Efficacy and Safety of Programmed Death 1/Programmed Death-Ligand 1 Plus Cytotoxic T-Lymphocyte-Associated Antigen 4 Inhibitors for Advanced or Metastatic Non-Small Cell Lung Cancer: A Meta-analysis Based on Randomized Controlled Trials.

BACKGROUND: This meta-analysis aims to investigate the efficacy and safety of programmed death 1 (PD-1)/programmed death-ligand 1 (PD-L1) combined with cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) inhibitors for patients with advanced or metastatic non-small cell lung cancer (NSCLC). METHODS: Authors conducted a comprehensive search of PubMed, Embase, Cochrane Library, Web of Science, Scopus, and Medline for randomized controlled trials comparing the prognosis and safety of PD-1/PD-L1 plus CTLA-4 inhibitors with other therapies for advanced or metastatic NSCLC. Hazard ratios (HRs) and 95% confidence intervals (CIs) were used as effect sizes. The primary outcomes of this study were overall survival (OS) and progression-free survival. RESULTS: A total of 4943 patients diagnosed with stage III/IV advanced or metastatic NSCLC were included in the analysis of the 6 randomized controlled trials. The results showed that patients receiving dual immunotherapy with PD-1/PD-L1 plus CTLA-4 inhibitors had a longer survival time compared with the control group (HR = 0.88, P = 0.044). However, no statistically significant difference was observed in progression-free survival (HR = 0.95, P = 0.579). Subgroup analysis revealed better OS in the interventional group for patients aged >65 years (HR = 0.88, P = 0.076), smokers (HR = 0.81, P = 0.036), and those with a tumor mutational burden (TMB) ≥20 mut/Mb (HR = 0.66, P < 0.001). Conversely, the control group demonstrated superior OS in patients with TMB <20 mut/Mb (HR = 1.14, P = 0.048). In addition, the statistical results indicated a lower incidence rate of any-grade anemia in the dual immunotherapy group compared with the control group (RR = 0.32, P = 0.04). CONCLUSIONS: This meta-analysis demonstrates the effectiveness and safety of dual immunotherapy with PD-1/PD-L1 plus CTLA-4 inhibitors for treating advanced or metastatic NSCLC. Its efficacy is influenced by certain clinical and pathological factors, such as age, smoking status, and TMB.

Deep Kernel Principal Component Analysis for multi-level feature learning.

Principal Component Analysis (PCA) and its nonlinear extension Kernel PCA (KPCA) are widely used across science and industry for data analysis and dimensionality reduction. Modern deep learning tools have achieved great empirical success, but a framework for deep principal component analysis is still lacking. Here we develop a deep kernel PCA methodology (DKPCA) to extract multiple levels of the most informative components of the data. Our scheme can effectively identify new hierarchical variables, called deep principal components, capturing the main characteristics of high-dimensional data through a simple and interpretable numerical optimization. We couple the principal components of multiple KPCA levels, theoretically showing that DKPCA creates both forward and backward dependency across levels, which has not been explored in kernel methods and yet is crucial to extract more informative features. Various experimental evaluations on multiple data types show that DKPCA finds more efficient and disentangled representations with higher explained variance in fewer principal components, compared to the shallow KPCA. We demonstrate that our method allows for effective hierarchical data exploration, with the ability to separate the key generative factors of the input data both for large datasets and when few training samples are available. Overall, DKPCA can facilitate the extraction of useful patterns from high-dimensional data by learning more informative features organized in different levels, giving diversified aspects to explore the variation factors in the data, while maintaining a simple mathematical formulation.

Tree growth and density enhanced, while diversity and spatial clustering reduced soil mycorrhizal C and N sequestration: Strong interaction with soil properties in northeastern China.

