Ant assemblages in isolated trees are more sensitive to species loss and replacement than their woodland counterparts

Isolated trees possess an arthropod assemblage different to that found in woodland trees. While isolated trees become an increasingly dominant part of many landscapes, with ‘off reserve’ habitat conservation potential, we know little about the drivers of their assemblage structure. While sampling bimonthly for 12 months in the seasonally dry tropics of Mexico, we characterized the ant species most likely to occupy isolated trees in comparison to small woody patches (‘matorral’; 0.13–0.74 ha), and examined the influence of environmental variables on the respective ant assemblages at both canopy and ground level. Isolated trees possessed a predictable ant assemblage: when compared to the woodland patches, isolated trees were characterised by a lack of specialised arboreal species and an increase in generalised terrestrial species reaching the canopy. Arboreal woodland ant species were as affected by tree isolation as the terrestrial woodland ant fauna. Ant assemblages at isolated trees correlated with a series of microenvironmental (microclimate and biophysical) variables, but this was not the case for the ant assemblages in woodlands. This suggests that at very small habitat sizes (e.g., isolated trees), microenvironment influences assemblage composition by favouring more environmentally tolerant or opportunistic species. Although we were unable to identify alternative variables (e.g., patch area, connectivity) which correlated with assemblage composition in larger habitat patches, it appears that in such patches, local microenvironment is less closely associated with assemblage structure, and variables such as patch and landscape configuration become increasingly important. In a practical sense, micro-habitat restoration aimed at augmentation of vegetation surrounding isolated trees may therefore be an effective means of increasing matrix habitat quality and increasing the partitioning of the arboreal and terrestrial faunas, thereby conserving a broader range of species. More generally, movement of matrix species into habitat patches appears to apply universally over a range of scales and taxa, and provides a distinct contrast to the predictions based on the Theory of Island Biogeography.     

Extra-pair young in house wren broods are more likely to be male than female

Sex-allocation theory predicts that females should preferentially produce offspring of the sex with greater fitness potential. In socially monogamous animal species, extra-pair mating often increases the variance in fitness of sons relative to daughters. Thus, in situations where offspring sired by a female''s extra-pair mate(s) will typically have greater fitness potential than offspring sired by the within-pair mate, sex-allocation theory predicts that females will bias the sex of offspring sired by extra-pair mates towards male. We examined the relationship between offspring sex and paternity over six breeding seasons in an Illinois population of the house wren (Troglodytes aedon), a cavity-nesting songbird. Out of the 2345 nestlings that had both sex and paternity assigned, 350 (15%) were sired by extra-pair males. The sex ratio of extra-pair offspring, 0.534, was significantly greater than the sex ratio of within-pair offspring, 0.492, representing an increase of 8.5 per cent in the proportion of sons produced. To our knowledge, this is the first confirmed report of female birds increasing their production of sons in association with extra-pair fertilization. Our results are consistent with the oft-mentioned hypothesis that females engage in extra-pair mating to increase offspring quality.     

Encephalomyocarditis viruses with short poly(C) tracts are more virulent than their mengovirus counterparts.

We have constructed three cDNA clones of encephalomyocarditis virus strain R (EMCV-R) with poly(C) tracts of C4, C9, and C20. RNA transcribed from these cDNAs was infectious to HeLa cells, and the resultant viruses grew well in this system, albeit with plaque sizes that were proportional to the poly(C) length. When injected into mice, the progeny viruses were only slightly less pathogenic than EMCV-R, and the observed degree of attenuation was not nearly as dramatic as for equivalent mengoviruses with similar short poly(C)s. Short-tract poly(C)-mediated attenuation is therefore highly dependent on viral genomic context.     

