Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection

1. Download : Download high-res image (212KB)
2. Download : Download full-size image

     

Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization

Cyrtandra (Gesneriaceae) is a genus of flowering plants with over 800 species distributed throughout Southeast Asia and the Pacific Islands. On the Hawaiian Islands, 60 named species and over 89 putative hybrids exist, most of which are identified on the basis of morphology. Despite many previous studies on the Hawaiian Cyrtandra lineage, questions regarding the reconciliation of morphology and genetics remain, many of which can be attributed to the relatively young age and evidence of hybridization between species. We utilized targeted enrichment, high‐throughput sequencing, and modern phylogenomics tools to test 31 Hawaiian Cyrtandra samples (22 species, two putative hybrids, four species with two samples each, one species with four samples) and two outgroups for species relationships and hybridization in the presence of incomplete lineage sorting (ILS). Both concatenated and species‐tree methods were used to reconstruct species relationships, and network analyses were conducted to test for hybridization. We expected to see high levels of ILS and putative hybrids intermediate to their parent species. Phylogenies reconstructed from the concatenated and species‐tree methods were highly incongruent, most likely due to high levels of incomplete lineage sorting. Network analyses inferred gene flow within this lineage, but not always between taxa that we expected. Multiple hybridizations were inferred, but many were on deeper branches of the island lineages suggesting a long history of hybridization. We demonstrated the utility of high‐throughput sequencing and a phylogenomic approach using 569 loci to understanding species relationships and gene flow in the presence of ILS.     

Behaviour, natural history, and annual cycle of the Henderson Island rail Porzana atra (Aves: Rallidae)

The little known endemic Henderson Island rail (or Henderson rail) Porzflna atra , inhabits forest on the coastal plain and upraised plateau of Henderson Island. Rails were studied for 15 months from January 1991 to March 1992. The population was estimated at c. 6200 individuals living in pairs or cooperative groups of 3–4 adults on territories averaging about 1 ha. Two or three eggs were laid in covered or open nests near the ground from mid-July to mid-February. Up to five consecutive nesting attempts were made in cases where eggs or young chicks were lost. Adults laid a second clutch when chicks were fully feathered at about one month of age. Both sexes incubated and helped rear the young. Older chicks sometimes helped feed younger siblings. Dispersal of juveniles from the natal territory took place in April. Adult birds underwent a rapid, simultaneous post-nuptial moult of the remiges in February-April; the post-juvenile moult involved body feathers only. Data on morphometries, breeding ecology, courtship behaviour and voice are compared with available information for the spotless crake P. tabuensis , the Henderson rail's closest relative and probable ancestor. These comparisons provide some information on how these two taxa have differentiated since rails arrived on Henderson Island some time in the last 380000 years.     

Morphometric variation in nearly unstudied populations of the most studied mammal: The non-commensal house mouse (Mus musculus domesticus) in the Near East and Northern Africa

The phenotypic consequences in the house mouse (Mus musculus domesticus) of the transition from an ordinary field-dwelling rodent to a species that is dependent on human populations was studied by investigating the morphometric variation of non-commensal populations of M. m. domesticus from Syria, Jordan, SW Iran, and Libya and comparing them with that of conspecific commensal populations from Eastern Turkey, Greece, and Bulgaria. Commensal populations of M. musculus musculus from the Czech Republic were used as an outgroup. About 849 adult specimens of M. musculus were analysed by multivariate procedures based on standard molar, skull and body measurements. As expected, there was considerable variation among the studied populations and a good correspondence between morphometric and geographic distances. The resulting morphometric tree was consistent with the hypothesis that the original radiation of M. m. domesticus took place somewhere in the Near East. Commensal populations of M. m. domesticus form a single derived branch. Specimens originating from four different sites in eastern Syria showed the greatest similarity to one another and possessed relatively bigger molars than the other studied populations. Commensal populations were characterised by longer tails when compared to non-commensal populations, which suggests an adaptation for living in a more three-dimensionally heterogeneous environment for commensal populations.     