In this paper, the effects of species diversity, tree growth, and spatial clustering on mycorrhizal carbon and nitrogen sequestration and the interaction of soil physicochemical properties in Northeast China were investigated. Based on 720 10 m ∗ 10 m plots in Harbin Experimental Forest Farm of Northeast Forestry University, we determined mycorrhizal biomarkers of easily extractable Glomalin-related soil protein (EEG) and total Glomalin-related soil protein (TG). Four plant diversity indices, seven structural metrics, and five soil properties were also measured. We found that: 1) The low tree diversity plots had 1.08-1.23 times higher TG, EEG, TG-N/TN (proportion of N in TG to TN), and TG-C/SOC (proportion of C in TG to SOC) than the high plots. 2) Tree diameter was negatively correlated with EEG and TG, but positively correlated with the EEG and TG contribution to soil TN and SOC. Soil EEG and TG were positively correlated with under-branch height and tree density. W (Uniform Angle Index, higher W indicates more clustering of tree distribution in the plot) was negatively correlated with the above four ratios and positively correlated with EEG/TG. 3) pH was the most powerful explainer for the GRSP variations (6.8 %, strongest negative association with GRSP/TN, R2 > 0.13), followed by soil electrical conductance (6.5 %, positive relation with TG, p < 0.05), AP (3.2 %). 4) Plant diversity mainly affected GRSP traits through the interaction with soils (0.07), tree growth and density directly increased TG, TG-N/TN, and TG-C/SOC, while tree spatial distribution directly reduced TG-N/TN. Our finding highlighted the important effects of tree diversity and forest structural traits on GRSP amount, carbon sequestration, and nutrient retentions, and could support glomalin-related forest soil management of temperate forests in the high-latitude northern hemisphere.

Low Dimensional Trajectory Hypothesis is True: DNNs Can Be Trained in Tiny Subspaces.

Deep neural networks (DNNs) usually contain massive parameters, but there is redundancy such that it is guessed that they could be trained in low-dimensional subspaces. In this paper, we propose a Dynamic Linear Dimensionality Reduction (DLDR) based on the low-dimensional properties of the training trajectory. The reduction method is efficient, supported by comprehensive experiments: optimizing DNNs in 40-dimensional spaces can achieve comparable performance as regular training over thousands or even millions of parameters. Since there are only a few variables to optimize, we develop an efficient quasi-Newton-based algorithm, obtain robustness to label noise, and improve the performance of well-trained models, which are three follow-up experiments that can show the advantages of finding such low-dimensional subspaces. The code is released (Pytorch: https://github.com/nblt/DLDR and Mindspore: https://gitee.com/mindspore/docs/tree/r1.6/docs/sample_code/dimension_reduce_training).

HMCES modulates the transcriptional regulation of nodal/activin and BMP signaling in mESCs.

Despite the fundamental roles of TGF-ß family signaling in cell fate determination in all metazoans, the mechanism by which these signals are spatially and temporally interpreted remains elusive. The cell-context-dependent function of TGF-ß signaling largely relies on transcriptional regulation by SMAD proteins. Here, we discover that the DNA repair-related protein, HMCES, contributes to early development by maintaining nodal/activin- or BMP-signaling-regulated transcriptional network. HMCES binds with R-SMAD proteins, co-localizing at active histone marks. However, HMCES chromatin occupancy is independent on nodal/activin or BMP signaling. Mechanistically, HMCES competitively binds chromatin to limit binding by R-SMAD proteins, thereby forcing their dissociation and resulting in repression of their regulatory effects. In Xenopus laevis embryo, hmces KD causes dramatic development defects with abnormal left-right axis asymmetry along with increasing expression of lefty1. These findings reveal HMCES transcriptional regulatory function in the context of TGF-ß family signaling.

Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex.

