miR-34a is a tumor suppressor in zebrafish and its expression levels impact metabolism, hematopoiesis and DNA damage.

Li-Fraumeni syndrome is caused by inherited TP53 tumor suppressor gene mutations. MicroRNA miR-34a is a p53 target and modifier gene. Interestingly, miR-34 triple-null mice exhibit normal p53 responses and no overt cancer development, but the lack of miR-34 promotes tumorigenesis in cancer-susceptible backgrounds. miR-34 genes are highly conserved and syntenic between zebrafish and humans. Zebrafish miR-34a and miR-34b/c have similar expression timing in development, but miR-34a is more abundant. DNA damage by camptothecin led to p53-dependent induction of miR-34 genes, while miR-34a mutants were adult-viable and had normal DNA damage-induced apoptosis. Nevertheless, miR-34a-/- compound mutants with a gain-of-function tp53R217H/ R217H or tp53-/- mutants were more cancer-prone than tp53 mutants alone, confirming the tumor-suppressive function of miR-34a. Through transcriptomic comparisons at 28 hours post-fertilization (hpf), we characterized DNA damage-induced transcription, and at 8, 28 and 72 hpf we determined potential miR-34a-regulated genes. At 72 hpf, loss of miR-34a enhanced erythrocyte levels and up-regulated myb-positive hematopoietic stem cells. Overexpression of miR-34a suppressed its reporter mRNA, but not p53 target induction, and sensitized injected embryos to camptothecin but not to γ-irradiation.

Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas.

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.

Temporal changes in allele frequencies in a small marble trout Salmo marmoratus population threatened by extreme flood events.

The effect of extreme floods on the genetic composition of marble trout Salmo marmoratus living in Lipovscek, a tributary of the Soca River in Slovenia, which has been affected by multiple destructive flood events for centuries was investigated. By monitoring genetic variability during the period 2004-2011, apparent signatures of genetic erosion including a decline in observed and expected heterozygosities and allelic richness were observed. Contemporary effective population size was estimated between 11 and 55 individuals, which is congruent with census data. The data suggest asymmetric gene flow between the two sections of the river. The existence of substantial downstream migration (15-19%) was confirmed by paternity analysis. A small (1-3%) upstream migration was also suggested, which was confirmed by tagging data. Overall, low genetic diversity has not prevented the survival of the Lipovscek population, which might be a common feature of salmonid freshwater populations.

Matching oceanography and genetics at the basin scale. Seascape connectivity of the Mediterranean shore crab in the Adriatic Sea.

Investigating the interactions between the physical environment and early life history is crucial to understand the mechanisms that shape the genetic structure of marine populations. Here, we assessed the genetic differentiation in a species with larval dispersal, the Mediterranean shore crab (Carcinus aestuarii) in the Adriatic Sea (central Mediterranean), and we investigated the role of oceanic circulation in shaping population structure. To this end, we screened 11 polymorphic microsatellite loci from 431 individuals collected at eight different sites. We found a weak, yet significant, genetic structure into three major clusters: a northern Adriatic group, a central Adriatic group and one group including samples from southern Adriatic and Ionian seas. Genetic analyses were compared, under a seascape genetics approach, with estimates of potential larval connectivity obtained with a coupled physical-biological model that integrates a water circulation model and a description of biological traits affecting dispersal. The cross-validation of the results of the two approaches supported the view that genetic differentiation reflects an oceanographic subdivision of the Adriatic Sea into three subbasins, with circulation patterns allowing the exchange of larvae through permanent connections linking north Adriatic sites and ephemeral connections like those linking the central Adriatic with northern and southern locations.

Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus).

This study provides a first description of the phylogeographic patterns and evolutionary history of two species of the mudskipper genus Periophthalmus. These amphibious gobies are distributed throughout the whole Indo-Pacific region and Atlantic coast of Africa, in peritidal habitats of soft-bottom coastal ecosystems. Three sequence datasets of two widely distributed species, Periophthalmus argentilineatus and P. kalolo, were obtained by amplifying and sequencing two mtDNA markers (D-loop and 16S rDNA) and the nDNA rag1 region. The three datasets were then used to perform phylogeographic, demographic and population genetic analyses. Our results indicate that tectonic events and past climatic oscillations strongly contributed to shape present genetic differentiation, phylogeographic and demographic patterns. We found support for the monophyly of P. kalolo, and only shallow genetic differentiation between East-African and Indo-Malayan populations of this species. However, our collections of the morphospecies P. argentilineatus include three molecularly distinct lineages, one of them more closely related to P. kalolo. The presence of Miocenic timings for the most recent common ancestors of some of these morphologically similar clades, suggests the presence of strong stabilising selection in mudskippers' habitats. At population level, demographic analyses and palaeoecological records of mangrove ecosystems suggest that Pleistocene bottlenecks and expansion plus secondary contact events of the studied species were associated with recurrent sea transgressions during interglacials, and sea regressions or stable regimes during glacials, respectively.

Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation.

Determining the timing, extent and underlying causes of interspecific gene exchange during or following speciation is central to understanding species' evolution. Antarctic notothenioid fish, thanks to the acquisition of antifreeze glycoproteins during Oligocene transition to polar conditions, experienced a spectacular radiation to >100 species during Late Miocene cooling events. The impact of recent glacial cycles on this group is poorly known, but alternating warming and cooling periods may have affected species' distributions, promoted ecological divergence into recurrently opening niches and/or possibly brought allopatric species into contact. Using microsatellite markers and statistical methods including Approximate Bayesian Computation, we investigated genetic differentiation, hybridization and the possible influence of the last glaciation/deglaciation events in three icefish species of the genus Chionodraco. Our results provide strong evidence of contemporary and past introgression by showing that: (i) a substantial fraction of contemporary individuals in each species has mixed ancestry, (ii) evolutionary scenarios excluding hybridization or including it only in ancient times have small or zero posterior probabilities, (iii) the data support a scenario of interspecific gene flow associated with the two most recent interglacial periods. Glacial cycles might therefore have had a profound impact on the genetic composition of Antarctic fauna, as newly available shelf areas during the warmer intervals might have favoured secondary contacts and hybridization between diversified groups. If our findings are confirmed in other notothenioids, they offer new perspectives for understanding evolutionary dynamics of Antarctic fish and suggest a need for new predictions on the effects of global warming in this group.

A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing.

Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control's 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach.

Phylogenetic relationships and demographic histories of the Atherinidae in the Eastern Atlantic and Mediterranean Sea re-examined by Bayesian inference.

The aim of our study is to examine the phylogenetic relationship, divergence times and demographic history of the five close-related Mediterranean and North-eastern Atlantic species/forms of Atherina using the full Bayesian framework for species tree estimation recently implemented in ∗BEAST. The inference is made possible by multilocus data using three mitochondrial genes (12S rRNA, 16S rRNA, control region) and one nuclear gene (rhodopsin) from multiple individuals per species available in GenBank. Bayesian phylogenetic analysis of the complete gene dataset produced a tree with strong support for the monophyly of each species, as well as high support for higher level nodes. An old origin of the Atherina group was suggested (19.2 MY), with deep split events within the Atherinidae predating the Messinian Salinity Crisis. Regional genetic substructuring was observed among populations of A. boyeri, with AMOVA and MultiDimensional Scaling suggesting the existence of five groupings (Atlantic/West Mediterranean, Adriatic, Greece, Black Sea and Tunis). The level of subdivision found might be consequence of the hydrographic isolation within the Mediterranean Sea. Bayesian inference of past demographic histories showed a clear signature of demographic expansion for the European coast populations of A. presbyter, possibly linked to post-glacial colonizations, but not for the Azores/Canary Islands, which is expected in isolated populations because of the impossibility of finding new habitats. Within the Mediterranean, signatures of recent demographic expansion were only found for the Adriatic population of A. boyeri, which could be associated with the relatively recent emergence of the Adriatic Sea.

Spatial asymmetry of the paternity success in nests of a fish with alternative reproductive tactics.

Guard-sneaker tactics are widespread among fish, where territorial males defend a nest and provide parental care while sneakers try to steal fertilizations. Territorials and sneakers adopt diverse pre- and post-mating strategies, adjusting their ejaculate investment and/or behavioural responses to the presence of competitors. The relative distance of competitors from the spawning female plays a major role in influencing male mating strategies and the resulting paternity share. However, territorial male quality and sneaking intensity do not fully account for the variability in the relative siring success occurring among species. An often neglected factor potentially affecting sneakers proximity to females is the nest structure. We conducted a field experiment using the black goby, whose nests show two openings of different size. We found that territorial males defend more and sneaking pressure is higher at the front, larger access of the nest than at the back, smaller one. Moreover, microsatellite paternity analysis shows that territorials sire more offspring at the back of their nest. Such a predictable spatial distribution of the paternity share suggests that nest structure might work as an indirect cue of male relative siring success, potentially influencing the territorial male investment in parental care and/or the female egg deposition strategy.

Inferring the demographic history of the Adriatic Flexopecten complex.

