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Abstract Accurate classification of rail transit stations is crucial for successful Transit-Oriented Development (TOD) and sustainable urban growth. This paper introduces a novel classification model integrating traditional methodologies with advanced machine learning algorithms. By employing mathematical models, clustering methods, and neural network techniques, the model enhances the precision of station classification, allowing for a refined evaluation of station attributes. A comprehensive case study on the Chengdu rail transit network validates the model’s efficacy, highlighting its value in optimizing TOD strategies and guiding decision-making processes for urban planners and policymakers. The study employs several regression models trained on existing data to generate accurate ridership forecasts, and data clustering using mathematical algorithms reveals distinct categories of stations. Evaluation metrics confirm the rationality and accuracy of the results. Additionally, a neural network achieving high accuracy on labeled data enhances the model’s predictive capabilities for unlabeled instances. The research demonstrates high accuracy, with the Mean Squared Error (MSE) for regression models (Multiple Linear Regression (MLR), Deep-Learning Neural Network (DNN), and K-Nearest Neighbor (KNN)) remaining below 0.012, while the neural networks used for station classification achieve 100% accuracy across seven time intervals and 98.15% accuracy for the eighth, ensuring reliable ridership forecasts and classification outcomes. Accuracy in rail transit station classification is critical, as it not only strengthens the model’s predictive capabilities but also ensures more reliable data-driven decisions for transit planning and development, allowing for more precise ridership forecasts and evidence-based strategies for optimizing TOD. This classification model provides stakeholders with valuable insights into the dynamics and features of rail transit stations, supporting sustainable urban development planning.

Abstract The intracellular bacterial pathogen Legionella pneumophila modulates host cell functions by secreting multiple effectors with diverse biochemical activities. In particular, effectors of the SidE family interfere with host protein ubiquitination in a process that involves production of phosphoribosyl ubiquitin (PR-Ub). Here, we show that effector LnaB converts PR-Ub into ADP-ribosylated ubiquitin, which is further processed to ADP-ribose and functional ubiquitin by the (ADP-ribosyl)hydrolase MavL, thus maintaining ubiquitin homeostasis in infected cells. Upon being activated by actin, LnaB also undergoes self-AMPylation on tyrosine residues. The activity of LnaB requires a motif consisting of Ser, His and Glu (SHxxxE) present in a large family of toxins from diverse bacterial pathogens. Thus, our study sheds light on the mechanisms by which a pathogen maintains ubiquitin homeostasis and identifies a family of enzymes capable of protein AMPylation.

Abstract Background Larval settlement and metamorphosis represent critical events in the life history of marine benthic animals. Myoinhibitory peptide (MIP) plays a pivotal role in larval settlement of marine invertebrates. However, the molecular mechanisms of MIP involved in this process are not well understood. Results In this study, we evaluated the effects of thirteen MIP mature peptides on triggering the larval settlement of Urechis unicinctus (Xenopneusta, Urechidae), and determined that MIP2 was the principal neuropeptide. Transcriptomic analysis was employed to identify differentially expressed genes (DEGs) between the MIP2-treated larvae and normal early-segmentation larvae. Both cAMP and calcium signaling pathways were enriched in the DEGs of the MIP2-treated larvae, and two neuropeptide receptor genes (Spr, Fmrfar) were up-regulated in the MIP2-treated larvae. The activation of the SPR-cAMP pathway by MIP2 was experimentally validated in HEK293T cells. Furthermore, fourteen cilia-related genes, including Tctex1d2, Cfap45, Ift43, Ift74, Ift22, Cav1 and Mns1, etc. exhibited down-regulated expression in the MIP2-treated larvae. Whole-mount in situ hybridization identified two selected ciliary genes, Tctex1d2 and Cfap45, were specially expressed in circumoral ciliary cells of the early-segmentation larvae. Knocking down Tctex1d2 mRNA levels by in vivo RNA interference significantly increased the larval settlement rate. Conclusion Our findings suggest that MIP2 inhibits the function of the cilia-related genes, such as Tctex1d2, through the SPR-cAMP-PKA pathway, thereby inducing larval settlement in U. unicinctus. The study contributes important data to the understanding of neuropeptide regulation in larval settlement.

