![128433-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/128433-Thumbnail%20Image.png?versionId=Qn33kjelWQz0nFNzIysk_SeSpisw9.JI&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240616/us-west-2/s3/aws4_request&X-Amz-Date=20240616T054339Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=63fe8185163f4d2eefcaefa77dc5346daa6acdbe6eb647fb4f408533e80e2b8d&itok=6EJHLmXo)
MicroRNAs (miRNAs) regulate gene output by targeting degenerate elements in mRNAs and have undergone drastic expansions in higher metazoan genomes. The evolutionary advantage of maintaining copies of highly similar miRNAs is not well understood, nor is it clear what unique functions, if any, miRNA family members possess. Here, we study evolutionary patterns of metazoan miRNAs, focusing on the targeting preferences of the let-7 and miR-10 families. These studies reveal hotspots for sequence evolution with implications for targeting and secondary structure. High-throughput screening for functional targets reveals that each miRNA represses sites with distinct features and regulates a large number of genes with cooperative function in regulatory networks. Unexpectedly, given the high degree of similarity, single-nucleotide changes grant miRNA family members with distinct targeting preferences. Together, our data suggest complex functional relationships among miRNA duplications, novel expression patterns, sequence change, and the acquisition of new targets.
![128506-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/128506-Thumbnail%20Image.png?versionId=lM0BtN6nSthZtsgT_xat9h9nVruO.L3R&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T025803Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=287d8231549f8444e230f7e503eb5df096a998e7685683ae427212790c0a91ea&itok=9g2j6AR5)
A data set of observed daily precipitation, maximum and minimum temperature, gridded to a 1/16° (~6 km) resolution, is described that spans the entire country of Mexico, the conterminous U.S. (CONUS), and regions of Canada south of 53° N for the period 1950-2013. The dataset improves previous products in spatial extent, orographic precipitation adjustment over Mexico and parts of Canada, and reduction of transboundary discontinuities. The impacts of adjusting gridded precipitation for orographic effects are quantified by scaling precipitation to an elevation-aware 1981-2010 precipitation climatology in Mexico and Canada. Differences are evaluated in terms of total precipitation as well as by hydrologic quantities simulated with a land surface model. Overall, orographic correction impacts total precipitation by up to 50% in mountainous regions outside CONUS. Hydrologic fluxes show sensitivities of similar magnitude, with discharge more sensitive than evapotranspiration and soil moisture. Because of the consistent gridding methodology, the current product reduces transboundary discontinuities as compared with a commonly used reanalysis product, making it suitable for estimating large-scale hydrometeorologic phenomena.
![128511-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/128511-Thumbnail%20Image.png?versionId=rx82Vuya.Uoj_WW1zyvX1r5XsDqjDNis&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240616/us-west-2/s3/aws4_request&X-Amz-Date=20240616T024418Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=b4e6f02da8093816fbaebc5f8fbb1520202908ea4e9ee60f93b1382a6299f2e8&itok=xoMHuav5)
Network reconstruction is a fundamental problem for understanding many complex systems with unknown interaction structures. In many complex systems, there are indirect interactions between two individuals without immediate connection but with common neighbors. Despite recent advances in network reconstruction, we continue to lack an approach for reconstructing complex networks with indirect interactions. Here we introduce a two-step strategy to resolve the reconstruction problem, where in the first step, we recover both direct and indirect interactions by employing the Lasso to solve a sparse signal reconstruction problem, and in the second step, we use matrix transformation and optimization to distinguish between direct and indirect interactions. The network structure corresponding to direct interactions can be fully uncovered. We exploit the public goods game occurring on complex networks as a paradigm for characterizing indirect interactions and test our reconstruction approach. We find that high reconstruction accuracy can be achieved for both homogeneous and heterogeneous networks, and a number of empirical networks in spite of insufficient data measurement contaminated by noise. Although a general framework for reconstructing complex networks with arbitrary types of indirect interactions is yet lacking, our approach opens new routes to separate direct and indirect interactions in a representative complex system.
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.
Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.
Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
![154421-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-09/154421-Thumbnail%20Image.png?versionId=eb_Ei3dfUjVF0fxymqLeCK3vSQmP4lam&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240616/us-west-2/s3/aws4_request&X-Amz-Date=20240616T033537Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=52afc905739eba9b6645906ba183fa021e7ea82fcde5e8acbfe1206f4506fadb&itok=-LzR9zif)
Recent transcriptome data from yeast, worm, plants, and humans has shown that alternative polyadenylation (APA), a mechanism that enables expression of multiple 3′UTR isoforms for the same gene, is widespread in eukaryotic organisms. It is still poorly understood why metazoans require multiple 3′UTRs for the same gene, but accumulating evidence suggests that APA is largely regulated at a tissue-specific level. APA may direct combinatorial variation between cis-elements and microRNAs, perhaps to regulate gene expression in a tissue-specific manner. Apart from a few single gene anecdotes, this idea has not been systematically explored.
This dissertation research employs a systems biology approach to study the somatic tissue dynamics of APA and its impact on microRNA targeting networks in the small nematode C. elegans. In the first aim, tools were developed and applied to isolate and sequence mRNA from worm intestine and muscle tissues, which revealed pervasive tissue-specific APA correlated with microRNA regulation. The second aim provides genetic evidence that two worm genes use APA to escape repression by microRNAs in the body muscle. Finally, in aim three, mRNA from five additional somatic worm tissues was sequenced and their 3′ends mapped, allowing for an integrative study of APA and microRNA targeting dynamics in worms. Together, this work provides evidence that APA is a pervasive mechanism operating in somatic tissues of C. elegans with the potential to significantly rearrange their microRNA regulatory networks and precisely dose their gene expression.
