CDKN1C/p57kip2 Is a Candidate Tumor Suppressor Gene in Human Breast Cancer

BACKGROUND. CDKN1C (also known as p57KIP2) is a cyclin-dependent kinase inhibitor previously implicated in several types of human cancer. Its family members (CDKN1A/p21CIP1 and B/p27KIP1) have been implicated in breast cancer, but information about CDKN1C's role is limited. We hypothesized that decreased CDKN1C may be involved in human breast carcinogenesis in vivo. METHODS. We determined rates of allele imbalance or loss of heterozygosity (AI/LOH) in CDKN1C, using an intronic polymorphism, and in the surrounding 11p15.5 region in 82 breast cancers. We examined the CDKN1C mRNA level in 10 cancers using quantitative real-time PCR (qPCR), and the CDKN1C protein level in 20 cancers using immunohistochemistry (IHC). All samples were obtained using laser microdissection. Data were analyzed using standard statistical tests. RESULTS. AI/LOH at 11p15.5 occurred in 28/73 (38%) informative cancers, but CDKN1C itself underwent AI/LOH in only 3/16 (19%) cancers (p = ns). In contrast, CDKN1C mRNA levels were reduced in 9/10 (90%) cancers (p < 0.0001), ranging from 2–60% of paired normal epithelium. Similarly, CDKN1C protein staining was seen in 19/20 (95%) cases' normal epithelium but in only 7/14 (50%) cases' CIS (p < 0.004) and 5/18 (28%) cases' IC (p < 0.00003). The reduction appears primarily due to loss of CDKN1C expression from myoepithelial layer cells, which stained intensely in 17/20 (85%) normal lobules, but in 0/14 (0%) CIS (p < 0.00001). In contrast, luminal cells displayed less intense, focal staining fairly consistently across histologies. Decreased CDKN1C was not clearly associated with tumor grade, histology, ER, PR or HER2 status. CONCLUSION. CDKN1C is expressed in normal epithelium of most breast cancer cases, mainly in the myothepithelial layer. This expression decreases, at both the mRNA and protein level, in the large majority of breast cancers, and does not appear to be mediated by AI/LOH at the gene. Thus, CDKN1C may be a breast cancer tumor suppressor.Department of Defense Breast Cancer Research Program (DAMD 17-99-1-9573); National Institutes of Health PHS (CA081078); LaPann Fun

MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes

Premise of the study: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. Methods and Results: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. Conclusions: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development

Polyploidy : an evolutionary and ecological force in stressful times

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent non-random long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than non-polyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus non-polyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy

Mini Tomato Production In Organic System Under Greenhouse With Partial Control Of Meteorological Elements

The objective of this research was to evaluate the meteorological elements of the environments and the production components of mini tomato crop in organic system in different forms of cultivation, biofertilizer doses and technological levels of protected environments. The research was conducted in completely randomized design in a 3 x 2 x 5 factorial scheme, corresponding to three greenhouses (A - climatized, B - mobile screen and C - fixed screen), two forms of cultivation (pots and beds) and five doses of a commercial biofertilizer (0, 50, 100, 150 and 200% of dose indicated), with five replicates. The treatments affected the analyzed variables, except for biofertilizer doses and interaction of treatments. Air temperature was unchanged among the environments and the mean and minimum relative humidity were within the control range in the climatized greenhouse. The greenhouse with mobile screen showed the best production results for the cultivation in beds and the biofertilizer doses were indifferent for all treatments.20980080

Pediatric Feeding Disorder: Consensus Definition and Conceptual Framework

Pediatric feeding disorders (PFDs) lack a universally accepted definition. Feeding disorders require comprehensive assessment and treatment of 4 closely related, complementary domains (medical, psychosocial, and feeding skill-based systems and associated nutritional complications). Previous diagnostic paradigms have, however, typically defined feeding disorders using the lens of a single professional discipline and fail to characterize associated functional limitations that are critical to plan appropriate interventions and improve quality of life. Using the framework of the World Health Organization International Classification of Functioning, Disability, and Health, a unifying diagnostic term is proposed: “Pediatric Feeding Disorder” (PFD), defined as impaired oral intake that is not age-appropriate, and is associated with medical, nutritional, feeding skill, and/or psychosocial dysfunction. By incorporating associated functional limitations, the proposed diagnostic criteria for PFD should enable practitioners and researchers to better characterize the needs of heterogeneous patient populations, facilitate inclusion of all relevant disciplines in treatment planning, and promote the use of common, precise, terminology necessary to advance clinical practice, research, and health-care policy