Abstract ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster. Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.

Abstract This study investigated attapulgite-modified loess as an efficient and cost-effective method for creating an impermeable liner for landfills in regions with scarce clay resources. Laboratory permeability tests were conducted using a flexible wall permeameter to determine the permeability of compacted loess and attapulgite mixtures under varying osmotic conditions. The relationship between the permeability coefficient, attapulgite dosage, radial pressure, and osmotic pressure was analyzed. Nuclear magnetic resonance and scanning electron microscopy were also used to observe the microstructure of the modified loess. The results showed that attapulgite dosage significantly reduced the permeability coefficient, but the effect became limited when the content surpassed 10%. The decrease of the permeability coefficient of the modified loess is mainly due to the filling of pores between the loess by attapulgite, which makes the pore size and throat size of the modified loess smaller. The modified loess displayed a sheet structure that contributed to an increased permeability coefficient due to increased radial pressure. This study provides valuable insights into using attapulgite-modified loess as a material for landfill lining in regions with scarce clay resources.

In this study, crumpled graphene oxide balls (CGBs) were prepared via capillary compression using a rapidly evaporating aerosol droplet method. The CGBs were observed using scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), and Raman spectroscopy. The size distributions of crumpled particles were obtained using a laser nanometer particle size analyzer (DLS). The dispersibility of the water and the ionic liquid (IL) was tested by ultrasonic dispersion. The tribological properties of water or ionic liquids containing crumpled graphene oxide ball additives (W/IL-CGB) were tested by a reciprocating friction tester and compared with water/ionic liquids with graphene oxide. The morphology of the wear scar was observed by a three-dimensional optical microscope and its lubrication mechanism was analyzed. The results show that the CGBs were successfully prepared by rapid evaporation of aerosol droplets, and the obtained CGBs were crumpled paper spheres. The CGBs had good water dispersion and ionic liquid dispersion, and IL-CGB has excellent anti-friction and anti-wear effects on steel–steel friction pairs. During the friction process, the CGB was adsorbed at the interface of the steel–steel friction pair to form a protective layer, which avoids the direct contact of the friction pair, thereby reducing friction and wear.

Abstract Nowadays, Transit-Oriented Development (TOD) plays a vital role for public transport planners in developing potential city facilities. Knowing the necessity of this concept indicates that TOD effective parameters such as network accessibility (node value) and station-area land use (place value) should be considered in city development projects. To manage the coordination between these two factors, we need to consider ridership and peak and off-peak hours as essential enablers in our investigations. To aim this, we conducted our research on Chengdu rail-transit stations as a case study to propose our Node-Place-Ridership-Time (NPRT) model. We applied the Multiple Linear Regression (MLR) to examine the impacts of node value and place value on ridership. Finally, K-Means and Cube Methods were used to classify the stations based on the NPRT model results. This research indicates that our NPRT model could provide accurate results compared with the previous models to evaluate rail-transit stations.

Abstract In this paper, we investigated the effect of space irradiation on the lubricating properties of IL/(GO-MWCNT) solid–liquid lubricating coatings. The solid–liquid lubricating coatings consist of ionic liquids (IL), graphene oxide (GO), and multi-walled carbon nanotubes (MWCNT). Irradiation experiments were carried out using ground simulation equipment. Atomic oxygen (AO), ultraviolet (UV), proton (Pr), and electron (El) irradiation alter the composition, structure, morphology, and tribological properties of solid–liquid lubricating coatings. The experimental results show the composition changes induced by irradiation, including the decomposition of ILs lubricants. The damage to the lubricating material was the most serious by Pr irradiation and the least by UV irradiation.

