Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation

Indexación: Web of Science.Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e(-5). None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).http://journal.frontiersin.org/article/10.3389/fmicb.2016.02035/ful

Correlation between Cu ion migration behaviour and deNO x activity in Cu-SSZ-13 for the standard NH 3 -SCR reaction

Here we present the results of a synchrotron-based in situ, time-resolved PXRD study during activation of two Cu-SSZ-13 catalysts under O2/He and one during standard NH3-SCR reaction conditions to obtain insight into the behaviour of Cu ions. The results obtained indicate that deNOx activity is inexorably linked with occupancy of the zeolite 6r

A Technique for Obtaining True Approximations for kk-Center with Covering Constraints

There has been a recent surge of interest in incorporating fairness aspects into classical clustering problems. Two recently introduced variants of the $k$-Center problem in this spirit are Colorful $k$-Center, introduced by Bandyapadhyay, Inamdar, Pai, and Varadarajan, and lottery models, such as the Fair Robust $k$-Center problem introduced by Harris, Pensyl, Srinivasan, and Trinh. To address fairness aspects, these models, compared to traditional $k$-Center, include additional covering constraints. Prior approximation results for these models require to relax some of the normally hard constraints, like the number of centers to be opened or the involved covering constraints, and therefore, only obtain constant-factor pseudo-approximations. In this paper, we introduce a new approach to deal with such covering constraints that leads to (true) approximations, including a $4$-approximation for Colorful $k$-Center with constantly many colors---settling an open question raised by Bandyapadhyay, Inamdar, Pai, and Varadarajan---and a $4$-approximation for Fair Robust $k$-Center, for which the existence of a (true) constant-factor approximation was also open. We complement our results by showing that if one allows an unbounded number of colors, then Colorful $k$-Center admits no approximation algorithm with finite approximation guarantee, assuming that $\mathrm{P} \neq \mathrm{NP}$. Moreover, under the Exponential Time Hypothesis, the problem is inapproximable if the number of colors grows faster than logarithmic in the size of the ground set

Capacitated Center Problems with Two-Sided Bounds and Outliers

In recent years, the capacitated center problems have attracted a lot of research interest. Given a set of vertices $V$, we want to find a subset of vertices $S$, called centers, such that the maximum cluster radius is minimized. Moreover, each center in $S$ should satisfy some capacity constraint, which could be an upper or lower bound on the number of vertices it can serve. Capacitated $k$-center problems with one-sided bounds (upper or lower) have been well studied in previous work, and a constant factor approximation was obtained. We are the first to study the capacitated center problem with both capacity lower and upper bounds (with or without outliers). We assume each vertex has a uniform lower bound and a non-uniform upper bound. For the case of opening exactly $k$ centers, we note that a generalization of a recent LP approach can achieve constant factor approximation algorithms for our problems. Our main contribution is a simple combinatorial algorithm for the case where there is no cardinality constraint on the number of open centers. Our combinatorial algorithm is simpler and achieves better constant approximation factor compared to the LP approach

Online unit clustering in higher dimensions

We revisit the online Unit Clustering and Unit Covering problems in higher dimensions: Given a set of $n$ points in a metric space, that arrive one by one, Unit Clustering asks to partition the points into the minimum number of clusters (subsets) of diameter at most one; while Unit Covering asks to cover all points by the minimum number of balls of unit radius. In this paper, we work in $\mathbb{R}^d$ using the $L_\infty$ norm. We show that the competitive ratio of any online algorithm (deterministic or randomized) for Unit Clustering must depend on the dimension $d$. We also give a randomized online algorithm with competitive ratio $O(d^2)$ for Unit Clustering}of integer points (i.e., points in $\mathbb{Z}^d$, $d\in \mathbb{N}$, under $L_{\infty}$ norm). We show that the competitive ratio of any deterministic online algorithm for Unit Covering is at least $2^d$. This ratio is the best possible, as it can be attained by a simple deterministic algorithm that assigns points to a predefined set of unit cubes. We complement these results with some additional lower bounds for related problems in higher dimensions.Comment: 15 pages, 4 figures. A preliminary version appeared in the Proceedings of the 15th Workshop on Approximation and Online Algorithms (WAOA 2017

Correlation between Cu ion migration behaviour and deNO(x) activity in Cu-SSZ-13 for the standard NH3-SCR reaction (vol 52, pg 6170, 2016)

Correction for ‘Correlation between Cu ion migration behaviour and deNOx activity in Cu-SSZ-13 for the standard NH3-SCR reaction’ by A. M. Beale et al., Chem. Commun., 2016, 52, 6170–6173. W. A. Slawinski was incorrectly spelt in the published article; the correct version is shown here. The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers

Capsular synovial metaplasia mimicking silicone leak of a breast prosthesis: a case report