Plant stages with biotic,indirect defences are more palatable and suffer less herbivory than their undefended counterparts

Plants have evolved several anti‐herbivory strategies, including direct defences, such as mechanical and chemical defences, and indirect or biotic defences, such as the recruitment of defending animals. We examined whether the investment plants make in direct defences differs between those which do and do not invest in biotic defences, by comparing standing herbivory and palatability of congeneric species with and without indirect defences at two ontogenetic stages: before and after the onset of indirect defences. We used Cordia alliodora and Croton suberosus as the species with indirect defences and Cordia elaeagnoides and Croton pseudoniveus as the species without indirect defences. We predicted that herbivores would prefer to eat species and stages with indirect defences to those without them. As predicted, we found that herbivores preferred species and ontogenetic stages with indirect defences in all cases. Overall, however, natural levels of herbivory were lower in species with indirect defences. We conclude that indirect defences offer effective protection against herbivores and posit that their recruitment allows plants to reduce investment in other defence mechanisms. Our results support the notion that plants trade‐off between direct and indirect defensive strategies. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 536–543.     

Antibodies to nontypeable Haemophilus influenzae in blood donors. A comparison between different assay methods

Abstract Antibodies to nontypeable Haemophilus influenzae were determined in sera from healthy blood donors with complement fixation (CF) test, diffusion-in-gel enzyme-linked immunosorbent assay (DIG-ELISA), and enzyme-linked immunosorbent assay (ELISA). In most sera, antibodies to H. influenzae could be detected with all three methods, but DIG-ELISA as well as ELISA demonstrated a greater sensitivity than the CF test. Furthermore, the ELISA methods allowed analysis of separate immunoglobulin classes, which is of great advantage when sera from infected patients are to be analysed.     

FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease

Background  

Candidate single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) were often selected for validation based on their functional annotation, which was inadequate and biased. We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically prioritize candidate SNPs from GWASs.     

FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease

Background

Candidate single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) were often selected for validation based on their functional annotation, which was inadequate and biased. We propose to use the more than 200,000 microarray studies in the Gene Expression Omnibus to systematically prioritize candidate SNPs from GWASs.

Results

We analyzed all human microarray studies from the Gene Expression Omnibus, and calculated the observed frequency of differential expression, which we called differential expression ratio, for every human gene. Analysis conducted in a comprehensive list of curated disease genes revealed a positive association between differential expression ratio values and the likelihood of harboring disease-associated variants. By considering highly differentially expressed genes, we were able to rediscover disease genes with 79% specificity and 37% sensitivity. We successfully distinguished true disease genes from false positives in multiple GWASs for multiple diseases. We then derived a list of functionally interpolating SNPs (fitSNPs) to analyze the top seven loci of Wellcome Trust Case Control Consortium type 1 diabetes mellitus GWASs, rediscovered all type 1 diabetes mellitus genes, and predicted a novel gene (KIAA1109) for an unexplained locus 4q27. We suggest that fitSNPs would work equally well for both Mendelian and complex diseases (being more effective for cancer) and proposed candidate genes to sequence for their association with 597 syndromes with unknown molecular basis.

Conclusions

Our study demonstrates that highly differentially expressed genes are more likely to harbor disease-associated DNA variants. FitSNPs can serve as an effective tool to systematically prioritize candidate SNPs from GWASs.     

Brucella-Salmonella lipopolysaccharide chimeras are less permeable to hydrophobic probes and more sensitive to cationic peptides and EDTA than are their native Brucella sp. counterparts.

