Cryptic differentiation and geographic variation in genetic diversity of Hall's Babbler Pomatostomus halli

Sequence variation was examined in domain I of the mitochondrial control region in three Queensland populations of Hall's Babbler Pomatostomus halli , a geographically restricted, monotypic songbird in eastern Australia. Surprisingly, we found that domain I sequences were strongly differentiated into two major clades differing by 3.29%. These two clades exhibited nearly complete geographic concordance with northern and southern populations, except for two haplotypes which were sampled in the north of the range but were phylogenetically allied to the southern clade. We also found a seven-fold higher level of genetic diversity in the northern than in the southern populations. Neutrality and molecular clock tests suggested that selection or differences in substitution rates were not responsible for this difference in diversity. However, a maximum likelihood analysis of gene flow between the north and south suggested that the difference in diversity could be due to both greater population size in the north and asymmetric gene flow dominated by south to north dispersal events. A likelihood ratio test rejected a model in which population sizes were equal and rates of gene flow symmetric, and came close to rejecting a model in which only population sizes were constrained to be equal. These results suggest that different population sizes and asymmetric gene flow could be a major source of differences in genetic variation between populations of Hall's Babbler, although ecological and biogeographic causes for these differences are obscure.     

Lectin microarray profiling of metastatic breast cancers

Altered protein glycosylation compared with the disease-free state is a universal feature of cancer cells. It has long been established that distinct glycan structures are associated with specific forms of cancer, but far less is known about the complete array of glycans associated with certain tumors. The cancer glycome has great potential as a source of biomarkers, but progress in this field has been hindered by a lack of available techniques for the elucidation of disease-associated glycosylation. In the present study, lectin microarrays consisting of 45 lectins with different binding preferences covering N- and O-linked glycans were coupled with evanescent-field activated fluorescent detection in the glycomic analysis of primary breast tumors and the serum and urine of patients with metastatic breast cancer. A single 50 μm section of a primary breast tumor or <1 μL of breast cancer patient serum or urine was sufficient to detect glycosylation alterations associated with metastatic breast cancer, as inferred from lectin-binding patterns. The high-throughput, sensitive and relatively simple nature of the simultaneous analysis of N- and O-linked glycosylation following minimal sample preparation and without the need for protein deglycosylation makes the lectin microarray analysis described a valuable tool for discovery phase glycomic profiling.     

An improved understanding of soil Cd risk to humans and low cost methods to phytoextract Cd from contaminated soils to prevent soil Cd risks

We believe greater consideration should be given the agronomic and nutritional/bioavailability factors that influence risk from Cd-contaminated soils. We have argued that the ability of rice to accumulate soil Cd in grain while excluding Fe, Zn and Ca (even though the soil contains 100-times more Zn than Cd) was important in adverse effects of soil Cd is farm families in Asia. Further, polished rice grain is deficient in Fe, Zn and Ca for humans, which promotes Cd absorption into duodenal cells. New kinetic studies clarified that dietary Cd is absorbed into duodenum enterocytes; 109Cd from a single meal remained in the duodenum for up to 16 days; part of the turnover pool 109Cd moved to the liver and kidneys by the end of the 64-day 'chase' period. Thus malnutrition induced by subsistence rice diets caused a higher absorption of dietary Cd and much higher potential risk from soil Cd than other crops. Because rice-induced Fe-Zn-Ca-malnutrition is so important in soil Cd risk, it seems evident that providing nutritional supplements to populations of exposed subsistence rice farmers could protect them against soil Cd during a period of soil remediation. In the long term, high Cd rice soils need to be remediated. Remediation by removal and replacement of contaminated soil is very expensive (on the order of $3 million/ha); while phytoextraction using the high Cd accumulating ecotypes of the Zn-Cd hyperaccumulator, Thlaspi caerulescens, should provide low cost soil Cd remediation.     

Tracking metastatic tumor cell extravasation with quantum dot nanocrystals and fluorescence emission-scanning microscopy

Metastasis is an impediment to the development of effective cancer therapies. Our understanding of metastasis is limited by our inability to follow this process in vivo. Fluorescence microscopy offers the potential to follow cells at high resolution in living animals. Semiconductor nanocrystals, quantum dots (QDs), offer considerable advantages over organic fluorophores for this purpose. We used QDs and emission spectrum scanning multiphoton microscopy to develop a means to study extravasation in vivo. Although QD labeling shows no deleterious effects on cultured cells, concern over their potential toxicity in vivo has caused resistance toward their application to such studies. To test if effects of QD labeling emerge in vivo, tumor cells labeled with QDs were intravenously injected into mice and followed as they extravasated into lung tissue. The behavior of QD-labeled tumor cells in vivo was indistinguishable from that of unlabeled cells. QDs and spectral imaging allowed the simultaneous identification of five different populations of cells using multiphoton laser excitation. Besides establishing the safety of QDs for in vivo studies, our approach permits the study of multicellular interactions in vivo.     

