Accelerated evolution of chosen genes

Orthogonal replication enables rapid continuous biomolecular evolution in Escherichia coli.

[Updates of colonoscopy surveillance guidelines after screening and polypectomy, and related research progress]

With the widespread application of colorectal cancer screening, the surveillance and management of the increasing number of screened population has become a pivotal aspect in preventing and controlling colorectal cancer. In recent years, researches have been conducted on the risk of colorectal cancer incidence and mortality in the population after screening. At the same time, various organizations in Europe and the United States have continuously updated colonoscopy surveillance after screening and polypectomy based on the latest research evidence. In this review, we summarized the current progress of studies on colorectal cancer risk in post-screening colorectal cancer populations and the key points of relevant guideline updates, in order to provide a reference for conducting relevant studies and formulating surveillance guidelines or consensus in China.

Discovery of VH domains that allosterically inhibit ENPP1

Ectodomain phosphatase/phosphodiesterase-1 (ENPP1) is overexpressed on cancer cells and functions as an innate immune checkpoint by hydrolyzing extracellular cyclic guanosine monophosphate adenosine monophosphate (cGAMP). Biologic inhibitors have not yet been reported and could have substantial therapeutic advantages over current small molecules because they can be recombinantly engineered into multifunctional formats and immunotherapies. Here we used phage and yeast display coupled with in cellulo evolution to generate variable heavy (VH) single-domain antibodies against ENPP1 and discovered a VH domain that allosterically inhibited the hydrolysis of cGAMP and adenosine triphosphate (ATP). We solved a 3.2 Å-resolution cryo-electron microscopy structure for the VH inhibitor complexed with ENPP1 that confirmed its new allosteric binding pose. Finally, we engineered the VH domain into multispecific formats and immunotherapies, including a bispecific fusion with an anti-PD-L1 checkpoint inhibitor that showed potent cellular activity.

Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate

When nature maintains or evolves a gene's function over millions of years at scale, it produces a diversity of homologous sequences whose patterns of conservation and change contain rich structural, functional, and historical information about the gene. However, natural gene diversity likely excludes vast regions of functional sequence space and includes phylogenetic and evolutionary eccentricities, limiting what information we can extract. We introduce an accessible experimental approach for compressing long-term gene evolution to laboratory timescales, allowing for the direct observation of extensive adaptation and divergence followed by inference of structural, functional, and environmental constraints for any selectable gene. To enable this approach, we developed a new orthogonal DNA replication (OrthoRep) system that durably hypermutates chosen genes at a rate of >10 -4 substitutions per base in vivo . When OrthoRep was used to evolve a conditionally essential maladapted enzyme, we obtained thousands of unique multi-mutation sequences with many pairs >60 amino acids apart (>15% divergence), revealing known and new factors influencing enzyme adaptation. The fitness of evolved sequences was not predictable by advanced machine learning models trained on natural variation. We suggest that OrthoRep supports the prospective and systematic discovery of constraints shaping gene evolution, uncovering of new regions in fitness landscapes, and general applications in biomolecular engineering.

In vitro evaluation of different protective techniques to reduce titanium particle contamination during implantoplasty

OBJECTIVES

Our aim is to study titanium remains in a bone model during standardized implantoplasty under different isolation and protective modalities.

MATERIAL AND METHODS

Forty implants were placed in artificial spongy bone blocks mimicking a horizontal bone loss and implant neck protrusion of 5 mm. Samples were randomly divided into four groups (n = 10), which were treated as follows: rubber dam (A), a dental adhesive paste (B), bone wax (C), and an unprotected positive control (D). Implantoplasty was performed using carbide and diamond burs under strict water cooling and standardized suction. After removal of the respective isolation materials, the bone blocks were thoroughly rinsed with tap water for 3 min and titanium chips were collected using a filter integrated in the model. The filter paper was removed and dissolved in 37% hydrochloric acid for 2 h at 120 °C and the titanium remnants were quantified using atomic absorption spectrometry.

RESULTS

None of the test groups were able to completely prevent titanium particle contamination. Rubber dam (691 ± 249 µg) and bone wax (516 ± 157 µg) were found to be significantly more protective than the positive control (2313 ± 747 µg) (p < 0.001) with respect to the amount of titanium particles that remained in the bone model after implantoplasty. The adhesive paste group (1863.5 ± 538 µg) was not significantly different from the positive control (p = 0.19).

CONCLUSIONS

Despite some limitations of the present study, titanium particles resulting from a standardized implantoplasty can be assumed to be significantly reduced when the tissues/bone were protected with rubber dam and bone wax, or a combination, depending on individual accessibility.

CLINICAL RELEVANCE

Tissue protective measures to reduce or avoid particle contamination during implantoplasty is possible and should be considered and further clinically assessed to avoid iatrogenic inflammatory reactions.

[Principle and routine operation of laser assisted periodontal surgery]

Periodontitis is one of the most common infectious oral diseases, which can cause destruction of periodontal supporting tissues and even tooth mobility and loss. Controlling infection, eliminating inflammation, restoring the physiological shape of periodontal tissues, and meeting functional and aesthetic needs are the main goals of periodontal treatment. When periodontitis develops to a more severe stage, surgical treatment is necessary to handle soft and hard tissues for good treatment results. Since the development of the first Nd:YAG laser dedicated to dental medicine by Myers in 1990, over 30 years of clinical and basic research have shown that lasers have tremendous potential in assisting periodontal surgery. This article summarizes the principles and operational routines of laser-assisted periodontal surgery, aiming to provide clinical reference for diagnosis and treatment.

Lactobacillus coryniformis subsp. torquens inhibits bone loss in obese mice via modification of the gut microbiota

High-fat diet (HFD)-induced obesity results in bone loss associated with an imbalanced gut microbiota and altered immune status. Probiotics are live microorganisms that are beneficial to the host and are important in maintaining bone health and gut homeostasis. In this study, the probiotic Lactobacillus coryniformis subsp. torquens (T3L) was isolated from traditional yak milk cheese produced in Lhasa and showed distinct acid and bile salt resistance as potential probiotics. Our data indicated that T3L not only reversed HFD-induced gut dysbiosis, as indicated by decreased Firmicutes-to-Bacteroidetes ratios but also reduced bone loss. The anti-obesity, microbiome-modulating, and bone-protective effects were transmissible via horizontal faeces transfer from T3L-treated mice to HFD-fed mice. The protective effects of T3L on bone mass were associated with regulatory T (Treg) cell-mediated inhibition of osteoclast differentiation. Our data indicate that T3L is a regulator of the gut microbiota and bone homeostasis in an animal model.

[Interpretation of updated guidelines for colorectal cancer screening in average-risk individuals in the United States]

In recent years, due to changes in the epidemiology of colorectal cancer in the United States, the update of evidence-based medical evidence for screening, and the emergence of various new screening methods, various organizations in the United States, such as American College of Gastroenterology、Preventive Services Task Force, have updated guidelines for colorectal cancer screening in average-risk individuals. These guidelines have different recommendation levels in terms of starting and ending age, screening methods and frequency for colorectal cancer screening. A comprehensive understanding of the key points of these guideline updates and the similarities and differences recommended by different guidelines has important reference value for the colorectal cancer screening in China.

