Foreword to the thematic cluster: the Arctic in Rapid Transition — marine ecosystems

The Arctic is warming and losing sea ice. Happening at a much faster rate than previously expected, these changes are causing multiple ecosystem feedbacks in the Arctic Ocean. The Arctic in Rapid Transition (ART) initiative was developed by early-career scientists as an integrative, international, multidisciplinary, long-term pan-Arctic network to study changes and feedbacks among the physical and biogeochemical components of the Arctic Ocean and their ultimate impacts on biological productivity on different timescales. In 2012, ART jointly organized with the Association of Polar Early Career Scientists their second science workshop—Overcoming Challenges of Observation to Model Integration in Marine Ecosystem Response to Sea Ice Transitions—at the Institute of Oceanology, Polish Academy of Sciences, in Sopot. This workshop aimed to identify linkages and feedbacks between atmosphere–ice–ocean forcing and biogeochemical processes, which are critical for ecosystem function, land–ocean interactions and productive capacity of the Arctic Ocean. This special thematic cluster of Polar Research brings together seven papers that grew out of workgroup discussions. Papers examine the climate change impacts on various ecosystem elements, providing important insights on the marine ecological and biogeochemical processes on various timescales. They also highlight priority areas for future research

Learning biophysically-motivated parameters for alpha helix prediction

<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p

Trophic structure of the macrobenthic community of Hornsund, Spitsbergen, based on the determination of stable carbon and nitrogen isotopic signatures

International audienc

Time-series benthic community composition and biomass and associated environmental characteristics in the Chukchi Sea during the RUSALCA 2004–2012 program

Benthic macrofaunal and epifaunal composition and biomass and associated environmental drivers were evaluated for time-series stations occupied during three cruises of the RUSALCA (Russian-American Long-term Census of the Arctic) program undertaken in August 2004, September 2009, and September 2012. We focus on the benthic communities collected at repeat stations in the southern Chukchi Sea and the key environmental characteristics that could influence benthic population structure and biomass. These characteristics included bottom water temperature, salinity, and chlorophyll a (chl a); integrated chl a; export production via sediment oxygen uptake rates as an indicator of food supply to the benthos; and surface sediment parameters that are known to influence benthic population community composition and biomass, such as grain size, carbon content, and chl a. Overall, both the macrofaunal and epibenthic community composition at the time-series sites in the southern Chukchi Sea have remained relatively constant over the time period of this study (2004–2012). However, some of the more sedentary macrofauna are showing significant declines in biomass since 2004, particularly in the center of a macrobenthic hotpot that has been persistent for decades in the southern Chukchi Sea. While biomass estimates were more variable for the more motile epibenthic fauna, there was also an indication of declining epifaunal biomass since 2009. We highlight here as a case study the benthic time-series efforts during RUSALCA that are also part of the Distributed Biological Observatory (DBO) international network, which is tracking the status and trends of Arctic ecosystem response to the changing physical drivers in the southern Chukchi Sea

Global and single-nucleotide resolution detection of 7-methylguanosine in RNA

RNA modifications, including N-7-methylguanosine (m7G), are pivotal in governing RNA stability and gene expression regulation. The accurate detection of internal m7G modifications is of paramount significance, given recent associations between altered m7G deposition and elevated expression of the methyltransferase METTL1 in various human cancers. The development of robust m7G detection techniques has posed a significant challenge in the field of epitranscriptomics. In this study, we introduce two methodologies for the global and accurate identification of m7G modifications in human RNA. We introduce borohydride reduction sequencing (Bo-Seq), which provides base resolution mapping of m7G modifications. Bo-Seq achieves exceptional performance through the optimization of RNA depurination and scission, involving the strategic use of high concentrations of NaBH4, neutral pH and the addition of 7-methylguanosine monophosphate (m7GMP) during the reducing reaction. Notably, compared to NaBH4-based methods, Bo-Seq enhances the m7G detection performance, and simplifies the detection process, eliminating the necessity for intricate chemical steps and reducing the protocol duration. In addition, we present an antibody-based approach, which enables the assessment of m7G relative levels across RNA molecules and biological samples, however it should be used with caution due to limitations associated with variations in antibody quality between batches. In summary, our novel approaches address the pressing need for reliable and accessible methods to detect RNA m7G methylation in human cells. These advancements hold the potential to catalyse future investigations in the critical field of epitranscriptomics, shedding light on the complex regulatory roles of m7G in gene expression and its implications in cancer biology.</p

Ecosystem characteristics and processes facilitating persistent macrobenthic biomass hotspots and associated benthivory in the Pacific Arctic

The northern Bering and Chukchi Seas are areas in the Pacific Arctic characterized by high northward advection of Pacific Ocean water, with seasonal variability in sea ice cover, water mass characteristics, and benthic processes. In this review, we evaluate the biological and environmental factors that support communities of benthic prey on the continental shelves, with a focus on four macrofaunal biomass hotspots. For the purpose of this study, we define hotspots as macrofaunal benthic communities with high biomass that support a corresponding ecological guild of benthivorous seabird and marine mammal populations. These four benthic hotspots are regions within the influence of the St. Lawrence Island Polynya (SLIP), the Chirikov Basin between St. Lawrence Island and Bering Strait (Chirikov), north of Bering Strait in the southeast Chukchi Sea (SECS), and in the northeast Chukchi Sea (NECS). Detailed benthic macrofaunal sampling indicates that these hotspot regions have been persistent over four decades of sampling due to annual reoccurrence of seasonally consistent, moderate-to-high water column production with significant export of carbon to the underlying sediments. We also evaluate the usage of the four benthic hotspot regions by benthic prey consumers to illuminate predator-prey connectivity. In the SLIP hotspot, spectacled eiders and walruses are important winter consumers of infaunal bivalves and polychaetes, along with epibenthic gastropods and crabs. In the Chirikov hotspot, gray whales have historically been the largest summer consumers of benthic macrofauna, primarily feeding on ampeliscid amphipods in the summer, but they are also foraging further northward in the SECS and NECS hotspots. Areas of concentrated walrus foraging occur in the SLIP hotspot in winter and early spring, the NECS hotspot in summer, and the SECS hotspot in fall. Bottom up forcing by hydrography and food supply to the benthos influences persistence and composition of benthic prey that then influences the distributions of benthivorous upper trophic level populations