A rough (R) Brucella abortus 45/20 mutant was more sensitive to the bactericidal activity of polymyxin B and lactoferricin B than was its smooth (S) counterpart but considerably more resistant than Salmonella montevideo. The outer membrane (OM) and isolated lipopolysaccharide (LPS) of S. montevideo showed a higher affinity for these cationic peptides than did the corresponding B. abortus OM and LPS. We took advantage of the moderate sensitivity of R B. abortus to cationic peptides to construct live R B. abortus-S-LPS chimeras to test the activities of polymyxin B, lactoferricin B, and EDTA. Homogeneous and abundant peripheral distribution of the heterologous S-LPS was observed on the surface of the chimeras, and this coating had no effect on the viability or morphology of the cells. When the heterologous LPS corresponded to the less sensitive bacterium S B. abortus S19, the chimeras were more resistant to cationic peptides; in contrast, when the S-LPS was from the more sensitive bacterium S. montevideo, the chimeras were more susceptible to the action of peptides and EDTA. A direct correlation between the amount of heterologous S-LPS on the surface of chimeric Brucella cells and peptide sensitivity was observed. Whereas the damage produced by polymyxin B in S. montevideo and B. abortus-S. montevideo S-LPS chimeras was manifested mainly as OM blebbing and inner membrane rolling, lactoferricin B caused inner membrane detachment, vacuolization, and the formation of internal electron-dense granules in these cells. Native S and R B. abortus strains were permeable to the hydrophobic probe N-phenyl-1-naphthylamine (NPN). In contrast, only reduced amounts of NPN partitioned into the OMs of the S. montevideo and B. abortus-S. montevideo S-LPS chimeras. Following peptide exposure, accelerated NPN uptake similar to that observed for S. montevideo was detected for the B. abortus-S. montevideo LPS chimeras. The partition of NPN into native or EDTA-, polymyxin B-, or lactoferricin B-treated LPS micelles of S. montevideo or B. abortus mimicked the effects observed with intact cells, and this was confirmed by using micelle hybrids of B. abortus and S. montevideo LPSs. The results showed that LPS is the main cause of B. abortus' resistance to bactericidal cationic peptides, the OM-disturbing action of divalent cationic chelants, and OM permeability to hydrophobic substances. It is proposed that these three features are related to the ability of Brucella bacteria to multiply within phagocytes.     

MCL-1–dependent leukemia cells are more sensitive to chemotherapy than BCL-2–dependent counterparts

Myeloid cell leukemia sequence 1 (MCL-1) and B cell leukemia/lymphoma 2 (BCL-2) are anti-apoptotic proteins in the BCL-2 protein family often expressed in cancer. To compare the function of MCL-1 and BCL-2 in maintaining cancer survival, we constructed complementary mouse leukemia models based on Eμ-Myc expression in which either BCL-2 or MCL-1 are required for leukemia maintenance. We show that the principal anti-apoptotic mechanism of both BCL-2 and MCL-1 in these leukemias is to sequester pro-death BH3-only proteins rather than BAX and BAK. We find that the MCL-1–dependent leukemias are more sensitive to a wide range of chemotherapeutic agents acting by disparate mechanisms. In common across these varied treatments is that MCL-1 protein levels rapidly decrease in a proteosome-dependent fashion, whereas those of BCL-2 are stable. We demonstrate for the first time that two anti-apoptotic proteins can enable tumorigenesis equally well, but nonetheless differ in their influence on chemosensitivity.     

Combined exposure to cigarette smoke and nontypeable Haemophilus influenzae drives development of a COPD phenotype in mice

Background

Cigarette smoke (CS) is the major etiologic factor of chronic obstructive pulmonary disease (COPD). CS-exposed mice develop emphysema and mild pulmonary inflammation but no airway obstruction, which is also a prominent feature of COPD. Therefore, CS may interact with other factors, particularly respiratory infections, in the pathogenesis of airway remodeling in COPD.

Methods

C57BL/6 mice were exposed to CS for 2 h a day, 5 days a week for 8 weeks. Mice were also exposed to heat-killed non-typeable H. influenzae (HK-NTHi) on days 7 and 21. One day after the last exposure to CS, mice were sacrificed and lung inflammation and mechanics, emphysematous changes, and goblet cell metaplasia were assessed. Mice exposed to CS or HK-NTHi alone or room air served as controls. To determine the susceptibility to viral infections, we also challenged these mice with rhinovirus (RV).

Results

Unlike mice exposed to CS or HK-NTHi alone, animals exposed to CS/HK-NTHi developed emphysema, lung inflammation and goblet cell metaplasia in both large and small airways. CS/HK-NTHi-exposed mice also expressed increased levels of mucin genes and cytokines compared to mice in other groups. CS/HK-NTHi-exposed mice infected with RV demonstrated increased viral persistence, sustained neutrophilia, and further increments in mucin gene and chemokine expression compared to other groups.

