On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei

Background: Although technical advances in genomics and proteomics research have yielded a better understanding of the coding capacity of a genome, one major challenge remaining is the identification of all expressed proteins, especially those less than 100 amino acids in length. Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle. Results: Starting with 993 T. brucei transcripts, previously shown by RNA-Sequencing not to coincide with annotated coding sequences (CDS), homology searches revealed that 173 predicted short open reading frames in these transcripts are conserved across kinetoplastids with 13 also conserved in representative eukaryotes. Mining mass spectrometry data sets revealed 42 transcripts encoding at least one matching peptide. RNAi-induced down-regulation of these 42 transcripts revealed seven to be essential in insect-form trypanosomes with two also required for the bloodstream life cycle stage. To validate the specificity of the RNAi results, each lethal phenotype was rescued by co-expressing an RNAi-resistant construct of each corresponding CDS. These previously non-annotated essential small proteins localized to a variety of cell compartments, including the cell surface, mitochondria, nucleus and cytoplasm, inferring the diverse biological roles they are likely to play in T. brucei. We also provide evidence that one of these small proteins is required for replicating the kinetoplast (mitochondrial) DNA. Conclusions: Our studies highlight the presence and significance of small proteins in a protist and expose potential new targets to block the survival of trypanosomes in the insect vector and/or the mammalian host

The linear multiplet and ectoplasm

In the framework of the superconformal tensor calculus for 4D N=2 supergravity, locally supersymmetric actions are often constructed using the linear multiplet. We provide a superform formulation for the linear multiplet and derive the corresponding action functional using the ectoplasm method (also known as the superform approach to the construction of supersymmetric invariants). We propose a new locally supersymmetric action which makes use of a deformed linear multiplet. The novel feature of this multiplet is that it corresponds to the case of a gauged central charge using a one-form potential not annihilated by the central charge (unlike the standard N=2 vector multiplet). Such a gauge one-form can be chosen to describe a variant nonlinear vector-tensor multiplet. As a byproduct of our construction, we also find a variant realization of the tensor multiplet in supergravity where one of the auxiliaries is replaced by the field strength of a gauge three-form.Comment: 31 pages; v3: minor corrections and typos fixed, version to appear in JHE

Dipole Interactions and Electrical Polarity in Nanosystems -- the Clausius-Mossotti and Related Models

Point polarizable molecules at fixed spatial positions have solvable electrostatic properties in classical approximation, the most familiar being the Clausius-Mossotti (CM) formula. This paper generalizes the model and imagines various applications to nanosystems. The behavior is worked out for a sequence of octahedral fragments of simple cubic crystals, and the crossover to the bulk CM law is found. Some relations to fixed moment systems are discussed and exploited. The one-dimensional dipole stack is introduced as an important model system. The energy of interaction of parallel stacks is worked out, and clarifies the diverse behavior found in different crystal structures. It also suggests patterns of self-organization which polar molecules in solution might adopt. A sum rule on the stack interaction is found and tested. Stability of polarized states under thermal fluctuations is discussed, using the one-dimensional domain wall as an example. Possible structures for polar hard ellipsoids are considered. An idea is formulated for enhancing polarity of nanosystems by intentionally adding metallic coatings.Comment: 18 pages (includes 6 embedded figures and 3 tables). New references, and other small improvements. Scheduled for publication by J. Chem. Phys., Jan. 200

Six-dimensional Supergravity and Projective Superfields

We propose a superspace formulation of N=(1,0) conformal supergravity in six dimensions. The corresponding superspace constraints are invariant under super-Weyl transformations generated by a real scalar parameter. The known variant Weyl super-multiplet is recovered by coupling the geometry to a super-3-form tensor multiplet. Isotwistor variables are introduced and used to define projective superfields. We formulate a locally supersymmetric and super-Weyl invariant action principle in projective superspace. Some families of dynamical supergravity-matter systems are presented.Comment: 39 pages; v3: some modifications in section 2; equations (2.3), (2.14b), (2.16) and (2.17) correcte

