Live-cell quantitative imaging of proteome degradation by stimulated Raman scattering

Protein degradation is a regulatory process essential to cell viability and its dysfunction is implicated in many diseases, such as aging and neurodegeneration. In this report, stimulated Raman scattering microscopy coupled with metabolic labeling with ^(13)C-phenylalanine is used to visualize protein degradation in living cells with subcellular resolution. We choose the ring breathing modes of endogenous ^(12)C-phenylalanine and incorporated ^(13)C-phenylalanine as protein markers for the original and nascent proteomes, respectively, and the decay of the former wasquantified through ^(12)C/(^(12)C + ^(13)C) ratio maps. We demonstrate time-dependent imaging of proteomic degradation in mammalian cells under steady-state conditions and various perturbations, including oxidative stress, cell differentiation, and huntingtin protein aggregation

Rumor Detection with a novel graph neural network approach

The wide spread of rumors on social media has caused a negative impact on people's daily life, leading to potential panic, fear, and mental health problems for the public. How to debunk rumors as early as possible remains a challenging problem. Existing studies mainly leverage information propagation structure to detect rumors, while very few works focus on correlation among users that they may coordinate to spread rumors in order to gain large popularity. In this paper, we propose a new detection model, that jointly learns both the representations of user correlation and information propagation to detect rumors on social media. Specifically, we leverage graph neural networks to learn the representations of user correlation from a bipartite graph that describes the correlations between users and source tweets, and the representations of information propagation with a tree structure. Then we combine the learned representations from these two modules to classify the rumors. Since malicious users intend to subvert our model after deployment, we further develop a greedy attack scheme to analyze the cost of three adversarial attacks: graph attack, comment attack, and joint attack. Evaluation results on two public datasets illustrate that the proposed MODEL outperforms the state-of-the-art rumor detection models. We also demonstrate our method performs well for early rumor detection. Moreover, the proposed detection method is more robust to adversarial attacks compared to the best existing method. Importantly, we show that it requires a high cost for attackers to subvert user correlation pattern, demonstrating the importance of considering user correlation for rumor detection.Comment: 10 pages, 5 figure

Live-cell quantitative imaging of proteome degradation by stimulated Raman scattering

Protein degradation is a regulatory process essential to cell viability and its dysfunction is implicated in many diseases, such as aging and neurodegeneration. In this report, stimulated Raman scattering microscopy coupled with metabolic labeling with ^(13)C-phenylalanine is used to visualize protein degradation in living cells with subcellular resolution. We choose the ring breathing modes of endogenous ^(12)C-phenylalanine and incorporated ^(13)C-phenylalanine as protein markers for the original and nascent proteomes, respectively, and the decay of the former wasquantified through ^(12)C/(^(12)C + ^(13)C) ratio maps. We demonstrate time-dependent imaging of proteomic degradation in mammalian cells under steady-state conditions and various perturbations, including oxidative stress, cell differentiation, and huntingtin protein aggregation

Apomixis for no bacteria-induced thelytoky in Diglyphus wani (Hymenoptera: Eulophidae)

In Hymenoptera species, the reproductive mode is usually arrhenotoky, where haploid males arise from unfertilized eggs and diploid females from fertilized eggs. In addition, a few species reproduce by thelytoky, where diploid females arise from unfertilized eggs. Diploid females can be derived through various cytological mechanisms in thelytokous Hymenoptera species. Hitherto, these mechanisms were revealed mainly in endosymbiont-induced thelytokous Hymenoptera species. In contrast, thelytokous Hymenoptera species in which a reproductive manipulator has not been verified or several common endosymbionts have been excluded were paid less attention in their cytological mechanisms, for instance, Diglyphus wani (Hymenoptera: Eulophidae). Here, we investigated the cytological mechanism of D. wani using cytological methods and genetic markers. Our observations indicated that the diploid karyotypes of two strains of D. wani consist of four pairs of relatively large metacentric chromosomes and one pair of short submetacentric chromosomes (2n = 10). The arrhenotokous strains could complete normal meiosis, whereas the thelytokous strain lacked meiosis and did not expulse any polar bodies. This reproductive type of lacking meiosis is classified as apomictic thelytoky. Moreover, a total of 636 microsatellite sequences were obtained from thelytokous D. wani, dominated by dinucleotide repeats. Genetic markers results showed all three generations of offspring from thelytokous strain maintained the same genotype as their parents. Our results revealed that D. wani is the first eulophid parasitoid wasp in Hymenoptera whose thelytoky was not induced by bacteria to form an apomictic thelytoky. These findings provide a baseline for future inner molecular genetic studies of ameiotic thelytoky

