EDomics: a comprehensive and comparative multi-omics database for animal evo-devo.

Evolutionary developmental biology (evo-devo) has been among the most fascinating interdisciplinary fields for decades, which aims to elucidate the origin and evolution of diverse developmental processes. The rapid accumulation of omics data provides unprecedented opportunities to answer many interesting but unresolved evo-devo questions. However, the access and utilization of these resources are hindered by challenges particularly in non-model animals. Here, we establish a comparative multi-omics database for animal evo-devo (EDomics, http://edomics.qnlm.ac) containing comprehensive genomes, bulk transcriptomes, and single-cell data across 40 representative species, many of which are generally used as model organisms for animal evo-devo study. EDomics provides a systematic view of genomic/transcriptomic information from various aspects, including genome assembly statistics, gene features and families, transcription factors, transposable elements, and gene expressional profiles/networks. It also exhibits spatiotemporal gene expression profiles at a single-cell level, such as cell atlas, cell markers, and spatial-map information. Moreover, EDomics provides highly valuable, customized datasets/resources for evo-devo research, including gene family expansion/contraction, inferred core gene repertoires, macrosynteny analysis for karyotype evolution, and cell type evolution analysis. EDomics presents a comprehensive and comparative multi-omics platform for animal evo-devo community to decipher the whole history of developmental evolution across the tree of life.

Fine Tuning Metal-Organic Frameworks with Halogen Functional Groups for Ethylene Purification.

One-step C2H4 purification from a mixture of C2H2/C2H4/C2H6 could be achieved by metal-organic framework (MOF) NTUniv-70 with an F-functional group. The selectivities of C2H4/C2H6 and C2H4/C2H2 of NTUnvi-70 based on ideal adsorbed solution theory were at least twice that of the original MOF platform, which was in line with the enthalpy of adsorption (Qst) and breakthrough testing. Grand canonical Monte Carlo simulations indicated that the C-H···F interactions played an important role in enhanced C2H4/C2H6 and C2H4/C2H2 adsorption selectivities.

Tuning Multiple Counter-Anions in Porous Coordination Polymers with lcy Topology for Acetylene/Ethylene Separation.

The efficient separation of acetylene (C2H2) and ethylene (C2H4) is an important and complex process in the industry. Herein, we report a new family of lcy-topologic coordination frameworks (termed NTU-90 to NTU-92) with Cu3MF6 (M = Si, Ti, and Zr) nodes. These charged frameworks are compensated by different counterbalanced ions (MF62-, BF4-, and Cl-), yielding changes in the size of the window apertures. Among these frameworks, NTU-92-a (activated NTU-92) shows good adsorption selectivity of C2H2/C2H4 and also significant ability in recovering both highly pure C2H4 (99.95%) and C2H2 (99.98%). Our work not only presents a potential alternative for energy-saving purification of C2 hydrocarbons but also provides a new approach for tuning the function of charged porous materials.

Flow Channel with Wrinkles and Calcium Sites in a Ca-MOF for Direct One-Step Ethylene Purification from C2 Gases and MTO Products Separation.

The strategy of flow channel with wrinkles and calcium sites for single-step C2H4 purification from C2 gases and methanol-to-olefins (MTO) products separation was realized in FJI-Y9. The adsorption amounts showed a total reversal order of C3H6 > C2H6 > C2H2 > C2H4 at 298 K. Modeling indicated that the wrinkles and Ca2+ facilitated the full contact of C3H6 and C2H6. Breakthrough experiments illustrated that FJI-Y9 could yield pure C2H4 in a single step with a productivity of 0.78 mmol g-1. In a lone adsorption/desorption cycle for MTO product separation, the productivities of C3H6 and C2H4 were 1.96 and 1.29 mol g-1, standing as the highest recorded values.

A novel KRIT1/CCM1 mutation accompanied by a NOTCH3 mutation in a Chinese family with multiple cerebral cavernous malformations.