INTRODUCTION The nuclear pore complex (NPC) resides on the nuclear envelope (NE) and mediates nucleocytoplasmic cargo transport. As one of the largest cellular machineries, a vertebrate NPC consists of cytoplasmic filaments, a cytoplasmic ring (CR), an inner ring, a nuclear ring, a nuclear basket, and a luminal ring. Each NPC has eight repeating subunits. Structure determination of NPC is a prerequisite for understanding its functional mechanism. In the past two decades, integrative modeling, which combines x-ray structures of individual nucleoporins and subcomplexes with cryo-electron tomography reconstructions, has played a crucial role in advancing our knowledge about the NPC. The CR has been a major focus of structural investigation. The CR subunit of human NPC was reconstructed by cryo-electron tomography through subtomogram averaging to an overall resolution of ~20 Å, with local resolution up to ~15 Å. Each CR subunit comprises two Y-shaped multicomponent complexes known as the inner and outer Y complexes. Eight inner and eight outer Y complexes assemble in a head-to-tail fashion to form the proximal and distal rings, respectively, constituting the CR scaffold. To achieve higher resolution of the CR, we used single-particle cryo-electron microscopy (cryo-EM) to image the intact NPC from the NE of Xenopus laevis oocytes. Reconstructions of the core region and the Nup358 region of the X. laevis CR subunit had been achieved at average resolutions of 5 to 8 Å, allowing identification of secondary structural elements. RATIONALE Packing interactions among the components of the CR subunit were poorly defined by all previous EM maps. Additional components of the CR subunit are strongly suggested by the EM maps of 5- to 8-Å resolution but remain to be identified. Addressing these issues requires improved resolution of the cryo-EM reconstruction. Therefore, we may need to enhance sample preparation, optimize image acquisition, and develop an effective data-processing strategy. RESULTS To reduce conformational heterogeneity of the sample, we spread the opened NE onto the grids with minimal force and used the chemical cross-linker glutaraldehyde to stabilize the NPC. To alleviate orientation bias of the NPC, we tilted sample grids and imaged the sample with higher electron dose at higher angles. We improved the image-processing protocol. With these efforts, the average resolutions for the core and the Nup358 regions have been improved to 3.7 and 4.7 Å, respectively. The highest local resolution of the core region reaches 3.3 Å. In addition, a cryo-EM structure of the N-terminal α-helical domain of Nup358 has been resolved at 3.0-Å resolution. These EM maps allow the identification of five copies of Nup358, two copies of Nup93, two copies of Nup205, and two copies of Y complexes in each CR subunit. Relying on the EM maps and facilitated by AlphaFold prediction, we have generated a final model for the CR of the X. laevis NPC. Our model of the CR subunit includes 19,037 amino acids in 30 nucleoporins. A previously unknown C-terminal fragment of Nup160 was found to constitute a key part of the vertex, in which the short arm, long arm, and stem of the Y complex meet. The Nup160 C-terminal fragment directly binds the ß-propeller proteins Seh1 and Sec13. Two Nup205 molecules, which do not contact each other, bind the inner and outer Y complexes through distinct interfaces. Conformational elasticity of the two Nup205 molecules may underlie their versatility in binding to different nucleoporins in the proximal and distal CR rings. Two Nup93 molecules, each comprising an N-terminal extended helix and an ACE1 domain, bridge the Y complexes and Nup205. Nup93 and Nup205 together play a critical role in mediating the contacts between neighboring CR subunits. Five Nup358 molecules, each in the shape of a shrimp tail and named "the clamp," hold the stems of both Y complexes. The innate conformational elasticity allows each Nup358 clamp to adapt to a distinct local environment for optimal interactions with neighboring nucleoporins. In each CR subunit, the α-helical nucleoporins appear to provide the conformational elasticity; the 12 ß-propellers may strengthen the scaffold. CONCLUSION Our EM map-based model of the X. laevis CR subunit substantially expands the molecular mass over the reported composite models of vertebrate CR subunit. In addition to the Y complexes, five Nup358, two Nup205, and two Nup93 molecules constitute the key components of the CR. The improved EM maps reveal insights into the interfaces among the nucleoporins of the CR. [Figure: see text].

