Paramecium Genetics, Genomics, and Evolution.

The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.

Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica.

Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.

Dietary fish oil improves autistic behaviors and gut homeostasis by altering the gut microbial composition in a mouse model of fragile X syndrome.

Fragile X syndrome (FXS) is the most common inherited intellectual disability, caused by a lack of the fragile X mental retardation protein (FMRP). Individuals with neurodevelopmental disorders frequently experience gastrointestinal problems that are primarily linked to gut microbial dysbiosis, inflammation, and increased intestinal permeability. Omega-3 polyunsaturated fatty acids (omega-3 PUFAs) are non-pharmacological agents that exert potential therapeutic effects against neurological disorders. However, it is unclear whether omega-3 PUFAs improve autistic behaviors in fragile X syndrome (FXS) by altering the gut microbial composition. Here, we describe gastrointestinal problems in Fmr1 knockout (KO) mice. FMRP deficiency causes intestinal homeostasis dysfunction in mice. Fish oil (FO) as a source of omega-3 PUFAs reduces intestinal inflammation but increases the mRNA and protein levels of TJP3 in the colon of juvenile Fmr1 KO mice. Fecal microbiota transplantation from FO-fed Fmr1 KO mice increased the gut abundance of Akkermansia and Gordonibacter in recipient Fmr1 KO mice and improved gut homeostasis and autistic behaviors. Our findings demonstrate that omega-3 PUFAs improve autistic behaviors and gut homeostasis in FMRP-deficient mice by suppressing gut microbiota dysbiosis, thereby presenting a novel therapeutic approach for juvenile FXS treatment.

In-line reflected fiber sensor for simultaneous measurement of temperature and liquid level based on tapered few-mode fiber.

An in-line reflective dual-parameters fiber-optic sensor is proposed in this work, whereas it is experimentally verified by measuring both the liquid level and the local temperature distribution simultaneously. The proposed sensor configuration comprises a single-mode fiber (SMF), a tapered few-mode fiber (TFMF), as well as a silver-coated capillary tube. The extracted experimental results indicate that the liquid level only affects the power of the resonant dips, while having little impact on the wavelength. On the other hand, both the wavelength and the power of the resonant dips vary with the temperature change. Therefore, the simultaneous measurement of the liquid level and temperature can be realized according to the different responses of the resonant dips to the liquid level and temperature. The obtained liquid level and temperature sensitivities can reach the values of 0.106 dB/mm and 0.029 dB/°C, 35 pm/°C, respectively. The sensor exhibits the advantages of high stability and low cost, the demodulation relates on only one wavelength which can shorten the scanning wavelength range during measurement. The proposed sensor can be potentially applied where accurate and simultaneous measurements of both temperature and liquid level are required.

Integrated Methylome and Transcriptome Analysis Provides Insights into the DNA Methylation Underlying the Mechanism of Cytoplasmic Male Sterility in Kenaf (Hibiscus cannabinus L.).

Cytoplasmic male sterility (CMS) is widely exploited in hybrid seed production. Kenaf is an important fiber crop with high heterosis. The molecular mechanism of kenaf CMS remains unclear, particularly in terms of DNA methylation. Here, using the anthers of a kenaf CMS line (P3A) and its maintainer line (P3B), comparative physiological, DNA methylation, and transcriptome analyses were performed. The results showed that P3A had considerably lower levels of IAA, ABA, photosynthetic products and ATP contents than P3B. DNA methylome analysis revealed 650 differentially methylated genes (DMGs) with 313 up- and 337 down methylated, and transcriptome analysis revealed 1788 differentially expressed genes (DEGs) with 558 up- and 1230 downregulated genes in P3A compared with P3B. Moreover, 45 genes were characterized as both DEGs and DMGs, including AUX,CYP, BGL3B, SUS6, AGL30 and MYB21. Many DEGs may be regulated by related DMGs based on methylome and transcriptome studies. These DEGs were involved in carbon metabolism, plant hormone signal transduction, the TCA cycle and the MAPK signaling pathway and were shown to be important for CMS in kenaf. These results provide new insights into the epigenetic mechanism of CMS in kenaf and other crops.

Antifungal Substances Produced by Xenorhabdus bovienii and Its Inhibition Mechanism against Fusarium solani.

