The human genome and gene expression profiling

The mapping and sequencing of the human genome has generated a large resource for answering questions about human disease. This achievement is akin in scientific importance to developing the periodic table of elements. Plastic surgery has always been at the frontier medical research. This resource will help us to improve our understanding on the many unknown physiological and pathogical conditions we deal with daily, such as wound heating keloid scar formation, Dupuytren's disease, rheumatoid arthritis, vascular malformation and carcinogenesis. We are primed in obtaining both disease and normal tissues to use this resource and applying it to clinical use. This review is about the human genome, the basis of gene expression profiling and how it will affect our clinical and research practices in the future and for those embarking on the use of this new technology as a research tool, we provide a brief insight on its limitations and pitfalls. (C) 2006 The British Association of Plastic Surgeons. Published by Elsevier Ltd. All rights reserved.

Identification of genes downstream of endothelin-3 signaling: characterization of WSB1 and SPC12

Signaling of endothelin-3 (Edn3) through its receptor, endothelin receptor B (EdnrB), has been shown to be indispensable for the development of certain neural crest derivatives. Since no research has been directed to investigate what the downstream targets of this signaling pathway are, the purpose of this study was to identify and characterize genes that are transcriptionally regulated by Edn3 signaling. Data from Differential Display RT-PCR of Edn-3 induced cDNA vs. non-induced cDNA obtained from primary neural crest cultures was analyzed. Thirty bands that were differentially expressed were sequenced and submitted for a homology search (BLAST). Among the genes identified were WSB 1 (a member of the SOCS family of negative regulators) and SPC 12 (the smallest subunit, 12kDa, of mammalian signal peptidase). Using whole-mount in-situ hybridization, the expression patterns of EdnrB, WSB 1 and SPC 12 were characterized. WSB 1 and SPC 12 expression patterns were found to overlap with that of EdnrB, suggesting that Edn3 might regulate the transcription of these genes in specific neural crest derived lineages.

Nutrigenómica de la tilapia, ("Oreochromis niloticus") alimentada con diferentes fuentes de ácidos grasos

El pescado es uno de los productos alimenticios básicos más comercializados en el mundo y desempeña un papel importante en la seguridad alimentaria y nutritiva, por ser una fuente de ácidos grasos omega 3 de cadena larga (EPA y DHA). El creciente interés por esta fuente de ácidos grasos ha incrementado su precio y, con ello, los costos de producción en la acuicultura. Todo esto ha llevado a la búsqueda de nuevas fuentes alternativas de ácidos grasos omega 3 de cadena larga para reemplazarlos. El objetivo de esta tesis fue investigar los efectos producidos en el metabolismo de los ácidos grasos y en los procesos de estrés en la Tilapia del Nilo (Oreochromis niloticus), al sustituir el aceite de pescado (fuente de ácidos grasos omega-3 de cadena larga) de su dieta por aceites vegetales (aceite de lino, aceite de girasol y aceite de girasol alto-oleico). Utilizando muestras de cerebro, músculo e hígado, se evaluaron los perfiles de expresión génica por Differential Display y la expresión relativa de genes candidatos mediante RT-PCR cuantitativa. Los resultados mostraron que las dietas basadas en aceites vegetales produjeron un aumento significativo en la expresión de genes que participan en la elongación y desaturación de los ácidos grasos (que permiten la conversión de ácidos grasos esenciales linoleico y linolénico en PUFA de cadena larga: AA, EPA y DHA) y una disminución en la expresión de enzimas que se activan en situaciones de estrés por osmorregulación, choque térmico y respuesta inmune. Estos resultados aportan una prueba más de que es posible sustituir el aceite de pescado por aceites vegetales en la dieta de Tilapia del Nilo, sin generar efectos negativos en el bienestar animal...

Reciprocal subtraction differential RNA display: An efficient and rapid procedure for isolating differentially expressed gene sequences

A reciprocal subtraction differential RNA display (RSDD) approach has been developed that permits the rapid and efficient identification and cloning of both abundant and rare differentially expressed genes. RSDD comprises reciprocal subtraction of cDNA libraries followed by differential RNA display. The RSDD strategy was applied to analyze the gene expression alterations resulting during cancer progression as adenovirus-transformed rodent cells developed an aggressive transformed state, as documented by elevated anchorage-independence and enhanced in vivo oncogenesis in nude mice. This approach resulted in the identification and cloning of both known and a high proportion (>65%) of unknown sequences, including cDNAs displaying elevated expression as a function of progression (progression-elevated gene) and cDNAs displaying suppressed expression as a function of progression (progression-suppressed gene). Sixteen differentially expressed genes, including five unknown progression-elevated genes and six unknown progression-suppressed genes, have been characterized. The RSDD scheme should find wide application for the effective detection and isolation of differentially expressed genes.

