Colicin Immunity Proteins of Pathogenic Bacteria Detected by Antibiotic-Induced SOS Response, Plasmid Sequencing, MALDI-TOF-TOF Mass Spectrometry, and Top-Down Proteomic Analysis.

Rationale: Plasmids can play a major role in the survival of pathogenic bacteria. Plasmids are acquired through horizontal gene transfer resulting in their spread across various strains, species and genera of bacteria. Colicins are bacterial protein toxins expressed by plasmid genes and released against co-located bacterial competitors.

Unusual modifications of protein biomarkers expressed by plasmid, prophage, and bacterial host of pathogenic Escherichia coli identified using top-down proteomic analysis.

Rationale: Pathogenic bacteria often carry prophage (bacterial viruses) and plasmids (small circular pieces of DNA) that may harbor toxin, antibacterial, and antibiotic resistance genes. Proteomic characterization of pathogenic bacteria should include the identification of host proteins and proteins produced by prophage and plasmid genomes.

Methods: Protein biomarkers of two strains of Shiga toxin-producing Escherichia coli (STEC) were identified using antibiotic induction, matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) with post-source decay (PSD), top-down proteomic (TDP) analysis, and plasmid sequencing.

Toxin and phage production from pathogenic E. coli by antibiotic induction analyzed by chemical reduction, MALDI-TOF-TOF mass spectrometry and top-down proteomic analysis.

Rationale: Shiga toxin-producing Escherichia coli (STEC) are an ongoing threat to public health and agriculture. Our laboratory has developed a rapid method for identification of Shiga toxin (Stx), bacteriophage, and host proteins produced from STEC. We demonstrate this technique on two genomically sequenced STEC O145:H28 strains linked to two major outbreaks of foodborne illness occurring in 2007 (Belgium) and 2010 (Arizona).

Managing Mortality and Aging Risks with a Time-Varying Lee-Carter Model.

Influential existing research has suggested that rather than being static, mortality declines decelerate at young ages and accelerate at old ages. Without accounting for this feature, the forecast mortality rates of the popular Lee-Carter (LC) model are less reliable in the long run. To provide more accurate mortality forecasting, we introduce a time-varying coefficients extension of the LC model by adopting the effective kernel methods.

A discussion on the robust vector autoregressive models: novel evidence from safe haven assets.

The vector autoregressive (VAR) model has been popularly employed in operational practice to study multivariate time series. Despite its usefulness in providing associated metrics such as the impulse response function (IRF) and forecast error variance decomposition (FEVD), the traditional VAR model estimated via the usual ordinary least squares is vulnerable to outliers. To handle potential outliers in multivariate time series, this paper investigates two robust estimation methods of the VAR model, the reweighted multivariate least trimmed squares and the multivariate MM-estimation.

Definition of customer requirements in big data using word vectors and affinity propagation clustering.

Customer requirements (CRs) have a significant impact on product design. The existing methods of defining CRs, such as customer surveys and expert evaluations, are time-consuming, inaccurate and subjective. This paper proposes an automatic CRs definition method based on online customer product reviews using the big data analysis.

Multiple investigations of aqueous Eu(III)-oxalate complexes: the reduction in coordination number and validation of spectral linear correlation.

Detailed information on the An(iii)/Ln(iii) complexation properties in solution is essential for separation chemistry and the prediction of their potential for radionuclide migration from nuclear waste repositories into natural aquifers. In the present study, to better reveal and confirm the structural information of [Eu(Ox)x (H2O)h-2x]3-2x (h = 8, 9; x = 0-3) aqueous species, especially the variable coordination number (CN), and explore the validity of the spectral linear correlation between the luminescence lifetime and the residual hydration number in the first coordination sphere of Eu(iii) compounds in solution, a comparison between the spectral results and the theoretical calculations in a wide parametric space in terms of the pH value and oxalate concentration was carried out by combining time-resolved luminescence spectroscopy (TRLS) with speciation modelling and density functional theory (DFT) calculations. We have found direct and clear evidence for the 9-fold to 8-fold coordination number reduction of Eu(iii) atoms upon coordination with more than one oxalate in an aqueous medium, and as well systematically validated the applicability of the spectral linear correlation in an aqueous system (otherwise solid state) involving multiple species with the support of relatively reliable and clear speciation modelling.

A retrospective analysis of the dynamic transmission routes of the COVID-19 in mainland China.