![128149-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/128149-Thumbnail%20Image.png?versionId=4_eVSm1oZUBvO8UkgByGWHMIsOpo9RqO&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T025803Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=1dd1dc04119eec4d04f11614fc0a4139731782c2c6c3fff97395d5453fa591f9&itok=OzjD69Sx)
Wetlands are the world's largest natural source of methane, a powerful greenhouse gas. The strong sensitivity of methane emissions to environmental factors such as soil temperature and moisture has led to concerns about potential positive feedbacks to climate change. This risk is particularly relevant at high latitudes, which have experienced pronounced warming and where thawing permafrost could potentially liberate large amounts of labile carbon over the next 100 years. However, global models disagree as to the magnitude and spatial distribution of emissions, due to uncertainties in wetland area and emissions per unit area and a scarcity of in situ observations. Recent intensive field campaigns across the West Siberian Lowland (WSL) make this an ideal region over which to assess the performance of large-scale process-based wetland models in a high-latitude environment. Here we present the results of a follow-up to the Wetland and Wetland CH4 Intercomparison of Models Project (WETCHIMP), focused on the West Siberian Lowland (WETCHIMP-WSL). We assessed 21 models and 5 inversions over this domain in terms of total CH4 emissions, simulated wetland areas, and CH4 fluxes per unit wetland area and compared these results to an intensive in situ CH4 flux data set, several wetland maps, and two satellite surface water products. We found that (a) despite the large scatter of individual estimates, 12-year mean estimates of annual total emissions over the WSL from forward models (5.34 ± 0.54 Tg CH4 yr-1), inversions (6.06 ± 1.22 Tg CH4 yr-1), and in situ observations (3.91 ± 1.29 Tg CH4 yr-1) largely agreed; (b) forward models using surface water products alone to estimate wetland areas suffered from severe biases in CH4 emissions; (c) the interannual time series of models that lacked either soil thermal physics appropriate to the high latitudes or realistic emissions from unsaturated peatlands tended to be dominated by a single environmental driver (inundation or air temperature), unlike those of inversions and more sophisticated forward models; (d) differences in biogeochemical schemes across models had relatively smaller influence over performance; and (e) multiyear or multidecade observational records are crucial for evaluating models' responses to long-term climate change.
![128234-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/128234-Thumbnail%20Image.png?versionId=GRXeudbZwgkaa2aFssymjDdV2qPByazv&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T081253Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=e5d9e209dd532b40a7eeb38b726382567dea56af4b605ffa4d783d3d40ecf358&itok=_cRu_DOG)
Climate factors including soil temperature and moisture, incident solar radiation, and atmospheric carbon dioxide concentration are important environmental controls on methane (CH4) emissions from northern wetlands. We investigated the spatiotemporal distributions of the influence of these factors on northern high-latitude wetland CH4 emissions using an enhanced version of the Variable Infiltration Capacity (VIC) land surface model. We simulated CH4 emissions from wetlands across the pan-Arctic domain over the period 1948–2006, yielding annual average emissions of 36.1 ± 6.7 Tg CH4 yr-1 for the period 1997–2006. We characterized historical sensitivities of CH4 emissions to air temperature, precipitation, incident long- and shortwave radiation, and atmospheric [CO2] as a function of average summer air temperature and precipitation. Emissions from relatively warm and dry wetlands in the southern (permafrost-free) portion of the domain were positively correlated with precipitation and negatively correlated with air temperature, while emissions from wetter and colder wetlands further north (permafrost) were positively correlated with air temperature. Over the entire period 1948–2006, our reconstructed CH4 emissions increased by 20 %, the majority of which can be attributed to an increasing trend in summer air temperature. We estimated future emissions in response to 21st century warming as predicted by CMIP5 (Coupled Model Intercomparison Project Phase 5) model projections to result in end-of-century CH4 emissions 38–53 % higher than our reconstructed 1997–2006 emissions, accompanied by the northward migration of warmer and drier than optimal conditions for CH4 emissions, implying a reduced role for temperature in driving future increases in emissions.
![128820-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/128820-Thumbnail%20Image.png?versionId=h1lPuUuhnf_D46z.zOBeJjmh3xYCozMa&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T152121Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=ffe74af80afe6e602bb53005b77adfc76cd07b2551f97fc8a73eea15421bcce5&itok=ioNLP5Pv)
In vitro rearing is an important and useful tool for honey bee (Apis mellifera L.) studies. However, it often results in intercastes between queens and workers, which are normally are not seen in hive-reared bees, except when larvae older than three days are grafted for queen rearing. Morphological classification (queen versus worker or intercastes) of bees produced by this method can be subjective and generally depends on size differences. Here, we propose an alternative method for caste classification of female honey bees reared in vitro, based on weight at emergence, ovariole number, spermatheca size and size and shape, and features of the head, mandible and basitarsus. Morphological measurements were made with both traditional morphometric and geometric morphometrics techniques. The classifications were performed by principal component analysis, using naturally developed queens and workers as controls. First, the analysis included all the characters. Subsequently, a new analysis was made without the information about ovariole number and spermatheca size. Geometric morphometrics was less dependent on ovariole number and spermatheca information for caste and intercaste identification. This is useful, since acquiring information concerning these reproductive structures requires time-consuming dissection and they are not accessible when abdomens have been removed for molecular assays or in dried specimens. Additionally, geometric morphometrics divided intercastes into more discrete phenotype subsets. We conclude that morphometric geometrics are superior to traditional morphometrics techniques for identification and classification of honey bee castes and intermediates.