Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

MOTIVATION: The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity. RESULTS: We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions, and predict performances of biomacromolecules. AVAILABILITY AND IMPLEMENTATION: Our tool is publicly available at https://github.com/BGI-SynBio/PyMOL-PUB.

DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage.

DNA storage is one of the most promising ways for future information storage due to its high data storage density, durable storage time and low maintenance cost. However, errors are inevitable during synthesizing, storing and sequencing. Currently, many error correction algorithms have been developed to ensure accurate information retrieval, but they will decrease storage density or increase computing complexity. Here, we apply the Bloom Filter, a space-efficient probabilistic data structure, to DNA storage to achieve the anti-error, or anti-contamination function. This method only needs the original correct DNA sequences (referred to as target sequences) to produce a corresponding data structure, which will filter out almost all the incorrect sequences (referred to as non-target sequences) during sequencing data analysis. Experimental results demonstrate the universal and efficient filtering capabilities of our method. Furthermore, we employ the Counting Bloom Filter to achieve the file version control function, which significantly reduces synthesis costs when modifying DNA-form files. To achieve cost-efficient file version control function, a modified system based on yin-yang codec is developed.

A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid.

Synthetic auxotrophy in which cell viability depends on the presence of an unnatural amino acid (unAA) provides a powerful strategy to restrict unwanted propagation of genetically modified organisms (GMOs) in open environments and potentially prevent industrial espionage. Here, we describe a generic approach for robust biocontainment of budding yeast dependent on unAA. By understanding escape mechanisms, we specifically optimize our strategies by introducing designed "immunity" to the generation of amber-suppressor tRNAs and developing the transcriptional- and translational-based biocontainment switch. We further develop a fitness-oriented screening method to easily obtain multiplex safeguard strains that exhibit robust growth and undetectable escape frequency (<~10-9) on solid media for 14 days. Finally, we show that employing our multiplex safeguard system could restrict the proliferation of strains of interest in a real fermentation scenario, highlighting the great potential of our yeast biocontainment strategy to protect the industrial proprietary strains.

Competing risks analysis of external versus internal radiation in patients with hepatocellular carcinoma after controlling for immortal time bias.

PURPOSE: In cohort studies on liver cancer, there are often immortal time bias and interference of competing risk events. This study proposes to explore the role of internal and external radiotherapy for hepatocellular carcinoma using SEER data, using a competing risk model and controlling immortal time bias. METHODS: Data of SEER from 2004 till 2015 was included. To analyze whether there was a difference in survival between HCC (hepatocellular carcinoma) patients receiving external radiation and internal radiation, we used a competing risk analysis after excluding immortal time bias, and created a nomogram to assess the risk of cancer-specific death (CSD) in hepatocellular carcinoma patients receiving radiotherapy. RESULTS: Potential confounding factors adjusted, there was no significant difference in CSD between external and internal radiation therapy [HR and its 95% CI = 1.098 (0.874-1.380)]. The constructed nomogram performed better than the traditional AJCC model. The AUC and calibration curve results showed that this well-calibrated nomogram could be used to make clinical decisions regarding the prognosis and personalized treatment of hepatocellular carcinoma treated. There was no difference in the cumulative risk of death between patients with liver cancer treated with external radiation therapy and internal radiation therapy. CONCLUSION: There is no difference in the cumulative risk of death between patients with liver cancer treated with external radiation therapy and internal radiation therapy. The nomogram predicts the results more accurately. These results can be used to guide the choice of treatment options for patients with HCC and to predict their survival prognosis.

Novel function of a putative TaCOBL ortholog associated with cold response.

The plant COBRA protein family plays an important role in secondary cell wall biosynthesis and the orientation of cell expansion. The COBRA gene family has been well studied in Arabidopsis thaliana, maize, rice, etc., but no systematic studies were conducted in wheat. In this study, the full-length sequence of TaCOBLs was obtained by homology cloning from wheat, and a conserved motif analysis confirmed that TaCOBLs belonged to the COBRA protein family. qRT-PCR results showed that the TaCOBL transcripts were induced by abiotic stresses, including cold, drought, salinity, and abscisic acid (ABA). Two haplotypes of TaCOBL-5B (Hap5B-a and Hap5B-b), harboring one indel (----/TATA) in the 5' flanking region (- 550 bp), were found on chromosome 5BS. A co-dominant marker, Ta5BF/Ta5BR, was developed based on the polymorphism of the two TaCOBL-5B haplotypes. Significant correlations between the two TaCOBL-5B haplotypes and cold resistance were observed under four environmental conditions. Hap5B-a, a favored haplotype acquired during wheat polyploidization, may positively contribute to enhanced cold resistance in wheat. Based on the promoter activity analysis, the Hap5B-a promoter containing a TATA-box was more active than that of Hap5B-b without the TATA-box under low temperature. Our study provides valuable information indicating that the TaCOBL genes are associated with cold response in wheat.

