Male reproductive traits are differentially affected by dietary macronutrient balance but unrelated to adiposity.

Dietary factors influence male reproductive function in both experimental and epidemiological studies. However, there are currently no specific dietary guidelines for male preconception health. Here, we use the Nutritional Geometry framework to examine the effects of dietary macronutrient balance on reproductive traits in C57BL/6 J male mice. Dietary effects are observed in a range of morphological, testicular and spermatozoa traits, although the relative influence of protein, fat, carbohydrate, and their interactions differ depending on the trait being examined. Interestingly, dietary fat has a positive influence on sperm motility and antioxidant capacity, differing to typical high fat diet studies where calorie content is not controlled for. Moreover, body adiposity is not significantly correlated with any of the reproductive traits measured in this study. These results demonstrate the importance of macronutrient balance and calorie intake on reproductive function and support the need to develop specific, targeted, preconception dietary guidelines for males.

Multimorbidity, depression with anxiety symptoms, and decrements in health in 47 low- and middle-income countries.

BACKGROUND: Comorbid depression and anxiety is associated with worse health outcomes compared to depression or anxiety occurring in isolation, but there is little data on its association with multimorbidity. Thus, we investigated this association across 47 low- and middle-income countries, and further explored whether having anxiety symptoms in addition to depression is associated with significant declines in health outcomes among those with multimorbidity. METHODS: Cross-sectional, predominantly nationally representative, community-based data were analyzed from the World Health Survey. DSM-IV depression was assessed with the Composite International Diagnostic Interview. Anxiety symptoms referred to severe/extreme problems with worry or anxiety. Ten chronic conditions and health status across five domains (cognition, interpersonal activities, sleep/energy, self-care, pain/discomfort) were assessed. Multivariable regression analyses conducted. RESULTS: Data included 237,952 adults aged ≥18 years [mean age (SD) 38.4 (16.0); 50.8 % females]. Compared to no chronic conditions, 2 (OR = 6.86; 95%CI = 5.59-8.42), 3 (OR = 12.33; 95%CI = 9.72-15.63), and ≥4 (OR = 26.55; 95%CI = 20.21-35.17) chronic conditions were associated with significantly higher odds for comorbid depression/anxiety symptoms (vs. no depression or anxiety symptoms) in the multinomial logistic regression model. Among those with depression and multimorbidity, anxiety symptoms were associated with significantly worse health status across all domains. LIMITATIONS: Cross-sectional design, depression and anxiety symptoms were not based on a clinical assessment. CONCLUSIONS: Comorbid depression/anxiety is common in people with multimorbidity, and anxiety symptoms in people with depression and multimorbidity signify worse health status. Future studies should assess the utility of screening for and treating comorbid depression/anxiety in patients with multimorbidity in terms of clinical outcomes.

Thirty-day suicidal thoughts and behaviours in the Spanish adult general population during the first wave of the Spain COVID-19 pandemic.

AIMS: To investigate the prevalence of suicidal thoughts and behaviours (STB; i.e. suicidal ideation, plans or attempts) in the Spanish adult general population during the first wave of the Spain coronavirus disease 2019 (COVID-19) pandemic (March-July, 2020), and to investigate the individual- and population-level impact of relevant distal and proximal STB risk factor domains. METHODS: Cross-sectional study design using data from the baseline assessment of an observational cohort study (MIND/COVID project). A nationally representative sample of 3500 non-institutionalised Spanish adults (51.5% female; mean age = 49.6 [s.d. = 17.0]) was taken using dual-frame random digit dialing, stratified for age, sex and geographical area. Professional interviewers carried out computer-assisted telephone interviews (1-30 June 2020). Thirty-day STB was assessed using modified items from the Columbia Suicide Severity Rating Scale. Distal (i.e. pre-pandemic) risk factors included sociodemographic variables, number of physical health conditions and pre-pandemic lifetime mental disorders; proximal (i.e. pandemic) risk factors included current mental disorders and a range of adverse events-experiences related to the pandemic. Logistic regression was used to investigate individual-level associations (odds ratios [OR]) and population-level associations (population attributable risk proportions [PARP]) between risk factors and 30-day STB. All data were weighted using post-stratification survey weights. RESULTS: Estimated prevalence of 30-day STB was 4.5% (1.8% active suicidal ideation; n = 5 [0.1%] suicide attempts). STB was 9.7% among the 34.3% of respondents with pre-pandemic lifetime mental disorders, and 1.8% among the 65.7% without any pre-pandemic lifetime mental disorder. Factors significantly associated with STB were pre-pandemic lifetime mental disorders (total PARP = 49.1%) and current mental disorders (total PARP = 58.4%), i.e. major depressive disorder (OR = 6.0; PARP = 39.2%), generalised anxiety disorder (OR = 5.6; PARP = 36.3%), post-traumatic stress disorder (OR = 4.6; PARP = 26.6%), panic attacks (OR = 6.7; PARP = 36.6%) and alcohol/substance use disorder (OR = 3.3; PARP = 5.9%). Pandemic-related adverse events-experiences associated with STB were lack of social support, interpersonal stress, stress about personal health and about the health of loved ones (PARPs 32.7-42.6%%), and having loved ones infected with COVID-19 (OR = 1.7; PARP = 18.8%). Up to 74.1% of STB is potentially attributable to the joint effects of mental disorders and adverse events-experiences related to the pandemic. CONCLUSIONS: STB at the end of the first wave of the Spain COVID-19 pandemic was high, and large proportions of STB are potentially attributable to mental disorders and adverse events-experiences related to the pandemic, including health-related stress, lack of social support and interpersonal stress. There is an urgent need to allocate resources to increase access to adequate mental healthcare, even in times of healthcare system overload. STUDY REGISTRATION NUMBER: NCT04556565.

