How to improve scaling from traits to ecosystem processes

Scaling approaches in ecology assume that traits are the main attributes by which organisms influence ecosystem functioning. However, several recent empirical papers have found only weak links between traits and ecosystem functioning, questioning the usefulness of trait-based ecology (TBE). We argue that these studies often suffer from one or more widespread misconceptions. Specifically, these studies often (i) conflict with the conceptual foundations of TBE, (ii) lack theory- or hypothesis-driven selection and use of traits, (iii) tend to ignore intraspecific variation, and (iv) use experimental or study designs that are not well suited to make strong tests of TBE assumptions. Addressing these aspects could significantly improve our ability to scale from traits to ecosystem functioning.     

Genetic variability in the European bison

In the European bison, Bison bonasus (L), 15 proteins coded by 20 loci have been studied. Two of these loci (Es-3 and Ca) are polymorphic and the remaining 18 are monomorphic. The average heterozygosity of bisons in Polish herds is 3.5%. The value does not differ from those found in populations of other large mammals in spite of restoration of the European bison population from a mere 13 individuals.     

Electron microscopy can be used to measure DNA supertwisting

Incorporation of starch or casein into protoplast-regeneration medium facilitated shotgun cloning of -amylase and neutral protease genes from an unidentified Bacillus sp. in Bacillus subtilis by polyethylene glycol-induced protoplast transformation. This modification and the use of the plasmid vector pPL603b enabled us to simultaneously select for promoter-bearing recombinant plasmids that expressed amylase or protease activity. The inserts were found to be 4 and 4.6 kb, respectively. Although protease activity directed by the cloned gene was only 2- to 4-fold higher than for the donor strain, that of -amylase was 28-fold higher.     

Patterns of genetic variation in US federal bison herds

Like many wide‐ranging mammals, American bison (Bison bison) have experienced significant range contraction over the past two centuries and are maintained in artificially isolated populations. A basic understanding of the distribution of genetic variation among populations is necessary to facilitate long‐term germplasm preservation and species conservation. The 11 herds maintained within the US federal system are a critically important source of germplasm for bison conservation, as they include many of the oldest herds in the USA and have served as a primary resource for the establishment of private and public herds worldwide. In this study, we used a panel of 51 nuclear markers to investigate patterns of neutral genetic variation among these herds. Most of these herds have maintained remarkably high levels of variation despite the severe bottleneck suffered in the late 1800s. However, differences were noted in the patterns of variation and levels of differentiation among herds, which were compared with historical records of establishment, supplementation, herd size, and culling practices. Although some lineages have been replicated across multiple herds within the US federal system, other lineages with high levels of genetic variation exist in isolated herds and should be considered targets for the establishment of satellite herds. From this and other studies, it is clear that the genetic variation represented in the US federal system is unevenly distributed among National Park Service and Fish and Wildlife Service herds, and that these resources must be carefully managed to ensure long‐term species conservation.     

Daytime naps can be used to supplement night-time sleep in athletes

ABSTRACT

This study examined the efficacy of daytime napping to supplement night-time sleep in athletes. Twelve well-trained male soccer players completed three conditions in a randomised, counterbalanced order: 9 h in bed overnight with no daytime nap (9 h + 0 h); 8 h in bed overnight with a 1-h daytime nap (8 h + 1 h); and 7 h in bed overnight with a 2-h daytime nap (7 h + 2 h). Sleep was assessed using polysomnography. The total amount of sleep obtained in the three conditions was similar, i.e. 8.1 h (9 h + 0 h), 8.2 h (8 h + 1 h), and 8.0 h (7 h + 2 h). Daytime napping may be an effective strategy to supplement athletes’ night-time sleep.     

