Pathogenic bacteria exploit transferrin receptor transcytosis to penetrate the blood-brain barrier.

The human blood-brain barrier (BBB) comprises a single layer of brain microvascular endothelial cells (HBMECs) protecting the brain from bloodborne pathogens. Meningitis is among the most serious diseases, but the mechanisms by which major meningitis-causing bacterial pathogens cross the BBB to reach the brain remain poorly understood. We found that Streptococcus pneumoniae, group B Streptococcus, and neonatal meningitis Escherichia coli commonly exploit a unique vesicle fusion mechanism to hitchhike on transferrin receptor (TfR) transcytosis to cross the BBB and illustrated the details of this process in human BBB model in vitro and mouse model. Toll-like receptor signals emanating from bacteria-containing vesicles (BCVs) trigger K33-linked polyubiquitination at Lys168 and Lys181 of the innate immune regulator TRAF3 and then activate the formation of a protein complex containing the guanine nucleotide exchange factor RCC2, the small GTPase RalA and exocyst subcomplex I (SC I) on BCVs. The distinct function of SEC6 in SC I, interacting directly with RalA on BCVs and the SNARE protein SNAP23 on TfR vesicles, tethers these two vesicles and initiates the fusion. Our results reveal that innate immunity triggers a unique modification of TRAF3 and the formation of the HBMEC-specific protein complex on BCVs to authenticate the precise recognition and selection of TfR vesicles to fuse with and facilitate bacterial penetration of the BBB.

CsiR-mediated signal transduction pathway in response to low iron conditions promotes Escherichia coli K1 invasion and penetration of the blood-brain barrier.

Escherichia coli K1 is the leading cause of neonatal Gram-negative bacterial meningitis, but the pathogenesis of E. coli K1 meningitis remains unclear. Blood-brain barrier (BBB) penetration is a crucial step in E. coli meningitis development. Here, we uncovered the crucial role of CsiR, a GntR family regulator, in E. coli K1 virulence. During infection, csiR expression was induced due to the derepression by Fur in the blood and human brain microvascular endothelial cells (HBMECs). CsiR positively regulated ilvB expression, which is associated with branched chain amino acid synthesis. Furthermore, we revealed that IlvB activated the FAK/PI3 K pathway of HBMECs to induce actin cytoskeleton rearrangements, thereby promoting the bacterial invasion and penetration of the BBB. Overall, this study reveals a CsiR-mediated virulence regulation pathway in E. coli K1, which may provide a useful target for the prevention or therapy of E. coli meningitis.

A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors.

Plant nucleotide-binding and leucine-rich repeat (NLR) receptors recognize avirulence effectors directly through their integrated domains (IDs) or indirectly via the effector-targeted proteins. Previous studies have succeeded in generating designer NLR receptors with new recognition profiles by engineering IDs or targeted proteins based on prior knowledge of their interactions with the effectors. However, it is yet a challenge to design a new plant receptor capable of recognizing effectors that function by unknown mechanisms. Several rice NLR immune receptors, including RGA5, possess an integrated heavy metal-associated (HMA) domain that recognizes corresponding Magnaporthe oryzae Avrs and ToxB-like (MAX) effectors in the rice blast fungus. Here, we report a designer rice NLR receptor RGA5HMA2 carrying an engineered, integrated HMA domain (RGA5-HMA2) that can recognize the noncorresponding MAX effector AvrPib and confers the RGA4-dependent resistance to the M. oryzae isolates expressing AvrPib, which originally triggers the Pib-mediated blast resistance via unknown mechanisms. The RGA5-HMA2 domain is contrived based on the high structural similarity of AvrPib with two MAX effectors, AVR-Pia and AVR1-CO39, recognized by cognate RGA5-HMA, the binding interface between AVR1-CO39 and RGA5-HMA, and the distinct surface charge of AvrPib and RAG5-HMA. This work demonstrates that rice NLR receptors with the HMA domain can be engineered to confer resistance to the M. oryzae isolates noncorresponding but structurally similar MAX effectors, which manifest cognate NLR receptor-mediated resistance with unknown mechanisms. Our study also provides a practical approach for developing rice multilines and broad race spectrum-resistant cultivars by introducing a series of engineered NLR receptors.