Mobile and Self-Sustained Data Storage in an Extremophile Genomic DNA.

DNA has been pursued as a novel biomaterial for digital data storage. While large-scale data storage and random access have been achieved in DNA oligonucleotide pools, repeated data accessing requires constant data replenishment, and these implementations are confined in professional facilities. Here, a mobile data storage system in the genome of the extremophile Halomonas bluephagenesis, which enables dual-mode storage, dynamic data maintenance, rapid readout, and robust recovery. The system relies on two key components: A versatile genetic toolbox for the integration of 10-100 kb scale synthetic DNA into H. bluephagenesis genome and an efficient error correction coding scheme targeting noisy nanopore sequencing reads. The storage and repeated retrieval of 5 KB data under non-laboratory conditions are demonstrated. The work highlights the potential of DNA data storage in domestic and field scenarios, and expands its application domain from archival data to frequently accessed data.

[Multiple Correspondence of Abnormal Birth History with Genetic and Environmental Risk Factors].

Objective To investigate the multiple correspondence of genetic and environmental risk factors with abnormal birth history and provide a scientific basis for improving the birth defects surveillance system and reducing the incidence of birth defects. Methods Data were collected from all the perinatal infants from 28-week-old fetuses to 7-day-old infants born in all the hospitals with obstetrical department in Xi'an from 2003 to 2015. Results A total of 1 236 937 perinatal infants were surveyed,including 10 619 with birth defects.The average incidence rate of birth defects was 0.86% (0.70%-1.15%).Multiple correspondence analysis showed that the women who had had 1 or 2 children with birth defects were associated with the history of spontaneous abortion,family history of birth defects,and history of exposure to toxic and harmful substances.The women who had had 3 or more children with birth defects showed stronger association with family history of birth defects.The birth defects in women with history of spontaneous abortion (257/10 619) was ranked in the order of congenital heart disease,polydactyly,neural tube defects,congenital hydrocephalus,cleft lip with cleft palate,and simple cleft lip.The birth defects in women who had given birth to children with birth defects (135/10 619) followed the order of cleft lip with cleft palate,anencephaly,hydrocephalus,neural tube defects,cleft lip,and talipes equinovarus. Conclusions Abnormal birth history is associated with family history of birth defects and history of exposure to environmental risk factors.Giving birth to three or more children with birth defects is highly correlated with the family history of birth defects.

Meta-analysis of Association Studies of Selenoprotein Gene Polymorphism and Kashin-Beck Disease: an Updated Systematic Review.

To evaluate the association between selenoprotein gene polymorphisms and Kashin-Beck disease (KBD) susceptibility through a systematic review and updated meta-analysis. PubMed, Google Scholar, Cochrane library, and Chinese National Knowledge Infrastructure (CNKI) were electronically searched using the terms "selenoprotein" and "Kashin-Beck disease" or "KBD" with a search time from the establishment of the database to January 2021. The Newcastle-Ottawa Scale (NOS) was used for methodological quality evaluation of the included studies. Stata 14.0 software was used to pooled odds ratio (OR) and 95% confidence interval. There were a total of eight included case-control studies covering 2025 KBD patients and 1962 controls. Meta-analysis results show that the pooled odds ratios (OR) and 95% confidence intervals (CI) for DIO2 (rs225014) were 0.69 (0.52, 0.91), 0.69 (0.50, 0.96), and 0.72 (0.52, 0.99) in the allele, heterozygote, and dominant models, respectively. The OR and 95%CI for SEPS1 (-105G>A) were 2.47 (1.85, 3.29), 9.36 (4.58, 19.12), 2.17 (1.53, 3.08), and 8.60 (4.25, 17.38) in the allele, homozygote, dominant, and recessive models, respectively. In addition, the OR and 95%CI for Sep15 (rs5859) were 2.05 (1.06, 3.96) in the allele model. These results illustrate that there was a significant association between DIO2 (rs225014), SEPS1 (-105G>A), Sep15 (rs5859), and KBD. For GPX1 (rs1050450, rs1800668, rs3811699), DIO2 (rs225014, rs1352815, rs1388382), TrxR2 (rs1139793, rs5746841), GPX4 (rs713041, rs4807542), and SEPP1 (rs7579, 25191g/a), there was no significant statistical difference between the KBD and control groups (P>0.05). We conclude that the DIO2 (rs225014), SEPS1 (-105G>A), and Sep15 (rs5859) gene polymorphism are associated with susceptibility to KBD.