Family cerebral cavernous malformations (FCCMs) are mainly inherited through the mutation of classical CCM genes, including CCM1/KRIT1, CCM2/MGC4607, and CCM3/PDCD10. FCCMs can cause severe clinical symptoms, including epileptic seizures, intracranial hemorrhage (ICH), or functional neurological deficits (FNDs). In this study, we reported a novel mutation in KRIT1 accompanied by a NOTCH3 mutation in a Chinese family. This family consists of 8 members, 4 of whom had been diagnosed with CCMs using cerebral MRI (T1WI, T2WI, SWI). The proband (II-2) and her daughter (III-4) had intracerebral hemorrhage and refractory epilepsy, respectively. Based on whole-exome sequencing (WES) data and bioinformatics analysis from 4 patients with multiple CCMs and 2 normal first-degree relatives, a novel KRIT1 mutation, NG_012964.1 (NM_194456.1): c.1255-1G > T (splice-3), in intron 13 was considered a pathogenic gene in this family. Furthermore, based on 2 severe and 2 mild CCM patients, we found an SNV missense mutation, NG_009819.1 (NM_000435.2): c.1630C > T (p.R544C), in NOTCH3. Finally, the KRIT1 and NOTCH3 mutations were validated in 8 members using Sanger sequencing. This study revealed a novel KRIT1 mutation, NG_012964.1 (NM_194456.1): c.1255-1G > T (splice-3), in a Chinese CCM family, which had not been reported previously. Moreover, the NOTCH3 mutation NG_009819.1 (NM_000435.2): c.1630C > T (p.R544C) might be a second hit and associated with the progression of CCM lesions and severe clinical symptoms.

Polarimetric calibration method for the fore-optics of a channeled spectropolarimeter.

A channeled spectropolarimeter is a powerful tool for the simultaneous measurement of the intensity, spectral, and polarization information of a target. However, the fore-optics introduce additional polarization information, which leads to inaccurate reconstruction of the Stokes parameters. In this study, we propose a simple method for polarimetric calibration and Stokes parameters reconstruction for a fieldable channeled spectropolarimeter. The polarization effects of the fore-optics and phase factors of the high-order retarders at varying view angles are considered and calibrated independently using a single reference beam. Moreover, the misalignment of the retarders is also considered. Simulation results demonstrate that the polarization effects of fore-optics can be precisely determined, enhancing the measurement accuracy of the Stokes parameters by approximately an order of magnitude. The effectiveness of the proposed method is also verified experimentally.

Deep learning for sub-Nyquist sampling scanning white light interferometry.

This Letter introduces sub-Nyquist sampling vertical scanning white light interferometry (SWLI) using deep learning. The method designs Envelope-Deep Residual Shrinkage Networks with channel-wise thresholds (E-DRSN-cw), a network model extracting oversampling envelopes from undersampled signals. The model improves the training efficiency, accuracy, and robustness by following the soft thresholding nonlinear layer approach, pre-padding undersampled interference signals with zeros, using LayerNorm for augmenting inputs and labels, and predicting regression envelopes. Simulation data train the network, and experiments demonstrate its superior performance over classical methods in the accuracy and the robustness. The E-DRSN-cw provides a swift measurement solution for SWLI, removing the need for prior knowledge.

Fine-Tuning MOFs with Amino Group for One-Step Ethylene Purification from the C2 Hydrocarbon Mixture.

Due to the similar kinetic diameters of C2H2, C2H4, and C2H6, one-step purification of C2H4 from a ternary C2H2/C2H4/C2H6 mixture by adsorption separation is still a challenge. Based on a C2H6-trapping platform and crystal engineering strategy, the N atom and amino group were introduced into NTUniv-58 and NTUniv-59, respectively. Gas adsorption testing of NTUniv-58 showed that both the C2H2 and C2H4 uptake capacities and the C2H2/C2H4 separation ability were boosted compared with the original platform. However, the C2H4 uptake value exceeds the C2H6 adsorption data. For NTUniv-59, the C2H2 uptake at low pressure increased and the C2H4 uptake decreased; thus, the C2H2/C2H4 selectivity was enhanced and the one-step purification of C2H4 from a ternary C2H2/C2H4/C2H6 mixture was realized, which was supported by the enthalpy of adsorption (Qst) and breakthrough testing. Grand canonical monte carlo (GCMC) simulation indicated that the preference for C2H2 over C2H4 originates from multiple hydrogen-bonding interactions between amino groups and C2H2 molecules.