The habitat occupied by flatfish fry differs considerably in light regime from that of the adult. The diversity of opsins and their expression patterns appear greatest for flatfishes to experience variable light environments. Yet, opsin repertoires and expression patterns in this group of fishes are poorly described. To understand how the visual system has adapted to such changes, we unveil that Japanese flounder (Paralichthys olivaceus) has a visual system adapted to a benthic environment by fine-tuning paralogous opsins (SWS2A and RH2) for wavelength shift and regulated expression. P. olivaceus express five basic opsin genes (M/LWS, SWS1, SWS2, RH1 and RH2) and gene-specific duplications were observed in RH2 and SWS2 paralogues. The expression of the three short-wavelength sensitive genes, SWS2Aα, SWS2Aβ, and SWS2B, is significantly elevated at the benthic stages, especially in SWS2Aβ a striking expression change is observed. The four middle-wavelength sensitive genes exhibit divergent expressions, the expression of RH2A-1 and RH2A-2 increased, while that of RH2B-1 and RH2B-2 decreased significantly from pelagic to benthic stage, especially RH2A-2. At present, changes at a total of 26 sites are known to have modified the λmax of various visual pigments during vertebrate evolution. Thus, these tuning site variations in our P. olivaceus are suspected to cause a green-shift in the λmax of SWS2Aα pigments and blue-shift in that of in RH2A-2. Together, our results suggest that RH2 and SWS2 opsin repertoires serve to optimize visual function under variable light environments by gene family duplications, differential expressions, and maximum absorption wavelength (λmax) variations.

Rail-transit hub classification in TOD refers to the categorization of transit stations based on their level of connectivity and ridership and the potential for development around them as part of a Transit-Oriented Development (TOD) strategy. TOD, as an essential concept in developing smart cities and public transportation accessibility, has attracted the focus of many policymakers. To this end, many research projects have been dedicated to classifying the rail-transit stations, although the necessity of integrated models for rail-transit hubs could have been mentioned in previous papers. Therefore, this parametric case study is directed to apply the Node–Place–Ridership–Time (NPRT) model to provide a logical classification model for Chengdu rail-transit hubs at the junctions of high-speed railway and subway stations. Multiple Linear Regression (MLR) provided a series of equations, including the effective parameters of the NPRT model. These equations were then verified by the Artificial Neural Network (ANN) to provide the effect of each node and place values on the integrated ridership of rail-transit hubs in different time periods. The results proved the consistent contribution of the integrated ANN-NPRT-HUB algorithm to the TOD concept for smart cities.

During the early development of marine invertebrates, planktic larvae usually occur, and their body surfaces often form specific types of cilia that are involved in locomotion and feeding. The echiuran worm Urechis unicinctus sequentially undergoes the formation and disappearance of different types of body surface cilia during embryonic and larval development. The morphological characteristics and molecular mechanisms involved in the process remain unclear. In this study, we found that body surface cilia in U. unicinctus embryos and larvae can be distinguished into four types: body surface short cilia, apical tufts, circumoral cilia and telotrochs. Further, distribution and genesis of the body surface cilia were characterized using light microscope and electron microscope. To better understand the molecular mechanism during ciliogenesis, we revealed the embryonic and larval transcriptome profile of the key stages of ciliogenesis in U. unicinctus using RNA-Seq technology. A total of 29,158 differentially expressed genes (DEGs) were obtained from 24 cDNA libraries by RNA-Seq. KEGG pathway enrichment results showed that Notch, Wnt and Ca2+ signaling pathways were significantly enriched during the occurrence of apical tufts and circumoral cilia. Furthermore, all DEGs were classified according to their expression pattern, and DEGs with similar expression pattern were grouped into a module. All DEG co-expression modules were correlated with traits (body surface short cilia, apical tufts, circumoral cilia and telotrochs) by WGCNA, the results showed DEGs were divided into 13 modules by gene expression patterns and that the genes in No. 7, No. 8 and No. 10 modules were to be highly correlated with the occurrence of apical tufts, circumoral cilia and telotrochs. The top 10 hub genes in the above three modules were identified to be highly correlated with ciliogenesis, including the reported cilium-related gene Cnbd2 and unreported cilium-related candidate genes FAM181B, Capsl, Chst3, TMIE and Innexin. Notably, Innexin was included in the top10 hub genes of the two modules (No. 7 and No. 8), suggesting that Innexin may play an important role in U. unicinctus apical tufts, circumoral cilia and telotrochs genesis. This study revealed the characteristics of ciliogenesis on the body surface of U. unicinctus embryos and larvae, providing basic data for exploring the molecular mechanism of ciliogenesis on the body surface.