Differential expression of MSTN, IGF2BP1, and FABP2 across different embryonic ages and sexes in white Muscovy ducks.

To explore the effects of growth-related genes in both sexes and at different growth and development stages, male and female white Muscovy ducks at embryonic day E13, E17, E21, E25 and E29 were assessed in this study. RT-qPCR was used to determine the mRNA transcription levels of selected growth-related genes in the leg muscles of Muscovy ducks of both sexes and at different growth and developmental stages. MSTN, IGF2BP1 and FABP2 mRNAs were expressed in the leg muscles of male and female Muscovy ducks, but with different expression patterns. The MSTN and IGF2BP1 mRNA expression patterns were wavelike. MSTN mRNA expression was elevated at E13, increased at E17, decreased rapidly to the lowest level at E21, increased again at E25, and then decreased. IGF2BP1 mRNA expression was elevated at E13, increased at E17, decreased rapidly at E21, decreased rapidly to the lowest level at E25, and increased at E29. The expression trend of FABP2 mRNA was approximately "⊥" shape; the expression was the lowest at E13, increased slowly from E17 to E25, and increased extremely significantly at E29. In addition, the expression of MSTN in male Muscovy ducks was significantly higher than that in female ducks at E25 (P < 0.05). The expression of IGF2BP1 in male Muscovy ducks was extremely significantly higher than that in female ducks at E17 (P < 0.01). However, the expression of FABP2 in female Muscovy ducks was extremely significantly higher than that in male Muscovy ducks at E21 and E29 (P < 0.01). In conclusion, the mRNA expression of MSTN, IGF2BP1 and FABP2 in white Muscovy ducks is gestational age specific and sex specific. The differential gene expression patterns observed in this study provide a basis for understanding the physiological changes in white Muscovy ducks at different embryonic ages and in both sexes, supplementing the existing research on duck embryo muscle development. In addition, the findings provide a new framework for further discussion of poultry breeding.

Cryo-EM structure of the inner ring from the Xenopus laevis nuclear pore complex.

Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an average resolution of 4.2 Å. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin hetero-trimer of Nup62/58/54 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure reveals the molecular basis for the IR subunit assembly of a vertebrate NPC.

Cryo-EM structure of the nuclear ring from Xenopus laevis nuclear pore complex.

Nuclear pore complex (NPC) shuttles cargo across the nuclear envelope. Here we present single-particle cryo-EM structure of the nuclear ring (NR) subunit from Xenopus laevis NPC at an average resolution of 5.6 Å. The NR subunit comprises two 10-membered Y complexes, each with the nucleoporin ELYS closely associating with Nup160 and Nup37 of the long arm. Unlike the cytoplasmic ring (CR) or inner ring (IR), the NR subunit contains only one molecule each of Nup205 and Nup93. Nup205 binds both arms of the Y complexes and interacts with the stem of inner Y complex from the neighboring subunit. Nup93 connects the stems of inner and outer Y complexes within the same NR subunit, and places its N-terminal extended helix into the axial groove of Nup205 from the neighboring subunit. Together with other structural information, we have generated a composite atomic model of the central ring scaffold that includes the NR, IR, and CR. The IR is connected to the two outer rings mainly through Nup155. This model facilitates functional understanding of vertebrate NPC.

Center-Aware Adversarial Autoencoder for Anomaly Detection.