RNA interference can be used to disrupt gene function in tardigrades

How morphological diversity arises is a key question in evolutionary developmental biology. As a long-term approach to address this question, we are developing the water bear Hypsibius dujardini (Phylum Tardigrada) as a model system. We expect that using a close relative of two well-studied models, Drosophila (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda), will facilitate identifying genetic pathways relevant to understanding the evolution of development. Tardigrades are also valuable research subjects for investigating how organisms and biological materials can survive extreme conditions. Methods to disrupt gene activity are essential to each of these efforts, but no such method yet exists for the Phylum Tardigrada. We developed a protocol to disrupt tardigrade gene functions by double-stranded RNA-mediated RNA interference (RNAi). We showed that targeting tardigrade homologs of essential developmental genes by RNAi produced embryonic lethality, whereas targeting green fluorescent protein did not. Disruption of gene functions appears to be relatively specific by two criteria: targeting distinct genes resulted in distinct phenotypes that were consistent with predicted gene functions and by RT-PCR, RNAi reduced the level of a target mRNA and not a control mRNA. These studies represent the first evidence that gene functions can be disrupted by RNAi in the phylum Tardigrada. Our results form a platform for dissecting tardigrade gene functions for understanding the evolution of developmental mechanisms and survival in extreme environments.     

Complexity charts can be used to map functional domains in DNA

We measured local compositional complexity (LCC) of DNA sequences by calculating Shannon information content over mononucleotide frequencies. Eukaryotic DNA appeared to be "simpler" than bacterial DNA even at the level of short oligonucleotides. Moreover, different DNA functional domains displayed different compositional complexity in a systematic manner. In particular, the complexity of exon sequences was systematically higher than the complexity of corresponding introns. We therefore present examples of complexity charts (plots of complexity versus position in sequence) for pre-mRNA sequences from higher eukaryotes. By taking a window width of 100 nucleotides and a window step of 1 nucleotide, introns can be distinguished from exons in the majority of cases studied. Complexity charts of immunoglobulin variable regions allowed correct mapping of exons and introns in these sequences as well, a task that was impossible with commercial programs available to date.     

Apoptotic markers can be used to forecast the freezeability of stallion spermatozoa

In an attempt to identify valuable markers for potential freezeability of the equine spermatozoa, three ejaculates were collected from five Andalusian stallions and frozen using a standard protocol. Before freezing, three apoptotic cell markers were studied by flow cytometry (early changes in sperm membranes, mitochondrial membrane potential and caspase activity). Post-thaw, spermatozoa were again evaluated for these parameters. Sperm kinematics using CASA were also studied before and after freezing and thawing. Receiving operating system curves were used to evaluate the relative value of the apoptotic markers herein studied, as forecast for potential freezeability. From all parameters studied, the outcome of JC-1 (as proportion of spermatozoa showing simultaneously orange and green fluorescence) had the highest diagnostic power. For potentially bad freezers (less than 25% of intact spermatozoa post-thaw), the significant area under the ROC-curve was 0.985, with a 100% sensitivity and 99.8% specificity for a cut off value of 55.7.     

Pepsin can be used to subculture viable mammary epithelial cells

Normal mouse mammary epithelial cells in primary culture can be passaged as viable single cells using 0.5 to 1.0 mg/ml pepsin in Hanks' salt solution. After 5 min the pepsin treatment preferentially removes fibroblasts, leaving a monolayer of purified epithelial cells that can be removed by pipetting and transferred to new culture vessels or injected into animals.     

Pepsin can be used to subculture viable mammary epithelial cells

Summary Normal mouse mammary epithelial cells in primary culture can be passaged as viable single cells using 0.5 to 1.0 mg/ml pepsin in Hanks’ salt solution. After 5 min the pepsin treatment preferentially removes fibroblasts, leaving a monolayer of purified epithelial cells that can be removed by pipetting and transferred to new culture vessels or injected into animals. This study was supported by Contract CB-43907 from the National Institutes of Health.     

How electron interference can be used in probing the surface of minute bioobjects and in fast reading of polynucleotides

A method is proposed for examining the surface of small biological objects such as macromolecules and their complexes. Based on interference of low-energy electrons, it allows constructing analogs of optical holograms but with a resolution on the order of interatomic distances. A set of such holograms obtained at different electron energies can provide sufficient information for identifying the surface groups of the object. Thus the method can be used for fast reading of e.g. polynucleotide sequences.