species of ghost moth, Oxycanus ephemerous sp. nov., O. flavoplumosus sp. nov., and O. petalous sp. nov. are described from South Australia, New South Wales, and south-west Western Australia, respectively. We illustrate these species and compare morphological and molecular (mtDNA COI gene) characters with similar Oxycanus Walker, 1856 species from Australia. Comparative images of Oxycanus subvaria (Walker, 1856), O. byrsa (Pfitzner, 1933), and O. determinata (Walker, 1856) are figured. The type material of the three new species are held in the Australian National Insect Collection, Canberra, the Western Australian Museum, Perth, and in the South Australian Museum, Adelaide. The type specimens of Oxycanus hildae Tindale, 1964 syn. n. were also examined and the taxon is here considered synonymous with O. subvaria. Concerns are raised about the conservation status of all three new species due to few or localised distribution records.

Four new species of Splendid Ghost Moths (Lepidoptera: Hepialidae: Aenetus) from Australia and Papua New Guinea.

Four new Aenetus Herrich-Schäffer species are described from northern Australasia; Aenetus simonseni sp. nov. from the top-end of the Northern Territory, Australia, A. maiasinus sp. nov. from the Kimberley region of Western Australia, A. trigonogrammus sp. nov. from south-eastern Queensland, Australia, and A. albadamanteum sp. nov. from eastern Papua New Guinea. Aenetus simonseni sp. nov. and A. maiasinus sp. nov. appear to belong to the tegulatus-group of species (sensu Grehan et al. 2018), A. trigonogrammus sp. nov. is part of the splendens-group of species (sensu Simonsen 2018), while A. albadamanteum sp. nov. shares morphological similarities with A. hampsoni (Joicey Noakes, 1914), A. crameri Viette, 1956, and A. toxopeusi Viette, 1956, from New Guinea, and A. cohici Viette, 1961 from New Caledonia. The four new species are illustrated and compared with superficially similar species in morphology and, for two species, molecular (mtDNA COI gene) sequences.

APOBEC3G induces a hypermutation gradient: purifying selection at multiple steps during HIV-1 replication results in levels of G-to-A mutations that are high in DNA, intermediate in cellular viral RNA, and low in virion RNA.

BACKGROUND: Naturally occurring Vif variants that are unable to inhibit the host restriction factor APOBEC3G (A3G) have been isolated from infected individuals. A3G can potentially induce G-to-A hypermutation in these viruses, and hypermutation could contribute to genetic variation in HIV-1 populations through recombination between hypermutant and wild-type genomes. Thus, hypermutation could contribute to the generation of immune escape and drug resistant variants, but the genetic contribution of hypermutation to the viral evolutionary potential is poorly understood. In addition, the mechanisms by which these viruses persist in the host despite the presence of A3G remain unknown. RESULTS: To address these questions, we generated a replication-competent HIV-1 Vif mutant in which the A3G-binding residues of Vif, Y(40)RHHY(44), were substituted with five alanines. As expected, the mutant was severely defective in an A3G-expressing T cell line and exhibited a significant delay in replication kinetics. Analysis of viral DNA showed the expected high level of G-to-A hypermutation; however, we found substantially reduced levels of G-to-A hypermutation in intracellular viral RNA (cRNA), and the levels of G-to-A mutations in virion RNA (vRNA) were even further reduced. The frequencies of hypermutation in DNA, cRNA, and vRNA were 0.73%, 0.12%, and 0.05% of the nucleotides sequenced, indicating a gradient of hypermutation. Additionally, genomes containing start codon mutations and early termination codons within gag were isolated from the vRNA. CONCLUSION: These results suggest that sublethal levels of hypermutation coupled with purifying selection at multiple steps during the early phase of viral replication lead to the packaging of largely unmutated genomes, providing a mechanism by which mutant Vif variants can persist in infected individuals. The persistence of genomes containing mutated gag genes despite this selection pressure indicates that dual infection and complementation can result in the packaging of hypermutated genomes which, through recombination with wild-type genomes, could increase viral genetic variation and contribute to evolution.

A structural investigation into the compaction behavior of pharmaceutical composites using powder X-ray diffraction and total scattering analysis.

PURPOSE: To use advanced powder X-ray diffraction (PXRD) to characterize the structure of anhydrous theophylline following compaction, alone, and as part of a binary mixture with either alpha-lactose monohydrate or microcrystalline cellulose. MATERIALS AND METHODS: Compacts formed from (1) pure theophylline and (2) each type of binary mixture were analyzed intact using PXRD. A novel mathematical technique was used to accurately separate multi-component diffraction patterns. The pair distribution function (PDF) of isolated theophylline diffraction data was employed to assess structural differences induced by consolidation and evaluated by principal components analysis (PCA). RESULTS: Changes induced in PXRD patterns by increasing compaction pressure were amplified by the PDF. Simulated data suggest PDF dampening is attributable to molecular deviations from average crystalline position. Samples compacted at different pressures were identified and differentiated using PCA. Samples compacted at common pressures exhibited similar inter-atomic correlations, where excipient concentration factored in the analyses involving lactose. CONCLUSIONS: Practical real-space structural analysis of PXRD data by PDF was accomplished for intact, compacted crystalline drug with and without excipient. PCA was used to compare multiple PDFs and successfully differentiated pattern changes consistent with compaction-induced disordering of theophylline as a single component and in the presence of another material.

HIV-1 recombination: an experimental assay and a phylogenetic approach.