Anomaly detection based on subspace learning has attracted much attention, in which the compactness of subspace is commonly considered as the core concern. Most related studies directly optimize the distance from the subspace representation to the fixed center, and the influence of the anomaly level of each normal sample is not considered to adjust the normal concentrated areas. In such cases, it is difficult to isolate the normal areas from the anomaly ones by making the subspace compact. To this end, we propose a center-aware adversarial autoencoder (CA-AAE) method, which detects anomaly samples by acquiring more compact and discriminative subspace representations. To fully exploit the subspace information to improve the compactness, anomaly-level description and feature learning are novelly integrated herein by dividing the output space of the encoder into presubspace and postsubspace. In presubspace, the toward-center prior distribution is imposed by the adversarial learning mechanism, and the anomaly level of normal samples can be described from a probabilistic perspective. In postsubspace, a novel center-aware strategy is established to enhance the compactness of the postsubspace, which achieves adaptive adjustment of the normal areas by constructing a weighted center based on the anomaly level. Then, a flexible anomaly score function is constructed in the testing stage, in which both the toward-center loss and the reconstruction loss are combined to balance the information in the learned subspace and the original space. Compared to other related methods, the proposed CA-AAE shows the effectiveness and advantages in numerical experiments.

Toward Deep Adaptive Hinging Hyperplanes.

The adaptive hinging hyperplane (AHH) model is a popular piecewise linear representation with a generalized tree structure and has been successfully applied in dynamic system identification. In this article, we aim to construct the deep AHH (DAHH) model to extend and generalize the networking of AHH model for high-dimensional problems. The network structure of DAHH is determined through a forward growth, in which the activity ratio is introduced to select effective neurons and no connecting weights are involved between the layers. Then, all neurons in the DAHH network can be flexibly connected to the output in a skip-layer format, and only the corresponding weights are the parameters to optimize. With such a network framework, the backpropagation algorithm can be implemented in DAHH to efficiently tackle large-scale problems and the gradient vanishing problem is not encountered in the training of DAHH. In fact, the optimization problem of DAHH can maintain convexity with convex loss in the output layer, which brings natural advantages in optimization. Different from the existing neural networks, DAHH is easier to interpret, where neurons are connected sparsely and analysis of variance (ANOVA) decomposition can be applied, facilitating to revealing the interactions between variables. A theoretical analysis toward universal approximation ability and explicit domain partitions are also derived. Numerical experiments verify the effectiveness of the proposed DAHH.

Lysosomal degradation of the maternal dorsal determinant Hwa safeguards dorsal body axis formation.

The Spemann and Mangold Organizer (SMO) is of fundamental importance for dorsal ventral body axis formation during vertebrate embryogenesis. Maternal Huluwa (Hwa) has been identified as the dorsal determinant that is both necessary and sufficient for SMO formation. However, it remains unclear how Hwa is regulated. Here, we report that the E3 ubiquitin ligase zinc and ring finger 3 (ZNRF3) is essential for restricting the spatial activity of Hwa and therefore correct SMO formation in Xenopus laevis. ZNRF3 interacts with and ubiquitinates Hwa, thereby regulating its lysosomal trafficking and protein stability. Perturbation of ZNRF3 leads to the accumulation of Hwa and induction of an ectopic axis in embryos. Ectopic expression of ZNRF3 promotes Hwa degradation and dampens the axis-inducing activity of Hwa. Thus, our findings identify a substrate of ZNRF3, but also highlight the importance of the regulation of Hwa temporospatial activity in body axis formation in vertebrate embryos.

The relationship between dairy products intake and breast cancer incidence: a meta-analysis of observational studies.

BACKGROUND: The effect of dairy products intake on breast cancer (BC) is highly controversial. This study aims to investigate the relationship between dairy intake and BC incidence. METHODS: A search was carried out in PubMed, EBSCO, Web of Science, and Cochrane Library databases before January 2021. The primary objective was the risk of BC and intake of dairy products were exposure variables. RESULTS: The meta-analysis comprised 36 articles with 1,019,232 participants. Total dairy products have a protective effect on female population (hazard ratio (HR) =0.95, 95% confidence interval (CI) =0.91-0.99, p = 0.019), especially for estrogen receptor-positive (ER+) (HR = 0.79, p = 0.002) and progesterone receptor-positive (PR+) BC (HR = 0.75, p = 0.027). For ER+/PR+ BC, there is a trend of protection, but it has not reached statistical significance (HR = 0.92, p = 0.075). Fermented dairy products can reduce BC risk in postmenopausal population (HR = 0.96, 95%CI = 0.93-0.99, p = 0.021), but have no protective effect on premenopausal population (HR = 0.98, 95%CI = 0.94-1.03, p = 0.52). Non-fermented dairy products have no significant effect on BC occurrence (p > 0.05). High-fat dairy products are harmful to women, without statistical difference (HR = 1.06, 95%CI = 1.00-1.13, p = 0.066). On the contrary, low-fat dairy products can protect the premenopausal population (HR = 0.94, 95%CI = 0.89-1.00, p = 0.048). CONCLUSION: The intake of dairy products can overall reduce BC risk in the female population, but different dairy products have varying effects on different BC subtypes and menopausal status.

