Bostonia: The Boston University Alumni Magazine. Volume 10

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Effective swimming strategies in low Reynolds number flows

The optimal strategy for a microscopic swimmer to migrate across a linear shear flow is discussed. The two cases, in which the swimmer is located at large distance, and in the proximity of a solid wall, are taken into account. It is shown that migration can be achieved by means of a combination of sailing through the flow and swimming, where the swimming strokes are induced by the external flow without need of internal energy sources or external drives. The structural dynamics required for the swimmer to move in the desired direction is discussed and two simple models, based respectively on the presence of an elastic structure, and on an orientation dependent friction, to control the deformations induced by the external flow, are analyzed. In all cases, the deformation sequence is a generalization of the tank-treading motion regimes observed in vesicles in shear flows. Analytic expressions for the migration velocity as a function of the deformation pattern and amplitude are provided. The effects of thermal fluctuations on propulsion have been discussed and the possibility that noise be exploited to overcome the limitations imposed on the microswimmer by the scallop theorem have been discussed.Comment: 14 pages, 5 figure

Hydrodynamic Synchronisation of Model Microswimmers

We define a model microswimmer with a variable cycle time, thus allowing the possibility of phase locking driven by hydrodynamic interactions between swimmers. We find that, for extensile or contractile swimmers, phase locking does occur, with the relative phase of the two swimmers being, in general, close to 0 or pi, depending on their relative position and orientation. We show that, as expected on grounds of symmetry, self T-dual swimmers, which are time-reversal covariant, do not phase-lock. We also discuss the phase behaviour of a line of tethered swimmers, or pumps. These show oscillations in their relative phases reminiscent of the metachronal waves of cilia.Comment: 17 pages, 8 figure

Bostonia: The Boston University Alumni Magazine. Volume 12

Founded in 1900, Bostonia magazine is Boston University’s main alumni publication

Dynamics of N removal over annual time periods in a suburban river network

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): G03038, doi:10.1029/2007JG000660.River systems are dynamic, highly connected water transfer networks that integrate a wide range of physical and biological processes. We used a river network nitrogen (N) removal model with daily temporal resolution to evaluate how elevated N inputs, saturation of the denitrification and total nitrate removal processes, and hydrologic conditions interact to determine the amount, timing and distribution of N removal in the fifth-order river network of a suburban 400 km2 basin. Denitrification parameters were based on results from whole reach 15NO3 tracer additions. The model predicted that between 15 and 33% of dissolved inorganic nitrogen (DIN) inputs were denitrified annually by the river system. Removal approached 100% during low flow periods, even with the relatively low and saturating uptake velocities typical of surface water denitrification. Annual removal percentages were moderate because most N inputs occurred during high flow periods when hydraulic conditions and temperatures are less favorable for removal by channel processes. Nevertheless, the percentage of annual removal occurring during above average flow periods was similar to that during low flow periods. Predicted river network removal proportions are most sensitive to loading rates, spatial heterogeneity of inputs, and the form of the removal process equation during typical base flow conditions. However, comparison with observations indicates that removal by the river network is higher than predicted by the model at moderately high flows, suggesting additional removal processes are important at these times. Further increases in N input to the network will lead to disproportionate increases in N exports due to the limits imposed by process saturation.This work was funded by NSF-DEB- 0614282, NSF-OCE-9726921, NSF-DEB-0111410, and NSF-BCS- 0709685

Differences in genotype and virulence among four multidrug-resistant <i>Streptococcus pneumoniae</i> isolates belonging to the PMEN1 clone

