Evaluating the transmission risk of SARS-CoV-2 from sewage pollution.

The presence of SARS-CoV-2 in untreated sewage has been confirmed in many countries but its incidence and infection risk in contaminated waters is poorly understood. The River Thames in the UK receives untreated sewage from 57 Combined Sewer Overflows (CSOs), with many discharging dozens of times per year. This study investigated if such discharges provide a pathway for environmental transmission of SARS-CoV-2. Samples of wastewater, surface water, and sediment collected close to six CSOs on the River Thames were assayed over eight months for SARS-CoV-2 RNA and infectious virus. Bivalves were also sampled as an indicator species of viral bioaccumulation. Sediment and water samples from the Danube and Sava rivers in Serbia, where raw sewage is also discharged in high volumes, were assayed as a positive control. No evidence of SARS-CoV-2 RNA or infectious virus was found in UK samples, in contrast to RNA positive samples from Serbia. Furthermore, this study shows that infectious SARS-CoV-2 inoculum is stable in Thames water and sediment for <3 days, while SARS-CoV-2 RNA is detectable for at least seven days. This indicates that dilution of wastewater likely limits environmental transmission, and that detection of viral RNA alone is not an indication of pathogen spillover.

Ecological speciation in sympatric palms: 2. Pre- and post-zygotic isolation.

We evaluated reproductive isolation in two species of palms (Howea) that have evolved sympatrically on Lord Howe Island (LHI, Australia). We estimated the strength of some pre- and post-zygotic mechanisms in maintaining current species boundaries. We found that flowering time displacement between species is consistent across in and ex situ common gardens and is thus partly genetically determined. On LHI, pre-zygotic isolation due solely to flowering displacement was 97% for Howea belmoreana and 80% for H. forsteriana; this asymmetry results from H. forsteriana flowering earlier than H. belmoreana and being protandrous. As expected, only a few hybrids (here confirmed by genotyping) at both juvenile and adult stages could be detected in two sites on LHI, in which the two species grow intermingled (the Far Flats) or adjacently (Transit Hill). Yet, the distribution of hybrids was different between sites. At Transit Hill, we found no hybrid adult trees, but 13.5% of younger palms examined there were of late hybrid classes. In contrast, we found four hybrid adult trees, mostly of late hybrid classes, and only one juvenile F1 hybrid in the Far Flats. This pattern indicates that selection acts against hybrids between the juvenile and adult stages. An in situ reciprocal seed transplant between volcanic and calcareous soils also shows that early fitness components (up to 36 months) were affected by species and soil. These results are indicative of divergent selection in reproductive isolation, although it does not solely explain the current distribution of the two species on LHI.

Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy.

Ecological speciation requires divergent selection, reproductive isolation and a genetic mechanism to link the two. We examined the role of gene expression and coding sequence evolution in this process using two species of Howea palms that have diverged sympatrically on Lord Howe Island, Australia. These palms are associated with distinct soil types and have displaced flowering times, representing an ideal candidate for ecological speciation. We generated large amounts of RNA-Seq data from multiple individuals and tissue types collected on the island from each of the two species. We found that differentially expressed loci as well as those with divergent coding sequences between Howea species were associated with known ecological and phenotypic differences, including response to salinity, drought, pH and flowering time. From these loci, we identified potential 'ecological speciation genes' and further validate their effect on flowering time by knocking out orthologous loci in a model plant species. Finally, we put forward six plausible ecological speciation loci, providing support for the hypothesis that pleiotropy could help to overcome the antagonism between selection and recombination during speciation with gene flow.

The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant.

The location and timing of domestication of the olive tree, a key crop in Early Mediterranean societies, remain hotly debated. Here, we unravel the history of wild olives (oleasters), and then infer the primary origins of the domesticated olive. Phylogeography and Bayesian molecular dating analyses based on plastid genome profiling of 1263 oleasters and 534 cultivated genotypes reveal three main lineages of pre-Quaternary origin. Regional hotspots of plastid diversity, species distribution modelling and macrofossils support the existence of three long-term refugia; namely the Near East (including Cyprus), the Aegean area and the Strait of Gibraltar. These ancestral wild gene pools have provided the essential foundations for cultivated olive breeding. Comparison of the geographical pattern of plastid diversity between wild and cultivated olives indicates the cradle of first domestication in the northern Levant followed by dispersals across the Mediterranean basin in parallel with the expansion of civilizations and human exchanges in this part of the world.

