Expansion and contraction of lake basin shape the genetic structure of Sinocyclocheilus (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China.

Geological events can strongly affect the genetic structures and differentiation of fish populations. Especially, as an endemic fish of the genus Sinocyclocheilus in the Yunnan-Guizhou Plateau, the effects of key geological events on the distributions and genetic structures remain poorly understood. Examining the phylogeographic patterns of Sinocyclocheilus fishes can be useful for elucidating the spatio-temporal dynamics of their population size, dispersal history and extent of geographical isolation, thereby providing a theoretical basis for their protection. Here, we used single nucleotide polymorphisms (SNP) method to investigate the phylogeographic patterns of Sinocyclocheilus fishes. Our analysis supports the endemicity of Sinocyclocheilus, but the samples of different regions of Sinocyclocheilus contain multiple ancestral components, which displayed more admixed and diversified genetic components, this may be due to the polymorphism of the ancestors themselves, or gene infiltration caused by hybridization between adjacent species of Sinocyclocheilus. We estimate that the most recent common ancestor (MRCA) of Sinocyclocheilus fish in the Central Yunnan Basin at approximately 3.75~3.11 Ma, and infer that the evolution of Sinocyclocheilus in the central Yunnan Basin is closely related to the formation of plateau lakes (around 4.0~0.02 Ma), and identifies the formation of Dianchi Lake and Fuxian Lake as key geological events shaping Sinocyclocheilus population structure. It is also the first time to prove that the altitude change has a great influence on the genetic variation among the populations of Sinocyclocheilus.

Structural and biochemical characterization of the key components of an auxin degradation operon from the rhizosphere bacterium Variovorax.

Plant-associated bacteria play important regulatory roles in modulating plant hormone auxin levels, affecting the growth and yields of crops. A conserved auxin degradation (iad) operon was recently identified in the Variovorax genomes, which is responsible for root growth inhibition (RGI) reversion, promoting rhizosphere colonization and root growth. However, the molecular mechanism underlying auxin degradation by Variovorax remains unclear. Here, we systematically screened Variovorax iad operon products and identified 2 proteins, IadK2 and IadD, that directly associate with auxin indole-3-acetic acid (IAA). Further biochemical and structural studies revealed that IadK2 is a highly IAA-specific ATP-binding cassette (ABC) transporter solute-binding protein (SBP), likely involved in IAA uptake. IadD interacts with IadE to form a functional Rieske non-heme dioxygenase, which works in concert with a FMN-type reductase encoded by gene iadC to transform IAA into the biologically inactive 2-oxindole-3-acetic acid (oxIAA), representing a new bacterial pathway for IAA inactivation/degradation. Importantly, incorporation of a minimum set of iadC/D/E genes could enable IAA transformation by Escherichia coli, suggesting a promising strategy for repurposing the iad operon for IAA regulation. Together, our study identifies the key components and underlying mechanisms involved in IAA transformation by Variovorax and brings new insights into the bacterial turnover of plant hormones, which would provide the basis for potential applications in rhizosphere optimization and ecological agriculture.

Anti-bacterial mechanism of baicalin-tobramycin combination on carbapenem-resistant Pseudomonas aeruginosa.

BACKGROUND: Pseudomonas aeruginosa (P. aeruginosa) is an important cause of nosocomial infections, and contributes to high morbidity and mortality, especially in intensive care units. P. aeruginosa is considered a 'critical' category bacterial pathogen by the World Health Organization to encourage an urgent need for research and development of new antibiotics against its infections. AIM: To investigate the effectiveness of baicalin combined with tobramycin therapy as a potential treatment method for carbapenem-resistant P. aeruginosa (CRPA) infections. METHODS: Polymerase chain reaction (PCR) and RT-PCR were used to detect the expression levels of drug-resistant genes (including VIM, IMP and OprD2) and biofilm-related genes (including algD, pslA and lasR) in CRPA that confer resistance to tobramycin, baicalin and tobramycin combined with baicalin (0, 1/8, 1/4, 1/2 and 1MIC). RESULTS: There was a correlation between biofilm formation and the expression of biofilm-related genes. In addition, VIM, IMP, OprD2, algD, pslA and lasR that confer biofilm production under different concentrations in CRPA were significantly correlated. The synergistic effect of baicalin combined with tobramycin was a significant down-regulation of VIM, IMP, algD, pslA and lasR. CONCLUSION: Baicalin combined with tobramycin therapy can be an effective treatment method for patients with CRPA infection.