Expanding MOF with Unexpanded Channel via Ketone Decorated Ligand for Ethylene Purification and Stability Enhancement.

The concept of an expanding MOF with unexpanded channel size was realized in MOF NTUniv-61 by the utilization of a ketone-functional-group-decorated semirigid ligand and pillar-layer platform. After this unusual expansion, the preferential C2H6 adsorption was preserved via the unchanged pore size, and the functional group was inserted into the MOF. Interestingly, the C2H2 uptake ability, C2H4 selective adsorption ability, and structural stability were obviously enhanced due to the incorporation of the ketone functional group, which were further verified by isosteric heats of adsorption (Qst), GCMC modeling, and breakthrough experiments.

Creating an Ethane Trap in a Ketone-Decorated MOF for One-Step Ethylene Separation from C2 Hydrocarbons.

One-step C2H4 purification from a mixture of C2H2/C2H4/C2H6 by physical adsorption separation was realized via creating an ethane trap in MOF NTUniv-63 by the utilization of a ketone-decorated semirigid ligand, which has further been verified by the breakthrough experiment, isosteric heats of adsorption (Qst), and Grand Canonical Monte Carlo (GCMC) modeling.

Channeled spectropolarimeter with arbitrary retarder orientation settings.

A channeled spectropolarimeter can simultaneously obtain intensity, spectral, and polarization information. In the traditional model, the retarders must be oriented at specific angles. However, misalignments of the retarders are inevitable during assembly, and the status of the retarders is sensitive to environmental perturbations, which affects the performance of the channeled spectropolarimeter. In this study, a general channeled spectropolarimeter model was derived, in which the retarder orientations can be arbitrary and unknown. Meanwhile, the system is unaffected by environmental perturbation because it can self-calibrate to avoid fluctuations in the retarder orientations and phase retardations. The effectiveness and robustness of the model were verified through simulations and experiments.

Significantly Enhanced Carbon Dioxide Selective Adsorption via Gradual Acylamide Truncation in MOFs: Experimental and Theoretical Research.

A gradual amide truncation strategy was presented to tune the pore chemistry and CO2 capture performance of a series of tetracarboxylate-based Cu-MOFs. These MOFs exhibited a high density of Lewis basic sites (LBSs) and open metal sites and were prepared with the goal to enhance CO2 selective adsorption capacity. [Cu2(L1)(H2O)2]n (NJU-Bai42: NJU-Bai for Nanjing University Bai's group), [Cu2(L2) (H2O)2]n (NJU-Bai17), and [Cu2(L3)(H2O)2]n (NTUniv-60: NTUniv for Nantong University) were synthesized, and we observed that the CO2 adsorption capacities and MOF structures were impacted by subtle changes in ligands. Interestingly, although the NTUniv-60 was decorated with the least LBSs in these three MOFs, its CO2 adsorption capacity reached 270 (53.0 wt %) and 164 (32.2 wt %) cm3 g-1 at 273 and 296 K under 1 bar, respectively, which is the highest data reported for MOFs under similar conditions. From the grand canonical Monte Carlo (GCMC) simulation, the cooperative interactions between the CO2 molecules within the shuttle-shaped cages of NTUniv-60 could potentially explain why the CO2 uptake is high in this material.

MOF Pillaring Method: Ligand-to-Ligand and Axial-to-Axial Cross-Linking of "Paddlewheels".

By shortening the previous shortest tetracarboxylate ligand, the first ligand-to-ligand and axial-to-axial pillaring method was realized in the prototype MOF NTUniv-56 (NTUniv = Nantong University), which exhibit a rare (2,4,6)-connected net with a new topology and interesting gas adsorption performance.

