Temporal dynamics of the microbial heterogeneity-diversity relationship in microcosmic systems.

Spatial heterogeneity significantly enhances biodiversity, representing one of the ecology's most enduring paradigms. However, many studies have found decreasing, humped, and neutral correlations between spatial heterogeneity and biodiversity (heterogeneity-diversity relationships, HDR). These findings have pushed this widely accepted theory back into controversy. Microbial HDR research has lagged compared to that of plants and animals. Nevertheless, microbes have features that add a temporal-scale perspective to HDR research that is critical to understanding patterns of HDR. In this study, 157 microcosms with different types spatial heterogeneity were set up to map the HDR of microorganisms and their temporal dynamics using high-throughput sequencing techniques. The results show that the following: 1. Spatial heterogeneity can significantly alter microbial diversity in microcosmic systems. Changes in microbial diversity, in turn, lead to changes in environmental conditions. These changes caused microorganisms to exhibit increasing, decreasing, humped, U-shaped, and neutral HDR patterns. 2. The emergence of HDR patterns is characterized by temporal dynamics. Additionally, the HDR patterns generated by spatial structural and compositional heterogeneity exhibit inconsistent emergence times. These results suggest that the temporal dynamics of HDR may be one of the reasons for the coexistence of multiple patterns in previous studies. The feedback regulation between spatial heterogeneity-biodiversity-environmental conditions is an essential reason for the temporally dynamics of HDR patterns. All future ecological studies should pay attention to the temporal dynamic patterns of ecological factors.

Natural recovery from fire disturbance is more favorable than assisted recovery for the restoration of soil nematode-trapping fungi.

A fire is usually considered a severe disturbance factor in the environment. Globally, rising temperatures and increasing human activities have intensified the severity and frequency of fire incidents, and research on post-fire recovery has inevitably become an important focus for ecologists. In terms of the restoration of burned areas, there are usually two primary approaches: natural recovery and assisted recovery. However, very few relevant studies have systematically compared these recovery alternatives, suggesting which one is more favorable to the overall restoration of an ecosystem, especially to the soil microbes that function as indispensable components of ecosystems. In this study, the restoration of soil nematode-trapping fungi (NTF) in natural and assisted recovery environments was compared. The results showed that although the NTF community structures differed among the sample sites, the counts and diversity of the NTF communities in the upper and lower soil layers in the natural recovery area were higher than those in the assisted recovery and unburned control areas. These findings suggest that artificial efforts to help ecosystem recovery after fire negatively affect the speed and quality of soil NTF community recovery. Instead, natural recovery appears to be a more suitable land management choice after fire disturbance.

Bacterial Signatures of "Red-Operculum" Disease in the Gut of Crucian Carp (Carassius auratus).

Fish gut microbiota play important roles in fish immunity, nutrition, and the adaptation to environmental changes. To date, few studies have focused on the interactions among environmental factors, fish diseases, and gut microbiota compositions. We compared the gut bacterial communities of healthy crucian carps (Carassius auratus) with those of individuals affected by "red-operculum" disease and corresponding water and sediment microbiota in four fish farm ponds. Distinct gut bacterial communities were observed in healthy and diseased fish. The bacterial communities of diseased fish were less diverse and stable than those of healthy individuals. The differences in bacterial community compositions between diseased and healthy fish were explained by the changes in the relative abundances of some specific bacterial OTUs, which belonged to the genera such as Vibrio, Aeromonas, and Shewanella, and they were prevalent in diseased fish, but rare or even absent in environmental samples. Water temperature and ammonia concentration were the two most important environmental factors that impacted gut microbiota in diseased fish. These results highlighted the surge of some potential pathogens as bacterial signatures that were associated with "red-operculum" disease in crucian carps.

Changes in the Intestinal Microbiota of Gibel Carp (Carassius gibelio) Associated with Cyprinid herpesvirus 2 (CyHV-2) Infection.

Gut microbiota are integral to the host, and have received increased attention in recent years. However, information regarding the intestinal microbiota of many aquaculture animals is insufficient; elucidating the dynamics of the intestinal microbiota can be beneficial for nutrition, immunity, and disease control. In this study, we used 16S rRNA sequencing to observe changes in the intestinal microbiota of gibel carp (Carassius auratus gibelio) associated with cyprinid herpesvirus 2 (CyHV-2) infection. Our results indicate that the diversity of the intestinal microbiota was strongly reduced, and the composition was dramatically altered following CyHV-2 infection. The most dominant species in healthy fish were Cetobacterium, Rhodobacter, and Crenothrix; meanwhile, Cetobacterium, Plesiomonas, Bacteroides, and Flavobacterium were the most abundant species in sick fish. Plesiomonas was highly abundant in infected samples, and could be used as a microbial biomarker for CyHV-2 infection. Chemical properties of the aquaculture water were significantly correlated with the microbial community structure; however, it is difficult to determine whether these changes are a cause or consequence of infection. However, it may be possible to use probiotics or prebiotics to restore the richness of the host intestinal microbiota in infected animals to maintain host health.

