Fast Bayesian inference for large occupancy datasets

In recent years, the study of species' occurrence has benefited from the increased availability of large-scale citizen-science data. While abundance data from standardized monitoring schemes are biased toward well-studied taxa and locations, opportunistic data are available for many taxonomic groups, from a large number of locations and across long timescales. Hence, these data provide opportunities to measure species' changes in occurrence, particularly through the use of occupancy models, which account for imperfect detection. These opportunistic datasets can be substantially large, numbering hundreds of thousands of sites, and hence present a challenge from a computational perspective, especially within a Bayesian framework. In this paper, we develop a unifying framework for Bayesian inference in occupancy models that account for both spatial and temporal autocorrelation. We make use of the Pólya-Gamma scheme, which allows for fast inference, and incorporate spatio-temporal random effects using Gaussian processes (GPs), for which we consider two efficient approximations: subset of regressors and nearest neighbor GPs. We apply our model to data on two UK butterfly species, one common and widespread and one rare, using records from the Butterflies for the New Millennium database, producing occupancy indices spanning 45 years. Our framework can be applied to a wide range of taxa, providing measures of variation in species' occurrence, which are used to assess biodiversity change.     

Invagination of Ectodermal Placodes Is Driven by Cell Intercalation-Mediated Contraction of the Suprabasal Tissue Canopy

Ectodermal organs such as teeth, hair follicles, and mammary glands begin their development as placodes. These are local epithelial thickenings that invaginate into mesenchymal space. There is currently little mechanistic understanding of the cellular processes driving the early morphogenesis of these organs and of why they lead to invagination rather than simple tissue thickening. Here, we show that placode invagination depends on horizontal contraction of superficial layers of cells that form a shrinking and thickening canopy over underlying epithelial cells. This contraction occurs by cell intercalation and is mechanically coupled to the basal layer by peripheral basal cells that extend apically and centripetally while remaining attached to the basal lamina. This process is topologically analogous to well-studied apical constriction mechanisms, but very different from them both in scale and molecular mechanism. Mechanical cell–cell coupling is propagated through the tissue via E-cadherin junctions, which in turn depend on tissue-wide tension. We further present evidence that this mechanism is conserved among different ectodermal organs and is, therefore, a novel and fundamental morphogenetic motif widespread in embryonic development.     

Metal Phytoremediation by the Halophyte Limoniastrum monopetalum (L.) Boiss: Two Contrasting Ecotypes

The phytoremediation potential of the halophyte Limoniastrum monopetalum for the removal of Cd and Pb from polluted sites is assessed in this work. Two pot experiments were conducted; the first with wild L. monopetalum grown on soil polluted with Cd and Pb irrigated at different salinities, and the second with commonly cultivated ornamental L. monopetalum grown on soil polluted with Cd irrigated also at different salinities. The data revealed that wild L. monopetalum is a Cd and Pb tolerant plant able to accumulate at least 100 ppm of cadmium in its shoots without showing any significant decrease in terms of biomass production, chlorophyll content or water content suggesting that it could be an accumulator of Cd. Pb above-ground accumulation was kept at low levels with the majority of Pb localized in the roots. On the other hand, contrasting results were obtained for ornamental L. monopetalum which although it was found to be also Cd tolerant, Cd accumulation in its tissues was kept at significantly lower levels especially compared to that of the wild ecotype. In addition for ornamental L. monopetalum salinity did not have a positive effect on Cd accumulation and translocation as observed in the wild type and in other halophytes. Analysis of the salt excretion crystals on the leaf surface confirmed that wild and cultivated ornamental L. monopetalum excrete cadmium and lead through their salt glands as a possible metal detoxification mechanism, although the amount excreted by the ornamental L. monopetalum is significantly less.     

Modification of human β-globin locus PAC clones by homologous recombination in Escherichia coli

We report here modifications of human β-globin PAC clones by homologous recombination in Escherichia coli DH10B, utilising a plasmid temperature sensitive for replication, the recA gene and a wild-type copy of the rpsL gene which allows for an efficient selection for plasmid loss in this host. High frequencies of recombination are observed even with very small lengths of homology and the method has general utility for introducing insertions, deletions and point mutations. No rearrangements were detected with the exception of one highly repetitive genomic sequence when either the E.coli RecA- or the lambdoid phage encoded RecT and RecE-dependent recombination systems were used.     