Phylogenetic analysis of DNA sequences can be a useful tool in taxonomical studies, which has important implications in terms of species traceability. The aim of our study is to solve the controversy regarding the taxonomical status of the Flexopecten group, which includes two putative sister species (F. glaber and F. proteus) that co-occur in the Adriatic Sea and are clearly distinguishable on the basis of morphometric characters. Our molecular analysis using three mitochondrial genes (COI, 12S rRNA and 16S rRNA) and one nuclear gene (Histone H3) suggest that F. glaber and F. proteus are the same species, as evidenced by both putative species appearing mixed in all genetic trees with no clustering according to species. Using a Bayesian approach, we inferred the demographic history of the Flexopecten group, which suggests that first F. glaber occurred in the Mediterranean, then F. glaber colonized the Adriatic sometime in the last 18,000 years, and finally the F. proteus morph appeared only recently in the Adriatic Sea. We propose F. proteus to be synonymized with F. glaber, which should have priority and be used in the future.

Genetic variability is unrelated to growth and parasite infestation in natural populations of the European eel (Anguilla anguilla).

Positive correlations between individual genetic heterozygosity and fitness-related traits (HFCs) have been observed in organisms as diverse as plants, marine bivalves, fish or mammals. HFCs are not universal and the strength and stability of HFCs seem to be variable across species, populations and ages. We analysed the relationship between individual genetic variability and two different estimators of fitness in natural samples of European eel, growth rate (using back-calculated length-at-age 1, 2 and 3) and parasite infestation by the swimbladder nematode Anguillicola crassus. Despite using a large data set of 22 expressed sequence tags-derived microsatellite loci and a large sample size of 346 individuals, no heterozygote advantage was observed in terms of growth rate or parasite load. The lack of association was evidenced by (i) nonsignificant global HFCs, (ii) a Multivariate General Linear Model showing no effect of heterozygosity on fitness components, (iii) single-locus analysis showing a lower number of significant tests than the expected false discovery rate, (iv) sign tests showing only a significant departure from expectations at one component, and, (v) a random distribution of significant single-locus HFCs that was not consistent across fitness components or sampling sites. This contrasts with the positive association observed in farmed eels in a previous study using allozymes, which can be explained by the nature of the markers used, with the allozyme study including many loci involved in metabolic energy pathways, while the expressed sequence tags-linked microsatellites might be located in genes or in the proximity of genes uncoupled with metabolism/growth.

Genetic composition of Atlantic and Mediterranean recruits of European eel Anguilla anguilla based on EST-linked microsatellite loci.

Anguilla anguilla glass eels arriving at two Mediterranean and two Atlantic sites were tested for differences in genetic composition between regions using a total of 23 microsatellite loci developed from an expressed sequence tag (EST) library. Hierarchical analysis of molecular variance indicated a non-significant difference between regions (Mediterranean v. Atlantic), which contrasted with the significant differences observed between samples within regions. The existence of a single spawning site for all A. anguilla individuals and extensive migration loop with great opportunity for mixing of individuals might explain the homogeneity in genetic composition found between regions. The observation of a (small-scale) pattern of genetic patchiness among intra-annual samples (arrival waves) within geographic regions does not conflict with the lack of (large-scale) geographic sub-structuring found between the Mediterranean and Atlantic regions, but most likely is a consequence of the strong dependence of A. anguilla on oceanic conditions in the Sargasso Sea that might result in a limited parental contribution to each spawning event. The comparison of Atlantic and Mediterranean A. anguilla glass eel recruits based on EST-linked microsatellite loci provides evidence supporting the hypothesis of panmixia A. anguilla across Europe.

Association of ethnicity, Fitzpatrick skin type, and hirsutism: A retrospective cross-sectional study of women with polycystic ovarian syndrome.

BACKGROUND: The complex interplay between ethnicity, Fitzpatrick skin type (FST), and hirsutism in patients with polycystic ovarian syndrome (PCOS) is poorly understood. OBJECTIVE: In this cross-sectional, retrospective analysis, we examined the prevalence, severity, and distribution of hirsutism with clinician-rated site-specific and total modified Ferriman-Gallwey (mFG) visual scoring in a diverse cohort of American patients with PCOS. METHODS: Independent analyses were conducted on the basis of patient-reported FST ratings and ethnicity. RESULTS: In this PCOS cohort, a correlation was found between hirsutism and ethnicity and the highest prevalence of hirsutism and total mFG scores was observed in Hispanic, Middle Eastern, African American, and South Asian patients. A positive correlation between hirsutism and FST was also observed with an increasing prevalence of hirsutism in the group of patients with higher FSTs. Significant trends in the anatomic distribution of hirsutism were observed between ethnic groups as well. A higher facial mFG score was found in African American patients but higher mFG scores in the truncal and extremity regions were observed in Middle Eastern patients. Truncal hirsutism was also associated with higher FSTs. CONCLUSIONS: Ethnicity and FST may be important variables in both the quantitative and qualitative presentations of hirsutism in women with PCOS and should be considered in the diagnostic evaluation of any patient who is suspected of having the condition. Previously published studies that examined ethnicity, FST, and hirsutism in homogeneous cohorts limited comparison and generalizability but the strength of this study lies in its detailed analysis within a single large and diverse PCOS cohort. Validated studies are needed to determine whether clinical criteria for hirsutism should be adjusted for ethnicity and FST in the PCOS population and particularly within diverse cohorts and patients of mixed ancestry.

