In contexts such as suspension feeding in marine ecologies there is an interplay between brownian motion of nonmotile particles and their advection by flows from swimming microorganisms. As a laboratory realization, we study passive tracers in suspensions of eukaryotic swimmers, the alga Chlamydomonas reinhardtii. While the cells behave ballistically over short intervals, the tracers behave diffusively, with a time-dependent but self-similar probability distribution function of displacements consisting of a gaussian core and robust exponential tails. We emphasize the role of flagellar beating in creating oscillatory flows that exceed brownian motion far from each swimmer.

The spherical alga Volvox swims by means of flagella on thousands of surface somatic cells. This geometry and its large size make it a model organism for studying the fluid dynamics of multicellularity. Remarkably, when two nearby Volvox colonies swim close to a solid surface, they attract one another and can form stable bound states in which they "waltz" or "minuet" around each other. A surface-mediated hydrodynamic attraction combined with lubrication forces between spinning, bottom-heavy Volvox explains the formation, stability, and dynamics of the bound states. These phenomena are suggested to underlie observed clustering of Volvox at surfaces.Long after he made his great contributions to microscopy and started a revolution in biology, Antony van Leeuwenhoek peered into a drop of pond water and discovered one of nature's geometrical marvels [1]. This was the freshwater alga which, years later, in the very last entry of his great work on biological taxonomy, Linnaeus named Volvox [2] for its characteristic spinning motion about a fixed body axis. Volvox is a spherical colonial green alga (Fig. 1), with thousands of biflagellated cells anchored in a transparent extracellular matrix (ECM) and daughter colonies inside the ECM. Since the work of Weismann [3], Volvox has been seen as a model organism in the study of the evolution of multicellularity [4][5][6].Because it is spherical, Volvox is an ideal organism for studies of biological fluid dynamics, being an approximate realization of Lighthill's "squirmer" model [7] of self-propelled bodies having a specified surface velocity. Such models have elucidated nutrient uptake at high Péclet numbers [6,8] by single organisms, and pairwise hydrodynamic interactions between them [9]. Volvocine algae may also be used to study collective dynamics of selfpropelled objects [10], complementary to bacterial suspensions (E. coli, B. subtilis) exhibiting large-scale coherence in thin films [11] and bulk [12].While investigating Volvox suspensions in glass-topped chambers, we observed stable bound states, in which pairs of colonies orbit each other near the chamber walls. Volvox is "bottomheavy" due to clustering of daughter colonies in the posterior, so an isolated colony swims

Vitamin B(12) (cobalamin) is a dietary requirement for humans because it is an essential cofactor for two enzymes, methylmalonyl-CoA mutase and methionine synthase (METH). Land plants and fungi neither synthesize or require cobalamin because they do not contain methylmalonyl-CoA mutase, and have an alternative B(12)-independent methionine synthase (METE). Within the algal kingdom, approximately half of all microalgal species need the vitamin as a growth supplement, but there is no phylogenetic relationship between these species, suggesting that the auxotrophy arose multiple times through evolution. We set out to determine the underlying cellular mechanisms for this observation by investigating elements of B(12) metabolism in the sequenced genomes of 15 different algal species, with representatives of the red, green, and brown algae, diatoms, and coccolithophores, including both macro- and microalgae, and from marine and freshwater environments. From this analysis, together with growth assays, we found a strong correlation between the absence of a functional METE gene and B(12) auxotrophy. The presence of a METE unitary pseudogene in the B(12)-dependent green algae Volvox carteri and Gonium pectorale, relatives of the B(12)-independent Chlamydomonas reinhardtii, suggest that B(12) dependence evolved recently in these lineages. In both C. reinhardtii and the diatom Phaeodactylum tricornutum, growth in the presence of cobalamin leads to repression of METE transcription, providing a mechanism for gene loss. Thus varying environmental conditions are likely to have been the reason for the multiple independent origins of B(12) auxotrophy in these organisms. Because the ultimate source of cobalamin is from prokaryotes, the selective loss of METE in different algal lineages will have had important physiological and ecological consequences for these organisms in terms of their dependence on bacteria.

Quantitative proteomics holds considerable promise for elucidation of basic biology and for clinical biomarker discovery. However, it has been difficult to fulfill this promise due to over-reliance on identification-based quantitative methods and problems associated with chromatographic separation reproducibility. Here we describe new algorithms termed "Landmark Matching" and "Peak Matching" that greatly reduce these problems. Landmark Matching performs time base-independent propagation of peptide identities onto accurate mass LC-MS features in a way that leverages historical data derived from disparate data acquisition strategies. Peak Matching builds upon Landmark Matching by recognizing identical molecular species across multiple LC-MS experiments in an identity-independent fashion by clustering. We have bundled these algorithms together with other algorithms, data acquisition strategies, and experimental designs to create a Platform for Experimental Proteomic Pattern Recognition (PEPPeR). These developments enable use of established statistical tools previously limited to microarray analysis for treatment of proteomics data. We demonstrate that the proposed platform can be calibrated across 2.5 orders of magnitude and can perform robust quantification of ratios in both simple and complex mixtures with good precision and error characteristics across multiple sample preparations. We also demonstrate de novo marker discovery based on statistical significance of unidentified accurate mass components that changed between two mixtures. These markers were subsequently identified by accurate mass-driven MS/MS acquisition and demonstrated to be contaminant proteins associated with known proteins whose concentrations were designed to change between the two mixtures. These results have provided a real world validation of the platform for marker discovery. There is tremendous interest in the use of mass spectrometry as a quantitative technology to measure peptide and protein abundances for comprehensive, system-wide biological research (1, 2). Quantitative proteomics may be used to systematically identify and quantify proteins and their modifications as a function of cell cycle, differentiation, or chemical treatment to obtain novel insights into basic cellular biology. Proteomics also holds promise for discovery of proteins in readily accessible biofluids that are diagnostic or prognostic of a disease condition. Such proteins are termed "biomarkers."The need for robust methods to obtain relative quantification is particularly acute in proteomics-based biomarker discovery where comparative data across multiple patient samples should be obtained (3). Biomarker discovery usually uses biofluids that greatly increase the magnitude of the challenge for quantitative proteomics due to the very high dynamic range of protein abundance (Ϸ10 12 for blood) and the enormous diversity of proteins present in such samples (4).Currently available MS platforms for quantitative proteomics fall roughly into three categories: 1) identity-ba...

In a multitude of life's processes, cilia and flagella are found indispensable. Recently, the biflagellated chlorophyte alga Chlamydomonas has become a model organism for the study of ciliary motility and synchronization. Here, we use high-speed, high-resolution imaging of single pipette-held cells to quantify the rich dynamics exhibited by their flagella. Underlying this variability in behaviour are biological dissimilarities between the two flagella—termed cis and trans, with respect to a unique eyespot. With emphasis on the wild-type, we derive limit cycles and phase parametrizations for self-sustained flagellar oscillations from digitally tracked flagellar waveforms. Characterizing interflagellar phase synchrony via a simple model of coupled oscillators with noise, we find that during the canonical swimming breaststroke the cis flagellum is consistently phase-lagged relative to, while remaining robustly phase-locked with, the trans flagellum. Transient loss of synchrony, or phase slippage, may be triggered stochastically, in which the trans flagellum transitions to a second mode of beating with attenuated beat envelope and increased frequency. Further, exploiting this alga's ability for flagellar regeneration, we mechanically induced removal of one or the other flagellum of the same cell to reveal a striking disparity between the beatings of the cis and trans flagella, in isolation. These results are evaluated in the context of the dynamic coordination of Chlamydomonas flagella.