DNA barcoding of Antarctic marine zooplankton for species identification and recognition

Polar zooplankton are particularly sensitive to climate change, and have been used as rapid-responders to indicate climate-induced changes in the fragile Antarctic ecosystem. DNA barcoding provides an alternative approach for rapid zooplankton species identification. Ninety-four specimens belonging to 32 Antarctic zooplankton species were barcoded to construct a comprehensive reference library. An 830 to 1 050 base-pair region of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene was obtained as DNA barcodes. The intraspecific variation of the gene ranged from 0 to 2.6% (p-distance), with an average of 0.67% (SD=0.67%). The distance between species within the same genera ranged from 0.1% (Calanus) to 29.3%, with an average of 15.3% (SD=8.4%). The morphological and genetic similarities between Calanus propinquus and C. simillimus raise new questions about the taxonomic status of C. simillimus. With the exception of the two Calanus species, the intraspecific genetic divergence was much smaller than the interspecific divergence among congeneric species, confirming the existence of a barcode gap for Antarctic zooplankton. In addition, species other than Calanus sp. formed a monophyletic group. Therefore, we have confirmed DNA barcoding as an accurate and efficient approach for zooplankton identification in the Antarctic area (except for Hydromedusa, Tunicata, and other gelatinous zooplankton). Indicator vector analysis further confirmed this conclusion. The new primer sets issued here may facilitate the study of Antarctic marine zooplankton species composition by environmental metagenetic analysis

Carbonaceous matter in the atmosphere and glaciers of the Himalayas and the Tibetan plateau: An investigative review

Carbonaceous matter, including organic carbon (OC) and black carbon (BC), is an important climate forcing agent and contributes to glacier retreat in the Himalayas and the Tibetan Plateau (HTP). The HTP – the so-called “Third Pole” – contains the most extensive glacial area outside of the polar regions. Considerable research on carbonaceous matter in the HTP has been conducted, although this research has been challenging due to the complex terrain and strong spatiotemporal heterogeneity of carbonaceous matter in the HTP. A comprehensive investigation of published atmospheric and snow data for HTP carbonaceous matter concentration, deposition and light absorption is presented, including how these factors vary with time and other parameters. Carbonaceous matter concentrations in the atmosphere and glaciers of the HTP are found to be low. Analysis of water-insoluable organic carbon and BC from snowpits reveals that concentrations of OC and BC in the atmosphere and glacier samples in arid regions of the HTP may be overestimated due to contributions from inorganic carbon in mineral dust. Due to the remote nature of the HTP, carbonaceous matter found in the HTP has generally been transported from outside the HTP (e.g., South Asia), although local HTP emissions may also be important at some sites. This review provides essential data and a synthesis of current thinking for studies on atmospheric transport modeling and radiative forcing of carbonaceous matter in the HTP

Regression of Gastric Cancer by Systemic Injection of RNA Nanoparticles Carrying Both Ligand and siRNA

Gastric cancer is the second leading cause of cancer-related death worldwide. RNA nanotechnology has recently emerged as an important field due to recent finding of its high thermodynamic stability, favorable and distinctive in vivo attributes. Here we reported the use of the thermostable three-way junction (3WJ) of bacteriophage phi29 motor pRNA to escort folic acid, a fluorescent image marker and BRCAA1 siRNA for targeting, imaging, delivery, gene silencing and regression of gastric cancer in animal models. In vitro assay revealed that the RNA nanoparticles specifically bind to gastric cancer cells, and knock-down the BRCAA1 gene. Apoptosis of gastric cancer cells was observed. Animal trials confirmed that these RNA nanoparticles could be used to image gastric cancer in vivo, while showing little accumulation in crucial organs and tissues. The volume of gastric tumors noticeably decreased during the course of treatment. No damage to important organs by RNA nanoparticles was detectible. All the results indicated that this novel RNA nanotechnology can overcome conventional cancer therapeutic limitations and opens new opportunities for specific delivery of therapeutics to stomach cancer without damaging normal cells and tissues, reduce the toxicity and side effect, improve the therapeutic effect, and exhibit great potential in clinical tumor therapy

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

The Columbia Cancer Target Discovery and Development (CTD2) Center is developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA-seq) profiles of 25 cell lines perturbed with similar to 400 clinical oncology drugs, to study a tumor-specific drug mechanism of action. Here, this resource serves as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions. Dose-response and perturbational profiles for 32 kinase inhibitors are provided to 21 teams who are blind to the identity of the compounds. The teams are asked to predict high-affinity binding targets of each compound among similar to 1,300 targets cataloged in DrugBank. The best performing methods leverage gene expression profile similarity analysis as well as deep-learning methodologies trained on individual datasets. This study lays the foundation for future integrative analyses of pharmacogenomic data, reconciliation of polypharmacology effects in different tumor contexts, and insights into network-based assessments of drug mechanisms of action.Peer reviewe

Black carbon and organic carbon dataset over the Third Pole

The Tibetan Plateau and its surroundings, also known as the Third Pole, play an important role in the global and regional climate and hydrological cycle. Carbonaceous aerosols (CAs), including black carbon (BC) and organic carbon (OC), can directly or indirectly absorb and scatter solar radiation and change the energy balance on the Earth. CAs, along with the other atmospheric pollutants (e.g., mercury), can be frequently transported over long distances into the inland Tibetan Plateau. During the last decades, a coordinated monitoring network and research program named “Atmospheric Pollution and Cryospheric Changes” (APCC) has been gradually set up and continuously operated within the Third Pole regions to investigate the linkage between atmospheric pollutants and cryospheric changes. This paper presents a systematic dataset of BC, OC, water-soluble organic carbon (WSOC), and water-insoluble organic carbon (WIOC) from aerosols (20 stations), glaciers (17 glaciers, including samples from surface snow and ice, snow pits, and 2 ice cores), snow cover (2 stations continuously observed and 138 locations surveyed once), precipitation (6 stations), and lake sediment cores (7 lakes) collected across the Third Pole, based on the APCC program. These data were created based on online (in situ) and laboratory measurements. High-resolution (daily scale) atmospheric-equivalent BC concentrations were obtained by using an Aethalometer (AE-33) in the Mt. Everest (Qomolangma) region, which can provide new insight into the mechanism of BC transportation over the Himalayas. Spatial distributions of BC, OC, WSOC, and WIOC from aerosols, glaciers, snow cover, and precipitation indicated different features among the different regions of the Third Pole, which were mostly influenced by emission sources, transport pathways, and deposition processes. Historical records of BC from ice cores and lake sediment cores revealed the strength of the impacts of human activity since the Industrial Revolution. BC isotopes from glaciers and aerosols identified the relative contributions of biomass and fossil fuel combustion to BC deposition on the Third Pole. Mass absorption cross sections of BC and WSOC from aerosol, glaciers, snow cover, and precipitation samples were also provided. This updated dataset is released to the scientific communities focusing on atmospheric science, cryospheric science, hydrology, climatology, and environmental science. The related datasets are presented in the form of excel files. BC and OC datasets over the Third Pole are available to download from the National Cryosphere Desert Data Center (10.12072/ncdc.NIEER.db0114.2021; Kang and Zhang, 2021)