N-Glycan Profiles of Neuraminidase from Avian Influenza Viruses.

The cleavage of sialic acids by neuraminidase (NA) facilitates the spread of influenza A virus (IV) descendants. Understanding the enzymatic activity of NA aids research into the transmission of IVs. An effective method for purifying NA was developed using p-aminophenyloxamic acid-modified functionalized hydroxylated magnetic particles (AAMPs), and from 0.299 to 0.401 mg of NA from eight IV strains was isolated by 1 mg AAMP. A combination of lectin microarrays and MALDI-TOF/TOF-MS was employed to investigate the N-glycans of isolated NAs. We found that more than 20 N-glycans were identified, and 16 glycan peaks were identical in the strains derived from chicken embryo cultivation. Multi-antennae, bisected, or core-fucosylated N-glycans are common in all the NAs. The terminal residues of N-glycans are predominantly composed of galactose and N-acetylglucosamine residues. Meanwhile, sialic acid residue was uncommon in these N-glycans. Further computational docking analysis predicted the interaction mechanism between NA and p-aminophenyloxamic acid.

Coaxial interferometry for camera-based ultrasound-modulated optical tomography with paired illumination.

Ultrasound-modulated optical tomography (UOT), which combines the advantages of both light and ultrasound, is a promising imaging modality for deep-tissue high-resolution imaging. Among existing implementations, camera-based UOT gains huge advances in modulation depth through parallel detection. However, limited by the long exposure time and the slow framerate of modern cameras, the measurement of UOT signals always requires holographic methods with additional reference beams. This requirement increases system complexity and is susceptible to environmental disturbances. To overcome this challenge, we develop coaxial interferometry for camera-based UOT in this work. Such a coaxial scheme is enabled by employing paired illumination with slightly different optical frequencies. To measure the UOT signal, the conventional phase-stepping method in holography can be directly transplanted into coaxial interferometry. Specifically, we performed both numerical investigations and experimental validations for camera-based UOT under the proposed coaxial scheme. One-dimensional imaging for an absorptive target buried inside a scattering medium was demonstrated. With coaxial interferometry, this work presents an effective way to reduce system complexity and cope with environmental disturbances for camera-based UOT.

Atomic-scale insights on hydrogen trapping and exclusion at incoherent interfaces of nanoprecipitates in martensitic steels.

Hydrogen is well known to embrittle high-strength steels and impair their corrosion resistance. One of the most attractive methods to mitigate hydrogen embrittlement employs nanoprecipitates, which are widely used for strengthening, to trap and diffuse hydrogen from enriching at vulnerable locations within the materials. However, the atomic origin of hydrogen-trapping remains elusive, especially in incoherent nanoprecipitates. Here, by combining in-situ scanning Kelvin probe force microscopy and aberration-corrected transmission electron microscopy, we unveil distinct scenarios of hydrogen-precipitate interaction in a high-strength low-alloyed martensitic steel. It is found that not all incoherent interfaces are trapping hydrogen; some may even exclude hydrogen. Atomic-scale structural and chemical features of the very interfaces suggest that carbon/sulfur vacancies on the precipitate surface and tensile strain fields in the nearby matrix likely determine the hydrogen-trapping characteristics of the interface. These findings provide fundamental insights that may lead to a better coupling of precipitation-strengthening strategy with hydrogen-insensitive designs.

Cryo-shift: reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization.

MOTIVATION: Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep learning methods have been proven to be highly accurate and efficient for subtomogram classification, but suffer from limited applicability due to scarcity of annotated data. While generating simulated data for training supervised models is a potential solution, a sizeable difference in the image intensity distribution in generated data as compared with real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms. RESULTS: In this work, we present Cryo-Shift, a fully unsupervised domain adaptation and randomization framework for deep learning-based cross-domain subtomogram classification. We use unsupervised multi-adversarial domain adaption to reduce the domain shift between features of simulated and experimental data. We develop a network-driven domain randomization procedure with 'warp' modules to alter the simulated data and help the classifier generalize better on experimental data. We do not use any labeled experimental data to train our model, whereas some of the existing alternative approaches require labeled experimental samples for cross-domain classification. Nevertheless, Cryo-Shift outperforms the existing alternative approaches in cross-domain subtomogram classification in extensive evaluation studies demonstrated herein using both simulated and experimental data. AVAILABILITYAND IMPLEMENTATION: https://github.com/xulabs/aitom. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Weakly Supervised 3D Semantic Segmentation Using Cross-Image Consensus and Inter-Voxel Affinity Relations.