Hormones and liver mitochondria: Influence of growth hormone,thyroxine, testosterone,and insulin on thermotropic effects of respiration and fatty acid composition of membranes

The effects of hypophysectomy and subsequent administration of growth hormone, thyroxine, insulin, and testosterone were examined in rat liver for the relationship between the thermotropic effects on State 3 respiration (ADP induced) and fatty acid composition of the phospholipid fraction of intact mitochondria as well as of inner membrane vesicles. The Arrhenius profile for energy-linked (succinate) State 3 respiration of mitochondria from hypophysectomized rats lacked the discontinuity at 23.5 °C seen with mitochondria from normal rats. After injections of the hormones the discontinuity representing the transition temperature from gel to liquid crystalline state of lipids occurred at different temperatures: 18.5 °C for growth hormone, 26.0 °C for thyroxine, 19.5 °C for growth hormone + thyroxine, 27.6 °C for insulin, and 25.3 °C for testosterone. The energy of activation between 37.5 and 23.5 °C was 1.9 times greater for hypophysectomy than for controls. Growth hormone was the most effective in restoring the energy of activation to normal, above as well as below transition temperature. The effect of thyroxine appears to be due to a larger stimulation of the State 4 respiration than that of growth hormone, insulin, or testosterone, especially at higher temperatures. Phospholipids extracted from intact mitochondria or inner membrane vesicles of hypophysectomized rats contained less arachidonic acid (20:4) and more linoleic acid (18:2) than those of normal rats. In addition, the contents of some of the minor fatty acids were also changed. Calculated unsaturation index showed an 18.8 and 14.9% depletion in unsaturation in whole mitochondria and inner membranes, respectively. Among the different hormones used to treat the hypophysectomized rats, growth hormone was the most effective in restoring the transition temperature and fatty acid composition to normal levels and increasing the gain in body weight. Although the other hormones increased total unsaturation index to some extent, some of the individual fatty acids were affected differently. Good correlation exists between the unsaturation index of mitochondrial fatty acids and transition temperature of State 3 respiration. These results strongly suggest a role for the hormones, particularly growth hormone, in the control of mitochondrial membrane fluidity of hypophysectomized rat liver, through fatty acid composition of phospholipids.     

Intraspecific variation in host plant traits mediates taxonomic and functional composition of local insect herbivore communities

1. Host plant phenotypic traits affect the structure of the associated consumer community and mediate species interactions. Intraspecific variation in host traits is well documented, although a functional understanding of variable traits that drive herbivore community response is lacking. We address this gap by modelling the trait-environment relationship using insect traits and host plant traits in a multilevel model. 2. We compare herbivore assemblages from the canopy of the phenotypically variable tree Metrosideros polymorpha on Hawai‘i Island. Multiple distinct varieties of M. polymorpha frequently co-occur, with variation in morphological traits. Using this system, we identify host and insect traits that underlie patterns of herbivore abundance and quantify the strength of host-insect trait interactions. 3. This work examines plant-insect interactions at a community scale, across 36 herbivore species in three orders. We find that co-occurring trees of varying phenotype support distinct communities. Leaf traits, including specific leaf area, trichome presence, and leaf nutrients, explain 46% of variation in insect communities. We find that feeding guild and nymphal life history are correlated with host plant traits, and we show that model predictions are improved by including the host and insect trait interaction. 4. This study demonstrates how insect herbivores traits influence community response to morphologically variable hosts. Environmental heterogeneity indirectly affected herbivore community structure via intraspecific variation in host plants, providing an important source of variation for maintaining diversity in the broader community.     

Modulation of the immune response by Middle East respiratory syndrome coronavirus

Coronavirus (CoV) infections are commonly associated with respiratory and enteric disease in humans and animals. In 2012, a new human disease called Middle East respiratory syndrome (MERS) emerged in the Middle East. MERS was caused by a virus that was originally called human coronavirus-Erasmus Medical Center/2012 but was later renamed as Middle East respiratory syndrome coronavirus (MERS-CoV). MERS-CoV causes high fever, cough, acute respiratory tract infection, and multiorgan dysfunction that may eventually lead to the death of the infected individuals. The exact origin of MERS-CoV remains unknown, but the transmission pattern and evidence from virological studies suggest that dromedary camels are the major reservoir host, from which human infections may sporadically occur through the zoonotic transmission. Human to human transmission also occurs in healthcare facilities and communities. Recent studies on Middle Eastern respiratory continue to highlight the need for further understanding the virus-host interactions that govern disease severity and infection outcome. In this review, we have highlighted the major mechanisms of immune evasion strategies of MERS-CoV. We have demonstrated that M, 4a, 4b proteins and Plppro of MERS-CoV inhibit the type I interferon (IFN) and nuclear factor-κB signaling pathways and therefore facilitate innate immune evasion. In addition, nonstructural protein 4a (NSP4a), NSP4b, and NSP15 inhibit double-stranded RNA sensors. Therefore, the mentioned proteins limit early induction of IFN and cause rapid apoptosis of macrophages. MERS-CoV strongly inhibits the activation of T cells with downregulation of antigen presentation. In addition, uncontrolled secretion of interferon ɣ-induced protein 10 and monocyte chemoattractant protein-1 can suppress proliferation of human myeloid progenitor cells.