A comparative analysis of the mechanisms underlying speciation on Lord Howe Island.

On Lord Howe Island, speciation is thought to have taken place in situ in a diverse array of distantly related plant taxa (Metrosideros, Howea and Coprosma; Proc. Natl Acad. Sci. USA 108, 2011, 13188). We now investigate whether the speciation processes were driven by divergent natural selection in each genus by examining the extent of ecological and genetic divergence. We present new and extensive, ecological and genetic data for all three genera. Consistent with ecologically driven speciation, outlier loci were detected using genome scan methods. This mechanism is supported by individual-based analyses of genotype-environment correlations within species, demonstrating that local adaptation is currently widespread on the island. Genetic analyses show that prezygotic isolating barriers within species are currently insufficiently strong to allow further population differentiation. Interspecific hybridization was found in both Howea and Coprosma, and species distribution modelling indicates that competitive exclusion may result in selection against admixed individuals. Colonization of new niches, partly fuelled by the rapid generation of new adaptive genotypes via hybridization, appears to have resulted in the adaptive radiation in Coprosma - supporting the 'Syngameon hypothesis'.

Impedance spectroscopy in monitoring the maturation of stem cell-derived retinal pigment epithelium.

The development and differentiation of stem cell-derived impermeable retinal pigment epithelium (RPE) with tight junctions (TJs) is a gradual process that is, at confluence, controlled by cell-to-cell contact. The objective of this study was to evaluate the use of electric impedance spectroscopy (EIS) to follow the maturation and development of barrier function in human embryonic stem cell-derived RPE (hESC-RPE). Barrier function was assessed using EIS, permeability measurements, and microscopic inspection in intact cells and following calcium sequestration with ethylene glycol tetraacetic acid (EGTA). The results showed that the cultures with the most mature morphology had the highest impedance and the lowest permeability values. The EIS of samples of high integrity fitted well to the equivalent model of a single RC circuit, whereas the semicircular shape of the Nyquist plots was distorted for samples of lower integrity. EGTA treatment resulted in lower impedance values and changes in the shapes of plots. Our results show that EIS-as a measure of overall maturity and integrity of the epithelium-is useful when evaluating the maturity of cell cultures. It is highly warranted in future transplantation therapies and in in vitro cell culture models in drug development.

Hybrid external fixation in treatment of proximal tibial fractures: a good outcome in AO/ASIF type-C fractures.

INTRODUCTION: The treatment of proximal tibial fractures is often challenging, and internal fixation is occasionally associated with problems in wound healing due to frequently co-existing soft tissue injuries. External fixation of these fractures have yielded satisfactory results, but some studies have reported problems in the achievement and maintenance of fracture reduction. The purpose of the present study was to evaluate the performance of a hybrid external fixator in the treatment of different types of proximal tibial fractures. MATERIALS AND METHODS: Thirty-three proximal tibial fractures, of which 20 were high energetic, were treated with a hybrid external fixator (Tenxor Strker-Howmedica) in the acute phase. Fracture categorisation was done according to AO/ASIF, and the reduction was performed most often by closed means or through mini-open reduction (26/78.8%). The patients were followed up to an average of 12.7 months (range 10-22) and were evaluated with radiographs and clinical examinations. RESULTS: Five AO/ASIF type-C intraarticular fractures had a poor postoperative reduction, and were thus treated with internal fixation in a second operation. Of the remaining 28 patients, local and transient pin tract infection was observed in seven patients, and one had septic arthritis of the knee. All 13 C1 and five of six C2/C3 fractures united in mean time of 15.1 weeks, whereas three of nine type-A fractures failed to unite, albeit an adequate reduction, and needed a second operation (odds ratio 11.4, 95% CI 1.0-143, compared with type-C fractures). For the remaining six type-A fractures, the mean healing time was 24 weeks (mean difference 8.9, 95% CI 6-12 weeks compared with type-C fractures). Age over 48 and the presence of an open fracture, but not fracture type, gender, or the level of injury energy, correlated to a poor subjective outcome. CONCLUSIONS: The hybrid external fixation method we have used is safe, and type-C1 fractures are particularly suitable to be treated with this method. However, even C2/C3 fractures may be candidates for this method, but a meticulous fracture reduction should be performed. Type-A fractures are liable to healing problems when the fixator is used as a rigid complex.