Identification of a highly polymorphic tetranucleotide repeat locus (DXpS) at Xp and development of a DXpS/HUMARA biplex methylation-based PCR assay that enhances detection of X-chromosome inactivation

The methylation-based PCR assay at the polymorphic (CAG)n repeat in exon 1 of the human androgen receptor _AR_ gene (HUMARA) is a standard method for determination of the methylation state of alleles in active X (Xa) and inactive X (Xi) chromosomes. HUMARA assay is endowed with heterozygosity rates ~85% worldwide. This means that in a proportion of females it is uninformative. The HUMARA genotype is not neutral, being linked to Kennedy&#xb4;s disease. Moreover, allele designation and quantification from trinucleotide repeats demand normalizing for minor (stutter) products differing from the original template by multiples of the repeat unit. Here, we report on the identification of a highly polymorphic tetranucleotide repeat (named DXpS) mapping to within a CpG island on Xp. This island is 191 bp downstream from the start of the repeat element, and contains sites for the HhaI, HpaII and BstUI methyl-sensitive restriction enzymes. We developed the DXpS and the HUMARA markers into a biplex methylation-based quantitative fluorescent PCR assay. For DXpS we observed twelve alleles with negligible stuttering. DXpS exhibited a heterozygosity rate of 87% (n = 60), matching that of HUMARA. The combined informativeness of the biplex assay was 98%. Random and nonrandom X-inactivation patterns inferred with DXpS in phenotypically normal females and haemophiliac females carrying a defective F8 gene were highly concordant (r^2^ = 0.96) with HUMARA patterns. DXpS represents a notable advancement in detecting X-chromosome inactivation due to the observed high rate of heterozygosity, negligible stuttering, concordance with HUMARA, and the apparent neutrality of allelic variants. Financial support: FAPESP (09/10615-7), FAPERJ, CNPq

Cloud fragmentation and proplyd-like features in HII regions imaged by HST

We have analyzed HST ACS and WFPC2 new and archival images of eight HII regions to look for new proto-planetary disks (proplyds) similar to those found in the Orion Nebula. We find a wealth of features similar in size (though many are larger) to the bright cusps around the Orion Nebula proplyds. None of them, however, contains a definitive central star. From this, we deduce that the new cusps may not be proplyds, but instead are fragments of molecular cloud material. Out of all the features found in the eight HII regions examined, only one, an apparent edge-on silhouette in M17, may have a central star. This feature might join the small number of bona fide proplyds found outside the Orion Nebula, in M8, M20 and possibly in M16. In line with the results found recently by Smith et al. (2005), the paucity of proplyds outside the Orion Nebula, may be explained by their transient nature as well as by the specific environmental conditions under whichthey can be observed.Comment: 51 pages; 19 figures; 5 tables. Accepted by A

ISOLATION AND CHARACTERIZATION OF NOVEL MICROSATELLITE MARKERS FOR ARCTIUM MINUS (COMPOSITAE)

[EN] Premise of the study: Microsatellite primers were developed for the invasive plant Arctium minus to investigate the effects of facultative self-pollination and the biannual habit on population genetic structure, as well as the colonization of the Americas by this Eurasian species. Methods and Results: Sixteen di- and trinucleotide microsatellite loci were identifi ed in six populations. The number of alleles per locus ranged from one to 10, observed heterozygosities ranged from 0.000 to 0.897, and the mean value of F IS was 0.316. Conclusions: These results indicate the utility of these loci in future studies of population genetics in A. minus .Peer reviewe