Komagataeibacter cocois sp. nov., a novel cellulose-producing strain isolated from coconut milk.

Phylogenetic analysis was performed on a cellulose-producing strain, designated WE7T, isolated from contaminated coconut milk. The analysis utilized nearly complete 16S rRNA gene sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, and allowed identification of the strain as belonging to the genus Komagataeibacter. DNA-DNA correlation or average nucleotide identity analysis was performed between WE7T and its closest phylogenetic neighbours, and the resulting values were below the species level (<70 % and <95 %), suggesting that the strain represents a novel species in genus Komagataeibacter. Strain WE7T was coupled with Komagataeibacter species more tightly than with Gluconacetobacter species in a 16S rRNA gene sequence phylogenetic tree. Strain WE7T can be differentiated from closely related Komagataeibacter and Gluconacetobacter entanii species by the ability to grow on the carbon sources d-mannitol, sodium d-gluconate and glycerol, the ability to form acid by d-fructose, sucrose, d-mannitol, d-galactose and ethanol, and the ability to grow without acetic acid. The major fatty acid of WE7T is C18 : 1ω9c (52.3 %). The DNA G+C content of WE7T is 63.2 mol%. The name Komagataeibacter cocois sp. nov. is proposed, with the type strain WE7T (=CGMCC 1.15338T=JCM 31140T).

An effective combination of whole-exome sequencing and runs of homozygosity for the diagnosis of primary ciliary dyskinesia in consanguineous families.

Primary ciliary dyskinesia (PCD) is clinically characterized by neonatal respiratory distress, chronic sinusitis, bronchiectasis and infertility, and situs inversus in 50% of the patients. PCD is a result of mutations in genes encoding proteins involved in ciliary function, and is primarily inherited in an autosomal recessive fashion. Diagnosis of PCD is often a challenging task due to its high clinical and genetic heterogeneities. In the present study, we attempted to use whole-exome sequencing (WES) combined with runs of homozygosity (ROH) approaches to identify the genetic defects in four Chinese consanguineous families with clinical PCD. We successfully identified three recently acknowledged PCD genes: DYX1C1, CCNO and ARMC4, and one well-characterized PCD gene, DNAI1. Our study provides compelling evidence that WES in combination with ROH analysis is an efficient diagnostic tool for identifying genetic causes of PCD in consanguineous families. Furthermore, our work expands the genetic mutation spectrum in PCD, and provides the additional tools to better serve the counseling of the families with PCD.

Detecting the somatic mutations spectrum of Chinese lung cancer by analyzing the whole mitochondrial DNA genomes.

To detect the somatic mutations and character its spectrum in Chinese lung cancer patients. In this study, we sequenced the whole mitochondrial DNA (mtDNA) genomes for 10 lung cancer patients including the primary cancerous, matched paracancerous normal and distant normal tissues. By analyzing the 30 whole mtDNA genomes, eight somatic mutations were identified from five patients investigated, which were confirmed with the cloning and sequencing of the somatic mutations. Five of the somatic mutations were detected among control region and the rests were found at the coding region. Heterogeneity was the main character of the somatic mutations in Chinese lung cancer patients. Further potential disease-related screening showed that, except the C deletion at position 309 showed AD-weakly associated, most of them were not disease-related. Although the role of aforementioned somatic mutations was unknown, however, considering the relative higher frequency of somatic mutations among the whole mtDNA genomes, it hints that detecting the somatic mutation(s) from the whole mtDNA genomes can serve as a useful tool for the Chinese lung cancer diagnostic to some extent.

The role of the QseC quorum-sensing sensor kinase in epinephrine-enhanced motility and biofilm formation by Escherichia coli.

Biofilms play a pivotal role in infections related to devices. Biofilm formation in Escherichia coli is mediated by the quorum-sensing E. coli regulator C (QseC), the histidine sensor kinase that can sense epinephrine (EPI)/norepinephrine (NE). In this study, we evaluate the role of the QseC quorum-sensing sensor kinase in epinephrine-enhanced motility and biofilm formation by E. coli. An E. coli MC1000 qseC mutant was constructed. We investigated the role of the QseC in the formation of biofilms on the surface of medical-grade polyvinyl chloride using the E. coli K-12 MC1000 strain as well as a corresponding qseC mutant. Addition of EPI/NE increased biofilm formation by wild-type K-12 MC1000 but not by the isogenic qseC mutant. Scanning confocal laser microscopy corroborated these results by showing that EPI/NE addition significantly increased biofilm's thickness. As expected, the addition of EPI/NE to the qseC mutant, which lacks the ability to sense the hormones, failed to stimulate biofilm formation. Since EPI/NE addition increased bacterial motility, we proposed that their stimulatory effects on biofilm formation occur by enhancing bacterial motility and altering biofilm architecture. We also found that EPI/NE regulate motility and the biofilm phenotype via QseC, as motility was diminished and biofilm formation was significantly decreased in a qseC deletion mutant. These results indicate that EPI/NE induce E. coli biofilm formation on the surface of polyvinyl chloride through QseC. Cross-talk between E. coli (quorum sensing) and host hormones may explain the pathogen-caused opportunistic infections that occur in patients with prosthetic devices used during hormone level fluctuations in the host.

