A Standardized Reference Data Set for Vertebrate Taxon Name Resolution

Taxonomic names associated with digitized biocollections labels have flooded into repositories such as GBIF, iDigBio and VertNet. The names on these labels are often misspelled, out of date, or present other problems, as they were often captured only once during accessioning of specimens, or have a history of label changes without clear provenance. Before records are reliably usable in research, it is critical that these issues be addressed. However, still missing is an assessment of the scope of the problem, the effort needed to solve it, and a way to improve effectiveness of tools developed to aid the process. We present a carefully human-vetted analysis of 1000 verbatim scientific names taken at random from those published via the data aggregator VertNet, providing the first rigorously reviewed, reference validation data set. In addition to characterizing formatting problems, human vetting focused on detecting misspelling, synonymy, and the incorrect use of Darwin Core. Our results reveal a sobering view of the challenge ahead, as less than 47% of name strings were found to be currently valid. More optimistically, nearly 97% of name combinations could be resolved to a currently valid name, suggesting that computer-aided approaches may provide feasible means to improve digitized content. Finally, we associated names back to biocollections records and fit logistic models to test potential drivers of issues. A set of candidate variables (geographic region, year collected, higher-level clade, and the institutional digitally accessible data volume) and their 2-way interactions all predict the probability of records having taxon name issues, based on model selection approaches. We strongly encourage further experiments to use this reference data set as a means to compare automated or computer-aided taxon name tools for their ability to resolve and improve the existing wealth of legacy data.     

A New Apparatus for Standardized Rat Kidney Biopsy

Survival biopsies are frequently applied in rat kidney disease models, but several drawbacks such as surgical kidney trauma, bleeding risk and variable loss of kidney tissue are still unsolved. Therefore, we developed an easy-to-use core biopsy instrument and evaluated whether two consecutive kidney biopsies within the same kidney can be carried out in a standardized manner. On day 0, 18 Lewis rats underwent a right nephrectomy and 9 of these rats a subsequent first biopsy of the left kidney (Bx group). 9 control rats had a sham biopsy of the left kidney (Ctrl group). On day 7, a second kidney biopsy/sham biopsy was performed. On day 42, all animals were sacrificed and their kidneys were removed for histology. Biopsy cylinders contained 57±28 glomeruli per transversal section, representing an adequate sample size. PAS staining showed that the biopsy depth was limited to the renal cortex whereas surgical tissue damage was limited to the area immediately adjacent to the taken biopsy cylinder. On day 42, the reduction of functional renal mass after two biopsies was only 5.2% and no differences of body weight, blood pressure, proteinuria, serum creatinine, glomerulosclerosis, interstitial fibrosis or number of ED-1 positive macrophages were found between both groups. In summary, our apparatus offers a safe method to perform repetitive kidney biopsies with minimal trauma and sufficient sample size and quality even in experimental disease models restricted to one single kidney.     

Stimulus Set Meaningfulness and Neurophysiological Differentiation: A Functional Magnetic Resonance Imaging Study

A meaningful set of stimuli, such as a sequence of frames from a movie, triggers a set of different experiences. By contrast, a meaningless set of stimuli, such as a sequence of ‘TV noise’ frames, triggers always the same experience—of seeing ‘TV noise’—even though the stimuli themselves are as different from each other as the movie frames. We reasoned that the differentiation of cortical responses underlying the subject’s experiences, as measured by Lempel-Ziv complexity (incompressibility) of functional MRI images, should reflect the overall meaningfulness of a set of stimuli for the subject, rather than differences among the stimuli. We tested this hypothesis by quantifying the differentiation of brain activity patterns in response to a movie sequence, to the same movie scrambled in time, and to ‘TV noise’, where the pixels from each movie frame were scrambled in space. While overall cortical activation was strong and widespread in all conditions, the differentiation (Lempel-Ziv complexity) of brain activation patterns was correlated with the meaningfulness of the stimulus set, being highest in the movie condition, intermediate in the scrambled movie condition, and minimal for ‘TV noise’. Stimulus set meaningfulness was also associated with higher information integration among cortical regions. These results suggest that the differentiation of neural responses can be used to assess the meaningfulness of a given set of stimuli for a given subject, without the need to identify the features and categories that are relevant to the subject, nor the precise location of selective neural responses.     