We report on the comparative genomics and characterization of the virulence phenotypes of four &lt;i&gt;S. pneumoniae&lt;/i&gt; strains that belong to the multidrug resistant clone PMEN1 (Spain&lt;sup&gt;23F&lt;/sup&gt; ST81). Strains SV35-T23 and SV36-T3 were recovered in 1996 from the nasopharynx of patients at an AIDS hospice in New York. Strain SV36-T3 expressed capsule type 3 which is unusual for this clone and represents the product of an in vivo capsular switch event. A third PMEN1 isolate - PN4595-T23 - was recovered in 1996 from the nasopharynx of a child attending day care in Portugal, and a fourth strain - ATCC700669 - was originally isolated from a patient with pneumococcal disease in Spain in 1984. We compared the genomes among four PMEN1 strains and 47 previously sequenced pneumococcal isolates for gene possession differences and allelic variations within core genes. In contrast to the 47 strains - representing a variety of clonal types - the four PMEN1 strains grouped closely together, demonstrating high genomic conservation within this lineage relative to the rest of the species. In the four PMEN1 strains allelic and gene possession differences were clustered into 18 genomic regions including the capsule, the blp bacteriocins, erythromycin resistance, the MM1-2008 prophage and multiple cell wall anchored proteins. In spite of their genomic similarity, the high resolution chinchilla model was able to detect variations in virulence properties of the PMEN1 strains highlighting how small genic or allelic variation can lead to significant changes in pathogenicity and making this set of strains ideal for the identification of novel virulence determinant

Tau Neutrinos Favored over Sterile Neutrinos in Atmospheric Muon Neutrino Oscillations

The previously published atmospheric neutrino data did not distinguish whether muon neutrinos were oscillating into tau neutrinos or sterile neutrinos, as both hypotheses fit the data. Using data recorded in 1100 live-days of the Super-Kamiokande detector, we use three complementary data samples to study the difference in zenith angle distribution due to neutral currents and matter effects. We find no evidence favoring sterile neutrinos, and reject the hypothesis at the 99% confidence level. On the other hand, we find that oscillation between muon and tau neutrinos suffices to explain all the results in hand.Comment: 9 pages with 2 figures, submitted to PR

A circle swimmer at low Reynolds number

Swimming in circles occurs in a variety of situations at low Reynolds number. Here we propose a simple model for a swimmer that undergoes circular motion, generalising the model of a linear swimmer proposed by Najafi and Golestanian (Phys. Rev. E 69, 062901 (2004)). Our model consists of three solid spheres arranged in a triangular configuration, joined by two links of time-dependent length. For small strokes, we discuss the motion of the swimmer as a function of the separation angle between its links. We find that swimmers describe either clockwise or anticlockwise circular motion depending on the tilting angle in a non-trivial manner. The symmetry of the swimmer leads to a quadrupolar decay of the far flow field. We discuss the potential extensions and experimental realisation of our model.Comment: 9 pages, 9 Figure

Co-Expression of miRNA Targeting the Expression of PERK, but Not PKR, Enhances Cellular Immunity from an HIV-1 Env DNA Vaccine

Small non-coding micro-RNAs (miRNA) are important post-transcriptional regulators of mammalian gene expression that can be used to direct the knockdown of expression from targeted genes. We examined whether DNA vaccine vectors co-expressing miRNA with HIV-1 envelope (Env) antigens could influence the magnitude or quality of the immune responses to Env in mice. Human miR-155 and flanking regions from the non-protein encoding gene mirhg155 were introduced into an artificial intron within an expression vector for HIV-1 Env gp140. Using the miR-155-expressing intron as a scaffold, we developed novel vectors for miRNA-mediated targeting of the cellular antiviral proteins PKR and PERK, which significantly down-modulated target gene expression and led to increased Env expression in vitro. Finally, vaccinating BALB/c mice with a DNA vaccine vector delivering miRNA targeting PERK, but not PKR, was able to augment the generation of Env-specific T-cell immunity. This study provides proof-of-concept evidence that miRNA effectors incorporated into vaccine constructs can positively influence vaccine immunogenicity. Further testing of vaccine-encoded miRNA will determine if such strategies can enhance protective efficacy from vaccines against HIV-1 for eventual human use

A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar

The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies