Comparative urine analysis by liquid chromatography-mass spectrometry and multivariate statistics: method development, evaluation, and application to proteinuria

We describe a platform for the comparative profiling of urine using reversed-phase liquid chromatography-mass spectrometry (LC-MS) and multivariate statistical data analysis. Urinary compounds were separated by gradient elution and subsequently detected by electrospray Ion-Trap MS. The lower limit of detection (5.7-21 nmol/L), within-day (2.9-19%) and between-day (4.8-19%) analytical variation of peak areas, linearity (R2: 0.918-0.999), and standard deviation for retention time (<0.52 min) of the method were assessed by means of addition of seven 3-8 amino acid peptides (0-500 nmol/L). Relating the amount of injected urine to the area under the curve (AUC) of the chromatographic trace at 214 nm better reduced the coefficient of variation (CV) of the AUC of the total ion chromatogram (CV = 10.1%) than relating it to creatinine (CV = 38.4%). LC-MS data were processed, and the common peak matrix was analyzed by principal component analysis (PCA) after supervised classification by the nearest shrunken centroid algorithm. The feasibility of the method to discriminate urine samples of differing compositions was evaluated by (i) addition of seven peptides at nanomolar concentrations to blank urine samples of different origin and (ii) a study of urine from kidney patients with and without proteinuria. (i) The added peptides were ranked as highly discriminatory peaks despite significant biological variation. (ii) Ninety-two peaks were selected best discriminating proteinuric from nonproteinuric samples, of which 6 were more intense in the majority of the proteinuric samples. Two of these 6 peaks were identified as albumin-derived peptides, which is in accordance with the early rise of albumin during glomerular proteinuria. Interestingly, other albumin-derived peptides were nondiscriminatory indicating preferential proteolysis at some cleavage sites.     

Functional variation among frugivorous birds: implications for rainforest seed dispersal in a fragmented subtropical landscape

Seed dispersal plays a critical role in rainforest regeneration patterns, hence loss of avian seed dispersers in fragmented landscapes may disrupt forest regeneration dynamics. To predict whether or not a plant will be dispersed in fragmented forests, it is necessary to have information about frugivorous bird distribution and dietary composition. However, specific dietary information for frugivorous birds is often limited. In such cases, information on the seed-crushing behaviour, gape width and relative dietary dominance by fruit may be used to describe functional groups of bird species with respect to their potential to disperse similar seeds. We used this information to assess differences in the seed dispersal potential of frugivorous bird assemblages in a fragmented rainforest landscape of southeast Queensland, Australia. The relative abundance of frugivorous birds was surveyed in extensive, remnant and regrowth rainforest sites (16 replicates of each). Large-gaped birds with mixed diets and medium-gaped birds with fruit-dominated diets were usually less abundant in remnants and regrowth than in continuous forest. Small-gaped birds with mixed diets and birds with fruit as a minor dietary component were most abundant in regrowth. We recorded a similar number of seed-crushing birds and large-gaped birds with fruit-dominated diets across site types. Bird species that may have the greatest potential to disperse a large volume and wide variety of plants, including large-seeded plants, tended to be less abundant outside of extensive forests, although one species, the figbird Sphecotheres viridis, was much more abundant in these areas. The results suggest that the dispersal of certain plant taxa would be limited in this fragmented landscape, although the potential for the dispersal of large-seeded plants may remain, despite the loss of several large-gaped disperser species.     

Using Web‐Based Technology to Bring Hands‐On Urban Material Flow Analysis to the Classroom

The main objective of this article is to introduce an open‐source, online software tool called OMAT as a teaching tool for performing economy wide‐material flow analysis (EW‐MFA) at urban or regional level in industrial ecology curricula. To that intent, we present a classroom and project activity that was developed for a masters‐level industrial ecology course offered by the Autonomous University of Barcelona. Insights are provided with regards to the outcome of the classroom exercise as well as lessons learned from both an academic and a software development point of view. The OMAT software provides users with a specialized tool to enter and process MFA data in a simple, intuitive way. The usefulness of OMAT as a teaching tool was tested by engaging students in a classroom activity that entailed using OMAT as a tool to perform an EW‐MFA applied to the Metropolitan Area of Barcelona for the years 2005‐2011. The aim of this exercise was to teach students specific skills required in performing an EW‐MFA, not through theory classes, but hands‐on through a learn‐as‐you‐go approach. The exercise not only equipped the students with knowledge about MFA, but also introduced them to solving problems as a team, meeting project deadlines, and communicating effectively with colleagues from different disciplines and backgrounds. Even though there is room for further improvements, this exercise showed that OMAT provided a useful addition to traditional methods that allowed students to get a more practical and thorough understanding of the MFA methodology.     