The cytokine FAM3B/PANDER is an FGFR ligand that promotes posterior development in Xenopus.

Fibroblast growth factor (FGF)/extracellular signal-regulated kinase (ERK) signaling plays a crucial role in anterior-posterior (A-P) axial patterning of vertebrate embryos by promoting posterior development. In our screens for novel developmental regulators in Xenopus embryos, we identified Fam3b as a secreted factor regulated in ectodermal explants. Family with sequence similarity 3 member B (FAM3B)/PANDER (pancreatic-derived factor) is a cytokine involved in glucose metabolism, type 2 diabetes, and cancer in mammals. However, the molecular mechanism of FAM3B action in these processes remains poorly understood, largely because its receptor is still unidentified. Here we uncover an unexpected role of FAM3B acting as a FGF receptor (FGFR) ligand in Xenopus embryos. fam3b messenger RNA (mRNA) is initially expressed maternally and uniformly in the early Xenopus embryo and then in the epidermis at neurula stages. Overexpression of Xenopus fam3b mRNA inhibited cephalic structures and induced ectopic tail-like structures. Recombinant human FAM3B protein was purified readily from transfected tissue culture cells and, when injected into the blastocoele cavity, also caused outgrowth of tail-like structures at the expense of anterior structures, indicating FGF-like activity. Depletion of fam3b by specific antisense morpholino oligonucleotides in Xenopus resulted in macrocephaly in tailbud tadpoles, rescuable by FAM3B protein. Mechanistically, FAM3B protein bound to FGFR and activated the downstream ERK signaling in an FGFR-dependent manner. In Xenopus embryos, FGFR activity was required epistatically downstream of Fam3b to mediate its promotion of posterior cell fates. Our findings define a FAM3B/FGFR/ERK-signaling pathway that is required for axial patterning in Xenopus embryos and may provide molecular insights into FAM3B-associated human diseases.

Phase separation of Axin organizes the ß-catenin destruction complex.

In Wnt/ß-catenin signaling, the ß-catenin protein level is deliberately controlled by the assembly of the multiprotein ß-catenin destruction complex composed of Axin, adenomatous polyposis coli (APC), glycogen synthase kinase 3ß (GSK3ß), casein kinase 1α (CK1α), and others. Here we provide compelling evidence that formation of the destruction complex is driven by protein liquid-liquid phase separation (LLPS) of Axin. An intrinsically disordered region in Axin plays an important role in driving its LLPS. Phase-separated Axin provides a scaffold for recruiting GSK3ß, CK1α, and ß-catenin. APC also undergoes LLPS in vitro and enhances the size and dynamics of Axin phase droplets. The LLPS-driven assembly of the destruction complex facilitates ß-catenin phosphorylation by GSK3ß and is critical for the regulation of ß-catenin protein stability and thus Wnt/ß-catenin signaling.

Efficacy of Huanglian root decoction on kidney injury in rat's model of metabolic syndrome.

