Hypercellular graphs: partial cubes without Q3−Q_3^- as partial cube minor

We investigate the structure of isometric subgraphs of hypercubes (i.e., partial cubes) which do not contain finite convex subgraphs contractible to the 3-cube minus one vertex $Q^-_3$ (here contraction means contracting the edges corresponding to the same coordinate of the hypercube). Extending similar results for median and cellular graphs, we show that the convex hull of an isometric cycle of such a graph is gated and isomorphic to the Cartesian product of edges and even cycles. Furthermore, we show that our graphs are exactly the class of partial cubes in which any finite convex subgraph can be obtained from the Cartesian products of edges and even cycles via successive gated amalgams. This decomposition result enables us to establish a variety of results. In particular, it yields that our class of graphs generalizes median and cellular graphs, which motivates naming our graphs hypercellular. Furthermore, we show that hypercellular graphs are tope graphs of zonotopal complexes of oriented matroids. Finally, we characterize hypercellular graphs as being median-cell -- a property naturally generalizing the notion of median graphs.Comment: 35 pages, 6 figures, added example answering Question 1 from earlier draft (Figure 6.

Molecular cloning and transcriptional activity of a new Petunia calreticulin gene involved in pistil transmitting tract maturation, progamic phase, and double fertilization

Calreticulin (CRT) is a highly conserved and ubiquitously expressed Ca2+-binding protein in multicellular eukaryotes. As an endoplasmic reticulum-resident protein, CRT plays a key role in many cellular processes including Ca2+ storage and release, protein synthesis, and molecular chaperoning in both animals and plants. CRT has long been suggested to play a role in plant sexual reproduction. To begin to address this possibility, we cloned and characterized the full-length cDNA of a new CRT gene (PhCRT) from Petunia. The deduced amino acid sequence of PhCRT shares homology with other known plant CRTs, and phylogenetic analysis indicates that the PhCRT cDNA clone belongs to the CRT1/CRT2 subclass. Northern blot analysis and fluorescent in situ hybridization were used to assess PhCRT gene expression in different parts of the pistil before pollination, during subsequent stages of the progamic phase, and at fertilization. The highest level of PhCRT mRNA was detected in the stigma–style part of the unpollinated pistil 1 day before anthesis and during the early stage of the progamic phase, when pollen is germinated and tubes outgrow on the stigma. In the ovary, PhCRT mRNA was most abundant after pollination and reached maximum at the late stage of the progamic phase, when pollen tubes grow into the ovules and fertilization occurs. PhCRT mRNA transcripts were seen to accumulate predominantly in transmitting tract cells of maturing and receptive stigma, in germinated pollen/growing tubes, and at the micropylar region of the ovule, where the female gametophyte is located. From these results, we suggest that PhCRT gene expression is up-regulated during secretory activity of the pistil transmitting tract cells, pollen germination and outgrowth of the tubes, and then during gamete fusion and early embryogenesis

The search for black hole binaries using a genetic algorithm

In this work we use genetic algorithm to search for the gravitational wave signal from the inspiralling massive Black Hole binaries in the simulated LISA data. We consider a single signal in the Gaussian instrumental noise. This is a first step in preparation for analysis of the third round of the mock LISA data challenge. We have extended a genetic algorithm utilizing the properties of the signal and the detector response function. The performance of this method is comparable, if not better, to already existing algorithms.Comment: 11 pages, 4 figures, proceeding for GWDAW13 (Puerto Rico

Trypanosoma Brucei Mitochondrial DNA POLIB Cell Cycle Localization and Effect on POLIC when POLIB is Depleted

Trypanosoma brucei is the causative agent of Human African Trypanosomiasis (HAT), also known as African sleeping sickness. T. brucei is unique in several ways that distinguish this organism from other eukaryotes. One of the unique features of T. brucei is the organism’s mitochondrial DNA, which is organized in a complex structure called kinetoplast DNA (kDNA). Since kDNA is unique to the kinetoplastids, kDNA may serve as a good drug target against T. brucei. Previews studies have shown that kDNA has 4 different family A mitochondrial DNA polymerases. Three of these mitochondrial DNA polymerases (POLIB, POLIC, and POLID) are essential components of kDNA synthesis and replication. POLID and POLIC dynamically localize throughout the cell cycle. POLID is found dispersed in the matrix before the kDNA has undergone replication and is re-localized at the antipodal sites when the kDNA is dividing. POLIC is found in the kinetoflagellar zone (KFZ) at low concentrations when the kDNA is not replicating and relocalizes to the antipodal sites when dividing. Based on the dynamic localization of these two DNA polymerases, we hypothesize that POLIB undergoes dynamic localization at some point during the cell cycle stage. Here, a POLIB/PTP single expressor cell line was analyzed by immunofluorescence microscopy in an unsynchronized population. We characterized the localization pattern of POLIB-PTP at different cell cycle stages and found different localization patterns throughout cell cycle. Cells at 1N1K (the majority of cell in an unsynchronized population) have single foci, but at 1N1Kdiv two different patterns are mainly observed, diffuse and segregated. When the kDNAs are separated POLIB-PTP is again seen as a distinct foci in each kDNA. By doing TdT labeling and a quantitative analysis, we found that at early stages of minicircles replication POLIB-PTP start relocalizing to the kDNA disk with a diffuse pattern being the main. By the time the minicircles are being reattached in the disk (late TdT), POLIB is seen in the disk as a bilobe shape

