The FunGenES Database: A Genomics Resource for Mouse Embryonic Stem Cell Differentiation

Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the “Functional Genomics in Embryonic Stem Cells” consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the results in an interactive database with a number of features and tools. Specifically, we have generated clusters of transcripts that behave the same way under the entire spectrum of the sixty-seven experimental conditions; we have assembled genes in groups according to their time of expression during successive days of ES cell differentiation; we have included expression profiles of specific gene classes such as transcription regulatory factors and Expressed Sequence Tags; transcripts have been arranged in “Expression Waves” and juxtaposed to genes with opposite or complementary expression patterns; we have designed search engines to display the expression profile of any transcript during ES cell differentiation; gene expression data have been organized in animated graphs of KEGG signaling and metabolic pathways; and finally, we have incorporated advanced functional annotations for individual genes or gene clusters of interest and links to microarray and genomic resources. The FunGenES database provides a comprehensive resource for studies into the biology of ES cells

Vampires in the village Žrnovo on the island of Korčula: following an archival document from the 18th century

Središnja tema rada usmjerena je na raščlambu spisa pohranjenog u Državnom arhivu u Mlecima (fond: Capi del Consiglio de’ Dieci: Lettere di Rettori e di altre cariche) koji se odnosi na događaj iz 1748. godine u korčulanskom selu Žrnovo, kada su mještani – vjerujući da su se pojavili vampiri – oskvrnuli nekoliko mjesnih grobova. U radu se podrobno iznose osnovni podaci iz spisa te rečeni događaj analizira u širem društvenom kontekstu i prate se lokalna vjerovanja.The main interest of this essay is the analysis of the document from the State Archive in Venice (file: Capi del Consiglio de’ Dieci: Lettere di Rettori e di altre cariche) which is connected with the episode from 1748 when the inhabitants of the village Žrnove on the island of Korčula in Croatia opened tombs on the local cemetery in the fear of the vampires treating. This essay try to show some social circumstances connected with this event as well as a local vernacular tradition concerning superstitions

Potential of mitochondrial DNA for providing insights into the origin of the Etruscans

This report of a small pilot survey of mitochondrial DNA (mtDNA) variation in ten individuals whose maternal lineages were from Tuscany emphasizes the problems and potential contributions of mtDNA studies regarding the origin of the Etruscans. An average of 20% of the mtDNA was studied for variations in patterns and nine different patterns were observed. These patterns are common in Europe and encompass most of European mtDNA variation. Consequently, contemporary Tuscan populations do not appear to harbor peculiar mtDNAs which could be attributed to the original Etruscan population. It is suggested that a study of mtDNA variation in skeletons excavated from authentic Etruscan grave sites might reveal mtDNA patterns whose distribution and frequency could be compared to those observed in Tuscans and other modern populations, and in human remains from other burial sites. This comparison could provide clues as to where the Etruscans may have originated

Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma

Giant congenital naevi are pigmented childhood lesions that frequently lead to melanoma, the most aggressive skin cancer. The mechanisms underlying this malignancy are largely unknown, and there are no effective therapies. Here we describe a mouse model for giant congenital naevi and show that naevi and melanoma prominently express Sox10, a transcription factor crucial for the formation of melanocytes from the neural crest. Strikingly, Sox10 haploinsufficiency counteracts Nras(Q61K)-driven congenital naevus and melanoma formation without affecting the physiological functions of neural crest derivatives in the skin. Moreover, Sox10 is also crucial for the maintenance of neoplastic cells in vivo. In human patients, virtually all congenital naevi and melanomas are SOX10 positive. Furthermore, SOX10 silencing in human melanoma cells suppresses neural crest stem cell properties, counteracts proliferation and cell survival, and completely abolishes in vivo tumour formation. Thus, SOX10 represents a promising target for the treatment of congenital naevi and melanoma in human patients

Vibrational Spectroscopy of Fluorescent Proteins: A Tool to Investigate the Structure of the Chromophore and Its Environment

The design of fluorescent protein (FP) mutants with tailored properties benefits from the comprehension of chromophore structure, interactions, energy landscapes, and dynamics. Vibrational spectroscopy can often provide detailed information on these characteristics for proteins in their natural aqueous environment, during their (photo)dynamics and without the need of crystallization. Here we will review the experimental and theoretical techniques that have been used to analyze the relations between vibrational spectra and different structural, photophysical, and chemical properties of FPs, in particular the ones able to selectively address the chromophore and its close environment, like (pre)resonance Raman, difference-IR absorption measurements, and their computational simulations. Starting from the preliminary results aimed at identifying vibrational modes in the neutral and anionic GFP chromophore, we will discuss selected experiments that unraveled, often thanks to comparison with theoretical studies, the structure of the chromophore in some FP mutants, the impact of cis\u2013trans isomerization and different protonation states in reversibly photoswitchable proteins, and the structural changes and proton-transfer pathway in the photoexcited state