A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies

A member of the Alu family of repeated DNA elements has been identified on the long arm of the human Y chromosome, Yq11. This element, referred to as the Y Alu polymorphic (YAP) element, is present at a specific site on the Y chromosome in some humans and is absent in others. Phylogenetic comparisons with other Alu sequences reveal that the YAP element is a member of the polymorphic subfamily-3 (PSF-3), a previously undefined subfamily of Alu elements. The evolutionary relationships of PSF-3 to other Alu subfamilies support the hypothesis that recently inserted elements result from multiple source genes. The frequency of the YAP element is described in 340 individuals from 14 populations, and the data are combined with those from other populations. There is both significant heterogeneity among populations and a clear pattern in the frequencies of the insertion: sub-Saharan Africans have the highest frequencies, followed by northern Africans, Europeans, Oceanians, and Asians. An interesting exception is the relatively high frequency of the YAP element in Japanese. The greatest genetic distance is observed between the African and non-African populations. The YAP is especially useful for studying human population history from the perspective of male lineages.      

Maternal diet influences gene expression in intestine of offspring in chicken (Gallus gallus)

The diet of the mother during pregnancy influences the onset of different diseases and health-related traits in the offspring. We investigated the influence of the mother hen diet on the intestinal gene expression pattern in the offspring. Hens received for 11 weeks either a commercial feed or a commercial feed supplemented with vitamins and minerals. The offspring of the two groups showed no changes in growth rate or feed conversion. Of this offspring, gene expression patterns in the intestine were measured at 3 and 14 days of age with an intestinal cDNA-microarray. Between the two groups, 11 genes were found to be differentially expressed both at 3 and 14 days of age. Thus, these genes were differently regulated when the intestine is developing as well as when the intestine is more mature. Genes that are differentially expressed at day 3 and/or day 14 affect intestinal turnover, proliferation and development, metabolism and feed absorption. To confirm that differences in gene expression are related to intestinal development, we investigated intestinal proliferation. This indeed also showed differences in proliferation between the two groups at day 3 and day 14 of age. The gene expression and proliferation results indicate that feed of the hens influences the functionality of intestine of the offspring at day 3 and 14 of age.     

The effect of genistein supplementation on performance and antioxidant status of Japanese Quail under heat stress

Genistein, a phytoestrogen found in soybeans, is a powerful antioxidant. We evaluated the effects of genistein supplementation on performance, carcass characteristics, levels of malondialdehyde (MDA), homocysteine, vitamins C, E, A in Japanese quail (Coturnix coturnix japonica) exposed to high ambient temperature of 34°C. Two hundred and forty Japanese quails (10 d old) were randomly assigned to eight treatment groups consisting of 10 replicates of three birds. The birds were kept in an environmental controlled room either for 24 h/d at 22°C with (thermoneutral, TN groups) or for 16 h/d at 22°C and for 8 h/d (09.00 am to 05.00 pm) at 34°C (heat stress, HS groups). Birds were fed either a basal (control) diet (TN and HS) or the basal diet supplemented with 200, 400 or 800 mg of genistein per kg of diet. Heat exposure decreased birds' performance when basal diet was fed. Increase in feed intake and body weight, and improvement of feed efficiency and carcass traits were found in genistein-supplemented quails reared under heat stress conditions. Growth rate and feed efficiency improved in quails reared under thermo-neutral conditions as well. Concentration of serum vitamins C, E, and A increased in supplemented birds reared at high temperature, while non-significant changes occurred in TN groups. With genistein supplementation homocysteine levels in serum and MDA levels in serum and liver decreased in all birds of both TN and HS groups. Effects of genistein were relatively greater in heat-stressed quails than in quails kept under thermo-neutral conditions. Results of the present study suggest that supplementation with genistein can be considered to be protective by reducing the negative effects of oxidative stress induced by heat stress in quail.     

Relative importance of top-down and bottom-up forces in food webs of Sarracenia pitcher communities at a northern and a southern site

The relative importance of resources (bottom-up forces) and natural enemies (top-down forces) for regulating food web dynamics has been debated, and both forces have been found to be critical for determining food web structure. How the relative importance of top-down and bottom-up forces varies between sites with different abiotic conditions is not well understood. Using the pitcher plant inquiline community as a model system, I examine how the relative importance of top-down and bottom-up effects differs between two disparate sites. Resources (ant carcasses) and top predators (mosquito larvae) were manipulated in two identical 4 × 4 factorial press experiments, conducted at two geographically distant sites (Michigan and Florida) within the range of the purple pitcher plant, Sarracenia purpurea, and the aquatic community that resides in its leaves. Overall, top predators reduced the density of prey populations while additional resources bolstered them, and the relative importance of top-down and bottom-up forces varied between sites and for different trophic levels. Specifically, top-down effects on protozoa were stronger in Florida than in Michigan, while the opposite pattern was found for rotifers. These findings experimentally demonstrate that the strength of predator–prey interactions, even those involving the same species, vary across space. While only two sites are compared in this study, I hypothesize that site differences in temperature, which influences metabolic rate, may be responsible for variation in consumer–resource interactions. These findings warrant further investigation into the specific factors that modify the relative importance of top-down and bottom-up effects.