Structure and assembly of type VI secretion system cargo delivery vehicle.

Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS delivery tube via its core components: Hcp, VgrG, or PAAR. Here, we report 2.8-Å resolution cryo-EM structure of intact T6SS Hcp5-VgrG-PAAR cargo delivery system and crystal structure of unbound Hcp5 from B. fragilis NCTC 9343. Loading of Hcp5 hexameric ring onto VgrG causes expansion of its inner cavity and external surface, explaining how structural changes could be propagated to regulate co-polymerization and surrounding contractile sheath. High-affinity binding between Hcp and VgrG causes entropically unfavorable structuring of long loops. Furthermore, interactions between VgrG trimer and Hcp hexamer are asymmetric, with three of the six Hcp monomers exhibiting a major loop flip. Our study provides insights into the assembly, loading, and firing of T6SS nanomachine that contributes to bacterial inter-species competition and host interactions.

Mechanistic and structural insights into the bifunctional enzyme PaaY from Acinetobacter baumannii.

PaaY is a thioesterase that enables toxic metabolites to be degraded through the bacterial phenylacetic acid (PA) pathway. The Acinetobacter baumannii gene FQU82_01591 encodes PaaY, which we demonstrate to possess γ-carbonic anhydrase activity in addition to thioesterase activity. The crystal structure of AbPaaY in complex with bicarbonate reveals a homotrimer with a canonical γ-carbonic anhydrase active site. Thioesterase activity assays demonstrate a preference for lauroyl-CoA as a substrate. The AbPaaY trimer structure shows a unique domain-swapped C-termini, which increases the stability of the enzyme in vitro and decreases its susceptibility to proteolysis in vivo. The domain-swapped C-termini impact thioesterase substrate specificity and enzyme efficacy without affecting carbonic anhydrase activity. AbPaaY knockout reduced the growth of Acinetobacter in media containing PA, decreased biofilm formation, and impaired hydrogen peroxide resistance. Collectively, AbPaaY is a bifunctional enzyme that plays a key role in the metabolism, growth, and stress response mechanisms of A. baumannii.

Nonhomologous Black Carbon Decoupled Char and Soot Sequestration Based on Stable Carbon Isotopes in Tibetan Plateau Lake Sediment.

Combustion-derived black carbon (BC) is an important component of sedimentary carbon pool. Due to different physicochemical properties, determining the source of char and soot is crucial for BC cycling, especially for nonhomologous char and soot in the Tibetan Plateau (TP). This study analyzed the sequestration and source of BC, char, and soot in the Dagze Co (inner TP) sediment core via the content and δ13C, revealing the biomass and fossil fuel driving on nonsynchronous char and soot and their response to local anthropogenic activities and atmospheric transmission. The results showed that BC concentration increased from 1.19 ± 0.35 mg g-1 (pre-1956) to 2.03 ± 1.05 mg g-1 (after 1956). The variation of char was similar to BC, while nonhomologous growth was detected in char and soot (r = 0.29 and p > 0.05). The source apportionment showed that biomass burning for 71.52 ± 10.23% of char and promoted char sequestration. The contribution of fossil fuel combustion to soot (46.67 ± 14.07%) is much higher than char (28.48 ± 10.23%). Redundancy analysis confirmed that local anthropogenic activities significantly influenced BC burial and atmospheric transport from outside TP-regulated BC burial. The contribution of biomass and fossil fuels to nonsynchronous char and soot is conducive to understanding the anthropogenic effect on BC burial in the TP.

Polycyclic aromatic hydrocarbons in remote lakes from the Tibetan Plateau: Concentrations, source, ecological risk, and influencing factors.