OBJECTIVE: To evaluate the efficacy of Huanglian root decoction (, HLD) on kidney injury in rat's model of metabolic syndrome (MetS), and investigate the possible mechanism. METHODS: A fructose-induced MetS rat model and human renal tubular epithelial cell-line model were used to compare the efficacy of HLD with that of berberine and tauroursodeoxycholic acid (TUDCA). Blood pressure, biochemical parameters, histopathological changes and the expression levels of oxidative stress markers were evaluated in the animal model at the end of an 8-week treatment regimen. Oxidative stress markers and molecules of the signal pathway of endoplasmic reticulum (ER) stress were evaluated in the human cell-line model. RESULTS: Levels of fasting insulin, systolic blood pressure and diastolic blood pressure were significantly decreased in rats in the Huanglian group compared to those in the MetS group (P < 0.05). Rats treated with HLD and TUDCA exhibited a significant reduction in blood levels of malondialdehyde compared to those in rats in the MetS group (P < 0.05). Significant increases in glutathione peroxidase in human tubular epithelial cells was found in the Huanglian group compared to that in the MetS group (14.02 vs 18.31, P < 0.05). The mRNA expression of protein kinase RNA-like endoplasmic reticulum kinase and eukaryotic translation initiation factor 2 α decreased significantly in Huanglian groups compared with that in the MetS group. CONCLUSION: HLD has therapeutic efficacy on kidney injury in the MetS rat's model, and is non-inferior to berberine and TUDCA.

Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex.

The nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ring (LR) of the NPC from Xenopus laevis oocyte. The observed key structural features of the LR are independently confirmed by single-particle cryo-electron microscopy (cryo-EM) analysis. The LR comprises eight butterfly-shaped subunits, each containing two symmetric wings. Each wing consists of four elongated, tubular protomers. Within the LR subunit, the eight protomers form a Finger domain, which directly contacts the fusion between the inner and outer nuclear membranes and a Grid domain, which serves as a rigid base for the Finger domain. Two neighboring LR subunits interact with each other through the lateral edges of their wings to constitute a Bumper domain, which displays two major conformations and appears to cushion neighboring NPCs. Our study reveals previously unknown features of the LR and potentially explains the elastic property of the NPC.

Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis.

The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.

Expression of the hormonal FGF co-receptor Klotho beta in the Xenopus laevis model.

Klotho beta (Klb), a single-pass transmembrane protein, has been described as a co-receptor for endocrine FGFs, such as FGF15/19 and FGF21, to regulate critical metabolic processes in multiple organs and tissues in adult mice. However, its function during early embryonic development remains largely unknown. In this paper, we evaluated for the first time the expression of klb mRNA during early development of Xenopus laevis by RT-PCR and whole mount in situ hybridization. RT-PCR experiments showed that the expression of klb was initially detected at late gastrula stage followed by a quick increasing and continued expression throughout embryonic development. Whole mount in situ hybridization detected specific expression of klb in many primordial organs at tailbud stage such as liver primordium and pancreatic buds, implying that the hormonal FGF signaling may play a role in the foregut development. The dynamic and specific expression patterns of klb also suggest that Xenopus laevis can serve a convenient model for the function of the hormonal FGF signaling in organogenesis and metabolism regulation during embryonic development.

Maternal Huluwa dictates the embryonic body axis through ß-catenin in vertebrates.

The vertebrate body is formed by cell movements and shape change during embryogenesis. It remains undetermined which maternal signals govern the formation of the dorsal organizer and the body axis. We found that maternal depletion of huluwa, a previously unnamed gene, causes loss of the dorsal organizer, the head, and the body axis in zebrafish and Xenopus embryos. Huluwa protein is found on the plasma membrane of blastomeres in the future dorsal region in early zebrafish blastulas. Huluwa has strong dorsalizing and secondary axis-inducing activities, which require ß-catenin but can function independent of Wnt ligand/receptor signaling. Mechanistically, Huluwa binds to and promotes the tankyrase-mediated degradation of Axin. Therefore, maternal Huluwa is an essential determinant of the dorsal organizer and body axis in vertebrate embryos.