The generation of genetic diversity is a fundamental characteristic of HIV-1 replication, allowing the virus to successfully evade the immune response and antiviral therapies. Although mutations are the first step towards diversity, mixing of the mutations through the process of recombination increases the variation and allows for the faster establishment of advantageous strains within the viral population. Therefore, studying recombination of HIV-1 provides insights into not only the mechanisms of HIV-1 replication but also into the potential for spread of antiviral drug resistance mutations within and across viral subtypes. This chapter describes, in detail, a highly sensitive recombination assay designed to measure the frequency of recombination between two viruses. This assay allows us to investigate the requirements, mechanisms, and final products of recombination. Additionally, software-based phylogenetic tools are described in this chapter, which allow for the identification of specific recombination events within patient samples or viral progeny from the recombination assay.

The complete mitochondrial genome of the brown pansy butterfly, Junonia stygia (Aurivillius, 1894), (Insecta: Lepidoptera: Nymphalidae).

The brown pansy, Junonia stygia (Aurivillius, 1894) (Lepidoptera: Nymphalidae), is a widespread West African forest butterfly. Genome skimming by Illumina sequencing allowed assembly of a complete 15,233 bp circular mitogenome from J. stygia consisting of 79.5% AT nucleotides. Mitochondrial gene order and composition is identical to other butterfly mitogenomes. Junonia stygia COX1 features an atypical CGA start codon, while ATP6, COX1, COX2, ND4, and ND4L exhibit incomplete stop codons. Phylogenetic reconstruction supports a monophyletic Subfamily Nymphalinae, Tribe Junoniini, and genus Junonia. The phylogenetic tree places Junonia iphita and J. stygia as basal mitogenome lineages sister to the remaining Junonia sequences.

The use of net analyte signal orthogonalization in the separation of multi-component diffraction patterns obtained from X-ray powder diffraction of intact compacts.

X-ray powder diffraction (XRPD) analysis of intact multi-component consolidated mixtures has significant potential owing to the ability to non-destructively quantify and discriminate between solid phases in composite bodies with minimal sample preparation. There are, however, limitations to the quantitative power using traditional univariate methods on diffraction data containing features from all components in the system. The ability to separate multi-component diffraction data into patterns representing single constituents allows both composition as well as physical phenomena associated with the individual components of complex systems to be probed. Intact, four-component compacts, consisting of two crystalline and two amorphous constituents were analyzed using XRPD configured in both traditional Bragg-Brentano reflectance geometry and parallel-beam transmission geometry. Two empirical, model-based methods consisting of a multiple step net analyte signal (NAS) orthogonalization are presented as ways to separate multi-component XRPD patterns into single constituent patterns. Multivariate figures of merit (FOM) were calculated for each of the isolated constituents to compare method-specific parameters such as sensitivity, selectivity, and signal-to-noise, enabling quantitative comparisons between the two modes of XRPD analysis.

1-Isopropyl-4-nitro-6-meth-oxy-1H-benzimidazole.

There are two independent mol-ecules in the asymmetric unit of the title compound, C(11)H(13)N(3)O(3). The inter-planar angles for the two rings of the benzimidazole ring system is 2.21 (12)° in one mol-ecule and 0.72 (12)° in the other. The nitro group is twisted in the same direction relative to the least-squares plane through its attached benzene ring in both mol-ecules, with inter-planar angles of 15.22 (9) and 18.02 (8)°. In the crystal structure, mol-ecules are stacked along the a axis through π-π inter-actions (centroid-centroid distance 4.1954 Å). C-H⋯O hydrogen bonds are also present.

RIPK1 is a critical modulator of both tonic and TLR-responsive inflammatory and cell death pathways in human macrophage differentiation.

In this study, we took advantage of human-induced pluripotent stem cells (hiPSC) and CRISPR/Cas9 technology to investigate the potential roles of RIPK1 in regulating hematopoiesis and macrophage differentiation, proinflammatory activation, and cell death pathways. Knock-out of RIPK1 in hiPSCs demonstrated that this protein is not required for erythro-myeloid differentiation. Using a well-established macrophage differentiation protocol, knock-out of RIPK1 did not block the differentiation of iPSC-derived macrophages, which displayed a similar phenotype to WT hiPSC-derived macrophages. However, knock-out of RIPK1 leads to a TNFα-dependent apoptotic death of differentiated hiPSC-derived macrophages (iPS-MΦ) and progressive loss of iPS-MΦ production irrespective of external pro-inflammatory stimuli. Live video analysis demonstrated that TLR3/4 activation of RIPK1 KO hiPSC-derived macrophages triggered TRIF and RIPK3-dependent necroptosis irrespective of caspase-8 activation. In contrast, TLR3/4 activation of WT macrophages-induced necroptosis only when caspases were inhibited, confirming the modulating effect of RIPK1 on RIPK3-mediated necroptosis through the FADD, Caspase-8 pathway. Activation of these inflammatory pathways required RIPK3 kinase activity while RIPK1 was dispensable. However, loss of RIPK1 sensitizes macrophages to activate RIPK3 in response to inflammatory stimuli, thereby exacerbating a potentially pathological inflammatory response. Taken together, these results reveal that RIPK1 has an important role in regulating the potent inflammatory pathways in authentic human macrophages that are poised to respond to external stimuli. Consequently, RIPK1 activity might be a valid target in the development of novel therapies for chronic inflammatory diseases.