经典好句

Modeling conversion and transport phenomena in solid-state fermentation:a review and perspectives,Biotechnol特别注意标点符号的规范使用、指示代词、介词、复合句*Chemoeffectors are detected by chemoreceptors, and typically each receptor will sense one or at most a few compounds; for example, the chemoreceptor Tar (also known as McpII) from E. coli senses the attractants aspartate, maltose and phenol and the repellents Ni2+ and Co2+. *In addition,the utilization of these agro-industrial wastes, on the one hand, provides alternative substrates and, on the other, helps in solving pollution problems ,which otherwise may cause their disposal.The aim of this paper is to review the potential application of SSF for the production of several metabolites of great interest to the food industry.In addition,different types of bioreactor for SSF processes are described. The different disadvantages detected in the above mentioned bioreactor designs to perform SSF processes have promoted the necessity of developing new bioreactor configurations or modifying the already existing designs. These bioreactor configurations should be able to operate in continuous mode with high productivity for prolonged periods of time without operational problems as well as permit the scale-up of the process.Our research group has been working in this field ,resulting in the design of a new bioreactor, called immersion bioreactor.The first category comprises many designs, more or less sophisticated,while the second category, which is used mainly at industrial level, is markedly less varied. Within each category, some of the bioreactors can operate in aseptic conditions.Interesting approaches have been used by several workers not only to characterize the oxygen transfer and the effects of air pressure oscillation amplitude ,but also to attempt to better understand the behaviour of the micro-organism in such solid state systems .But, despite this success, little improvements were carried out from the traditional Koji equipment and, in most cases,the scaling-up has only consisted in mechanizing the trayfermenter.Without forced aeration and agitation, only thetemperature of the room,where they are incubated,is regulated.Easy to use in large numbers,they are particularly well adapted for the screening of substrates or micro-organisms in the first steps.SSF resembles the natural habitat of microorganism and is,therefore, preferred choice For microorganisms to grow and produce useful value added products.Bioremediation is againa very important aspect where SSF has proved its credibility.Thus there is hardly any bioprocess untouched by SSF.SSF is on the way to commercialization even for processes which were earlier thought feasible only for SmF. It has been found economicallyviable for various processes, including pharmaceutica products. Still,continuous efforts are needed in the direction of automation of the process,which could prove it equally efficient to SmF.Biorefineries has added more value to SSF,as biomass is the only foreseeable source of energy to meet needs of the future generation,Which adds to the importance of agro-residual waste. However, mathematical models have now reached a level of sophistication which makes this not only possible,but also necessary;it is only through the use of mathematical models as tools during the design process and in the optimization of operation that SSF bioreactors will perform at their full potential land there by maximize the economic performance of SSF processes.There is a need for experimental work to determine these parameters for SSF bioreactors as also to test these theoretical approaches by applying them in the development of real large-scale SSF bioreactors. Nowadays there is a continuously increasing worldwide concern for development of alternative water reuse technologies,mainly focused on agriculture and industry.In this context,Advanced Oxidation Processes (AOPs)are considered a highly competitive water treatment technology for the removal of those organic pollutants not treatable by conventional techniques due to their high chemical stability and/or low biodegradability.The second greenhouse experiment quantified the extent to which each species in monoculture was affected by negative soil feedbacks.Figure2a shows how planted and realized species richness related to each other.We found no effect of plant diversity on the extent to which roots were colonized by AMF.Finally,two of the three species that grew in low-diversity assemblages that were most mycorrhizal responsive in a separate greenhouse experiment were not negatively influenced by fungicide,as one might expect of fungicide-induced suppression of mycorrhizal infection negatively effected plant performance.Here,we did find that fungicide reduced AMF root infection,but fungicide-induced reductions in mycorrhizal root infection were similar in magnitude across the diversity gradient,contrary to what one might expect if this was an important driver of our results.If true, niche-based ⁄ competitive processes and soil pathogen effects are not mutually exclusive mechanisms but rather may act in concert. Thus, negative density-dependent effects of soil pathogens may both suppress the productivity of low-diversity assemblages,while helping to maintain the diversity of more species-rich assemblages.As we could not tease apart effects of species and functional richness on productivity,determining which component of diversity more stronglyaffects productivity and pathogen attack awaits further study.