Efeitos da ocratoxina no desempenho do camarão-branco-do-pacífico (Litopenaeus vannamei, Bonne) / The effects of ochratoxina in performance pacific white shrimp (Litopenaeus vannamei Bonne)

A ocratoxina é um dos maiores grupos de micotoxinas; são metabólitos secundários produzidos principalmente por fungos dos gêneros Aspergillus e Penicillium. Possui propriedades tóxicas e nefrotóxicas, está relacionada à nefropatia endêmica dos Bálcãs, a tumores do trato urinário e foi classificada pela Agência Internacional de Pesquisa do Câncer (IARC) como pertencente ao grupo 2B, por ser possivelmente carcinogênica para humanos. O objetivo do presente estudo foi avaliar os efeitos da ocratoxina A (OTA) no desempenho do camarão-branco-do-pacífico (Litopenaues vannamei). O experimento foi feito simulando o manejo produtivo de uma fazenda de camarão marinho do litoral localizada em Luís Correia, Piauí. Foram utilizados cinco tratamentos com diferentes níveis de micotoxinas: T1- 100µg/kg de OTA; T2- 500µg/kg de OTA; T3- 1000µg/kg de OTA; T4- 100µg/kg de OTA e 500µg/kg afatoxina B1 e T5 - 0,0µg/kg de OTA. A produção de OTA foi realizada por meio da fermentação do milho, utilizando-se a cepa de Aspergillus ochraceus. Rações comerciais foram contaminadas com os núcleos de milho. A detecção e a quantificação de OTA dos núcleos, das rações comerciais e dos tecidos do camarão (cefalotórax e abdome) foram realizadas por cromatografia líquida de alta eficiência (CLAE). Para simular o sistema de criação da fazenda, os animais foram cultivados por um período de oito semanas, sendo 20 animais por caixa, recebendo alimentação duas vezes por dia. O menor ganho de peso observado foi no T2 e no T4 e os maiores ganhos de peso foram obtidos no T1 e no T5, que também apresentaram a melhor conversão alimentar. Após 56 dias de experimento, foi detectada OTA residual nas amostras de abdome apenas nos camarões do T1. Logo, camarões alimentados com rações contaminadas com OTA têm seu desempenho produtivo comprometido, o que gera impactos econômicos negativos para a indústria carcinicultora, além de ser um risco à saúde do consumidor, devido aos resíduos em sua musculatura.(AU)

Ochratoxin A is the second largest group of mycotoxins. It is a secondary metabolite produced mainly by fungi of the genera Aspergillus and Penicillium, and has toxic and nephrotoxic properties that are associated with the Balkan endemic nephropathy and urinary tract tumors. The International Agency for Research on Cancer (IARC) classifies it as group 2B: possibly carcinogenic to humans. The aim of this study was to evaluate the effects of ochratoxin A (OTA) on the performance of the Pacific white shrimp (Litopenaues vannamei). The experiment simulated the productive management of a shrimp farm located on the marine coast of Luis Correia, Piauí State. Five treatments with different levels of mycotoxins were used: T1- 100µg/kg of OTA; T2- 500µg/kg of OTA; T3 - 1000µg/kg of OTA; T4- 100µg/kg of OTA and 500µg/kg afatoxina B1 and T5 - 0.0µg/kg of OTA. OTA was produced by fermenting corn, using the Aspergillus ochraceus strain. Commercial feeds were contaminated with the corn kernels. OTA in the kernels, commercial feeds and shrimp tissues (cephalothorax and abdomen) were detected and quantified via high performance liquid chromatography (HPLC). To simulate the farming system, totaling 20 animals per box. The animals were fed twice a day and raised under these conditions for eight weeks. The shrimp gained weight during the weeks of the test, when subjected to different OTA treatments. The lowest weight gain was observed in T2 and T4 and the highest weight gains were in T1 and T5, which also presented the best feed conversion ratio. After 56 days, residual OTA was detected in samples of shrimp abdomen only in T1. Therefore, the productive performance of shrimp that are fed with OTA-contaminated feed is compromised, which has a negative economic impact on the shrimp industry, and is a health risk to consumers due to residues in the muscles.(AU)

Pap test accuracy and severity of squamous intraepithelial lesion.

BACKGROUND: Cytology smears and guided biopsies are the most widely used diagnostic standards for cervical cancer (CC) screening in the developing countries. AIM: To evaluate the performance of conventional cytology in estimating the presence and grade of cervical disease against the reference standard of histopathology. SETTINGS AND DESIGN: After primary screening for CC, directed biopsies were performed and compared with histopathology results. MATERIALS AND METHODS: Papanicolaou (Pap) smears and biopsies from 3194 women in the age group of 14-98 years were included. Cytology results were provided by doctors who performed the cervical biopsies. STATISTICAL ANALYSIS: The accuracy of Pap smear was measured by sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) calculated using the statistical analysis program PSPP 0.7.8. RESULTS: The sensitivity of conventional cytology (Pap smear) for women with low-grade cervical intraepithelial neoplasia or less serious lesions (CIN1-) was 93% and specificity was 73%. The sensitivity and specificity of cytology for women with high-grade cervical intraepithelial neoplasia or cancer (CIN2+) was 64% and 84%, respectively. CONCLUSION: Cytology is a sufficiently sensitive test for detection of cervical lesions and can be used as a primary testing tool to triage.

Landscape structure in the Pirapó, Paranapanema 3 and 4 Hydrographic Unit, in the state of Paraná, Brazil.

The aim of this study is to characterize the Pirapó, Paranapanema 3 and 4 Hydrographic Unit, emphasizing its physical attributes and processes of use and occupation, responsible for the structure of the current landscape and the state of its water resources. The recognition of the landscape's spatial structure in the hydrographic unit and its drainage basins was obtained by integrated analysis of the main elements that compose it: geology, landforms (hypsometric and slope), soils, climate and land use. Analysis revealed that within each drainage basin several variations in the spatial structure of the landscape occur which produce an internal compartmentalization. Each compartment is defined by its own geo-ecological structure, physiognomic standards and dynamics, reflected in its potentialities and vulnerabilities and in the conditions of water resources in the wake of occupation and use over time.

Landscape structure in the Pirapó, Paranapanema 3 and 4 Hydrographic Unit, in the state of Paraná, Brazil / Estrutura da paisagem na Unidade Hidrográfica Pirapó, Paranapanema 3 e 4, no estado do Paraná, Brasil

The aim of this study is to characterize the Pirapó, Paranapanema 3 and 4 Hydrographic Unit, emphasizing its physical attributes and processes of use and occupation, responsible for the structure of the current landscape and the state of its water resources. The recognition of the landscape’s spatial structure in the hydrographic unit and its drainage basins was obtained by integrated analysis of the main elements that compose it: geology, landforms (hypsometric and slope), soils, climate and land use. Analysis revealed that within each drainage basin several variations in the spatial structure of the landscape occur which produce an internal compartmentalization. Each compartment is defined by its own geo-ecological structure, physiognomic standards and dynamics, reflected in its potentialities and vulnerabilities and in the conditions of water resources in the wake of occupation and use over time.

