Using the extended quarter degree grid cell system to unify mapping and sharing of biodiversity data

Information on the distribution of animal populations is essential for conservation planning and management. Unfortunately, shared coordinate-level data may have the potential to compromise sensitive species and generalized data are often shared instead to facilitate knowledge discovery and communication regarding species distributions. Sharing of generalized data is, unfortunately, often ad hoc and lacks scalable conventions that permit consistent sharing at larger scales and varying resolutions. One common convention in African applications is the Quarter Degree Grid Cells (QDGC) system. However, the current standard does not support unique references across the Equator and Prime Meridian. We present a method for extending QDGC nomenclature to support unique references at a continental scale for Africa. The extended QDGC provides an instrument for sharing generalized biodiversity data where laws, regulations or other formal considerations prevent or prohibit distribution of coordinate-level information. We recommend how the extended QDGC may be used as a standard, scalable solution for exchange of biodiversity information through development of tools for the conversion and presentation of multi-scale data at a variety of resolutions. In doing so, the extended QDGC represents an important alternative to existing approaches for generalized mapping and can help planners and researchers address conservation issues more efficiently.     

LUMOS - A Sensitive and Reliable Optode System for Measuring Dissolved Oxygen in the Nanomolar Range

Most commercially available optical oxygen sensors target the measuring range of 300 to 2 μmol L^-1. However these are not suitable for investigating the nanomolar range which is relevant for many important environmental situations. We therefore developed a miniaturized phase fluorimeter based measurement system called the LUMOS (Luminescence Measuring Oxygen Sensor). It consists of a readout device and specialized “sensing chemistry” that relies on commercially available components. The sensor material is based on palladium(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorphenyl)-porphyrin embedded in a Hyflon AD 60 polymer matrix and has a K_SV of 6.25 x 10^-3 ppmv^-1. The applicable measurement range is from 1000 nM down to a detection limit of 0.5 nM. A second sensor material based on the platinum(II) analogue of the porphyrin is spectrally compatible with the readout device and has a measurement range of 20 μM down to 10 nM. The LUMOS device is a dedicated system optimized for a high signal to noise ratio, but in principle any phase flourimeter can be adapted to act as a readout device for the highly sensitive and robust sensing chemistry. Vise versa, the LUMOS fluorimeter can be used for read out of less sensitive optical oxygen sensors based on the same or similar indicator dyes, for example for monitoring oxygen at physiological conditions. The presented sensor system exhibits lower noise, higher resolution and higher sensitivity than the electrochemical STOX sensor previously used to measure nanomolar oxygen concentrations. Oxygen contamination in common sample containers has been investigated and microbial or enzymatic oxygen consumption at nanomolar concentrations is presented.     

Elemental Content of Calcium Oxalate Stones from a Canine Model of Urinary Stone Disease

One of the most common types of urinary stones formed in humans and some other mammals is composed of calcium oxalate in ordered hydrated crystals. Many studies have reported a range of metals other than calcium in human stones, but few have looked at stones from animal models such as the dog. Therefore, we determined the elemental profile of canine calcium oxalate urinary stones and compared it to reported values from human stones. The content of 19 elements spanning 7-orders of magnitude was quantified in calcium oxalate stones from 53 dogs. The elemental profile of the canine stones was highly overlapping with human stones, indicating similar inorganic composition. Correlation and cluster analysis was then performed on the elemental profile from canine stones to evaluate associations between the elements and test for potential subgrouping based on elemental content. No correlations were observed with the most abundant metal calcium. However, magnesium and sulfur content correlated with the mineral hydration form, while phosphorous and zinc content correlated with the neuter status of the dog. Inter-elemental correlation analysis indicated strong associations between barium, phosphorous, and zinc content. Additionally, cluster analysis revealed subgroups within the stones that were also based primarily on barium, phosphorous, and zinc. These data support the use of the dog as a model to study the effects of trace metal homeostasis in urinary stone disease.     

Evidence for long‐term migration on the Balkan Peninsula using dental and cranial nonmetric data: Early interaction between Corinth (Greece) and its colony at Apollonia (Albania)

This article seeks to identify “Greeks” and “non‐Greeks” in “mixed” mortuary contexts in a Greek colony. Specifically, we test the hypothesis that Illyrian and Greek individuals lived and were buried together at the Corinthian colony of Apollonia, Albania (established ca. 600 BC). The pattern of human biological interaction at Apollonia is tested by identifying variation in genetic relatedness using biodistance analysis of dental and cranial nonmetric traits for three sites: Apollonia (n = 116), its founder‐city Corinth (n = 69), and Lofkënd (n = 108), an inland site near Apollonia pre‐dating colonization. Logistic regression analysis estimates that individuals from colonial Apollonia are most closely related to prehistoric Illyrian populations (from Lofkënd and prehistoric Apollonia), rather than Greeks (from Corinth). The phenotypic similarity between colonial Apollonia and prehistoric Illyria suggests that there was a large Illyrian contribution to the gene pool at the colony of Apollonia. However, some trait combinations show low biological distances among all groups, suggesting homogeneity among Illyrian and Greek populations (assessed through pseudo‐Mahalanobis' D²). The degree of phenotypic similarity suggests shared ancestry and long‐term migration throughout these regions. The impacts of missing data and small sample sizes are also considered. Am J Phys Anthropol 153:236–248, 2014. © 2013 Wiley Periodicals, Inc.     

TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment

Phosphorylation of plasma membrane proteins frequently initiates signal transduction pathways or attenuate plasma membrane transport processes. Because of the low abundance and hydrophobic features of many plasma membrane proteins and the low stoichiometry of protein phosphorylation, studies of the plasma membrane phosphoproteome are challenging. We present an optimized analytical strategy for plasma membrane phosphoproteomics that combines efficient plasma membrane protein preparation with TiO(2)-based phosphopeptide enrichment and high-performance mass spectrometry for phosphopeptide sequencing. We used sucrose centrifugation in combination with sodium carbonate extraction to achieve efficient and reproducible purification of low microgram levels of plasma membrane proteins from human mesenchymal stem cells (hMSCs, 10(7) cells), achieving more than 70% yield of membrane proteins. Phosphopeptide enrichment by titanium dioxide chromatography followed by capillary liquid chromatography-tandem mass spectrometry allowed us to assign 703 unique phosphorylation sites in 376 phosphoproteins. Our experiments revealed that treatment of cell cultures with three different types of protein phosphatase inhibitors produces distinct phosphopeptide populations and an increase of 10-40% of the number of detected and sequenced phosphoserine, phosphothreonine and phosphotyrosine containing peptides. In summary, our analytical strategy enables functional phosphoproteomic analysis of stem cell differentiation and cell surface biomarker discovery using very low amounts of starting material.