A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments

Background  

For gene expression data obtained from a time-course microarray experiment, Liu et al. [1] developed a new algorithm for clustering genes with similar expression profiles over time. Performance of their proposal was compared with three other methods including the order-restricted inference based methodology of Peddada et al. [2, 3]. In this note we point out several inaccuracies in Liu et al. [1] and conclude that the order-restricted inference based methodology of Peddada et al. (programmed in the software ORIOGEN) indeed operates at the desired nominal Type 1 error level, an important feature of a statistical decision rule, while being computationally substantially faster than indicated by Liu et al. [1].     

Expression of active human sialyltransferase ST6GalNAcI in Escherichia coli

Background  

The presence of terminal, surface-exposed sialic acid moieties can greatly enhance the in vivo half-life of glycosylated biopharmaceuticals and improve their therapeutic efficacy. Complete and homogeneous sialylation of glycoproteins can be efficiently performed enzymically in vitro but this process requires large amounts of catalytically active sialyltransferases. Furthermore, standard microbial hosts used for large-scale production of recombinant enzymes can only produce small quantities of glycosyltransferases of animal origin, which lack catalytic activity.     

Regulation of Mammary Stem/Progenitor Cells by PTEN/Akt/β-Catenin Signaling

Recent evidence suggests that many malignancies, including breast cancer, are driven by a cellular subcomponent that displays stem cell-like properties. The protein phosphatase and tensin homolog (PTEN) is inactivated in a wide range of human cancers, an alteration that is associated with a poor prognosis. Because PTEN has been reported to play a role in the maintenance of embryonic and tissue-specific stem cells, we investigated the role of the PTEN/Akt pathway in the regulation of normal and malignant mammary stem/progenitor cell populations. We demonstrate that activation of this pathway, via PTEN knockdown, enriches for normal and malignant human mammary stem/progenitor cells in vitro and in vivo. Knockdown of PTEN in normal human mammary epithelial cells enriches for the stem/progenitor cell compartment, generating atypical hyperplastic lesions in humanized NOD/SCID mice. Akt-driven stem/progenitor cell enrichment is mediated by activation of the Wnt/β-catenin pathway through the phosphorylation of GSK3-β. In contrast to chemotherapy, the Akt inhibitor perifosine is able to target the tumorigenic cell population in breast tumor xenografts. These studies demonstrate an important role for the PTEN/PI3-K/Akt/β-catenin pathway in the regulation of normal and malignant stem/progenitor cell populations and suggest that agents that inhibit this pathway are able to effectively target tumorigenic breast cancer cells.     

Phosphorylation of CLIP-170 by Plk1 and CK2 promotes timely formation of kinetochore�Cmicrotubule attachments

CLIP‐170 is implicated in the formation of kinetochore–microtubule attachments through direct interaction with the dynein/dynactin complex. However, whether this important function of CLIP‐170 is regulated by phosphorylation is unknown. Herein, we have identified polo‐like kinase 1 (Plk1) and casein kinase 2 (CK2) as two kinases of CLIP‐170 and mapped S195 and S1318 as their respective phosphorylation sites. We showed that a CK2 unphosphorylatable mutant lost its ability to bind to dynactin and to localize to kinetochores during prometaphase, indicating that the CK2 phosphorylation of CLIP‐170 is involved in its dynactin‐mediated kinetochore localization. Furthermore, we provide evidence that Plk1 phosphorylation of CLIP‐170 at S195 enhances its association with CK2. Finally, we detected defects in the formation of kinetochore fibres in cells expressing the CLIP‐S195A and ‐S1318A, but not the CLIP‐S195E and ‐S1318D, confirming that Plk1‐ and CK2‐associated phosphorylations of CLIP‐170 are involved in the timely formation of kinetochore–microtubule attachments in mitosis.     

Hypertrophy-driven adipocyte death overwhelms recruitment under prolonged weight gain

Fat pads dynamically regulate energy storage capacity under energy excess and deficit. This remodeling process is not completely understood, with controversies regarding differences between fat depots and plasticity of adipose cell number. We examined changes of mouse adipose cell-size distributions in epididymal, inguinal, retroperitoneal, and mesenteric fat under both weight gain and loss. With mathematical modeling, we specifically analyzed the recruitment, growth/shrinkage, and loss of adipose cells, including the size dependence of these processes. We found a qualitatively universal adipose tissue remodeling process in all four fat depots: 1), There is continuous recruitment of new cells under weight gain; 2), the growth and shrinkage of larger cells (diameter >50 μm) is proportional to cell surface area; and 3), cell loss occurs under prolonged weight gain, with larger cells more susceptible. The mathematical model gives a predictive integrative picture of adipose tissue remodeling in obesity.     

<Emphasis Type="Italic">Cryptococcus gattii</Emphasis>: Clinical Importance and Emergence in North America

Cryptococcus gattii is an emerging fungal pathogen in the Pacific Northwest of North America, where it has caused more than 50 human infections since its emergence in 2004. Among residents of British Columbia, where the disease emerged in 1999 on Vancouver Island, many infections have occurred in immunocompetent persons. The cause for the emergence is currently unknown. The pathogenic profile of Cryptococcus gattii in North American patients appears to be different from that seen previously for C. gattii and from the profile of infection among patients with Cryptococcus neoformans. Treatment duration and the need for patient follow-up may be different between patients infected with C. gattii and C. neoformans. For this reason, physicians treating atypical patients with Cryptococcal spp infection, particularly HIV-uninfected patients, should obtain a travel history and obtain a species identity for Cryptococcus isolates.     