Phylogeny, biogeography, and ecology of Ficus section Malvanthera (Moraceae).

We conducted the first molecular phylogenetic study of Ficus section Malvanthera (Moraceae; subgenus Urostigma) based on 32 Malvanthera accessions and seven outgroups representing other sections of Ficus subgenus Urostigma. We used DNA sequences from the nuclear ribosomal internal and external transcribed spacers (ITS and ETS), and the glyceraldehyde-3-phosphate dehydrogenase (G3pdh) region. Phylogenetic analysis using maximum parsimony, maximum likelihood and Bayesian methods recovered a monophyletic section Malvanthera to the exclusion of the rubber fig, Ficus elastica. The results of the phylogenetic analyses do not conform to any previously proposed taxonomic subdivision of the section and characters used for previous classification are homoplasious. Geographic distribution, however, is highly conserved and Melanesian Malvanthera are monophyletic. A new subdivision of section Malvanthera reflecting phylogenetic relationships is presented. Section Malvanthera likely diversified during a period of isolation in Australia and subsequently colonized New Guinea. Two Australian series are consistent with a pattern of dispersal out of rainforest habitat into drier habitats accompanied by a reduction in plant height during the transition from hemi-epiphytic trees to lithophytic trees and shrubs. In contradiction with a previous study of Pleistodontes phylogeny suggesting multiple changes in pollination behaviour, reconstruction of changes in pollination behaviour on Malvanthera, suggests only one or a few gains of active pollination within the section.

Measuring the fate of plant diversity: towards a foundation for future monitoring and opportunities for urgent action.

Vascular plants are often considered to be among the better known large groups of organisms, but gaps in the available baseline data are extensive, and recent estimates of total known (described) seed plant species range from 200000 to 422000. Of these, global assessments of conservation status using International Union for the Conservation of Nature (IUCN) categories and criteria are available for only approximately 10000 species. In response to recommendations from the Conference of the Parties to the Convention on Biological Diversity to develop biodiversity indicators based on changes in the status of threatened species, and trends in the abundance and distribution of selected species, we examine how existing data, in combination with limited new data collection, can be used to maximum effect. We argue that future work should produce Red List Indices based on a representative subset of plant species so that the limited resources currently available are directed towards redressing taxonomic and geographical biases apparent in existing datasets. Sampling the data held in the world's major herbaria, in combination with Geographical Information Systems techniques, can produce preliminary conservation assessments and help to direct selective survey work using existing field networks to verify distributions and gather population data. Such data can also be used to backcast threats and potential distributions through time. We outline an approach that could result in: (i) preliminary assessments of the conservation status of tens of thousands of species not previously assessed, (ii) significant enhancements in the coverage and representation of plant species on the IUCN Red List, and (iii) repeat and/or retrospective assessments for a significant proportion of these. This would result in more robust Sampled Red List Indices that can be defended as more representative of plant diversity as a whole; and eventually, comprehensive assessments at species level for one or more major families of angiosperms. The combined results would allow scientifically defensible generalizations about the current status of plant diversity by 2010 as well as tentative comments on trends. Together with other efforts already underway, this approach would establish a firmer basis for ongoing monitoring of the status of plant diversity beyond 2010 and a basis for comparison with the trend data available for vertebrates.

Pertrochanteric femoral fractures treated with a dynamic hip screw or a proximal femoral nail. A randomised study comparing post-operative rehabilitation.

