Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

Zaremba-Niedzwiedzka K, Viklund J, Zhao W, et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology. 2013;14(11): R130.BACKGROUND: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. RESULTS: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. CONCLUSIONS: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host

Soil Moisture Availability at Early Growth Stages Strongly Affected Root Growth of Bothriochloa ischaemum When Mixed With Lespedeza davurica

Rainfall is the main resource of soil moisture in the semiarid areas, and the altered rainfall pattern would greatly affect plant growth and development. Root morphological traits are critical for plant adaptation to changeable soil moisture. This study aimed to clarify how root morphological traits of Bothriochloa ischaemum (a C4 herbaceous species) and Lespedeza davurica (a C3 leguminous species) in response to variable soil moisture in their mixtures. The two species were co-cultivated in pots at seven mixture ratios under three soil water regimes [80% (HW), 60% (MW), and 40% (LW) of soil moisture field capacity (FC)]. At the jointing, flowering, and filling stages of B. ischaemum, the LW and MW treatments were rewatered to MW or HW, respectively. At the end of growth season, root morphological traits of two species were evaluated. Results showed that the root morphological response of B. ischaemum was more sensitive than that of L. davurica under rewatering. The total root length (TRL) and root surface area (RSA) of both species increased as their mixture ratio decreased, which suggested that mixed plantation of the two species would be beneficial for their own root growth. Among all treatments, the increase of root biomass (RB), TRL, and RSA reached the highest levels when soil water content increased from 40 to 80% FC at the jointing stage. Our results implied that species-specific response in root morphological traits to alternated rainfall pattern would greatly affect community structure, and large rainfall occurring at early growth stages would greatly increase their root growth in the semiarid environments

Volatile Constituents, Inorganic Elements and Primary Screening of Bioactivity of Black Coral Cigarette Holders

Black corals (BC) have been used for a long time in Chinese medicine, and may have some pharmaceutical functions when used as material for cigarette holders in southeast China. This study is aimed to investigate the bioactivities of volatile constituents in BC and to explore the folklore behind the use of BC cigarette holders (BCCHs). We extracted the volatile constituents of BC by supercritical fluid extraction (SFE) with carbon dioxide (CO2-SFE), then identified and analyzed the constituents by gas chromatography-mass spectrometry (GC-MS). In total, 15 components were reliably identified in BC and found to be biologically active. These included triethyl phosphate, butylated hydroxytoluene, cedrol, n-hexadecanoic acid, squalene, and cholesterol. Meanwhile 13 inorganic elements (P, Ca, Mg, S, B, Si, Fe, Cu, Zn, Ba, etc.) were determined by inductively coupled plasma spectrometer (ICPS). In the bioactivity tests, the BC extract (BCE) showed a scavenging activity of 2,2-diphenyl-1-picrylhydrazyl free radicals and hydroxyl radicals by phenanthroline-Fe (II) oxidation and moderate inhibition of Gram-positive microorganisms. The antioxidant and antimicrobial activities of BC, which are related to the active chemical composition, may explain the perceived benefit for cigarette smokers who use BCCHs

Effects of brine- and NaCl- fermented carrots on lipid metabolism and gut microbiota in high-fat diet-fed mice

This study investigated the alterations in the phytochemical components and the antioxidant abilities of brine- and NaCl-fermented carrots and their effects on the lipid metabolism and microbial community in high-fat diet (HFD)-fed mice. Results showed that brine-fermentation significantly improved the contents of total dietary fiber, total phenols and β-carotene by 57 %, 48 % and 117 %, respectively. Fermented carrots possessed a higher level of antioxidant activities (P < 0.05). Furthermore, fermented carrot attenuated the increase in body weight, alleviated liver injury and oxidative stress but also promoted the lipid metabolism and reduced fatty acid accumulation in vivo, which were correlated with the total phenols and dietary fiber contents. Further investigation demonstrated that fermented carrots can attenuate HFD-induced lipid accumulation through the AMPK pathway and restoring the gut microbiota in HFD mice. Overall, fermented carrots can modulate the lipid accumulation in the HFD mice through the AMPK pathway and the microbiota community

Pulsed-chaos MIMO radar based on a single flat-spectrum and Delta-like autocorrelation optical chaos source