Fungal colonization can severely damage artifacts. Nematode endosymbiotic bacteria exhibit good prospects in protecting artifacts from fungal damage. We previously found that supernatant from the fermentation of nematode endosymbiotic bacterium, Xenorhabdus bovienii, is effective in inhibiting the growth of Fusarium solani NK-NH1, the major disease fungus in the Nanhai No.1 Shipwreck. Further experiments proved that X. bovienii produces volatile organic compounds (VOCs) that inhibit NK-NH1. Here, using metabolomic analysis, GC-MS, and transcriptomic analysis, we explored the antifungal substances and VOCs produced by X. bovienii and investigated the mechanism underlying its inhibitory effect against NK-NH1. We show that X. bovienii produces several metabolites, mainly lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. The VOCs produced by X. bovienii showed two specific absorption peaks, and based on the library ratio results, these were predicted to be of 2-pentanone, 3-(phenylmethylene) and 1-hexen-3-one, 5-methyl-1-phenyl. The inhibition of F. solani by VOCs resulted in upregulation of genes related to ribosome, ribosome biogenesis, and the oxidative phosphorylation and downregulation of many genes associated with cell cycle, meiosis, DNA replication, and autophagy. These results are significant for understanding the inhibitory mechanisms employed by nematode endosymbiotic bacteria and should serve as reference in the protection of artifacts.

Systematic analysis of CCCH zinc finger family in Brassica napus showed that BnRR-TZFs are involved in stress resistance.

BACKGROUND: CCCH zinc finger family is one of the largest transcription factor families related to multiple biotic and abiotic stresses. Brassica napus L., an allotetraploid oilseed crop formed by natural hybridization between two diploid progenitors, Brassica rapa and Brassica oleracea. A systematic identification of rapeseed CCCH family genes is missing and their functional characterization is still in infancy. RESULTS: In this study, 155 CCCH genes, 81 from its parent B. rapa and 74 from B. oleracea, were identified and divided into 15 subfamilies in B. napus. Organization and syntenic analysis explained the distribution and collinearity relationship of CCCH genes, the selection pressure and evolution of duplication gene pairs in B. napus genome. 44 diploid duplication gene pairs and 4 triple duplication gene groups were found in B. napus of CCCH family and the segmental duplication is attributed to most CCCH gene duplication events in B. napus. Nine types of CCCH motifs exist in B. napus CCCH family members, and motif C-X7/8-C-X5-C-X3-H is the most common and a new conserved CCH motif (C-X5-C-X3-H) has been identified. In addition, abundant stress-related cis-elements exist in promoters of 27 subfamily IX (RR-TZF) genes and their expression profiles indicated that RR-TZF genes could be involved in responses to hormone and abiotic stress. CONCLUSIONS: The results provided a foundation to understand the basic characterization and genes evolution of CCCH gene family in B. napus, and provided potential targets for genetic engineering in Brassicaceae crops in pursuit of stress-tolerant traits.

T porous PtIr bimetallic nanotubes with core shell structure for enhanced electrocatalysis on methanol oxidation.

Sluggish methanol oxidation brings challenges to the commercialization of the direct methanol fuel cells (DMFCs). Herein, porous PtIr bimetallic nanotubes were prepared via galvanic replacement using Ag nanowires as template. These PtIr catalysts show a core-shell nanostructure with a tunable Pt-rich surface. The mass activity of methanol oxidation reaction (MOR) at these porous PtIr nanotubes can reach up to 1.42 A mg-1based on Pt loading, which is better than the commercial Pt/C catalysts and can be comparable with most of one-dimensional Pt-based MOR catalysts reported recently. In addition, these PtIr catalysts can maintain structural integrity after long-term durability test. The superior catalytic performance of the novel porous PtIr nanotubes will make it possible used in the commercial DMFCs as advanced MOR catalysts at industrial scale.

Temperature and liquid refractive index sensor using P-D fiber structure-based Sagnac loop.

A cost-efficient P-D fiber structure-based Sagnac loop sensor is proposed and experimentally demonstrated for measuring temperature and liquid refractive index (RI). The P-D structure is fabricated by fusion splicing a section of polarization-maintaining fiber (PMF) to a piece of multimode D-shaped optical fiber (MMDF). Then the P-D structure is built into a Sagnac loop using a 3dB coupler. The temperature and RI characteristics of the sensor are investigated experimentally. The results show that two resonant dips have different spectral responses of temperature and RI, which indicate that the sensor can realize simultaneous temperature and RI measurement. The high sensitivities of -1.804nm/°C and -131.49nm/RIU are achieved. The obtained resolutions of temperature and RI of the proposed sensor can reach 0.01°C and 2.46 × 10-4RIU, respectively. The proposed sensor has the potential application in biological and chemical fields.

