Host-specific bacterial communities associated with six cold-seep sponge species in the South China Sea

The cold-seep sponge holobionts are attracting growing attention in recent years. In this study, we utilized 16S rRNA amplicons to characterize the bacterial communities of six deep-sea sponge species found in sponge grounds at the Formosa Ridge cold seep in the South China Sea. Bacterial communities in these geographically proximal sponge species are dominated by Proteobacteria (mainly Gammaproteobacteria and Alphaproteobacteria) but exhibit distinct diversity and compositions among communities. Further analysis revealed that the SUP05 clade (Thioglobaceae) dominated most of the sponge samples. Meanwhile, phylogenetic analysis showed that the six sponge species harbored diverse SUP05 OTU phylotypes, indicating significant divergence within this clade. Additionally, operational taxonomic units (OTUs) of the family Methylomonadaceae, another abundant group in these sponges, displayed a significant genetic distance both from each other and from known species. Our findings support the hypothesis of the host-species specificity of sponge-associated bacterial communities, a widely accepted concept in shallow-water and other deep-sea sponges. The presence of dominant functional microbes, such as sulfur- and methanol-oxidizing bacteria, suggests their crucial role as chemosynthetic symbionts in facilitating the niche adaption of sponge hosts to the cold seep ecosystem. In conclusion, our study reveals the diverse and novel bacterial communities in deep-sea sponges from cold seep environments, contributing new knowledge to the host-species specificity of bacterial communities within sponges and highlighting the potential significance of functional microbes in cold seep ecosystems with dynamic energy supplies

Topological Interface-State Lasing in a Polymer-Cholesteric Liquid Crystal Superlattice

The advance of topological photonics has heralded a revolution for manipulating light as well as for the development of novel photonic devices such as topological insulator lasers. Here, we demonstrate topological lasing of circular polarization in a polymer-cholesteric liquid crystal (P-CLC) superlattice, tunable in the visible wavelength regime. By use of the femtosecond-laser direct-writing and self-assembling techniques, we establish the P-CLC superlattice with a controlled mini-band structure and a topological interface defect, thereby achieving a low threshold for robust topological lasing at about 0.4 uJ. Thanks to the chiral liquid crystal, not only the emission wavelength is thermally tuned, but the circularly polarized lasing is readily achieved. Our results bring about the possibility to realize compact and integrated topological photonic devices at low cost, as well as to engineer an ideal platform for exploring topological physics that involves light-matter interaction in soft-matter environments.Comment: 14 pages, 4 figure

High-Throughput Construction of Intron-Containing Hairpin RNA Vectors for RNAi in Plants

With the wide use of double-stranded RNA interference (RNAi) for the analysis of gene function in plants, a high-throughput system for making hairpin RNA (hpRNA) constructs is in great demand. Here, we describe a novel restriction-ligation approach that provides a simple but efficient construction of intron-containing hpRNA (ihpRNA) vectors. The system takes advantage of the type IIs restriction enzyme BsaI and our new plant RNAi vector pRNAi-GG based on the Golden Gate (GG) cloning. This method requires only a single PCR product of the gene of interest flanked with BsaI recognition sequence, which can then be cloned into pRNAi-GG at both sense and antisense orientations simultaneously to form ihpRNA construct. The process, completed in one tube with one restriction-ligation step, produced a recombinant ihpRNA with high efficiency and zero background. We demonstrate the utility of the ihpRNA constructs generated with pRNAi-GG vector for the effective silencing of various individual endogenous and exogenous marker genes as well as two genes simultaneously. This method provides a novel and high-throughput platform for large-scale analysis of plant functional genomics

