Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes

Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two nonexclusive alternative approaches have recently been developed, the "fossilized birth-death" (FBD) model and "total-evidence dating." While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated data sets, and compare its performance to that of the FBD model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the FBD model. By applying our approach to a large data set including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for transoceanic dispersal of cichlids and other groups of teleost fishes. [Bayesian inference; calibration density; Cichlidae; fossil record; marine dispersal; phylogeny; relaxed molecular clock]

The content of polyphenols and antioxidant activity in leaves and flowers of wild garlic (Allium ursinum L.)

Wild garlic (Allium ursinum L.) is a wildly growing plant that grows in forests and next to the streams. It has a specific aroma and taste resembling garlic. Wild garlic is increasingly favoured in gastronomy, food industry, and modern food technologies. The aim of this study was to analyse the dynamics of changes in total polyphenols content (TPC) and antioxidant activity (AOA) in wild garlic leaves and flowers during the vegetation period (from April to June). The samples of plant material were collected from the area of Bratislava – Železná studienka. The samples of fresh leaves and flowers were homogenized and a methanolic extract was prepared. These extracts were used for analyses. Total polyphenol content in the samples ranged from 726±10 mg GAE/kg FW to 14.1×102±13 mg GAE/kg FW. The values of antioxidant activity were from 10.7±1.57 to 25.9±1.06% inhibition FW

Bioaccumulation of chemical elements at post-industrial freshwater sites varies predictably between habitats, elements and taxa: A power law approach

Elevated environmental levels of elements originating from anthropogenic activities threaten natural communities and public health, as these elements can persist and bioaccumulate in the environment. However, their environmental risks and bioaccumulation patterns are often habitat-, species- and element-specific. We studied the bioaccumulation patterns of 11 elements in seven freshwater taxa in post-mining habitats in the Czech Republic, ranging from less polluted mining ponds to highly polluted fly ash lagoons. We found nonlinear, power-law relationships between the environmental and tissue concentrations of the elements, which may explain differences in bioaccumulation factors (BAF) reported in the literature. Tissue concentrations were driven by the environmental concentrations in non-essential elements (Al, As, Co, Cr, Ni, Pb and V), but this dependence was limited in essential elements (Cu, Mn, Se and Zn). Tissue concentrations of most elements were also more closely related to substrate than to water concentrations. Bioaccumulation was habitat specific in eight elements: stronger in mining ponds for Al and Pb, and stronger in fly ash lagoons for As, Cu, Mn, Pb, Se, V and Zn, although the differences were often minor. Bioaccumulation of some elements further increased in mineral-rich localities. Proximity to substrate, rather than trophic level, drove increased bioaccumulation levels across taxa. This highlights the importance of substrate as a pollutant reservoir in standing freshwaters and suggests that benthic taxa, such as molluscs (e.g., Physella) and other macroinvertebrates (e.g., Nepa), constitute good bioindicators. Despite the higher environmental risks in fly ash lagoons than in mining ponds, the observed ability of freshwater biota to sustain pollution supports the conservation potential of post-industrial sites. The power law approach used here to quantify and disentangle the effects of various bioaccumulation drivers may be helpful in additional contexts, increasing our ability to predict the effects of other contaminants and environmental hazards on biota.info:eu-repo/semantics/publishedVersio

Dependence of viscosity and diffusion on β-cyclodextrin and chloroquine diphosphate interactions