Dynamic tailoring of electromagnetic behaviors of graphene plasmonic oligomers by local chemical potential.

In the mid-infrared and terahertz (THz) regime, graphene supports tunable surface plasmon resonance (SPR) by controlling the chemical potential, which promotes light-matter interaction at the selected wavelength, showing exceptional promise for optoelectronic applications. In this article, we show that the electromagnetic (EM) response of graphene oligomers can be substantially modified by the modification of the local chemical potential, strengthening or reducing the intrinsic plasmonic modes. The effect mechanism is corroborated by a graphene nanocluster composed of 13 nanodisks with D6h symmetry; by transforming to D3h symmetry, the effect mechanism was retained and more available plasmonic resonance modes appeared. The intriguing properties open a new way to design nanodevices made of graphene oligomers with highly efficient photoresponse enhancement and tunable spectral selectivity for highly accurate photodetection.

Topologically protected edge states in graphene plasmonic crystals.

A two-dimensional graphene plasmonic crystal composed of periodically arranged graphene nanodisks is proposed. We show that the band topology effect due to inversion symmetry broken in the proposed plasmonic crystals is obtained by tuning the chemical potential of graphene nanodisks. Utilizing this kind of plasmonic crystal, we constructed N-shaped channels and realized topologically edged transmission within the band gap. Furthermore, topologically protected exterior boundary propagation, which is immune to backscattering, was also achieved by modifying the chemical potential of graphene nanodisks. The proposed graphene plasmonic crystals with ultracompact size are subject only to intrinsic material loss, which may find potential applications in the fields of topological plasmonics and high density nanophotonic integrated systems.

Electromagnetic field coupling characteristics in graphene plasmonic oligomers: from isolated to collective modes.

In this paper, we propose a plasmonic tetramer composed of coupled graphene nanodisks. The transformation from the isolated to the collective modes of the proposed structure is investigated by analysing the whispering-gallery modes and extinction spectra with various inter-nanodisk gap distances. In addition, the effect of introducing a central nanodisk into the tetramer on the extinction spectra is explored, which leads to Fano resonance. Furthermore, the refractive index sensing properties of the proposed graphene plasmonic oligomer have been demonstrated. The proposed nanostructures might pave the road toward the application of graphene plasmonic oligomers in fields such as nanophotonics, and chemical or biochemical sensing.

Improved pestalotiollide B production by deleting competing polyketide synthase genes in Pestalotiopsis microspora.

Pestalotiollide B, an analog of dibenzodioxocinones which are inhibitors of cholesterol ester transfer proteins, is produced by Pestalotiopsis microspora NK17. To increase the production of pestalotiollide B, we attempted to eliminate competing polyketide products by deleting the genes responsible for their biosynthesis. We successfully deleted 41 out of 48 putative polyketide synthases (PKSs) in the genome of NK17. Nine of the 41 PKS deleted strains had significant increased production of pestalotiollide B (P < 0.05). For instance, deletion of pks35, led to an increase of pestalotiollide B by 887%. We inferred that these nine PKSs possibly lead to branch pathways that compete for precursors with pestalotiollide B, or that convert the product. Deletion of some other PKS genes such as pks8 led to a significant decrease of pestalotiollide B, suggesting they are responsible for its biosynthesis. Our data demonstrated that improvement of pestalotiollide B production can be achieved by eliminating competing polyketides.

Identification of genes related to high royal jelly production in the honey bee (Apis mellifera) using microarray analysis.

China is the largest royal jelly producer and exporter in the world, and high royal jelly-yielding strains have been bred in the country for approximately three decades. However, information on the molecular mechanism underlying high royal jelly production is scarce. Here, a cDNA microarray was used to screen and identify differentially expressed genes (DEGs) to obtain an overview on the changes in gene expression levels between high and low royal jelly producing bees. We developed a honey bee gene chip that covered 11,689 genes, and this chip was hybridised with cDNA generated from RNA isolated from heads of nursing bees. A total of 369 DEGs were identified between high and low royal jelly producing bees. Amongst these DEGs, 201 (54.47%) genes were up-regulated, whereas 168 (45.53%) were down-regulated in high royal jelly-yielding bees. Gene ontology (GO) analyses showed that they are mainly involved in four key biological processes, and pathway analyses revealed that they belong to a total of 46 biological pathways. These results provide a genetic basis for further studies on the molecular mechanisms involved in high royal jelly production.

