Three differentiation states risk-stratify bladder cancer into distinct subtypes

Current clinical judgment in bladder cancer (BC) relies primarily on pathological stage and grade. We investigated whether a molecular classification of tumor cell differentiation, based on a developmental biology approach, can provide additional prognostic information. Exploiting large preexisting gene-expression databases, we developed a biologically supervised computational model to predict markers that correspond with BC differentiation. To provide mechanistic insight, we assessed relative tumorigenicity and differentiation potential via xenotransplantation. We then correlated the prognostic utility of the identified markers to outcomes within gene expression and formalin-fixed paraffin-embedded (FFPE) tissue datasets. Our data indicate that BC can be subclassified into three subtypes, on the basis of their differentiation states: basal, intermediate, and differentiated, where only the most primitive tumor cell subpopulation within each subtype is capable of generating xenograft tumors and recapitulating downstream populations. We found that keratin 14 (KRT14) marks the most primitive differentiation state that precedes KRT5 and KRT20 expression. Furthermore, KRT14 expression is consistently associated with worse prognosis in both univariate and multivariate analyses. We identify here three distinct BC subtypes on the basis of their differentiation states, each harboring a unique tumor-initiating population.     

Cytokines in the stools of children with complicated shigellosis.

The pathogenesis of the systemic complications, leukemoid reaction and hemolytic uremic syndrome, associated with Shigella dysenteriae type 1 infection is not well understood. The excessive production of proinflammatory cytokines, including tumor necrosis factor alpha (TNF-alpha) and interleukin 6 (IL-6), has been suggested as a possible factor. We measured IL-6 and TNF-alpha in stools of 56 children with S. dysenteriae 1 infection and 29 children without any apparent infection, all age 12 to 60 months. Sixteen children with S. dysenteriae 1 infection had leukemoid reaction or hemolytic uremic syndrome (complicated shigellosis), while the others did not (uncomplicated shigellosis). Stool IL-6 and TNF-alpha concentrations were higher in children with uncomplicated shigellosis than in children with complicated shigellosis (P = 0.009 and < 0.001, respectively) or in uninfected children (P < 0.001). It is concluded that complicated infection is not associated with higher concentrations of the proinflammatory cytokines IL-6 and TNF-alpha in stool.     

Classification and selection of biomarkers in genomic data using LASSO

High-throughput gene expression technologies such as microarrays have been utilized in a variety of scientific applications. Most of the work has been done on assessing univariate associations between gene expression profiles with clinical outcome (variable selection) or on developing classification procedures with gene expression data (supervised learning). We consider a hybrid variable selection/classification approach that is based on linear combinations of the gene expression profiles that maximize an accuracy measure summarized using the receiver operating characteristic curve. Under a specific probability model, this leads to the consideration of linear discriminant functions. We incorporate an automated variable selection approach using LASSO. An equivalence between LASSO estimation with support vector machines allows for model fitting using standard software. We apply the proposed method to simulated data as well as data from a recently published prostate cancer study.     

Identification of new genetic regions more prevalent in nontypeable Haemophilus influenzae otitis media strains than in throat strains

Nontypeable (NT) Haemophilus influenzae strains cause significant respiratory illness and are isolated from up to half of middle ear aspirates from children with acute otitis media. Previous studies have identified two genes, lic2B and hmwA, that are associated with NT H. influenzae strains isolated from the middle ears of children with otitis media but that are not associated with NT H. influenzae strains isolated from the throats of healthy children, suggesting that they may play a role in virulence in otitis media. In this study, genomic subtraction was used to identify additional genetic regions unique to middle ear strains. The genome of NT H. influenzae middle ear strain G622 was subtracted from that of NT H. influenzae throat strain 23221, and the resultant gene regions unique to the middle ear strain were identified. Subsequently, the relative prevalence of the middle ear-specific gene regions among a large panel of otitis media and throat strains was determined by dot blot hybridization. By this approach, nine genetic regions were found to be significantly more prevalent in otitis media strains. Classification tree analysis of lic2B, hmwA, and the nine new potential otitis media virulence genes revealed two H. influenzae pathotypes associated with otitis media.     

