Metabolic scaling: consensus or controversy?

Background  

The relationship between body mass (M) and standard metabolic rate (B) among living organisms remains controversial, though it is widely accepted that in many cases B is approximately proportional to the three-quarters power of M.     

Junk DNA的功能诠释

在庞大的基因组序列中数量占绝对优势的序列因为不编码蛋白质或RNA产物,一直被人们称为junk DNA.事事讲究经济效率的生物在长期的进化中,应该不会让大量无功能的“垃圾”堆积在充满活力的生命细胞中.近年来的研究已揭示junk DNA具有重要的功能,随着研究的深入,一定会发现越来越多的junk DNA决非垃圾,而是基因组的宝贵财富.     

Whole Genome Duplications and a ‘Function’ for Junk DNA? Facts and Hypotheses

Background

The lack of correlation between genome size and organismal complexity is understood in terms of the massive presence of repetitive and non-coding DNA. This non-coding subgenome has long been called “junk” DNA. However, it might have important functions. Generation of junk DNA depends on proliferation of selfish DNA elements and on local or global DNA duplication followed by genic non-fonctionalization.

Methodology/Principal Findings

Evidence from genomic analyses and experimental data indicates that Whole Genome Duplications (WGD) are often followed by a return to the diploid state, through DNA deletions and intra/interchromosomal rearrangements. We use simple theoretical models and simulations to explore how a WGD accompanied by sequence deletions might affect the dosage balance often required among several gene products involved in regulatory processes. We find that potential genomic deletions leading to changes in nuclear and cell volume might potentially perturb gene dosage balance.

Conclusions/Significance

The potentially negative impact of DNA deletions can be buffered if deleted genic DNA is, at least temporarily, replaced by repetitive DNA so that the nuclear/cell volume remains compatible with normal living. Thus, we speculate that retention of non-functionalized non-coding DNA, and replacement of deleted DNA through proliferation of selfish elements, might help avoid dosage imbalances in cycles of polyploidization and diploidization, which are particularly frequent in plants.     

The ribosome-recycling step: consensus or controversy?

Ribosome recycling, the last step in translation, is now accepted as an essential process for prokaryotes. In 2005, three laboratories showed that ribosome-recycling factor (RRF) and elongation factor G (EF-G) cause dissociation of ribosomes into subunits, solving the long-standing problem of how this essential step of translation occurs. However, there remains ongoing controversy regarding the other actions of RRF and EF-G during ribosome recycling. We propose that the available data are consistent with the notion that RRF and EF-G not only split ribosomes into subunits but also participate directly in the release of deacylated tRNA and mRNA for the next round of translation.     

Hammer or crescent wrench? Stone-tool form and function in the Aurignacian of southwest Germany

The early Upper Paleolithic of Europe is associated with the appearance of blade/bladelet technology (e.g., Aurignacian). These industries include a wider range of formal tool types than seen in the Middle Paleolithic. Greater diversity in tool types is often interpreted as specialized tools created for specific tasks. This, in turn, is said to reflect dramatic behavioral shifts between Neandertals and modern humans. In order to test previous interpretations, it is necessary to have a detailed understanding of early Upper Paleolithic stone-tool function. Toward this end, analyses of microscopic residue and use-wear were undertaken on 109 stone tools from three Aurignacian sites in southwest Germany (Hohle Fels, Geissenkl?sterle, and Vogelherd). These cave sites evidenced remarkable residue preservation, with approximately 82% of the sample showing some form of functional evidence. Residues observed included hair, feathers, bone/antler, wood, plant tissue, phytoliths, starch grains, and resin. The results suggest that tool typology is not strongly linked to the processing of specific materials. For example, endscrapers from the sample show evidence of processing wood, charred wood, plants, starchy plants, birds, bone/antler, and animals (hair). Hairs are found on tools typologically classified as blades, flakes, borers, pointed blades, and combination tools (nosed endscraper-borer, burin-laterally-retouched blade). In the early Upper Paleolithic of southwest Germany, a wide range of tool types appears to have been used to process a diverse array of materials. These results suggest that the interpretation of behavioral patterns from stone tools must consider more than tool typology.     

Prion hypothesis: the end of the controversy?