In this study, fluorographene nanosheets (FG nanosheets) were prepared via the solvent-ultrasonic exfoliation method. The fluorographene sheets were observed using field-emission scanning electron microscopy (FE-SEM). The microstructure of the as-prepared FG nanosheets was characterized by X-ray diffraction (XRD) and a thermal analyzer (TG). The tribological properties of FG nanosheets as an additive in ionic liquids in high vacuum were compared to that of ionic liquid (IL) with graphene (IL-G). The wear surfaces and transfer films were analyzed via an optical microscope, Raman spectroscopy, scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS). The results show that FG nanosheets can be obtained from the simple solvent-ultrasonic exfoliation method. The prepared G nanosheets are a sheet, and the longer the ultrasonic time is, the thinner the sheet is. Ionic liquids with FG nanosheets had low friction and a low wear rate under high vacuum conditions. The improved frictional properties were attributed to the transfer film of FG nanosheets and more formation film of Fe-F.

Fibroblast growth factors (FGFs) are short polypeptides that play essential roles in various cellular biological processes, including cell migration, proliferation, and differentiation, as well as tissue regeneration, immune response, and organogenesis. However, studies focusing on the characterization and function of FGF genes in teleost fishes are still limited. In this study, we identified and characterized expression patterns of 24 FGF genes in various tissues of embryonic and adult specimens of the black rockfish (Sebates schlegelii). Nine FGF genes were found to play essential roles in myoblast differentiation, as well as muscle development and recovery in juvelines of S. schlegelii. Moreover, sex-biased expression pattern of multiple FGF genes was recorded in the species’ gonads during its development. Among them, expression of the FGF1 gene was recorded in interstitial and sertoli cells of testes, promoting germ-cell proliferation and differentiation. In sum, the obtained results enabled systematic and functional characterization of FGF genes in S. schlegelii, laying a foundation for further studies on FGF genes in other large teleost fishes.

Quantifying regional myocardial motion and deformation from cardiac magnetic resonance imaging (MRI) plays an important role in clinical applications. In this paper, we present a novel approach for the estimation of left ventricle myocardial motion based on iterative deformable graph matching for cine MRI. Graph matching is a shape matching approach that can be used to determine the correspondence between two objects. However, existing graph matching algorithms are unsuitable for applications with large deformations. In this paper, we propose an iterative deformable graph matching framework for estimating the correspondence between points extracted from left ventricle myocardium at the end-diastolic and end-systolic phases to estimate cardiac motion. A new cost function for graph matching is defined to measure the discrepancy between the nodes and edges of two graphs under a transformation. By introducing a spatial transformation with a sparsity constraint, we can estimate a robust deformation field, alleviating the influence of inevitable graph mismatches. The correspondence between points is then updated by mapping the source graph using the estimated transformation. The cost function is optimized by alternatively optimizing for correspondence and spatial transformation. Furthermore, we propose a multilayer framework to improve correspondence accuracy using a bottom-up matching procedure. This framework estimates the deformation field between an image at the end-systolic phase and an image at the end-diastolic phase in an MRI sequence. Evaluations of two public cardiac datasets indicate that the proposed framework outperforms traditional graph matching algorithms in accuracy and robustness.