Lysobacter chengduensis sp. nov. Isolated from the Air of Captive Ailuropoda melanoleuca Enclosures in Chengdu, China.

A novel bacterial strain, designated as CF21(T), was isolated from the air of Ailuropoda melanoleuca enclosures in China. Cells were gram-negative, aerobic, non-motile, and rod shaped. Strain CF21(T) grew at 10-40 °C (optimum 28-30 °C) and pH 6.0-9.0 (optimum pH 7.0-8.0) and in the presence of NaCl concentrations ranging from 0.0% (w/v) to 2.0 % (optimum 0.0-1.0%). 16SrRNA gene sequence analysis indicated that strain CF21(T) belonged to genus Lysobacter within class Gammaproteobacteria and was most closely related to Luteimonas dalianensi OB44-3(T) (95.8% similarity), Lysobacter ruishenii CTN-1(T) (95.1%), Lysobacter spongiicola KMM329(T) (94.8 %), and Lysobacter daejeonensis GH1-9T (94.6%). The genomic G+C DNA content was 68.72 mol%. Major cellular fatty acids of CF21(T) were iso-C16:0 (30.22%), iso-C15:0 (25.70%), and the sum of 10-methyl C16 : 0 and/or iso-C17 : 1ω9c (21.94%). The prominent isoprenoid quinone was ubiquinone 8 (Q-8). Primary polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid. DNA sequence relatedness between strain CF21(T) and L. ruishenii CTN-1(T) was 56%, which was clearly below the 70% threshold for prokaryotic species delineation. These analyses indicated that CF21(T) is a novel member of genus Lysobacter, for which the name Lysobacter chengduensis sp. nov. is proposed. The type strain is CF21(T) (=CGMCC1.15145(T) = DSM 100306(T)).

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans.

BACKGROUND: Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species. RESULTS: Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains. CONCLUSIONS: The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains.

De novo assembly and analysis of RNA-seq data.

We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.

genBlastG: using BLAST searches to build homologous gene models.

MOTIVATION: BLAST users frequently expect to obtain homologous genes with certain similarity to their query genes. But what they get from BLAST searches are often collections of local alignments called high-scoring segment pairs (HSPs). On the other hand, most homology-based gene finders have been built using computation-intensive algorithms, without taking full advantage of BLAST searches that have been perfected over the last decades. RESULTS: Here we report an efficient algorithm, genBlastG that directly uses the HSPs reported by BLAST to define high-quality gene models. AVAILABILITY: http://genome.sfu.ca/genblast/download.html

Walking and taking vitamin C alleviates oxidative stress and inflammation in overweight students, even in the short-term.

Objective: Obese or overweight is a risk factor for some chronic diseases, and oxidative stress and inflammation may be one of the molecular mechanisms leading to the persistence of these chronic diseases. Discovering interventions to alleviate oxidative stress and inflammation in the overweight/obese population, is very important for public health and health education. Methods: A two-week panel intervention study (Run 0-Run 1-Run 2) was conducted. The subjects were 77 overweight/obese undergraduates attending Dali University, with a BMI>24 kg/m2. The physical indices measured at the end of each run included BMI, waist circumference, serum ROS, TNF-α, IL-1ß and urinary 8-OHdG. Students were allocated to one of four intervention groups: No intervention (control); walking; taking vitamin C; and walking + taking vitamin C. Results: The results demonstrated (1) Walking significantly alleviated ROS levels, and this was consistent in Run 1 and Run 2; (2) During Run1, all three intervention modes reduced levels of 8-OHdG, but there was a statistically insignificant increase during Run 2; (3) No alleviating effects of the three intervention modes on TNF-α levels during Run 1 and Run 2 were observed; (4) The alleviating effects of the three intervention modes on IL-1ß levels during Run 1 and Run 2 were clear. Conclusion: Walking and taking vitamin C can reduce levels of ROS, 8-OHdG and IL-1ß, but not TNF-α, in overweight/obese participants. These interventions may become potential preventive measures for the overweight against obese-induced oxidative stress and inflammation.

