A General Upper Bound on the Size of Constant-Weight Conflict-Avoiding Codes

Conflict-avoiding codes are used in the multiple-access collision channel without feedback. The number of codewords in a conflict-avoiding code is the number of potential users that can be supported in the system. In this paper, a new upper bound on the size of conflict-avoiding codes is proved. This upper bound is general in the sense that it is applicable to all code lengths and all Hamming weights. Several existing constructions for conflict-avoiding codes, which are known to be optimal for Hamming weights equal to four and five, are shown to be optimal for all Hamming weights in general.Comment: 10 pages, 1 figur

Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation

Bacteroidetes are abundant pathogen-suppressing members of the plant microbiome that contribute prominently to rhizosphere phosphorus mobilisation, a frequent growth-limiting nutrient in this niche. However, the genetic traits underpinning their success in this niche remain largely unknown, particularly regarding their phosphorus acquisition strategies. By combining cultivation, multi-layered omics and biochemical analyses we first discovered that all plant-associated Bacteroidetes express constitutive phosphatase activity, linked to the ubiquitous possession of a unique phosphatase, PafA. For the first time, we also reveal a subset of Bacteroidetes outer membrane SusCD-like complexes, typically associated with carbon acquisition, and several TonB-dependent transporters, are induced during Pi-depletion. Furthermore, in response to phosphate depletion, the plant-associated Flavobacterium used in this study expressed many previously characterised and novel proteins targeting organic phosphorus. Collectively, these enzymes exhibited superior phosphatase activity compared to plant-associated Pseudomonas spp. Importantly, several of the novel low-Pi-inducible phosphatases and transporters, belong to the Bacteroidetes auxiliary genome and are an adaptive genomic signature of plant-associated strains. In conclusion, niche adaptation to the plant microbiome thus appears to have resulted in the acquisition of unique phosphorus scavenging loci in Bacteroidetes, enhancing their phosphorus acquisition capabilities. These traits may enable their success in the rhizosphere and also present exciting avenues to develop sustainable agriculture

Comparative Proteomic, Glycoproteomic And Phosphoproteomic Analyses Of Breast Cancer Tissues

Breast cancer is the second-most leading cause of death among women worldwide. This is true in the Malaysian population as well; breast cancer is one of the most common types of cancer among women. This study was aimed to identify potential tumour proteins that are characteristic of breast carcinogenesis. In order to detect the tumour-specific proteins, differential proteomic profiling was conducted using advanced proteomics techniques in healthy and tumour breast tissue samples. In this study, protein profiles of breast tumour and their adjacent normal tissues from Malaysian women were obtained and examined using GELFREE separation, LTQ-Orbitrap LC-MS/MS identification, and bioinformatic analyses. Findings of the current proteomic profile showed that among the proteins that were detected, several proteins were found with post-translation modifications (PTMs) such as phosphorylation and glycosylation. The analysis of proteins resulted in the identification of 137 proteins, out of that 21 proteins were significantly abundant in tumour tissues. In addition, 81 phosphoproteins were identified, out of that 12 proteins were found significantly higher in abundance in tumour tissues than compared to that their normal counterparts. Furthermore, the analysis identified a total of 73 glycoproteins, out of these 10 glycoproteins were recorded to be significantly abundant in tumour tissues. Generally, most of the identified proteins were found to be involved in physiological processes such as proliferation, cell survival, motility, invasion, angiogenesis, metastasis and stem cell self-renewal and cell structure signalling pathways

Fibronectin peptides and murine embryonic stem cells : an in vitro study

Murine embryonic stem cells are cells that are obtained from the inner cell mass of the embryo blastocyst at day 3.5. These cells have the novel capability of differentiating into almost any cell lineage in the mammal and this characteristic has resulted in them being referred to as pluripotent. Fibronectin is involved in a number of different functions including differentiation, growth, migration and the adhesion of cells. In addition it is well known to interact with the extracellular matrix. Fibronectin also has an essential role to play in early development of the embryo as studies have shown that knocking out either fibronectin or its primary receptor eg 51 integrin receptor is lethal to the developing embryo. The section of fibronectin identified as being essential for binding and activation of 51 integrin receptor has been identified as the 9th and 10th type III fibronectin domain. This peptide of fibronectin has subsequently been generated. In this study, the effect of this fibronectin peptide on murine embryonic stem cells was examined. In particular it was identified that the generation of 2-D orientated fibronectin peptide displays in no way enhances the cell attachment potential of the fibronectin peptides. The optimal conformation of the peptides for the attachment of embryonic stem cell colonies was identified as being the dimeric form of the peptide. The fact that these fibronectin peptides have no effect on the proliferation of embryonic stem cells was also determined. There was an apparent morphological change in embryonic stem cells grown on the fibronectin peptides. These embryonic stem cells were flatter and reminiscent of differentiated embryonic stem cells. This occurred even when the embryonic stem cells were cultured in the presence of LIF, the cytokine essential to maintain embryonic stem cells in a state of self renewal. Alkaline phosphatase staining confirmed that while there was a morphological change the embryonic stem cells maintained their undifferentiated state when grown on fibronectin peptides in the presence of LIF. Finally Quantitative Polymerase Chain Reaction was carried out in an attempt to ascertain why there appeared to be a morphological change in embryonic stem cells grown on fibronectin peptides as opposed to embryonic stem cells grown on gelatin controls. In the presence of LIF, there was a transient increase in the number of Oct-4, Brachyury and Nestin transcripts. Up regulation of these genes is known in some cases to come from a pro differentiation signal. However concomitant with these transcriptional up regulations, the levels of Nanog, the gene well known to resist and/or reverse changes in gene expression states in embryonic stem cells also increased upon growth on fibronectin peptides. It is possible that in the presence of LIF, Nanog increases to inhibit the differentiation inducing signals produced by interaction of the fibronectin peptides with the 51 integrin receptor. When grown in complete media containing foetal calf serum in the absence of LIF, there were no obvious transcriptional changes that gave an indication to which, if any, lineage the fibroenctin peptides may be instructing the embryonic stem cells to differentiate into. Upon using serum replacement media as opposed to foetal calf serum and allowing the embryonic stem cells to differentiate more obvious transcriptional changes were observed. ES cells grown on the fibronectin peptides appeared to be inhibited from increasing the levels of transcripts with known roles in cardiac and neuroectodermal differentiation. However there was a transient increase in the levels of FoxA2, a gene involved in the differentiation of embryonic stem cells into endodermal tissue. This increase was shortly followed by a significant decrease in the levels of transcripts when grown on the fibronectin peptides as opposed to gelatin controls. Importantly it appears that allowing the differentiation of embryonic stem cells to occur in a monolayer instead of the classically used embryoid bodies could potentially be used as an alternative model to study embryonic stem cell differentiation