Bone defect development in experimental canine peri-implantitis models: a systematic review

PURPOSE

To provide a systematic overview of preclinical research regarding bone defect formation around different implant surfaces after ligature-induced peri-implantitis models in dogs. Two focused questions were formulated: 'How much bone loss can be expected after a certain time of ligature induced peri-implantitis?' and 'Do different implant types, dog breeds and study protocols differ in their extent of bone loss?'

MATERIALS AND METHODS

A systematic literature search was conducted on four databases (MEDLINE, Web of Science, EMBASE and Scopus). Observations, which consisted of bone defects measured directly after ligature removal in canine models, were included and analysed. Two approaches were used to analyse the relatively heterogeneous studies that fulfilled the inclusion criteria. First, separate simple linear regressions were calculated for each study and implant surface, for which observations were available across multiple time points. Second, a linear mixed model was specified for the observations at 12 weeks after ligature initiation, and assessing the potential influencing factors on defect depth was explored using lasso regularisation.

RESULTS

Thirty-six studies with a total of 1082 implants were included after. Bone loss was determined at different time points, either with clinical measurements radiographically or histologically. Different implant groups [e.g. turned, sand-blasted-acid-etched (SLA), titanium-plasma-sprayed (TPS) and other rough surfaces] were assessed and described in the studies. A mean incremental defect depth increase of 0.08 mm (SD: -0.01-0.28 mm) per week was observed. After 12 weeks, the defect depths ranged between 0.7 and 5 mm. Based on the current data set, implant surface could not be statistically identified as an essential factor in defect depth after 12 weeks of ligature-induced peri-implantitis.

CONCLUSION

Expectable defect depth after a specific time of ligature-induced peri-implantitis can vary robustly. It is currently impossible to delineate apparent differences in bone loss around different implant surfaces.

Using continuous directed evolution to improve enzymes for plant applications

Continuous directed evolution of enzymes and other proteins in microbial hosts is capable of outperforming classical directed evolution by executing hypermutation and selection concurrently in vivo, at scale, with minimal manual input. Provided that a target enzyme's activity can be coupled to growth of the host cells, the activity can be improved simply by selecting for growth. Like all directed evolution, the continuous version requires no prior mechanistic knowledge of the target. Continuous directed evolution is thus a powerful way to modify plant or non-plant enzymes for use in plant metabolic research and engineering. Here, we first describe the basic features of the yeast (Saccharomyces cerevisiae) OrthoRep system for continuous directed evolution and compare it briefly with other systems. We then give a step-by-step account of three ways in which OrthoRep can be deployed to evolve primary metabolic enzymes, using a THI4 thiazole synthase as an example and illustrating the mutational outcomes obtained. We close by outlining applications of OrthoRep that serve growing demands (i) to change the characteristics of plant enzymes destined for return to plants, and (ii) to adapt ("plantize") enzymes from prokaryotes-especially exotic prokaryotes-to function well in mild, plant-like conditions.

[DALYs for breast cancer in China, 2000-2050: trend analysis and prediction based on GBD 2019]

Objective: Based on the data of Global Burden of Disease 2019 data, to analyze the past, current, and future burden of disability-adjusted life years (DALYs) in China and compare with the international status. Methods: The total number of DALYs, age-standardized DALY rate, and the composition of different subgroups were extracted and described to analyze the time trend in 2000-2019 and the current situation in 2019 for Chinese female breast cancer. The burden of DALYs in 2050 was predicted by Joinpoint using average annual percent change (AAPC). Results: In 2000-2019, the ranking of DALYs caused by female breast cancer in China rose from the fourth to the second in all female cancers. The total DALYs increased by 48.4%, of which the years lived with disability increased from 4.8% to 8.8%. The age-standardized DALY rate only slightly decreased (AAPC=-0.3%; which increased during 2016-2019, AAPC=1.6%). In 2019, the age-standardized DALY rate for breast cancer in China was 278.0/100 000. The DALYs were 2.88 million (accounting for 14.2% of the global burden and 12.1% of all female cancers burden in China), 26.5% of which attributed known risk factors (overweight and obesity were the largest: 0.34 million DALYs, but some common breast cancer risk factors were not available on the platform, such as menstruation and fertility). In 2050, the prediction suggests that the total DALYs caused by female breast cancer in China will reach 3.80 million person-years-5.16 million person-years, increasing 32.1%-79.4% over 2019. From 2000 to 2019, the peak age of DALYs and DALY rate became older, and the DALYs among females aged 65 years and above increased faster than those younger than 65 years (AAPC were 4.8% and 1.3%, respectively). In 2019, females aged 45-74 (the starting age recommended by local guidelines for breast cancer screening) contributed 74.3% of the total DALYs. Conclusions: Over the past 20 years, the age-standardized DALY rate for breast cancer in female populations in China has not changed obviously. Without the continuous expansion of effective intervention and population aging, the burden of DALYs for female breast cancer in China will increase. DALYs for breast cancer attributed leading risk factors were still limited.

Integrating continuous hypermutation with high-throughput screening for optimization of cis,cis-muconic acid production in yeast

Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection and amplification. While powerful, systematic searches through large sequence-spaces is a labour-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here, we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generate enzyme variants using the recently developed orthogonal replication system, OrthoRep and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a rate-limiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers > 13-fold compared with reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.

Evolving Small-Molecule Biosensors with Improved Performance and Reprogrammed Ligand Preference Using OrthoRep

Genetically encoded biosensors are valuable for the optimization of small-molecule biosynthesis pathways, because they transduce the production of small-molecule ligands into a readout compatible with high-throughput screening or selection in vivo. However, engineering biosensors with appropriate response functions and ligand preferences remains challenging. Here, we show that the continuous hypermutation system, OrthoRep, can be effectively applied to evolve biosensors with a high dynamic range, reprogrammed activity toward desired noncognate ligands, and proper operational range for coupling to biosynthetic pathways. In particular, we encoded the allosteric transcriptional factor, BenM, on OrthoRep such that the propagation of host yeast cells resulted in BenM's rapid and continuous diversification. When these cells were subjected to cycles of culturing and sorting on BenM activity in the presence and absence of its cognate ligand, muconic acid, or the noncognate ligand, adipic acid, we obtained multiple BenM variants that respond to their corresponding ligands. These biosensors outperform previously engineered BenM-based biosensors by achieving a substantially greater dynamic range (up to ∼180-fold induction) and broadened operational range. The expression of select BenM variants in the presence of a muconic acid biosynthetic pathway demonstrated sensitive biosensor activation without saturating response, which should enable pathway and host engineering for higher production of muconic and adipic acids. Given the streamlined manner in which high-performance and versatile biosensors were evolved using OrthoRep, this study provides a template for generating custom biosensors for metabolic pathway engineering and other biotechnology goals.

Investigation of the association between gall bladder wall thickness and hypoalbuminaemia in dogs

OBJECTIVES

To assess the correlation between gallbladder wall thickness and serum/plasma albumin concentrations in dogs.

MATERIALS AND METHODS

Retrospective searches of digital medical record databases were conducted to identify dogs that had either severely low serum/plasma albumin concentration (<1.5 g/dL) or ultrasonographic evidence of gallbladder wall thickening (>2 mm). Analysis of covariance models were used to analyze gallbladder wall thickness with sample type (serum vs plasma), age, etiology, albumin, and albumin ' etiology as the covariates.