We propose a novel weakly supervised approach for 3D semantic segmentation on volumetric images. Unlike most existing methods that require voxel-wise densely labeled training data, our weakly-supervised CIVA-Net is the first model that only needs image-level class labels as guidance to learn accurate volumetric segmentation. Our model learns from cross-image co-occurrence for integral region generation, and explores inter-voxel affinity relations to predict segmentation with accurate boundaries. We empirically validate our model on both simulated and real cryo-ET datasets. Our experiments show that CIVA-Net achieves comparable performance to the state-of-the-art models trained with stronger supervision.

Research on ecosystem services of water conservation and soil retention: a bibliometric analysis.

Water conservation and soil retention are two essential regulating services that are closely related, and their relationship might produce synergies or trade-offs. Distinguishing the current status and evolution of research in this field could provide a scientific foundation for subsequent research. "Water conservation" and "soil retention" were selected as keywords for a search of Web of Science for publications during 1976-2018. A total of 4489 periodical articles were obtained. Using bibliometric and social network analysis tools, the scientific output performance, national research contributions, potential hot topics, and connections between keywords and the levels of cooperation between countries at different stages were explored to reveal the related development trends. The results showed that the literature on water conservation and soil retention increased rapidly, especially after 2008. The USA, China, and India were the most productive countries, and the USA, the UK, and Canada were the most influential countries regarding international cooperation. Agriculture, water resource utilization, water-soil erosion, and ecosystem services were closely related topics, and the connections between these topics have increased since 1998. In addition to sustainability, the response of water conservation and soil retention to global environmental change, such as water resource management, land use, and land conservation, are potential emerging research hotspots.

A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation.

BACKGROUND: Cryo-electron tomography is an important and powerful technique to explore the structure, abundance, and location of ultrastructure in a near-native state. It contains detailed information of all macromolecular complexes in a sample cell. However, due to the compact and crowded status, the missing edge effect, and low signal to noise ratio (SNR), it is extremely challenging to recover such information with existing image processing methods. Cryo-electron tomogram simulation is an effective solution to test and optimize the performance of the above image processing methods. The simulated images could be regarded as the labeled data which covers a wide range of macromolecular complexes and ultrastructure. To approximate the crowded cellular environment, it is very important to pack these heterogeneous structures as tightly as possible. Besides, simulating non-deformable and deformable components under a unified framework also need to be achieved. RESULT: In this paper, we proposed a unified framework for simulating crowded cryo-electron tomogram images including non-deformable macromolecular complexes and deformable ultrastructures. A macromolecule was approximated using multiple balls with fixed relative positions to reduce the vacuum volume. A ultrastructure, such as membrane and filament, was approximated using multiple balls with flexible relative positions so that this structure could deform under force field. In the experiment, 400 macromolecules of 20 representative types were packed into simulated cytoplasm by our framework, and numerical verification proved that our method has a smaller volume and higher compression ratio than the baseline single-ball model. We also packed filaments, membranes and macromolecules together, to obtain a simulated cryo-electron tomogram image with deformable structures. The simulated results are closer to the real Cryo-ET, making the analysis more difficult. The DOG particle picking method and the image segmentation method are tested on our simulation data, and the experimental results show that these methods still have much room for improvement. CONCLUSION: The proposed multi-ball model can achieve more crowded packaging results and contains richer elements with different properties to obtain more realistic cryo-electron tomogram simulation. This enables users to simulate cryo-electron tomogram images with non-deformable macromolecular complexes and deformable ultrastructures under a unified framework. To illustrate the advantages of our framework in improving the compression ratio, we calculated the volume of simulated macromolecular under our multi-ball method and traditional single-ball method. We also performed the packing experiment of filaments and membranes to demonstrate the simulation ability of deformable structures. Our method can be used to do a benchmark by generating large labeled cryo-ET dataset and evaluating existing image processing methods. Since the content of the simulated cryo-ET is more complex and crowded compared with previous ones, it will pose a greater challenge to existing image processing methods.

Effects of External Environments on the Fixed Elongation and Tensile Properties of the VAE Emulsion-Cement Composite Joint Sealant.

Joint sealant is affected by various environmental factors in service, such as different temperatures, water soaking, ultraviolet and so on. In this paper, the VAE emulsion-cement compositejoint sealant was pretreated under multiple simulation environments. Thereafter, the degradation rules of fixed elongation and tensile properties of joint sealants at different mix proportions were systemically investigated under the action of external environments (temperature, water soaking and ultraviolet), and the influence mechanisms of diverse environmental factors were analyzed. The research results suggested that, under the action of external environments, the VAE emulsion-cement composite joint sealants exhibited degradation effects to varying degrees. After the addition of plasticizer, the joint sealants had reduced cohesion strength in low temperature environment and enhanced flexible deformability. The addition of water repellent improved the water resistance of joint sealants. Meanwhile, adding ultraviolet shield agent partially improved the ultraviolet radiation aging resistance. A greater powder-liquid ratio led to the lower flexibility of joint sealants, but superior water resistance and ultraviolet radiation aging resistance.