Development and application of a multiplex PCR system for forensic salivary identification.

In forensics, accurate identification of the origin of body fluids is essential for reconstructing a crime scene or presenting strong evidence in court. Microorganisms have demonstrated great potential in body fluid identification. We developed a multiplex PCR system for forensic salivary identification, which contains five types of bacteria:Streptococcus salivarius, Neisseria subflava, Streptococcus. mutans, Bacteroides thetaiotaomicron, and Bacteroides. uniformis. And the validated studies were carried out following the validation guidelines for DNA analysis methods developed by the Scientific Working Group on DNA Analysis Methods (SWGDAM), which included tests for sensitivity, species specificity, repeatability, stability, and mixed samples, trace samples, case samples, and a population study. Our result depicted that the lowest detection limit of the system was 0.01 ng template DNA. Moreover, the corresponding bacteria can still be detected when the amount of saliva input is low to 0.1 µL for DNA extraction. In addition, the target bacteria were not detected in the DNA of human, seven common animals, and seven bacteria DNA and in nine other body fluid samples (skin, semen, blood, menstrual blood, nasal mucus, sweat, tears, urine, and vaginal secretions). Six common inhibitors such as indigo, EDTA, hemoglobin, calcium ions, alcohol and humic acid were well tolerated by the system. What is more, the salivary identification system recognized the saliva component in all mixed samples and simulated case samples. Among 400 unrelated individuals from the Chinese Han population analyzed by this novel system, the detection rates of N. subflava, S. salivarius, and S. mutans were 97.75%, 70.75%, and 19.75%, respectively, with 100% identification of saliva. In conclusion, the salivary identification system has good sensitivity, specificity, stability, and accuracy, which can be a new effective tool for saliva identification.

Management of balloon dilatation in cases of subglottic stenosis in children: success and failure.

PURPOSE: To assess efficacy and prognostic factors of endoscopic balloon dilatation for the treatment of subglottic stenosis in children. METHODS: A retrospective review was performed on 49 pediatric patients with subglottic stenosis treated at the Shanghai Children's Hospital between December 2017 and December 2021. Specific demographic data, type and severity of the stenosis, number of balloon dilatations and outcomes were recorded and analyzed. RESULTS: Forty-nine children (30 male, 19 female) were included in the study with a median age at diagnosis of 24 (13-36.5) months, of which 7 (14.3%) had received open laryngotracheal reconstruction previously. The degree of subglottic stenosis was grade I in six patients, grade II in 16 patients, grade III in 20 patients and grade IV in seven patients. After various numbers of balloon dilatations (1-7 times), 29 patients showed a good outcome (decannulation or prevention of tracheostomy) and the success rate in that series was 59.2%. Overall, prognosis of balloon dilatation was not dependent on pathogeny (congenital or acquired) or open surgical history(P > 0.05), but rather on the severity grade of stenosis and the number of dilatations (P < 0.05). CONCLUSIONS: Endoscopic balloon dilatation can be safe and effective in the treatment of subglottic stenosis in children, except for more serious cases (grade IV). Open surgery should be considered if no significant improvement is observed after dilatation, especially after three or more dilatations.

Epidemiology and Predictors for Cervical Burn Scar Contractures: A Multicenter Cohort Study.