Functional verification of the diphtheria toxin A gene in a recombinant system

Abstract Diphtheria toxin A (DTA), a segment of the diphtheria toxin (tox), inhibits protein synthesis in cells. When released from a cell, DTA is nontoxic and cannot enter other cells independently without the help of diphtheria toxin B. In this study, we artificially synthesized the DTA gene sequence and cloned it into pEGFP-N1 to generate the recombinant vector pEGFP-N1-DTA. This recombinant vector was then transfected into 293T cells to observe the effect of DTA protein expression on enhanced green fluorescent protein (EGFP) protein expression and the proliferation of 293T cells. After 48 h, high levels of EGFP expression were seen in control pEGFP-N1-transfected cells, whereas very low levels were seen in cells transfected with pEGFP-N1-DTA. Reverse transcription polymerase chain reaction confirmed the expression of the DTA gene in cells transfected with pEGFP-N1-DTA. Further, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay revealed a significant difference in cell proliferation between the control group and the pEGFP-N1-DTA-transfected group. Using the expression of EGFP expression as an indicator, this study revealed that DTA expression can inhibit intracellular protein synthesis and cell proliferation.</p

Coupling of Defect Modes in Cholesteric Liquid Crystals Separated by Isotropic Polymeric Layers

Cholesteric liquid crystal structures with multiple isotropic defect layers exhibit localized optical modes (defect modes). Coupling effects between these modes were simulated using the finite difference time domain method. Analogous to the well-known result of the tight-binding approximation in solid state physics, splitting of the defect modes takes place, as soon as the structure contains more than one defect layer. The dispersion relation of the mini-bands forming within the photonic band gap of the structure is calculated numerically. The structures might have promising applications for multiwavelength filters and low-threshold lasers

Proteome of mouse oocytes at different developmental stages

The mammalian oocyte possesses powerful reprogramming factors, which can reprogram terminally differentiated germ cells (sperm) or somatic cells within a few cell cycles. Although it has been suggested that use of oocyte-derived transcripts may enhance the generation of induced pluripotent stem cells, the reprogramming factors in oocytes are undetermined, and even the identified proteins composition of oocytes is very limited. In the present study, 7,000 mouse oocytes at different developmental stages, including the germinal vesicle stage, the metaphase II (MII) stage, and the fertilized oocytes (zygotes), were collected. We successfully identified 2,781 proteins present in germinal vesicle oocytes, 2,973 proteins in MII oocytes, and 2,082 proteins in zygotes through semiquantitative MS analysis. Furthermore, the results of the bioinformatics analysis indicated that different protein compositions are correlated with oocyte characteristics at different developmental stages. For example, specific transcription factors and chromatin remodeling factors are more abundant in MII oocytes, which may be crucial for the epigenetic reprogramming of sperm or somatic nuclei. These results provided important knowledge to better understand the molecular mechanisms in early development and may improve the generation of induced pluripotent stem cells

Efficiency of cloning of pRNAi-GG at different restriction-ligation times.

<p>The number of recombinant colonies for each transformation was counted. Restriction-ligation was performed with continuous incubation at 37°C or for 20–50 cycles (2 min 37°C+5 min16°C). Cloning for pRNAi-GFP and pRNAi-GFP/PDS were performed in duplicate. The negative control was performed without BsaI enzyme. NT, not tested.</p><p>For each transformation, 12 clones (when less than 12, pick all) were identified by PCR using vector specific primes P21 and P22, and insert reverse primer P12 (for pRNAi-GFP) or P16 (for pRNAi-GFP/PDS). All the clones showed the expected bands, as part of the results was shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038186#pone-0038186-g002" target="_blank">Fig. 2A</a>.</p

Schematic diagram of ihpRNA construction with pRNAi-GG (Golden Gate) vector.

<p>(A) The cassette of pRNAi-GG. The duplicated 35S CaMV promoter, two copies of <i>ccdB</i> gene, the Pdk intron, four BsaI recognition sites with designed adaptors (cleavage site sequences of BsaI) are cloned between the HindIII and SacI of T-DNA vector pBI121. Adaptors with the same color have the same sequences but opposite orientation. A chloramphenicol-resistant gene (Cm^r) was contained in the Pdk intron. (B) One-step construction of ihpRNA. The target fragment of the gene of interest is PCR amplified using gene-specific primers carrying BsaI sites and adaptors complementary to the appropriate sequences on the vector. The purified PCR product is mixed, in one tube, with pRNAi-GG vector, BsaI enzyme and T4 ligase for a one-step restriction-ligation reaction.</p