Sample size and sampling error in geometric morphometric studies of size and shape

Geometric morphometric studies are increasingly becoming common in systematics and palaeontology. The samples in such studies are often small, due to the paucity of material available for analysis. However, very few studies have tried to assess the impact of sampling error on analytical results. Here, this issue is addressed empirically using repeated randomized selection experiments to build progressively smaller samples from an original dataset of ∼400 vervet monkey (Cercopithecus aethiops) skulls. Size and shape parameters (including mean size and shape, size and shape variances, angles of allometric trajectories) that are commonly used in geometric morphometric studies, are estimated first in the original sample and then in the random subsamples. Estimates are then compared to give an indication of what is the minimum desirable sample size for each parameter. Mean size, standard deviation of size and variance of shape are found to be fairly accurate even in relatively small samples. In contrast, mean shapes and angles between static allometric trajectories are strongly affected by sampling error. If confirmed in other groups, our findings may have substantial implications for studies of morphological variation in present and fossil species. By performing rarefaction analyses like those presented in our study, morphometricians can be easily provided with important clues on how a simple but crucial factor like sample size can alter results of their studies.     

Highly purified lipopolysaccharides from Burkholderia cepacia complex clinical isolates induce inflammatory cytokine responses via TLR4-mediated MAPK signalling pathways and activation of NFkappaB

In cystic fibrosis (CF), bacteria of the Burkholderia cepacia complex (Bcc) can induce a fulminant inflammation with pneumonitis and sepsis. Lipopolysaccharide (LPS) may be an important virulence factor associated with this decline but little is known about the molecular pathogenesis of Bcc LPS. In this study we have investigated the inflammatory response to highly purified LPS from different Bcc clinical isolates and the cellular signalling pathways employed. The inflammatory response (TNFalpha, IL-6) was measured in human MonoMac 6 monocytes and inhibition experiments were used to investigate the Toll-like receptors and associated adaptor molecules and pathways utilized. LPS from all clinical Bcc isolates induced significant pro-inflammatory cytokines and utilized TLR4 and CD14 to mediate activation of mitogen-activated protein kinase pathways, IkappaB-alpha degradation and NFkappaB activation. However, LPS from different clinical isolates of the same clonal strain of Burkholderia cenocepacia were found to induce a varied inflammatory response. LPS from clinical isolates of Burkholderia multivorans was found to activate the inflammatory response via MyD88-independent pathways. This study suggests that LPS alone from clinical isolates of Bcc is an important virulence factor in CF and utilizes TLR4-mediated signalling pathways to induce a significant inflammatory response.     

Monitoring Rarity: The Critically Endangered Saharan Cheetah as a Flagship Species for a Threatened Ecosystem

Deserts are particularly vulnerable to human impacts and have already suffered a substantial loss of biodiversity. In harsh and variable desert environments, large herbivores typically occur at low densities, and their large carnivore predators occur at even lower densities. The continued survival of large carnivores is key to healthy functioning desert ecosystems, and the ability to gather reliable information on these rare low density species, including presence, abundance and density, is critical to their monitoring and management. Here we test camera trap methodologies as a monitoring tool for an extremely rare wide-ranging large felid, the critically endangered Saharan cheetah (Acinonyx jubatus hecki). Two camera trapping surveys were carried out over 2–3 months across a 2,551km² grid in the Ti-n-hağğen region in the Ahaggar Cultural Park, south central Algeria. A total of 32 records of Saharan cheetah were obtained. We show the behaviour and ecology of the Saharan cheetah is severely constrained by the harsh desert environment, leading them to be more nocturnal, be more wide-ranging, and occur at lower densities relative to cheetah in savannah environments. Density estimates ranged from 0.21–0.55/1,000km², some of the lowest large carnivore densities ever recorded in Africa, and average home range size over 2–3 months was estimated at 1,583km². We use our results to predict that, in order to detect presence of cheetah with p>0.95 a survey effort of at least 1,000 camera trap days is required. Our study identifies the Ahaggar Cultural Park as a key area for the conservation of the Saharan cheetah. The Saharan cheetah meets the requirements for a charismatic flagship species that can be used to “market” the Saharan landscape at a sufficiently large scale to help reverse the historical neglect of threatened Saharan ecosystems.     

SLC24A5 encodes a trans-Golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis

A non-synonymous single nucleotide polymorphism in the human SLC24A5 gene is associated with natural human skin color variation. Multiple sequence alignments predict that this gene encodes a member of the potassium-dependent sodium-calcium exchanger family denoted NCKX5. In cultured human epidermal melanocytes we show using affinity-purified antisera that native human NCKX5 runs as a triplet of approximately 43 kDa on SDS-PAGE and is partially localized to the trans-Golgi network. Removal of the NCKX5 protein through small interfering RNA-mediated knockdown disrupts melanogenesis in human and murine melanocytes, causing a significant reduction in melanin pigment production. Using a heterologous expression system, we confirm for the first time that NCKX5 possesses the predicted exchanger activity. Site-directed mutagenesis of NCKX5 and NCKX2 in this system reveals that the non-synonymous single nucleotide polymorphism in SLC24A5 alters a residue that is important for NCKX5 and NCKX2 activity. We suggest that NCKX5 directly regulates human epidermal melanogenesis and natural skin color through its intracellular potassium-dependent exchanger activity.     

Photosynthesis in aquatic adventitious roots of the halophytic stem-succulent Tecticornia pergranulata (formerly Halosarcia pergranulata)

In flood-tolerant species, a common response to inundation is growth of adventitious roots into the water column. The capacity for these roots to become photosynthetically active has received scant attention. The experiments presented here show the aquatic adventitious roots of the flood-tolerant, halophytic stem-succulent, Tecticornia pergranulata (subfamily Salicornioideae, Chenopodiaceae) are photosynthetic and quantify for the first time the photosynthetic capacity of aquatic roots for a terrestrial species. Fluorescence microscopy was used to determine the presence of chloroplasts within cells of aquatic roots. Net O₂ production by excised aquatic roots, when underwater, was measured with varying light and CO₂ regimes; the apparent maximum capacity ( P _max) for underwater net photosynthesis in aquatic roots was 0.45  µ mol O₂ m⁻² s⁻¹. The photosynthetic potential of these roots was supported by the immunolocalization of PsbA, the major protein of photosystem II, and ribulose-1-5-bisphosphate carboxylase/oxygenase (Rubisco) in root protein extracts. Chlorophyllous aquatic roots of T. pergranulata are photosynthetically active, and such activity is a previously unrecognized source of O₂, and potentially carbohydrates, in flooded and submerged plants.     

Efficacy of curcumin in the treatment of experimental vulvovaginal candidiasis

BackgroundCandida albicans is the main agent that causes vulvovaginal candidiasis. Resistance among isolates to azole antifungal agents has been reported.AimsDue to the well-known antifungal potential of curcumin, the purpose of this work was to evaluate the in vitro anticandidal activity of curcumin and its effect in the treatment of experimental vulvovaginal candidiasis.MethodsThe anticandidal activity of curcumin was investigated against eight Candida strains by the broth microdilution assay, and its mechanism of action was evaluated by testing the binding to ergosterol. Then, the effect of curcumin in the treatment of vulvovaginal candidiasis was evaluated in an immunosuppressed, estrogen treated rat model.ResultsCurcumin showed minimum inhibitory concentration values of 125–1000 μg/ml, and the best result was observed against Candida glabrata. The compound was shown to be able to bind to the ergosterol present in the membrane, event that may be the mechanism of action. In addition, in the in vivo model of vulvovaginal candidiasis with C. albicans, treatments reduced the vaginal fungal burden in infected rats after seven days of treatment with different doses.ConclusionsCurcumin could be considered a promising effective antifungal agent in the treatment of vulvovaginal candidiasis.     