Forty-three years have passed since it was first proposed that a protein could be the sole component of the infectious agent responsible for the enigmatic prion diseases. Many discoveries have strongly supported the prion hypothesis, but only recently has this once heretical hypothesis been widely accepted by the scientific community. In the past 3 years, researchers have achieved the 'Holy Grail' demonstration that infectious material can be generated in vitro using completely defined components. These breakthroughs have proven that a misfolded protein is the active component of the infectious agent, and that propagation of the disease and its unique features depend on the self-replication of the infectious folding of the prion protein. In spite of these important discoveries, it remains unclear whether another molecule besides the misfolded prion protein might be an essential element of the infectious agent. Future research promises to reveal many more intriguing features about the rogue prions.     

Should I stay or should I go? Cadherin function and regulation in the neural crest

Our increasing comprehension of neural crest cell development has reciprocally advanced our understanding of cadherin expression, regulation, and function. As a transient population of multipotent stem cells that significantly contribute to the vertebrate body plan, neural crest cells undergo a variety of transformative processes and exhibit many cellular behaviors, including epithelial‐to‐mesenchymal transition (EMT), motility, collective cell migration, and differentiation. Multiple studies have elucidated regulatory and mechanistic details of specific cadherins during neural crest cell development in a highly contextual manner. Collectively, these results reveal that gradual changes within neural crest cells are accompanied by often times subtle, yet important, alterations in cadherin expression and function. The primary focus of this review is to coalesce recent data on cadherins in neural crest cells, from their specification to their emergence as motile cells soon after EMT, and to highlight the complexities of cadherin expression beyond our current perceptions, including the hypothesis that the neural crest EMT is a transition involving a predominantly singular cadherin switch. Further advancements in genetic approaches and molecular techniques will provide greater opportunities to integrate data from various model systems in order to distinguish unique or overlapping functions of cadherins expressed at any point throughout the ontogeny of the neural crest.     

Anatomical and functional imaging techniques: basically similar or fundamentally different?

Accurate and early detection of coronary artery disease (CAD) is essential, as the disease remains one of the leading causes of death in the industrialised world. For this purpose, several invasive as well as noninvasive modalities are available. The current gold standard to detect significant narrowing of the coronary arteries is invasive coronary angiography, which allows direct visualisation of the coronary arteries with high spatial and temporal resolution. In addition, if abnormalities are demonstrated, direct intervention is possible. However, it is also an invasive technique that is associated with substantial patient discomfort, costs and a small but distinct risk of potentially life-threatening complications.     

Exosomes and retroviruses: the chicken or the egg?

Retroviruses appropriate pre‐existing cellular machineries to propagate. In the last decade, impressive similarities have been observed in the generation and dissemination in the host cells of retroviruses and small cellular vesicles known as exosomes. These cellular vesicles are thought to facilitate intercellular communication processes and mediate immune functions. However, their link to the retroviral life cycle has given rise to distinct hypotheses and puzzling dilemmas. Are exosomes the antecessors of retroviruses or do retroviruses merely exploit the same cellular machinery designated for exosome biosynthesis? Here, we address these fascinating evolutionary questions by reviewing recent discoveries and analysing the controversies surrounding them.     

Deep pools of the Danube River: ecological function or turbulent sink?

Danube main channel deep pools are in-stream habitats of high ecological relevance. We used dual-frequency identification sonar to investigate seasonal and diel fish abundance in two hydrodynamically different deep pools in the main channel of the Danube River in 2008. In general, fish of different species were present in both deep pools throughout the year, irrespective of water level. High fish abundance was recorded during autumn and winter, low abundance during spring and summer. During low discharge and low temperature and particularly during low flow velocity, low kinetic energy and low shear stress, high fish abundance in densely packed aggregations were observed, a clear indication for the refuge capacity of deep pools. In contrast, during turbulent hydraulic conditions with high flow velocity, high turbulent kinetic energy and high shear stress, low fish abundance occurred, mainly consisting of single fish, small fish shoals and benthic fish specimens. Furthermore, we could reveal that calm as well as turbulent pools fulfil the requirements as refuge and feeding habitat of eurytopic, piscivorous catfish throughout the year. The application of a multiple linear model based on the hydrological parameters discharge and water temperature as well as the hydraulic parameters flow velocity, turbulent kinetic energy and shear stress provided highly significant evidence between the observed and the expected seasonal fish abundance in the deep pools (R ² = 0.77, P < 0.001). For the first time these results make clear that the main channel deep pools are important refuge and resource habitats of different species of the Danube fish community. Deep pools are key habitats for the in-stream fish community of the Danube River.