Feather isotope analysis discriminates age-classes of Western, Least, and Semipalmated sandpipers when plumage methods are unreliable

ABSTRACT Avian age‐class discrimination is typically based on the completeness of the first prebasic molt. In several calidrid sandpiper species, juvenal flight feathers grown on Arctic breeding grounds are retained through the first three migrations. Thereafter, flight feathers are grown annually at temperate migratory stopover sites during the fall or on the subtropical wintering grounds. Standard methods for distinguishing age classes of sandpipers rely on a combination of traits, including body plumage, coloration of protected inner median covert edges, and extent of flight feather wear. We tested the ability of stable hydrogen isotope ratios in flight feathers (δD_f) to distinguish young birds in their first winter through second fall from older adults in three calidrid sandpiper species, Western (Calidris mauri), Least (C. minutilla), and Semipalmated (C. pusilla) sandpipers. We compared the apparent reliability of the isotope approach to that of plumage‐based aging. The large expected differences in δD_f values of flight feathers grown at Arctic versus non‐Arctic latitudes enabled use of this technique to discriminate between age‐classes. We determined δD_f values of known Arctic‐grown feathers from juveniles that grew their flight feathers on the breeding grounds. Flight feather δD_f values of southward‐migrating adults showed bimodal distributions for all three species. Negative values overlapped with species‐specific juvenile values, identifying putative second fall birds with high‐latitude grown juvenal feathers retained from the previous year. The more positive values identified older adults who grew their feathers at mid‐ and low latitudes. Importantly, δD_f analysis successfully identified first‐winter and second‐fall birds not detected by plumage‐based aging. Flight feather wear alone was a poor basis for age classification because scores overlapped extensively between putative second fall birds and older adults. Flight feather hydrogen isotope analysis enables more definitive assignment of age classes when standard plumage methods are unreliable.     

Copy Number Analysis Identifies Novel Interactions Between Genomic Loci in Ovarian Cancer

Ovarian cancer is a heterogeneous disease displaying complex genomic alterations, and consequently, it has been difficult to determine the most relevant copy number alterations with the scale of studies to date. We obtained genome-wide copy number alteration (CNA) data from four different SNP array platforms, with a final data set of 398 ovarian tumours, mostly of the serous histological subtype. Frequent CNA aberrations targeted many thousands of genes. However, high-level amplicons and homozygous deletions enabled filtering of this list to the most relevant. The large data set enabled refinement of minimal regions and identification of rare amplicons such as at 1p34 and 20q11. We performed a novel co-occurrence analysis to assess cooperation and exclusivity of CNAs and analysed their relationship to patient outcome. Positive associations were identified between gains on 19 and 20q, gain of 20q and loss of X, and between several regions of loss, particularly 17q. We found weak correlations of CNA at genomic loci such as 19q12 with clinical outcome. We also assessed genomic instability measures and found a correlation of the number of higher amplitude gains with poorer overall survival. By assembling the largest collection of ovarian copy number data to date, we have been able to identify the most frequent aberrations and their interactions.     

A secreted effector protein of Salmonella dublin is translocated into eukaryotic cells and mediates inflammation and fluid secretion in infected ileal mucosa

Enteritis induced by non-typhoid pathogenic Salmonella is characterized by fluid secretion and inflammatory responses in the infected ileum. The inflammatory response provoked by Salmonella initially consists largely of a neutrophil (PMN) migration into the intestinal mucosa and the gut lumen. The interactions between Salmonella and intestinal epithelial cells are known to play an essential role in inducing the inflammatory response. Upon interaction with epithelial cells salmonellae are able to elicit transepithelial signalling to neutrophils. This signalling is recognized as a key virulence feature underlying Salmonella -induced enteritis. However, the nature and mechanism of such signalling has not been clarified to date. Here, we characterize SopB, a novel secreted effector protein of Salmonella dublin , and present data implying that SopB is translocated into eukaryotic cells via a sip -dependent pathway to promote fluid secretion and inflammatory responses in the infected ileum.     