Cervical burn scar contracture (BSC) affects many important neck functions and the patients' quality of life. However, it remains unclear which patients have a higher risk of neck BSCs. This study aimed to describe the epidemiology and identify the independent risks of cervical BSC formation and severity. Clinical and demographic data of 106 patients with burn scars were retrospectively collated and analyzed from 3 different Chinese hospitals between December 2016 and December 2020. Both univariate and multivariate logistic regression analyses were performed to identify the independent risks for BSC formation and severity at 12 months postburn. Lateral flexion was the most common plane of motion (POM) limited by contractures (29.4%), whereas the POM most commonly limited by severe contractures was the extension (24.6%). Most patients with contractures had those in 3 to 4 POMs (72.1%). Neck skin grafting was an independent risk factor for BSC formation, and cervical and cervicothoracic skin grafting were independent risk factors for BSC severity. These results may help to identify high-risk patients with contractures in the early stages of burns to carry out individualized early prevention and treatment.

Neonatal Meningitis-Causing Escherichia coli Induces Microglia Activation which Acts as a Double-Edged Sword in Bacterial Meningitis.

Bacterial meningitis is a devastating disease occurring worldwide, with up to half of survivors left with permanent neurological sequelae. Neonatal meningitis-causing Escherichia coli (NMEC) is the most common Gram-negative bacillary organism that causes meningitis, particularly during the neonatal period. Here, RNA-seq transcriptional profiles of microglia in response to NMEC infection show that microglia are activated to produce inflammatory factors. In addition, we found that the secretion of inflammatory factors is a double-edged sword that promotes polymorphonuclear neutrophil (PMN) recruitment to the brain to clear the pathogens but, at the same time, induces neuronal damage, which may be related to the neurological sequelae. New neuroprotective therapeutic strategies must be developed for the treatment of acute bacterial meningitis. We found that transforming growth factor-ß (TGF-ß) may be a strong candidate in the treatment of acute bacterial meningitis, as it shows a therapeutic effect on bacterial-meningitis-induced brain damage. Prevention of disease and early initiation of the appropriate treatment in patients with suspected or proven bacterial meningitis are the key factors in reducing morbidity and mortality. Novel antibiotic and adjuvant treatment strategies must be developed, and the main goal for new therapies will be dampening the inflammatory response. Based on this view, our findings may help develop novel strategies for bacterial meningitis treatment.

Novel Therapeutic Potential of Retinoid-Related Orphan Receptor α in Cardiovascular Diseases.

The retinoid-related orphan receptor α (RORα) is one subfamily of nuclear hormone receptors (NRs). This review summarizes the understanding and potential effects of RORα in the cardiovascular system and then analyzes current advances, limitations and challenges, and further strategy for RORα-related drugs in cardiovascular diseases. Besides regulating circadian rhythm, RORα also influences a wide range of physiological and pathological processes in the cardiovascular system, including atherosclerosis, hypoxia or ischemia, myocardial ischemia/reperfusion injury, diabetic cardiomyopathy, hypertension, and myocardial hypertrophy. In terms of mechanism, RORα was involved in the regulation of inflammation, apoptosis, autophagy, oxidative stress, endoplasmic reticulum (ER) stress, and mitochondrial function. Besides natural ligands for RORα, several synthetic RORα agonists or antagonists have been developed. This review mainly summarizes protective roles and possible mechanisms of RORα against cardiovascular diseases. However, there are also several limitations and challenges of current research on RORα, especially the difficulties on the transformability from the bench to the bedside. By the aid of multidisciplinary research, breakthrough progress on RORα-related drugs to combat cardiovascular disorder may appear.

Microbial Synthesis of Heme b: Biosynthetic Pathways, Current Strategies, Detection, and Future Prospects.

Heme b, which is characterized by a ferrous ion and a porphyrin macrocycle, acts as a prosthetic group for many enzymes and contributes to various physiological processes. Consequently, it has wide applications in medicine, food, chemical production, and other burgeoning fields. Due to the shortcomings of chemical syntheses and bio-extraction techniques, alternative biotechnological methods have drawn increasing attention. In this review, we provide the first systematic summary of the progress in the microbial synthesis of heme b. Three different pathways are described in detail, and the metabolic engineering strategies for the biosynthesis of heme b via the protoporphyrin-dependent and coproporphyrin-dependent pathways are highlighted. The UV spectrophotometric detection of heme b is gradually being replaced by newly developed detection methods, such as HPLC and biosensors, and for the first time, this review summarizes the methods used in recent years. Finally, we discuss the future prospects, with an emphasis on the potential strategies for improving the biosynthesis of heme b and understanding the regulatory mechanisms for building efficient microbial cell factories.