Resumo O objetivo deste trabalho é caracterizar a Unidade Hidrográfica do Pirapó, Paranapanema 3 e 4, ressaltando os seus atributos físicos e os processos de uso e ocupação, responsáveis pela estrutura da paisagem atual e pelo estado dos seus recursos hídricos. O reconhecimento da estrutura espacial da paisagem na unidade hidrográfica e nas suas bacias foi obtido por meio da análise integrada dos principais elementos que a compõe: geologia, relevo, solos, clima e uso da terra. A análise mostrou que no interior de cada bacia hidrográfica ocorrem variações na estrutura espacial da paisagem que produzem uma compartimentação interna. Cada compartimento se define por uma estrutura geoecológica, padrões fisionômicos e dinâmicos próprios o que se reflete nas suas potencialidades e vulnerabilidades e nas condições dos seus recursos hídricos, em face das formas de ocupação e uso ao longo do tempo.

Landscape structure in the Pirapó, Paranapanema 3 and 4 Hydrographic Unit, in the state of Paraná, Brazil

The aim of this study is to characterize the Pirapó, Paranapanema 3 and 4 Hydrographic Unit, emphasizing its physical attributes and processes of use and occupation, responsible for the structure of the current landscape and the state of its water resources. The recognition of the landscapes spatial structure in the hydrographic unit and its drainage basins was obtained by integrated analysis of the main elements that compose it: geology, landforms (hypsometric and slope), soils, climate and land use. Analysis revealed that within each drainage basin several variations in the spatial structure of the landscape occur which produce an internal compartmentalization. Each compartment is defined by its own geo-ecological structure, physiognomic standards and dynamics, reflected in its potentialities and vulnerabilities and in the conditions of water resources in the wake of occupation and use over time.

Resumo O objetivo deste trabalho é caracterizar a Unidade Hidrográfica do Pirapó, Paranapanema 3 e 4, ressaltando os seus atributos físicos e os processos de uso e ocupação, responsáveis pela estrutura da paisagem atual e pelo estado dos seus recursos hídricos. O reconhecimento da estrutura espacial da paisagem na unidade hidrográfica e nas suas bacias foi obtido por meio da análise integrada dos principais elementos que a compõe: geologia, relevo, solos, clima e uso da terra. A análise mostrou que no interior de cada bacia hidrográfica ocorrem variações na estrutura espacial da paisagem que produzem uma compartimentação interna. Cada compartimento se define por uma estrutura geoecológica, padrões fisionômicos e dinâmicos próprios o que se reflete nas suas potencialidades e vulnerabilidades e nas condições dos seus recursos hídricos, em face das formas de ocupação e uso ao longo do tempo.

Spatial and temporal variation in artisanal catches of dolphinfish Coryphaena hippurus off north-eastern Brazil.

The sampling of fish from the artisanal fleet operating with surface lines off north-eastern Brazil was carried out between 1998 and 2000. Generalized linear models (GLMs) were used to standardize mean abundance indices using catch and fishing effort data on dolphinfish Coryphaena hippurus and to identify abundance trends in time and space, using 1215 surface line deployments. A standard relative abundance index (catch per unit effort, CPUE) was estimated for the most frequent vessels used in the sets, employing factors and coefficients generated in the GLMs. According to the models, C. hippurus catches are affected by the operating characteristics and power of different fishing vessels. These differences highlight the need for standardization of catch and effort data for artisanal fisheries. The highest mean abundance values for C. hippurus were off the state of Rio Grande do Norte, with an increasing tendency in areas with greater depths and more distant from the coast, reaching maximal values in areas whose depths range from 200 to 500 m. The highest mean abundance values occurred between April and June. The higher estimated abundance of C. hippurus in this period off the state of Rio Grande do Norte and within the 200-500 m depth range may be related to a migration pattern of food sources, as its main prey, the flying fish Hirundichthys affinis, uses floating algae as refuge and to deposit its pelagic eggs.

PU.1 is essential for MLL leukemia partially via crosstalk with the MEIS/HOX pathway.

Mixed lineage leukemia (MLL) fusion proteins directly activate the expression of key downstream genes such as MEIS1, HOXA9 to drive an aggressive form of human leukemia. However, it is still poorly understood what additional transcriptional regulators, independent of the MLL fusion pathway, contribute to the development of MLL leukemia. Here we show that the transcription factor PU.1 is essential for MLL leukemia and is required for the growth of MLL leukemic cells via the promotion of cell-cycle progression and inhibition of apoptosis. Importantly, PU.1 expression is not under the control of MLL fusion proteins. We further identified a PU.1-governed 15-gene signature, which contains key regulators in the MEIS-HOX program (MEIS1, PBX3, FLT3, and c-KIT). PU.1 directly binds to the genomic loci of its target genes in vivo, and is required to maintain active expression of those genes in both normal hematopoietic stem and progenitor cells and in MLL leukemia. Finally, the clinical significance of the identified PU.1 signature was indicated by its ability to predict survival in acute myelogenous leukemia patients. Together, our findings demonstrate that PU.1 contributes to the development of MLL leukemia, partially via crosstalk with the MEIS/HOX pathway.