Increased frequency of micronuclei in the lymphocytes of patients chronically infected with hepatitis B or hepatitis C virus

In this study, we analysed the frequency of micronuclei (MN), nucleoplasmic bridges (NPBs) and nuclear buds (NBUDs) and evaluated mutagen-induced sensitivity in the lymphocytes of patients chronically infected with hepatitis B virus (HBV) or hepatitis C virus (HCV). In total, 49 patients with chronic viral hepatitis (28 HBV-infected and 21 HCV-infected patients) and 33 healthy, non-infected blood donor controls were investigated. The frequencies (‰) of MN, NPBs and NBUDs in the controls were 4.41 ± 2.15, 1.15 ± 0.97 and 2.98 ± 1.31, respectively. The frequencies of MN and NPBs were significantly increased (p < 0.0001) in the patient group (7.01 ± 3.23 and 2.76 ± 2.08, respectively) compared with the control group. When considered separately, the HBV-infected patients (7.18 ± 3.57) and HCV-infected patients (3.27 ± 2.40) each had greater numbers of MN than did the controls (p < 0.0001). The HCV-infected patients displayed high numbers of NPBs (2.09 ± 1.33) and NBUDs (4.38 ± 3.28), but only the HBV-infected patients exhibited a significant difference (NPBs = 3.27 ± 2.40, p < 0.0001 and NBUDs = 4.71 ± 2.79, p = 0.03) in comparison with the controls. Similar results were obtained for males, but not for females, when all patients or the HBV-infected group was compared with the controls. The lymphocytes of the infected patients did not exhibit sensitivity to mutagen in comparison with the lymphocytes of the controls (p = 0.06). These results showed that the lymphocytes of patients who were chronically infected with HBV or HCV presented greater chromosomal instability.     

Comparative analysis of optogenetic actuators in cultured astrocytes

Astrocytes modulate synaptic transmission via release of gliotransmitters such as ATP, glutamate, d-serine and l-lactate. One of the main problems when studying the role of astrocytes in vitro and in vivo is the lack of suitable tools for their selective activation. Optogenetic actuators can be used to manipulate astrocytic activity by expression of variants of channelrhodopsin-2 (ChR2) or other optogenetic actuators with the aim to initiate intracellular events such as intracellular Ca²⁺ ([Ca²⁺]_i) and/or cAMP increases. We have developed an array of adenoviral vectors (AVV) with ChR2-like actuators, including an enhanced ChR2 mutant (H134R), and a mutant with improved Ca²⁺ permeability (Ca²⁺ translocating channelrhodopsin, CatCh). We show here that [Ca²⁺]_i elevations evoked by ChR2(H134R) and CatCh in astrocytes are largely due to release of Ca²⁺ from the intracellular stores. The autocrine action of ATP which is released under these conditions and acts on the P2Y receptors also contributes to the [Ca²⁺]_i elevations. We also studied effects evoked using light-sensitive G-protein coupled receptors (opto-adrenoceptors). Activation of optoα1AR (Gq-coupled) and optoβ2AR (G_s-coupled) resulted in astrocytic [Ca²⁺]_i increases which were suppressed by blocking the corresponding intracellular signalling cascade (phospholipase C and adenylate cyclase, respectively). Interestingly, the bulk of [Ca²⁺]_i responses evoked using either optoAR was blocked by an ATP degrading enzyme, apyrase, or a P2Y1 receptor blocker, MRS 2179, indicating that they are to a large extent triggered by the autocrine action of ATP. We conclude that, whilst optimal tools for control of astrocytes are yet to be generated, the currently available optogenetic actuators successfully initiate biologically relevant signalling events in astrocytes.     

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this “RAD-sex” method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, “male genotypes” became males and some “female genotypes” also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.     