宏蛋白质组学:研究微生物群落的一种新策略

宏蛋白质组学是一种运用蛋白质组技术对特定微生物群落所产生的全部蛋白质进行大规模研究与分析的新技术。简要概述宏蛋白组学的产生、研究策略及其应用情况,并对其应用前景进行展望。     

胚胎干细胞研究的新工具:RNA干扰

胚胎干细胞研究是20世纪90年代以来在生物医学领域中最引人注目的热点之一,而新近发展起来的RNA干扰技术,能快速有效地沉默基因表达,将成为胚胎干细胞生物学研究的得力工具。现对RNA干扰的作用机制,以及RNA干扰应用于胚胎干细胞研究的方法与RNA干扰在胚胎干细胞研究领域的进展作一综述,以期为今后这方面的研究提供参考。     

A New Methodology for Studying the Activity of Underground Mammals

Biology Bulletin - A new methodology for studying the activity of underground mammals with the use of a digital portable voice recorder has been elaborated. Previously, mole rats were visually...     

Bank of Standardized Stimuli (BOSS) Phase II: 930 New Normative Photos

Researchers have only recently started to take advantage of the developments in technology and communication for sharing data and documents. However, the exchange of experimental material has not taken advantage of this progress yet. In order to facilitate access to experimental material, the Bank of Standardized Stimuli (BOSS) project was created as a free standardized set of visual stimuli accessible to all researchers, through a normative database. The BOSS is currently the largest existing photo bank providing norms for more than 15 dimensions (e.g. familiarity, visual complexity, manipulability, etc.), making the BOSS an extremely useful research tool and a mean to homogenize scientific data worldwide. The first phase of the BOSS was completed in 2010, and contained 538 normative photos. The second phase of the BOSS project presented in this article, builds on the previous phase by adding 930 new normative photo stimuli. New categories of concepts were introduced, including animals, building infrastructures, body parts, and vehicles and the number of photos in other categories was increased. All new photos of the BOSS were normalized relative to their name, familiarity, visual complexity, object agreement, viewpoint agreement, and manipulability. The availability of these norms is a precious asset that should be considered for characterizing the stimuli as a function of the requirements of research and for controlling for potential confounding effects.     

A New Chamber for Studying the Behavior of Drosophila

Methods available for quickly and objectively quantifying the behavioral phenotypes of the fruit fly, Drosophila melanogaster, lag behind in sophistication the tools developed for manipulating their genotypes. We have developed a simple, easy-to-replicate, general-purpose experimental chamber for studying the ground-based behaviors of fruit flies. The major innovative feature of our design is that it restricts flies to a shallow volume of space, forcing all behavioral interactions to take place within a monolayer of individuals. The design lessens the frequency that flies occlude or obscure each other, limits the variability in their appearance, and promotes a greater number of flies to move throughout the center of the chamber, thereby increasing the frequency of their interactions. The new chamber design improves the quality of data collected by digital video and was conceived and designed to complement automated machine vision methodologies for studying behavior. Novel and improved methodologies for better quantifying the complex behavioral phenotypes of Drosophila will facilitate studies related to human disease and fundamental questions of behavioral neuroscience.     

X-Ray Fluorescence Imaging: A New Tool for Studying Manganese Neurotoxicity

The neurotoxic effect of manganese (Mn) establishes itself in a condition known as manganism or Mn induced parkinsonism. While this condition was first diagnosed about 170 years ago, the mechanism of the neurotoxic action of Mn remains unknown. Moreover, the possibility that Mn exposure combined with other genetic and environmental factors can contribute to the development of Parkinson''s disease has been discussed in the literature and several epidemiological studies have demonstrated a correlation between Mn exposure and an elevated risk of Parkinson''s disease. Here, we introduce X-ray fluorescence imaging as a new quantitative tool for analysis of the Mn distribution in the brain with high spatial resolution. The animal model employed mimics deficits observed in affected human subjects. The obtained maps of Mn distribution in the brain demonstrate the highest Mn content in the globus pallidus, the thalamus, and the substantia nigra pars compacta. To test the hypothesis that Mn transport into/distribution within brain cells mimics that of other biologically relevant metal ions, such as iron, copper, or zinc, their distributions were compared. It was demonstrated that the Mn distribution does not follow the distributions of any of these metals in the brain. The majority of Mn in the brain was shown to occur in the mobile state, confirming the relevance of the chelation therapy currently used to treat Mn intoxication. In cells with accumulated Mn, it can cause neurotoxic action by affecting the mitochondrial respiratory chain. This can result in increased susceptibility of the neurons of the globus pallidus, thalamus, and substantia nigra pars compacta to various environmental or genetic insults. The obtained data is the first demonstration of Mn accumulation in the substantia nigra pars compacta, and thus, can represent a link between Mn exposure and its potential effects for development of Parkinson''s disease.     