Regulation of MEIS1 by distal enhancer elements in acute leukemia.

Aberrant activation of the three-amino-acid-loop extension homeobox gene MEIS1 shortens the latency and accelerates the onset and progression of acute leukemia, yet the molecular mechanism underlying persistent activation of the MEIS1 gene in leukemia remains poorly understood. Here we used a combined comparative genomics analysis and an in vivo transgenic zebrafish assay to identify six regulatory DNA elements that are able to direct green fluorescent protein expression in a spatiotemporal manner during zebrafish embryonic hematopoiesis. Analysis of chromatin characteristics and regulatory signatures suggests that many of these predicted elements are potential enhancers in mammalian hematopoiesis. Strikingly, one of the enhancer elements (E9) is a frequent integration site in retroviral-induced mouse acute leukemia. The genomic region corresponding to enhancer E9 is differentially marked by H3K4 monomethylation and H3K27 acetylation, hallmarks of active enhancers, in multiple leukemia cell lines. Decreased enrichment of these histone marks is associated with downregulation of MEIS1 expression during hematopoietic differentiation. Further, MEIS1/HOXA9 transactivate this enhancer via a conserved binding motif in vitro, and participate in an autoregulatory loop that modulates MEIS1 expression in vivo. Our results suggest that an intronic enhancer regulates the expression of MEIS1 in hematopoiesis and contributes to its aberrant expression in acute leukemia.

Mixture design applied for the study of the tartaric acid effect on starch/polyester films.

Tartaric acid (TA), a dicarboxylic acid, can act as a compatibiliser in starch/polyester blends. A mixture design was proposed to evaluate the effect of TA on the properties of starch/poly (butylene adipate co-terephthalate) (PBAT) blown films plasticised with glycerol. The interaction between the starch/PBAT and the TA has a positive effect on the tensile strength and puncture force. Additionally, greater proportions of TA increased Young's modulus. The starch+PBAT/TA and Gly/TA interactions contributed to a reduction in the water vapour permeability of the films. The inclusion of TA did not change the crystallinity of the samples. Formulations with intermediate proportions of TA (0.8 g/100 g) were shown to produce the best compatibilising effect. This was observed by DMA analysis as a consequence of the perfect equilibrium between the contributions of TA as a compatibiliser and in the acidolysis of starch, resulting in films with a tensile strength of 5.93 MPa, a possible alternative to non-biodegradable packaging.

In vitro scan for enhancers at the TCF7L2 locus.

AIMS/HYPOTHESIS: Recent functional characterisations of genome-wide association study (GWAS) loci suggest that cis-regulatory variation may be a common paradigm for complex disease susceptibility. Several studies point to a similar mechanism at the transcription factor 7-like 2 (TCF7L2) GWAS locus for type 2 diabetes. To address this possibility, we carried out an in vitro scan of this diabetes-associated locus to fine-map cis-regulatory sequences within this genomic interval. METHODS: A systematic cell-based enhancer strategy was employed to interrogate all sequences within the 92 kb type-2-diabetes-association interval for cis-regulatory activity in a panel of cell lines (HCT-116, Neuro-2a, C2C12, U2OS, MIN6 and HepG2). We further evaluated chromatin state at a subset of these regions in HCT-116 and U2OS cells and examined allelic-specific enhancer properties at the type-2-diabetes-associated single nucleotide polymorphism (SNP) rs7903146. RESULTS: In total, we assigned cis-regulatory activity to approximately 30% (9/28) of constructs tested. Notably, a subset of enhancers was active across multiple cell lines and overlapped with key epigenetic markers suggestive of cis-regulatory sequences. We further replicated the allelic-specific properties for SNP rs7903146 in pancreatic beta cells and additionally demonstrate identical allelic-specific enhancer effects in other cell lines. CONCLUSIONS: These results provide a detailed map of cis-regulatory elements within the TCF7L2 GWAS locus and support the hypothesis of cis-regulatory variation leading to type 2 diabetes predisposition. The detection of allelic-specific effects for SNP rs7903146 in multiple cell lines further alludes to the likelihood of a peripheral defect in disease aetiology.

