Identification two novel nacrein-like proteins involved in the shell formation of the Pacific oyster Crassostrea gigas

Nacrein-like proteins have carbonic anhydrase (CA)-like domains, but their coding regions are flanked by inserted repeat sequence, such as Gly-X-Asn. Reportedly, nacrein-like proteins show the highest similarity to human carbonic anhydrase 1(α-CA1), possess CA catalytic functions, and play a key role in shell biomineralization. In the present study, two novel nacrein-like proteins were firstly identified from the shell-forming mantle of the Pacific oyster Crassostrea gigas. With numerous analyses, it was identified and characterized that both the nacrein-like proteins F1 and F2 were secreted and most closely related to the nacrein-like protein of California mussel Mytilus californianus via phylogenetic analysis. RT-PCR analysis showed that the nacrein-like proteins F1 and F2 were expressed in multiple tissues and the expression levels remarkably rose after entering the spat stage, which were basically consistent with the increase of calcite fractions in the total shell volume. Surprisingly, the Gly-X-Asn repeat domain, which is distinctive in most nacrein-like proteins, was absent in the two newly identified nacrein-like proteins in C. gigas and replaced with a series of acidic amino acids (D/E). Regardless, nacrein-like proteins in mollusks seem to be vital to the deposition of calcium carbonate and likely perform diverse functions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11033-014-3298-z) contains supplementary material, which is available to authorized users

Dynamic Kernel Sparsifiers

A geometric graph associated with a set of points $P= \{x_1, x_2, \cdots, x_n \} \subset \mathbb{R}^d$ and a fixed kernel function $\mathsf{K}:\mathbb{R}^d\times \mathbb{R}^d\to\mathbb{R}_{\geq 0}$ is a complete graph on $P$ such that the weight of edge $(x_i, x_j)$ is $\mathsf{K}(x_i, x_j)$. We present a fully-dynamic data structure that maintains a spectral sparsifier of a geometric graph under updates that change the locations of points in $P$ one at a time. The update time of our data structure is $n^{o(1)}$ with high probability, and the initialization time is $n^{1+o(1)}$. Under certain assumption, we can provide a fully dynamic spectral sparsifier with the robostness to adaptive adversary. We further show that, for the Laplacian matrices of these geometric graphs, it is possible to maintain random sketches for the results of matrix vector multiplication and inverse-matrix vector multiplication in $n^{o(1)}$ time, under updates that change the locations of points in $P$ or change the query vector by a sparse difference

Gray Matter Atrophy in Parkinson’s Disease and the Parkinsonian Variant of Multiple System Atrophy: A Combined ROI- and Voxel-Based Morphometric Study

OBJECTIVES: Parkinson’s disease (PD) and the parkinsonian variant of multiple system atrophy (MSA-P) are distinct neurodegenerative disorders that share similar clinical features of parkinsonism. The morphological alterations of these diseases have yet to be understood. The purpose of this study was to evaluate gray matter atrophy in PD and MSA-P using regions of interest (ROI)-based measurements and voxel-based morphometry (VBM). METHODS: We studied 41 patients with PD, 20 patients with MSA-P, and 39 controls matched for age, sex, and handedness using an improved T1-weighted sequence that eased gray matter segmentation. The gray matter volumes were measured using ROI and VBM. RESULTS: ROI volumetric measurements showed significantly reduced bilateral putamen volumes in MSA-P patients compared with those in PD patients and controls (po0.05), and the volumes of the bilateral caudate nucleus were significantly reduced in both MSA-P and PD patients compared with those in the controls (po0.05). VBM analysis revealed multifocal cortical and subcortical atrophy in both MSA-P and PD patients, and the volumes of the cerebellum and temporal lobes were remarkably reduced in MSA-P patients compared with the volumes in PD patients (po0.05). CONCLUSIONS: Both PD and MSA-P are associated with gray matter atrophy, which mainly involves the bilateral putamen, caudate nucleus, cerebellum, and temporal lobes. ROI and VBM can be used to identify these morphological alterations, and VBM is more sensitive and repeatable and less time-consuming, which may have potential diagnostic value