Towards practical and robust DNA-based data archiving using the yin-yang codec system.

DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense of introducing biocompatibility challenges or decoding failure. Here we propose a robust transcoding algorithm named the yin-yang codec, using two rules to encode two binary bits into one nucleotide, to generate DNA sequences that are highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200 nt oligo pools and in vivo as a ~54 kbps DNA fragment in yeast cells. Sequencing results show that the yin-yang codec exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.9% above 104 molecule copies and an achieved recovery rate of 87.53% at ≤102 copies. Additionally, the in vivo storage demonstration achieved an experimentally measured physical density close to the theoretical maximum.

Systematical Engineering of Synthetic Yeast for Enhanced Production of Lycopene.

Synthetic biology allows the re-engineering of biological systems and promotes the development of bioengineering to a whole new level, showing great potential in biomanufacturing. Here, in order to make the heterologous lycopene biosynthesis pathway compatible with the host strain YSy 200, we evolved YSy200 using a unique Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system that is built in the Sc2.0 synthetic yeast. By inducing SCRaMbLE, we successfully identified a host strain YSy201 that can be served as a suitable host to maintain the heterologous lycopene biosynthesis pathway. Then, we optimized the lycopene biosynthesis pathway and further integrated into the rDNA arrays of YSy201 to increase its copy number. In combination with culturing condition optimization, we successfully screened out the final yeast strain YSy222, which showed a 129.5-fold increase of lycopene yield in comparison with its parental strain. Our work shows that, the strategy of combining the engineering efforts on both the lycopene biosynthesis pathway and the host strain can improve the compatibility between the heterologous pathway and the host strain, which can further effectively increase the yield of the target product.

Elucidating the Influence of Sulfur Vacancies on Nonradiative Recombination Dynamics in Cu2ZnSnS4 Solar Absorbers.

We report a time-domain ab initio simulation of charge carrier trapping and relaxation dynamics in pristine and defect-containing kesterite Cu2ZnSnS4 (CZTS) structures. Our simulations show that introduction of a neutral sulfur vacancy in the CZTS system leads to a decrease of the charge recombination rate by a factor of ∼4, and the doubly positively charged sulfur vacancy results in a minor decrease of carrier lifetime, as compared to the pristine CZTS system. The neutral sulfur vacancy weakens the nonadiabatic (NA) electron-phonon coupling by moderately localizing charge density and accelerates the pure dephasing process, extending charge carrier lifetime. Therefore, the neutral sulfur vacancy is electrically benign. The doubly positively charged sulfur vacancy introduces a subgap state which is hardly populated, and recombination of the electron and hole bypassing the trap state dominates. As a result, the recombination rate decreases in the doubly charged sulfur vacancy structure. The reported results identified the key role of the sulfur-related vacancy on charge carrier trapping and relaxation of CZTS materials, carrying important implications for further optimization of CZTS and other thin-film solar cell materials.

Two new steroidal alkaloids from the rhizomes of Veratrum nigrum L. and their anti-TYLCV activity.

Two new steroidal alkaloids (1-2), together with seven known related steroidal alkaloids (3-9), were isolated from the rhizomes of Veratrum nigrum L. Their structures were elucidated by extensive spectroscopic analysis, and by comparison with literature data. Compound 1 possessed a rare 1, 3-oxazolidine unit within varazine-type alkaloids, and 2 was a 9-hydroxy-4-one derivative of 3-veratroylgermine. All isolates were evaluated inhibit tomato yellow leaf curl virus (TYLCV) activity. Compounds 5 and 7 (40 µg/mL) showed a significant anti-TYLCV activity in the host Nicotiana benthamiana with inhibition rates 74.6% and 63.4%, respectively, which are higher than that of the positive control ningnanmycin (51.4%).