Establishment and validation of a nomogram to predict the neck contracture after skin grafting in burn patients: A multicentre cohort study.

Cervical burn contracture is one of the burn contractures with the highest incidence and severity, and there is no effective method to predict the risk of neck contracture. This study aimed to investigate the effect of combined cervicothoracic skin grafting on the risk of neck contracture in burn patients and to develop a nomogram to predict the risk of neck contracture after skin grafting in burn patients. Data from 212 patients with burns who underwent neck skin grafting were collected from three hospitals, and the patients were randomly divided into training and validation sets. Independent predictors were identified through univariate and multivariate logistic regression analyses and incorporated into a prognostic nomogram. Its performance was assessed using the receiver operating characteristic area under the curve, calibration curve, and decision curve analysis. Burn depth, combined cervicothoracic skin grafting, graft thickness, and neck graft size were significantly associated with neck contractures. In the training cohort, the nomogram had an area under the curve of 0.894. The calibration curve and decision curve analysis indicated good clinical applicability of the nomogram. The results were tested using a validation dataset. Combined cervicothoracic skin grafting is an independent risk factor for neck contracture. Our nomogram demonstrated excellent performance in predicting neck contracture risk.

Lactate attenuates astrocytic inflammation by inhibiting ubiquitination and degradation of NDRG2 under oxygen-glucose deprivation conditions.

BACKGROUND: Brain lactate concentrations are enhanced in response to cerebral ischemia and promote the formation of reactive astrocytes, which are major components of the neuroinflammatory response and functional recovery, following cerebral ischemia. NDRG2 is upregulated during reactive astrocyte formation. However, its regulation and function are unclear. We studied the relationship between lactate and NDRG2 in astrocytes under conditions of ischemia or oxygen-glucose deprivation (OGD). METHODS: We examined astrocytic NDRG2 expression after middle cerebral artery occlusion (MCAO) using western blot and immunofluorescence staining. Under hypoxia conditions, we added exogenous L-lactate sodium (lactate) to cultured primary astrocytes to explore the effects of lactate on the ubiquitination modification of NDRG2. We profiled the transcriptomic features of NDRG2 silencing in astrocytes after 8 h of OGD conditions as well as exogenous lactate treatment by performing RNA-seq. Finally, we evaluated the molecular mechanisms of NDRG2 in regulating TNFα under OGD conditions using western blot and immunohistochemistry. RESULTS: Reactive astrocytes strongly expressed NDRG2 in a rat model of MCAO. We also showed that lactate stabilizes astrocytic NDRG2 by inhibiting its ubiquitination. NDRG2 inhibition in astrocytes increased inflammation and upregulated immune-associated genes and signaling pathways. NDRG2 knockdown induced TNFα expression and secretion via c-Jun phosphorylation. CONCLUSIONS: We revealed that under OGD conditions, lactate plays an important anti-inflammatory role and inhibits TNFα expression by stabilizing NDRG2, which is beneficial for neurological functional recovery. NDRG2 may be a new therapeutic target for cerebral ischemia.

Development and validation of a forensic multiplex InDel assay: The AGCU InDel 60 kit.