Cloning and functional analysis of the SiRLK35 gene in Setaria italic L.

Receptor like protein kinases (RLKs) play vital roles in both plant development and stress conditions. Using drought-treated "Yugu 1" as materials, a drought-responsive RLK gene, SiRLK35, was isolated through iTRAQ analysis. In this study, the further analyses of the gene functions were carried out. First, full-length SiRLK35 was amplified by PCR using the cDNA of foxtail millet seedlings as a template. The expression patterns of SiRLK35 under NaCl, PEG, ABA, GA and MeJA treatment were analyzed by quantitative real-time PCR (qRT-PCR), and we found that the expression of SiRLK35 could be induced under different treatments, especially under NaCl treatment. Second, the prokaryotic expression plasmid of SiRLK35 was constructed, and the salt resistance of SiRLK35 was detected by the bacterial plaque growth method. And we uncovered that the growth and tolerance of SiRLK35-containing Escherichia coli strains were in better conditions than control under the NaCl stress. Lastly, pCambia1301P-SiRLK35 was constructed and transformed into rice to obtain transgenic plants. The tolerance of transgenic rice plants to salt stress was higher than that of controls through physiological analysis. We propose that SiRLK35 may participate in salt and stress resistance processes, which could provide potential theoretical foundation for the stress resistance varieties cultivation and breeding of foxtail millet.

Halomonas urumqiensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkaline lake.

A moderately halophilic, aerobic bacterium, strain BZ-SZ-XJ27T, belonging to the genus Halomonas, was isolated from a saline-alkaline lake in the Xinjiang Uyghur Autonomous Region of China. Phylogenetic analysis based on 16S rRNA gene sequences and a multilocus sequence analysis using the 16S rRNA, gyrB and rpoD genes demonstrated that strain BZ-SZ-XJ27T represents a member of the genus Halomonas. On the basis of 16S rRNA gene sequence similarity, the closest relatives were Halomonas campaniensis 5AGT, H. fontilapidosi 5CRT, H. korlensis XK1T and H. sinaiensis ALO SharmT, with similarities of 96.2-97.2 %. DNA-DNA hybridization with H. korlensis CGMCC 1.6981T (the nearest phylogenetic neighbour) and H. campaniensis DSM 15293T (the highest 16S rRNA gene sequence similarity) showed relatedness values of 53 and 38 %, respectively, demonstrating the separateness of the three taxa. The bacterium stained Gram-negative and the cells were motile and rod-shaped. The strain formed creamy-white colonies and grew under optimal conditions of 1.42 M Na+ (range 0.22-4.32 M Na+), pH 8.0-8.5 (range pH 6.0-10.0) and 39 °C (range 4-43 °C). The dominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 36.6 %), C16 : 0 (25.9 %) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 21.2 %). The dominant polar lipids were two unknown phospholipids, phosphatidylethanolamine and phosphatidylglycerol, and the main respiratory quinones were ubiquinone 9 (Q-9; 89 %) and ubiquinone 8 (Q-8; 10 %). The genomic DNA G+C content was 61.7 ± 0.8 mol% (Tm). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BZ-SZ-XJ27T is proposed to represent a novel species, Halomonas urumqiensis sp. nov., within the genus Halomonas of the family Halomonadaceae. The type strain is BZ-SZ-XJ27T ( = JCM 30202T = CGMCC 1.12917T).

A B-type histone acetyltransferase Hat1 regulates secondary metabolism, conidiation, and cell wall integrity in the taxol-producing fungus Pestalotiopsis microspora.

In filamentous fungi, many gene clusters for the biosynthesis of secondary metabolites often stay silent under laboratory culture conditions because of the absence of communication with its natural environment. Epigenetic processes have been demonstrated to be critical in the expression of the genes or gene clusters. Here, we report the identification of a B-type histone acetyltransferase, Hat1, and demonstrate its significant roles in secondary metabolism, conidiation, and the cell wall integrity in the fungus Pestalotiopsis microspora. An hat1 deletion strain shows a dramatic decrease of SMs in this fungus, suggesting hat1 functions as a global regulator on secondary metabolism. Moreover, the mutant strain hat1Δ delays to produce conidia with significantly decreased number of conidia, while shows little effect on vegetative growth, suggesting that it plays a critical role in conidiation. The hypersensitivity of hat1Δ to Congo red demonstrates that disruption of hat1 impairs the integrity of cell wall. Overexpression of the wild-type hat1 allele enhances conidiation by boosting the number of conidia. This is the first report on the role of a B-type histone acetyltransferase in fungal secondary metabolism and cell wall integrity.

