Benefit or Liability? The Ectomycorrhizal Association May Undermine Tree Adaptations to Fire After Long-term Fire Exclusion

Ecosystems - Long-term fire exclusion may weaken ecosystem resistance to the return of fire. We investigated how a surface wildfire that occurred after several decades of fire exclusion affected a...     

Bias in vegetation databases? A comparison of stratified‐random and preferential sampling

Aim: Vegetation plots collected since the early 20th century and stored in large vegetation databases are an important source of ecological information. These databases are used for analyses of vegetation diversity and estimation of vegetation parameters, however such analyses can be biased due to preferential sampling of the original data. In contrast, modern vegetation survey increasingly uses stratified‐random instead of preferential sampling. To explore how these two sampling schemes affect vegetation analyses, we compare parameters of vegetation diversity based on preferentially sampled plots from a large vegetation database with those based on stratified‐random sampling. Location: Moravian Karst and Silesia, Czech Republic. Methods: We compared two parallel analyses of forest vegetation, one based on preferentially sampled plots taken from a national vegetation database and the other on plots sampled in the field according to a stratified‐random design. We repeated this comparison for two different regions in the Czech Republic. We focussed on vegetation properties commonly analysed using data from large vegetation databases, including alpha (within‐plot) diversity, cover and participation of different species groups, such as endangered and alien species within plots, total species richness of data sets, beta diversity and ordination patterns. Results: The preferentially sampled data sets obtained from the database contained more endangered species and had higher beta diversity, whereas estimates of alpha diversity and representation of alien species were not consistently different between preferentially and stratified‐randomly sampled data sets. In ordinations, plots from the preferential samples tended to be more common at margins of plot scatters. Conclusions: Vegetation data stored in large databases are influenced by researcher subjectivity in plot positioning, but we demonstrated that not all of their properties necessarily differ from data sets obtained by stratified‐random sampling. This indicates the value of vegetation databases for use in biodiversity studies; however, some analyses based on these databases are clearly biased and their results must be interpreted with caution.     

Postcranial Functional Morphology of <Emphasis Type="Italic">Hyracotherium</Emphasis> (Equidae,Perissodactyla) and Locomotion in the Earliest Horses

A nearly complete skeleton of Hyracotherium grangeri is described from the early Wasatchian (early Eocene) of the Clarks Fork Basin in northwestern Wyoming. This specimen includes a virtually complete, well-preserved pre-caudal vertebral column allowing the first thorough investigation of the locomotory abilities of these early Eocene horses. The posterior thorax (T) and lumbus (L) are divided into a facultatively dorsostable region (T15-L3) and an obligately dorsostable region (L3-L7). The facultatively dorsostable region is characterized by robust, cranially-oriented neural spines and well-developed attachment sites for epaxial musculature, whereas the obligately dorsostable region is characterized by embracing zygapophyses and less developed spines and attachment sites. Limb morphology exhibits a mixture of primitive characters and derived features associated with cursoriality. As described by previous authors, limb mobility is restricted at the elbow and ankle due to interlocking humero-radial and tibio-astragalar articulations, respectively. In contrast, the presence of a rounded femoral head and well-developed pelvic and femoral attachment sites for hindlimb adductor muscles suggests a highly mobile hip joint. Limited inversion of the manus and pes may have been possible via differential movement between the proximal and distal carpal elements and at the transverse tarsal joint, respectively. The obligately dorsostable region of the vertebral column likely resisted variably-oriented torque applied by hip musculature, thereby preventing dislocation of the pelvis and lumbus. The facultatively dorsostable region would have facilitated dynamic positioning of the center of mass during rapid acceleration. Brief comparisons with Orohippus and Mesohippus postcrania are used to discuss the selective pressures imposed by changes in body mass and habitat on the postcranial evolution of Paleogene horses.     

Mucous solids and liquid secretion by airways: studies with normal pig, cystic fibrosis human, and non-cystic fibrosis human bronchi

To better understand how airways produce thick airway mucus, nonvolatile solids were measured in liquid secreted by bronchi from normal pig, cystic fibrosis (CF) human, and non-CF human lungs. Bronchi were exposed to various secretagogues and anion secretion inhibitors to induce a range of liquid volume secretion rates. In all three groups, the relationship of solids concentration (percent nonvolatile solids) to liquid volume secretion rate was curvilinear, with higher solids concentration associated with lower rates of liquid volume secretion. In contrast, the secretion rates of solids mass and water mass as functions of liquid volume secretion rates exhibited positive linear correlations. The y-intercepts of the solids mass-liquid volume secretion relationships for all three groups were positive, thus accounting for the higher solids concentrations in airway liquid at low rates of secretion. Predictive models derived from the solids mass and water mass linear equations fit the experimental percent solids data for the three groups. The ratio of solids mass secretion to liquid volume secretion was 5.2 and 2.4 times higher for CF bronchi than for pig and non-CF bronchi, respectively. These results indicate that normal pig, non-CF human, and CF human bronchi produce a high-percent-solids mucus (>8%) at low rates of liquid volume secretion (≤1.0 μl·cm(-2)·h(-1)). However, CF bronchi produce mucus with twice the percent solids (~8%) of pig or non-CF human bronchi at liquid volume secretion rates ≥4.0 μl·cm(-2)·h(-1).     

Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial

We analyzed HIV-1 genome sequences from 68 newly infected volunteers in the STEP HIV-1 vaccine trial. To determine whether the vaccine exerted selective T cell pressure on breakthrough viruses, we identified potential T cell epitopes in the founder sequences and compared them to epitopes in the vaccine. We found greater distances to the vaccine sequence for sequences from vaccine recipients than from placebo recipients. The most significant signature site distinguishing vaccine from placebo recipients was Gag amino acid 84, a site encompassed by several epitopes contained in the vaccine and restricted by human leukocyte antigen (HLA) alleles common in the study cohort. Moreover, the extended divergence was confined to the vaccine components of the virus (HIV-1 Gag, Pol and Nef) and not found in other HIV-1 proteins. These results represent what is to our knowledge the first evidence of selective pressure from vaccine-induced T cell responses on HIV-1 infection in humans.     

A case study in explanatory power: John Snow's conclusions about the pathology and transmission of cholera

In the mid-1800s, there was much debate about the origin or ‘exciting cause’ of cholera. Despite much confusion surrounding the disease, the so-called miasma theory emerged as the prevalent account about cholera’s cause. Going against this mainstream view, the British physician John Snow inferred several things about cholera’s origin and pathology that no one else inferred. Without observing the vibrio cholerae, however,—data unavailable to Snow and his colleagues—, there was no way of settling the question of what exactly was causing cholera and how, or if, it was passed on. The question then arises as to how Snow arrived at conclusions so systematically different from those of his opponents. In this paper, I want to look at Snow’s reasoning in some detail, and show that there were certain principles, explanatory power in particular, that were epistemologically important to Snow in their own right. I will show that Snow himself takes explanatory power to be an epistemic property, and makes explicit links between explanatory power and confirmation. Systematically juxtaposing Snow’s claims and his opponents’, I will show that Snow was right to tout the explanatory power of his theory, and that his conclusions about the epistemic superiority of his theory over that of the miasmatists’ were justified.     

GO for integration of expression data

The low reproducibility of differential expression of individual genes in microarray experiments has led to the suggestion that experiments be analyzed in terms of gene characteristics, such as GO categories or pathways, in order to enhance the robustness of the results. An implicit assumption of this approach is that the different experiments in effect randomly sample the genes participating in an active process. We argue that by the same rationale it is possible to perform this higher-level analysis on the aggregation of genes that are differentially-expressed in different expression-based studies, even if the experiments used different platforms. The aggregation increases the reliability of the results, it has the potential for uncovering signals that are liable to escape detection in the individual experiments, and it enables a more thorough mining of the ever more plentiful microarray data. We present here a proof-of-concept study of these ideas, using ten studies describing the changes in expression profiles of human host genes in response to infection by Retroviridae or Herpesviridae viral families. We supply a tool (accessible at www.cs.bgu.ac.il/～waytogo) which enables the user to learn about genes and processes of interest in this study.     

Coordinated regulation of niche and stem cell precursors by hormonal signaling

Stem cells and their niches constitute units that act cooperatively to achieve adult body homeostasis. How such units form and whether stem cell and niche precursors might be coordinated already during organogenesis are unknown. In fruit flies, primordial germ cells (PGCs), the precursors of germ line stem cells (GSCs), and somatic niche precursors develop within the larval ovary. Together they form the 16-20 GSC units of the adult ovary. We show that ecdysone receptors are required to coordinate the development of niche and GSC precursors. At early third instar, ecdysone receptors repress precocious differentiation of both niches and PGCs. Early repression is required for correct morphogenesis of the ovary and for protecting future GSCs from differentiation. At mid-third instar, ecdysone signaling is required for niche formation. Finally, and concurrent with the initiation of wandering behavior, ecdysone signaling initiates PGC differentiation by allowing the expression of the differentiation gene bag of marbles in PGCs that are not protected by the newly formed niches. All the ovarian functions of ecdysone receptors are mediated through early repression, and late activation, of the ecdysone target gene broad. These results show that, similar to mammals, a brain-gland-gonad axis controls the initiation of oogenesis in insects. They further exemplify how a physiological cue coordinates the formation of a stem cell unit within an organ: it is required for niche establishment and to ensure that precursor cells to adult stem cells remain undifferentiated until the niches can accommodate them. Similar principles might govern the formation of additional stem cell units during organogenesis.     

Elevated hypothalamic TCPTP in obesity contributes to cellular leptin resistance

In obesity, anorectic responses to leptin are diminished, giving rise to the concept of "leptin resistance." Increased expression of protein tyrosine phosphatase 1B (PTP1B) has been associated with the attenuation of leptin signaling and development of cellular leptin resistance. Here we report that hypothalamic levels of the tyrosine phosphatase TCPTP are also elevated in obesity to attenuate the leptin response. We show that mice that lack TCPTP in neuronal cells have enhanced leptin sensitivity and are resistant to high-fat-diet-induced weight gain and the development of leptin resistance. Also, intracerebroventricular administration of a TCPTP inhibitor enhances leptin signaling and responses in mice. Moreover, the combined deletion of TCPTP and PTP1B in neuronal cells has additive effects in the prevention of diet-induced obesity. Our results identify TCPTP as a critical negative regulator of hypothalamic leptin signaling and causally link elevated TCPTP to the development of cellular leptin resistance in obesity.