The Burkholderia cenocepacia iron starvation σ factor, OrbS, possesses an on-board iron sensor.

Burkholderia cenocepacia is an opportunistic pathogen that causes severe infections of the cystic fibrosis (CF) lung. To acquire iron, B. cenocepacia secretes the Fe(III)-binding compound, ornibactin. Genes for synthesis and utilisation of ornibactin are served by the iron starvation (IS) extracytoplasmic function (ECF) σ factor, OrbS. Transcription of orbS is regulated in response to the prevailing iron concentration by the ferric uptake regulator (Fur), such that orbS expression is repressed under iron-sufficient conditions. Here we show that, in addition to Fur-mediated regulation of orbS, the OrbS protein itself responds to intracellular iron availability. Substitution of cysteine residues in the C-terminal region of OrbS diminished the ability to respond to Fe(II) in vivo. Accordingly, whilst Fe(II) impaired transcription from and recognition of OrbS-dependent promoters in vitro by inhibiting the binding of OrbS to core RNA polymerase (RNAP), the cysteine-substituted OrbS variant was less responsive to Fe(II). Thus, the cysteine residues within the C-terminal region of OrbS contribute to an iron-sensing motif that serves as an on-board 'anti-σ factor' in the presence of Fe(II). A model to account for the presence two regulators (Fur and OrbS) that respond to the same intracellular Fe(II) signal to control ornibactin synthesis and utilisation is discussed.

Dually Distribution Pulling Network for Cross-Resolution Person Reidentification.

Person reidentification (Re-ID) aims at recognizing the same identity across different camera views. However, the cross resolution of images [high resolution (HR) and low resolution (LR)] is unavoidable in a realistic scenario due to the various distances among cameras and pedestrians of interest, thus leading to cross-resolution person Re-ID problems. Recently, most cross-resolution person Re-ID methods focus on solving the resolution mismatch problem, while the distribution mismatch between HR and LR images is another factor that significantly impacts the person Re-ID performance. In this article, we propose a dually distribution pulling network (DDPN) to tackle the distribution mismatch problem. DDPN is composed of two modules, that is: 1) super-resolution module and 2) person Re-ID module. They attempt to pull the distribution of LR images closer to the distribution of HR images from image and feature aspects, respectively, through optimizing the maximum mean discrepancy losses. Extensive experiments have been conducted on three benchmark datasets and the results demonstrate the effectiveness of DDPN. Remarkably, DDPN shows a great advantage when compared to the state-of-the-art methods, for instance, we achieve rank-1 accuracy of 76.9% on VR-Market1501, which outperforms the best existing cross-resolution person Re-ID method by 10%.

CGAN-TM: A novel domain-to-domain transferring method for person re-identification.

Person re-identification (re-ID) is a technique aiming to recognize person cross different cameras. Although some supervised methods have achieved favorable performance, they are far from practical application owing to the lack of labeled data. Thus, unsupervised person re-ID methods are in urgent need. Generally, the commonly used approach in existing unsupervised methods is to first utilize the source image dataset for generating a model in supervised manner, and then transfer the source image domain to the target image domain. However, images may lose their identity information after translation, and the distributions between different domains are far away. To solve these problems, we propose an image domain-to-domain translation method by keeping pedestrian's identity information and pulling closer the domains' distributions for unsupervised person re-ID tasks. Our work exploits the CycleGAN to transfer the existing labeled image domain to the unlabeled image domain. Specially, a Self-labeled Triplet Net is proposed to maintain the pedestrian identity information, and maximum mean discrepancy is introduced to pull the domain distribution closer. Extensive experiments have been conducted and the results demonstrate that the proposed method performs superiorly than the state-ofthe- art unsupervised methods on DukeMTMC-reID and Market- 1501.

Person Re-Identification with Feature Pyramid Optimization and Gradual Background Suppression.

Compared with face recognition, the performance of person re-identification (re-ID) is still far from practical application. Among various interferences, there are two factors seriously limiting the performance improvement, i.e., the feature discriminability determined by "external network effectiveness", and the image quality determined by "internal background clutters". Target at the "external network effectiveness" problem, feature pyramids are effective to learn discriminative features because they can learn both detailed features from high-resolution shallow layers and semantical features from low-resolution deep layers, however, it can only achieve slight improvement on re-ID tasks because of the error back propagation problem. To handle the problem and utilize the effectiveness of feature pyramids, we propose a strategy called Feature Pyramid Optimization (FPO). Instead of concatenating features directly, the selected layers are optimized independently in a top-bottom order. Target at the "internal background clutters" problem, background suppression is generally considered for removing the environmental interference and improving the image quality. Several mask-based methods are used attempting to totally remove background clutters but achieve limited promotion because of the mask sharpening effect. We propose a novel strategy, i.e., Gradual Background Suppression (GBS) to reduce the background clutters and keep the smoothness of images simultaneously. Extensive experiments have been conducted and the results demonstrate the effectiveness of both FPO and GBS.

Distinct Modes of Promoter Recognition by Two Iron Starvation σ Factors with Overlapping Promoter Specificities.