Analysis of differential gene expression by display of 3' end restriction fragments of cDNAs.

We have developed an approach to study changes in gene expression by selective PCR amplification and display of 3' end restriction fragments of double-stranded cDNAs. This method produces highly consistent and reproducible patterns, can detect almost all mRNAs in a sample, and can resolve hidden differences such as bands that differ in their sequence but comigrate on a gel. Bands corresponding to known cDNAs move to predictable positions on the gel, making this a powerful approach to correlate gel patterns with cDNA data bases. Applying this method, we have examined differences in gene expression patterns during T-cell activation. Of a total of 700 bands that were evaluated in this study, as many as 3-4% represented mRNAs that are upregulated, while approximately 2% were down-regulated within 4 hr of activation of Jurkat T cells. These and other results suggest that this approach is suitable for the systematic, expeditious, and nearly exhaustive elucidation of subtle changes in the patterns of gene expression in cells with altered physiologic states.

Identification of the human prostatic carcinoma oncogene PTI-1 by rapid expression cloning and differential RNA display.

Elucidating the relevant genomic changes mediating development and evolution of prostate cancer is paramount for effective diagnosis and therapy. A putative dominant-acting nude mouse prostatic carcinoma tumor-inducing gene, PTI-1, has been cloned that is expressed in patient-derived human prostatic carcinomas but not in benign prostatic hypertrophy or normal prostate tissue. PTI-1 was detected by cotransfecting human prostate carcinoma DNA into CREF-Trans 6 cells, inducing tumors in nude mice, and isolating genes displaying increased expression in tumor-derived cells by using differential RNA display (DD). Screening a human prostatic carcinoma (LNCaP) cDNA library with a 214-bp DNA fragment found by DD permitted the cloning of a full-length 2.0-kb PTI-1 cDNA. Sequence analysis indicates that PTI-1 is a gene containing a 630-bp 5' sequence and a 3' sequence homologous to a truncated and mutated form of human elongation factor 1 alpha. In vitro translation demonstrates that the PTI-1 cDNA encodes a predominant approximately 46-kDa protein. Probing Northern blots with a DNA fragment corresponding to the 5' region of PTI-1 identifies multiple PTI-1 transcripts in RNAs from human carcinoma cell lines derived from the prostate, lung, breast, and colon. In contrast, PTI-1 RNA is not detected in human melanoma, neuroblastoma, osteosarcoma, normal cerebellum, or glioblastoma multiforme cell lines. By using a pair of primers recognizing a 280-bp region within the 630-bp 5' PTI-1 sequence, reverse transcription-PCR detects PTI-1 expression in patient-derived prostate carcinomas but not in normal prostate or benign hypertrophic prostate tissue. In contrast, reverse transcription-PCR detects prostate-specific antigen expression in all of the prostate tissues. These results indicate that PTI-1 may be a member of a class of oncogenes that could affect protein translation and contribute to carcinoma development in human prostate and other tissues. The approaches used, rapid expression cloning with the CREF-Trans 6 system and the DD strategy, should prove widely applicable for identifying and cloning additional human oncogenes.

Identification of Novel Immunoregulatory Molecules in Human Thymic Regulatory CD4(+)CD25(+) T Cells by Phage Display

Thymic CD4(+)CD25(+) cells play an important role in immune regulation and are continuously developed in the thymus as an independent lineage. How these cells are generated, what are their multiple pathways of suppressive activity and which are their specific markers are questions that remain unanswered. To identify molecules involved in the function and development of human CD4(+)CD25(+) T regulatory cells we targeted thymic CD4(+)CD25(+) cells by peptide phage display. A phage library containing random peptides was screened ex vivo for binding to human thymic CD4(+)CD25(+) T cells. After four rounds of selection on CD4(+)CD25(+) enriched populations of thymocytes, we sequenced several phage displayed peptides and selected one with identity to the Vitamin D Receptor (VDR). We confirmed the binding of the VDR phage to active Vitamin D in vitro, as well as the higher expression of VDR in CD4(+)CD25(+) cells. We suggest that differential expression of VDR on natural Tregs may be related to the relevance of Vitamin D in function and ontogeny of these cells.

