Pan-Genome of Wild and Cultivated Soybeans.

Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.

Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.

Ubiquitination constitutes one of the most important signaling mechanisms in eukaryotes. Conventional ubiquitination is catalyzed by the universally conserved E1-E2-E3 three-enzyme cascade in an ATP-dependent manner. The newly identified SidE family effectors of the pathogen Legionella pneumophila ubiquitinate several human proteins by a different mechanism without engaging any of the conventional ubiquitination machinery. We now report the crystal structures of SidE alone and in complex with ubiquitin, NAD, and ADP-ribose, thereby capturing different conformations of SidE before and after ubiquitin and ligand binding. The structures of ubiquitin bound to both mART and PDE domains reveal several unique features of the two reaction steps catalyzed by SidE. Further, the structural and biochemical results demonstrate that SidE family members do not recognize specific structural folds of the substrate proteins. Our studies provide both structural explanations for the functional observations and new insights into the molecular mechanisms of this non-canonical ubiquitination machinery.

Performance evaluation of the effect of humic acid on Anammox granular sludge: Apparent morphology, nitrogen removal and microbial community.

Humic acid (HA) is a typical refractory organic matter, so it is of great significance to investigate its effect on the performance of Anammox granular sludge. When the dosage of HA ≤ 50 mg/L, HA promotes the total nitrogen removal rate (NRR) to 1.45 kg/(m3·day). When HA was between 50 and 100 mg/L, the NRR of Anammox was stable. At this time, the adsorption of HA causes the sludge to gradually turn from red to brown, but the activities of heme and enzymes showed that its capacity was not affected. When HA levels reached 250 mg/L, the NRR dropped to 0.11 kg/(m3·day). Moderate HA levels promoted the release of extracellular polymeric substance (EPS), but excessive HA levels lead to a decrease in EPS concentrations. HA inhibited Anammox activity, which indirectly hindered the transmission of substrate and accumulated substrate toxicity. Although HA promoted the increase of heterotrophic microbial abundance in Anammox system, the microbial diversity decreased gradually. With the increase of HA concentration, the abundance of Candidatus_Brocadia, the main functional microorganism of Anammox system, decreased gradually, while the abundance of Candidatus_Kuenenia increased gradually.

A review on the transformation of birnessite in the environment: Implication for the stabilization of heavy metals.

Birnessite is ubiquitous in the natural environment where heavy metals are retained and easily transformed. The surface properties and structure of birnessite change with the changes in external environmental conditions, which also affects the fate of heavy metals. Clarifying the effect and mechanism of the birnessite phase transition process on heavy metals is the key to taking effective measures to prevent and control heavy metal pollution. Therefore, the four transformation pathways of birnessite are summarized first in this review. Second, the relationship between transformation pathways and environmental conditions is proposed. These relevant environmental conditions include abiotic (e.g., co-existing ions, pH, oxygen pressure, temperature, electric field, light, aging, pressure) and biotic factors (e.g., microorganisms, biomolecules). The phase transformation is achieved by the key intermediate of Mn(III) through interlayer-condensation, folding, neutralization-disproportionation, and dissolution-recrystallization mechanisms. The AOS (average oxidation state) of Mn and interlayer spacing are closely correlated with the phase transformation of birnessite. Last but not least, the mechanisms of heavy metals immobilization in the transformation process of birnessite are summed up. They involve isomorphous substitution, redox, complexation, hydration/dehydration, etc. The transformation of birnessite and its implication on heavy metals will be helpful for understanding and predicting the behavior of heavy metals and the crucial phase of manganese oxides/hydroxides in natural and engineered environments.

Gram-level NH3 Electrosynthesis via NOx reduction on a Cu Activated Co Electrode.

Ambient electrochemical ammonia (NH3 ) synthesis is one promising alternative to the energy-intensive Haber-Bosch route. However, the industrial requirement for the electrochemical NH3 production with amperes current densities or gram-level NH3 yield remains a grand challenge. Herein, we report the high-rate NH3 production via NO2 - reduction using the Cu activated Co electrode in a bipolar membrane (BPM) assemble electrolyser, wherein BPM maintains the ion balance and the liquid level of electrolyte. Benefited from the abundant Co sites and optimal structure, the target modified Co foam electrode delivers a current density of 2.64 A cm-2 with the Faradaic efficiency of 96.45 % and the high NH3 yield rate of 279.44 mg h-1 cm-2 in H-type cell using alkaline electrolyte. Combined with in situ experiments and theoretical calculations, we found that Cu optimizes the adsorption behavior of NO2 - and facilitates the hydrogenation steps on Co sites toward a rapid NO2 - reduction process. Importantly, this activated Co electrode affords a large NH3 production up to 4.11 g h-1 in a homemade reactor, highlighting its large-scale practical feasibility.