Multi analyte profiling and variability of inflammatory markers in blood and induced sputum in patients with stable COPD

Background

We analyzed serial concentrations of multiple inflammatory mediators from serum and induced sputum obtained from patients with stable COPD and controls. The objective was to determine which proteins could be used as reliable biomarkers to assess COPD disease state and severity.

Methods

Forty-two subjects; 21 with stable COPD and 21 controls, were studied every 2 weeks over a 6-week period. Serum and induced sputum were obtained at each of 3 visits and concentrations of 19 serum and 22 sputum proteins were serially assessed using multiplex immunoassays. We used linear mixed effects models to test the distribution of proteins for an association with COPD and disease severity. Measures of within- and between-subject coefficients of variation were calculated for each of the proteins to assess reliability of measurement.

Results

There was significant variability in concentrations of all inflammatory proteins over time, and variability was greater for sputum proteins (median intra-subject coefficient of variation 0.58) compared to proteins measured in serum (median intra-subject coefficient of variation 0.32, P = 0.03). Of 19 serum proteins and 22 sputum proteins tested, only serum CRP, myeloperoxidase and VEGF and sputum IL-6, IL-8, TIMP-1, and VEGF showed acceptable intra and inter-patient reliability and were significantly associated with COPD, the severity of lung function impairment, and dyspnea.

Conclusions

Levels of many serum and sputum biomarkers cannot be reliably ascertained based on single measurements. Multiple measurements over time can give a more reliable and precise estimate of the inflammatory burden in clinically stable COPD patients.     

Multilocus Sequence Type Analysis Reveals both Clonality and Recombination in Populations of Candida glabrata Bloodstream Isolates from U.S. Surveillance Studies

The human commensal yeast Candida glabrata is becoming increasingly important as an agent of nosocomial bloodstream infection. However, relatively little is known concerning the genetics and population structure of this species. We have analyzed 230 incident bloodstream isolates from previous and current population-based surveillance studies by using multilocus sequence typing (MLST). Our results show that in the U.S. cities of Atlanta, GA; Baltimore, MD; and San Francisco, CA during three time periods spanning 1992 to 2009, five populations of C. glabrata bloodstream isolates are defined by a relatively small number of sequence types. There is little genetic differentiation in the different C. glabrata populations. We also show that there has been a significant temporal shift in the prevalence of one major subtype in Atlanta. Our results support the concept that both recombination and clonality play a role in the population structure of this species.In the most recently available survey of nosocomial bloodstream infections, Candida species were the fourth most common organism, surpassed only by Staphylococcus and Enterococcus species (24). Although Candida albicans remains the most commonly isolated Candida species worldwide, the incidence of Candida glabrata infection has been increasing steadily so that it is now the second most common cause of Candida infection in the United States (14). C. glabrata is considered a normal component of the human epithelial flora but is capable of causing serious systemic infections in susceptible hosts. This increase in the relative proportion of infections due to C. glabrata has come during the period of the introduction and prophylactic use of azole antifungal drugs (21) and may be a reflection of the decreased susceptibility of C. glabrata to these azole antifungal drugs (7, 15). Many questions regarding the epidemiology of C. glabrata infections have a direct impact on public health and still remain unanswered. Is the decreased susceptibility due to a small number of clones expanding in a population, or are all isolates capable of developing resistance to azole drugs? Are some isolates more virulent than others and therefore more prevalent in a population? Can we monitor the expansion of clonal isolates that may be more virulent or have increased drug resistance? A better understanding of the population genetics of C. glabrata may allow us to answer some of these questions.Many DNA fingerprinting methods have been developed for the investigation of the population genetics of Candida species (19). Two of the most important aspects of a typing system are reproducibility between laboratories and the ability to archive strain types. Multilocus sequence typing (MLST) has been developed as a typing system which allows highly reproducible strain discrimination as well as the development of genotypic strain archives that can be stored digitally for both prospective and retrospective analysis of isolates (13, 22). An MLST system which utilizes six housekeeping genes on six separate chromosomes was developed for C. glabrata (4), and an online archive of sequence types (STs) was established (http://cglabrata.mlst.net). Several studies utilizing this typing system have described the molecular population structure of both regional and worldwide collections of C. glabrata isolates (4, 5, 11, 12).During the past 2 decades, the Centers for Disease Control and Prevention (CDC) and our partners have undertaken three active, population-based surveillance studies in order to determine the incidence of candidemia, the distribution of species causing bloodstream infection, and the prevalence of antifungal drug resistance (8, 10). In each case, two major metropolitan areas were included: San Francisco, CA, and Atlanta, GA (1992 to 1993); Baltimore, MD, and the state of Connecticut (1998 to 2000); and Atlanta, GA, and Baltimore, MD (2008 to 2010). Population-based surveillance is unique in that it includes the total population of a particular geographic area and avoids the biases associated with single or select institutional studies. During each of the surveillance studies, incident bloodstream isolates from all hospitals within each defined geographic area were collected and identified to the species level. While C. glabrata isolates comprised a smaller percentage of the isolates in the 1992-to-1993 and 1998-to-2000 surveillance studies (8, 10), they represent almost a third of the isolates collected during the current surveillance (N. Iqbal and S. Lockhart, unpublished observations).In the present work, we have characterized by MLST analysis 230 isolates of C. glabrata from five populations (excluding Connecticut) separated both geographically and temporally. This unique collection of isolates allowed an analysis of the changing population genetics of this organism. We identified 31 unique STs and showed the maintenance of a major ST both geographically and temporally that is unique to the United States. An analysis of the relatedness of specific C. glabrata populations and a strong indication for recombination within and between populations are provided.