Differential gene expression during Trypanosoma cruzi metacyclogenesis

The transformation of epimastigotes into metacyclic trypomastigotes involves changes in the pattern of expressed genes, resulting in important morphological and functional differences between these developmental forms of Trypanosoma cruzi. In order to identify and characterize genes involved in triggering the metacyclogenesis process and in conferring to metacyclic trypomastigotes their stage specific biological properties, we have developed a method allowing the isolation of genes specifically expressed when comparing two close related cell populations (representation of differential expression or RDE). The method is based on the PCR amplification of gene sequences selected by hybridizing and subtracting the populations in such a way that after some cycles of hybridization-amplification genes specific to a given population are highly enriched. The use of this method in the analysis of differential gene expression during T. cruzi metacyclogenesis (6 hr and 24 hr of differentiation and metacyclic trypomastigotes) resulted in the isolation of several clones from each time point. Northern blot analysis showed that some genes are transiently expressed (6 hr and 24 hr differentiating cells), while others are present in differentiating cells and in metacyclic trypomastigotes. Nucleotide sequencing of six clones characterized so far showed that they do not display any homology to gene sequences available in the GeneBank.

Differential Gene Expression between Fall- and Spring-Run Chinook Salmon Assessed by Long Serial Analysis of Gene Expression

Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes: and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data.

Transcript profiling suggests that differential metabolic adaptation of mice to a high fat diet is associated with changes in liver to muscle lipid fluxes.

Genetically homogenous C57Bl/6 mice display differential metabolic adaptation when fed a high fat diet for 9 months. Most become obese and diabetic, but a significant fraction remains lean and diabetic or lean and non-diabetic. Here, we performed microarray analysis of "metabolic" transcripts expressed in liver and hindlimb muscles to evaluate: (i) whether expressed transcript patterns could indicate changes in metabolic pathways associated with the different phenotypes, (ii) how these changes differed from the early metabolic adaptation to short term high fat feeding, and (iii) whether gene classifiers could be established that were characteristic of each metabolic phenotype. Our data indicate that obesity/diabetes was associated with preserved hepatic lipogenic gene expression and increased plasma levels of very low density lipoprotein and, in muscle, with an increase in lipoprotein lipase gene expression. This suggests increased muscle fatty acid uptake, which may favor insulin resistance. In contrast, the lean mice showed a strong reduction in the expression of hepatic lipogenic genes, in particular of Scd-1, a gene linked to sensitivity to diet-induced obesity; the lean and non-diabetic mice presented an additional increased expression of eNos in liver. After 1 week of high fat feeding the liver gene expression pattern was distinct from that seen at 9 months in any of the three mouse groups, thus indicating progressive establishment of the different phenotypes. Strikingly, development of the obese phenotype involved re-expression of Scd-1 and other lipogenic genes. Finally, gene classifiers could be established that were characteristic of each metabolic phenotype. Together, these data suggest that epigenetic mechanisms influence gene expression patterns and metabolic fates.

Differential methylation of TCF7L2 promoter in peripheral blood DNA in newly diagnosed, drug-naïve patients with type 2 diabetes

TCF7L2 is the susceptibility gene for Type 2 diabetes (T2D) with the largest effect on disease risk that has been discovered to date. However, the mechanisms by which TCF7L2 contributes to the disease remain largely elusive. In addition, epigenetic mechanisms, such as changes in DNA methylation patterns, might have a role in the pathophysiology of T2D. This study aimed to investigate the differences in terms of DNA methylation profile of TCF7L2 promoter gene between type 2 diabetic patients and age- and Body Mass Index (BMI)- matched controls. We included 93 type 2 diabetic patients that were recently diagnosed for T2D and exclusively on diet (without any pharmacological treatment). DNA was extracted from whole blood and DNA methylation was assessed using the Sequenom EpiTYPER system. Type 2 diabetic patients were more insulin resistant than their matched controls (mean HOMA IR 2.6 vs 1.8 in controls, P<0.001) and had a poorer beta-cell function (mean HOMA B 75.7 vs. 113.6 in controls, P<0.001). Results showed that 59% of the CpGs analyzed in TCF7L2 promoter had significant differences between type 2 diabetic patients and matched controls. In addition, fasting glucose, HOMA-B, HOMA-IR, total cholesterol and LDL-cholesterol correlated with methylation in specific CpG sites of TCF7L2 promoter. After adjustment by age, BMI, gender, physical inactivity, waist circumference, smoking status and diabetes status uniquely fasting glucose, total cholesterol and LDL-cholesterol remained significant. Taken together, newly diagnosed, drug-naïve type 2 diabetic patients display specific epigenetic changes at the TCF7L2 promoter as compared to age- and BMI-matched controls. Methylation in TCF7L2 promoter is further correlated with fasting glucose in peripheral blood DNA, which sheds new light on the role of epigenetic regulation of TCF7L2 in T2D.