Failure to achieve reduction on developmental dysplasia of hip: an ultrasound evaluation.

BACKGROUND: Ultrasound examination of the medial side of the hip joint has been rarely used to evaluate the status of developmental dysplasia of the hip (DDH) in Pavlik harness treatment according to the literature. PURPOSE: To analyze the effects of cartilaginous acetabulum, hip joint labrum, and acetabular tissue on the reduction of DDH. MATERIAL AND METHODS: A total of 50 cases (100 hips) were detected by the Graf method with a high-frequency linear transducer (L 5-12), and there were 59 dislocated hips and 41 non-dislocated hips. Patients were treated with a Pavlik harness. Ultrasound examination of the medial side of the hip joint was performed for follow-up. The hip joints were divided into three groups: the non-dislocated group; the reducible group; and the non-reducible group. RESULTS: The success rate of reduction was significantly higher when the acetabulum cartilage was located on the cephalic side (chi-square = 28.12, P < 0.001). The success rate was also significantly higher when the hip joint labrum was located on the cephalic side (chi-square = 17.21, P < 0.001). Type III and D had a higher success rate of reduction than type IV (P < 0.001). The pairwise comparison of the measurements of acetabular tissue between the non-dislocated group, the reducible group, and the non-reducible group showed statistical differences (P < 0.001). CONCLUSION: The present study confirmed that the location of acetabulum cartilage and hip joint labrum affected the outcome of treatment. The degree of dislocation and the amount of acetabular tissue were correlated with the success rate of treatment.

Colorimetric High-Throughput Screening Method for Directed Evolution of Prazole Sulfide Monooxygenase.

Baeyer-Villiger monooxygenases (BVMOs) are important biocatalysts for the enzymatic synthesis of chiral sulfoxides, including chiral sulfoxide-type proton pump inhibitors for the treatment of gastrointestinal diseases. However, native BVMOs are not yet suitable for practical application due to their unsatisfactory activity and thermostability. Although protein engineering approaches can help address these issues, few feasible high-throughput methods are available for the engineering of such enzymes. Herein, a colorimetric detection method to distinguish sulfoxides from sulfides and sulfones was developed for prazole sulfide monooxygenases. Directed evolution enabled by this method has identified a prazole sulfide monooxygenase CbBVMO variant with improved activity and thermostability that catalyzes the asymmetric oxidation of lansoprazole sulfide. A 71.3 % increase in conversion and 6 °C enhancement in the melting point were achieved compared with the wild-type enzyme. This new method is feasible for high-throughput screening of prazole sulfide monooxygenase variants with improved activity, thermostability, and/or substrate specificity.

Deep eutectic solvent for spent lithium-ion battery recycling: comparison with inorganic acid leaching.

Deep eutectic solvents (DESs) as novel green solvents are potential options to replace inorganic acids for hydrometallurgy. Compared with inorganic acids, the physicochemical properties of DESs and their applications in recycling of spent lithium-ion batteries were summarized. The viscosity, metal solubility, toxicological properties and biodegradation of DESs depend on the hydrogen bond donor (HBD) and acceptor (HBA). The viscosity of ChCl-based DESs increased according to the HBD in the following order: alcohols < carboxylic acids < sugars < inorganic salts. The strongly coordinating HBDs increased the solubility of metal oxide via surface complexation reactions followed by ligand exchange for chloride in the bulk solvent. Interestingly, the safety and degradability of DESs reported in the literature are superior to those of inorganic acids. Both DESs and inorganic acids have excellent metal leaching efficiencies (>99%). However, the reaction kinetics of DESs are 2-3 orders of magnitude slower than those of inorganic acids. A significant advantage of DESs is that they can be regenerated and recycled multiple times after recovering metals by electrochemical deposition or precipitation. In the future, the development of efficient and selective DESs still requires a lot of attention.

Use of ultrasonography to evaluate early outcomes of reduction in developmental dysplasia of the hip.