A C-terminal glutamine recognition mechanism revealed by E3 ligase TRIM7 structures.

The E3 ligase TRIM7 has emerged as a critical player in viral infection and pathogenesis. However, the mechanism governing the TRIM7-substrate association remains to be defined. Here we report the crystal structures of TRIM7 in complex with 2C peptides of human enterovirus. Structure-guided studies reveal the C-terminal glutamine residue of 2C as the primary determinant for TRIM7 binding. Leveraged by this finding, we identify norovirus and SARS-CoV-2 proteins, and physiological proteins, as new TRIM7 substrates. Crystal structures of TRIM7 in complex with multiple peptides derived from SARS-CoV-2 proteins display the same glutamine-end recognition mode. Furthermore, TRIM7 could trigger the ubiquitination and degradation of these substrates, possibly representing a new Gln/C-degron pathway. Together, these findings unveil a common recognition mode by TRIM7, providing the foundation for further mechanistic characterization of antiviral and cellular functions of TRIM7.

Loaches of Vanmanenia (Cypriniformes: Gastromyzontidae) from Yunnan, China with Description of a New Species.

After comparing specimens of Vanmanenia collected from the Lancang-jiang (the upper Mekong River), Yuan-jiang (the upper Red River), Lixian-jiang (first branch of the Red River), and Jinsha-jiang (the upper Yangtze River) drainages in Yunnan, China, we considered the specimens of Vanmanenia from Shunbi Township, Yangbi County, Yunnan (a branch of the Lancang-jiang drainage basin, the upper Mekong River) a new species, herein named V. microcephala sp. nov. Our investigation also suggested that V. striata should be restored as a valid species. On the basis of the systematic comparison of morphological characteristics of the genus Vanmanenia and based on the combination of the characteristics of the rostral fold, rostral barbels, the bars/marks on the flank, the rows of spots on the paired fins, and the markings on the caudal-fin base, the loaches of Vanmanenia should be divided into three groups: 1) the barred group, characterized by bars on the flank, 2), the cusped rostral fold group, characterized by the rostral fold lobes forming a cusp process, and 3) the barbeled rostral fold group, characterized by the rostral fold lobes specialized as secondary barbels. The barred group differs from congeners in Vanmanenia by the following combination of characters: three rostral lobes with a smooth and arcuate outer edge, a pattern of bars on the flank, and spotless paired fins. This group includes six species: V. crassicauda, V. microcephala sp. nov., V. serrilineata, V. striata, V. tetraloba, and Vanmanenia pseudostriata. The new species, V. microcephala, differs from the other species in the barred group by the following combination of characters: the lateral side of the body with 14-22 vermiculations with widths smaller than the diameter of the eye; the dorsal side of the head covered with a large black blotch; the gill opening smaller and its upper angle aligned with the lower edge of the eye; and the head smaller, head depth 45.2-47.1% head length. The characteristic evolutionary trends, origin, and taxonomic status of the barred group in the genus Vanmanenia are also discussed.

Deep Representation Learning for Complex Free-Energy Landscapes.

In this Letter, we analyzed the inductive bias underlying complex free-energy landscapes (FELs) and exploited it to train deep neural networks that yield reduced and clustered representation for the FEL. Our parametric method, called information distilling of metastability (IDM), is end-to-end differentiable and thus scalable to ultralarge data sets. IDM is able to perform clustering in the meantime of reducing the dimensionality. Besides, as an unsupervised learning method, IDM differs from many existing dimensionality reduction and clustering methods in that it requires neither a cherry-picked distance metric nor the ground-true number of clusters defined a priori, and it can be used to unroll and zoom in on the hierarchical FEL with respect to different time scales. Through multiple experiments, we show that IDM can achieve physically meaningful representations that partition the FEL into well-defined metastable states that hence are amenable for downstream tasks such as mechanism analysis and kinetic modeling.

Loaches of Homatula (Teleostei: Nemacheilidae) from the upper Salween River in Yunnan, China with description of three new species.

Seven loaches of Homatula are distributed in a narrow geographical area between the upper Black River (or Song Da in Vietnam, that is a major tributary of the Red River, including the tributaries Lixian-jiang and Tengtiao-jiang in Yunnan, China) and the upper Salween River drainage (including tributaries of the Nu-jiang and Nanding-he, the latter is a major tributary of the Salween River in Yunnan, China). These seven species are distinguished from other Homatula by the combination of having the body densely-scaled, the lateral line complete, and a short adipose crest along the dorsal midline of the caudal peduncle that does not reach the posterior end of anal-fin base or does not extend beyond the middle of the anal-fin base. Based on a comparison with the described species of the densely-scaled group of Homatula, we can confirm that the specimens collected from the Nu-jiang drainage in western Yunnan are different from known species and are described herein as Homatula anteridorsalis sp. nov., Homatula cryptoclathrata sp. nov., and Homatula nigra sp. nov.

Mechanisms by which Bisphenol A affect the photosynthetic apparatus in cucumber (Cucumis sativus L.) leaves.

Bisphenol A (BPA), a widely distributed pollutant, suppresses photosynthesis in leaves. In previous studies on higher plants, the plants were treated by BPA through irrigation to root. This method cannot distinguish whether the BPA directly suppresses photosynthesis in leaves, or indirectly influences photosynthesis through affecting the function of root. Here, only the leaves but not the roots of cucumber were infiltrated with BPA solution. The photosystem II and I (PSII, PSI) were insensitive to BPA under darkness. BPA aggravated the PSII but not the PSI photoinhibition under light. BPA also inhibited CO2 assimilation, and the effect of BPA on PSII photoinhibition disappeared when the CO2 assimilation was blocked. The H2O2 accumulated in BPA-treated leaves under light. And the BPA-caused PSII photoinhibition was prevented under low (2%) O2. We also proved that the BPA-caused PSII photoinhibition depend on the turnover of D1 protein. In conclusion, this study proved that BPA could directly suppress photosynthesis in leaves, however, BPA does not damage PSII directly, but inhibits CO2 assimilation and over-reduces the electron transport chain under light, which increases the production of reactive oxygen species (H2O2), the over-accumulated ROS inhibits the turnover of D1 protein and consequently aggravates PSII photoinhibition.

CDNs-STING Interaction Mechanism Investigations and Instructions on Design of CDN-Derivatives.

Cyclic dinucleotides (CDNs) present thousand-fold differences of dissociation constants to STING, a pivotal protein in cytosolic dsDNA immunity. To understand how subtle chemical changes in CDNs lead to these substantial variances, a precise ranking of binding affinity is needed. However, the large size and flexibility of CDNs elevate the entropic effect and pose a challenge for this precise prediction. Therefore, in this paper, we developed a new protocol, a combination of selective-integrated tempering sampling of ligands and molecular docking, to take into account the entropic effects originating from extensive ligand configurational space and solvation on binding affinity evaluations. The calculated ranking orders of CDNs and CDN-derivatives to wild type STING and R232H mutant are in agreement with experimental measurements. Further molecular dynamics analysis revealed that the interaction between phosphonate groups and 232R differentiates the binding affinities. The 2'-5' linked phosphonate groups have a larger tendency to form hydrogen bonds with 232R than those with 3'-5' linkages. Moreover, the new protocol identified structural features that enhanced CDNs-STING binding, such as anti-glycosidic bonds and large pro-R distances, which explains the high binding affinity of dithio-RpRp-2'3'-CDA to STING and is expected to provide valuable guidance in the lead-drug optimization.

Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex.

Subtle changes in protein sequences are able to alter ligand-protein interactions. Unraveling the mechanism of such phenomena is important for understanding ligand-protein interactions, including the DMXAA-STING interaction. DMXAA specifically binds to mouse STING instead of human STING. However, the S162A mutation and a newly discovered E260I mutation endow human STINGAQ with DMXAA sensitivity. Through molecular dynamics simulations, we revealed how these single mutations alter the DMXAA-STING interaction. Compared to mutated systems, structural correlations in the interaction of STINGAQ with DMXAA are stronger, and the correlations are cross-protomers in the dimeric protein. Analyses on correlation coefficients lead to the identification of two key interactions that mediate the strong cross-protomer correlation in the DMXAA-STINGAQ interaction network: DMXAA-267T-162S* and 238R-260E*. These two interactions are partially and totally interrupted by the S162A and E260I mutations, respectively. Moreover, a smaller number of water molecules are displaced upon DMXAA binding to STINGAQ than that on binding to its mutants, leading to a larger entropic penalty for the former. Considering the sensitivity of STINGAQ and two of its mutants to DMXAA, a strong structural correlation appears to discourage DMXAA-STING binding. Such an observation suggests that DMXAA derivatives, which are deprived of hydrogen-bond interaction with both 162S* and 267T, are potential agonists of human STING.