4-alkoxy-3-arylfuran-2(5H)-ones as inhibitors of tyrosyl-tRNA synthetase: synthesis, molecular docking and antibacterial evaluation.

A series of novel 4-alkoxy-3-arylfuran-2(5H)-ones as tyrosyl-tRNA synthetase inhibitors were synthesized. Of these compounds, 3-(4-hydroxyphenyl)-4-(2-morpholinoethoxy)furan-2(5H)-one (27) was the most potent. The binding model and structure-activity relationship indicate that replacement of morpholine-ring in the side chain of 27 with a substituent containing more hydrophilic groups would be more suitable for further modification. Antibacterial assay revealed that the synthetic compounds are effective against growth of Gram-positive organisms, and 27 is the most potent agent against Staphylococcus aureus ATCC 25923 with MIC(50) value of 0.23 µg/mL.

4-(2-Chloro-anilino)-3-phenyl-furan-2(5H)-one.

The title compound, C(16)H(12)ClNO(2), featuring a furan-2(5H)-one (γ-butyrolactone) core, contains two mol-ecules (A and B) in the asymmetric unit, with different dihedral angles between the central ring and the pendant phenyl and chloro-benzene rings [43.33 (8) and 20.16 (8)°, respectively, for A, and 47.79 (8) and 13.87 (8)°, respectively, for B]. In the crystal, the A mol-ecules are linked into [001] chains by single C-H⋯O inter-actions. The B mol-ecules also form [001] chains, but their relative orientations in the chains are quite different to those of the A mol-ecules so that adjacent B mol-ecules are linked by two C-H⋯O hydrogen bonds. Finally, C-H⋯O inter-actions and aromatic π-π stacking contacts [centroid-centroid separations = 3.754 (1) and 3.817 (1) Å] link the chains into a two-dimensional array parallel to (010).

L-theanine inhibits foam cell formation via promoting the scavenger receptor A degradation.

Atherosclerosis is one of the most common cardiovascular diseases with highly mortality worldwide. The formation of foam cell plays an important role in the early stage of atherosclerosis pathogenesis. L-theanine is the most abundant free amino acid in tea, which possesses anti-inflammatory, anti-tumor and anti-atherosclerosis effects. However, little is known about the effects of L-theanine on the foam cell formation. In our study, RAW264.7 cells and primary mouse peritoneal macrophages were exposed to oxidized low density lipoprotein (ox-LDL) for inducing foam cell formation. We found that L-theanine significantly impeded cholesterol accumulation in macrophages, while inhibiting the formation of foam cell. Our further experiments showed that L-theanine attenuated the cholesterol uptake of RAW264.7 cells and primary mouse peritoneal macrophages by reducing the protein level of macrophage scavenger receptor A (SR-A), but not the level of mRNA suggesting that L-theanine regulates scavenger receptor A at the translational rather than transcriptional level. The present results demonstrated that L-theanine obviously promoted the degradation of scavenger receptor A protein and scavenger receptor A was degraded by ubiquitination dependent manner. Collectively, our research indicates that L-theanine suppresses the formation of macrophage foam cell by promoting the ubiquitination dependent degradation of scavenger receptor A.

An Individualized Intra-Articular Stabilization Device Designed Based on 3D Printing Technology for Traumatic Instability of the Ulnohumeral Joint.

We aimed to design an individualized intra-articular stabilization device based on 3D printing technology and investigate the clinical effects of this device for treating traumatic instability of the ulnohumeral joint. This study enrolled nine patients with traumatic instability of the ulnohumeral joint (age: 47.2 ± 1.80 years) who received treatment between March 2018 and March 2019 in our hospital. All patients underwent a thin-layer computed tomography (CT) scan of the elbow before surgery. The original injury and repair models of the elbow were printed using 3D printing technology based on CT data. An individualized intra-articular stabilization device was designed with a 2.0 mm Kirschner wire based on the repair model. Nine patients agreed to receive surgical treatment for elbow disease and placement of the intra-articular stabilization device. The nine patients underwent open reduction through a posterior median approach, and the intra-articular stabilization device was placed in the elbow. Operation time, intraoperative blood loss, and postoperative complications were recorded and followed up. The device was removed at two postoperative months, and the Mayo score was used to evaluate elbow function. Four months after removing the intra-articular stabilization device, elbow joint function was evaluated again using the Mayo score. The mean operation time was 100.1 ± 8.2 min, and the mean intraoperative blood loss was 35.5 ± 7.1 ml. No complications occurred after operation. Two months after surgery, eight patients received an excellent Mayo score, and one patient received a good Mayo score. Four months after removal of the intra-articular stabilization device, eight patients received an excellent Mayo score, and one patient received a good Mayo score. The individualized intra-articular stabilization device can increase ulnohumeral stability and achieve rapid functional recovery of the elbow.