DNA storage: research landscape and future prospects.

The global demand for data storage is currently outpacing the world's storage capabilities. DNA, the carrier of natural genetic information, offers a stable, resource- and energy-efficient and sustainable data storage solution. In this review, we summarize the fundamental theory, research history, and technical challenges of DNA storage. From a quantitative perspective, we evaluate the prospect of DNA, and organic polymers in general, as a novel class of data storage medium.

Prevention and control strategies for children Kashin-Beck disease in China: A systematic review and meta-analysis.

BACKGROUND: To evaluate prevention and control strategies for children with Kashin-Beck disease (KBD) in China through a systematic review and meta-analysis. METHODS: We conducted literature searches of articles indexed in Web of Knowledge, PubMed, Springerlink, Elsevier, the Chinese National Knowledge Infrastructure, and Wanfang data until February 2019. Search terms included "Kashin-Beck disease" or "KBD," and "improvement of water" or "change of grain" or "salt-rich selenium" or "comprehensive measures." Eligible studies were prospective trials of interventions in endemic area. Data extraction was performed by 2 independent authors using predefined data fields that also included quality evaluation. RESULTS: We screened 1183 potentially relevant articles, and included 22 studies that reported 24 trials, with data from 3700 healthy children and 2961 children KBD. The pooled odds ratios (ORs) and confidence intervals (95% CIs) for primary prevention new incidence in healthy children following interventions to comprehensive measures, change of grain, salt-rich selenium, and improvements of water were 0.15 (0.02, 0.95), 0.15 (0.03, 0.70), 0.19 (0.09, 0.38), and 0.20 (0.09, 0.42), respectively. The OR (95% CI) for clinical improvement in children KBD following interventions to improvement of water, salt-rich selenium, comprehensive measures, and change of grain were 5.03 (3.21, 7.89), 4.39 (3.15, 6.11), 2.98 (1.61, 5.52), and 2.35 (1.59, 3.47), respectively. All interventions showed significant differences and were effective (P < .05). CONCLUSION: Comprehensive measures and change of grain were the most effective measures in preventing new case, whereas improvement of water and salt-rich selenium resulted in clinical improvements in children KBD.

Carbon-based archiving: current progress and future prospects of DNA-based data storage.

The information explosion has led to a rapid increase in the amount of data requiring physical storage. However, in the near future, existing storage methods (i.e., magnetic and optical media) will be insufficient to store these exponentially growing data. Therefore, data scientists are continually looking for better, more stable, and space-efficient alternatives to store these huge datasets. Because of its unique biological properties, highly condensed DNA has great potential to become a storage material for the future. Indeed, DNA-based data storage has recently emerged as a promising approach for long-term digital information storage. This review summarizes state-of-the-art methods, including digital-to-DNA coding schemes and the media types used in DNA-based data storage, and provides an overview of recent progress achieved in this field and its exciting future.

Comparison of Apoptosis and Autophagy in Human Chondrocytes Induced by the T-2 and HT-2 Toxins.

In this report, we have investigated the apoptosis and autophagy of chondrocytes induced by the T-2 and HT-2 toxins. The viability of chondrocytes was measured by the MTT assay. Malondialdehyde (MDA) and superoxide dismutase (SOD) kits were used to measure the oxidative stress of chondrocytes. The apoptosis of chondrocytes was measured using flow cytometry. Hoechst 33258 and MDC staining agents were introduced to analyze apoptosis and autophagy induction in chondrocytes, respectively. Protein expression of Bax, caspase-9, caspase-3, and Beclin1 was examined by western blotting analysis. The T-2 and HT-2 toxins significantly decreased the viability of chondrocytes in a time-dependent manner. The level of oxidative stress in chondrocytes induced by the T-2 toxin was significantly higher when compared with that of the HT-2 toxin. The apoptosis rate of chondrocytes induced by the T-2 toxin increased from 3.26 ± 1.03%, 18.38 ± 1.28%, 34.5 ± 1.40% to 49.67 ± 5.31%, whereas apoptosis rate of chondrocytes induced by the HT-2 toxin increased from 3.82 ± 1.03%, 11.61 ± 1.27%, 25.72 ± 2.95% to 36.28 ± 2.81% in 48 h incubation time. Hoechst 33258 staining confirmed that apoptosis of chondrocytes induced by the T-2 toxin was significantly higher than that observed when the chondrocytes were incubated with the HT-2 toxin. MDC staining revealed that the autophagy rate of chondrocytes induced by the T-2 toxin increased from 6.38% to 63.02%, whereas this rate induced by the HT-2 toxin changed from 6.08% to 53.33%. The expression levels of apoptosis and autophagy related proteins, Bax, caspase-9, caspase-3, and Beclin1 in chondrocytes induced by the T-2 toxin were significantly higher when compared with those levels induced by the HT-2 toxin.