We propose and demonstrate a pulsed-chaos multiple-input-multiple-output (MIMO) radar system in this paper. In the proposed MIMO radar system, multi-channel pulsed chaotic signals are extracted from an optical seed chaos source with Delta-like autocorrelation and flat spectrum. The seed chaos source is generated by passing the chaotic output of an external-cavity semiconductor laser through a dispersive self-feedback phase-modulation loop and used for MIMO radar signal generation. The cross-correlation characteristics of MIMO radar signals, the maximum channel number of separable mixed echoes, as well as the performances of multi-target ranging and anti-interference in the proposed pulsed-chaos MIMO radar system are systematically investigated. The results indicate that multi-channel pulsed-chaos signals with Delta-like autocorrelation can be simultaneously generated from the seed chaos source, and excellent quasi-orthogonality of transmission radar signals can be guaranteed. Moreover, it is demonstrated that the proposed pulsed-chaos MIMO radar supports multi-target ranging with a centimeter-level resolution and can maintain satisfactory performance under low SNR scenarios with various interferences

Enhancement of local anti-demagnetization ability of permanent magnet by selected area grain boundary diffusion toward high-speed motors

The working environment of permanent magnets in high-speed motors is harsh, because they are seriously affected by multi-physical fields such as temperature, stress, weak magnetic control field, etc., and irreversible demagnetization is easy to occur under the extreme working conditions. In this work, a model of high-speed Interior Permanent magnet Motor is established, the easy demagnetization area of the permanent magnet is simulated by electromagnetic and thermal simulations to determine, and its local anti-demagnetization optimization is performed. Dy/Tb co-infiltration is carried out in the easy demagnetization region of the permanent magnets, and the process of selective zone diffusion is analyzed based on the principle of selective zone grain boundary diffusion. Through microscopic observation and macroscopic magnetic performance test, the effect of local anti-demagnetization performance enhancement of the optimized permanent magnets is verified. The results show that the magnetic properties of the optimized permanent magnets are obviously improved after the optimization of the selected zones. The present approach is important for the follow-up less heavy-rare-earth research of permanent magnet and its application in high-speed motors

Tool wear influence on surface roughness, burrs and cracks in milling unidirectional carbon fiber reinforced plastics (UD-CFRP)

This study delves into the machining defects encountered during the milling of Carbon Fiber Reinforced Plastics (CFRP), with a special focus on fishbone-like cracks on the machined surface, which have never been focused before. Through a series of experiments, models for post-machining fiber burrs and matrix cracks were developed and analyzed, uncovering the causes of fishbone crack formation. The research reveals that the formation mechanisms of burrs vary with fiber orientation, burrs are not only from fiber bending under tool pressure but also from fiber buckling. Fishbone cracks are believed to be induced by growing burrs as the tool wear, and propagate along the in-plane and subsurface. Propagation downwards is along the fiber direction, while propagation inward is at an angle of approximately 40° ± 3°. This research is vital for enhancing the machining quality of composite materials and their engineering applications

Anticoagulant Activity and Structural Characterization of Polysaccharide from Abalone (Haliotis discus hannai Ino) Gonad

In this study, we aimed at characterizing the structure and the anticoagulant activity of a polysaccharide fraction (AGP33) isolated from the gonads of Haliotis discus hannai Ino. AGP33 was extracted by enzymatic hydrolysis and purified by ion-exchange and gel-filtration chromatography. The backbone fraction of AGP33 (BAGP33), which appeared to contain of mannose, glucose and galactose, was prepared by partial acid hydrolysis. According to methylation and nuclear magnetic resonance (NMR) spectroscopy, the backbone of AGP33 was identified as mainly consisting of 1→3-linked, 1→4-linked, and 1→6-linked monosaccharides. AGP33 is a sulfated polysaccharide with sulfates occur at 3-O- and 4-O-positions. It prolonged thromboplastin time (APTT), thrombin time (TT) and prothrombin time (PT) compared to a saline control solution in a dosage-dependent manner. AGP33 exhibited an extension (p &lt; 0.01) of APTT compared to the saline group at concentrations higher than 5 μg/mL. AGP33 exhibited higher anticoagulant activity than its desulfated product (AGP33-des) and BAGP33. The results showed that polysaccharide with higher molecular weight and sulfate content demonstrated greater anticoagulant activity