Isolation and characterization of bacterial phosphorous metabolism genes from complex microbial communities

Phosphorous (P) is an essential nutrient, playing a central role in the life of a bacterial cell. It is involved in cellular metabolic pathways, cell signaling and is a component of many of the cell’s macromolecules. Since a majority of the biosphere’s microorganisms have not yet been cultured, much more can be learned about the biochemical and genetic mechanisms that govern bacterial P metabolism. The function-driven approach to metagenomics was applied to study P metabolism in the bacterial communities present in pulp and municipal wastewater treatment plant activated sludge and soil, leading to the isolation and identification of three new phosphatases, genes involved in P transport, regulation of P related functions and additional genes which may be important for the bacterial cell’s adaptation to the above communities. The identification of two new nonspecific acid phosphatases (NSAPs) phoNACX6.13 and phoNBCX4.10 and an alkaline phosphatase, phoAACX6.71, belonging to the nucleotide pyrophosphatase phosphodiesterase (NPP) family is reported here. The genes for the three phosphatases were cloned, sequenced, and analysed for upstream regulatory sequences in addition to biochemical characterization of their protein products. PhoB-binding sites were found upstream to phoAACX6.71 and NSAP phoNACX6.13, suggesting these genes are governed by the mechanisms of the previously described “pho” regulon. The two NSAPs have pH optima in the acidic neutral range while the alkaline phosphatase has an optimal pH at 9.5. The three phosphatases appear to be distantly related to known bacterial phosphatase enzymes. Phylogenetic analysis shows the newly identified NSAPs appear on a separate clade from known bacterial NSAPs. Key amino acid residues involved in the catalytic site of these NSAPs were identified in PhoNACX6.13 and PhoNBCX4.10.In PhoAACX6.71, key amino acid residues involved in catalysis and metal cofactor coordination were identified. The roles of these residues were confirmed based on the predicted molecular structure of these proteins. The structures indicate the three proteins are globular with folding patterns suitable for catalytic residues to bind and cleave the P substrate. This is the first report of functional characterization of phosphatases from uncultured bacteria. In addition to exploring the hydrolysis of phosphate esters, the transport and metabolism of other P compounds was also investigated. By phenotypic complementation of phosphonate growth deficient mutants of the legume symbiont, Sinorhizobium meliloti and large scale sequencing of selected metagenomic clones, 92 ORFs were isolated. As expected, about 25% of these ORFs are P transport proteins and P related regulators. Genes involved in other regulatory functions made up about 12% of the total while genes related to Nitrogen metabolism and assimilation account for about 8% of the newly identified ORFs. About 30% of the ORFs encoded general cellular functions or hypothetical proteins of unknown function. The results of this investigation demonstrate the effectiveness of functional metagenomics in studying genetic diversity of bacteria inhabiting complex microbial communities and in identifying new proteins of interest

An architecture for sensate robots : real time social-gesture recognition using a full body array of touch sensors

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.Includes bibliographical references.Touch plays a central role in social expression but, so far, research into social touch behaviors for robots has been almost. non-existent. Embodied machines have the unique capability to sense human body language, which will enable robots to better comprehend, anticipate and respond to their human companions in a natural way.This thesis addresses the novel field of sensate touch by (1) creating the first. robot with full Body sensate touch and with on-screen visualization, (2) establishing a library of salient social gestures through behavioral studies, (3) implementing a first-pass touch gesture recognition system in real-time, an(d (4) running a small pilot study with children to evaluate classifications and test the device's acceptance/utility with humans. Such research is critical path to conceiving and advancing thee use of machine touch to better integrate robots in.to human social environments.All of the above will be incorporated into the huggable robotic teddy bear at the MIT Media Lab's Personal Robotics group and makes use of the Sensitive Skins circuit design created in Dan Stiehl's Masters thesis. This implementation substantially reduces his proposed total sensor numbers and type, modularizes sensors into two uniform shapes, and extends his valuable work on a single body sections to an evaluation of sensors over the entire surface of the robot.Heather-Marie Callanan Knight.M.Eng