Multiple stressors on biotic interactions: how climate change and alien species interact to affect pollination

Global change may substantially affect biodiversity and ecosystem functioning but little is known about its effects on essential biotic interactions. Since different environmental drivers rarely act in isolation it is important to consider interactive effects. Here, we focus on how two key drivers of anthropogenic environmental change, climate change and the introduction of alien species, affect plant–pollinator interactions. Based on a literature survey we identify climatically sensitive aspects of species interactions, assess potential effects of climate change on these mechanisms, and derive hypotheses that may form the basis of future research. We find that both climate change and alien species will ultimately lead to the creation of novel communities. In these communities certain interactions may no longer occur while there will also be potential for the emergence of new relationships. Alien species can both partly compensate for the often negative effects of climate change but also amplify them in some cases. Since potential positive effects are often restricted to generalist interactions among species, climate change and alien species in combination can result in significant threats to more specialist interactions involving native species.     

Complete Genome Sequence and Genome Analysis of Eggplant mottled dwarf virus‐Iranian Isolate

The full‐length nucleotide sequence of the Iranian isolate of Eggplant mottled dwarf virus (EMDV), a phytorhabdovirus, was determined using the random polymerase chain reaction method (rPCR) followed by PCR with specific primers to fill in the gaps. The negative‐sense RNA genome of the Iranian isolate of EMDV contains 13154 nucleotides and seven open‐reading frames (ORFs) in the order 3′‐leader‐N‐X‐P‐Y‐M‐G‐L‐trailer‐5′. These ORFs encode the nucleocapsid, X protein (of unknown function), phosphoprotein, Y protein (putative movement protein), matrix protein, glycoprotein and RNA‐dependent RNA polymerase, respectively. EMDV has a 199 nt 3′ leader RNA and a 151 nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. Phylogenetic analyses indicate that EMDV is most closely related to Potato yellow dwarf virus, which has a distinctly different geographical distribution.     

Analysis of individual cells identifies cell‐to‐cell variability following induction of cellular senescence

Senescent cells play important roles in both physiological and pathological processes, including cancer and aging. In all cases, however, senescent cells comprise only a small fraction of tissues. Senescent phenotypes have been studied largely in relatively homogeneous populations of cultured cells. In vivo, senescent cells are generally identified by a small number of markers, but whether and how these markers vary among individual cells is unknown. We therefore utilized a combination of single‐cell isolation and a nanofluidic PCR platform to determine the contributions of individual cells to the overall gene expression profile of senescent human fibroblast populations. Individual senescent cells were surprisingly heterogeneous in their gene expression signatures. This cell‐to‐cell variability resulted in a loss of correlation among the expression of several senescence‐associated genes. Many genes encoding senescence‐associated secretory phenotype (SASP) factors, a major contributor to the effects of senescent cells in vivo, showed marked variability with a subset of highly induced genes accounting for the increases observed at the population level. Inflammatory genes in clustered genomic loci showed a greater correlation with senescence compared to nonclustered loci, suggesting that these genes are coregulated by genomic location. Together, these data offer new insights into how genes are regulated in senescent cells and suggest that single markers are inadequate to identify senescent cells in vivo.     

LiDAR‐derived canopy structure supports the more‐individuals hypothesis for arthropod diversity in temperate forests

Despite considerable progress in the ability to measure the complex 3‐D structure of forests with the improvement of remote‐sensing techniques, our mechanistic understanding of how biodiversity is linked to canopy structure is still limited. Here we tested whether the increase in arthropod abundance and richness in beech forest canopies with increasing canopy complexity supports the more‐individuals hypothesis or the habitat‐heterogeneity hypothesis. We used fogging to collect arthropod samples from 80 standardized plots from canopies of single‐ to multi‐layered mature montane European beech stands. Tree height and an independent measure of vertical heterogeneity – the vertical distribution ratio – on each arthropod sampling plot were derived from high‐resolution full‐waveform airborne laser scanning data. Mixed‐model path analysis based on almost 20 000 specimens of 762 species from 11 orders provided support for the more‐individuals hypothesis, with higher arthropod abundance but not higher species richness in stands with a more equal vertical distribution of plant biomass. By contrast, we found no support for the habitat‐heterogeneity hypothesis. The increase in the number of individuals with increasing vertical distribution of biomass might be caused either by increasing leaf area, as indicated by higher space filling and productivity in multi‐layered stands, or by higher persistence of arthropod populations owing to better shelter, reduced competition and more refuges under harsh conditions, or by both. High‐resolution airborne laser scanning, with its ability to penetrate dense canopies under leaf‐on conditions, has proved suitable for measuring vertical structures as a predictor for canopy diversity. Expanding combinations of remote‐sensing and canopy‐biodiversity data opens many avenues for improving our understanding of the link between diversity and forest structures.