Effect of antimicrobial use density on resistance rate of Stenotrophomonas maltophilia / 中国感染控制杂志

Objective To analyze the correlation between antimicrobial use density (AUD) and change in antimicrobial resistance rate of Stenotrophomonas maltophilia (SM), and explore the influencing factors of antimicrobial resistance of SM. Methods Antimicrobial resistance rate of SM and AUD of commonly used antimicrobial agents in patients in a hospital from 2012 to 2017 were summarized, correlation was analyzed with Pearson correlation method. Results A total of 23 994 strains of gram-negative bacteria were isolated, of which 1 331 strains (5.55％) were SM, mainly from sputum (54.02％) and distributed in intensive care unit (21.49％). Resistance rates of SM to ceftazidime, levofloxacin, and compound sulfamethoxazole were 21.79％, 7.66％, and 13.37％ respectively, resistance rates to levofloxacin showed an increasing trend year by year (P＜0.05). Resistance rate of SM to levofloxacin was positively correlated with the use intensity of β-lactamase inhibitors, carbapenems, fluoroquinolones, and oxazolidinones (all P＜0.05); resistance rate to compound sulfamethoxazole was positively correlated with the use intensity of macrolides (P＜0.05).Conclusion Change in resistance rates of SM to levofloxacin and compound sulfamethoxazole are positively correlated with the use intensity of some commonly used antimicrobial agents, reducing AUD is beneficial to the control and reducing of the resistance of SM.

Coupled Mutations-Enabled Glycerol Transportation in an Aquaporin Z Mutant.

Aquaporins are transmembrane channel proteins with key function being transportation of water or other small substrates. Escherichia coli Aqp Z transports water molecules only, whereas Glp F is permeable to glycerol. It is intriguing to explore the possibility to induce glycerol permeability in Aqp Z by targeted mutations. The Aqp Z mutants with mutated selectivity filter (SF) residues exhibit poor permeability for both glycerol and water. For addressing the complexity of protein systems, pair correlation information in protein sequence analyses is instructive to identify residues that are coupled by coevolution and motion. In this study, we analyze the correlation between residues and unravel the clustering patterns of coupled residues, beyond SF residues, in aquaglyceroporins (AQGPs). The identified coupled motifs are proposed to be sequenced into aquaporin (Aqp Z) to introduce glycerol permeability. These residues are located in the vicinity of SF region, C-loop, and M6-M7 linkage domain. Significant enlargement of SF pore size of the proposed Aqp Z mutant is observed by an all-atom replica exchange molecular dynamics simulation, which is critical to facilitate considerable glycerol passage as characterized in calculated free-energy landscapes. Clearly, the hidden connections among residues play crucial roles in water/glycerol selectivity. In contrast, single-site mutation-based scheme may even lead to undesirable effects in AQGPs, such as the blocking of water transportation by aromatic π-stacked gate. As demonstrated in this work, the pair correlation analysis guided rational mutagenesis provides a feasible strategy to modulate proteins' functions.

Polymorphisms of 23 Y-chromosome STR Loci in A Han Population in Jiangsu Province.

Objective To investigate the polymorphisms of 23 Y-STR loci in a Han population in Jiangsu province. Methods Blood samples were collected from 4821 unrelated healthy Han males in Jiangsu province. DNA templates were amplified by PowerPlex Y23 kit,and the amplification products were detected by 3500xL genetic analyzer. Then,we calculated the allele frequencies and gene diversities respectively,as well as the haplotype frequencies and haplotype diversities. Results The gene diversity of these 23 Y-STR loci ranged 0.4099-0.9696. A total of 4781 haplotypes were detected,of which 4743 were found once. The haplotype diversity was 0.99999812. Conclusion The 23 Y-STR loci used in this study are highly polymorphic in Han individuals in Jiangsu province and therefore suitable for population genetic study and forensic individual identification.