<p>Abstract</p> <p>Introduction</p> <p>Synovial metaplasia around a prosthesis and in particular around silicone breast implants has been noted by various investigators, but has unknown clinical significance. We report on a patient where a large amount of synovial fluid mimicked rupture of an implant. We believe this to be an unusual clinical presentation of this phenomenon. Review of the English language literature failed to identify a comparable case.</p> <p>Case presentation</p> <p>A 25-year-old woman had undergone bilateral breast augmentation for cosmetic reasons. One implant was subsequently subjected to two attempts at expansion to correct asymmetry. The patient was later found to have a large quantity of viscous fluid around the port of that same prosthesis. Histological assessment of the implant had consequently confirmed capsular synovial metaplasia. This had initially caused the suspicion of a silicone 'bleed' from the implant and had resulted in an unnecessary explantation.</p> <p>Conclusion</p> <p>Capsular synovial metaplasia should be ruled out before the removal of breast implants where a leak is suspected. Manipulation and expansion of an implant may be risk factors for the development of synovial metaplasia.</p

Impact of calcium on salivary α-amylase activity, starch paste apparent viscosity and thickness perception

Thickness perception of starch-thickened products during eating has been linked to starch viscosity and salivary amylase activity. Calcium is an essential cofactor for α-amylase and there is anecdotal evidence that adding extra calcium affects amylase activity in processes like mashing of beer. The aims of this paper were to (1) investigate the role of salivary calcium on α-amylase activity and (2) to measure the effect of calcium concentration on apparent viscosity and thickness perception when interacting with salivary α-amylase in starch-based samples. α-Amylase activity in saliva samples from 28 people was assessed using a typical starch pasting cycle (up to 95 °C). The activity of the enzyme (as measured by the change in starch apparent viscosity) was maintained by the presence of calcium, probably by protecting the enzyme from heat denaturation. Enhancement of α-amylase activity by calcium at 37 °C was also observed although to a smaller extent. Sensory analysis showed a general trend of decreased thickness perception in the presence of calcium, but the result was only significant for one pair of samples, suggesting a limited impact of calcium enhanced enzyme activity on perceived thickness

Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage.

Sequence type (ST) 59 is an epidemic lineage of community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) isolates. Taiwanese CA-MRSA isolates belong to ST59 and can be grouped into 2 distinct clones, a virulent Taiwan clone and a commensal Asian-Pacific clone. The Taiwan clone carries the Panton-Valentine leukocidin (PVL) genes and the staphylococcal chromosomal cassette mec (SCCmec) VT, and is frequently isolated from patients with severe disease. The Asian-Pacific clone is PVL-negative, carries SCCmec IV, and a frequent colonizer of healthy children. Isolates of both clones were characterized by their ability to adhere to respiratory A549 cells, cytotoxicity to human neutrophils, and nasal colonization of a murine and murine sepsis models. Genome variation was determined by polymerase chain reaction of selected virulence factors and by multi-strain whole genome microarray. Additionally, the expression of selected factors was compared between the 2 clones. The Taiwan clone showed a much higher cytotoxicity to the human neutrophils and caused more severe septic infections with a high mortality rate in the murine model. The clones were indistinguishable in their adhesion to A549 cells and persistence of murine nasal colonization. The microarray data revealed that the Taiwan clone had lost the ø3-prophage that integrates into the β-hemolysin gene and includes staphylokinase- and enterotoxin P-encoding genes, but had retained the genes for human immune evasion, scn and chps. Production of the virulence factors did not differ significantly in the 2 clonal groups, although more α-toxin was expressed in Taiwan clone isolates from pneumonia patients. In conclusion, the Taiwan CA-MRSA clone was distinguished by enhanced virulence in both humans and an animal infection model. The evolutionary acquisition of PVL, the higher expression of α-toxin, and possibly the loss of a large portion of the β-hemolysin-converting prophage likely contribute to its higher pathogenic potential than the Asian-Pacific clone

Radiological and pathological findings of a metastatic composite paraganglioma with neuroblastoma in a man: a case report

INTRODUCTION: Composite tumors of the adrenal medulla or paraganglia are extremely rare and present a diagnostic dilemma. These tumors consist of a neuroendocrine component mixed with a neural component.We describe the imaging characteristics together with the corresponding pathological findings of a composite tumor. Apart from any component-specific imaging findings, the hallmark of this entity is the presence of histologically distinguishable components. CASE PRESENTATION: A 61-year-old Caucasian man was referred to our hospital due to a suspect lesion found on chest computed tomography carried out for unclear thoracic pain. An abdominal computed tomography scan and ultrasound examination detected a retroperitoneal tumor comprising two different tumor components. Twenty-four-hour urine revealed high levels of normetanephrine, characteristic of a neuroendocrine tumor. An octreoscan prior to surgical procedures revealed multiple osseous and intra-hepatic metastases. The final histopathological workup revealed a composite paraganglioma with neuroblastoma. Our patient died ten months after the initial diagnosis from tumor-associated complications. CONCLUSIONS: Composite paragangliomas with neuroblastoma are rare tumors of the retroperitoneum. Such tumors should be considered in the differential diagnosis of retroperitoneal masses