Gut bacteria associated with different diets in reared Nephrops norvegicus

The impact of different diets on the gut microbiota of reared Nephrops norvegicus was investigated based on bacterial 16S rRNA gene diversity. Specimens were collected from Pagasitikos Gulf (Greece) and kept in experimental rearing tanks, under in situ conditions, for 6 months. Treatments included three diets: frozen natural (mussel) food (M), dry formulated pellet (P) and starvation (S). Gut samples were collected at the initiation of the experiment, and after 3 and 6 months. Tank water and diet samples were also analyzed for bacterial 16S rRNA gene diversity. Statistical analysis separated the two groups fed or starved (M and P vs. S samples). Most gut bacteria were not related to the water or diet bacteria, while bacterial diversity was higher in the starvation samples. M and P samples were dominated by Gammaproteobacteria, Epsilonproteobacteria and Tenericutes. Phylotypes clustering in Photobacterium leiognathi, Shewanella sp. and Entomoplasmatales had high frequencies in the M and P samples but low sequence frequencies in S samples. The study showed that feeding resulted in the selection of specific species, which also occurs in the natural population, and might be associated with the animal's nutrition.     

Total Phenolic Fraction (TPF) from Extra Virgin Olive Oil: Induction of apoptotic-like cell death in Leishmania spp. promastigotes and in vivo potential of therapeutic immunomodulation

BackgroundLeishmaniasis is a serious multifactorial parasitic disease with limited treatment options. Current chemotherapy is mainly consisted of drugs with serious drawbacks such as toxicity, variable efficacy and resistance. Alternative bioactive phytocompounds may provide a promising source for discovering new anti-leishmanial drugs. Extra Virgin Olive Oil (EVOO), a key-product in the Mediterranean diet, is rich in phenols which are associated with anti-inflammatory, anti-cancer and anti-microbial effects. In this study, we investigate the anti-leishmanial effect of Total Phenolic Fraction (TPF) derived from EVOO in both in vitro and in vivo systems by investigating the contributing mechanism of action.Methodology/Principal findingsWe tested the ability of TPF to cause apoptotic-like programmed cell death in L. infantum and L. major exponential-phase promastigotes by evaluating several apoptotic indices, such as reduction of proliferation rate, sub-G0/G1 phase cell cycle arrest, phosphatidylserine externalization, mitochondrial transmembrane potential disruption and increased ROS production, by using flow cytometry and microscopy techniques. Moreover, we assessed the therapeutic effect of TPF in L. major-infected BALB/c mice by determining skin lesions, parasite burden in popliteal lymph nodes, Leishmania-specific antibodies and biomarkers of tissue site cellular immune response, five weeks post-treatment termination. Our results show that TPF triggers cell-cycle arrest and apoptotic-like changes in Leishmania spp. promastigotes. Moreover, TPF treatment induces significant reduction of parasite burden in draining lymph nodes together with an antibody profile indicative of the polarization of Th1/Th2 immune balance towards the protective Th1-type response, characterized by the presence of IFN-γ-producing CD4+ T-cells and increased Tbx21/GATA-3 gene expression ratio in splenocytes.Conclusions/SignificanceTPF exhibits chemotherapeutic anti-leishmanial activity by inducing programmed cell death on cell-free promastigotes and immunomodulatory properties that induce in vivo T cell-mediated responses towards the protective Th1 response in experimental cutaneous leishmaniasis. These findings enable deeper understanding of TPF’s dual mode of action that encourages further studies.     

