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Background: It is critical to understand the wide-ranging clinical and non-clinical effects of genome sequencing (GS) for parents in the NICU context. We assessed parents’ experiences with GS as a first-line diagnostic tool for infants with suspected genetic conditions in the NICU. Methods: Parents of newborns (N = 62) suspected of having a genetic condition were recruited across five hospitals in the southeast United States as part of the SouthSeq study. Semi-structured interviews (N = 78) were conducted after parents received their child’s sequencing result (positive, negative, or variants of unknown significance). Thematic analysis was performed on all interviews. Results: Key themes included that (1) GS in infancy is important for reproductive decision making, preparing for the child’s future care, ending the diagnostic odyssey, and sharing results with care providers; (2) the timing of disclosure was acceptable for most parents, although many reported the NICU environment was overwhelming; and (3) parents deny that receiving GS results during infancy exacerbated parent–infant bonding, and reported variable impact on their feelings of guilt. Conclusion: Parents reported that GS during the neonatal period was useful because it provided a “backbone” for their child’s care. Parents did not consistently endorse negative impacts like interference with parent–infant bonding.

Since Antonie van Leeuwenhoek first observed microbes, we have come to learn that life on our planet includes not only the macroscopic lifeforms visible to the unaided eye that Charles Darwin studied but also an immense diversity of microbes (Fig 1). We have learned that microorganisms influence nearly every aspect of human existence with beneficial or detrimental effects. With their pivotal roles in biomass conversion, biogeochemical cycles, photosynthesis, and in promoting plant growth, life on this planet ultimately depends on the activities of microorganisms. On the other hand, microorganisms are the etiological agents of many diseases in humans, animals, and plants, causing massive economic losses yearly. Microorganisms also contribute significantly to the production of greenhouse gases such as CO2 and CH4 and, thus, contribute to global warming. In the past decade, we have also learned that microorganisms inhabiting the human body, i.e., the human microbiome, have profound effects on human physiology. Not to forget, some of our most delicious food products and beverages get their distinct qualities from microorganisms, and the pharmaceutical and biotechnological industry relies heavily on microbes. In terms of research, many technological breakthroughs in molecular biology, such as DNA cloning, PCR, and CRISPR-Cas technologies have their origin in microbes. Therefore, research in microbiology is as important now as it ever was.

PURPOSE: SouthSeq is a translational research study that performed genome sequencing (GS) for infants with symptoms suggestive of a genetic disorder. Recruitment targeted racial/ethnic minorities and rural, medically underserved areas in the Southeastern US that are historically under-represented in genomic medicine research. METHODS: GS and analysis were performed for 367 infants to detect disease-causal variation concurrent with standard of care evaluation and testing. RESULTS: Definitive diagnostic (DD) or likely diagnostic (LD) genetic findings were identified in 30% of infants and 14% harbored an uncertain result. Only 43% of DD/LD findings were identified via concurrent clinical genetic testing suggesting that GS testing is better for obtaining early genetic diagnosis. We also identified phenotypes that correlate with the likelihood of receiving a DD/LD finding, such as craniofacial, ophthalmologic, auditory, skin, and hair abnormalities. We did not observe any differences in diagnostic rates between racial/ethnic groups. CONCLUSION: We describe one of the largest-to-date GS cohorts of ill infants, enriched for African American and rural patients. Our results demonstrate the utility of GS as it provides early in life detection of clinically relevant genetic variation not identified via current clinical genetic testing, particularly for infants exhibiting certain phenotypic features.

SummaryThe Bengal cat breed was developed from intercrosses between the Asian leopard cat,Prionailurus bengalensis, and the domestic cat,Felis silvestris catus, with a last common ancestor 6 million years ago. Predicted to contain ~95% of their genome from domestic cats, regions of the leopard cat genome are thought to account for unique pelage traits and ornate color patterns of the Bengal breed, which are similar to those of ocelots and jaguars. We explore ancestry distribution and selection signatures in the Bengal breed using reduced representation and whole genome sequencing from 905 cats. Overall, leopard cat introgressions are reduced twofold from expectation and include examples of genetic incompatibility—reduced expression of a leopard cat gene in a domestic cat background—underlying the color traitsCharcoaland contributing to coat color variation. Leopard cat introgressions do not show strong signatures of selection; instead, selective sweeps in Bengal cats are associated with domestic, rather than leopard cat haplotypes, and harbor candidate genes for pelage and color pattern. We identify the molecular and phenotypic basis of one selective sweep as reduced expression of theFgfr2gene, which underliesGlitter, a desirable trait that affects hair texture and light reflectivity.

SUMMARYColor variation is a frequent evolutionary substrate for camouflage in small mammals but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus, exhibits a range of colors including the cinnamon morph which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (P < 10−13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that impaired protein localization and decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos, but is not fixed across the range.HIGHLIGHTSThe cinnamon morph of American black bears and brown bears have different missense mutations in TYRP1 that account for their similar colorationTYRP1 variants in American black bears and brown bears are loss-of-function alleles associated with impaired protein localization to melanosomesIn American black bears, the variant causing the cinnamon morph arose 9,360 years ago in the western lineage where it provides an adaptive advantage, and has spread northwards and eastwards by migration

Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC’s ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life., Larison et al. report epigenetic aging models in plains zebras (Equus quagga) using the epigenetic clock and epigenetic pacemaker approaches. Their epigenetic clock allows age to be accurately estimated in endangered sister species, and the pacemaker model identifies an association between inbreeding and accelerating aging.