Marker sets based on insertion/deletion polymorphisms (InDels) combine the characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms and have served as effective complementary or stand-alone systems for human identification in forensics. We developed a novel multiplex amplification detection system, designated the AGCU InDel 60 kit, containing 57 autosomal InDels, 2 Y-chromosomal InDels, and the amelogenin locus and validated the kit in a series of studies, which included tests of the PCR conditions; tests for sensitivity, species specificity, reproducibility, stability, and mock case samples; degradation studies; and a population study. The results indicated that the AGCU InDel 60 kit was accurate, specific, reproducible, stable, and robust. Complete DNA profiles were obtained even with 125 pg of human DNA. In tests of artificially degraded samples, we found that the number of alleles detected by the validated kit was considerably greater than that detected by the STR-based AGCU 21+1 kit, even as the degree of degradation increased. Additionally, 564 unrelated individuals from three Han groups were investigated using this novel system, and the values of combined power of discrimination and combined power of exclusion were not less than 1-4.9026 × 10-24 and 1-3.1123 × 10-5 , respectively. Thus, the results indicated that the novel kit was more powerful than the previous version of the InDel kit (the AGCU InDel 50 kit). Our results suggest that the AGCU InDel 60 kit can serve as an efficient tool for human forensics and a supplementary kit for population genetics research.

miR-124: A Promising Therapeutic Target for Central Nervous System Injuries and Diseases.

Central nervous system injuries and diseases, such as ischemic stroke, spinal cord injury, neurodegenerative diseases, glioblastoma, multiple sclerosis, and the resulting neuroinflammation often lead to death or long-term disability. MicroRNAs are small, non-coding, single-stranded RNAs that regulate posttranscriptional gene expression in both physiological and pathological cellular processes, including central nervous system injuries and disorders. Studies on miR-124, one of the most abundant microRNAs in the central nervous system, have shown that its dysregulation is related to the occurrence and development of pathology within the central nervous system. Herein, we review the molecular regulatory functions, underlying mechanisms, and effective delivery methods of miR-124 in the central nervous system, where it is involved in pathological conditions. The review also provides novel insights into the therapeutic target potential of miR-124 in the treatment of human central nervous system injuries or diseases.

Magnetic Luffa-Leaf-Derived Hierarchical Porous Biochar for Efficient Removal of Rhodamine B and Tetracycline Hydrochloride.

Luffa leaf (LL) is an agricultural waste produced by loofah. In this work, LL was used as biomass carbon source for biochars for the first time. After carbonization, activation, and chemical co-precipitation treatments, a magnetic lignocellulose-derived hierarchical porous biochar was obtained. The specific surface area and total pore volume were 2565.4 m2/g and 1.4643 cm3/g, and the surface was rich in carbon and oxygen functional groups. The synthetic dye rhodamine B (RhB) and the antibiotic tetracycline hydrochloride (TH) were selected as organic pollutant models to explore the ability to remove organic pollutants, and the results showed good adsorption performances. The maximum adsorption capacities were 1701.7 mg/g for RhB and 1755.9 mg/g for TH, which were higher than most carbon-based adsorbents. After 10 cycles of use, the removal efficiencies were still maintained at more than 70%, showing good stability. This work not only verified the feasibility of lignocellulose LL as a carbon source to prepare biochar but also prepared a magnetic hierarchical porous adsorbent with good performances that can better treat RhB and TH, which provided a new idea and direction for the efficient removal of organic pollutants in water.

Prognostic nomogram for hepatocellular carcinoma with radiofrequency ablation: a retrospective cohort study.

BACKGROUND: Radiofrequency ablation (RFA) is an effective treatment option for hepatocellular carcinoma (HCC). This study aimed to analyze the prognostic factors of HCC patients treated with RFA and to develop nomograms for outcome prediction. METHODS: A total of 3142 HCC patients treated with RFA were recruited, and their data were collected from the Surveillance, Epidemiology, and End Results database. Univariate and multifactor Cox analyses were performed to identify independent prognostic factors. These factors were integrated into a nomogram to predict 3- and 5-year cancer-specific survival (CSS) and overall survival (OS). Consistency indices and calibration plots were used to assess the accuracy of the nomograms in both the internal and external cohorts. RESULTS: The median follow-up periods for HCC patients treated with RFA were 27 and 29 months for OS and CSS, respectively. Marital status, age, race, histological grade of differentiation, tumor size, T stage, and serum alpha-fetoprotein levels at the time of diagnosis were identified as prognostic factors for OS and CSS. Additionally, M stage was identified as risk factors for OS. These risk factors are included in the nomogram. The calibration plots of the OS and CSS nomograms showed excellent consistency between actual survival and nomogram predictions. The bootstrap-corrected concordance indices of the OS and CSS nomograms were 0.637 (95% CI, 0.628-0.646) and 0.670 (95% 0.661-0.679), respectively. Importantly, our nomogram performed better discriminatory compared with 8th edition tumor-node-metastasis (TNM) stage system for predicting OS and CSS. CONCLUSIONS: We identified prognostic factors for HCC patients treated with RFA and provided an accurate and personalized survival prediction scheme.