Developmental change in translation initiation alters the localization of a common microbial protein necessary for Toxoplasma chronic infection

The Toxoplasma gondii cyst stage is resistant to drug therapy. To identify potential targets for new therapeutics, we screened insertional mutants of T. gondii for a reduced ability to form cysts in the brains of mice. In one of these mutants, named 38C3, the mutagenesis plasmid inserted into the mRNA of a protein that is highly conserved in microbes but is not present in humans. The mutation in 38C3 causes reduced brain cyst production during chronic infection, but does not affect acute virulence, so the disrupted gene and protein are called T. gondii Brain Colonization Protein 1 (TgBCP1). TgBCP1 has three potential in frame start codons that produce 51, 33 or 25 kDa proteins. In rapidly replicating tachyzoites, translation initiates at the third methionine, producing the 25 kDa form that is conserved in many bacteria and protozoans. Brain cysts exclusively express the 51 kDa form of TgBCP1, which is secreted from the parasites and localizes to the cyst wall. Only expression of the long form of TgBCP1 restored cyst formation in the 38C3 mutant. TgBCP1 is essential for cyst formation and is the first example of a developmental regulation in translation initiation site preference for a T. gondii protein.     

Ikarugamycin: A Natural Product Inhibitor of Clathrin‐Mediated Endocytosis

Ikarugamycin (IKA) is a previously discovered antibiotic, which has been shown to inhibit the uptake of oxidized low‐density lipoproteins in macrophages. Furthermore, several groups have previously used IKA to inhibit clathrin‐mediated endocytosis (CME) in plant cell lines. However, detailed characterization of IKA has yet to be performed. Consequently, we performed biochemistry and microscopy experiments to further characterize the effects of IKA on CME. We show that IKA has an IC₅₀ of 2.7 μm in H1299 cells and acutely inhibits CME, but not other endocytic pathways, in a panel of cell lines. Although long‐term incubation with IKA has cytotoxic effects, the short‐term inhibitory effects on CME are reversible. Thus, IKA can be a useful tool for probing routes of endocytic trafficking.      

Rapid identification of ubiquitination and SUMOylation target sites by microfluidic peptide array

SUMOylation and ubiquitination are two essential post translational modifications (PTMs) involved in the regulation of important biological processes in eukaryotic cells. Identification of ubiquitin (Ub) and small ubiquitin-related modifier (SUMO)-conjugated lysine residues in proteins is critical for understanding the role of ubiquitination and SUMOylation, but remains experimentally challenging. We have developed a powerful in vitro Ub/SUMO assay using a novel high density peptide array incorporated within a microfluidic device that allows rapid identification of ubiquitination and SUMOylation sites on target proteins. We performed the assay with a panel of human proteins and a microbial effector with known target sites for Ub or SUMO modifications, and determined that 80% of these proteins were modified by Ub or specific SUMO isoforms at the sites previously determined using conventional methods. Our results confirm the specificity for both SUMO isoform and individual target proteins at the peptide level. In summary, this microfluidic high density peptide array approach is a rapid screening assay to determine sites of Ub and SUMO modification of target substrates, which will provide new insights into the composition, selectivity and specificity of these PTM target sites.     

Repression of arginase and agmatine amidinohydrolase by urea in the lichen Evernia prunastri

Two forms of arginase (EC 3.5.3.1) have been found in Evernia prunastri: (1) a light-arginase (M_r, 180 000) induced by l-arginine—urea causes repression which is reversed by cyclic AMP; (2) a constitutive heavy-arginase (M_r, 330 000) which is not affected by cyclic AMP. Agmatine amidinohydrolase (EC 3.5.3.11) is also repressed by urea but this effect is carried out at catabolite concentrations higher than those required to prevent the synthesis of the light-arginase. This repression is also relieved by cyclic AMP.