We treated 108 patients with a pertrochanteric femoral fracture using either the dynamic hip screw or the proximal femoral nail in this prospective, randomised series. We compared walking ability before fracture, intra-operative variables and return to their residence. Patients treated with the proximal femoral nail (n = 42) had regained their pre-operative walking ability significantly (p = 0.04) more often by the four-month review than those treated with the dynamic hip screw (n = 41). Peri-operative or immediate post-operative measures of outcome did not differ between the groups, with the exception of operation time. The dynamic hip screw allowed a significantly greater compression of the fracture during the four-month follow-up, but consolidation of the fracture was comparable between the two groups. Two major losses of reduction were observed in each group, resulting in a total of four revision operations. Our results suggest that the use of the proximal femoral nail may allow a faster post-operative restoration of walking ability, when compared with the dynamic hip screw.

Femoral shaft medialisation and neck-shaft angle in unstable pertrochanteric femoral fractures.

We analysed the time-dependent mean changes in the femoral neck length, neck-shaft angle and hip offset in a randomised study comprising 48 patients who were treated with the dynamic hip screw (DHS) or the proximal femoral nail (PFN) for an unstable intertrochanteric femoral fracture. As a consequence of fracture compression, the mean post-operative neck length was significantly shorter in patients treated with the DHS. During the first 6 weeks after the operation, a mean decrease of 4.6 degrees was observed in the neck-shaft angle, but there was not a significant difference between the treatment groups. The radiographic measures remained virtually unaffected during the interval from 6 weeks to 4 months in both groups. When the operated hip was compared to the opposite hip, patients who had received the DHS showed significantly greater medialisation of the femoral shaft at 4 months than those treated with the PFN. We thus recommend that unstable intertrochanteric fractures should be initially reduced in a slight valgus position in order to achieve an outcome after healing that is as normal as possible. As a result of differences in operative technique and implant stability, the PFN may be superior to the DHS in retaining the anatomical relations in the hip region in unstable intertrochanteric fractures.

Testing genetic susceptibility loci for alcoholic heart muscle disease.

BACKGROUND: Although many heavy alcohol users have subclinical alcoholic heart muscle disease, only a very few develop severe dilated cardiomyopathy. Therefore, and because cardiac abnormalities correlate only weakly with the duration or quantity of drinking, individual susceptibility differences may exist. In this work we examined whether common gene variants previously associated with cardiac hypertrophy or altered alcohol metabolism could modify the effects of alcohol on the heart. METHODS: We studied 700 middle-aged male victims of sudden death who underwent a medicolegal autopsy. In addition to routine postmortem examination, the weights and the cavity and wall dimensions of the left and right ventricle were measured. Coronary artery stenoses were determined from a silicone rubber cast of the arteries. Alcohol consumption and cardiovascular risk factors were assessed by a structured interview of the spouse. The following gene polymorphisms were determined by using polymerase chain reaction restriction fragment length polymorphism and solid-phase minisequencing techniques: angiotensin converting enzyme I/D, angiotensin II type 1 receptor 1166A/C, aldosterone synthase -344C/T, alcohol dehydrogenases 2 and 3, acetaldehyde dehydrogenase 2, and cytochrome P-450 2E1 DraI, PstI, RsaI, and MspI. RESULTS: The most consistent effects of alcohol (p < 0.05) were a higher total heart weight and a larger right ventricle size with increasing daily drinking. However, these and other effects of alcohol were statistically fully independent of the studied genotypes. CONCLUSIONS: The gene polymorphisms selected for and analyzed in our study are unlikely to modify the effects of alcohol on the heart. Other unknown factors determine the individual susceptibility to alcoholic heart muscle disease.

Evolution of the angiosperms: calibrating the family tree.

Growing evidence of morphological diversity in angiosperm flowers, seeds and pollen from the mid Cretaceous and the presence of derived lineages from increasingly older geological deposits both imply that the timing of early angiosperm cladogenesis is older than fossil-based estimates have indicated. An alternative to fossils for calibrating the phylogeny comes from divergence in DNA sequence data. Here, angiosperm divergence times are estimated using non-parametric rate smoothing and a three-gene dataset covering ca. 75% of all angiosperm families recognized in recent classifications. The results provide an initial hypothesis of angiosperm diversification times. Using an internal calibration point, an independent evaluation of angiosperm and eudicot origins is performed. The origin of the crown group of extant angiosperms is indicated to be Early to Middle Jurassic (179-158 Myr), and the origin of eudicots is resolved as Late Jurassic to mid Cretaceous (147-131 Myr). Both estimates, despite a conservative calibration point, are older than current fossil-based estimates.