Declines in PDE4B activity promote myopia progression through downregulation of scleral collagen expression.

Myopia is the most common cause of a visual refractive error worldwide. Cyclic adenosine monophosphate (cAMP)-linked signaling pathways contribute to the regulation of myopia development, and increases in cAMP accumulation promote myopia progression. To pinpoint the underlying mechanisms by which cAMP modulates myopia progression, we performed scleral transcriptome sequencing analysis in form-deprived mice, a well-established model of myopia development. Form deprivation significantly inhibited the expression levels of genes in the cAMP catabolic pathway. Quantitative real-time polymerase chain reaction analysis validated that the gene expression level of phosphodiesterase 4B (PDE4B), a cAMP hydrolase, was downregulated in form-deprived mouse eyes. Under visually unobstructed conditions, loss of PDE4B function in Pde4b-knockout mice increased the myopic shift in refraction, -3.661 ± 1.071 diopters, more than that in the Pde4b-wildtype littermates (P < 0.05). This suggests that downregulation and inhibition of PDE4B gives rise to myopia. In guinea pigs, subconjunctival injection of rolipram, a selective inhibitor of PDE4, led to myopia in normal eyes, and it also enhanced form-deprivation myopia (FDM). Subconjunctival injection of dibutyryl-cyclic adenosine monophosphate, a cAMP analog, induced only a myopic shift in the normal visually unobstructed eyes, but it did not enhance FDM. As myopia developed, axial elongation occurred during scleral remodeling that was correlated with changes in collagen fibril thickness and distribution. The median collagen fibril diameter in the FDM + rolipram group, 55.09 ± 1.83 nm, was thinner than in the FDM + vehicle group, 59.33 ± 2.06 nm (P = 0.011). Thus, inhibition of PDE4 activity with rolipram thinned the collagen fibril diameter relative to the vehicle treatment in form-deprived eyes. Rolipram also inhibited increases in collagen synthesis induced by TGF-ß2 in cultured human scleral fibroblasts. The current results further support a role for PDE enzymes such as PDE4B in the regulation of normal refractive development and myopia because either loss or inhibition of PDE4B function increased myopia and FDM development through declines in the scleral collagen fibril diameter.

The role of exosomal microRNAs in central nervous system diseases.

MicroRNAs (miRNA), endogenous non-coding RNAs approximately 22 nucleotides long, regulate gene expression by mediating translational inhibition or mRNA degradation. Exosomes are a tool for intercellular transmission of information in which miRNA exchange plays an important role. Under pathophysiological conditions in the central nervous system (CNS), cellular transmission of exosomal miRNAs can regulate signaling pathways. Exosomal miRNAs are involved in the occurrence and development of diverse CNS diseases, such as traumatic brain injury, spinal cord injury, stroke, neurodegenerative diseases, epilepsy, and glioma. The use of exosomes as transport vehicles for certain miRNAs provides a novel therapeutic strategy for CNS diseases. Furthermore, the exosomes in body fluids change with the occurrence of diseases, indicating that subtle changes in physiological and pathological processes in vivo could be recognized by analyzing exosomes. Exosomal analysis is expected to act as a novel tool for diagnosis and prediction of neurological diseases. In this review, we present the current understanding of the implications of miRNAs in CNS diseases and summarize the role and mechanism of action of exosomal miRNA in nervous system disease models.