Application of silk fibroin/chitosan/nano-hydroxyapatite composite scaffold in the repair of rabbit radial bone defect.

Silk fibroin (SF), chitosan (CS) and nano-hydroxyapatite (nHA) possess excellent biocompatibility, thus, these were used to construct a SF/CS/nHA composite scaffold. Previously published results identified that this material exhibited satisfactory physical and chemical properties, and therefore qualified as a repair material in bone tissue engineering. The aim of the present study was to investigate the capacity and mechanism of this composite scaffold in repairing bone defects. In total, 45 New Zealand white rabbits were used to model defect in the right radial bone. A radial bone defect was induced, and rabbits were divided into the following treatment groups (n=15 in each): Group A, in which the SF/CS/nHA scaffold was implanted; group B, in which the SF/CS scaffold was implanted; and group C, in which rabbits did not receive subsequent treatment. X-ray scanning, specimen observation and histopathological examination were implemented at 1, 2, 3 and 4 months after modeling, in order to evaluate the osteogenic capacity and mechanism. At 1 month after modeling, the bone density shadow in the X-ray scan was darker in group A as compared with that in group B. Observation of the pathological specimens indicated that normal bone tissues partially replaced the scaffold. At 2 months, the bone density shadow of group A was similar to normal bone tissues, and normal tissue began to replace the scaffold. At 3-4 months after modeling, the X-ray scan and histopathological observation indicated that the normal bone tissues completely replaced the scaffold in group A, with an unobstructed marrow cavity. However, the bone mass of group B was lower in comparison with that of group A. The bone defect induced in group C was filled with fibrous connective tissues. Therefore, it was concluded that the SF/CS/nHA composite scaffold may be a promising material for bone tissue engineering.

Isolation and characterization of a novel thermostable non-specific lipid transfer protein-like antimicrobial protein from motherwort (Leonurus japonicus Houtt) seeds.

In screening for potent antimicrobial proteins from plant seeds, a novel heat-stable antimicrobial protein, designated LJAMP2, was purified from seeds of the motherwort (Leonurus japonicus Houtt), a medicine herb, with a procedure involving cation exchange chromatography on a CM FF column, and reverse phase HPLCs on C8 column and C18 column. LJAMP2 exhibited a molecular mass of 6.2 kDa determined. Automated Edman degradation determined the partial N-terminal sequence of LJAMP2 to be NH2-AIGCNTVASKMAPCLPYVTGKGPLGGCCGGVKGLIDAARTTPDRQAVCNCLKTLAKSYSG, which displays homology with plant non-specific lipid transfer proteins (nsLTPs). In vitro bioassays showed that LJAMP2 inhibits the growth of a variety of microbes, including filamentous fungi, bacteria and yeast. The growth of three phytopathogenic fungi, Alternaria brassicae, Botrytis maydis, and Rhizoctonia cerealis, are inhibited at 7.5 microM of LJAMP2, whereas Bacillus subtilis is about 15 microM. The IC(50) of LJAMP2 for Aspergillus niger, B. maydis, Fusarium oxysporum, Penicillium digitatum and Saccharomyces cerevisiae are 5.5, 6.1, 9.3, 40.0, and 76.0 microM, respectively.

Psc-AFP, an antifungal protein with trypsin inhibitor activity from Psoralea corylifolia seeds.

An antifungal protein designated as Psc-AFP, with an apparent molecular mass of 18kDa, was isolated from a traditional Chinese herb, malaytea scurfpea (Psoralea corylifolia L.). The isolation procedure entailed extraction, cation exchange chromatography on CM FF, gel filtration chromatography on Superdex 75 and reversed-phase high performance liquid chromatography on SOURCE 5RPC column. Automated Edman degradation determined the partial N-terminal sequence of Psc-AFP to be NH2-EWEPVQNGGSSYYMVPRIWA, which displayed homology with plant trypsin inhibitors. The protease inhibitor activity of Psc-AFP was then confirmed by the inhibition on trypsin. Psc-AFP at 10 microM inhibited the mycelial growth of Alternari brassicae, Aspergillus niger, Fusarium oxysporum and Rhizoctonia cerealis, suggesting that Psc-AFP has a role in the defense against pathogens.