Trends and challenges of multi-drug resistance in childhood tuberculosis

Drug-resistant tuberculosis (DR-TB) in children is a growing global health concern, This review provides an overview of the current epidemiology of childhood TB and DR-TB, including prevalence, incidence, and mortality. We discuss the challenges in diagnosing TB and DR-TB in children and the limitations of current diagnostic tools. We summarize the challenges associated with treating multi-drug resistance TB in childhood, including limitations of current treatment options, drug adverse effects, prolonged regimens, and managing and monitoring during treatment. We highlight the urgent need for improved diagnosis and treatment of DR-TB in children. The treatment of children with multidrug-resistant tuberculosis will be expanded to include the evaluation of new drugs or new combinations of drugs. Basic research is needed to support the technological development of biomarkers to assess the phase of therapy, as well as the urgent need for improved diagnostic and treatment options

Relationship between biofilm formation and antibiotic resistance of Klebsiella pneumoniae and updates on antibiofilm therapeutic strategies

Klebsiella pneumoniae is a Gram-negative bacterium within the Enterobacteriaceae family that can cause multiple systemic infections, such as respiratory, blood, liver abscesses and urinary systems. Antibiotic resistance is a global health threat and K. pneumoniae warrants special attention due to its resistance to most modern day antibiotics. Biofilm formation is a critical obstruction that enhances the antibiotic resistance of K. pneumoniae. However, knowledge on the molecular mechanisms of biofilm formation and its relation with antibiotic resistance in K. pneumoniae is limited. Understanding the molecular mechanisms of biofilm formation and its correlation with antibiotic resistance is crucial for providing insight for the design of new drugs to control and treat biofilm-related infections. In this review, we summarize recent advances in genes contributing to the biofilm formation of K. pneumoniae, new progress on the relationship between biofilm formation and antibiotic resistance, and new therapeutic strategies targeting biofilms. Finally, we discuss future research directions that target biofilm formation and antibiotic resistance of this priority pathogen

Associations of HLA-DP Variants with Hepatitis B Virus Infection in Southern and Northern Han Chinese Populations: A Multicenter Case-Control Study

) locus has been reported to be associated with hepatitis B virus (HBV) infection in populations of Japan and Thailand. We aimed to examine whether the association can be replicated in Han Chinese populations. = 0.097∼0.697 and 0.198∼0.615 in northern Chinese population, respectively). loci were strongly associated with HBV infection in southern and northern Han Chinese populations, but not with HBV progression

The oyster genome reveals stress adaptation and complexity of shell formation

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. © 2012 Macmillan Publishers Limited. All rights reserved

An Improved Method of DNA Extraction from the Shell of the Pacific Oyster, Crassostrea gigas

We earlier developed a method to extract DNA from in vivo-sampled mantle tissue of the bivalve Pacific oyster (Crassostrea gigas) for molecular marker-assisted selection (MAS) in breeding. However, mortality was too high when using this method. In the current study, a more efficient and safer method of extracting DNA from the oyster shell was developed, based on the improved phenol-chloroform DNA extraction method. Both nuclear DNA and mitochondrial DNA were successfully extracted from the oyster shell, and mortality was 0%. These results illustrate the safety of extracting DNA from the bivalve shell. In addition, because DNA is a cellular component, the results provide molecular evidence that cells are likely involved in shell formation

Hyperspectral Image Inpainting Based on Robust Spectral Dictionary Learning

To address the problems of defective pixels and strips in hyperspectral images affecting subsequent processing and applications, we modeled the hyperspectral image (HSI) inpainting problem as a sparse signal reconstruction problem with incomplete observations using the theory of sparse representation, and proposed an HSI inpainting algorithm based on spectral dictionary learning. First, we studied the HSI observation model under the assumption of additive noise. We subsequently proposed a new algorithm for constructing a spectral dictionary directly from hyperspectral data by introducing an online learning optimization method and performing dictionary learning using a robust function. Afterwards, the image was sparsely encoded by applying the variable decomposition and augmented Lagrangian sparse regression method. Finally, the inpainted HSI was obtained by sparse reconstruction. The experimental results showed that compared with the existing algorithms, the algorithm proposed herein could effectively inpaint the defective HSI under different noise conditions with a shorter calculation time than those of existing methods and other dictionary learning inpainting algorithms