Supermultiplexed optical imaging and barcoding with engineered polyynes

Optical multiplexing has a large impact in photonics, the life sciences and biomedicine. However, current technology is limited by a 'multiplexing ceiling' from existing optical materials. Here we engineered a class of polyyne-based materials for optical supermultiplexing. We achieved 20 distinct Raman frequencies, as 'Carbon rainbow', through rational engineering of conjugation length, bond-selective isotope doping and end-capping substitution of polyynes. With further probe functionalization, we demonstrated ten-color organelle imaging in individual living cells with high specificity, sensitivity and photostability. Moreover, we realized optical data storage and identification by combinatorial barcoding, yielding to our knowledge the largest number of distinct spectral barcodes to date. Therefore, these polyynes hold great promise in live-cell imaging and sorting as well as in high-throughput diagnostics and screening

Subjective Cognitive Decline May Be Associated With Post-operative Delirium in Patients Undergoing Total Hip Replacement: The PNDABLE Study

Objective: Subjective cognitive decline (SCD) is associated with an increased risk of clinical cognitive disorders. Post-operative delirium (POD) is a common complication after total hip replacement. We aimed to investigate the relationship between SCD and POD in patients undergoing total hip replacement.Methods: Our study recruited 214 cognitively intact individuals from the Perioperative Neurocognitive Disorder And Biomarker Lifestyle (PNDABLE) study in the final analysis. SCD was diagnosed with Subjective Cognitive Decline Scale (SCDS), Mini-Mental State Examination (MMSE), and Montreal Cognitive Assessment (MoCA). The incidence of POD was evaluated by using Confusion Assessment Method (CAM), and POD severity was measured by using the Memorial Delirium Assessment Scale (MDAS). Preoperative cerebrospinal fluid (CSF) Aβ40, Aβ42, T-tau, and P-tau levels were measured by enzyme-linked immune-sorbent assay (ELISA).Results: Overall, the incidence of POD was 26.64% (57/214), including 32.43% (36/111) in the SCD group and 20.39% (21/103) in the NC group. With the increase of age, the incidence of POD in all age groups increased (P < 0.05). Logistic regression analysis showed that after adjusting for SCD, Aβ42, Aβ40, P-tau, and T-tau, SCD (OR 2.32, CI 1.18–4.55, P = 0.01) and the increased CSF level of P-tau (OR 1.04, CI 1.01–1.06, P < 0.001) were risk factors for POD, while the level of aβ42 (OR 0.99, CI 0.99–1.00, P < 0.001) was a protective factor for POD.Conclusion: SCD is one of the preoperative risk factors for POD.Clinical Trial Registration: This study was registered at China Clinical Trial Registry (Chictr200033439)

Characterization of ultra-deeply buried middle Triassic Leikoupo marine carbonate petroleum system (!) in the Western Sichuan depression, China