The fourth outbreak of the Coronaviruses, known as the COVID-19, has occurred in Wuhan city of Hubei province in China in December 2019. We propose a time-varying sparse vector autoregressive (VAR) model to retrospectively analyze and visualize the dynamic transmission routes of this outbreak in mainland China over January 31-February 19, 2020. Our results demonstrate that the influential inter-location routes from Hubei have become unidentifiable since February 4, 2020, whereas the self-transmission in each provincial-level administrative region (location, hereafter) was accelerating over February 4-15, 2020.

Macroscopic and spectroscopic characterization of U(VI) sorption on biotite.

Knowledge of the geochemical behavior of uranium is critical for the safe disposal of radioactive wastes. Biotite, a Fe(II)-rich phyllosilicate, is a common rock-forming mineral and a major component of granite or granodiorite. This work comprehensively studied the sorption of U(VI) on biotite surface with batch experiments and analyzed the uranium speciation with various spectroscopic techniques, including X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and time-resolved fluorescence spectra (TRFS).

Sorption of U(VI) onto natural soils and different mineral compositions: The batch method and spectroscopy analysis.

This research studied the sorption behavior of uranium(VI) onto two different kinds of soils: surface soil and undersurface soil that taken from the depth of 30 m undersurface. The soil samples were collected from a low and medium-level radioactive waste disposal site in the southwest of China. The effects of pH, solid-liquid ratio and contact time on the adsorption behavior were studied by batch adsorption method.

The Sources and Diversity of Immigrant Population Change in Australia, 1981-2011.

Australia has one of the largest percentages of immigrant populations in the developed world with a highly regulated system of immigration control and regular censuses to track their changes over time. However, the ability to explain the population change through the demographic components of immigration, emigration, and death by age and sex is complicated because of differences in measurement and sources of information. In this article, we explore three methods for reconciling the demographic accounts from 1981 to 2011 for the Australia-born and 18 foreign-born population groups.

A Versatile and Robust Approach to Stimuli-Responsive Protein Multilayers with Biologically Enabled Unique Functions.

Protein-based materials call for innovative processing techniques to integrate their unique biologically enabled functions with other materials of complementary features. Herein, we report the covalent protein layer-by-layer assembly via orthogonal "Tag-Catcher" reactions as a facile and robust approach to make entirely protein-based multilayers on a variety of substrates. Programmed assembly of native telechelic proteins not only endows the materials valuable stimuli-sensitive behaviors, but also unique properties unparalleled by any synthetic counterparts.

Influence of Fe(II) on the Se(IV) sorption under oxic/anoxic conditions using bentonite.

Se, one of the key radionuclides for nuclear waste disposal, threatens the quality of the environment, as well as human health. Therefore, it needs to be permanently isolated from the biosphere. The aim of the study was to investigate the effects of Fe(II)/Fe(III) on the removal of Se using bentonite in the pH range of 2.

BODIPY-based fluorescent thermometer as a lysosome-targetable probe: how the oligo(ethylene glycols) compete photoinduced electron transfer.

A novel BODIPY-based fluorescent thermometer, which shows a lysosome-targeting property, was successfully prepared. Due to the electron-donating ability of the oligo(ethylene glycols), the photoinduced electron-transfer pathway from morpholine to BODIPY dye is blocked. The fluorescence of the thermometer quenched by intramolecular rotation at room temperature was progressively enhanced during heating due to the increased microviscosity around the fluorophore.

BosR functions as a repressor of the ospAB operon in Borrelia burgdorferi.

The Lyme disease spirochete, Borrelia burgdorferi, must abundantly produce outer surface lipoprotein A (OspA) in the tick vector but downregulate OspA in mammals in order to evade the immune system and maintain its natural enzootic cycle. Here, we show that BosR binds two regulatory elements of the ospAB operon and that increasing BosR expression leads to downregulation of OspA. Both regulatory sequences, cisI and cisII, showed strong BosR-binding and cisII bound much tighter than cisI.

RpoS regulates essential virulence factors remaining to be identified in Borrelia burgdorferi.

Background: Since the RpoN-RpoS regulatory network was revealed in the Lyme disease spirochete Borrelia burgdorferi a decade ago, both upstream and downstream of the pathway have been intensively investigated. While significant progress has been made into understanding of how the network is regulated, most notably, discovering a relationship of the network with Rrp2 and BosR, only three crucial virulence factors, including outer surface protein C (OspC) and decorin-binding proteins (Dbps) A and B, are associated with the pathway. Moreover, for more than 10 years no single RpoS-controlled gene has been found to be critical for infection, raising a question about whether additional RpoS-dependent virulence factors remain to be identified.