Genomics and proteomics approaches to the study of cancer-stroma interactions.

BACKGROUND: The development and progression of cancer depend on its genetic characteristics as well as on the interactions with its microenvironment. Understanding these interactions may contribute to diagnostic and prognostic evaluations and to the development of new cancer therapies. Aiming to investigate potential mechanisms by which the tumor microenvironment might contribute to a cancer phenotype, we evaluated soluble paracrine factors produced by stromal and neoplastic cells which may influence proliferation and gene and protein expression. METHODS: The study was carried out on the epithelial cancer cell line (Hep-2) and fibroblasts isolated from a primary oral cancer. We combined a conditioned-medium technique with subtraction hybridization approach, quantitative PCR and proteomics, in order to evaluate gene and protein expression influenced by soluble paracrine factors produced by stromal and neoplastic cells. RESULTS: We observed that conditioned medium from fibroblast cultures (FCM) inhibited proliferation and induced apoptosis in Hep-2 cells. In neoplastic cells, 41 genes and 5 proteins exhibited changes in expression levels in response to FCM and, in fibroblasts, 17 genes and 2 proteins showed down-regulation in response to conditioned medium from Hep-2 cells (HCM). Nine genes were selected and the expression results of 6 down-regulated genes (ARID4A, CALR, GNB2L1, RNF10, SQSTM1, USP9X) were validated by real time PCR. CONCLUSIONS: A significant and common denominator in the results was the potential induction of signaling changes associated with immune or inflammatory response in the absence of a specific protein.

Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome.

BACKGROUND: Recurrent 15q13.3 microdeletions were recently identified with identical proximal (BP4) and distal (BP5) breakpoints and associated with mild to moderate mental retardation and epilepsy. METHODS: To assess further the clinical implications of this novel 15q13.3 microdeletion syndrome, 18 new probands with a deletion were molecularly and clinically characterised. In addition, we evaluated the characteristics of a family with a more proximal deletion between BP3 and BP4. Finally, four patients with a duplication in the BP3-BP4-BP5 region were included in this study to ascertain the clinical significance of duplications in this region. RESULTS: The 15q13.3 microdeletion in our series was associated with a highly variable intra- and inter-familial phenotype. At least 11 of the 18 deletions identified were inherited. Moreover, 7 of 10 siblings from four different families also had this deletion: one had a mild developmental delay, four had only learning problems during childhood, but functioned well in daily life as adults, whereas the other two had no learning problems at all. In contrast to previous findings, seizures were not a common feature in our series (only 2 of 17 living probands). Three patients with deletions had cardiac defects and deletion of the KLF13 gene, located in the critical region, may contribute to these abnormalities. The limited data from the single family with the more proximal BP3-BP4 deletion suggest this deletion may have little clinical significance. Patients with duplications of the BP3-BP4-BP5 region did not share a recognisable phenotype, but psychiatric disease was noted in 2 of 4 patients. CONCLUSIONS: Overall, our findings broaden the phenotypic spectrum associated with 15q13.3 deletions and suggest that, in some individuals, deletion of 15q13.3 is not sufficient to cause disease. The existence of microdeletion syndromes, associated with an unpredictable and variable phenotypic outcome, will pose the clinician with diagnostic difficulties and challenge the commonly used paradigm in the diagnostic setting that aberrations inherited from a phenotypically normal parent are usually without clinical consequences.

Automated construction of high-density comparative maps between rat, human, and mouse.

Animal models have been used primarily as surrogates for humans, having similar disease-based phenotypes. Genomic organization also tends to be conserved between species, leading to the generation of comparative genome maps. The emergence of radiation hybrid (RH) maps, coupled with the large numbers of available Expressed Sequence Tags (ESTs), has revolutionized the way comparative maps can be built. We used publicly available rat, mouse, and human data to identify genes and ESTs with interspecies sequence identity (homology), identified their UniGene relationships, and incorporated their RH map positions to build integrated comparative maps with >2100 homologous UniGenes mapped in more than one species (approximately 6% of all mammalian genes). The generation of these maps is iterative and labor intensive; therefore, we developed a series of computer tools (not described here) based on our algorithm that identifies anchors between species and produces printable and on-line clickable comparative maps that link to a wide variety of useful tools and databases. The maps were constructed using sequence-based comparisons, thus creating "hooks" for further sequence-based annotation of human, mouse, and rat sequences. Currently, this map enables investigators to link the physiology of the rat with the genetics of the mouse and the clinical significance of the human.