OBJECTIVE: To compare pubo-femoral distance (PFD) in normal hips and those treated for developmental dysplasia of the hip (DDH) and to investigate the value of ultrasonography from the medial hip in early follow-up of dislocated DDH after reduction. MATERIALS AND METHODS: This study included 58 infants (49 females) with DDH who presented with 65 dislocated hips (51 unilateral and 7 bilateral). Dislocation was treated by closed reduction for 53 and open reduction for 12 hips. Ultrasonography on the medial side of the hip was performed within 1-2 weeks and 4 weeks after reduction. The distance from the pubic bone to the femoral head (PFD) was measured to assess the reduction and stability of the femoral head and compared to that on the contralateral side (control) in cases of unilateral DDH. RESULTS: The PFD value for the normal group (2.9 ± 0.4 mm) was significantly less than that for the closed reduction group (4.9 ± 2.8 mm, P<0.001) and that for the open reduction group (4.4 ± 1.6 mm; P=0.02), but no difference in the PFD was observed between the closed reduction and the open reduction groups (P=0.73). Despite successful reduction, the PFD values in the successful reduction group remained higher than those of the normal hips. CONCLUSION: PFD measurement by ultrasonography of the medial hip can be used to evaluate the effectiveness of reduction procedures in DDH. The clinical implications of post-reduction ultrasound evaluation in the diagnosis and long-term follow-up of outcomes require further research.

Establishment and application of a qPCR diagnostic method for Theileria annulata.

Bovine theileriosis caused by several Theileria species including Theileria annulata, Theileria parva, Theileria orientalis, Theileria mutans, and Theileria sinensis is a significant hemoprotozoan tick-borne disease. Among these, Theileria species, T. annulata, which causes tropical theileriosis (TT), is regarded as one of the most pathogenic and is responsible for high mortality. At present, most conventional diagnostic methods for tropical theileriosis are time-consuming and laborious and cannot distinguish newfound T. sinensis in China. Therefore, a high sensitivity and specificity real-time quantitative PCR method based on the TA19140 target molecule was developed, and the method was found to be specific for T. annulata. No cross-reaction was observed with T. sinensis, T. orientalis, Babesia bovis, Babesia bigemina, or Hyalomma anatolicum which is negative for T. annulata. A total of 809 field samples from different regions of China were analyzed by using the developed qPCR and conventional PCR. The positive samples for T. annulata detected by real-time qPCR and conventional PCR were 66/809 (8.16%) and 20/809 (2.47%), respectively, and all positive amplicons by qPCR were confirmed by Sanger sequencing. The results showed that the developed qPCR for the T. annulata 19,140 gene was more sensitive than conventional PCR. In addition, we first discovered that TA19140 was mainly expressed at the schizont and merozoite stages of T. annulata by relative quantification. The protein encoded by the TA19140 gene may be used as a potential diagnostic antigen for tropical theileriosis. In conclusion, a real-time quantitative PCR diagnostic method targeting the TA19140 gene was successfully established and could be used for both the quantitative and qualitative analysis of T. annulata infection from cattle and vector ticks, which will greatly help to control and diagnosis of tropical theileriosis.

Analysis of changes in population's cross-city travel patterns in the pre- and post-pandemic era: A case study of China.

The coronavirus disease (COVID-19) outbreak has immensely changed people's travel behaviour. The changes in travel behaviour have had a huge impact on different industries, such as consumption, entertainment, commerce, office, and education. This study investigates the impact of COVID-19 on population travel patterns from three aspects: total trips, travel recovery degree, and travel distance. The result indicates that COVID-19 has reduced the total number of cross-city trips and flexible non-work travel; in the post-pandemic era, cross-city travel is mainly short-distance (distance <100 km). This study has significant policymaking implications for governments in countries where the population shares a similar change in travel behaviour.

Identification two key residues at the intersection of domains of a thioether monooxygenase for improving its sulfoxidation performance.

AcCHMO, a cyclohexanone monooxygenase from Acinetobacter calcoaceticus, is a typical Type I Baeyer-Villiger monooxygenase (BVMO). We previously obtained the AcCHMOM6 mutant, which oxidizes omeprazole sulfide (OPS) to the chiral sulfoxide drug esomeprazole. To further improve the catalytic efficiency of the AcCHMOM6 mutant, a focused mutagenesis strategy was adopted at the intersections of the FAD-binding domain, NADPH-binding domain, and α-helical domain based on structural characteristics of AcCHMO. By using focused mutagenesis and subsequent global evolution two key residues (L55 and P497) at the intersections of the domains were identified. Mutant of L55Y improved catalytic efficiency significantly, whereas the P497S mutant alleviated substrate inhibition remarkably. AcCHMOM7 (L55Y/P497S) was obtained by combining the two mutations, which increased the specific activity from 18.5 (M6) to 108 U/g, and an increase in the Ki of the substrate OPS from 34 to 265 µM. The results indicate that catalytic performance can be elevated by modification of the sensitive sites at the intersection of the domains of AcCHMO. The results also provided some insights for the engineering of other Type I BVMOs or other multidomain proteins.