[A Methane Detection System Using Distributed Feedback Laser at 1 654 nm].

A methane (CH4) detection system based on tunable diode laser absorption spectroscopy (TDLAS) technique was experimentally demonstrated. A distributed feedback (DFB) laser around 1 654 nm, an open reflective sensing probe and two InGaAs photodiodes were adopted in the system. The electrical part of the system mainly includes the laser temperature control & modulation module and the orthogonal lock-in amplifier module. Temperature and spectrum tests on the DFB laser indicate that, the laser temperature fluctuation can be limited to the range of -0.02-0.02 degrees C, the laser's emitting wavelength varies linearly with the temperature and injection current, and also good operation stability of the laser was observed through experiments. Under a constant working temperature, the center wavelength of the laser is varied linearly by adjusting the driving current. Meanwhile, a 5 kHz sine wave signal and a 10 Hz saw wave signal were provided by the driving circuit for the harmonic extraction purpose. The developed orthogonal lock-in amplifier can extract the If and 2f harmonic signals with the extraction error of 3.55% and 5% respectively. By using the open optical probe, the effective optical pass length was doubled to 40 cm. Gas detection experiment was performed to derive the relation between the harmonic amplitude and the gas concentration. As the concentration increases from 1% to 5%, the amplitudes of the 1f harmonic and the 2f harmonic signal were obtained, and good linear ration between the concentration and the amplitude ratio was observed, which proves the normal function of the developed detection system. This system is capable to detect other trace gases by using relevant DFB lasers.

[Online Detection System on Acetylene with Tunable Diode Laser Absorption Spectroscopy Method].

Based on tunable diode laser absorption spectroscopy (TDLAS) technique, an acetylene (C2H2) online detection system was developed by using the absorption band at the wavelength of 1.534 µm of C2H2 molecule. The sensing system consists of four modules including a distributed feedback (DFB) laser, a DFB laser driver, a gas cell with single optical path and a data processing module. With the prepared standard C2H2 gas sample, detailed measurements were carried out to study the detection performance of the system. Experimental results reveal that, the limit of the system (LOD) is about 0.02%; a good linear relationship is observed between C2H2 gas concentration and the amplitude of the 2f signal is within the range of 0.02%~1%. A long-term measurement lasting for 20 h on a 0.5% C2H2 gas sample was carried out to test the stability of the system. Compared with the C2H2 detection systems utilizing quantum cascaded lasers (QCLs) and wideband incandescence, this system has great advantage due to the capability of using long-distance and low-loss optical fiber for remote monitoring. With self-developed DFB laser driver and lock-in amplifier, the system has good prospects in industrial field because of its simple structure, low price and capability of easy to be integrated.

Cryptococcal phosphoglucose isomerase is required for virulence factor production, cell wall integrity and stress resistance.

Regulation of virulence factor production in the pathogen Cryptococcus neoformans remains to be fully illustrated. We present here a finding that a gene, encoding the glycolysis enzyme phosphoglucose isomerase (Pgi1), is critical for the biosynthesis of melanin and capsule, cell wall integrity and resistance to stress conditions. A leaky mutant of the yeast, LZM19, resulted from an insertion of T-DNA in the PGI1 promoter region, expressed PGI1 at a level only 1.9% of the wild type. LZM19 could synthesize the pigment melanin in the presence of 2% glucose, suggesting a status of LAC1 derepression. Phenotypically, capsule biosynthesis in LZM19 was remarkably reduced. Integrity of the cell wall and plasma membrane of LZM19 were impaired based on its sensitivity to Congo red and SDS. Also, LZM19 exhibited hypersensitivity to osmotic stress generated by 2 M NaCl or 1 M KCl, indicating possible impairment in the HOG signaling pathway. Furthermore, LZM19 failed to utilize mannose and fructose, suggesting a possible involvement of Pgi1 in the breakdown of these two sugars. Our results revealed a crucial role of PGI1 in coordination of the production of virulence factors, cell wall integrity and stress response in C. neoformans.