Drought Effects in Climate Change Manipulation Experiments: Quantifying the Influence of Ambient Weather Conditions and Rain-out Shelter Artifacts

Extreme drought events challenge ecosystem functioning. Ecological response to drought is studied worldwide in a growing number of field experiments by rain-out shelters. Yet, few meta-analyses face severe challenges in the comparability of studies. This is partly because build-up of drought stress in rain-out shelters is modified by ambient weather conditions. Rain-out shelters can further create confounding effects (radiation, temperature), which may influence plant responses. Yet, a quantification of ecophysiological effects within rain-out shelters under opposing ambient weather conditions and of microclimatological artifacts is missing. Here, we examined phytometers—standardized potted individuals of Plantago lanceolata—under rain-out shelter, rain-out shelter artifact control, and ambient control during opposing outside microclimatological conditions. Furthermore, we tested for artifacts of rain-out shelters on plant responses in a long-term semi-natural grassland experiment. Phytometer plants below the rain-out shelters showed lower stomatal conductance, maximum quantum efficiency, and leaf water potential during warm ambient conditions with high evaporative demand than during cold conditions with low evaporative demand. Plant performance was highly correlated with ambient temperature and vapor pressure deficit (VPD). Rain-out shelter artifacts on plant responses were nonsignificant. Rain-out shelters remain a viable tool for studying ecosystem responses to drought. However, drought manipulations using rain-out shelters are strongly modified by ambient weather conditions. Attributing the results from rain-out shelter studies to drought effects and comparability among studies and study years therefore requires the quantification of the realized drought stress, for example, by relating ecosystem responses to measured microclimatological parameters such as air temperature and VPD.     

CFD assessment of the effect of convective mass transport on the intracellular clearance of intracellular triglycerides in macrosteatotic hepatocytes

Donor livers available to transplant for patients with end-stage liver disease are in severe shortage. One possible avenue to expand the donor pool is to recondition livers that would be otherwise discarded due to excessive fat content. Severely steatotic livers (also known as fatty livers) are highly susceptible to ischemia-reperfusion injury and as a result, primary liver non-function post-transplantation. Prior studies in isolated perfused rat livers suggest that “defatting” may be possible in a timeframe of a few hours; thus, it is conceivable that fatty liver grafts could be recovered by machine perfusion to clear stored fat from the organ prior to transplantation. However, studies using hepatoma cells and adult hepatocytes made fatty in culture report that defatting may take several days. Because cell culture studies were done in static conditions, we hypothesized that the defatting kinetics are highly sensitive to flow-mediated transport of metabolites. To investigate this question, we experimentally evaluated the effect of increasing flow rate on the defatting kinetics of cultured HepG2 cells and developed an in silico combined reaction-transport model to identify possible rate-limiting steps in the defatting process. We found that in cultured fatty HepG2 cells, the time required to clear stored fat down to lean control cells can be reduced from 48 to 4–6 h by switching from static to flow conditions. The flow required resulted in a fluid shear of .008 Pa, which did not adversely affect hepatic function. The reaction-transport model suggests that the transport of l-carnitine, which is the carrier responsible for taking free fatty acids into the mitochondria, is the key rate-limiting process in defatting that was modulated by flow. Therefore, we can ensure higher levels of l-carnitine uptake by the cells by choosing flow rates that minimize the limiting mass transport while minimizing shear stress.     

Island‐wide aridity did not trigger recent megafaunal extinctions in Madagascar

Researchers are divided about the relative importance of people versus climate in triggering the Late Holocene extinctions of the endemic large‐bodied fauna on the island of Madagascar. Specifically, a dramatic and synchronous decline in arboreal pollen and increase in grass pollen ca 1000 yr ago has been alternatively interpreted as evidence for aridification, increased human activity, or both. As aridification and anthropogenic deforestation can have similar effects on vegetation, resolving which of these factors (if either) led to the demise of the megafauna on Madagascar has remained a challenge. We use stable nitrogen isotope (δ¹⁵N) values from radiocarbon‐dated subfossil vertebrates to disentangle the relative importance of natural and human‐induced changes. If increasing aridity were responsible for megafaunal decline, then we would expect an island‐wide increase in δ¹⁵N values culminating in the highest values at the time of proposed maximum drought at ca 1000 yr ago. Alternatively, if climate were relatively stable and anthropogenic habitat alteration explains the palynological signal, then we would anticipate little or no change in habitat moisture, and no systematic, directional change in δ¹⁵N values over time. After accounting for the confounding influences of diet, geographic region, and coastal proximity, we find no change in δ¹⁵N values over the past 10 000 yr, and no support for a period of marked, geographically widespread aridification culminating 900–950 yr ago. Instead, increases in grasses at around that time may signal a transition in human land use to a more dedicated agro‐pastoralist lifestyle, when megafaunal populations were already in decline. Land use changes ca 1000 yr ago would have simply accelerated the inevitable loss of Madagascar's megafauna.     

