A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors

Host proteins are essential for HIV entry and replication and can be important nonviral therapeutic targets. Large-scale RNA interference (RNAi)-based screens have identified nearly a thousand candidate host factors, but there is little agreement among studies and few factors have been validated. Here we demonstrate that a genome-wide CRISPR-based screen identifies host factors in a physiologically relevant cell system. We identify five factors, including the HIV co-receptors CD4 and CCR5, that are required for HIV infection yet are dispensable for cellular proliferation and viability. Tyrosylprotein sulfotransferase 2 (TPST2) and solute carrier family 35 member B2 (SLC35B2) function in a common pathway to sulfate CCR5 on extracellular tyrosine residues, facilitating CCR5 recognition by the HIV envelope. Activated leukocyte cell adhesion molecule (ALCAM) mediates cell aggregation, which is required for cell-to-cell HIV transmission. We validated these pathways in primary human CD4 + T cells through Cas9-mediated knockout and antibody blockade. Our findings indicate that HIV infection and replication rely on a limited set of host-dispensable genes and suggest that these pathways can be studied for therapeutic intervention

A generalized framework unifying image registration and respiratory motion models and incorporating image reconstruction, for partial image data or full images.

Surrogate-driven respiratory motion models relate the motion of the internal anatomy to easily acquired respiratory surrogate signals, such as the motion of the skin surface. They are usually built by first using image registration to determine the motion from a number of dynamic images, and then fitting a correspondence model relating the motion to the surrogate signals. In this paper we present a generalized framework that unifies the image registration and correspondence model fitting into a single optimization. This allows the use of 'partial' imaging data, such as individual slices, projections, or k-space data, where it would not be possible to determine the motion from an individual frame of data. Motion compensated image reconstruction can also be incorporated using an iterative approach, so that both the motion and a motion-free image can be estimated from the partial image data. The framework has been applied to real 4DCT, Cine CT, multi-slice CT, and multi-slice MR data, as well as simulated datasets from a computer phantom. This includes the use of a super-resolution reconstruction method for the multi-slice MR data. Good results were obtained for all datasets, including quantitative results for the 4DCT and phantom datasets where the ground truth motion was known or could be estimated

A generalized framework unifying image registration and respiratory motion models and incorporating image reconstruction, for partial image data or full images

Surrogate-driven respiratory motion models relate the motion of the internal anatomy to easily acquired respiratory surrogate signals, such as the motion of the skin surface. They are usually built by first using image registration to determine the motion from a number of dynamic images, and then fitting a correspondence model relating the motion to the surrogate signals. In this paper we present a generalized framework that unities the image registration and correspondence model fitting into a single optimization. This allows the use of 'partial' imaging data, such as individual slices, projections, or k-space data, where it would not be possible to determine the motion from an individual frame of data. Motion compensated image reconstruction can also be incorporated using an iterative approach, so that both the motion and a motion-free image can be estimated from the partial image data. The framework has been applied to real 4DCT, Cine CT, multi-slice CT, and multi-slice MR data, as well as simulated datasets from a computer phantom. This includes the use of a super-resolution reconstruction method for the multi-slice MR data. Good results were obtained for all datasets, including quantitative results for the 4DCT and phantom datasets where the ground truth motion was known or could be estimated.nifies the image registratio

Turner Review No. 8. Ecology and ecophysiology of grasstrees

Xanthorrhoea...is in habit one of the most remarkable genera of Terra Australis, and gives a peculiar character to the vegetation of that part of the country where it abounds’ Robert Brown (1814). Grasstrees (arborescent Xanthorrhoea, Dasypogon, Kingia), with their crown of long narrow leaves and blackened leafbase-covered trunk (caudex), are a characteristic growth form in the Australian flora. Xanthorrhoea is the most widespread genus, with 28 species that are prominent from heathlands to sclerophyll forests. While leaf production for X. preissii reaches a peak in spring–summer, growth never stops even in the cool winter or dry autumn seasons. Summer rain, accompanied by a rapid rise in leaf water potential, may be sufficient to stimulate leaf production, whereas root growth is confined to the usual wet season. Grasstrees are highly flammable yet rarely succumb to fire: while retained dead leaves may reach \u3e1000°C during fire, the temperature 100 mm above the stem apex remains \u3c60°C and the roots are insulated completely. Immediately following fire, leaf production from the intact apical meristem is up to six times greater than that at unburnt sites. For X. preissii, pre-fire biomass is restored within 40 weeks; the mass of live leaves remains uniform from thereon, whereas the mass of dead leaves increases steadily. Leaves usually survive for \u3e2 years. In X. preissii, the post-fire growth flush corresponds to a reduction in starch storage by desmium in the caudex. Minerals, especially P, are remobilised from the caudex to the crown following a spring fire, but accumulate there following an autumn fire. At least 80% of P is withdrawn from senescing leaves, while \u3e95% K and Na are leached from dead leaves. Most stored N and S are volatilised by fire, with 1–85% of all minerals returned as ash. Despite monthly clipping for 16 months, X. preissii plants recover, although starch reserves are depleted by 90%, indicating considerable resilience to herbivory. Analysis of colour band patterns in the leafbases of X. preissii shows that elongation of the caudex may vary more than 5–50 mm per annum, with 10–20 mm being typical. Exceptionally tall plants (\u3e3 m) may reach an age of 250 years, with a record at 450 years (6 m). Fires, recorded as black bands on the leafbases, in south-western Australia have been decreasing in frequency but increasing in variability since 1750–1850. Some grasstrees have survived a mean fire interval of 3–4 years over the last two centuries. In more recent times, some grasstrees have not been burnt for \u3e50 years. The band-analysis technique has been used to show a downward trend in plant δ13C of 2–5.5‰ from 1935 to the present. Grasstrees are most likely to flower in the first spring after fire. A single inflorescence is initiated from the apical meristem, elongating at up to 100 mm day–1 and reaching a length up to 3 m, with one recorded at 5.5 m. This rapid rate of elongation is achieved through leaf (and inflorescence) photosynthesis and desmium starch mobilisation. The developing spike and seeds are vulnerable to a moth larva. Leaf production recommences from axillary buds and the trade-off with reproduction is equivalent to 240 leaves in X. preissii. Flowering and seed production are affected by time of fire. Grasstrees are mainly insect-pollinated. Up to 8000 seeds per spike are produced, although pre-dispersal granivory is common. Seeds are released in autumn and persist in the soil for \u3c2 years. Most fresh seeds germinate in the laboratory but germination is inhibited by light. At any\u3etime, seedlings and juveniles may account for most plants in the population, although there may be up to an 80% reduction within 1 year of seedling emergence, often due to kangaroo herbivory. In the absence of fire, mortality of adults may be 4% per annum. Although few grasstree species are considered rare or threatened, their conservation requirements, especially in regard to a suitable fire regime, remain unknown. Grasstrees are particularly susceptible to the exotic root pathogen, Phytophthora cinnamomi, although recruitment among some species has been observed 20–30 years after pathogen invasion. Much remains to be known about the biology of this icon of the Australian bush