Search for: All records

Understanding and mitigating the e ects of our ongoing biodiversity crisis requires a deep-time perspective on how ecosystems recover in the aftermath of environmental catastrophes. The mass extinction event at the Cretaceous/Paleogene (K/Pg) boundary (ca. 66 Ma) represents a natural laboratory wherein the tempo and mode of biotic recovery can be studied with high chronostratigraphic resolution. Although the morphological evolution of mammals across this event has been reconstructed from skeletal remains, the exact nature of any changes in dietary preference remains unknown. A primary goal here is to fill this gap by investigating how ecological preferences of mammals, reflected by diet, changed from the Late Cretaceous, when they shared landscapes with dinosaurs, to the earliest Paleogene, when they did not. To accomplish this, carbon and oxygen isotope ratios of fossil tooth enamel (bioapatite) were measured using laserablation mass spectrometry in order to infer animal diet and drinking water sources, which vary depending on the niche occupied by an animal. Fossil teeth were collected from two sites located within 400 meters of one another within the West Bijou Creek field area of the Denver Basin, one 9 meters (~128 ky pre-K/Pg) below the boundary (teeth from ceratopsian and hadrosaurid dinosaurs and the multituberculate mammal Mesodma, as well as gar fish scales), and the other 4 meters (~57 ky post-K/Pg) above (Mesodma teeth and gar fish scales). Carbon isotope ratios (δ13C) of Mesodma tooth enamel vary significantly across the K/Pg boundary, with Late Cretaceous teeth having lower and more variable δ13C (-10.1 to -16.4‰, n=4) and early Paleocene teeth having higher and less variable δ13C (-5.3 to 9.0 ‰, n=5), the latter being similar to values for Late Cretaceous dinosaurs. These results suggest Mesodma had very di erent dietary behaviors following the extinction event, presumably a result of the disappearance of non-avian dinosaurs as well as 57% of North American plants, both of which made new food sources and niches available to them. These results also hint at a decoupling of behavioral change from morphological change, at least in the case of Mesodma, over 10 ky timescales. Isotopic analysis of teeth from other Late Cretaceous and earliest Paleogene mammalian taxa is ongoing and will hopefully allow for more detailed interpretations of ecological change across the K/Pg extinction event in the Denver Basin. 

Abstract BackgroundCost-effective production of biofuels from lignocellulose requires the fermentation ofd-xylose. Many yeast species within and closely related to the generaSpathasporaandScheffersomyces(both of the order Serinales) natively assimilate and ferment xylose. Other species consume xylose inefficiently, leading to extracellular accumulation of xylitol. Xylitol excretion is thought to be due to the different cofactor requirements of the first two steps of xylose metabolism. Xylose reductase (XR) generally uses NADPH to reduce xylose to xylitol, while xylitol dehydrogenase (XDH) generally uses NAD⁺to oxidize xylitol to xylulose, creating an imbalanced redox pathway. This imbalance is thought to be particularly consequential in hypoxic or anoxic environments. ResultsWe screened the growth of xylose-fermenting yeast species in high and moderate aeration and identified both ethanol producers and xylitol producers. Selected species were further characterized for their XR and XDH cofactor preferences by enzyme assays and gene expression patterns by RNA-Seq. Our data revealed that xylose metabolism is more redox balanced in some species, but it is strongly affected by oxygen levels. Under high aeration, most species switched from ethanol production to xylitol accumulation, despite the availability of ample oxygen to accept electrons from NADH. This switch was followed by decreases in enzyme activity and the expression of genes related to xylose metabolism, suggesting that bottlenecks in xylose fermentation are not always due to cofactor preferences. Finally, we expressedXYLgenes from multipleScheffersomycesspecies in a strain ofSaccharomyces cerevisiae. RecombinantS. cerevisiaeexpressingXYL1fromScheffersomyces xylosifermentans, which encodes an XR without a cofactor preference, showed improved anaerobic growth on xylose as the primary carbon source compared toS. cerevisiaestrain expressingXYLgenes fromScheffersomyces stipitis. ConclusionCollectively, our data do not support the hypothesis that xylitol accumulation occurs primarily due to differences in cofactor preferences between xylose reductase and xylitol dehydrogenase; instead, gene expression plays a major role in response to oxygen levels. We have also identified the yeastSc. xylosifermentansas a potential source for genes that can be engineered intoS. cerevisiaeto improve xylose fermentation and biofuel production. 

Abstract The amplification and diversification of genes into large multi-gene families often mark key evolutionary innovations, but this process often creates genetic redundancy that hinders functional investigations. When the model budding yeast Saccharomyces cerevisiae transitions to anaerobic growth conditions, the cell massively induces the expression of seven serine/threonine-rich anaerobically-induced cell wall mannoproteins (anCWMPs): TIP1, TIR1, TIR2, TIR3, TIR4, DAN1, and DAN4. Here, we show that these genes likely derive evolutionarily from a single ancestral anCWMP locus, which was duplicated and translocated to new genomic contexts several times both prior to and following the budding yeast whole genome duplication (WGD) event. Based on synteny and their phylogeny, we separate the anCWMPs into four gene subfamilies. To resolve prior inconclusive genetic investigations of these genes, we constructed a set of combinatorial deletion mutants to determine their contributions toward anaerobic growth in S. cerevisiae. We found that two genes, TIR1 and TIR3, were together necessary and sufficient for the anCWMP contribution to anaerobic growth. Overexpressing either gene alone was insufficient for anaerobic growth, implying that they encode non-overlapping functional roles in the cell during anaerobic growth. We infer from the phylogeny of the anCWMP genes that these two important genes derive from an ancient duplication that predates the WGD event, whereas the TIR1 subfamily experienced gene family amplification after the WGD event. Taken together, the genetic and molecular evidence suggests that one key anCWMP gene duplication event, several auxiliary gene duplication events, and functional divergence underpin the evolution of anaerobic growth in budding yeasts.