Computational phylogenetics and the internal structure of Pama-Nyungan

We present the first proposal of detailed internal subgrouping and higher-order structure of the Pama-Nyungan family of Australian languages. Previous work has identified more than twentyfive primary subgroups in the family, with little indication of ho

‘Sustaining masculinity’:a scoping review of anabolic androgenic steroid use by older males

In the past, research, policy and media have reported the use of anabolic androgenic steroids (AAS) primarily among younger males. However, recent studies have indicated the presence of an older cohort of men who use AAS in comparison to previous years. We carried out a scoping review of the extant literature to map and describe what is known about the use of AAS by older men (>40 years). A systematic search collected and analysed empirical research and grey literature relevant to the research question. Following application of inclusion and exclusion criteria, 44 studies were included which were subsequently charted and thematically analysed. The records included originated from the UK, USA, Canada, Australia, Slovenia, Norway, Spain, Turkey, Switzerland, Japan, and five global studies and were published between 1996 and 2021. Age ranged overall from 14 to 78 years old, however our review only discussed findings pertaining to those older than 40. Three main themes with subthemes were generated as follows: 1) Characteristics of AAS Use; Self-reported Adverse Effects from AAS Use; and Harms Diagnosed by Medical Professional. The review highlights the significant risks to hypothalamic-pituitary testicular function, cardiovascular health, and other organ systems as a result of the ageing man who is motivated to sustain masculine characteristics such as muscularity, youthfulness, sexual function, and perceived desirability and attractiveness. Future research is required to further understand the motivations of older men who use AAS. Furthermore, there is a need for age-specific research and recommendations to inform future policy and practice pertaining so that age-appropriate healthcare and policy decisions can be made in the future

Halocarbons associated with Arctic sea ice

Short-lived halocarbons were measured in Arctic sea-ice brine, seawater and air above the Greenland and Norwegian seas (∼81°N, 2 to 5°E) in mid-summer, from a melting ice floe at the edge of the ice pack. In the ice floe, concentrations of C2H5I, 2-C3H7I and CH2Br2 showed significant enhancement in the sea ice brine, of average factors of 1.7, 1.4 and 2.5 times respectively, compared to the water underneath and after normalising to brine volume. Concentrations of mono-iodocarbons in air are the highest ever reported, and our calculations suggest increased fluxes of halocarbons to the atmosphere may result from their sea-ice enhancement. Some halocarbons were also measured in ice of the sub-Arctic in Hudson Bay (∼55°N, 77°W) in early spring, ice that was thicker, colder and less porous than the Arctic ice in summer, and in which the halocarbons were concentrated to values over 10 times larger than in the Arctic ice when normalised to brine volume. Concentrations in the Arctic ice were similar to those in Antarctic sea ice that was similarly warm and porous. As climate warms and Arctic sea ice becomes more like that of the Antarctic, our results lead us to expect the production of iodocarbons and so of reactive iodine gases to increase

Genomic and geographical structure of human cytomegalovirus

Human cytomegalovirus (CMV) has infected humans since the origin of our species and currently infects most of the world’s population. Variability between CMV genomes is the highest of any human herpesvirus, yet large portions of the genome are conserved. Here, we show that the genome encodes 74 regions of relatively high variability each with 2 to 8 alleles. We then identified two patterns in the CMV genome. Conserved parts of the genome and a minority (32) of variable regions show geographic population structure with evidence for African or European clustering, although hybrid strains are present. We find no evidence that geographic segregation has been driven by host immune pressure affecting known antigenic sites. Forty-two variable regions show no geographical structure, with similar allele distributions across different continental populations. These “nongeographical” regions are significantly enriched for genes encoding immunomodulatory functions suggesting a core functional importance. We hypothesize that at least two CMV founder populations account for the geographical differences that are largely seen in the conserved portions of the genome, although the timing of separation and direction of spread between the two are not clear. In contrast, the similar allele frequencies among 42 variable regions of the genome, irrespective of geographical origin, are indicative of a second evolutionary process, namely balancing selection that may preserve properties critical to CMV biological function. Given that genetic differences between CMVs are postulated to alter immunogenicity and potentially function, understanding these two evolutionary processes could contribute important information for the development of globally effective vaccines and the identification of novel drug targets

Haplotype assignment of longitudinal viral deep-sequencing data using co-variation of variant frequencies

Longitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and transmit between hosts. Many analyses require haplotype reconstruction, identifying which variants are co-located on the same genomic element. Most current methods to perform this reconstruction are based on a high density of variants and cannot perform this reconstruction for slowly evolving viruses. We present a new approach, HaROLD (HAplotype Reconstruction Of Longitudinal Deep sequencing data), which performs this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We illustrate HaROLD on both RNA and DNA viruses with synthetic Illumina paired read data created from mixed human cytomegalovirus and norovirus genomes, and clinical datasets of human cytomegalovirus and norovirus samples, demonstrating high accuracy, especially when longitudinal samples are available

Manipulation of flavour and aroma compound sequestration and release using a glycosyltransferase with specificity for terpene alcohols.

Glycosides are an important potential source of aroma and flavour compounds for release as volatiles in flowers and fruit. The production of glycosides is catalysed by UDP-glycosyltransferases (UGTs) that mediate the transfer of an activated nucleotide sugar to acceptor aglycones. A screen of UGTs expressed in kiwifruit (Actinidia deliciosa) identified the gene AdGT4 which was highly expressed in floral tissues and whose expression increased during fruit ripening. Recombinant AdGT4 enzyme glycosylated a range of terpenes and primary alcohols found as glycosides in ripe kiwifruit. Two of the enzyme's preferred alcohol aglycones, hexanol and (Z)-hex-3-enol, contribute strongly to the 'grassy-green' aroma notes of ripe kiwifruit and other fruit including tomato and olive. Transient over-expression of AdGT4 in tobacco leaves showed that enzyme was able to glycosylate geraniol and octan-3-ol in planta whilst transient expression of an RNAi construct in Actinidia eriantha fruit reduced accumulation of a range of terpene glycosides. Stable over-expression of AdGT4 in transgenic petunia resulted in increased sequestration of hexanol and other alcohols in the flowers. Transgenic tomato fruit stably over-expressing AdGT4 showed changes in both the sequestration and release of a range of alcohols including 3-methylbutanol, hexanol and geraniol. Sequestration occurred at all stages of fruit ripening. Ripe fruit sequestering high levels of glycosides were identified as having a less intense, earthier aroma in a sensory trial. These results demonstrate the importance of UGTs in sequestering key volatile compounds in planta and suggest a future approach to enhancing aromas and flavours in flowers and during fruit ripening. Yauk YK1, Ged C, Wang MY, Matich AJ, Tessarotto L, Cooney JM, Chervin C, Atkinson RG

Correction: Aberrant iPSC-derived human astrocytes in Alzheimer's disease

The original version of this Article contained an error in Fig. 1, in which a number of incorrect fluorescence images were inadvertently incorporated into the panel. This has been corrected in both the PDF and HTML versions of the Article