Dose dependent but non-linear effects of alcohol on the left and right ventricle.

OBJECTIVE: To assess how left (LV) and right ventricular (RV) size, wall thickness, and mass depend on daily alcohol consumption. Among alcoholics, most common findings have been LV hypertrophy and mild systolic or diastolic dysfunction, accompanied occasionally by ventricular dilatation resembling dilated cardiomyopathy. Although it is commonly agreed that chronic heavy alcohol use is injurious to the heart, the dose-injury relation remains a matter of dispute. DESIGN: Prospective series of 700 Finnish men aged 33-70 years who died out of hospital and underwent a medicolegal necropsy. METHODS AND RESULTS: Data on alcohol use and other risk factors were obtained from the spouse. At necropsy, a transversal slice of the heart was traced on a transparent sheet and analysed later for LV and RV cavity areas and wall thicknesses. Coronary artery stenoses were measured from silicone casts of the arteries. In analyses of all men, daily alcohol dose predicted heart weight (beta = 0.17, p < 0.001) and RV cavity area (beta = 0.14, p = 0.007) independent of body size, age, coronary artery disease, hypertension, diabetes, and smoking. In the subgroup of men free of significant coronary artery disease, LV area averaged (SEM) 11.0 (1.0) cm(2) in men drinking < 12 g/day, 7.7 (0.7) cm(2) in those drinking 72-180 g/day, and 10.0 (0.9) cm(2) in those drinking > 180 g/day (p = 0.054). Very heavy drinking (> 180 g/day) was associated with an increase in RV cavity area (p = 0.005). CONCLUSIONS: The effects of alcohol on the heart in middle aged men are dose dependent but partly non-linear. In the absence of coronary artery disease, LV size shows a U shaped reduction with increasing daily alcohol use accompanied by an increase in RV size with very heavy drinking. These findings question the idea of progressive LV dilatation with increasing alcohol consumption among male victims of sudden death.

Evolutionary rates and species diversity in flowering plants.

Genetic change is a necessary component of speciation, but the relationship between rates of speciation and molecular evolution remains unclear. We use recent phylogenetic data to demonstrate a positive relationship between species numbers and the rate of neutral molecular evolution in flowering plants (in both plastid and nuclear genes). Rates of protein and morphological evolution also correlate with the neutral substitution rate, but not with species numbers. Our findings reveal a link between the rate of neutral molecular change within populations and the evolution of species diversity.

Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA, phytochrome B, rbcL, atpB, and morphology.

Phylogenetic relationships within Celastraceae (spindle-tree family) were inferred from nucleotide sequence characters from the 5' end of 26S nuclear ribosomal DNA (including expansion segments D1-D3; 84 species sampled), phytochrome B (58 species), rbcL (31 species), atpB (23 species), and morphology (94 species). Among taxa of questionable affinity, Forsellesia is a member of Crossosomataceae, and Goupia is excluded from Celastraceae. However, Brexia, Canotia, Lepuropetalon, Parnassia, Siphonodon, and Stackhousiaceae are supported as members of Celastraceae. Gymnosporia and Tricerma are distinct from Maytenus, Cassine is supported as distinct from Elaeodendron, and Dicarpellum is distinct from Salacia. Catha, Maytenus, and Pristimera are not resolved as natural genera. Hippocrateaceae (including Plagiopteron and Lophopetalum) are a clade nested within a paraphyletic Celastraceae. These data also suggest that the Loesener's classification of Celastraceae sensu stricto and Hallé's classification of Hippocrateaceae are artificial. The diversification of the fruit and aril within Celastraceae appears to be complex, with multiple origins of most fruit and aril forms.

Promoter polymorphism of the CD14 endotoxin receptor gene as a risk factor for alcoholic liver disease.