RESULTS

A total of 216 dogs met inclusion criteria. One-hundred and forty-six dogs had a thickened gallbladder wall (Group 1). Median serum/plasma albumin concentration for dogs in this group was 2.2 g/dL (1 to 5 g/dL), and 84 dogs (57.5%) had hypoalbuminemia (<2.5 g/dL). The search for dogs with severe hypoalbuminemia (< 1.5 g/dL) identified 70 dogs (Group 2). In this group, median gallbladder wall thickness was 1.3 mm (0.2 to 6.1 mm) and 17 dogs (24.3%) had a thickened gallbladder wall. Serum/plasma albumin concentration and gallbladder wall thickness were not significantly correlated for Group 1 (r = 0.0044, p = 0.9580) or Group 2 (r = -0.1137, p = 0.3487). A moderate negative correlation (-0.64) was identified between gallbladder wall thickness and albumin concentration in dogs with immune-mediated diseases (p = 0.03).

CLINICAL SIGNIFICANCE

Gallbladder wall thickness and serum/plasma albumin concentration are independent variables in dogs.

Rapid generation of potent antibodies by autonomous hypermutation in yeast

The predominant approach for antibody generation remains animal immunization, which can yield exceptionally selective and potent antibody clones owing to the powerful evolutionary process of somatic hypermutation. However, animal immunization is inherently slow, not always accessible and poorly compatible with many antigens. Here, we describe 'autonomous hypermutation yeast surface display' (AHEAD), a synthetic recombinant antibody generation technology that imitates somatic hypermutation inside engineered yeast. By encoding antibody fragments on an error-prone orthogonal DNA replication system, surface-displayed antibody repertoires continuously mutate through simple cycles of yeast culturing and enrichment for antigen binding to produce high-affinity clones in as little as two weeks. We applied AHEAD to generate potent nanobodies against the SARS-CoV-2 S glycoprotein, a G-protein-coupled receptor and other targets, offering a template for streamlined antibody generation at large.

Lineage tracing and analog recording in mammalian cells by single-site DNA writing

Studying cellular and developmental processes in complex multicellular organisms can require the non-destructive observation of thousands to billions of cells deep within an animal. DNA recorders address the staggering difficulty of this task by converting transient cellular experiences into mutations at defined genomic sites that can be sequenced later in high throughput. However, existing recorders act primarily by erasing DNA. This is problematic because, in the limit of progressive erasure, no record remains. We present a DNA recorder called CHYRON (Cell History Recording by Ordered Insertion) that acts primarily by writing new DNA through the repeated insertion of random nucleotides at a single locus in temporal order. To achieve in vivo DNA writing, CHYRON combines Cas9, a homing guide RNA and the template-independent DNA polymerase terminal deoxynucleotidyl transferase. We successfully applied CHYRON as an evolving lineage tracer and as a recorder of user-selected cellular stimuli.

[Diagnostic performance of quantitative fecal immunochemical test in detection of advanced colorectal neoplasia]

Objective: To evaluate the diagnostic performance of quantitative fecal immunochemical testing (FIT) and to provide reference for designing effective colorectal cancer (CRC) screening strategy in China. Methods: Based on an ongoing randomized controlled trial comparing the colorectal cancer screening strategies, this current study involved 3 407 participants aged 50-74 years who had undergone colonoscopies. All the feces samples were collected from the participants prior to receiving the colonoscopy. Fecal hemoglobin (Hb) was tested by FIT following a standardized operation process. Diagnosis-related indicators of FIT were calculated using the colonoscopy results as the gold standard. Results: Among the 3 407 participants, the mean age (SD) as 60.5 (6.3) years and 1 753 (51.5%) were males. The participants involved 28 (0.8%) CRCs, 255 (7.5%) advanced adenomas, 677 (19.9%) nonadvanced adenomas, and 2 447 (71.8%) benign or negative findings. With an overall positivity rate of 2.8% (96/3 407) at the recommended cutoff value of 20 μg Hb/g, the sensitivities of FIT for both CRC and advanced adenoma were 57.1% (95%CI: 37.2%-75.5%) and 11.0% (95%CI: 7.4%-15.5%), respectively, with the corresponding specificity as 98.4% (95%CI: 97.8%-98.8%). At a decreased cut-off value of 5 μg Hb/g, the sensitivities for detecting CRC and advanced adenoma increased to 64.3% (95%CI: 44.1%-81.4%) and 16.5% (95%CI: 12.1%-21.6%), respectively, but the specificity reduced to 95.2% (95%CI: 94.4%-95.9%). The areas under the ROC curve for CRC and advanced adenoma were 0.908 (95%CI: 0.842-0.973) and 0.657 (95%CI: 0.621-0.692), respectively. Of the diagnostic performance, there were no significant differences noticed by different sex and age groups. Conclusions: In our study, the quantitative FIT showed modest sensitivity in detecting CRC but limited sensitivity in detecting advanced adenoma. In population-based CRC screening programs, the quantitative FIT had the advantage of adjusting the positive threshold based on the targeted detection rate and available resource load of colonoscopy.

[Rates on the acceptance of colonoscopy, fecal immunochemical test and a novel risk-adapted screening approach in the screening programs of colorectal cancer as well as related associated factors]

Objective: To compare the rates of acceptance of colonoscopy, fecal immunochemical test (FIT), or a novel risk-adapted screening approach in the colorectal cancer (CRC) screening program. Related risk factors were also studied. Methods: The study has been based on an ongoing randomized controlled trial on colorectal cancer screening programs in six centers of research since May 2018. The involved participants were those who presented at the baseline screening phase. All the participants were randomly allocated into one of the following three intervention arms in a 1∶2∶2 ratio: colonoscopy group, FIT group, and a novel risk-adapted screening group. All the participants underwent risk assessment on CRC by an established risk score system. The subjects with high-risk were recommended to undertake the colonoscopy while the low-risk ones were receiving the FIT. Detailed epidemiological data was collected through questionnaires and clinical examinations. Rates of participation and compliance in all three groups were calculated. Multivariate logistic regression models were used to explore the potential associated factors related to the acceptance of screening. Results: There were 19 546 eligible participants involved in the study, including 3 916 in the colonoscopy group, 7 854 in the FIT group, and 7 776 in the novel risk-adapted screening group, respectively. Among the 19 546 participants, the mean age was 60.5 years (SD=6.5), and 8 154 (41.7%) were males. The rates of participation in the colonoscopy, FIT and the novel risk-adapted screening groups were 42.5%, 94.0% and 85.2%, respectively. In the novel risk-adapted screening group, the participation rate was 49.2% for the high-risk participants who need to undertake colonoscopy and was 94.0% for the low-risk ones who need to undertake FIT. Results from the multivariate logistic regression models demonstrated that there were several factors associated with the rates of participation in CRC screening, including age, background of education, history of smoking cigarettes, previous history of bowel examination, chronic inflammatory bowel disease and family history of CRC among the 1(st)-degree relatives. Conclusions: FIT and the novel risk-adapted screening approach showed superior participation rates to the colonoscopy. Further efforts including health promotion campaign for specific target population are needed to improve the engagement which ensures the effectiveness of CRC screening programs.

Ferromagnetic frustration in ternary nitride ZnFe3N

As a new antiperovskite nitride, ZnFe3N was synthesized and characterized by almost completely substituting iron atoms at corner positions of γ'-Fe4N. The magnetic interactions of the system with the space group Pm3[combining macron]m are fully investigated. The critical behavior was investigated based on the measured magnetic data around the ferromagnetic phase transition temperature. In this work, the values of critical exponents (β, γ and δ) were obtained systematically using the Kouvel-Fisher method in the critical region. The Widom scaling law (δ = 1 + γβ-1) and the scaling equation (m = f±(h)) were used to reveal the reliability of these values. The values of the critical exponents (β = 0.325, γ = 1.228, and δ = 4.778) are different from those predicted by the three-dimensional (3D) Heisenberg model and mean-field model, and are very close to those of the 3D-Ising model. Combined with ESR analysis, the spin clusters induced by changes in chemical bonds are considered to be the cause for the existence of an anisotropic short-range ordered state in this ferromagnetic system.