Stimulus selection (light) in four subspecies of deermice (Peromyscus maniculatus)

Abstract

Four subspecies of deermice (Peromyscus maniculatus) were selected from habitats along a gradient from mesic hardwood forests (gracilis), tall grass prairie (bairdi), short grass prairie (nebrascensis), to desert grassland (labecula) in effort to relate the light preferences of the mice to the habitat of their origin. Six individuals of each subspecies were maintained in dark chambers for 25 days, during which they could turn on a dim light for 30 seconds on ten of these days. Mice from the mesic habitats turned the lights on more frequently (light reinforcement) than mice from xeric habitats. The same subspecies that exhibited light reinforcement when raised in laboratory light conditions failed to show light reinforcement when raised in total darkness. The circadian periodicities also differed significantly among the subspecies. Conclusions drawn from the results were: (1) selection for light is genetically influenced as indicated by subspecific differences, (2) some genotypes are readily modified by environmental light conditions than others, and (3) natural selection in each environment appears to contribute to the degree of genetic fixation or genetic plasticity.     

A New Method for Studying Human Oocytes by Light and Electron Microscopy

Since ovarian follicles appear to be randomly oriented with respect to the plane of the section, the method of sectioning and examining follicles at their raimm diameter described here allows direct comparison between oocyte populations of women and small differences can be detected. Re-sectioning for EM allows selected follicles of interest to be examined at a higher resolution.     

High-Pressure Scanning Microcalorimetry – A New Method for Studying Conformational and Phase Transitions

The development of high-pressure scanning microcalorimetry and the first results studying transitions in proteins, lipids, and model polymers are reviewed. Special attention is given to changes (increments) in volume parameters upon transitions as well as the nature of these changes. It is demonstrated that the use of the model of compound transfer reaction in its purest form for assessment of denaturation volume effects failed due to serious difficulties.     

Identification of a New Set of Polypeptidic Sex Pheromones from Cuttlefish (Sepia officinalis)

Marine Biotechnology - The common English Channel cuttlefish (Sepia officinalis) reproduces every year on very localized coastal spawning areas after a west–east horizontal migration of...     

A Standardized Test for the Identification and Characterization of Melanins Using Electron Paramagnetic Resonance (EPR) Spectroscopy

Melanins are complex, incompletely understood polymeric pigments that historically have been difficult to investigate with common chemical, histochemical, and physicochemical techniques. Because these pigments uniquely contain a stable population of organic free radicals, electron paramagnetic resonance (EPR) spectroscopy is a particularly effective method for studying them, and a set of qualitative EPR criteria has been established for their identification. However, a number of practical problems have arisen in applying these criteria to identify and characterize unknown pigments in relatively scarce pathological specimens, indicating that a standardized approach is needed. As reported here, a standardized EPR test for melanin based on the EPR criteria has been developed, guided by the requirements that it be sensitive, accurate, simple, and easy to interpret. It has been evaluated using the well-characterized synthetic melanin prepared by alkaline autooxidation of 5,6-dihydroxyphenylalanine (Dopa) and initially applied to the identification and characterization of an unknown pigment purified from an unusual malignant lung tumor.     

Stimulus concordance and risk-assessment in hermit crabs (Coenobita clypeatus): implications for attention

Recent research has demonstrated that the topography of defensive reactions depends on factors that are extraneous to the stimulus that elicits the defensive response. For example, hermit crabs will withdraw more slowly to the approach of a simulated visual predator (i.e., the eliciting stimulus) when in the presence of a coincident acoustic stimulus. Multiple properties related to the magnitude (e.g., duration, amplitude) of the acoustic stimulus have been found to modulate the crabs' withdrawal response (Chan et al., 2010b). We demonstrate that the proximity in spatial location between a threatening visual stimulus and a potentially distracting extraneous auditory stimulus is an important determinant of anti-predator behavior in hermit crabs. We suggest that a distal relationship between the eliciting stimulus and an unrelated signal may produce greater distraction. This marks the first reported experimental evidence of this relationship in an invertebrate species.