Crisaborole and its potential role in treating atopic dermatitis: overview of early clinical studies.

Atopic dermatitis (AD), a chronic, relapsing, inflammatory skin disease that is characterized by intense pruritus and eczematous lesions with up to 90% of patients presenting with mild to moderate disease. Current topical treatments for AD have not changed in over 15 years and are associated with safety concerns. In AD, overactivity of phosphodiesterase 4 (PDE4), leads to inflammation and disease exacerbation. Crisaborole Topical Ointment, 2%, is a novel, nonsteroidal, topical anti-inflammatory PDE4 inhibitor currently being investigated for the treatment of mild to moderate AD. Preliminary studies in children and adults demonstrated favorable efficacy and safety profiles. Crisaborole may represent an anti-inflammatory option that safely minimizes the symptoms and severity of AD and that can be used for both acute and long-term management.

Tavaborole topical solution, 5% for the treatment of toenail onychomycosis.

Tavaborole topical solution, 5% (tavaborole) is a novel, boron-based, antifungal pharmaceutical agent indicated for treatment of toenail onychomycosis due to the dermatophytes Trichophyton rubrum or Trichophyton mentagrophytes. In preclinical studies, tavaborole effectively penetrated through full-thickness, non-diseased cadaver fingernails, including those with up to four layers of nail polish. Limited systemic absorption was observed following topical application of tavaborole. In phase III clinical trials involving patients with distal subungual onychomycosis affecting 20-60% of a target great toenail, significantly more patients treated with tavaborole versus vehicle achieved completely clear nail with negative mycology following daily application for 48 weeks. Treatment-emergent adverse events reported by at least 1% of patients treated with tavaborole and at a greater frequency versus vehicle included ingrown toenail, exfoliation, erythema and dermatitis. Treatment discontinuations were uncommon. Results from preclinical studies and phase III clinical trials establish tavaborole as a safe and efficacious treatment for toenail onychomycosis.

Genomic Resources Notes accepted 1 April 2015 - 31 May 2015.

This article documents the public availability of transcriptomic resources for (i) the stellate sturgeon Acipenser stellatus, (ii) the flowering plant Campanula gentilis and (iii) two endemic Iberian fish, Squalius carolitertii and Squalius torgalensis.

Molecular evidence for genetic subdivision of Antarctic krill (Euphausia superba Dana) populations.

Antarctic krill (Euphausia superba Dana) is a key species in the Antarctic food web and occurs on a circumcontinental scale. Population genetic structure of this species was investigated by sequence analysis of the ND1 mitochondrial gene in four population samples collected at different geographical localities around the Antarctic continent. Results indicate the existence of significant genetic differences between samples, and we suggest that oceanographic barriers could be sufficiently strong and temporally stable to restrict gene flow between distinct areas. Moreover, our data indicate that Antarctic krill is not at mutation-drift equilibrium and that the species possibly has a low effective population size as compared to the census size.

Release of membrane-associated growth factors during neural injury.

The release of membrane-associated growth factors after neural injury may influence the outcome of the recovery. For example, for remyelination to occur after neural injury it is critical for the glial cell to proliferate prior to remyelination in both the PNS and CNS. In the CNS, the relative response of the oligodendrocytes and astroglia to growth factors mobilized during neural injury may play a role in the cellular dynamics of repair of neural injury or scarring and subsequent failure to repair neural injury. In support of this view, we have studied the mitotic potential and cell cycle kinetics of cultured adult oligodendrocytes and found that these adult cells respond only weakly to factors such as FGF which are known to be potent mitogens for neonatal cells. However, given the same dose of FGF, adult astrocytes are mitotically stimulated to a much greater degree than are the adult oligodendrocytes (Vick and De Vries, unpublished observations). Given the pathways which may be operative in the release of growth factors after injury, it has not escaped our attention that, provided the released factors are in equilibrium with easily accessible and peripheral body fluids, these released factors may serve as new markers for neural injury. Further experiments are in progress to explore this possibility.

A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel.

Reduced representation genome sequencing such as restriction-site-associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome-wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome-wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19,703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long-term effective population size was estimated to range between 132,000 and 1,320,000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82,425 loci and 376,918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome.