Evolutionary sequence analysis of complete eukaryote genomes

BACKGROUND: Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation. RESULTS: Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies. CONCLUSION: Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes

Updated Clinical Guidelines for Diagnosing Fetal Alcohol Spectrum Disorders

The adverse effects of prenatal alcohol exposure constitute a continuum of disabilities (fetal alcohol spectrum disorders [FASD]). In 1996, the Institute of Medicine established diagnostic categories delineating the spectrum but not specifying clinical criteria by which diagnoses could be assigned. In 2005, the authors published practical guidelines operationalizing the Institute of Medicine categories, allowing for standardization of FASD diagnoses in clinical settings. The purpose of the current report is to present updated diagnostic guidelines based on a thorough review of the literature and the authors’ combined expertise based on the evaluation of >10 000 children for potential FASD in clinical settings and in epidemiologic studies in conjunction with National Institute on Alcohol Abuse and Alcoholism–funded studies, the Collaborative Initiative on Fetal Alcohol Spectrum Disorders, and the Collaboration on FASD Prevalence. The guidelines were formulated through conference calls and meetings held at National Institute on Alcohol Abuse and Alcoholism offices in Rockville, MD. Specific areas addressed include the following: precise definition of documented prenatal alcohol exposure; neurobehavioral criteria for diagnosis of fetal alcohol syndrome, partial fetal alcohol syndrome, and alcohol-related neurodevelopmental disorder; revised diagnostic criteria for alcohol-related birth defects; an updated comprehensive research dysmorphology scoring system; and a new lip/philtrum guide for the white population, incorporating a 45-degree view. The guidelines reflect consensus among a large and experienced cadre of FASD investigators in the fields of dysmorphology, epidemiology, neurology, psychology, developmental/behavioral pediatrics, and educational diagnostics. Their improved clarity and specificity will guide clinicians in accurate diagnosis of infants and children prenatally exposed to alcohol

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.publishe

Maternal Resolution of Grief After Preterm Birth: Implications for Infant Attachment Security

WHAT’S KNOWN ON THIS SUBJECT: For mothers of children with chronic medical conditions or disabilities, such as epilepsy or cerebral palsy, a history of maternal unresolved grief regarding the child’s diagnosis has been associated with insecure infant-mother attachment. WHAT THIS STUDY ADDS: Unresolved grief related to a preterm birth is associated with the development of insecure infant-mother attachment. Mothers with resolved grief after preterm birth are 2.9 times as likely to have securely attached infants, compared with mothers with unresolved grief. OBJECTIVE: This study explored the association between mothers ’ un-resolved grief regarding their infant’s preterm birth and infant-mother attachment security. We hypothesized that mothers with unresolved grief would be more likely to have insecurely attached infants at 1

The Influence of Early Temperament on Language Development: The Moderating Role of Maternal Input

Temperament is an individual aspect that strictly affects infants and children engagement with the environment and it is supposed to play a role in the acquiring of new competences. Several studies focused on the possible influence of temperament in the process of language acquisition in early childhood reporting not consistent findings. Since maternal input is a variable that has been widely associated with infant language development this longitudinal study aimed to explore the role of the quality of maternal input in the temperament-language association. We hypothesized that the longitudinal association between early infant temperament and language production is moderated by the quality of maternal input during the first year of life. Infant temperament at 3 months and maternal linguistic input (lexical diversity and syntactic complexity) during spontaneous mother–infant interactions at 6, 9, and 12 months were assessed. Language competences were evaluated at the end of the second year: language production at 18 months with the CDI and child syntactic complexity at 24 months during spontaneous speech. Results showed significant moderating effects of syntactic complexity and lexical variability of maternal input at 6 and 9 months on the association of duration of orienting abilities and later language production. Infants with greater attentional abilities and with mothers who spoke to them with a more complex and variable input showed the better language outcomes. The association between infant distress to limitations and child language was not moderated by maternal input. No effects were found when considering the temperamental scale smile and laugher. Attentional control temperamental characteristics could help the infant to be more focus on maternal input throughout the first year of life and could consequently facilitate language development. Our findings underlined the necessity to explore infant development considering the interaction between individual and contextual factors

COVID-19-related state-wise racial and ethnic disparities across the USA: an observational study based on publicly available data from The COVID Tracking Project.

OBJECTIVE: To evaluate COVID-19 infection and mortality disparities in ethnic and racial subgroups in a state-wise manner across the USA. METHODS: Publicly available data from The COVID Tracking Project at The Atlantic were accessed between 9 September 2020 and 14 September 2020. For each state and the District of Columbia, % infection, % death, and % population proportion for subgroups of race (African American/black (AA/black), Asian, American Indian or Alaska Native (AI/AN), and white) and ethnicity (Hispanic/Latino, non-Hispanic) were recorded. Crude and normalised disparity estimates were generated for COVID-19 infection (CDI and NDI) and mortality (CDM and NDM), computed as absolute and relative difference between % infection or % mortality and % population proportion per state. Choropleth map display was created as thematic representation proportionate to CDI, NDI, CDM and NDM. RESULTS: The Hispanic population had a median of 158% higher COVID-19 infection relative to their % population proportion (median 158%, IQR 100%-200%). This was followed by AA, with 50% higher COVID-19 infection relative to their % population proportion (median 50%, IQR 25%-100%). The AA population had the most disproportionate mortality, with a median of 46% higher mortality than the % population proportion (median 46%, IQR 18%-66%). Disproportionate impact of COVID-19 was also seen in AI/AN and Asian populations, with 100% excess infections than the % population proportion seen in nine states for AI/AN and seven states for Asian populations. There was no disproportionate impact in the white population in any state. CONCLUSIONS: There are racial/ethnic disparities in COVID-19 infection/mortality, with distinct state-wise patterns across the USA based on racial/ethnic composition. There were missing and inconsistently reported racial/ethnic data in many states. This underscores the need for standardised reporting, attention to specific regional patterns, adequate resource allocation and addressing the underlying social determinants of health adversely affecting chronically marginalised groups