This research study applied Artificial Neural Networks (ANNs) to predict and evaluate the structural responses of externally bonded FRP (EB-FRP)-strengthened RC T-beams under combined torsion and shear. Previous studies proved that, compared to reinforced concrete (RC) rectangular beams, RC T-beams performance in shear is significantly higher in structural analysis and design. The structural response of RC beams experiences a critical change while torsion moments are applied in load conditions. Fiber Reinforced Polymer (FRP) is used to retrofit the structural elements due to changing structural design codes and loadings, especially in earthquake-prone countries. We applied Finite Element Method (FEM) software, ABAQUS, to provide a precise numerical database of a set of experimentally tested FRP-retrofitted RC T-beams in previous research works. ANN predicted structural analysis results and Mean Square Error (MSE) and Multiple Determination Coefficients (R2) proved the accuracy of this study. The MSE values that were less than 0.0009 and R2 values greater than 0.9960 showed that the ANN precisely fits the data. The consistency between analyzed experimental and numerical results demonstrated the accurate implication of ANN, MSE, and R2 in predicting the structural responses of EB-FRP- strengthened RC T-beams.

This paper studied the anti-seepage ability of the modified loess by using attapulgite, which is abundant in local areas. The possibility of using the modified loess as the sustainable compacted soil liner material in a solid waste landfill was also considered in this research. The materials were then evaluated using Nuclear Magnetic Resonance (NMR), Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD), and an Impermeability Mechanism (IM). The experimental results showed that the permeability coefficient of the attapulgite-modified loess decreases significantly with increasing attapulgite content. However, it becomes less significant when the attapulgite level approaches 10%. Both cases can meet the landfill impermeability requirements, based on the attapulgite content remaining at 10%, adding 15% lime or 5% cement, respectively. The triaxial consolidation and drainage experiment was carried out to investigate the shear strength of the materials under three different working circumstances. The stress–strain curves of each specimen were produced, as were the cohesion and internal friction angle values. This research lays the groundwork for using attapulgite-modified loess as a landfill lining material. It establishes a solid platform for future studies on attapulgite adsorption and purifying performance in landfills.

The focus of this study was to investigate the effect of loess soil treated with lime on the lateral-seepage response. Three groups of box experiments were carried out to study the lateral-seepage effect under different types of loess-lime structures. Automated testing systems were designed to perform experiments and collect data. Additionally, numerical analysis of lateral-seepage impact and embankment settlement was performed. Finally, moisture content and settlement were monitored to quantify lateral-seepage effect results under corresponding loess-lime treatment. Results showed that loess-lime compaction piles and diaphragm wall structures could effectively prevent lateral seepage, and the latter was better. The simulated results are similar to the measured values of the box experiment, which indicates the accuracy of the simulation analysis and further supports the experimental results of this study.

Fiber-reinforced polymers (FRPs) retrofit reinforced concrete (RC) structures. ABAQUS finite element software was used to perform numerical parametric analysis on a group of RC beams in this research. All specimens were retrofitted by FRP strips as an external retrofitting and experimentally tested up to previous researchers’ failure points. The range of subjects examined in these RC beams included cracking torque, ultimate torque, angle of twist, and the effect of using FRP on these subjects. We applied artificial neural networks (ANNs) to predict the structural behavior of RC beams under combined torsion and bending to develop the research accuracy. After testing, the ANN results were compared with the ABAQUS results. Consequently, a reasonable examination of the determined mathematical and trial results confirmed this study’s logical accuracy in predicting retrofitted RC beams’ structural behavior under combined loading.