Formation of a Polar Flow Channel with Embedded Gas Recognition Pockets in a Yttrium-Based MOF for Enhanced C2H2/C2H4 and CO2 Selective Adsorptions.

A polar flow channel with embedded gas recognition pockets was made in a 10-connected hexanuclear yttrium-based metal-organic frameworks (MOF) NTUniv-57 (NTUniv = Nantong University) by lowering the symmetry of the ligand, which showed high chemical stability and obviously enhanced gas adsorption selectivities.

Finely Tuning Tridentate Carboxylic Acids for the Construction of Rod Scandium Metal-Organic Frameworks with High Chemical Stability and Selective Gas Adsorption.

By systematic ligand tuning for control of the secondary building units, the use of tridentate carboxylic acid to construct the rod scandium metal-organic framework NTUniv-55 (NTUniv = Nantong University) with high chemical stability and interesting selective gas adsorption was reported.

Co-exposure to fluoride and arsenic disrupts intestinal flora balance and induces testicular autophagy in offspring rats.

While numerous studies have shown that fluoride or arsenic exposure may damage the reproductive system, there are few reports of co-exposure to fluoride and arsenic. In addition, the literature on autophagy and intestinal flora composition in reproductive toxicity studies of co-exposure to fluoride and arsenic is insufficient. In this study, we developed a rat model of fluoride and arsenic exposure via drinking water from pre-pregnancy to 90 days postnatal. Sprague-Dawley rats were randomly divided into sterile water control group, fluoride group (100 mg/L NaF), arsenic group (50 mg/L NaAsO2) and combined exposure group (100 mg/L NaF+50 mg/L NaAsO2). Our results showed that fluoride and arsenic exposure caused a reduction in testicular weight and significant pathological damage to tissue. We found that the levels of follicle-stimulating hormone, luteinizing hormone, and testosterone were reduced to varying degrees. Meanwhile experiments showed that fluoride and arsenic exposure can modulate autophagic flux, causing increased levels of Beclin1 and LC3 expression and decreased p62 expression. Analogously, by performing 16S sequencing of rat feces, we found 24 enterobacterial genera that differed significantly among the groups. Furthermore, the flora associated with testicular injury were identified by correlation analysis of hormonal indices and autophagy alterations with intestinal flora composition at the genus level, respectively. In summary, our study shows that fluoride and arsenic co-exposure alters autophagic flux in the testis, causes testicular injury, and reveals an association between altered intestinal flora composition and testicular injury.

Proteomics and transcriptomics jointly identify the key role of oxidative phosphorylation in fluoride-induced myocardial mitochondrial dysfunction in rats.

The regulation of mitochondrial function, which is dominated by oxidative phosphorylation (OXPHOs), is important in fluoride induced cardiovascular disease. Based on the previous study of fluoride-induced mitochondrial structure and membrane potential abnormalities, this study integrated ITRAQ protein quantification and RNA-Seq methods to analyze the sequencing data of rat myocardial tissue under fluoride exposure (0, 30, 60 and 90 mg/L). A total of 22 differentially expressed genes associated with the OXPHOs pathway were screened by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) co-enrichment analysis, and were localizated by Interaction Network and calculated inter-genes and inter-omics correlations by Pearson correlation. In general, fluoride exposure can down-regulate genes related OXPHOs, particularly affecting the assembly of the complex I including Ndufa10, resulting in abnormal mitochondrial ATP synthesis and reduced myocardial energy supply. Most importantly, this study shows that the enriched information from the proteomics can explain the change process of energy production, but the specific molecules involved in energy supply cannot be obtained via transcriptomics information alone. Based on the results of transcriptional and protein analysis, our findings contribute to an innovative understanding of the pathways and molecular changes of myocardial injury induced by fluorosis.

Effects of arsenic exposure on lipid metabolism: a systematic review and meta-analysis.