Chryseobacterium chengduensis sp. nov. isolated from the air of captive giant panda enclosures in Chengdu, China.

A Gram-negative, aerobic, non-motile, rod-shaped bacterial strain, designated 25-1(T), was isolated from the air inside giant panda enclosures at the Chengdu Research Base of Giant Panda Breeding, China. Strain 25-1(T) grew optimally at pH 7.0-8.0, at 28-30 °C and in the presence of NaCl concentrations from 0.0% to 0.5 %. 16S rRNA gene sequence analysis indicated that strain 25-1(T) belongs to the genus Chryseobacterium within the family Flavobacteriaceae and is related most closely to C. carnis G81(T) (96.4% similarity), C. lathyri RBA2-6(T) (95.8% similarity), and C. zeae JM1085(T) (95.8% similarity). Its genomic DNA G+C molar composition was 36.2%. The major cellular fatty acids were iso-C15:0 (44.0%), iso-C17:0 3OH (19.8%) and C16:1 ω7c/16:1 ω6c (12.7%). The only isoprenoid quinone was menaquinone 6 (MK-6). The major polar lipids were phosphatidylethanolamine, two unidentified amino lipids and two unidentified lipids. The DNA-DNA relatedness between strain 25-1(T) and C. lathyri RBA2-6(T) was 38%. Phenotypic, genotypic, and phylogenetic characteristics indicated that strain 25-1(T) is a novel member of the genus Chryseobacterium, for which the name C. chengduensis sp. nov. is proposed. The type strain is 25-1(T) (CCTCC AB2015133(T)=DSM 100396(T)).

[Spatial distribution characteristics and correlation analysis of organic matter, total nitrogen and total phosphorus in topsoil around Chaohu Lake].

Sixty topsoil composite samples (0-20 cm) have been collected in 3 258 km2 surrounding area of Chaohu Lake. The concentrations of organic material (OM), total nitrogen (TN) and total phosphorus (TP) were determined, and their spatial distribution characteristics were studied by geo-statistics software named GS 7.0 +, Surfer 8.0 and Mapinfo 8.5. The correlations of these 3 kinds of nutrient were analyzed by SPSS 17.0 at the same time. Results showed that the average omega (OM), omega (TN) and omega (TP) in topsoil around Chaohu Lake were 19 500 mg x kg(-1), 1 027 mg x kg(-1) and 483 mg x kg(-1). The omega (OM) and omega (TN) in topsoil in the east of Chaohu Lake were both higher than those in the west of the lake, while omega (TP) was reverse. The omega (TP) in topsoil around Hangbu-Fengle River and Baishitianhe River which located in the southwest of Chaohu Lake was higher than that in any other rivers and with the serious soil erosion. Hence, to control the TP released by nonpoint pollution, attention should be paid on these two rivers. Furthermore, the semivariogram models of omega (OM), omega (TN) and omega (TP) followed linear model and they all had a strong spatial autocorrelation, the ratios of nugget to sill were 0.015, 0.202 and 0.128, respectively. The characteristics of spatial distribution of omega (OM), omega (TN) and omega (TP) were similar. Moreover, the Pearson correlation analysis showed that omega (OM), omega (TN) and omega (TP) were significantly correlated. The omega (TN) and omega (TP) can be calculated by two recommended formulas, and the results were acceptable in daily non-pint pollution management.

GenBlastA: enabling BLAST to identify homologous gene sequences.

BLAST is an extensively used local similarity search tool for identifying homologous sequences. When a gene sequence (either protein sequence or nucleotide sequence) is used as a query to search for homologous sequences in a genome, the search results, represented as a list of high-scoring pairs (HSPs), are fragments of candidate genes rather than full-length candidate genes. Relevant HSPs ("signals"), which represent candidate genes in the target genome sequences, are buried within a report that contains also hundreds to thousands of random HSPs ("noises"). Consequently, BLAST results are often overwhelming and confusing even to experienced users. For effective use of BLAST, a program is needed for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report. To achieve this goal, we have designed a graph-based algorithm, genBlastA, which automatically filters HSPs into well-defined groups, each representing a candidate gene in the target genome. The novelty of genBlastA is an edge length metric that reflects a set of biologically motivated requirements so that each shortest path corresponds to an HSP group representing a homologous gene. We have demonstrated that this novel algorithm is both efficient and accurate for identifying homologous sequences, and that it outperforms existing approaches with similar functionalities.