Influence of ionic crosslinkers (Ca2+/Ba2+/Zn2+) on the mechanical and biological properties of 3D Bioplotted Hydrogel Scaffolds

Three dimensional (3D) bioplotting requires appropriate crosslinkers to crosslink the hydrogel precursor while simultaneously maintaining the viability of embedded cells. However, the evaluation and comparison of various types of crosslinkers in bioplotting remains underexplored to date. This paper presents our study of the influence of three ionic crosslinkers—calcium chloride (CaCl₂), barium chloride (BaCl₂), and zinc chloride (ZnCl₂)—on the mechanical and biological properties of 3D bioplotted alginate scaffolds. The scaffold mechanical properties characterized included the elastic modulus, swelling, and degradation while the biological properties considered included Schwann cell viability and surface morphology. The mechanical and biological properties of the bioplotted scaffolds were both dependent on the crosslinkers used for fabrication; specifically, crosslinking ions resulted in the elastic modulus of the hydrogels decreasing in the order BaCl₂>CaCl₂>ZnCl₂ over 42 days while Schwann cell viability decreased in the order CaCl₂>BaCl₂>ZnCl₂ over 7 days. Taken together, these results offer insights that are effective in terms of manipulating the 3D bioplotting process so as to tune and optimize the mechanical and biological performance of the plotted scaffolds for tissue engineering applications.     

Genetic heterogeneity in northeastern India: Reflection of Tribe–Caste continuum in the genetic structure

We critically examined the gene frequency data for 11 genetic markers commonly available in the literature for 22 populations of northeastern India in the light of their geographic, linguistic, and ethnic affiliations. The markers investigated were three blood groups (A₁A₂BO, MNS, and Rh), four serum proteins (KM, Gc, Hp, and Tf), and four enzyme systems (AP, AK, EsD, and Hb). The neighbor‐joining tree and multidimensional scaling of the distance matrix suggest relatively high genetic differentiation among the Mongoloid groups, with probably diverse origins when compared to the Caucasoid Indo‐European populations, which had probably come from relatively more homogeneous backgrounds. Broadly speaking, the pattern of population affinities conforms to the ethno‐historic, linguistic, and geographic backgrounds. An interesting and important feature that emerges from this analysis is the reflection of the effect of the sociological process of a Tribe–Caste continuum on genetic structure. While on one end we have the cluster of Caucasoid caste populations, the other end consists of Mongoloid tribal groups. In between are the populations which were originally tribes but now have become semi‐Hinduized caste groups, viz., Rajbanshi, Chutiya, and Ahom. These groups have currently assumed caste status and speak Indo‐European languages. Therefore, one may infer that what appears to be a purely sociological phenomenon of a Tribe–Caste continuum may well reflect in their genetic structure. Am. J. Hum. Biol. 16:334–345, 2004. © 2004 Wiley‐Liss, Inc.     

Role of La autoantigen and polypyrimidine tract-binding protein in HCV replication

To determine if the cellular factors La autoantigen (La) and polypyrimidine tract-binding protein (PTB) are required for hepatitis C virus (HCV) replication, we used siRNAs to silence these factors and then monitored their effect on HCV replication using quantitative RT-PCR. In addition, we determined the influence of PTB on the activity of the 3' noncoding region (NCR) of HCV and investigated its interaction with the components of the HCV replicase complex. We found that La is essential for efficient HCV replication while PTB appears to partially repress replication. PTB does, however, block the binding of HCV RNA-dependent RNA polymerase (RdRp, NS5B) to the 3'NCR. Indirect immunofluorescence microscopy showed co-localization of cytoplasmic PTB with the HCV RdRp in hepatoma cells (Huh-7) expressing HCV proteins, while in vitro translation of viral proteins from the HCV replicon revealed the interaction of PTB isoforms with NS5B polymerase and NS3.     

Efficacy of soil-borne Enterobacter sp. for carbofuran degradation: HPLC quantitation of degradation rate

Excessive use of pesticides in agricultural fields is a matter of great concern for living beings as well as the environment across the world, in particular, the third world countries. Therefore, there is an urgent need to find out an effective way to degrade these hazardous chemicals from the soil in an environment-friendly way. In the current project, a bacterial species were isolated through enrichment culture from carbofuran-supplemented rice-field soil and identified as a carbofuran degrader. The rate of carbofuran degradation by this bacterial species was evaluated using reverse-phase high-performance liquid chromatography (RP-HPLC), which confirmed the ability to utilize as a carbon source up to 4 µg/ml of 99% technical grade carbofuran. The morphological, physiological, biochemical characteristics and phylogenetic analysis of the 16S rRNA sequence showed that this strain belongs to the genus of Enterobacter sp. (sequence accession number LC368285 in DDBJ), and the optimum growth condition for the isolated strain was 37°C at pH 7.0. Moreover, an antibiotic sensitivity test showed that it was susceptible to azithromycin, penicillin, ceftazidime, ciprofloxacin, and gentamycin, and the minimal inhibitory concentration value of gentamycin was 400 μg/ml against the bacteria. It shows beyond doubt from the RP-HPLC quantification that the isolated bacterium has the ability to detoxify carbofuran (99% pure). Finally, the obtained results imply that the isolated strain of Enterobacter can be used as a potential and effective carbofuran degrader for bioremediation of contaminated sites through bioaugmentation.