Superform formulation for vector-tensor multiplets in conformal supergravity

The recent papers arXiv:1110.0971 and arXiv:1201.5431 have provided a superfield description for vector-tensor multiplets and their Chern-Simons couplings in 4D N = 2 conformal supergravity. Here we develop a superform formulation for these theories. Furthermore an alternative means of gauging the central charge is given, making use of a deformed vector multiplet, which may be thought of as a variant vector-tensor multiplet. Its Chern-Simons couplings to additional vector multiplets are also constructed. This multiplet together with its Chern-Simons couplings are new results not considered by de Wit et al. in hep-th/9710212.Comment: 28 pages. V2: Typos corrected and references updated; V3: References updated and typo correcte

N=2 Conformal Superspace in Four Dimensions

We develop the geometry of four dimensional N=2 superspace where the entire conformal algebra of SU(2,2|2) is realized linearly in the structure group rather than just the SL(2,C) x U(2)_R subgroup of Lorentz and R-symmetries, extending to N=2 our prior result for N=1 superspace. This formulation explicitly lifts to superspace the existing methods of the N=2 superconformal tensor calculus; at the same time the geometry, when degauged to SL(2,C) x U(2)_R, reproduces the existing formulation of N=2 conformal supergravity constructed by Howe.Comment: 43 pages; v2 references added, acknowledgments update

Impairments in orienting to visual stimuli in monkeys following unilateral lesions of the superior sulcal polysensory cortex

Monkeys were tested for head and eye orientation to illuminated lamps in a hemisphere before and after serial, unilateral lesions of the polysensory superior temporal cortex (STS) or control lesions. Following STS lesions they were impaired in orienting to contralateral lamps; this impairment was more severe and persistent when a ipsilateral stimulus in the mirror-image position was simultaneously presented. These findings, together with deficits in manual reaching and grasping observed following STS lesions, support the view that the STS is part of a polysensory system controlling attention and exploratory movements.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26421/1/0000508.pd

Three form potential in (special) minimal supergravity superspace and supermembrane supercurrent

This contribution begins the study of the complete superfield Lagrangian description of the interacting system of D=4 N=1 supergravity (SUGRA) and supermembrane. Firstly, we review a 'three form supergravity' by Ovrut and Waldram, which we prefer to call 'special minimal supergravity'. This off-shell formulation of simple SUGRA is appropriate for our purposes as the supermembrane action contains the so-called Wess-Zumino term given by the integral over a three form potential in superspace, C3. We describe this formulation in the frame of Wess--Zumino superfield approach, showing how the basic variations of minimal SUGRA are restricted by the conditions of the existence of a three-form potential C3 in its superspace. In this language the effect of dynamical generation of cosmological constant, known to be characteristic for this formulation of SUGRA, appears in its superfield form, first described by Ogievetsky and Sokatchev in their formulation of SUGRA as a theory of axial vector superfield. Secondly, we vary the supermembrane action with respect to the special minimal SUGRA superfields (basic variations) and obtain the supercurrent superfields as well as the supergravity superfield equations with the supermembrane contributions.Comment: 18 pages, no figures. V2: Important references added. The abstract and presentation have been changed to reflect the overloop with that. Submitted to the QTS7 Proceedings. J. Phys. style use

Extended supersymmetric sigma models in AdS_4 from projective superspace

There exist two superspace approaches to describe N=2 supersymmetric nonlinear sigma models in four-dimensional anti-de Sitter (AdS_4) space: (i) in terms of N=1 AdS chiral superfields, as developed in arXiv:1105.3111 and arXiv:1108.5290; and (ii) in terms of N=2 polar supermultiplets using the AdS projective-superspace techniques developed in arXiv:0807.3368. The virtue of the approach (i) is that it makes manifest the geometric properties of the N=2 supersymmetric sigma-models in AdS_4. The target space must be a non-compact hyperkahler manifold endowed with a Killing vector field which generates an SO(2) group of rotations on the two-sphere of complex structures. The power of the approach (ii) is that it allows us, in principle, to generate hyperkahler metrics as well as to address the problem of deformations of such metrics. Here we show how to relate the formulation (ii) to (i) by integrating out an infinite number of N=1 AdS auxiliary superfields and performing a superfield duality transformation. We also develop a novel description of the most general N=2 supersymmetric nonlinear sigma-model in AdS_4 in terms of chiral superfields on three-dimensional N=2 flat superspace without central charge. This superspace naturally originates from a conformally flat realization for the four-dimensional N=2 AdS superspace that makes use of Poincare coordinates for AdS_4. This novel formulation allows us to uncover several interesting geometric results.Comment: 88 pages; v3: typos corrected, version published in JHE