Modelling optical micro-machines

A strongly focused laser beam can be used to trap, manipulate and exert torque on a microparticle. The torque is the result of transfer of angular momentum by scattering of the laser beam. The laser could be used to drive a rotor, impeller, cog wheel or some other microdevice of a few microns in size, perhaps fabricated from a birefringent material. We review our methods of computationally simulating the torque and force imparted by a laser beam. We introduce a method of hybridizing the T-matrix with the Finite Difference Frequency Domain (FDFD) method to allow the modelling of materials that are anisotropic and inhomogeneous, and structures that have complex shapes. The high degree of symmetry of a microrotor, such as discrete or continuous rotational symmetry, can be exploited to reduce computational time and memory requirements by orders of magnitude. This is achieved by performing calculations for only a given segment or plane that is repeated across the whole structure. This can be demonstrated by modelling the optical trapping and rotation of a cube.Comment: 4 pages, 3 figure

Phylogenetic analysis of planarian collagens and their roles in regeneration

Poster Presentation - Theme 3: Development & stem cellsStem cells are regulated by the microenvironment or niche they reside in, which consists of growth factors, niche cells and the extracellular matrix. The ECM acts as both a structural component and as a reservoir for growth factors that are released upon degradation. During regeneration, stem cells in the planarian are activated to migrate and proliferate; however, the role of the ECM in stem cell regulation is still unclear. Analysis of an EST library of planarian transcripts revealed nine fibrillar-related collagen chains (DjCol1-9). Sequence and structural analysis ...postprin

Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif

Bacterial DNA transposition is an important model system for studying DNA recombination events such as HIV-1 DNA integration and RAG-1-mediated V(D)J recombination. This communication focuses on the role of protein–phosphate contacts in manipulating DNA structure as a requirement for transposition catalysis. In particular, the participation of the nontransferred strand (NTS) 5′ phosphate in Tn5 transposition strand transfer is analyzed. The 5′ phosphate plays no direct catalytic role, nonetheless its presence stimulates strand transfer ∼30-fold. X-ray crystallography indicates that transposase–DNA complexes formed with NTS 5′ phosphorylated DNA have two properties that contrast with structures formed with complexes lacking the 5′ phosphate or complexes generated from in-crystal hairpin cleavage. Transposase residues R210, Y319 and R322 of the (R)YREK motif coordinate the 5′ phosphate rather than the subterminal NTS phosphate, and the 5′ NTS end is moved away from the 3′ transferred strand end. Mutation R210A impairs the 5′ phosphate stimulation. It is posited that DNA phosphate coordination by R210, Y319 and R322 results in movement of the 5′ NTS DNA away from the 3′-end thus allowing efficient target DNA binding. It is likely that this role for the newly identified RYR triad is utilized by other transposase-related proteins

Velocity-resolved high-J CO emission from massive star-forming clumps

(Abridged) Context. Massive star formation is associated with energetic processes, which result in significant gas cooling via far-infrared (IR) lines. Velocity-resolved observations can constrain the kinematics of the gas, allowing the identification of the physical mechanisms responsible for gas heating. Aims. Our aim is to quantify far-infrared CO line emission toward high-mass star-forming regions, identify the high-velocity gas component associated with outflows, and estimate the physical conditions required for the excitation of the observed lines. Methods. Velocity-resolved SOFIA/GREAT spectra of 13 high-mass star forming clumps of various luminosities and evolutionary stages are studied using CO 11-10 and 16-15 lines. Results. All targets show strong high-J CO emission in the far-IR, characterized by broad line wings associated with outflows, thereby significantly increasing the sample of sources with velocity-resolved high-J CO spectra. The contribution of the emission in the line wings does not correlate with the envelope mass or evolutionary stage. Gas rotational temperatures cover a narrow range of 120-220 K for the line wings. The non-LTE radiative transfer models indicate gas densities of 1e5-1e7 cm-3 and N(CO) of 1e17- 1e18 cm-2, similar to physical conditions in deeply-embedded low- and high-mass protostars. The velocity-integrated CO line fluxes correlate with the bolometric luminosity over 7 orders of magnitude including data on the low-mass protostars, suggesting similar processes are responsible for the high-J CO excitation over a significant range of physical scales. Conclusions. Velocity-resolved line profiles allow the detection of outflows toward massive star-forming clumps spanning a broad range of evolutionary stages. The lack of clear evolutionary trends suggest that mass accretion and ejection prevail during the entire lifetime of star-forming clumps.Comment: 21 pages, 19 figures, accepted to A&

T-cell subpopulations αβ and γδ in cord blood of very preterm infants : The influence of intrauterine infection

Open Access: This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are creditedPreterm infants are very susceptible to infections. Immune response mechanisms in this group of patients and factors that influence cord blood mononuclear cell populations remain poorly understood and are considered insufficient. However, competent immune functions of the cord blood mononuclear cells are also described. The aim of this work was to evaluate the T-cell population (CD3+) with its subpopulations bearing T-cell receptor (TCR) αβ or TCR γδ in the cord blood of preterm infants born before 32 weeks of gestation by mothers with or without an intrauterine infection. Being a pilot study, it also aimed at feasibility check and assessment of an expected effect size. The cord blood samples of 46 infants age were subjected to direct immunofluorescent staining with monoclonal antibodies and then analyzed by flow cytometry. The percentage of CD3+ cells in neonates born by mothers with diagnosis of intrauterine infection was significantly lower than in neonates born by mothers without infection (p = 0.005; Mann-Whitney U test). The number of cells did not differ between groups. Infection present in the mother did not have an influence on the TCR αβ or TCR γδ subpopulations. Our study contributes to a better understanding of preterm infants' immune mechanisms, and sets the stage for further investigations.Peer reviewedFinal Published versio

Postglacial expansion of the arctic keystone copepod calanus glacialis

Calanus glacialis, a major contributor to zooplankton biomass in the Arctic shelf seas, is a key link between primary production and higher trophic levels that may be sensitive to climate warming. The aim of this study was to explore genetic variation in contemporary populations of this species to infer possible changes during the Quaternary period, and to assess its population structure in both space and time. Calanus glacialis was sampled in the fjords of Spitsbergen (Hornsund and Kongsfjorden) in 2003, 2004, 2006, 2009 and 2012. The sequence of a mitochondrial marker, belonging to the ND5 gene, selected for the study was 1249 base pairs long and distinguished 75 unique haplotypes among 140 individuals that formed three main clades. There was no detectable pattern in the distribution of haplotypes by geographic distance or over time. Interestingly, a Bayesian skyline plot suggested that a 1000-fold increase in population size occurred approximately 10,000 years before present, suggesting a species expansion after the Last Glacial Maximum.GAME from the National Science Centre, the Polish Ministry of Science and Higher Education Iuventus Plus [IP2014 050573]; FCT-PT [CCMAR/Multi/04326/2013]; [2011/03/B/NZ8/02876

β-delayed γ-proton decay in 56Zn: analysis of the charged-particle spectrum

A study of the beta decay of the proton-rich T-z = 2 nucleus Zn-56 has been reported in a recent publication. A rare and exotic decay mode, beta-delayed gamma-proton decay, has been observed there for the first time in the fp shell. Here, we expand on some of the details of the data analysis, focussing on the charged particle spectrum