Direct Oxidation of Aliphatic C-H Bonds in Amino-Containing Molecules under Transition-Metal-Free Conditions.

By employing a simple, inexpensive, and transition-metal-free oxidation system, secondary C-H bonds in a series of phthaloyl protected primary amines and amino acid derivatives were oxidized to carbonyls with good regioselectivities. This method could also be applied to oxidize tertiary C-H bonds and modify synthetic dipeptides.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C-H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions.

Cyclic dinucleotides are able to trigger the innate immune system by activating STING. It was found that the binding affinity of asymmetric 2'3'-cGAMP to symmetric dimer of STING is 3 orders of magnitude higher than that of the symmetric 3'3'-cyclic dinucleotides. Such a phenomenon has not been understood yet. Here we show that the subtle changes in phosphodiester linkage of CDNs lead to their distinct structural properties which correspond to the varied binding affinities. 2'-5' and/or 3'-5' linked CDNs adopt specific while different types of ribose puckers and backbone conformations. That ribose conformations and base types have different propensities for anti or syn glycosidic conformations further affects the overall flexibility of CDNs. The counterbalance between backbone ring tension and electrostatic repulsion, both affected by the ring size, also contributes to the different flexibility of CDNs. Our calculations reveal that the free energy cost for 2'3'-cGAMP to adopt the STING-bound structure is smaller than that for 3'3'-cGAMP and cyclic-di-GMP. These findings may serve as a reference for design of CDN-analogues as vaccine adjuvants. Moreover, the cyclization pattern of CDNs closely related to their physiological roles suggests the importance of understanding structural properties in the study of protein-ligand interactions.

14-3-3epsilon contributes to tumour suppression in laryngeal carcinoma by affecting apoptosis and invasion.

BACKGROUND: 14-3-3epsilon regulates a wide range of biological processes, including cell cycle control, proliferation, and apoptosis, and plays a significant role in neurogenesis and the formation of malignant tumours. However, the exact function and regulatory mechanism of 14-3-3epsilon in carcinogenesis have not been elucidated. METHODS: The expression of 14-3-3epsilon was assessed by RT-PCR and western blotting. The invasiveness and viability of Hep-2 cells were determined by the transwell migration assay and MTT assay, respectively. Cell cycle and apoptosis of Hep-2 cells were detected by flow cytometry. RESULTS: The mRNA and protein expression of 14-3-3epsilon in larynx squamous cell carcinoma (LSCC) tissues were significantly lower than those in clear surgical margin tissues. Statistical analysis showed that the 14-3-3epsilon protein level in metastatic lymph nodes was lower than that in paired tumour tissues. In addition, the protein level of 14-3-3epsilon in stage III or IV tumours was significantly lower than that in stage I or II tumours. Compared with control Hep-2 cells, the percentages of viable cells in the 14-3-3epsilon-GFP and negative control GFP groups were 36.68 +/- 14.09% and 71.68 +/- 12.10%, respectively. The proportions of S phase were 22.47 +/- 3.36%, 28.17 +/- 3.97% and 46.15 +/- 6.82%, and the apoptotic sub-G1 populations were 1.23 +/- 1.02%, 2.92 +/- 1.59% and 13.72 +/- 3.89% in the control, negative control GFP and 14-3-3epsilon-GFP groups, respectively. The percentages of the apoptotic cells were 0.84 +/- 0.25%, 1.08 +/- 0.24% and 2.93 +/- 0.13% in the control, negative control GFP and 14-3-3epsilon-GFP groups, respectively. The numbers of cells that penetrated the filter membrane in the control, negative control GFP and 14-3-3epsilon-GFP groups were 20.65 +/- 1.94, 17.63 +/- 1.04 and 9.1 +/- 0.24, respectively, indicating significant differences among the different groups. CONCLUSIONS: Decreased expression of 14-3-3epsilon in LSCC tissues contributes to the initiation and progression of LSCC. 14-3-3epsilon can promote apoptosis and inhibit the invasiveness of LSCC.