OrbS and PvdS are extracytoplasmic function (ECF) σ factors that regulate transcription of operons required for the biosynthesis of the siderophores ornibactin and pyoverdine in the Burkholderia cepacia complex and Pseudomonas spp., respectively. Here we show that promoter recognition by OrbS requires specific tetrameric -35 and -10 element sequences that are strikingly similar to those of the consensus PvdS-dependent promoter. However, whereas Pseudomonas aeruginosa PvdS can serve OrbS-dependent promoters, OrbS cannot utilize PvdS-dependent promoters. To identify features present at OrbS-dependent promoters that facilitate recognition by OrbS, we carried out a detailed analysis of the nucleotide sequence requirements for promoter recognition by both OrbS and PvdS. This revealed that DNA sequence features located outside the sigma binding elements are required for efficient promoter utilization by OrbS. In particular, the presence of an A-tract extending downstream from the -35 element at OrbS-dependent promoters was shown to be an important contributor to OrbS specificity. Our observations demonstrate that the nature of the spacer sequence can have a major impact on promoter recognition by some ECF σ factors through modulation of the local DNA architecture.IMPORTANCE ECF σ factors regulate subsets of bacterial genes in response to environmental stress signals by directing RNA polymerase to promoter sequences known as the -35 and -10 elements. In this work, we identify the -10 and -35 elements that are recognized by the ECF σ factor OrbS. Furthermore, we demonstrate that efficient promoter utilization by this σ factor also requires a polyadenine tract located downstream of the -35 region. We propose that the unique architecture of A-tract DNA imposes conformational features on the -35 element that facilitates efficient recognition by OrbS. Our results show that sequences located between the core promoter elements can make major contributions to promoter recognition by some ECF σ factors.

Chronological Lifespan in Yeast Is Dependent on the Accumulation of Storage Carbohydrates Mediated by Yak1, Mck1 and Rim15 Kinases.

Upon starvation for glucose or any other macronutrient, yeast cells exit from the mitotic cell cycle and acquire a set of characteristics that are specific to quiescent cells to ensure longevity. Little is known about the molecular determinants that orchestrate quiescence entry and lifespan extension. Using starvation-specific gene reporters, we screened a subset of the yeast deletion library representing the genes encoding 'signaling' proteins. Apart from the previously characterised Rim15, Mck1 and Yak1 kinases, the SNF1/AMPK complex, the cell wall integrity pathway and a number of cell cycle regulators were shown to be necessary for proper quiescence establishment and for extension of chronological lifespan (CLS), suggesting that entry into quiescence requires the integration of starvation signals transmitted via multiple signaling pathways. The CLS of these signaling mutants, and those of the single, double and triple mutants of RIM15, YAK1 and MCK1 correlates well with the amount of storage carbohydrates but poorly with transition-phase cell cycle status. Combined removal of the glycogen and trehalose biosynthetic genes, especially GSY2 and TPS1, nearly abolishes the accumulation of storage carbohydrates and severely reduces CLS. Concurrent overexpression of GSY2 and TSL1 or supplementation of trehalose to the growth medium ameliorates the severe CLS defects displayed by the signaling mutants (rim15Δyak1Δ or rim15Δmck1Δ). Furthermore, we reveal that the levels of intracellular reactive oxygen species are cooperatively controlled by Yak1, Rim15 and Mck1, and the three kinases mediate the TOR1-regulated accumulation of storage carbohydrates and CLS extension. Our data support the hypothesis that metabolic reprogramming to accumulate energy stores and the activation of anti-oxidant defence systems are coordinated by Yak1, Rim15 and Mck1 kinases to ensure quiescence entry and lifespan extension in yeast.

The Yeast GSK-3 Homologue Mck1 Is a Key Controller of Quiescence Entry and Chronological Lifespan.

Upon starvation for glucose or any other core nutrient, yeast cells exit from the mitotic cell cycle and acquire a set of G0-specific characteristics to ensure long-term survival. It is not well understood whether or how cell cycle progression is coordinated with the acquisition of different G0-related features during the transition to stationary phase (SP). Here, we identify the yeast GSK-3 homologue Mck1 as a key regulator of G0 entry and reveal that Mck1 acts in parallel to Rim15 to activate starvation-induced gene expression, the acquisition of stress resistance, the accumulation of storage carbohydrates, the ability of early SP cells to exit from quiescence, and their chronological lifespan. FACS and microscopy imaging analyses indicate that Mck1 promotes mother-daughter cell separation and together with Rim15, modulates cell size. This indicates that the two kinases coordinate the transition-phase cell cycle, cell size and the acquisition of different G0-specific features. Epistasis experiments place MCK1, like RIM15, downstream of RAS2 in antagonising cell growth and activating stress resistance and glycogen accumulation. Remarkably, in the ras2∆ cells, deletion of MCK1 and RIM15 together, compared to removal of either of them alone, compromises respiratory growth and enhances heat tolerance and glycogen accumulation. Our data indicate that the nutrient sensor Ras2 may prevent the acquisition of G0-specific features via at least two pathways. One involves the negative regulation of the effectors of G0 entry such as Mck1 and Rim15, while the other likely to involve its functions in promoting respiratory growth, a phenotype also contributed by Mck1 and Rim15.