Ultra-deeply buried (>5000 m) marine carbonate reservoirs have gradually become important exploration targets. This research focuses on providing an understanding of the basic elements of the ultra-deeply buried Middle Triassic Leikoupo marine carbonate petroleum system within the Western Sichuan Depression, China. Comprehensive analyses of organic geochemistry, natural gas, and C–H–He–Ne–Ar isotope compositions suggest that the reservoir is charged with compound gases from four source rock units including the Permian Longtan, Middle Triassic Leikoupo, Late Triassic Maantang and Xiaotangzi formations. Approximately a 50-m thick outcrop and 100-m length of drilling cores were examined in detail, and 108 samples were collected from six different exploration wells in order to conduct petrographic and petrophysical analyses. Thin-section and scanning electron microscope (SEM) observations, helium porosity and permeability measurements, mercury injection capillary pressure (MICP) analysis, and wire-line logging (5,500–6,900 m) indicate that the reservoir lithologies include argillaceous algal limestones, dolograinstones, crystalline dolostones, and microbially-derived stromatolitic and thrombolitic dolostones. Reservoir properties exhibit extreme heterogeneity due to different paleogeographic environmental controls and mutual interactions between constructive (e.g., epigenetic paleo-karstification, burial dissolution, structural movement, pressure-solution and dolomitization) and destructive (e.g., physical/chemical compaction, cementation, infilling, recrystallization, and replacement) diagenetic processes. An unconformity-related epigenetic karstification zone was identified in the uppermost fourth member of the Leikoupo Formation, which has developed secondary solution-enhanced pores, vugs, and holes that resulted in higher porosity (1.8–14.2%) and permeability (0.2–7.7 mD). The homogeneity and tightness of the reservoir increases with depth below the unconformity, and it is characterized by primary intergranular and intracrystalline pores, solution pores, fractures, stylolites, and micropores with a lower helium porosity (0.6–4.1%) and permeability (0.003–125.2 mD). Regional seals consist of the Late Triassic Xujiahe Formation, comprised of ~300 m of mudstones that are overlain by ~5,000-m thick of Jurassic to Quaternary continental argillaceous overburden rocks. Effective traps are dominated by a combination of structural-stratigraphic types. Paleo- reservoir crude oil cracking, wet-gases, and dry-gases from three successive hydrocarbon generation processes supplied the sufficient hydrocarbon resources. The homogenization temperatures of the hydrocarbon-associated aqueous fluid inclusions range from 98–130 °C and 130–171 °C, which suggests hydrocarbon charging occurred between 220–170 Ma and 130–90 Ma, respectively. One-dimensional basin evolution models combined with structural geologic and seismic profiles across wells PZ1-XQS1-CK1-XCS1-TS1 show that hydrocarbon migration and entrapment mainly occurred via the unconformity and interconnected fault-fracture networks with migration and charging driven by formation overpressure, abnormal fluid flow pressure, and buoyancy forces during the Indosinian and Yanshanian orogenies, with experiencing additional transformation occurring during the Himalayan orogeny. The predicted estimated reserves reached ~300 × 109 m3. The results provide excellent scientific implications for similar sedimentary basin studies, it is believed that abundant analogous deeply buried marine carbonate hydrocarbon resources yet to be discovered in China and elsewhere worldwide in the near future

Genome Sequencing of the Sweetpotato Whitefly \u3cem\u3eBemisia tabaci\u3c/em\u3e MED/Q

The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 437 kb, and a total length of 658 Mb. Annotation of repetitive elements and coding regions resulted in 265.0 Mb TEs (40.3%) and 20 786 protein-coding genes with putative gene family expansions, respectively. Phylogenetic analysis based on orthologs across 14 arthropod taxa suggested that MED/Q is clustered into a hemipteran clade containing A. pisum and is a sister lineage to a clade containing both R. prolixus and N. lugens. Genome completeness, as estimated using the CEGMA and Benchmarking Universal Single-Copy Orthologs pipelines, reached 96% and 79%. These MED/Q genomic resources lay a foundation for future \u27pan-genomic\u27 comparisons of invasive vs. noninvasive, invasive vs. invasive, and native vs. exotic Bemisia, which, in return, will open up new avenues of investigation into whitefly biology, evolution, and management