Search for: All records

Genomic data can provide valuable insights into the evolutionary history of rapidly diversifying groups and the genetic basis of phenotypic differences among lineages. We used whole-genome sequencing of the warbler genus Myioborus to investigate dynamics of its recent diversification in Neotropical mountains. We found that mitochondrial and UCE phylogenies are mostly, but not fully, concordant, and we found phylogenetic support for a pattern of north-to-south and low-to-high elevation colonization in the genus. Within the ornatus-melanocephalus complex, which showed topological incongruence between our phylogenies, we found that genetic structure generally coincides with geographic variation in plumage, although three subspecies with striking plumage differences exhibit low mitochondrial divergence. The hybridizing taxa M. o. chrysops and M. m. bairdi show very shallow genomic differentiation, with marked peaks of divergence. Most of these are shared with other parulid warbler pairs, pointing to broad genomic features, like recombination rate, as the processes shaping these regions. However, other highly differentiated regions were unique to Myioborus, including one containing the gene CCDC91, which is associated with melanin-based plumage differences in several other birds. Lastly, we found higher levels of differentiation on the Z chromosome relative to autosomes, including two putative chromosomal inversions. Together, these results highlight the interplay of deep ancestral divergence, recent hybridization, and shared genomic architecture in shaping the evolution of phenotypic and genomic diversity within Myioborus. 

Abstract Downstream of Cape Hatteras, the vigorously meandering Gulf Stream forms anticyclonic warm core rings (WCRs) that carry warm Gulf Stream and Sargasso Sea waters into the cooler, fresher Slope Sea, and forms cyclonic cold core rings (CCRs) that carry Slope Sea waters into the Sargasso Sea. The Northwest Atlantic shelf and open ocean off the U.S. East Coast have experienced dramatic changes in ocean circulation and water properties in recent years, with significant consequences for marine ecosystems and coastal communities. Some of these changes may be related to a reported regime shift in the number of WCRs formed annually, with a doubling of WCRs shed after 2000. Since the regime shift was detected using a regional eddy‐tracking product, primarily based on sea surface temperatures and relies on analyst skill, we examine three global eddy‐tracking products as an automated and potentially more objective way to detect changes in Gulf Stream rings. Currently, global products rely on altimeter‐measured sea surface height (SSH), with WCRs registering as sea surface highs and CCRs as lows. To identify eddies, these products use either SSH contours or a Lagrangian approach, with particles seeded in satellite‐based surface geostrophic velocity fields. This study confirms the three global products are not well suited for statistical analysis of Gulf Stream rings and suggests that automated WCR identification and tracking comes at the price of accurate identification and tracking. Furthermore, a shift to a higher energy state is detected in the Northwest Atlantic, which coincides with the regime shift in WCRs. 

Abstract The Gulf Stream system is dominated by strong mesoscale variability that can obscure any seasonal signals in Gulf Stream strength. Nevertheless, seasonal variability of the Gulf Stream is important for local weather and climate and can influence amplification of hurricane intensity and storm tracks. We investigate seasonal variability of the speed of the Gulf Stream after it detaches from Cape Hatteras, using high‐resolution along‐track altimeter data. The altimeter data show a significant seasonal cycle in the Gulf Stream axis speed, peaking in summer. The seasonal variability in the Gulf Stream axis velocity is related to changes in the local wind stress curl and changes in the density difference across the Gulf Stream. Wind forcing affects the Gulf Stream year‐round, while changes in the density difference have the largest impact in summer. Overall, changes in the wind stress curl and upper ocean density difference across the Gulf Stream can explain roughly 40% of the seasonal Gulf Stream speed variability in summer. 

Abstract The Northwest Atlantic, which has exhibited evidence of accelerated warming compared to the global ocean, also experienced several notable marine heatwaves (MHWs) over the last decade. We analyze spatiotemporal patterns of surface and subsurface temperature structure across the Northwest Atlantic continental shelf and slope to assess the influences of atmospheric and oceanic processes on ocean temperatures. Here we focus on MHWs from 2015/16 and examine their physical drivers using observational and reanalysis products. We find that a combination of jet stream latitudinal position and ocean advection, mainly due to warm core rings shed by the Gulf Stream, plays a role in MHW development. While both atmospheric and oceanic drivers can lead to MHWs they have different temperature signatures with each affecting the vertical structure differently and horizontal spatial patterns of a MHW. Northwest Atlantic MHWs have significant socio-economic impacts and affect commercially important species such as squid and lobster. 

Abstract The strong sea‐surface temperature (SST) gradient associated with the Gulf Stream (GS) is widely acknowledged to play an important role in shaping mid‐latitude weather and climate. Despite this, an index for the GS SST gradient has not yet been standardized in the literature. This paper introduces a monthly index for the large‐scale SST gradient across the separated GS based on the time‐varying GS position detected from sea‐surface height. Analysis suggests that the variations in the monthly average SST gradient throughout the year result primarily from SST variability to the north of the GS, with little contribution from SST to the south. The index exhibits a weak periodicity at ∼2 years. Sea level pressure and turbulent heat flux patterns suggest that variability in the large‐scale SST gradient is related to atmospheric (rather than oceanic) forcing. Ocean‐to‐atmosphere feedback does not persist throughout the year, but there is some evidence of wintertime feedback. 

Purpose To develop a novel model composed solely of Col I and Col III with the lower and upper limits set to include the ratios of Col I and Col III at 3:1 and 9:1 in which the structural and mechanical behavior of the resident CM can be studied. Further, the progression of fibrosis due to change in ratios of Col I:Col III was tested. Methods Collagen gels with varying Col I:Col III ratios to represent a healthy (3:1) and diseased myocardial tissue were prepared by manually casting them in wells. Absorbance assay was performed to confirm the gelation of the gels. Rheometric analysis was performed on each of the collagen gels prepared to determine the varying stiffnesses and rheological parameters of the gels made with varying ratios of Col I:Col III. Second Harmonic Generation (SHG) was performed to observe the 3D characterization of the collagen samples. Scanning Electron microscopy was used for acquiring cross sectional images of the lyophilized collagen gels. AC16 CM (human) cell lines were cultured in the prepared gels to study cell morphology and behavior as a result of the varying collagen ratios. Cellular proliferation was studied by performing a Cell Trace Violet Assay and the applied force on each cell was measured by means of Finite Element Analysis (FEA) on CM from each sample. Results Second harmonic generation microscopy used to image Col I, displayed a decrease in acquired image intensity with an increase in the non-second harmonic Col III in 3:1 gels. SEM showed a fiber-rich structure in the 3:1 gels with well-distributed pores unlike the 9:1 gels or the 1:0 controls. Rheological analysis showed a decrease in substrate stiffness with an increase of Col III, in comparison with other cases. CM cultured within 3:1 gels exhibited an elongated rod-like morphology with an average end-to-end length of 86 ± 28.8 µm characteristic of healthy CM, accompanied by higher cell growth in comparison with other cases. Finite element analysis used to estimate the forces exerted on CM cultured in the 3:1 gels, showed that the forces were well dispersed, and not concentrated within the center of cells, in comparison with other cases. Conclusion This study model can be adopted to simulate various biomechanical environments in which cells crosstalk with the Collagen-matrix in diseased pathologies to generate insights on strategies for prevention of fibrosis. 

Large-language models (LLMs) such as GPT-4 caught the interest of many scientists. Recent studies suggested that these models could be useful in chemistry and materials science. To explore these possibilities, we organized a hackathon. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines. 

Abstract microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms’ role in ecology and human health.