Probing the localisation and function of a novel kinetoplast-associated protein in evolutionarily divergent protists

In evolutionary terms, the origin of the kinetoplast remains ambiguous. However, interestingly some components of the TAC are found in the genome of the free-living Bodo Saltans. This includes the protein designated Tb9260, which is important in kinetoplast organisation during cell division a fragment of the Bodo saltans Tb9260 orthologue, named Trett, will be expressed as recombinant protein in E.coli in order to raise a BsTrett antibody. This will be utilised for the in vivo targeting by confocal and super-resolution microscopy of BsTrett within Bodo saltans in order to ascertain its localisation. Additionally, Bodo saltans TAC65, TAC60, TAC40 and Trett orthologues will be cloned into a pNUS-GFPcH expression vector and transfected into Crithidia fasciculata. The localisations of these orthologous proteins are shown here with some surprising phenotypes. In addition, a cross species bioinformatic analysis of the Bodo saltans transcriptome against peptide sequences of putative proteins identified within the TbMitoCarta will aim to identify possible conserved orthologues and future protein targets. Bodo saltans is a divergent free-living ancestor of the parasitic trypanosomatids, including species of trypanosomes and Leishmania. Similarities between the Kinetoplastids have demonstrated the importance of understanding the evolutionary process which has led to parasitism and the question of whether it evolved from, or separately, to its free-living ancestor remains unanswered. Here I show the localisations of the aforementioned proteins and their similarities between the free-living and parasitic organisms

Transcriptional integration of paternal and maternal factors in the Arabidopsis zygote

In many plants, the asymmetric division of the zygote sets up the apical-basal axis of the embryo. Unlike animals, plant zygotes are transcriptionally active, implying that plants have evolved specific mechanisms to control transcriptional activation of patterning genes in the zygote. In Arabidopsis, two pathways have been found to regulate zygote asymmetry: YODA (YDA) mitogen-activated protein kinase (MAPK) signaling, which is potentiated by sperm-delivered mRNA of the SHORT SUSPENSOR (SSP) membrane protein, and up-regulation of the patterning gene WOX8 by the WRKY2 transcription factor. How SSP/YDA signaling is transduced into the nucleus and how these pathways are integrated have remained elusive. Here we show that paternal SSP/YDA signaling directly phosphorylates WRKY2, which in turn leads to the up-regulation of WOX8 transcription in the zygote. We further discovered the transcription factors HOMEODOMAIN GLABROUS11/12 (HDG11/12) as maternal regulators of zygote asymmetry that also directly regulate WOX8 transcription. Our results reveal a framework of how maternal and paternal factors are integrated in the zygote to regulate embryo patterning

Lorelei Localization and Ovule Ultrastructure in Arabidopsis Thaliana

Communication between the male and female gametophyte is vital to successful fertilization during sexual reproduction in plants. One of the proteins known to be important for communication between the male and female gametophyte is LORELEI (LRE). Several studies have shown that there are defects in pollen tube guidance and synergid degeneration, however this is the first study that shows that cell wall thickness in the female gametophyte may also be affected. Previous confocal studies have documented that LRE is present both in the filiform apparatus and found in puncta throughout the cytoplasm. This study confirmed this, but our studies suggest that the proportions maybe different; in the TEM sections we examined a majority of the LRE seems to be localizing to the filiform apparatus. This study also reported that three Arabidopsis WT accessions had very similar embryo sac ultrastructure, thus for electron microscopy studies data from all these accessions can be used to add robustness to a study with a low WT sample size

The Killing of African Trypanosomes by Ethidium Bromide

Introduced in the 1950s, ethidium bromide (EB) is still used as an anti-trypanosomal drug for African cattle although its mechanism of killing has been unclear and controversial. EB has long been known to cause loss of the mitochondrial genome, named kinetoplast DNA (kDNA), a giant network of interlocked minicircles and maxicircles. However, the existence of viable parasites lacking kDNA (dyskinetoplastic) led many to think that kDNA loss could not be the mechanism of killing. When recent studies indicated that kDNA is indeed essential in bloodstream trypanosomes and that dyskinetoplastic cells survive only if they have a compensating mutation in the nuclear genome, we investigated the effect of EB on kDNA and its replication. We here report some remarkable effects of EB. Using EM and other techniques, we found that binding of EB to network minicircles is low, probably because of their association with proteins that prevent helix unwinding. In contrast, covalently-closed minicircles that had been released from the network for replication bind EB extensively, causing them, after isolation, to become highly supertwisted and to develop regions of left-handed Z-DNA (without EB, these circles are fully relaxed). In vivo, EB causes helix distortion of free minicircles, preventing replication initiation and resulting in kDNA loss and cell death. Unexpectedly, EB also kills dyskinetoplastic trypanosomes, lacking kDNA, by inhibiting nuclear replication. Since the effect on kDNA occurs at a >10-fold lower EB concentration than that on nuclear DNA, we conclude that minicircle replication initiation is likely EB's most vulnerable target, but the effect on nuclear replication may also contribute to cell killing