Rapid generation of potent antibodies by autonomous hypermutation in yeast

The predominant approach for antibody generation remains animal immunization, which can yield exceptionally selective and potent antibody clones owing to the powerful evolutionary process of somatic hypermutation. However, animal immunization is inherently slow, has poor compatibility with certain antigens ( e . g ., integral membrane proteins), and suffers from self-tolerance and immunodominance, which limit the functional spectrum of antibodies that can be obtained. Here, we describe A utonomous H ypermutation y E ast surf A ce D isplay (AHEAD), a synthetic recombinant antibody generation technology that imitates somatic hypermutation inside engineered yeast. In AHEAD, antibody fragments are encoded on an error-prone orthogonal DNA replication system, resulting in Saccharomyces cerevisiae populations that continuously mutate surface-displayed antibody repertoires. Simple cycles of yeast culturing and enrichment for antigen binding drive the evolution of high-affinity antibody clones in a readily parallelizable process that takes as little as 2 weeks. We applied AHEAD to generate nanobodies against the SARS-CoV-2 S glycoprotein, a GPCR, and other targets. The SARS-CoV-2 nanobodies, concurrently evolved from an open-source naïve nanobody library in 8 independent experiments, reached subnanomolar affinities through the sequential fixation of multiple mutations over 3-8 AHEAD cycles that saw ∼580-fold and ∼925-fold improvements in binding affinities and pseudovirus neutralization potencies, respectively. These experiments highlight the defining speed, parallelizability, and effectiveness of AHEAD and provide a template for streamlined antibody generation at large with salient utility in rapid response to current and future viral outbreaks.

[Pathological diagnosis of lung cancer based on deep transfer learning]

Objective: To establish an artificial intelligence (AI)-assisted diagnostic system for lung cancer via deep transfer learning. Methods: The researchers collected 519 lung pathologic slides from 2016 to 2019, covering various lung tissues, including normal tissues, adenocarcinoma, squamous cell carcinoma and small cell carcinoma, from the Beijing Chest Hospital, the Capital Medical University. The slides were digitized by scanner, and 316 slides were used as training set and 203 as the internal test set. The researchers labeled all the training slides by pathologists and establish a semantic segmentation model based on DeepLab v3 with ResNet-50 to detect lung cancers at the pixel level. To perform transfer learning, the researchers utilized the gastric cancer detection model to initialize the deep neural network parameters. The lung cancer detection convolutional neural network was further trained by fine-tuning of the labeled data. The deep learning model was tested by 203 slides in the internal test set and 1 081 slides obtained from TCIA database, named as the external test set. Results: The model trained with transfer learning showed substantial accuracy advantage against the one trained from scratch for the internal test set [area under curve (AUC) 0.988 vs. 0.971, Kappa 0.852 vs. 0.832]. For the external test set, the transferred model achieved an AUC of 0.968 and Kappa of 0.828, indicating superior generalization ability. By studying the predictions made by the model, the researchers obtained deeper understandings of the deep learning model. Conclusions: The lung cancer histopathological diagnostic system achieves higher accuracy and superior generalization ability. With the development of histopathological AI, the transfer learning can effectively train diagnosis models and shorten the learning period, and improve the model performance.

Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities

Enzyme orthologs sharing identical primary functions can have different promiscuous activities. While it is possible to mine this natural diversity to obtain useful biocatalysts, generating comparably rich ortholog diversity is difficult, as it is the product of deep evolutionary processes occurring in a multitude of separate species and populations. Here, we take a first step in recapitulating the depth and scale of natural ortholog evolution on laboratory timescales. Using a continuous directed evolution platform called OrthoRep, we rapidly evolve the Thermotoga maritima tryptophan synthase β-subunit (TmTrpB) through multi-mutation pathways in many independent replicates, selecting only on TmTrpB's primary activity of synthesizing L-tryptophan from indole and L-serine. We find that the resulting sequence-diverse TmTrpB variants span a range of substrate profiles useful in industrial biocatalysis and suggest that the depth and scale of evolution that OrthoRep affords will be generally valuable in enzyme engineering and the evolution of biomolecular functions.

[Disease burden of colorectal cancer in China: any changes in recent years?]

Objective: To update the disease burden of colorectal cancer (CRC) in Chinese population by integrating the latest multi-source evidences. Methods: Groups of data from GLOBOCAN, series of Chinese Cancer Registry Annual Report (annual report), Cancer Incidence in Five Continents (CI5), Global Burden of Disease Project 2017 (GBD), China Death Cause Surveillance Datasets and China Health Statistical Yearbooks (yearbook) were used to extract the information. Data on incidence, mortality, disability-adjusted life year (DALY) and percentage distribution of sub-location of CRC were used to analyze the latest disease burden in China, and age-standardized rates by world standard population were mainly used. Joinpoint Trend Analysis Software 4.7.0.0 was applied for time trend analysis. Data related to the economic burden of CRC in China were gathered by literature review. Results: (1) Current status: according to the latest annual report, the incidence and mortality rates of CRC were 17.1 per 100 000 and 7.9 per 100 000, respectively among the covered registration sites in 2015. The incidence ratios of male to female and that of urban to rural were 1.5 and 1.4, with the mortality ratios were 1.6 and 1.4, respectively. Similar to data from the annual report, the mortality rate was reported as 6.9 per 100 000 in 2017 by the surveillance data sets. Data from the GBD project showed that, the DALYs caused by CRC in China in 2017 was 4.254 million person years (doubled compared with that of 1990), accounting for 22.4% of the global burden of CRC. (2) Time trends: according to the annual reports, from 2009 to 2015, the incidence rate and mortality rate of CRC in China decreased by 10.2% and 9.5%, respectively. The same trend was also observed in urban sites, but was opposite in rural areas (increased 20.0% in incidence and 15.2% in mortality). Results from the Joinpoint analysis showed that the averaged annual percentage change (AAPC) was estimated as -1.6% (P<0.05) in the national mortality rate. Similarly, in the incidence and mortality rates of urban sites appeared as AAPC=-1.5% and -1.4% (all P<0.05), but inversely in the incidence rate from the rural sites as AAPC=3.3% (P<0.05). The yearbook data showed a 9.8% increase in urban and 20.6% increase in rural on the mortality in 2017 when compared with 2004, but the Joinpoint analysis showed no statistical significance (P<0.05). (3) Distribution of sub-location of CRC: the annual report showed that among all the new CRC cases in China in 2015, colon, rectal and anal cancer accounted for 49.6%, 49.2% and 1.2%, respectively, while the proportions were 51.3%, 47.6% and 1.1%, respectively in 2009. The proportion of colon cancer was continuously higher in the urban (>52%) than that in the rural areas (<44%). The CI5 Ⅺ data showed that ascending and sigmoid colons were more commonly seen among all the colon cancers. (4) Economic burden: the average annual growth rate of the medical expenditure per CRC patient in China ranged from 6.9% to 9.2%, and the 1-year out-of-pocket expenditure of a newly diagnosed patient accounted for about 60% of their previous-year household income. Conclusions: In China, the overall disease burden of CRC might have been decreased slightly but generally remained stable in the last several years, however, the rising burden appeared in the rural areas should not be ignored. In consistent with findings from a previous review, men and people from the urban areas are considered the target populations for CRC. The finding of higher proportion of colon cancer in urban areas suggests the impact of development of socioeconomic and medical technologies on CRC development and detection. The economic burden of CRC continued to grow.

Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study

Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today's agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell's growth rate to the target gene's function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.

[Population's acceptance and attitude toward a novel fecal immunochemical test for colorectal cancer screening: a multi-center survey in China]

Objective: To investigate the acceptance and attitude toward a novel fecal immunochemical test (FIT) in colorectal cancer screening among populations in China. Methods: From May 2018 to May 2019, 2 474 people aged 50-74 years were recruited from five provinces of China (Zhejiang, Anhui, Jiangsu, Hunan and Yunnan). The general demographic characteristics, acceptance of the new FIT technology and operational difficulties through the whole screening process were obtained through questionnaire survey. Multivariate logistic regression model was used to analyze the factors related to difficulties encountered in sampling stool, reading and uploading results. Results: The subjects were (60.0±6.4) years old, and female, high school of above educated, unemployed/retired/other, married and with medical insurance status of "new rural cooperative medical care (NRCMC)" accounted for 61.7% (1 526), 29.0%(718), 34.3% (849), 92.7% (2 293) and 31.3%(775), respectively. The population's acceptance of the FIT technology was 94.8%. In the process of FIT screening, the percentage of occurred difficulties in sampling stool, reading and uploading results were 33.1% (819), 46.4% (1 147) and 62.9% (1 557), respectively. The main difficulties were the uncertainty about whether the sampling operation was standard (28.0%), the inability to accurately judge the result displayed (32.5%) and the need for help without using a smartphone (44.2%). The results of multivariate logistic regression model analysis showed that people aged 65-74 years old and with medical insurance status of "NRCMC" were more likely to encounter difficulties in sampling, and those who were unemployed/retired/other and living with 3 or more family members were less likely to encounter difficulties in sampling. Those aged 65-74 years old, farmers or migrant workers, and those with "NRCMC" were more likely to encounter difficulties in readingresults, and those with 3 or more family members were less likely to encounter difficulties in reading result. Those with "NRCMC" were more likely to encounter difficulties in uploading results, and those with education level of high school or above, living with more than 3 family members were less likely to encounter difficulties in uploading results. Conclusion: The acceptance of the new FIT technology is relatively high among the subjects. Age, education level, occupation, number of family members living together and medical insurance status might be related to difficulties encountered in sampling stool, reading and uploading results, and it can be further strengthened in terms of the technology and characteristics of sub-populations.

Automated Continuous Evolution of Proteins in Vivo

We present automated continuous evolution (ACE), a platform for the hands-free directed evolution of biomolecules. ACE pairs OrthoRep, a genetic system for continuous targeted mutagenesis of user-selected genes in vivo, with eVOLVER, a scalable and automated continuous culture device for precise, multiparameter regulation of growth conditions. By implementing real-time feedback-controlled tuning of selection stringency with eVOLVER, genes of interest encoded on OrthoRep autonomously traversed multimutation adaptive pathways to reach desired functions, including drug resistance and improved enzyme activity. The durability, scalability, and speed of biomolecular evolution with ACE should be broadly applicable to protein engineering as well as prospective studies on how selection parameters and schedules shape adaptation.

[Health economic evidence for colorectal cancer screening programs in China: an update from 2009-2018]

Objective: This study was to systematically update the economic evaluation evidence of colorectal cancer screening in mainland China. Methods: Based on a systematic review published in 2015, we expanded the scope of retrieval database (PubMed, EMbase, The Cochrane Library, Web of Science, CNKI, Wanfang Data, VIP, CBM) and extended it to December 2018. Focusing on the evidence for nearly 10 years (2009-2018), basic characteristics and main results were extracted. Costs were discounted to 2017 using the consumer price index of medical and health care being provided to the residents, and the ratio of incremental cost-effectiveness ratio (ICER) to per capita GDP in corresponding years were calculated. Results: A total of 12 articles (8 new ones) were included, of which 9 were population-based (all cross-sectional studies) and 3 were model-based. Most of the initial screening age was 40 years (7 articles), and most of the frequency was once in a lifetime (11 articles). Technologies used for primary screening included: questionnaire assessment, immunological fecal occult blood test (iFOBT) and endoscopy. The most commonly used indicator was the cost per colorectal cancer detected, and the median (range) of the 20 screening schemes was 52 307 Chinese Yuan (12 967-3 769 801, n=20). The cost per adenoma detected was 9 220 Yuan (1 859-40 535, n=10). In 3 articles, the cost per life year saved (compared with noscreening) was mentioned and the ratio of ICER to GDP was 0.673 (-0.013-2.459, n=11), which was considered by WHO as "very cost-effective" ; The range of ratios overlapped greatly among different technologies and screening frequencies, but the initial age for screening seemed more cost-effective at the age of 50 years (0.002, -0.013-0.015, n=3), than at the 40 year-olds (0.781, 0.321-2.459, n=8). Conclusions: Results from the population-based studies showed that the cost per adenoma detected was only 1/6 of the cost per colorectal cancer detected, and limited ICER evidence suggested that screening for colorectal cancer was generally cost-effective in Chinese population. Despite the inconclusiveness of the optimal screening technology, the findings suggested that the initial screening might be more cost-effective at older age. No high-level evidence such as randomized controlled trial evaluation was found.

[In vitro study on signal transduction in mice spiral ganglion cell stimulated by multi-wavelength laser based on calcium imaging]

Objective: To research the auditory nerve transduction effects under multi-wavelength pulsed laser stimulations within a safe and acceptable signal range. Methods: The real-time detection of intracellular calcium concentration was adopted by specific fluorescent indicator staining based on calcium imager. The spiral ganglion cells of mice were cultured in vitro. After fluorescent indicating, morphologic observation under optical microscope, Fura-2 calcium ion fluorescence excitation, intact morphology cells selection, fixing the optical fiber, the spiral ganglion cells were irradiated by different wavelength laser, including visible light (450 nm) and near infrared light (808 nm,1 065 nm). The intracellular calcium concentration was monitored by calcium ion imaging. Results: When 450 nm laser stimulated spiral ganglion cells, the intracellular calcium concentration was strongly increased, however, for other wavelength laser stimulation, there was no obvious relative response. And the sensitivity expression of the nerve cells under laser was related with the location of laser fiber. Cells closer to the fiber produced more obvious changes in calcium ion concentration, while for cells farther away from the fiber, the change amplitudes were weaker although the number of changes in calcium ion concentration was consistent. Conclusion: The spiral ganglion cells of mice can induce a signal transduction response under the action of laser, and the response has laser wavelength selectivity.