Patterns of population genetic structure and diversity across bumble bee communities in the Pacific Northwest

Patterns of genetic structure and diversity are largely mediated by a species’ ecological niche and sensitivity to climate variation. Some species with narrow ecological niches have been found to exhibit increased population differentiation, limited gene flow across populations, and reduced population genetic diversity. In this study, we examine patterns of population genetic structure and diversity of four bumble bee species that are broadly sympatric, but do not necessarily inhabit the same ecological niche in the Pacific Northwest of the United States. Testing for the effect of isolation by geographic distance (IBD) with linearized F _st and D _est found that Bombus sylvicola and B. mixtus exhibited significant IBD across populations. In contrast, both B. melanopygus and B. flavifrons, two species that are distributed across a broad elevation gradient, exhibited no IBD, a result further corroborated by Bayesian a priori population assignment tests. Furthermore, we discovered that B. sylvicola populations distributed on the Olympic Peninsula have significantly less average allelic diversity than populations distributed in the Cascade Mountains. Our results suggest that populations distributed in the Olympic Mountains represent a distinct genetic cluster relative to the Cascade Mountains, with B. sylvicola and B. mixtus likely experiencing the greatest degree of population genetic differentiation relative to B. flavifrons and B. melanopygus. While bumble bees are known to co-exist across a diversity of habitats, our results demonstrate that underlying population genetic structure and diversity may not necessarily be similar across species, and are largely governed by their respective niches.     

Autoinducer production and quorum-sensing dependent phenotypes of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> vary according to isolation site during colonization of intubated patients

Background  

Pseudomonas aeruginosa frequently colonizes and is responsible for severe ventilator-associated pneumonia in intubated patients. A quorum-sensing (QS) circuit, depending on the production of the two QS-signaling molecules (autoinducers, AIs) 3-oxo-C₁₂-HSL and C₄-HSL, regulates the production by P. aeruginosa of several virulence factors and is required for biofilm formation. Therefore QS-inhibition has been suggested as a new target for preventive and/or therapeutic strategies. However the precise role of QS during colonization and subsequent infections of intubated patients remains unclear.     

<Emphasis Type="Italic">Geobacillus zalihae</Emphasis> sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia

Background  

Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78°C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5–99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification.     

Amino acids and insulin act additively to regulate components of the ubiquitin-proteasome pathway in C2C12 myotubes

Background  

The ubiquitin-proteasome system is the predominant pathway for myofibrillar proteolysis but a previous study in C2C12 myotubes only observed alterations in lysosome-dependent proteolysis in response to complete starvation of amino acids or leucine from the media. Here, we determined the interaction between insulin and amino acids in the regulation of myotube proteolysis     

Two non-homologous brain diseases-related genes, <Emphasis Type="Italic">SERPINI1</Emphasis> and <Emphasis Type="Italic">PDCD10</Emphasis>, are tightly linked by an asymmetric bidirectional promoter in an evolutionarily conserved manner

Background  

Despite of the fact that mammalian genomes are far more spacious than prokaryotic genomes, recent nucleotide sequencing data have revealed that many mammalian genes are arranged in a head-to-head orientation and separated by a small intergenic sequence. Extensive studies on some of these neighboring genes, in particular homologous gene pairs, have shown that these genes are often co-expressed in a symmetric manner and regulated by a shared promoter region. Here we report the identification of two non-homologous brain disease-related genes, with one coding for a serine protease inhibitor (SERPINI1) and the other for a programmed cell death-related gene (PDCD10), being tightly linked together by an asymmetric bidirectional promoter in an evolutionarily conserved fashion. This asymmetric bidirectional promoter, in cooperation with some cis-acting elements, is responsible for the co-regulation of the gene expression pattern as well as the tissue specificity of SERPINI1 and PDCD10.     

A comprehensive evaluation of SAM,the SAM R-package and a simple modification to improve its performance

Background  

The Significance Analysis of Microarrays (SAM) is a popular method for detecting significantly expressed genes and controlling the false discovery rate (FDR). Recently, it has been reported in the literature that the FDR is not well controlled by SAM. Due to the vast application of SAM in microarray data analysis, it is of great importance to have an extensive evaluation of SAM and its associated R-package (sam2.20).