Polycyclic aromatic hydrocarbons (PAHs) have received worldwide attention due to their potential teratogenic, persistent, and carcinogenic characteristics. In this study, the PAHs concentrations in two dated sediment cores taken from central Tibetan Plateau (TP) were analyzed to study the deposition history, potential sources, ecological risks, and influencing factors. Total concentration of PAHs (∑PAHs) ranged from 50.0 to 195 ng g-1 and 51.9-133 ng g-1 in sediments of Pung Co (PC) and Dagze Co (DZC), respectively. 2-3-ring PAHs were dominant in the two lake sediments, accounting for an average of 77.5% and 80.1%, respectively. The historical trends of ∑PAHs in the two lakes allowed to distinguish three periods, namely, relative stability before the 1950s, a gradual increase between the 1950s and the 1990s, and then a decline to the present-day. In addition, the trend in the concentration level of each PAH composition was consistent with ∑PAHs before the 1990s, while they exhibited different trends since the 1990s, which may be the result of a combination of anthropogenic activities and climate change in recent years, whereas before the 1990s the PAH profile was mainly influenced by atmospheric deposition. The results of source apportionment examined according to diagnostic ratios and positive matrix factorization were consistent and revealed that PAHs were primarily derived from biomass and coal combustion. Significant correlations between PAHs and organic carbon (OC) indicate that OC might be a key factor influencing the concentration of PAHs in sediments. The ecological risk assessment demonstrated that PAHs in TP sediments occurred at a low risk level. Results of this study could be helpful to develop a deeper insight into the deposition history of PAHs in remote lakes of the TP region and explore the response of these variations to climate change and human activities.

Source apportionment of polycyclic aromatic hydrocarbons (PAHs) in a sediment core from Lake Dagze Co, Tibetan Plateau, China: Comparison of three receptor models.

Receptor models are a useful tool for identifying sources of polycyclic aromatic hydrocarbons (PAHs) in multiple environmental media. In this study, three different receptor models (including the principal component analysis-multiple linear regression (PCA-MLR), positive matrix factorization (PMF), and Unmix models) were used to apportion the sources of 16 priority PAHs in a sediment core of Lake Dagze Co. The ∑PAHs (sum of all 16 measured PAHs) concentrations ranged from 51.89 to 132.82 ng/g with an average of 80.39 ng/g. The ∑PAHs were dominated by 2-3 ring PAHs, accounting for 80.12% on average, thereby indicating that they mainly originated from biomass and coal combustion and/or from long-range atmospheric transportation. The three models produced consistent source apportionment results. The greatest contributor to ∑PAHs was biomass combustion, followed by coal combustion, vehicle emissions, and petrogenic sources. Moreover, the temporal variation of the common sources was well-correlated among models. The multi-method comparison and evaluation results showed that all three models were useful tools for source apportionment of PAHs, with the PMF model providing better results than the PCA-MLR and Unmix models. The temporal trends of factor contributions were verified by PAHs with different ring numbers. Significant correlations were found between the simulated concentrations of each source factor and the PAHs with different ring numbers (P<0.01), except for the petrogenic source identified by the Unmix model (P>0.05). This study can provide useful information for further investigation of source apportionment of PAHs in the sediment cores.

Neuropeptides as the Shared Genetic Crosstalks Linking Periodontitis and Major Depression Disorder.

BACKGROUND: The aim of this study was at investigating the association between major depressive disorder (MDD) and periodontitis based on crosstalk genes and neuropeptides. METHODS: Datasets for periodontitis (GSE10334, GSE16134, and GSE23586) and MDD (GSE38206 and GSE39653) were downloaded from GEO. Following batch correction, a differential expression analysis was applied (MDD: ∣log2FC | >0 and periodontitis ∣log2FC | ≥0.5, p < 0.05). The neuropeptide data were downloaded from NeuroPep and NeuroPedia. Intersected genes were potential crosstalk genes. The correlation between neuropeptides and crosstalk genes in MDD and periodontitis was analyzed with Pearson correlation coefficient. Subsequently, regression analysis was performed to calculate the differentially regulated link. Cytoscape was used to map the pathways of crosstalk genes and neuropeptides and to construct the protein-protein interaction network. Lasso regression was applied to screen neuropeptides, whereby boxplots were created, and receiver operating curve (ROC) analysis was conducted. RESULTS: The MDD dataset contained 30 case and 33 control samples, and the periodontitis dataset contained 430 case and 139 control samples. 35 crosstalk genes were obtained. A total of 102 neuropeptides were extracted from the database, which were not differentially expressed in MDD and periodontitis and had no intersection with crosstalk genes. Through lasso regression, 9 neuropeptides in MDD and 43 neuropeptides in periodontitis were obtained. Four intersected neuropeptide genes were obtained, i.e., ADM, IGF2, PDYN, and RETN. The results of ROC analysis showed that IGF2 was highly predictive in MDD and periodontitis. ADM was better than the other three genes in predicting MDD disease. A total of 13 crosstalk genes were differentially coexpressed with four neuropeptides, whereby FOSB was highly expressed in MDD and periodontitis. CONCLUSION: The neuropeptide genes ADM, IGF2, PDYN, and RETN were intersected between periodontitis and MDD, and FOSB was a crosstalk gene related to these neuropeptides on the transcriptomic level. These results are a basis for future research in the field, needing further validation.