Conclusions

These findings indicate that in addition to CS, bacteria may also contribute to development of COPD, particularly changes in airways. Mice exposed to CS/HK-NTHi are also more susceptible to subsequent viral infection than mice exposed to either CS or HK-NTHi alone.     

Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies

There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. In many EWASs, it is not possible to analyze the target tissue in large numbers of live humans, and consequently surrogate tissues are employed, most commonly blood. But there is as yet no evidence demonstrating that blood is more informative than buccal cells, the other easily accessible tissue. To assess the potential of buccal cells for use in EWASs, we performed a comprehensive analysis of a buccal cell methylome using whole-genome bisulfite sequencing. Strikingly, a buccal vs. blood comparison reveals > 6X as many hypomethylated regions in buccal. These tissue-specific differentially methylated regions (tDMRs) are strongly enriched for DNaseI hotspots. Almost 75% of these tDMRs are not captured by commonly used DNA methylome profiling platforms such as Reduced Representational Bisulfite Sequencing and the Illumina Infinium HumanMethylation450 BeadChip, and they also display distinct genomic properties. Buccal hypo-tDMRs show a statistically significant enrichment near SNPs associated to disease identified through GWASs. Finally, we find that, compared with blood, buccal hypo-tDMRs show significantly greater overlap with hypomethylated regions in other tissues. We propose that for non-blood based diseases/phenotypes, buccal will be a more informative tissue for EWASs.     

Seed addition experiments are more likely to increase recruitment in larger-seeded species

Colonisation theory predicts that large-seeded species are more likely to show increased seedling recruitment in response to seed addition than are small-seeded species. This is both because their seedlings tend to have better survivorship potential, and because their background density of germinating seedlings tends to be lower. We tested this hypothesis by combining data from a recent review of seed addition studies with seed mass data. Logistic regressions showed positive relationships between seed mass and propensity to increase seedling establishment in response to seed addition in experiments in which establishment success was assessed within 6 months or a year, but not in experiments in which establishment success was assessed more than a year after seed addition. When data for all time periods were combined, a generalised linear model including terms for seed mass, time and an interaction term showed a significant positive relationship between seed mass and species response to seed addition. Thus, knowing a species' seed mass significantly increased our ability to predict its response to seed supplementation.     

A clonal group of nontypeable Haemophilus influenzae with two IgA proteases is adapted to infection in chronic obstructive pulmonary disease

Strains of nontypeable Haemophilus influenzae show enormous genetic heterogeneity and display differential virulence potential in different clinical settings. The igaB gene, which encodes a newly identified IgA protease, is more likely to be present in the genome of COPD strains of H. influenzae than in otitis media strains. Analysis of igaB and surrounding sequences in the present study showed that H. influenzae likely acquired igaB from Neisseria meningitidis and that the acquisition was accompanied by a ~20 kb genomic inversion that is present only in strains that have igaB. As part of a long running prospective study of COPD, molecular typing of H. influenzae strains identified a clonally related group of strains, a surprising observation given the genetic heterogeneity that characterizes strains of nontypeable H. influenzae. Analysis of strains by 5 independent methods (polyacrylamide gel electrophoresis, multilocus sequence typing, igaB gene sequences, P2 gene sequences, pulsed field gel electrophoresis) established the clonal relationship among the strains. Analysis of 134 independent strains collected prospectively from a cohort of adults with COPD demonstrated that ~10% belonged to the clonal group. We conclude that a clonally related group of strains of nontypeable H. influenzae that has two IgA1 protease genes (iga and igaB) is adapted for colonization and infection in COPD. This observation has important implications in understanding population dynamics of H. influenzae in human infection and in understanding virulence mechanisms specifically in the setting of COPD.     

Evidence that human genes of modular proteins have retained significantly more ancestral introns than their fly or worm orthologues

Comparison of the exon-intron structures of human, fly and worm orthologues of mosaic genes assembled from class 1-1 modules by exon-shuffling has revealed that human genes retained significantly more of the original inter-module introns than their protostome orthologues. It is suggested that the much higher rate of intron loss in the worm- and insect lineages than in the chordate lineage reflects their greater tendency for genome compaction.