Lipid metabolism dysfunction is a risk factor for cardiovascular diseases. Reportedly, arsenic exposure could affect lipid metabolism, but this finding remains controversial. Herein, we updated and reevaluated evidence regarding the relationship between arsenic exposure and lipid metabolism. Electronic and manual searches were performed to determine the effect of arsenic exposure on lipid metabolism from inception up to 30 November 2019. Overall, five studies were included in our meta-analysis. Two reviewers independently extracted information. Standardized mean difference (SMD) and 95% confidence intervals (CI) were used to analyze the combined effects of four indicators related to lipid metabolism (total cholesterol [TC], triglyceride [TG], high-density lipoprotein [HDL], low-density lipoprotein [LDL]). Afterwards, subgroup and sensitivity analyses were performed to explore the source of heterogeneity. Publication bias was tested using funnel plots and Begg's test. In this study, we observed that arsenic exposure can affect lipid metabolism by reducing serum HDL levels and increasing serum LDL levels. Following subgroup analysis, the arsenic concentration appeared to affect lipid metabolism. Funnel plot and Begg's test suggested no asymmetry. In conclusion, we recommend that potential influencing factors, including age, exposure time, and multiple concentration gradients, should be considered to further explore the relationship between arsenic exposure and lipid metabolism.

ITRAQ-based proteomics reveals the potential mechanism of fluoride-induced myocardial contraction function damage.

Fluorosis is a worldwide public health problem, and its adverse effects on the heart have been confirmed by many studies. Abnormal myocardial contractions are often associated with impairment of cardiac function as a cause or consequence. We designed two-part experiments to search for biomarkers and clarify the underlying molecular mechanism of fluoride on myocardial contraction. First, we used Pressure-volume Loop analysis to evaluate changes in myocardial function indexes with multiple fluoride exposure levels in mice (0, 30, 70, and 150 mg/L) exposed for 4 weeks. The results showed that fluoride exposure affects the heart pump function and reduces cardiac contractility. Then, we established a rat model of fluoride exposure (0, 30, 60, and 90 mg/L) for 6 months to carry out proteomic analysis of fluoride-induced myocardial contractile injury. Hematoxylin-eosin (H&E) staining was used to determine the severity of myocardial injury, and myocardial tissue samples were submitted for isobaric tags for relative and absolute quantitation (ITRAQ) analysis. A total of 1607 proteins were successfully identified with 294 differentially expressed proteins (DEPs) in fluoride treated groups. According to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, 12 DEPs were confirmed to be involved in pathways related to myocardial contraction. Furthermore, we constructed a protein-protein interaction (PPI) network for these 12 core DEPs to illustrate the role and location of each DEP in the myocardial contraction pathway. The results of this study are helpful for identify a potential mechanism and biomarkers of fluoride-induced myocardial contraction function damage, moreover, which can provide a new insight into the heart toxicity of fluoride in animals at the proteomics level.

Prediction of potential distributions of Morina kokonorica and Morina chinensis in China.

Changes in the habitats of species can provide insights into the impact of climate change on their habitats. Species in the genus Morina (Morinoideae) are perennial herbaceous plants that are mainly distributed in the South Asian Mountains and Eastern Mediterranean. In China, there are four species and two varieties of this genus distributed across the Yunnan, Sichuan, Qinghai, and Gansu provinces. This study used the optimal MaxEnt model to simulate past, current, and future potentially suitable habitats of Morina kokonorica and Morina chinensis. Seventy data of M. kokonorica occurrences and 3 of M. chinensis were used in the model to predict potentially suitable habitats. The model prediction results indicated that both M. kokonorica and M. chinensis exhibited trends of northward migration to higher latitudes and westward migration along the Himalayas to higher elevations, suggesting that the northern valleys of Hengduan Mountains and northern and eastern parts of the Himalayas were potential refugia for M. kokonorica, and the potential refugia for M. chinensis was located in the eastern part of Qinghai-Tibet Plateau. The results of this niche analysis showed that the two species had higher levels of interspecific competition and that the environmental adaptability of M. chinensis was stronger. This research could help further understand the response pattern of Morina to environmental change, to understand the adaptability of species to the environment, and promote the protection of species.