Mirror-like Bright Al-Mn Coatings Electrodeposition from 1-Ethyl-3 Methylimidazolium Chloride-AlCl3-MnCl2 Ionic Liquids with Pyridine Derivatives.

The effects of three pyridine derivative additives, 4-hydroxypyridine, 4-picolinic acid, and 4-cyanopyridine, on Al-Mn coatings were investigated in 1-ethyl-3-methylimidazolium chloride-AlCl3-MnCl2 (EMIC-AlCl3-MnCl2) ionic liquids. The smooth mirror-like bright Al-Mn coatings were obtained only in the EMIC-AlCl3-MnCl2 ionic liquids containing 4-cyanopyridine, while the matte Al-Mn coatings were electrodeposited from EMIC-AlCl3-MnCl2 without additives or containing either 4-hydroxypyridine or 4-picolinic acid. The scanning electron microscope and X-ray diffraction showed that the bright Al-Mn coatings consisted of nanocrystals and had a strong (200) preferential orientation, while the particle size of matte Al-Mn coatings were within the micron range. The brightening mechanism of 4-cyanopyridine is due to it being adsorbed onto the cathode to produce the combined effect of (1) generating an overpotential to promote Al-Mn nucleation; (2) inhibiting the growth of the deposited nuclei and enabling them grow preferentially, making the coating composed of nanocrystals and with a smooth surface. The brightening effect of 4-cyanopyridine on the Al-Mn coatings was far better than that of the 4-hydroxypyridine and the 4-picolinic acid. In addition, the bright Al-Mn coating was prepared in a bath with 6 mmol·L-1 4-cyanopyridine and displayed superior corrosion resistance relative to the matte coatings, which could be attributed to its unique nanocrystalline structure that increased the number of grain boundaries and accelerated the formation of the protective layer of the corrosion products.

Anthropogenic-Driven Alterations in Black Carbon Sequestration and the Structure in a Deep Plateau Lake.

The continuous flux of organic carbon (OC) from terrestrial ecosystems into inland water is an important component of the global carbon cycle. The buried OC pool in inland water sediments is considerable, and black carbon (BC) is a significant contributor to this OC pool because of the continuous growth in BC emissions. Therefore, determining the effect of BC on total OC burial and variations in the structure of BC during the burial process will contribute significantly to our understanding of lacustrine carbon cycling. This study investigated BC burial and its structural variations in response to anthropogenic drivers using four dated sedimentary cores from a deep plateau lake in China. The BC burial rate rose from 0.96 ± 0.64 g·m-2·y-1 (mean of sedimentary cores pre-1960s) to 4.83 ± 1.25 g·m-2·y-1 (after 2000), which is a 5.48 ± 2.12-fold rise. The increase of char was similar to those of BC. The growth rate of soot was 7.20 ± 4.30 times, which is higher than that of BC and char, increasing from 0.12 ± 0.08 to 0.64 ± 0.23 g·m-2·y-1. There was a decreasing trend in the ratio of char and soot at a mean rate of 62.8 ± 6.46% (excluding core 3) in relation to increased fossil fuel consumption. The contribution of BC to OC burial showed a significant increasing trend from the past to the present, particularly in cores 3 and 4, and the mean contribution of the four cores was 11.78 ± 2.84%. Source tracer results from positive matrix factorization confirmed that the substantial use of fossil fuels has promoted BC burial and altered the BC structure. This has resulted in BC with a higher aromatic content in the lake sediment, which exhibits reduced reactivity and increased stability. The strong correlation between BC and allochthonous total OC indicates that the input pathways of the buried BC in this plateau lake sediment were terrestrial surface processes and not atmospheric deposition.

[Soil available nitrogen and phosphorus contents and the environmental impact factors across different land use types in typical karst rocky desertification area, Southwest China.] / å–€æ–¯ç‰¹çŸ³æ¼ åŒ–åœ°åŒºä¸åŒåœŸåœ°åˆ©ç”¨ç±»åž‹åœŸå£¤æ°®ç£·æœ‰æ•ˆæ€§åŠå ¶çŽ¯å¢ƒå½±å“å› å­.