First report on the spawning migration and early life development of a cyprinid species of the genus Telestes

Reproductive migration of a Telestes species is reported for the first time for the Balkan endemic Telestes pleurobipunctatus (Stephanidis, 1939) from Louros River (Northwestern Greece), while the embryonic and larval development is also described for the first time for this species and genus. Adult fish migrate in late winter upstream and spawn in a peak of 2–3 nights in the outflow of springs. Embryos at hatching measure approx. 6.0 mm notochord length (NL), flexion starts at 8.1 mm NL and food particles are noted in the digestive tract of larvae at 8.2 mm NL. The larval period is characterized by the sequential formation of fins and the development of scalation. Fin differentiation ends with the completion of pelvic fin rays and the disappearance of the pre-anal finfold at 20.0 mm. First scales appear at 17.0 mm standard length (SL) and scalation completes at 27.8 mm SL. We propose that the size at a specific ontogenetic event, the pigmentation pattern and the pre-anal myomeres' number comprise diagnostic characters that permit distinguishing T. pleurobipunctatus larvae from other sympatric cyprinids. We note the rare pattern of scale scalation and pigmentation pattern of the target species. Parapatric speciation in T. pleurobipunctatus possibly related to its spawning migration pattern, as well as the use of larval identification in monitoring and conservation programmes targeting threatened cyprinids exhibiting this type of reproductive behaviour are also discussed.     

Synthesis of derivatives of the keto-pyrrolyl-difluorophenol scaffold: Some structural aspects for aldose reductase inhibitory activity and selectivity

Seven novel ARIs (3a–c, 4a–c and 5) were synthesized with the implementation of an optimized and, partially, selective synthetic procedure, via a Friedel–Crafts acylation reaction. The synthesized ARIs have values of IC₅₀^ALR2 ranging from 0.19 μM (in case of compound 3b) to 2.3 μM (in case of compound 4a), while the values of selectivity index towards ALR1 range from 1 (in case of compound 3b) to 238 (in case of compound 3a). Finally, we found out that the presence of an additional (secondary) aromatic area is not a prerequisite feature for ARI activity.     

Host cystathionine-γ lyase derived hydrogen sulfide protects against Pseudomonas aeruginosa sepsis

Hydrogen sulfide (H₂S) has recently been recognized as a novel gaseous transmitter with several anti-inflammatory properties. The role of host- derived H₂S in infections by Pseudomonas aeruginosa was investigated in clinical and mouse models. H₂S concentrations and survival was assessed in septic patients with lung infection. Animal experiments using a model of severe systemic multidrug-resistant P. aeruginosa infection were performed using mice with a constitutive knock-out of cystathionine-γ lyase (Cse) gene (Cse^-/-) and wild-type mice with a physiological expression (Cse^+/+). Experiments were repeated in mice after a) treatment with cyclophosphamide; b) bone marrow transplantation (BMT) from a Cse^+/+ donor; c) treatment with H₂S synthesis inhibitor aminooxyacetic acid (ΑΟΑΑ) or propargylglycine (PAG) and d) H₂S donor sodium thiosulfate (STS) or GYY3147. Bacterial loads and myeloperoxidase activity were measured in tissue samples. The expression of quorum sensing genes (QS) was determined in vivo and in vitro. Cytokine concentration was measured in serum and incubated splenocytes. Patients survivors at day 28 had significantly higher serum H₂S compared to non-survivors. A cut- off point of 5.3 μΜ discriminated survivors with sensitivity 92.3%. Mortality after 28 days was 30.9% and 93.7% in patients with H₂S higher and less than 5.3 μΜ (p = 7 x 10⁻⁶). In mice expression of Cse and application of STS afforded protection against infection with multidrug-resistant P. aeruginosa. Cyclophosphamide pretreatment eliminated the survival benefit of Cse^+/+ mice, whereas BMT increased the survival of Cse^-/- mice. Cse^-/- mice had increased pathogen loads compared to Cse^+/+ mice. Phagocytic activity of leukocytes from Cse^-/- mice was reduced but was restored after H₂S supplementation. An H₂S dependent down- regulation of quorum sensing genes of P.aeruginosa could be demonstrated in vivo and in vitro. Endogenous H₂S is a potential independent parameter correlating with the outcome of P. aeruginosa. H₂S provides resistance to infection by MDR bacterial pathogens.