Mutual diffusion coefficients of chloroquine diphosphate (CDP) in aqueous solutions both without and with β-cyclodextrin (β-CD) were measured at concentrations from (0.0000 to 0.0100) mol dm−3 and 298.15 K, using the Taylor dispersion technique. Ternary mutual diffusion coefficients (Dik) measured by the same technique are reported for aqueous CDP + β-CD solutions at 298.15 K. The presence of β CD led to relevant changes in the diffusion process, as showed by nonzero values of the cross-diffusion coefficients, D12 and D21 . β-CD concentration gradients produced significant co-current coupled flows of CDP. In addition, the effects of β-CD on the transport of CDP are assessed by comparing the binary diffusion coefficient of aqueous CDP solutions with the main diffusion coefficient (D11 ) measured for ternary {CDP(1) + β-CD(2)} solutions. These observations are supported by viscosity analysis. All data allow to have a better interpretation on the effect of cyclodextrin on the transport behavior of CDP. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Coimbra Chemistry Centre - FundacAo para a Ciencia e a Tecnologia (FCT), Portuguese Agency for Scientific Research [UID/QUI/UI0313/2019]; COMPETE; Ministry of Education, Youth and Sports of the Czech Republic DKRVO [RP/CPS/2020/003]; University of Alcala (Spain)RP/CPS/2020/003; UID/QUI/UI0313/2019; Fundação para a Ciência e a Tecnologia, FCT; Universidad de Alcalá, UAH; Programa Operacional Temático Factores de Competitividade, POF

Effect of hofmeister ions on transport properties of aqueous solutions of sodium hyaluronate

Tracer diffusion coefficients obtained from the Taylor dispersion technique at 25.0◦C were measured to study the influence of sodium, ammonium and magnesium salts at 0.01 and 0.1 mol dm−3 on the transport behavior of sodium hyaluronate (NaHy, 0.1%). The selection of these salts was based on their position in Hofmeister series, which describe the specific influence of different ions (cations and anions) on some physicochemical properties of a system that can be interpreted as a salting-in or salting-out effect. In our case, in general, an increase in the ionic strength (i.e., concentrations at 0.01 mol dm−3 ) led to a significant decrease in the limiting diffusion coefficient of the NaHy 0.1%, indicating, in those circumstances, the presence of salting-in effects. However, the opposite effect (salting-out) was verified with the increase in concentration of some salts, mainly for NH4SCN at 0.1 mol dm−3 . In this particular salt, the cation is weakly hydrated and, consequently, its presence does not favor interactions between NaHy and water molecules, promoting, in those circumstances, less resistance to the movement of NaHy and thus to the increase of its diffusion (19%). These data, complemented by viscosity measurements, permit us to have a better understanding about the effect of these salts on the transport behaviour of NaHy. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Fundacao para a Ciencia e a Tecnologia (FCT) through COMPETE Programme (Operational Programme for Competitiveness) [UIDB/QUI/00313/2020]; Ministry of Education, Youth and Sports of the Czech Republic DKRVO [RP/CPS/2020/003]Ministerstvo Školství, Mládeže a Tělovýchovy, MŠMT: RP/CPS/2020/003; Fundação para a Ciência e a Tecnologia, FCT: UIDB/QUI/00313/202

Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes

Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage ancestral to R0a is more ancient than previously thought, with a relict distribution across the Mediterranean/Southwest Asia; (2) R0a has a much deeper presence in Arabia than previously thought, highlighting the role of at least one Pleistocene glacial refugium, perhaps on the Red Sea plains; (3) the main episode of dispersal into Eastern Africa, at least concerning maternal lineages, was at the end of the Late Glacial, due to major expansions from one or more refugia in Arabia; (4) there was likely a minor Late Glacial/early postglacial dispersal from Arabia through the Levant and into Europe, possibly alongside other lineages from a Levantine refugium; and (5) the presence of R0a in Southwest Arabia in the Holocene at the nexus of a trading network that developed after ~3 ka between Africa and the Indian Ocean led to some gene flow even further afield, into Iran, Pakistan and India