Establishing reference values for the pubofemoral distance in normal infant medial hips by ultrasound.

BACKGROUND: Measuring the pubofemoral distance (PFD) is important for evaluating the effectiveness of hip reduction in the treatment of developmental dysplasia of the hip (DDH). However, reference PFD values have not been established in normal infants. PURPOSE: To investigate variations in PFD values measured in normal infant medial hips stratified by age, laterality, and gender. MATERIAL AND METHODS: A total of 240 infants diagnosed with Graf type Ia and/or Graf type Ib hips by ultrasonography were stratified into eight age groups: 0-1 month; 1-2 months; 2-3 months; 3-4 months; 4-5 months; 5-6 months; 6-7 months; and 7-12 months. The bilateral medial hips were scanned with transinguinal ultrasound. The PFD was defined as the distance between the lateral edge of the superior ramus of pubic bone and the medial edge of the femoral head. Inter-observer reproducibility was assessed. RESULTS: Among the 240 infants, there were 371 Graf type Ia hips and 109 Graf type Ib hips. Mean ± SD bilateral PFD values of eight groups were measured separately. There were no significant differences in mean PFD values for left or right hips (t = 0.946, P = 0.345) or mean bilateral PFD values in male and female infants (t = 1.445, P = 0.149). Mean PFD values increased linearly with age (left: r = 0.680, P < 0.0001; right: r = 0.682, P < 0.0001). Inter-observer reproducibility was excellent. CONCLUSION: This study established reference PFD values from the medial hip in infants aged 0-12 months. PFD values increased with age, but were not significantly influenced by laterality or gender. These data provide detailed information that can support follow-up of infants treated for DDH.

Exploring potential impact(s) of cerium in mining wastewater on the performance of partial-nitrification process and nitrogen conversion microflora.

Cerium Ce(III) is one of the major pollutants contained in wastewater generated during Ce(III) mining. However, the effect(s) of Ce(III) on the functional genera responsible for removing nitrogen biologically from wastewater has not been studied and reported. In this study, the effects of Ce(III) on aspects of partial-nitritation-(PN) process including ammonia oxidation rate (AOR), process kinetics, and microbial activities were investigated. It was found that the effect of dosing Ce(III) in the PN system correlated strongly with the AOR. Compared to the control, batch assays dosed with 5 mg/L Ce(III) showed elevated PN efficiency of about 121%, an indication that maximum biological response was feasible upon Ce(III) dose. It was also found that, PN performance was not adversely affected, given that Ce(III) dose was ≤20 mg/L. Process kinetics investigated also suggested that the maximum Ce(III) dose without any visible inhibition to the activities of ammonium oxidizing bacteria was 1.37 mg/L, but demonstrated otherwise when Ce(III) dose exceeded 5.63 mg/L. Compared to the control, microbes conducted efficient Ce(III) removal (averaged 98.66%) via biosorption using extracellular polymeric substances (EPS). Notably, significant deposits of Ce(III) was found within the EPS produced as revealed by SEM, EDX, CLSM and FTIR. 2-dimensional correlation infrared-(2DCOS-IR) revealed ester group (uronic acid) as a major organic functional group that promoted Ce(III) removal. Excitation-emission matrix-(EEM) spectrum and 2DCOS-IR suggested the dominance of Fulvic acid, hypothesized to have promoted the performance of the PN process under Ce(III) dosage.

Tristability in mitochondrial permeability transition pore opening.

Mitochondrial permeability transition pore (PTP), a key regulator of cell life and death processes, is triggered by calcium ions (Ca2+) and potentiated by reactive oxygen species (ROS). Although the two modes of PTP opening, i.e., transient and persistent, have been identified for a long time, its dynamical mechanism is still not fully understood. To test a proposed hypothesis that PTP opening acts as a tristable switch, which is characterized by low, medium, and high open probability, we develop a three-variable model that focused on PTP opening caused by Ca2+ and ROS. For the system reduced to two differential equations for Ca2+ and ROS, both the stability analysis and the potential landscape feature that it exhibits tristability under standard parameters. For the full system, the bifurcation analysis suggests that it can achieve tristability over a wide range of input parameters. Furthermore, parameter sensitivity analysis demonstrates that the existence of tristability is a robust property. In addition, we show how the deterministic tristable property can be understood within a stochastic framework, which also explains the PTP dynamics at the level of a single channel. Overall, this study may yield valuable insights into the intricate regulatory mechanism of PTP opening.