Whole-body imaging of infection using bioluminescence.

Bioluminescence imaging is a powerful technique to visualize and monitor biological processes in numerous systems. This unit describes two strategies for bioluminescence imaging that can be used to study bacterial infection in mice. One method is to express a luciferase gene in the bacteria; the second method is to use bacteria that express both a luciferase and β-lactamase along with a substrate containing caged luciferin, which is released by β-lactamase hydrolysis and reacts with luciferase to generate light.

[Primary peripheral T-cell lymphoma of the penis: a case report and review of the literature].

Objective: To report a case of primary peripheral T-cell lymphoma of the penis.

Methods: We analyzed the clinicopathological characteristics of the case of primary peripheral T-cell lymphoma using histological, cytochemical and immunohistochemical methods and by review of the literature.

Results: The patient was a 65 years old man and presented with a diffuse enlargement of the penis as the initial sign, followed by erosive ulcer in the caput penis and inguinal lymphadenectasis.

Common and unique contributions of decorin-binding proteins A and B to the overall virulence of Borrelia burgdorferi.

As an extracellular bacterium, the Lyme disease spirochete Borrelia burgdorferi resides primarily in the extracellular matrix and connective tissues and between host cells during mammalian infection, where decorin and glycosaminoglycans are abundantly found, so its interactions with these host ligands potentially affect various aspects of infection. Decorin-binding proteins (Dbps) A and B, encoded by a 2-gene operon, are outer surface lipoproteins with similar molecular weights and share approximately 40% identity, and both bind decorin and glycosaminoglycans. To investigate how DbpA and DbpB contribute differently to the overall virulence of B.

Both decorin-binding proteins A and B are critical for the overall virulence of Borrelia burgdorferi.

Both decorin-binding proteins (DbpA and DbpB) of the Lyme disease spirochete Borrelia burgdorferi bind decorin and glycosaminoglycans, two important building blocks of proteoglycans that are abundantly found in the extracellular matrix (ECM) and connective tissues as well as on cell surfaces of mammals. As an extracellular pathogen, B. burgdorferi resides primarily in the ECM and connective tissues and between host cells during mammalian infection.

The dbpBA locus of Borrelia burgdorferi is not essential for infection of mice.

The Lyme disease spirochete Borrelia burgdorferi expresses a broad array of adhesive molecules, including the decorin-binding proteins A and B (DbpA and DbpB), which are believed to play important roles in mammalian infection. The dbpBA locus was deleted; resulting mutants were able to infect both immunodeficient and immunocompetent mice, indicating that neither DbpA nor DbpB is essential for the infection of mammals, although the DbpAB deficiency may significantly attenuate infectivity potential.

Cloning and expression analysis of two beta-1,3-glucanase genes from strawberry.

We isolated from strawberry (Fragariae x ananassa Duch) a genomic clone of a beta-1,3-glucanase gene, designated as FaBG2-2. In addition, a related cDNA clone, designated as FaBG2-3, was also isolated. FaBG2-2 and FaBG2-3 are similar in their coding regions, except that FaBG2-2 does not appear to contain a signal peptide coding sequence.

Identification of a zinc transporter gene in strawberry.

We have cloned a ZRT (Zn-regulated transporter), IRT (Fe-regulated transporter)-like protein (ZIP) gene from the strawberry plant (Fragaria x ananassa Duch). This gene, designated as FaZIP1, is composed of three exons and two introns. The locations of the two introns (546 and 157 base pairs) in the gene were confirmed by sequence analysis of cDNA clones obtained by using 3' and 5' RNA ligase mediated-rapid amplification of cDNA ends (RLM-RACE) PCR.

Classification of Streptomyces griseus (Krainsky 1914) Waksman and Henrici 1948 and related species and the transfer of 'Microstreptospora cinerea' to the genus Streptomyces as Streptomyces yanii sp. nov.

A soil actinomycete, strain 80-133(T), with the non-validly published name 'Microstreptospora cinerea', was the subject of a polyphasic study designed to clarify its taxonomic status. Comparative 16S rRNA gene sequence studies indicated that the organism belonged to the genus Streptomyces, a result in line with previous chemotaxonomic and morphological data. The strain belonged to the Streptomyces griseus clade, but could be distinguished from representatives of species assigned to this taxon by using DNA-DNA relatedness and phenotypic data.