Characterizing complex mixed-species bird flocks using an objective method for determining species participation

We developed sampling methods to characterize the participation of bird species in foraging flocks led by the Eastern Tufted Titmouse (Baeolophus bicolor) in North-central Florida during winter, because standard field methods, developed primarily for permanent resident Neotropical flocks, were intractable in our system. During January–February 2004 and November 2004–March 2005, we observed 55 mixed-species flocks, recorded 40 potential flocking species [mean of 12.4 species (SD = 3.8; range 3–20), 26.3 individuals (SD = 12.2; range 8–60), and 3.1 titmice (SD = 1.4; range 1–7), per flock]. Twenty-six species were observed frequently enough (>10% of observations) to be included in analyses. We paired 60-min flock observations with 10-min point counts conducted in locations used by flocks, but after flocks had moved more than 100 m away. This method yielded a measure of flocking propensity: the ratio of the number of individuals observed in the flock versus during the point count for each species. We used regression tree (RT) analysis to classify species into groupings according to their levels of flock participation, and to investigate relationships between flocking propensity and various environmental and social factors that we measured. Our analysis identified three clear species groups; “Nuclear/Regular Associate” (12 spp.; high/moderate), “Occasional Associate” (four spp.; moderate/low), and “Non-joiner/Accidental” (ten spp.; low/no flocking propensity). Groupings were similar to schemes produced via more time-intensive field methods. In order to contextualize grouping categories, we conducted a review of flocking group definitions and relevant autecological information (e.g., interspecific sociality) about our study species. We found this method to be useful for geographically extensive sampling of species’ participation in mixed-species flocks, despite high inter-flock variability in species composition and limited labor.     

Comparative proteomics using 2-D gel electrophoresis and mass spectrometry as tools to dissect stimulons and regulons in bacteria with sequenced or partially sequenced genomes

We propose two-dimensional gel electrophoresis (2-DE) and mass spectrometry to define the protein components of regulons and stimulons in bacteria, including those organisms where genome sequencing is still in progress. The basic 2-DE protocol allows high resolution and reproducibility and enables the direct comparison of hundreds or even thousands of proteins simultaneously. To identify proteins that comprise stimulons and regulons, peptide mass fingerprint (PMF) with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF-MS) analysis is the first option and, if results from this tool are insufficient, complementary data obtained with electrospray ionization tandem-MS (ESI-MS/MS) may permit successful protein identification. ESI-MS/MS and MALDI-TOF-MS provide complementary data sets, and so a more comprehensive coverage of a proteome can be obtained using both techniques with the same sample, especially when few sequenced proteins of a particular organism exist or genome sequencing is still in progress.     

The reduction of 5 alpha-cholestan-3-one and 5 beta-cholestan-3-one by some boranes and hydroborates.

This paper describes the high yield synthesis of 5 alpha-cholestan-3 alpha-ol and 5 beta-cholestan-3 beta-ol by the reduction of 5 alpha- and 5 beta-cholestan-3-one using using potassium and lithium-tri-sec-butyl-hydroborates as reducing reagents. Attempts to obtain the same alcohols using other bulky boranes resulted in the equatorial products.     

A review of clinical and experimental observations about antidepressant actions and side effects produced by Hypericum perforatum extracts

Hypericum perforatum is an herbaceous perennial plant, also known as "St. John's wort", used popularly as a natural antidepressant. Although some clinical and experimental studies suggest it has some properties similar to conventional antidepressants, the proposed mechanism of action seems to be multiple: a non-selective blockade of the reuptake of serotonin, noradrenaline and dopamine; an increase in density of serotonergic and dopaminergic receptors and an increased affinity for GABAergic receptors; moreover, the inhibition of monoaminoxidase enzyme activity has been involved. In any case, the increase of monoamine concentrations in the synaptic cleft resembles several actions exerted by clinically effective antidepressants. In the present article, we review some of the controversial evidence derived from clinical and experimental studies suggesting that H. perforatum exerts antidepressant-like actions, and we also review some of its side effects, such as nausea, rash, fatigue, restlessness, photosensitivity, acute neuropathy, and even episodes of mania and serotonergic syndrome when administered simultaneously with other antidepressant drugs. All of the foregoing suggests that H. perforatum extracts appear to exert potentially significant pharmacological activity involving several neurotransmission systems supposed to be involved in the pathophysiology of depression. However, little information regarding the safety of H. perforatum is available, including potential herb-drug interactions. There is a need for additional research on the pharmacological and biochemical activity of H. perforatum, as well as its side-effects and its several bioactive constituents to further elucidate the mechanisms of antidepressant actions.     

Molecular identification of Dunaliella sp. utilizing the 18S rDNA gene

The utilization of micro-algae for the production of food and fine chemicals is growing in importance. However, confusion of names and species makes comparison of results by different authors very difficult. In this work, five species of Dunaliella were characterized using their 18S ribosomal RNA genes. Conserved oligonucleotides complementary to 5' and 3' termini of the 18S rDNAs were designed and utilized to amplify theme, restriction fragment length polymorphism analysis of the polymerase chain reaction products was developed. Species-specific primers were also designed and utilized to corroborate the identification.     

Overlapping of the VP2-VP3 gene and the VP1 gene in the SV40 genome.

The nucleotide sequence of the SV40 Hind E fragment has been determined mainly by the partial chemical degradation procedure of Maxam and Gilbert (1977). The sequence of the strand with the same polarity as the late messenger RNA shows only one open reading frame for translation. Considering that VP3 corresponds to the carbosyl terminal part of VP2, and considering various evidence which indicates that the SV40 Hind E segment is part of the amino acid sequence of VP2-VP3. It continues clockwise in Hind K, where it terminates with a UAA signal. The latter is located 110 nucleotides beyond the initiation signal for the major structural protein VP1 (Fiers et al., 1975; Van de Voorde et al., 1976). Hence this small overlapping region of the genome codes for the synthesis of three different proteins in two different reading frames. The deduced amino acid sequence covers a major part of the vp3 poly peptide, and the amino acid composition is in good agreement with published values (Greenaway and Levine, 1973).     

Great spotted cuckoo eggshell microstructure characteristics can make eggs stronger

Obligate avian brood parasites lay stronger eggs than their hosts or non‐parasitic relatives because they are rounder and have a thicker eggshell. Additionally, some other characteristics of the brood parasitic eggshells related to their microstructure such as size and orientation of calcite crystal units could also contribute to generating even stronger shells. An eggshell microstructure formed by small randomly oriented calcite crystal units can increase the robustness of the eggshells of birds. Here, the eggshell microstructure of avian brood parasites as well as their hosts have been characterized in detail, using X‐ray diffraction analyses to estimate the size and degree of orientation of calcite crystal units making the eggshell. Specifically, the brood parasitic great spotted cuckoo Clamator glandarius and two hosts (jackdaws Corvus monedula and magpie Pica pica) and one non‐host species (the pigeon, Columba livia domestica) were considered. Calcite crystal of the eggshell of the brood parasitic species was smaller and more randomly oriented than those of the eggshells of non‐parasitic species, which suggest that eggshell microstructure would contribute to explain why parasitic eggs are more resistant to breakage than those of their hosts.     

Glycome mapping on DNA sequencing equipment

Here we provide a detailed protocol for the analysis of protein-linked glycans on DNA sequencing equipment. This protocol satisfies the glyco-analytical needs of many projects and can form the basis of 'glycomics' studies, in which robustness, high throughput, high sensitivity and reliable quantification are of paramount importance. The protocol routinely resolves isobaric glycan stereoisomers, which is much more difficult by mass spectrometry (MS). Earlier methods made use of polyacrylamide gel-based sequencers, but we have now adapted the technique to multicapillary DNA sequencers, which represent the state of the art today. In addition, we have integrated an option for HPLC-based fractionation of highly anionic 8-amino-1,3,6-pyrenetrisulfonic acid (APTS)-labeled glycans before rapid capillary electrophoretic profiling. This option facilitates either two-dimensional profiling of complex glycan mixtures and exoglycosidase sequencing, or MS analysis of particular compounds of interest rather than of the total pool of glycans in a sample.