De novo assembly of a wild pear (Pyrus betuleafolia) genome.

China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide-binding site (NBS)-type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR-NBS-LRR (TNL)-type genes, which represented the greatest number of TNL-type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism-related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high-quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.

SOX2 interferes with the function of CDX2 in bile acid-induced gastric intestinal metaplasia.

BACKGROUND: Intestinal metaplasia (IM) is a premalignant lesion associated with gastric cancer. Both animal and clinical studies have revealed that bile acid reflux and subsequent chronic inflammation are key causal factors of IM. Previous studies indicated that SOX2, the key transcription factor in gastric differentiation, was downregulated during IM development while CDX2, the pivotal intestine-specific transcription factor was upregulated significantly. However, it remains unclear whether the downregulation of SOX2 promotes gastric IM emergence or is merely a concomitant phenomenon. In addition, the underlying mechanisms of SOX2 downregulation during IM development are unclear. METHODS: Gastric cell lines were treated with deoxycholic acid (DCA) in a dose-dependent manner. The expression of CDX2 and miR-21 in gastric tissue microarray were detected by immunohistochemistry and in situ hybridization. Coimmunoprecipitation and immunofluorescence were performed to ascertain the interaction of SOX2 and CDX2. Luciferase reporter assays were used to detect the transcriptional activity of CDX2, and confirm miR-21 binding to SOX2 3'-UTR. The protein level of SOX2, CDX2 and downstream IM-specific genes were investigated using western blotting. mRNA level of miR-21, SOX2, CDX2 and downstream IM-specific genes were detected by qRT-PCR. RESULTS: Bile acid treatment could suppress SOX2 expression and simultaneously induce expression of CDX2 in gastric cell lines. Furthermore, we demonstrated that SOX2 overexpression could significantly inhibit bile acid- and exogenous CDX2-induced IM-specific gene expression, including KLF4, cadherin 17 and HNF4α expression. In contrast, SOX2 knockdown had the opposite effect. A dual-luciferase reporter assay demonstrated that SOX2 overexpression could significantly suppress CDX2 transcriptional activity in HEK293T cells. CDX2 and SOX2 could form protein complexes in the nucleus. In addition, bile acid induced the expression of miR-21. The inhibition of SOX2 in bile acid-treated gastric cell lines was rescued by miR-21 knockdown. CONCLUSIONS: These findings suggested that SOX2 can interfere with the transcriptional activity of CDX2 in bile acid-induced IM and that miR-21 might play a key role in this process, which shed new lights in the prevention of gastric cancer.

Neoadjuvant docetaxel, cisplatin and ifosfamide (ITP) combination chemotherapy for treating penile squamous cell carcinoma patients with terminal lymph node metastasis.

BACKGROUND: Chemotherapy may be a valuable treatment option as neoadjuvant treatment for locally advanced penile cancer according to some previous studies, but the rarity of the sample and the Lack of large-scale clinical trials hampered the attempt to establish a solid evidence base for its routine use. The purpose of this study was to evaluate the efficacy of the neoadjuvant chemotherapy combined with a ITP regimen including docetaxel, cisplatin and ifosfamide for treating advanced penile cancer patients. METHODS: A total of 19 patients who were classified into advanced penile cancer (PN3) received neoadjuvant chemotherapy of ITP regimen from June 2009 to June 2016 in our hospital. RESULTS: After chemotherapy 12 patients had a partial response (PR), 5 had stable disease (SD) and progressive disease (PD) in 2 cases. The 12 responders underwent penectomy, bilateral inguinal lymphadenectomy (ILND) and pelvic lymph node dissection (LPLND). In contrast, 7 cases who were non-responsive received palliative local radiotherapy. After a median follow-up of 30.6 months, there was statistically significant improvement in median PFS and OS among patients who experienced an objective response to neoadjuvant chemotherapy (group A) compared with those patients who did not respond to chemotherapy (group B) (log-rank test; P < 0.001). CONCLUSION: Neoadjuvant docetaxel, cisplatin and ifosfamide chemotherapy gave 63% (12/19) of patients who were diagnosed with stage n3 penile cancer the chance of radical resection of metastases, and their OS and PFS were significantly higher than those who could not be operated on and the therapeutic dose, toxic and side effects are acceptable in the Chinese Han population. Therefore, neoadjuvant ITP chemotherapy in the treatment of stage T3 penile cancer patients may have cheerful prospects in the Chinese Han population.