Genome Instability and Bleomicin Sensitivity Test

Procjena individualne osjetljivosti na mutagene često je dio istraživanja u epidemiološkim studijama koje prate pojavnost zloćudnih bolesti u populacijama. Posljedica djelovanja mutagena u genomu izloženih osoba jest nastanak određene, manje ili veće, količine oštećenja, uvjetovane individualnim razlikama u osjetljivosti. Viša razina takve genomske nestabilnosti znači opasnost (rizik) od razvoja zloćudnih bolesti. Interindividualne razlike u odgovoru na mutagene obično se povezuju i s promijenjenom (većinom smanjenom) sposobnosti (kapacitetom) za popravak DNA. Citogenetičke studije su pokazale da je genom tumorskih stanica nestabilniji od normalnih, a time i skloniji akumuliranju oštećenja, bilo da je nestabilnost uzrokovana nasljeđem, izloženošću ili kombinacijom tih dvaju učinaka. U oboljelih ispitanika utvrđena je povećana učestalost kromatidnih i kromosomskih aberacija naspram normalne populacije te sklonost razvoju određenih vrsta neoplazija. U praćenju povezanosti promijenjenog odgovora i pojavnosti tumora služe nam različiti biomarkeri. Kao indirektni pokazatelji uspješnosti popravka DNA često se rabe testovi osjetljivosti na mutagene u kulturama limfocita periferne krvi. Jedan od takvih testova je i bleomicinski test. Radiomimetik i citostatik, a po strukturi glikopeptid, bleomicin se u stanici prevodi u aktivni oblik sposoban cijepati molekulu DNA što uzrokuje brojne jednolančane i dvolančane lomove. Kao jednostavna i jeftina metoda, zasniva se na utvrđivanju ukupnog broja jednolančanih lomova u kromosomima limfocita uzgajanih u staničnoj kulturi koji su u uvjetima in vitro tijekom kasne G2-faze staničnog ciklusa bili izloženi bleomicinu. Ovaj revijalni rad daje pregled utjecaja raznih faktora na rezultate samog testa i pokazuje njegovu široku primjenu u proučavanju genomske nestabilnosti koju najčešće uzrokuje kombinacija raznih faktora.Estimation of individual susceptibility to mutagens is often a part of epidemiological studies monitoring the appearance of malignant disease in different populations. Genome exposure to mutagens can lead to DNA damage. The rate of damage depends on individual differences in response, which are usually associated with differences in DNA repair capacity. Cytogenetic studies have shown that the genome of tumour cells is less stable than normal cells and therefore accumulates more damage. Tumour patients show a higher frequency of chromatid and chromosomal aberrations and a predisposition to certain types of tumours. One of the common biomarkers used in monitoring tumour appearance and changed response to DNA damage is the bleomycin test. In its active form, bleomycin (glycopeptid) is a radiomimetic cytostatic that can damage the DNA molecule and cause multiple single and double strands. The bleomycin test is simple and inexpensive, and is based on scoring chromatid breaks in lymphocytes in vitro exposed to bleomycin during the late G2 phase of the cell cycle. This review looks into different factors that may affect test results and discusses its wide implementation in studies of genome instability usually caused by a combination of factors

Von Willebrand Factor Gene Variants Associate with Herpes simplex Encephalitis

Herpes simplex encephalitis (HSE) is a rare complication of Herpes simplex virus type-1 infection. It results in severe parenchymal damage in the brain. Although viral latency in neurons is very common in the population, it remains unclear why certain individuals develop HSE. Here we explore potential host genetic variants predisposing to HSE. In order to investigate this we used a rat HSE model comparing the HSE susceptible SHR (Spontaneously Hypertensive Rats) with the asymptomatic infection of BN (Brown Norway). Notably, both strains have HSV-1 spread to the CNS at four days after infection. A genome wide linkage analysis of 29 infected HXB/BXH RILs (recombinant inbred lines-generated from the prior two strains), displayed variable susceptibility to HSE enabling the definition of a significant QTL (quantitative trait locus) named Hse6 towards the end of chromosome 4 (160.89-174Mb) containing the Vwf (von Willebrand factor) gene. This was the only gene in the QTL with both cis-regulation in the brain and included several non-synonymous SNPs (single nucleotide polymorphism). Intriguingly, in human chromosome 12 several SNPs within the intronic region between exon 43 and 44 of the VWF gene were associated with human HSE pathogenesis. In particular, rs917859 is nominally associated with an odds ratio of 1.5 (95% CI 1.11-2.02; p-value = 0.008) after genotyping in 115 HSE cases and 428 controls. Although there are possibly several genetic and environmental factors involved in development of HSE, our study identifies variants of the VWF gene as candidates for susceptibility in experimental and human HSE