In this study, we collected soil samples from four different land use types (forest land, shrub land, grassland and abandoned land) in Huajiang valley of Guizhou Province, a typical karst rocky desertification area in Southwest China. Correlation analysis and redundancy analysis were used to examine the distribution of available nitrogen (N) and available phosphorus (P) in diffe-rent soil layers from 0 to 30 cm and the relationships between soil environmental factors (soil physical indexes, organic carbon components, electrochemical properties, metal oxides and enzyme activities) and the contents of available N and available P. The results showed that the concentrations of soil total N, total P, available N, available P decreased significantly with the increases of soil depth. The concentrations of soil available N and available P in forest land and shrub land were significantly higher than those in grassland and abandoned land, which were significantly positively correlated with soil organic carbon composition, enzyme activity, surface electrochemical properties and amorphous mental oxide while significantly negatively correlated with soil silt and free metal oxides. Results of the redundancy analysis showed that the environmental factors affecting soil availa-ble N and available P of the four land use types were basically the same, with soil particulate organic carbon, total organic carbon and soil specific surface area playing a key role in driving the variations of soil available N and available P. The efficient explanation of variation to soil available N and P contents by soil particulate organic carbon might be due to the reduction of soil nutrient loss by the storage of N and P in organic matter. Except for high enzyme activity and electrochemical properties of forest land and shrub land, the higher soil available N and available P concentrations compared with grassland and abandoned land might be resulted from the inhibition of free iron and aluminum oxides information by higher soil organic carbon content and the reduced adsorption and fixation of N and P by iron and aluminum oxides.

[Effects of land use change on soil organic carbon and its components in karst rocky desertification of southwest China]. / è¥¿å—å–€æ–¯ç‰¹çŸ³æ¼ åŒ–çŽ¯å¢ƒä¸‹åœŸåœ°åˆ©ç”¨å˜åŒ–å¯¹åœŸå£¤æœ‰æœºç¢³åŠå ¶ç»„åˆ†çš„å½±å“.

Soil organic carbon (SOC) is the dynamic medium of carbon transfer and the main pathway of carbon transfer in the karst ecosystem. SOC and its components are the important parts in soil carbon cycling of karst ecosystem. However, few studies have focused on SOC and its components in the karst ecosystem. We analyzed the effects of land use change on the SOC content, SOC reserve (SOCS), water-soluble organic carbon (WSOC), easily oxidizable organic carbon (EOC), particu-late organic carbon (POC), and light fraction organic carbon (LFOC), and heavy fraction organic carbon (HFOC) and their distribution ratio, with six different land-use patterns [Zanthoxylum bungeanum forest (HJ), Hylocereus undulates forest (HL), mixed forest of Z. bungeanum and H. undulates (HHL), Sabina chinensis forest (YB), mixed forest of S. chinensis and Ligustrum luci-dum (YBN), and slope cropland (PD)] in Huajiang Canyon of Guanling County, Guizhou Pro-vince. Results showed that SOC and SOCS in YB, YBN and HJ were significantly higher than those in HL, HHL and PD. In the 0-20 cm soil layer, the concentrations of SOCS followed the order of HJ＞YB＞YBN＞PD＞HHL＞HL. Contents of WSOC, EOC, POC, LFOC and HFOC in YB, YBN, and HJ were all higher than those in the other three patterns. Significant positive correlations existed between SOC and each of its components (WSOC, EOC, POC, LFOC and HFOC), also between any two of those components. Z. bungeanum could be used as a priority economic species for the ecological rehabilitation of karst rocky desertification and mountain agriculture development in Southwest China. WSOC, EOC, POC, LFOC and HFOC could be used as indicators of soil organic carbon pool.

Microarc oxidation coating covered Ti implants with micro-scale gouges formed by a multi-step treatment for improving osseointegration.

The sub-microporous microarc oxidation (MAO) coating covered Ti implant with micro-scale gouges has been fabricated via a multi-step MAO process to overcome the compromised bone-implant integration. The as-prepared implant has been further mediated by post-heat treatment to compare the effects of -OH functional group and the nano-scale orange peel-like morphology on osseointegration. The bone regeneration, bone-implant contact interface, and biomechanical push-out force of the modified Ti implant have been discussed thoroughly in this work. The greatly improved push-out force for the MAO coated Ti implants with micro-scale gouges could be attributed to the excellent mechanical interlocking effect between implants and biologically meshed bone tissues. Attributed to the -OH functional group which promotes synostosis between the biologically meshed bone and the gouge surface of implant, the multi-step MAO process could be an effective strategy to improve the osseointegration of Ti implant.