Boundary identification in the domain of a parabolic partial differential equation

Bakgrunden och inspirationen till föreliggande studie är tidigare forskning i tillämpningar på randidentifiering i metallindustrin. Effektiv randidentifiering möjliggör mindre säkerhetsmarginaler och längre serviceintervall för apparaturen i industriella högtemperaturprocesser, utan ökad risk för materielhaverier. I idealfallet vore en metod för randidentifiering baserad på uppföljning av någon indirekt variabel som kan mätas rutinmässigt eller till en ringa kostnad. En dylik variabel för smältugnar är temperaturen i olika positioner i väggen. Denna kan utnyttjas som insignal till en randidentifieringsmetod för att övervaka ugnens väggtjocklek. Vi ger en bakgrund och motivering till valet av den geometriskt endimensionella dynamiska modellen för randidentifiering, som diskuteras i arbetets senare del, framom en flerdimensionell geometrisk beskrivning. I de aktuella industriella tillämpningarna är dynamiken samt fördelarna med en enkel modellstruktur viktigare än exakt geometrisk beskrivning. Lösningsmetoder för den s.k. sidledes värmeledningsekvationen har många saker gemensamt med randidentifiering. Därför studerar vi egenskaper hos lösningarna till denna ekvation, inverkan av mätfel och något som brukar kallas förorening av mätbrus, regularisering och allmännare följder av icke-välställdheten hos sidledes värmeledningsekvationen. Vi studerar en uppsättning av tre olika metoder för randidentifiering, av vilka de två första är utvecklade från en strikt matematisk och den tredje från en mera tillämpad utgångspunkt. Metoderna har olika egenskaper med specifika fördelar och nackdelar. De rent matematiskt baserade metoderna karakteriseras av god noggrannhet och låg numerisk kostnad, dock till priset av låg flexibilitet i formuleringen av den modellbeskrivande partiella differentialekvationen. Den tredje, mera tillämpade, metoden kännetecknas av en sämre noggrannhet förorsakad av en högre grad av icke-välställdhet hos den mera flexibla modellen. För denna gjordes även en ansats till feluppskattning, som senare kunde observeras överensstämma med praktiska beräkningar med metoden. Studien kan anses vara en god startpunkt och matematisk bas för utveckling av industriella tillämpningar av randidentifiering, speciellt mot hantering av olinjära och diskontinuerliga materialegenskaper och plötsliga förändringar orsakade av “nedfallande” väggmaterial. Med de behandlade metoderna förefaller det möjligt att uppnå en robust, snabb och tillräckligt noggrann metod av begränsad komplexitet för randidentifiering.

Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion

Endocrine therapies target the activation of the oestrogen receptor alpha (ERα) via distinct mechanisms, but it is not clear whether breast cancer cells can adapt to treatment using drug-specific mechanisms. Here we demonstrate that resistance emerges via drug-specific epigenetic reprogramming. Resistant cells display a spectrum of phenotypical changes with invasive phenotypes evolving in lines resistant to the aromatase inhibitor (AI). Orthogonal genomics analysis of reprogrammed regulatory regions identifies individual drug-induced epigenetic states involving large topologically associating domains (TADs) and the activation of super-enhancers. AI-resistant cells activate endogenous cholesterol biosynthesis (CB) through stable epigenetic activation in vitro and in vivo. Mechanistically, CB sparks the constitutive activation of oestrogen receptors alpha (ERα) in AI-resistant cells, partly via the biosynthesis of 27-hydroxycholesterol. By targeting CB using statins, ERα binding is reduced and cell invasion is prevented. Epigenomic-led stratification can predict resistance to AI in a subset of ERα-positive patients

Differential Habituation of Male Betta Splendens to Qualitatively Different Stimuli

Habituation is a learning mechanism that functions to decrease the amount of energy and attention focused on a certain stimuli. Male Siamese Fighting Fish, Betta splendens, are territorial animals that defend their territories using a number of aggressive displays. Male Bettas have previously shown the ability to habituate to the presence of a conspecific male when visually exposed to each other. Due to the costly nature of many of the male Betta’s displays, I hypothesized that male Bettas should differentially habituate to qualitatively different stimuli. I presented each of three groups of male Betta splendens with a different stimulus, each presenting a different level of interactivity. I predicted that the Bettas would be more likely to habituate to a less interactive stimulus than a more interactive one. No significant habituation was observed in any of the groups and no significant differences in latency to display or length of display between all three groups were observed. However, overall data trends suggest that habituation was indeed occurring and that the three different stimuli elicited different levels of display. The limited amount of visual exposure to the stimuli in this experiment might account for why results were insignificant.