Identification and Functional Analysis of Tomato TPR Gene Family.

Tomato (Solanum lycopersicum) as an important vegetable grown around the world is threatened by many diseases, which seriously affects its yield. Therefore, studying the interaction between tomato and pathogenic bacteria is biologically and economically important. The TPR (Tetratricopeptide repeat) gene family is a class of genes containing TPR conserved motifs, which are widely involved in cell cycle regulation, gene expression, protein degradation and other biological processes. The functions of TPR gene in Arabidopsis and wheat plants have been well studied, but the research on TPR genes in tomato is not well studied. In this study, 26 TPR gene families were identified using bioinformatics based on tomato genome data, and they were analyzed for subcellular localization, phylogenetic evolution, conserved motifs, tissue expression, and GO (Gene Ontology) analysis. The qRT-PCR was used to detect the expression levels of each member of the tomato TPR gene family (SlTPRs) under biological stress (Botrytis cinerea) and abiotic stress such as drought and abscisic acid (ABA). The results showed that members of the tomato TPR family responded to various abiotic stresses and Botrytis cinerea stress, and the SlTPR2 and SlTPR4 genes changed significantly under different stresses. Using VIGS (Virus-induced gene silencing) technology to silence these two genes, the silenced plants showed reduced disease resistance. It was also shown that TPR4 can interact with atpA which encodes a chloroplast ATP synthase CF1 α subunit. The above results provide a theoretical basis for further exploring the molecular mechanism of TPR-mediated resistance in disease defense, and also provide a foundation for tomato disease resistance breeding.

Systematic design and in vitro validation of novel one-carbon assimilation pathways.

The utilization of one-carbon (C1) assimilation pathways to produce chemicals and fuels from low-cost C1 compounds could greatly reduce the substrate-related production costs, and would also alleviate the pressure of the resource supply for bio-manufacturing. However, the natural C1 assimilation pathways normally involve ATP consumption or the loss of carbon resources as CO2, resulting in low product yields, making the design of novel pathways highly pertinent. Here we present several new ATP-independent and carbon-conserving C1 assimilation cycles with 100% theoretical carbon yield, which were discovered by computational analysis of metabolic reaction set with 6578 natural reactions from MetaCyc database and 73 computationally predicted aldolase reactions from ATLAS database. Then, kinetic evaluation of these cycles was conducted and the cycles without kinetic traps were chosen for further experimental verification. Finally, we used the two engineered enzymes Gals and TalBF178Y for the artificial reactions to construct a novel C1 assimilation pathway in vitro and optimized the pathway to achieve 88% carbon yield. These results demonstrate the usefulness of computational design in finding novel metabolic pathways for the efficient utilization of C1 compounds and shedding light on other promising pathways.

CropDeep: The Crop Vision Dataset for Deep-Learning-Based Classification and Detection in Precision Agriculture.

Intelligence has been considered as the major challenge in promoting economic potential and production efficiency of precision agriculture. In order to apply advanced deep-learning technology to complete various agricultural tasks in online and offline ways, a large number of crop vision datasets with domain-specific annotation are urgently needed. To encourage further progress in challenging realistic agricultural conditions, we present the CropDeep species classification and detection dataset, consisting of 31,147 images with over 49,000 annotated instances from 31 different classes. In contrast to existing vision datasets, images were collected with different cameras and equipment in greenhouses, captured in a wide variety of situations. It features visually similar species and periodic changes with more representative annotations, which have supported a stronger benchmark for deep-learning-based classification and detection. To further verify the application prospect, we provide extensive baseline experiments using state-of-the-art deep-learning classification and detection models. Results show that current deep-learning-based methods achieve well performance in classification accuracy over 99%. While current deep-learning methods achieve only 92% detection accuracy, illustrating the difficulty of the dataset and improvement room of state-of-the-art deep-learning models when applied to crops production and management. Specifically, we suggest that the YOLOv3 network has good potential application in agricultural detection tasks.