Max-flow segmentation of the left ventricle by recovering subject-specific distributions via a bound of the Bhattacharyya measure.

This study investigates fast detection of the left ventricle (LV) endo- and epicardium boundaries in a cardiac magnetic resonance (MR) sequence following the optimization of two original discrete cost functions, each containing global intensity and geometry constraints based on the Bhattacharyya similarity. The cost functions and the corresponding max-flow optimization built upon an original bound of the Bhattacharyya measure yield competitive results in nearly real-time. Within each frame, the algorithm seeks the LV cavity and myocardium regions consistent with subject-specific model distributions learned from the first frame in the sequence. Based on global rather than pixel-wise information, the proposed formulation relaxes the need of a large training set and optimization with respect to geometric transformations. Different from related active contour methods, it does not require a large number of iterative updates of the segmentation and the corresponding computationally onerous kernel density estimates (KDEs). The algorithm requires very few iterations and KDEs to converge. Furthermore, the proposed bound can be used for several other applications and, therefore, can lead to segmentation algorithms which share the flexibility of active contours and computational advantages of max-flow optimization. Quantitative evaluations over 2280 images acquired from 20 subjects demonstrated that the results correlate well with independent manual segmentations by an expert. Moreover, comparisons with a related recent active contour method showed that the proposed framework brings significant improvements in regard to accuracy and computational efficiency.

Agromyces flavus sp. nov., an actinomycete isolated from soil.

A gram-positive, non-motile strain, designated CPCC 202695(T), was isolated from a soil sample collected from the Qinghai-Tibet plateau, north-west China. Strain CPCC 202695(T) contained rhamnose, glucose and galactose in the cell wall as diagnostic sugars and 2,4-diaminobutyric acid, alanine, glutamic acid and glycine in the peptidoglycan. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. MK-12 was the predominant menaquinone and anteiso-C(15 : 0) (34.2 %), iso-C(15 : 0) (19.8 %), iso-C(16 : 0) (12.7 %) and anteiso-C(17 : 0) (11.1 %) were the major fatty acids. 16S rRNA gene sequence similarities (94.2-97.1 %) between the isolate and the type strains of recognized species of the genus Agromyces indicated that strain CPCC 202695(T) was a member of the genus Agromyces. DNA-DNA relatedness clearly separated strain CPCC 202695(T) from its closest relatives. The phenotypic and genotypic data demonstrated that strain CPCC 202695(T) represents a novel species of the genus Agromyces, for which the name Agromyces flavus sp. nov. is proposed. The type strain is CPCC 202695(T) ( = KCTC 19578(T)  = CCM 7623(T)).

A parameterization of deformation fields for diffeomorphic image registration and its application to myocardial delineation.

This study investigates a new parameterization of deformation fields for image registration. Instead of standard displacements, this parameterization describes a deformation field with its transformation Jacobian and curl of end velocity field. It has two important features which make it appealing to image registration: 1) it relaxes the need of an explicit regularization term and the corresponding ad hoc weight in the cost functional; 2) explicit constraints on transformation Jacobian such as topology preserving and incompressibility constraints are straightforward to impose in a unified framework. In addition, this parameterization naturally describes a deformation field in terms of radial and rotational components, making it especially suited for processing cardiac data. We formulate diffeomorphic image registration as a constrained optimization problem which we solve with a step-then-correct strategy. The effectiveness of the algorithm is demonstrated with several examples and a comprehensive evaluation of myocardial delineation over 120 short-axis cardiac cine MRIs acquired from 20 subjects. It shows competitive performance in comparison to two recent segmentation based approaches.

Mutual information-based CT-MR brain image registration using generalized partial volume joint histogram estimation.

Mutual information (MI)-based image registration has been found to be quite effective in many medical imaging applications. To determine the MI between two images, the joint histogram of the two images is required. In the literature, linear interpolation and partial volume interpolation (PVI) are often used while estimating the joint histogram for registration purposes. It has been shown that joint histogram estimation through these two interpolation methods may introduce artifacts in the MI registration function that hamper the optimization process and influence the registration accuracy. In this paper, we present a new joint histogram estimation scheme called generalized partial volume estimation (GPVE). It turns out that the PVI method is a special case of the GPVE procedure. We have implemented our algorithm on the clinically obtained brain computed tomography and magnetic resonance image data furnished by Vanderbilt University. Our experimental results show that, by properly choosing the kernel functions, the GPVE algorithm significantly reduces the interpolation-induced artifacts and, in cases that the artifacts clearly affect registration accuracy, the registration accuracy is improved.