Estimating robust transformations based on noisy landmark correspondences is challenging and cannot be ensured to be exact. In this paper, we propose a novel sparse transformation model based on corresponding landmarks. First, we construct a new transformation model that uses compact supported radial basis functions (CSRBFs) with multiple supports, with a least-squares cost function constrained by the l1 and l2 norms of the elastic and affine deformation coefficients used to estimate the CSRBF coefficients. This sparse model can be used to select CSRBFs with different supports and construct a robust deformation field. Then, the relationship between the CSRBF coefficients and the bending energy of the deformation field is analyzed in a reproducing kernel Hilbert space; this bending energy is introduced into the cost function as a regularization term. The cost function is optimized by using the fast iterative shrinkagethreshold algorithm to compute coefficients in the transformation model. To demonstrate the performance of our sparse transformation model, we combine it with robust point matching to simultaneously estimate the correspondence and transformation between landmarks. Experiments on synthetic data, brain images, and cardiac images show that the transformations estimated by our sparse transformation model are robust to noised landmark correspondences, preserving registration accuracy, minimizing the bending energy of the deformation field, and preserving the topology of the deformation field.

Abstract Background Cardiac diseases represent the leading cause of sudden death worldwide. During the development of cardiac diseases, the left ventricle (LV) changes obviously in structure and function. LV motion estimation plays an important role for diagnosis and treatment of cardiac diseases. To estimate LV motion accurately for cine magnetic resonance (MR) cardiac images, we develop an algorithm by combining point set matching with surface structure features of myocardium. Methods The structure features of myocardial wall are described by estimating the normal directions of points locating on the myocardium contours using an approximation approach. The Gaussian mixture model (GMM) of structure features is used to represent LV structure feature distribution. A new cost function is defined to represent the differences between two Gaussian mixture models, which are the GMM of structure features and the GMM of positions of two point sets. To optimize the cost function, its gradient is derived to use the Quasi-Newton (QN). Furthermore, to resolve the dis-convergence issue of Quasi-Newton for high-dimensional parameter space, Stochastic Gradient Descent (SGD) is used and SGD gradient is derived. Finally, the new cost function is solved by optimization combining SGD with QN. With the closed form expression of gradient, this paper provided a computationally efficient registration algorithm. Results Three public datasets are employed to verify the performance of our algorithm, including cardiac MR image sequences acquired from 33 subjects, 14 inter-subject heart cases, and the data obtained in MICCAI 2009s 3D Segmentation Challenge for Clinical Applications. We compare our results with those of the other point set registration methods for LV motion estimation. The obtained results demonstrate that our algorithm shows inherent statistical robustness, due to the combination of SGD and Quasi-Newton optimization. Furthermore, our method is shown to outperform other point set matching methods in the registration accuracy. Conclusions We provide a novel effective algorithm for cardiac motion estimation by introducing LV surface structure feature to point set matching. A new cost function is defined to measure the discrepancy between GMMs of two point sets. The GMM of point positions and the GMM of surface structure descriptor are defined at the same time. Optimization by combining SGD and Quasi-Newton is performed to solve the cost function. We experimentally demonstrate that our algorithm shows improved registration accuracy, and is convergent when used in high-dimensional parameter space.

Ocean acidification (OA), which is caused by increasing levels of dissolved CO2 in the ocean, is a major threat to marine ecosystems. Multiple lines of scientific evidence show that marine bivalves, including scallops, are vulnerable to OA due to their poor capacities to regulate extracellular ions and acid-based status. However, the physiological mechanisms of scallops responding to OA are not well understood. In this study, we evaluated the effects of 45 days of exposure to OA (pH 7.5) on the energy metabolism and antioxidant capability of Yesso scallops. Some biochemical markers related to energy metabolism (e.g., content of glycogen and ATP, activity of ATPase, lactate dehydrogenase, glutamate oxaloacetate transaminase, and glutamate-pyruvate transaminase), antioxidant capacity (e.g., reactive oxygen species level, activity of superoxide dismutase, and catalase) and cellular damage (e.g., lipid peroxidation level) were measured. Our results demonstrate that the effects of the reduced pH (7.5) on scallops are varied in different tissues. The energy reserves are mainly accumulated in the adductor muscle and hepatopancreas. Yesso scallops exhibit energy modulation by increasing lactate dehydrogenase activities to stimulate anaerobic metabolism. The highly active Na+/K+-ATPase and massive ATP consumption in the mantle and gill indicate that a large amount of energy was allocated for the ion regulation process to maintain the acid-base balance in the reduced-pH environment. Moreover, the increase in the reactive oxygen species level and the superoxide dismutase and catalase activities in the gill and adductor muscle, indicate that oxidative stress was induced after long-term exposure to the reduced-pH environment. Our findings indicate that the effects of OA are tissue-specific, and physiological homeostasis could be modulated through different mechanisms for Yesso scallops.