Zooplankton-associated and free-living bacteria in the York River, Chesapeake Bay: comparison of seasonal variations and controlling factors

Zooplankton provide microhabitats for bacteria, but factors which influence zooplankton-associated bacterial abundance are not well known. Through a year-long field study, we measured the concentration of free-living bacteria and bacteria associated with the dominant mesozooplankters Acartia tonsa and Balanus sp. Free-living bacteria peaked in the summer, while zooplankton-associated bacteria peaked in summer and winter. No relationships were found between bacterial abundance per individual and zooplankter width, length, surface area or body volume. Multiple regression analyses indicated that free-living and Acartia-associated bacterial concentrations were explained by temperature, salinity, ammonium, chl a, and all term interactions. Balanus-associated bacterial concentration was explained by ammonium and phosphate. Ammonium significantly influenced all sampled bacterial communities. In laboratory experiments, copepods raised under high ammonium concentration had higher bacterial concentrations than those raised under low ammonium condition. Transplant experiments showed that high ammonium favored loosely attached bacteria, whereas low ammonium selected for firmly attached bacteria, suggesting greater exchange between free-living and zooplankton-associated bacterial communities in nutrient-rich systems. Additional sampling of other zooplankton taxa all showed high bacterial concentrations, supporting the notion that zooplankton function as microbial hotspots and may play an important, yet overlooked, role in marine biogeochemical cycles.     

Ecoenzymatic stoichiometry of microbial nutrient acquisition in tropical soils

The relative activities of soil enzymes involved in mineralizing organic carbon (C), nitrogen (N), and phosphorus (P) reveal stoichiometric and energetic constraints on microbial biomass growth. Although tropical forests and grasslands are a major component of the global C cycle, the effects of soil nutrient availability on microbial activity and C dynamics in these ecosystems are poorly understood. To explore potential microbial nutrient limitation in relation to enzyme allocation in low latitude ecosystems, we performed a meta-analysis of acid/alkaline phosphatase (AP), β-1,4-glucosidase (BG), and β-1,4-N-acetyl-glucosaminidase (NAG) activities in tropical soils. We found that BG:AP and NAG:AP ratios in tropical soils are significantly lower than those of temperate ecosystems overall. The lowest BG:AP and NAG:AP ratios were associated with old or acid soils, consistent with greater biological phosphorus demand relative to P availability. Additionally, correlations between enzyme activities and mean annual temperature and precipitation suggest some climatic regulation of microbial enzyme allocation in tropical soils. We used the results of our analysis in conjunction with previously published data on soil and biomass C:N:P stoichiometry to parameterize a biogeochemical equilibrium model that relates microbial growth efficiency to extracellular enzyme activity. The model predicts low microbial growth efficiencies in P-limited soils, indicating that P availability may influence C cycling in the highly weathered soils that underlie many tropical ecosystems. Therefore, we suggest that P availability be included in models that simulate microbial enzyme allocation, biomass growth, and C mineralization.     

A global model of the response of tropical and sub-tropical forest biodiversity to anthropogenic pressures

Habitat loss and degradation, driven largely by agricultural expansion and intensification, present the greatest immediate threat to biodiversity. Tropical forests harbour among the highest levels of terrestrial species diversity and are likely to experience rapid land-use change in the coming decades. Synthetic analyses of observed responses of species are useful for quantifying how land use affects biodiversity and for predicting outcomes under land-use scenarios. Previous applications of this approach have typically focused on individual taxonomic groups, analysing the average response of the whole community to changes in land use. Here, we incorporate quantitative remotely sensed data about habitats in, to our knowledge, the first worldwide synthetic analysis of how individual species in four major taxonomic groups—invertebrates, ‘herptiles’ (reptiles and amphibians), mammals and birds—respond to multiple human pressures in tropical and sub-tropical forests. We show significant independent impacts of land use, human vegetation offtake, forest cover and human population density on both occurrence and abundance of species, highlighting the value of analysing multiple explanatory variables simultaneously. Responses differ among the four groups considered, and—within birds and mammals—between habitat specialists and habitat generalists and between narrow-ranged and wide-ranged species.