Cytokine tear film profile determination in eyes of healthy dogs and those with inflammatory periocular and skin disorders

Alterations in serum cytokine levels and profiles have been reported in association with a variety of disease conditions (e.g., allergic, immune-mediated, etc.) in both humans and animals. In comparison to serum cytokine measurements, tear cytokine measurements might be expected to more accurately reflect the inflammatory milieu associated with periocular disease. The purpose of this study was to use a multiplexed assay to compare the cytokine profile of tears in healthy dogs to those with inflammatory skin and periocular disease. We were able to detect IL-2, IL-6, IL-8, and TNF-α in >47 % of tear samples from both healthy canine patients and those with inflammatory dermatologic disease (with or without concurrent periocular involvement). In contrast, IL-7, IL-10 and IFN-γ were rarely detected. Dogs with both dermatologic and periocular disease (but not dermatologic disease alone) had higher levels of IL-8 (P < 0.001, P > 0.05, respectively) relative to healthy dogs. Patients with concurrent dermatologic and periocular disease also demonstrated significantly greater variability in IL-8 concentrations between eyes than did healthy dogs (P < 0.0001). Our findings suggest that tear cytokine analysis may prove to be a useful tool to investigate the role and interactions of the local ocular immune response in patients with inflammatory periocular disease.

[Analysis on the consciousness of the cancer early detection and its influencing factors among urban residents in China from 2015 to 2017]

Objective: To understand the consciousness of the cancer early detection among urban residents and identify the influencing factors from 2015 to 2017. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. Self-designed questionnaires were used to collect population, socioeconomic indicators, self-cancer risk assessment, regular participation in physical examination and other information. The multivariate logistic regression model was used to identify the factors of people who had not regularly participated in the regular physical examination in the past five years. Results: The self-assessment results of 32 357 residents showed that there were 27.54% (8 882) of total study population with self-reported cancer risk, 45.48% (14 671) without cancer risk and 26.98% (8 704) with unclear judgement on their own cancer risk. Among population with cancer risk, 79.84% (7 091) considered physical examination accounted. In the past five years, there were 21 105 (65.43%) residents participated in regular physical examination and 11 148 (34.56%) participated in non-scheduled one, respectively. The multivariate logistic regression analysis showed that compared with unmarried and western region residents, divorced, middle and eastern region residents had a stronger consciousness to participate in the regular physical examination (P<0.05). Compare with residents with annual household income less than 20 000 CNY in 2014, cancer risk assessment/screening intervention population, and self-assessment with cancer risk, residents with annual household income between 20 000 CNY and 59 000 CNY in 2014, occupational population, community residents, cancer patients, self-reported cancer-free risk, and self-assessment with unclear judgement of cancer risk were less likely to participate in the regular physical examination (all P values <0.05). Conclusion: From 2015 to 2017, the Chinese urban residents had a acceptable consciousness of the cancer early detection. The marital status, annual household income, population group and self-assessment of cancer risk were related to the consciousness of the cancer early detection of people who had not participated in the regular physical examination in the past five years.

[Analysis on the demand, access and related factors of cancer prevention and treatment knowledge among urban residents in China from 2015 to 2017]

Objective: To investigate the demand and access to the cancer prevention and treatment knowledge and related factors among urban residents in China from 2015 to 2017. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. The self-designed questionnaire was used to collect the information of general demographic characteristics, the demand and access to cancer prevention and treatment knowledge, and the influencing factors of the attitude. The Chi-square test was used to analyze the difference of the demand of the cancer prevention knowledge among different groups and the corresponding factors of the cancer prevention and treatment knowledge were analyzed by using the logistic regression model. Results: The proportion of residents who need the cancer prevention and treatment knowledge was 79.5%. The demand rate of the inducement, symptom and diagnosis methods of cancer in the occupational population was highest, about 66.8%, 71.0% and 20.8%, respectively. The demand rate of treatment methods and cost in current cancer patients was the highest, about the 45.9% and 21.9%, respectively. The top three sources to acquire the cancer prevention and treatment knowledge were "broadcast or television" (69.5%), "books, newspapers, posters or brochures" (44.7%) and "family and friends" (33.8%). The multivariate analysis showed that compared with public institution personnel/civil servants, unmarried/cohabiting/divorced/widowed and others, annual household income less than 20 000 CNY, from the eastern region, people without cancer diagnosis and people with self-assessment of cancer risk, the demand rate of cancer prevention and treatment knowledge was higher in enterprise personnel/workers, married, annual household income between 60 000 CNY and 150 000 CNY, from the central region, people with cancer and people with unclear cancer risk (all P values <0.05). Conclusion: There was a high demand for the cancer prevention and treatment knowledge among urban residents in China from 2015 to 2017. The main access to the knowledge is from the radio or television. The occupation, marital status, annual household income, residential region, health status and risk of disease were the main factors of the demand of the cancer prevention and treatment knowledge.

[Study on the health literacy and related factors of the cancer prevention consciousness among urban residents in China from 2015 to 2017]

Objective: To understand the health literacy and relevant factors of cancer prevention consciousness in Chinese urban residents from 2015 to 2017. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. The self-designed questionnaire was used to collect the information of demographic characteristics and cancer prevention consciousness focusing on nine common risk factors, including smoking, alcohol, fiber food, food in hot temperature or pickled food, chewing betel nut, helicobacter pylori, moldy food, hepatitis B infection, estrogen, and exercise. The logistic regression model was adopted to identify the influencing factors. Results: The overall health literacy of the cancer prevention consciousness was 77.4% (24 980 participants), with 77.4% (12 018 participants), 79.9% (6 406 participants), 77.2% (1 766 participants) and 74.5% (4 709 participants) in each group (P<0.001). The correct response rates for nine risk factors ranged from 55.2% to 93.0%. The multivariate logistic regression analysis showed that compared with community residents, people with primary school level education or below, and the number of people living together in the family <3, the cancer risk assessment/screening intervention population, cancer patients, those with junior high school level educationor above and the number of people living in the family ≥3 had better health literacy of the cancer prevention consciousness (all P values <0.05). Compared with females, 39 years old and below, government-affiliated institutions or civil servants, from the eastern region, males, older than 40 years, company or enterprise employees, and from the middle or western region had worse health literacy of the cancer prevention consciousness (all P values <0.05). Conclusion: The health literacy of the cancer prevention consciousness in Chinese urban residents should be improved. The cancer screening intervention, gender, age, education, occupation, the number of people co-living in the family, and residential region were associated with the health literacy of the cancer prevention consciousness.

[Analysis on the health literacy of the cancer prevention and treatment and its related factors among urban residents in China from 2015 to 2017]

Objective: To understand the health literacy of the cancer prevention and treatment among urban residents of China, and explore the related factors. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China (CanSPUC) from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. The health literacy of the cancer prevention, early discovery, early diagnosis, early treatment and the demands of cancer prevention and treatment knowledge was analyzed. The level of health literacy among different groups were calculated and compared. The binary logistic regression model was used to analyze the influencing factors of the health literacy of the cancer prevention and treatment. Results: The level of health literacy of the cancer prevention and treatment was 56.97% among all study population; in each group it was 55.01% for community residents, 59.08% for cancer risk assessment/screening population, 61.99% for cancer patients and 57.31% for occupational population, respectively (P<0.001). The level of health literacy of the cancer prevention and treatment of residents aged 50 to 69 years old, other occupational groups, unmarried, the central and western region residents and the group with unclear self-assessment of cancer risk was significantly lower than that of residents younger than 40 years old, personnel of public institutions/civil servants, married, the eastern region residents and the group whose self-assessment without cancer risk (P<0.05) . The level of health literacy of cancer prevention and treatment of females, people who went to high school or over, cancer risk assessment/screening population, cancer patients and occupational population was significantly higher than that of males, people who had an education level of primary school or below and community residents (P<0.05) . Conclusion: The health literacy of the cancer prevention and treatment of urban residents in China was relatively high, but there was still room for improvement. Gender, age, educational level, occupation, region, marital status, self-assessment of cancer risk, and type of respondents were the key influencing factors of the health literacy of the cancer prevention and treatment. Male, 50-69 years old, lower educational level, central and western regions, unclear cancer risk self-assessment, and without specific environmental exposure to cancer prevention and treatment knowledge or related risk factors were the characteristics of the key intervention group of the health literacy of the cancer prevention and treatment.