The innate immune system plays a pivotal role in defending invasion of microorganisms for scallops. Previous studies on immune-related genes in the Yesso scallop, Patinopecten yessoensis (Jay, 1857) have mainly focused on characterization and expression pattern in response to bacterial challenge, no research has been carried out on the cytogenetic level yet. In the present study, eight fosmid clones containing the sequences of key immune-related genes (PyNFkB, PyTRAF2, PyTRAF4, PyTRAF7, PyMyd88-1, PyMyd88-3, PyMKK-7 and PyTNFR) were isolated and seven of them were successfully mapped on chromosomes of P. yessoensis utilizing fluorescence in situ hybridization. Wherein, PyMyd88-1, PyMyd88-3 and PyMKK-7 located on the same chromosome pair with adjacent positions and the other genes were mapped on four non-homologous chromosome pairs, showing a similar distribution to another five model species. The isolation and mapping of such genes of the Yesso scallop will lay a foundation for studies such as assignment of interested genes to chromosomes, construction cytogenetic maps and so on.

Four new polyketides: nectriacids A–C (1–3) and 12-epicitreoisocoumarinol (4), together with three known compounds: citreoisocoumarinol (5), citreoisocoumarin (6), and macrocarpon C (7) were isolated from the culture of the endophytic fungus Nectria sp. HN001, which was isolated from a fresh branch of the mangrove plant Sonneratia ovata collected from the South China Sea. Their structures were determined by the detailed analysis of NMR and mass spectroscopic data. The absolute configuration of the stereogenic carbons for compound 4 was further assigned by Mosher’s ester method. All of the isolated compounds were tested for their α-glucosidase inhibitory activity by UV absorbance at 405 nm, and new compounds 2 and 3 exhibited potent inhibitory activity with IC50 values of 23.5 and 42.3 μM, respectively, which were more potent than positive control (acarbose, IC50, 815.3 μM).

ADP-ribosylation is a post-translational modification involved in regulation of diverse cellular pathways. Interestingly, many pathogens have been identified to utilize ADP-ribosylation as a way for host manipulation. A recent study found that CteC, an effector from the bacterial pathogen Chromobacterium violaceum, hinders host ubiquitin (Ub) signaling pathways via installing mono-ADP-ribosylation on threonine 66 of Ub. However, the molecular basis of substrate recognition by CteC is not well understood. In this article, we probed the substrate specificity of this effector at protein and residue levels. We also determined the crystal structure of CteC in complex with NAD+, which revealed a canonical mono-ADP-ribosyltransferase fold with an additional insertion domain. The AlphaFold-predicted model differed significantly from the experimentally determined structure, even in regions not used in crystal packing. Biochemical and biophysical studies indicated unique features of the NAD+ binding pocket, while showing selectivity distinction between Ub and structurally close Ub-like modifiers and the role of the insertion domain in substrate recognition. Together, this study provides insights into the enzymatic specificities and the key structural features of a novel bacterial ADP-ribosyltransferase involved in host-pathogen interaction. [ABSTRACT FROM AUTHOR]