Twin concordance studies indicate that genetic factors influence the individual susceptibility for alcoholic liver disease (ALD). Both clinical and experimental data suggest that Kupffer cell activation by gut-derived endotoxins and other bacterial products is an important pathogenic factor. Activated Kupffer cells release proinflammatory cytokines, a process that is regulated by the CD14 endotoxin receptor (CD14). Recently, a C-->T (-159) polymorphism in the promoter region of the CD14 gene was detected and found to confer increased CD14 expression. In the present study, the association of CD14 promoter polymorphism with different forms of ALD was examined in 3 separate autopsy series. Among 442 men with valid alcohol-consumption data, 381 men had been moderate or heavy alcohol consumers. The allele frequency of the CD14 promoter genotype, determined by a modified cycle minisequencing technique, was 0.34 (CC), 0.51 (CT), and 0.16 (TT). The T allele was found to be associated with advanced ALD, i.e., with alcoholic hepatitis (odds ratio [OR]: 2.48; P = .018), and especially with cirrhosis (OR: 3.45; P = .004), but not with fatty liver, periportal fibrosis, or bridging fibrosis. The overall age-adjusted risk for cirrhosis was 3.08 (P = .01) for the carriers of the CT genotype, and 4.17 (P = .005) for the homozygous TT genotype. These results suggest that in the relatively isolated Finnish population, the T allele confers increased risk of alcoholic liver damage. In particular, TT homozygotes are at a high risk to develop cirrhosis.

Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology.

Phylogenetic relationships within Celastraceae were inferred using a simultaneous analysis of 61 morphological characters and 1123 base pairs of phytochrome B exon 1 from the nuclear genome. No gaps were inferred, and the gene tree topology suggests that the primers were specific to a single locus that did not duplicate among the lineages sampled. This region of phytochrome B was most useful for examining relationships among closely related genera. Fifty-one species from 38 genera of Celastraceae were sampled. The Celastraceae sensu lato (including Hippocrateaceae) were resolved as a monophyletic group. Loesener's subfamilies and tribes of Celastraceae were not supported. The Hippocrateaceae were resolved as a monophyletic group nested within a paraphyletic Celastraceae sensu stricto. Goupia was resolved as more closely related to Euphorbiaceae, Corynocarpaceae, and Linaceae than to Celastraceae. Plagiopteron (Flacourtiaceae) was resolved as the sister group of Hippocrateoideae. Brexia (Brexiaceae) was resolved as closely related to Elaeodendron and Pleurostylia. Canotia was resolved as the sister group of Acanthothamnus within Celastraceae. Perrottetia and Mortonia were resolved as the sister group of the rest of the Celastraceae. Siphonodon was resolved as a derived member of Celastraceae. Maytenus was resolved as three disparate groups, suggesting that this large genus needs to be recircumscribed.

Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences.

Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84:1-49), we present a phylogenetic analysis of flowering plants based on a second plastid gene, atpB, analyzed separately and in combination with rbcL sequences for 357 taxa. Despite some discrepancies, the atpB-based phylogenetic trees were highly congruent with those derived from the analysis of rbcL and 18S rDNA, and the combination of atpB and rbcL DNA sequences (comprising approximately 3000 base pairs) produced increased bootstrap support for many major sets of taxa. The angiosperms are divided into two major groups: noneudicots with inaperturate or uniaperturate pollen (monocots plus Laurales, Magnoliales, Piperales, Ceratophyllales, and Amborellaceae-Nymphaeaceae-Illiciaceae) and the eudicots with triaperturate pollen (particularly asterids and rosids). Based on rbcL alone and atpB/rbcL combined, the noneudicots (excluding Ceratophyllum) are monophyletic, whereas in the atpB trees they form a grade. Ceratophyllum is sister to the rest of angiosperms with rbcL alone and in the combined atpB/rbcL analysis, whereas with atpB alone, Amborellaceae, Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the base of the angiosperms. The phylogenetic information at each codon position and the different types of substitutions (observed transitions and transversions in the trees vs. pairwise comparisons) were examined; taking into account their respective consistency and retention indices, we demonstrate that third-codon positions and transitions are the most useful characters in these phylogenetic reconstructions. This study further demonstrates that phylogenetic analysis of large matrices is feasible.