[Analysis on the consciousness of the early cancer treatment and its influencing factors among urban residents in China from 2015 to 2017]

Objective: To understand the consciousness of the cancer early treatment and its demographic and socioeconomic factors. Methods: A cross-sectional survey was conducted in 16 provinces covered by the Cancer Screening Program in Urban China (CanSPUC) from 2015 to 2017. A total of 32 257 local residents aged ≥18 years old who could understand the investigation procedure were included in the study by using the cluster sampling method and convenient sampling method. All local residents were categorized into four groups, which contained 15 524 community residents, 8 016 cancer risk assessment/screening population, 2 289 cancer patients and 6 428 occupational population, respectively. The questionnaire collected personal information, the consciousness of the cancer early treatment and relevant factors. The Chi square test was used to compare the difference between the consciousness of the cancer early treatment and relevant factors among the four groups. The logistic regression model was used to analyze the influencing factors related to the consciousness of the cancer early treatment. Results: With the assumption of being diagnosed as precancer or cancer, 89.97% of community residents, 91.84% of cancer risk assessment/screening population, 93.00% of cancer patients and 91.52% of occupational population would accept active treatments (P<0.001). If the immediate family members were diagnosed as precancer or cancer, people who would encourage their family members to receive early treatment in the four groups accounted for 91.96%, 91.94%, 92.44% and 91.55%, respectively (P<0.001). The company employees, annual household income with 40 000 yuan and more and other three groups had a relatively better consciousness of the cancer early treatment (P<0.05). Male, widowed, unemployed and from the central and western regions had a relatively worse consciousness of the cancer early treatment (P<0.05). Conclusion: Residents in urban China participants had a good consciousness of the cancer early treatment. The marital status, occupation, annual household income and residential regions were major factors related to the consciousness of the cancer early treatment.

[Natural history of colorectal cancer: a Meta-analysis on global prospective cohort studies]

Objective: To acknowledge the availability and rates of annual transition of outcomes during the progression and regression stages of colorectal cancer (CRC) and related diseases, by pooling global follow-up studies on the natural history of CRC. Methods: Till March, 2017, data was collected through systematic literature review over multiple databases, including PubMed, Embase, Cochrane and Chinese Biology Medicine (CBM) disc. Information regarding the characteristics, classification system of health states, related outcomes and incidence rates on CRC or high-risk adenoma for the surveillance cohorts of the studies, were extracted and summarized. Both Meta and sensitivity analyses were performed on those outcomes if they appeared in more than 3 studies, using the random effects model. Annual transition rate with 95%CI was used to estimate each of the outcomes, Quality of the studies was assessed, using the Newcastle-Ottawa Scale. Results: A total of 29 cohort studies were included, with the mean follow-up period as 5.7 years. All studies except one, focused on adenoma-carcinoma pathway and reported the outcome parameters of adenomas by different risk, and some reported the findings on different sizes (n=6) of adenomas. These cohorts were divided into three groups (normal status, with low-risk or high-risk adenoma) according to the status of baseline endoscopic pathologic findings. Their available outcome parameters, corresponding number of involved articles, aggregated sample size and pooled annual transition rates were presented. Six parameters were obtained in the normal cohorts, including those from normal to low-risk adenoma (16 articles, 58 235, 0.030: 0.024-0.037), to high-risk adenoma (17 articles, 62 089, 0.003: 0.002-0.004), to diminutive adenoma (<5 mm, 4 articles, 1 277, 0.021: 0.013-0.029), to small adenoma (6-9 mm, 4 articles, 1 277, 0.006: 0.001-0.010), to large adenoma (≥10 mm, 7 articles, 3 531, 0.002: 0.000-0.003) and to CRC (19 articles, 104 836, 0.000 3: 0.000 2-0.000 5). Three parameters were obtained in low-risk adenoma in cohorts with polypectomy findings, including recurrence (9 articles, 4 788, 0.109: 0.062-0.157) from low-risk adenoma after polypectomy to high-risk adenoma (10 articles, 5 736, 0.009: 0.004-0.013) and to CRC (12 articles, 11 347, 0.000 6: 0.000 4-0.000 8). Three parameters were obtained on high-risk adenoma from cohorts with polypectomy findings, including recurrence (12 articles, 7 030, 0.038: 0.028-0.048) from high-risk adenoma after polypectomy to low-risk adenoma (8 articles, 2 489, 0.133: 0.081-0.185) and CRC (14 articles, 14 899, 0.002: 0.001-0.003). Except for normal to low-risk adenomas, results from the sensitivity analysis for the other parameters showed stable. Of the included studies, two presented incidence rates of CRC in different clinical stages and the another two were focusing on the parameters related to serrated pathway. Conclusions: Globally, follow-up studies reported data on natural history of colorectal cancer is of paucity. Compared to the "adenoma-carcinoma" pathway, transition parameters of the serrated lesion pathway are more limited. This Meta-analysis provided convincing evidence for optimizing the strategies regarding follow-up program on the disease, using the baseline endoscopic findings from global CRC Screening Program. These results also offered strong data-related support for Chinese population- specific interventional model on colorectal cancer.

Genetic Compatibility and Extensibility of Orthogonal Replication

We recently developed an orthogonal replication system (OrthoRep) in yeast that allows for the rapid continuous mutagenesis of a special plasmid without mutating the genome. Although OrthoRep has been successfully applied to evolve several proteins and enzymes, the generality of OrthoRep has not yet been systematically studied. Here, we show that OrthoRep is fully compatible with all Saccharomyces cerevisiae strains tested, demonstrate that the orthogonal plasmid can encode genetic material of at least 22 kb, and report a CRISPR/Cas9-based method for expedient genetic manipulations of OrthoRep. It was previously reported that the replication system upon which OrthoRep is based is only stable in respiration-deficient S. cerevisiae strains that have lost their mitochondrial genome (ρ⁰ strains). However, here we trace this biological incompatibility to the activity of the dispensable toxin/antitoxin system encoded on the wild-type orthogonal plasmid. Since the toxin/antitoxin system is replaced by genes of interest in any OrthoRep application, OrthoRep is a generally compatible platform for continuous in vivo evolution in S. cerevisiae.

[Economic burden of stomach cancer in China during 1996-2015: a systematic review]

Objective: To clarify the research status of economic burden of stomach cancer in China from 1996 to 2015. Methods: Based on three electronic literature databases (China Knowledge Resource Integrated Database, Wanfang Database and PubMed), a total of 2 873, 1 244 and 84 articles published during 1996 to 2015 were found, respectively, using keywords of"cancer","neoplasms","malignant tumor","tumor","economic burden","health expenditure","cost","cost of illness", and"China". According to the inclusion and exclusion criteria, 30 literatures were included in the final analysis. Then the basic information and study subjects, indicators and main results of economic burden were abstracted and analyzed. All the expenditure data were discounted to the values in 2013 by using China's percapita consumer price index. Results: Totally, 30 articles were included, covering 14 provinces and of which 16 were published during 2011-2015. One article was based on population-level and the remaining studies were all based on individual-level. The number of individual-level articles that reported direct medical, non-medical and indirectly economic burden was 29, 1 and 2, respectively. The main indicators of direct medical expenditure were expenditure per patient (22), per clinical visit (9) and per diem (11), respectively. The median expenditure per patient was 7 387-28 743 RMB (CNY), with average annual growth rate (AAGR) of 1.7% (1996-2013). The median expenditure per clinical visit was 18 504-41 871 RMB (2003-2013), with AAGR of 5.5%. The median expenditure per diem was 313-1 445 RMB (1996-2012), with AAGR of 3.7%. Difference was found among provinces. Conclusions: The evidence for economic burden of stomach cancer was still limited over the past two decades and mainly focused on individual and regional levels. An increase and differences in provinces were observed in direct medical expenditure. Evaluation on direct non-medical and indirect medical expenditure needs to be addressed.

Tunable Expression Systems for Orthogonal DNA Replication

We recently developed an orthogonal DNA replication (OrthoRep) system capable of driving the rapid continuous evolution of genes in vivo. However, OrthoRep uses a special transcription system, the components of which (e.g., promoters) have previously limited the strength with which OrthoRep-encoded genes can be expressed. Here, we report a collection of synthetic and evolved OrthoRep expression parts that allow OrthoRep-encoded genes to span expression levels matching those of endogenous Saccharomyces cerevisiae genes. Specifically, we found that various promoter mutations as well as a genetically encoded poly(A) tail enable us to tune the expression level of OrthoRep-encoded genes over a large range and up to levels 43-fold higher than were previously attained, reaching at least ∼40% of the strength of the genomic TDH3 promoter. We further show that expression level gains using our new parts are stable over passaging and consistent across multiple genes and OrthoRep systems of different mutation rates. This new set of expression parts further expands OrthoRep's applicability to the continuous in vivo evolution of proteins and pathways.

Site-Specific Incorporation of Sulfotyrosine Using an Expanded Genetic Code

Tyrosine sulfation is an important posttranslational modification found in bacteria and higher eukaryotes. However, the chemical synthesis or expression of homogenously sulfated proteins is particularly difficult, limiting our study and application of tyrosine-sulfated proteins. With the recent development of genomically recoded organisms and orthogonal translation components, we can often treat otherwise posttranslationally-modified amino acids as noncanonical amino acids (ncAAs) encoded by an expanded genetic code. Here, we describe methods for the co-translational incorporation of one or multiple sulfotyrosines into proteins using standard or genomically recoded Escherichia coli stains, thereby achieving the direct expression of site-specifically tyrosine sulfated proteins in vivo.

Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds

Directed evolution is a powerful approach for engineering biomolecules and understanding adaptation. However, experimental strategies for directed evolution are notoriously labor intensive and low throughput, limiting access to demanding functions, multiple functions in parallel, and the study of molecular evolution in replicate. We report OrthoRep, an orthogonal DNA polymerase-plasmid pair in yeast that stably mutates ∼100,000-fold faster than the host genome in vivo, exceeding the error threshold of genomic replication that causes single-generation extinction. User-defined genes in OrthoRep continuously and rapidly evolve through serial passaging, a highly straightforward and scalable process. Using OrthoRep, we evolved drug-resistant malarial dihydrofolate reductases (DHFRs) in 90 independent replicates. We uncovered a more complex fitness landscape than previously realized, including common adaptive trajectories constrained by epistasis, rare outcomes that avoid a frequent early adaptive mutation, and a suboptimal fitness peak that occasionally traps evolving populations. OrthoRep enables a new paradigm of routine, high-throughput evolution of biomolecular and cellular function.

Correction to: CDK5 Regulates PD-L1 Expression and Cell Maturation in Dendritic Cells of CRSwNP

The article CDK5 Regulates PD-L1 Expression and Cell Maturation in Dendritic Cells of CRSwNP, written by C. C. Liu, H. L. Zhang, L. L. Zhi, P. Jin, L. Zhao, T. Li, X. M. Zhou, D. S. Sun, G. H. Cheng, Q. Xin, L. Shi, and M. Xia was originally published electronically on the publisher's internet.

Mutually Orthogonal DNA Replication Systems In Vivo

The yeast cytoplasmically localized pGKL1/TP-DNAP1 plasmid/DNA polymerase pair forms an orthogonal DNA replication system whose mutation rate can be drastically increased without influencing genomic replication, thereby supporting in vivo continuous evolution. Here, we report that the pGKL2/TP-DNAP2 plasmid/DNA polymerase pair forms a second orthogonal replication system. We show that custom genes can be encoded and expressed from pGKL2, that error-prone TP-DNAP2s can be engineered, and that pGKL2 replication by TP-DNAP2 is both orthogonal to genomic replication in Saccharomyces cerevisiae and mutually orthogonal with pGKL1 replication by TP-DNAP1. This demonstration of two mutually orthogonal DNA replication systems with tunable error rates and properties should enable new applications in cell-based continuous evolution, genetic recording, and synthetic biology at large.

Selection of Differential Isolates of Magnaporthe oryzae for Postulation of Blast Resistance Genes

A set of differential isolates of Magnaporthe oryzae is needed for the postulation of blast resistance genes in numerous rice varieties and breeding materials. In this study, the pathotypes of 1,377 M. oryzae isolates from different regions of China were determined by inoculating detached rice leaves of 24 monogenic lines. Among them, 25 isolates were selected as differential isolates based on the following characteristics: they had distinct responses on the monogenic lines, contained the minimum number of avirulence genes, were stable in pathogenicity and conidiation during consecutive culture, were consistent colony growth rate, and, together, could differentiate combinations of the 24 major blast resistance genes. Seedlings of rice cultivars were inoculated with this differential set of isolates to postulate whether they contain 1 or more than 1 of the 24 blast resistance genes. The results were consistent with those from polymerase chain reaction analysis of target resistance genes. Establishment of a standard set of differential isolates will facilitate breeding for blast resistance and improved management of rice blast disease.

Characterization of a Sulfated Anti-HIV Antibody Using an Expanded Genetic Code

Tyrosine sulfation is a crucial post-translational modification for certain antibodies that neutralize HIV. One of the most neutralizing sulfated anti-HIV antibodies, E51, contains a region in its V_HCDR3 loop with five tyrosine (Tyr) residues, which are hypothesized to be partially or fully sulfated to bind to HIV's gp120 coat protein. However, the gp120-binding contribution of each sulfate or more complex sulfation patterns is unknown. In addition, natural sulfation of Tyr-rich loops usually yields a mixture of multiply sulfated products, complicating attempts to dissect the function of individual E51 sulfoforms with unique sulfation patterns. Here, we use an upgraded expanded genetic code for sulfotyrosine (sY) to express homogeneous E51 sulfoforms containing up to five sulfates. Through characterization of the 32 possible sulfoforms of E51, we show that only a subset of E51 sulfoforms with two, three, or four sYs bind to gp120 with potency similar to that of post-translationally sulfated E51, which we find is a mixture of sulfoforms. We show that sulfation of Tyr100i is necessary for gp120 binding whereas sulfation of Tyr100n is detrimental to binding. These results reveal that gp120 binding by E51 requires very specific sulfation patterns and should aid in the further design of sulfated E51-based peptides and immunoadhesins against HIV.