Publisher Correction: Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae.

The transient larva-bearing biphasic life cycle is the hallmark of many metazoan phyla, but how metazoan larvae originated remains a major enigma in animal evolution. There are two hypotheses for larval origin. The 'larva-first' hypothesis suggests that the first metazoans were similar to extant larvae, with later evolution of the adult-added biphasic life cycle; the 'adult-first' hypothesis suggests that the first metazoans were adult forms, with the biphasic life cycle arising later via larval intercalation. Here, we investigate the evolutionary origin of primary larvae by conducting ontogenetic transcriptome profiling for Mollusca-the largest marine phylum characterized by a trochophore larval stage and highly variable adult forms. We reveal that trochophore larvae exhibit rapid transcriptome evolution with extraordinary incorporation of novel genes (potentially contributing to adult shell evolution), and that cell signalling/communication genes (for example, caveolin and innexin) are probably crucial for larval evolution. Transcriptome age analysis of eight metazoan species reveals the wide presence of young larval transcriptomes in both trochozoans and other major metazoan lineages, therefore arguing against the prevailing larva-first hypothesis. Our findings support an adult-first evolutionary scenario with a single metazoan larval intercalation, and suggest that the first appearance of proto-larva probably occurred after the divergence of direct-developing Ctenophora from a metazoan ancestor.

Integration of Biochemical, Cellular, and Genetic Indicators for Understanding the Aging Process in a Bivalve Mollusk Chlamys farreri.

The major causal factors for the irreversible decline in physical vitality during organismal aging are postulated to be a chronic state of cellular redox imbalance, metabolic toxicity, and impaired energy homeostasis. We assessed whether the relevant enzyme activity, oxidative stress, and intracellular ATP might be causally involved in the aging of short-lived Chlamys farreri (life span 4~5 years). A total of eight related biochemical and cellular indicators were chosen for the subsequent analysis. All the indicators were measured in seven different tissues from scallops aged one to four years, and our data support that the aging of C. farreri is associated with attenuated tissue enzyme activity as well as a decreased metabolic rate. Through principal component analysis, we developed an integrated vigor index for each tissue for comprehensive age-related fitness evaluation. Remarkably, all tissue-integrated vigor indexes significantly declined with age, and the kidney was observed to be the most representative tissue. Further transcriptional profiling of the enzymatic genes provided additional detail on the molecular responses that may underlie the corresponding biochemical results. Moreover, these critical molecular responses may be attributed to the conserved hierarchical regulators, e.g., FOXO, AMPKs, mTOR, and IGF1R, which were identified as potentially novel markers for chronic fitness decline with age in bivalves. The present study provides a systematic approach that could potentially benefit the global assessment of the aging process in C. farreri and provide detailed evaluation of the biochemical, cellular, and genetic indicators that might be involved. This information may assist in a better understanding of bivalve adaptability and life span.

Genome-wide identification and expression profiling of the Wnt gene family in three bivalve molluscs.

Cellular signaling initiated by various secreted, cysteine-rich Wnt proteins plays essential roles in regulating animal development and cell stemness. By virtue of its functional diversity and importance, the Wnt gene family has received substantial research interests in a variety of animal species, from invertebrates to vertebrates. However, for bivalve molluscs, one of the ancient bilaterian groups with high morphological diversity, systematic identification and analysis of the Wnt gene family remain lacking. To shed some light on the evolutionary dynamics of this gene family and obtain a more comprehensive understanding, we analyzed the characteristics of the Wnt gene family in three bivalve molluscs, with both genome and extensive transcriptomic resources. Investigation of genomic signatures, functional domains as well as phylogenetic relationships was conducted, and 12, 11, 12 subfamilies were identified in Yesso scallop, Zhikong scallop and Pacific oyster respectively. Spatiotemporal expression profiling suggested that, some bivalve Wnts might coordinate and participate in adult organ/tissue morphogenesis and homeostasis as well as early embryonic development. The transcriptional regulation of oyster Wnt genes showed dynamic and responsive patterns under different environmental stresses, indicating that Wnts may play a role in coping with challenging intertidal environments in bivalves. To our best knowledge, this study presents the first genome-wide study of Wnt gene family in bivalves, and our findings would assist in better understanding of Wnt function and evolution in bivalve molluscs.