*Instead, it seems to be related to the lysophosphatidic acid acyl transferase family, which is responsible for the transfer of anacyl Chain from either acyl-ACP or acyl-CoA to lysophosphatidic Acid, resulting in the production of phosphatidic acid.*However, with the identification of AHLs With Long Acyl chains, the idea that all AHLs are freely diffusible has come into question.*This is in contrast to the C4-HSL also produced by P.aeruginosa, which freely diffuses into and out the cells.*It is not yet known if pumps similar to the MexAB-type pumpare involved in AHL transport in those organisms.*The symbiotic interaction results in the reduction of atmospheric dinitrogen to ammonia by the bacteroids,which is then utilized by the host plant.*Analysis of these plant mutants promises to be a very active area of study in the near future.*The empty nodules elicited by mutants unable to make either exopolysaccharide appear to be arrested at an intermediate state of nodule development.*It is unclear what functions are carried on these plasmids.*It was demonstrated that rhiABC was controlled by RhiR and that (千万不能省略)flavonoids repressed the expression of both rhiR andrhiABC.*Recent work has also identified a cluster of genes on pRL1JI with homology to the trb operon of A.tumefaciens.*These observations provide some of the most compelling evidence supporting the idea that quorum sensing is involved in symbiosis, even though the mechanisms through which quorum sensing acts is still a mystery.*Only two AHLs have been described in R.etli CFN42, 3-oxo-C8-HSL, synthesized byTraI, and a putative3-OH-C8-HSL, whose function and synthase remain to be identified.*Quorum-sensing system might exist to regulate the transfer of pNGR234a, (which is)similar to the regulation of Ti plasmid transfer in A.tumefaciens.*A traI mutant still produces a compound comigrating with (=with homology to)3-oxo-C8-HSL,suggesting that one or more additional AHL synthases may be present.*As expected, traI seems to be autoregulated by TraR and 3-oxo-C8-HSL and TraR activity is inhibited by TraM, which corresponds to properties of the A.tumefacienstra system.*Another possible explanation lies in the fact that it is possible that these do not function in conjugation, leading to the overall conjugal deficiency *Expression of TraR increased the production of the other AHLsproduced by NGR234and, in the presence of 3-oxo-C8-HSL, resulted in Growth inhibition.*Disruption of the sin system correlates with(与某种结果相联系) a delay in the appearance of nitrogen-fixing nodules, as well as with an overall decrease in the number of pink nodules, suggesting a role for quorum sensingin establishing a successful symbiosis with medicagosativa .注意比较下面两句话（标点符号的区别）ExpR is a positive regulator of the exp genes,which are responsible for EPSII biosynthesisExpR is a positive regulator of the exp genes which are responsible for EPSII biosynthesis*It was proposed that these short-chain AHLs are part of a second quorum-sensing system in Rm1021,termed the mel system.*The tra system, named for its homology to the tra systems in A.tumefaciens and Rhizobium.*Interestingly, transfer frequency of plj101, as in NGR234,(与NGR中是一样的)also Occurs at a fairly low frequency.*Early work showed that nod genes seemed to be repressed at high cell densities, suggesting a quorum-sensing phenomenon, but to date no evidence of AHL production has been found.*Synthesis of bradyoxetin was found to be iron regulated, with maximalproduction under iron-depleted conditions.*It is therefore important to develop rigorous analyses of how bacteria communicate within and between species and how eukaryotic hosts talk back.*The rhizobia serve as an excellent quorum-sensing model system for such studies.*LuxI encodes the AHL synthase, which(先行词AHL synthase) synthesizes 3-oxo-C6-HSL from acyl-ACP and SAM substrates.*In some species, luxS has been linked to regulatory functions, such as control of toxin productionin and of the virulence , but the role of the autoinducer remains largely unknown.*The genes underlying QS（QS系统囊括的基因）are distributed in a discontinuous manner among the bacteria, suggesting that they have been subject to（遭受）loss or horizontal transfer.*In this regard（在这点上）, gene phylogenies for the components of QS Systems can provide evidence as to whether they are ancestra land lost in some species or have been acquired from distantly related lineages(血缘).*We use these phylogenies to address the basis for the observed distributions of QS genes in bacteria.*Specifically,we examine(1)the extent to which LuxI and LuxR have coevolved versus the extent to which they have switched partners and(2)the extent to which the distributions of LuxI/R and LuxS reflect vertical transmission along the organism alphylogeny versus horizontal transmission among lineages.*Here, we present phylogenetic analyses of genes underlying the two QS systems, LuxI/R and LuxS.*The genes that are regularly referred to as the LuxI/R families in fact constitute two families in each case.*In bacteria, the perception of the environment can direct cellular differentiation by influencing the expression of genes underlying a variety of biological pathways.*Although (the quorum sensing, 在十分明确句子主语的情形下，此处为了句子的简便性，句中主语是可以省略的) initially considered to be a specialized system of V .fischeri and related species ,experimental work later revealed homologous systems with diverse biological roles in other proteobacterial species.*These included Pseudomonas aeruginosa, a human pathogen in which two circuits act in parallel to control the expression of a number of virulence factors*The mechanisms underlying QS were established very early in the evolution of bacteria.*Furthermore, only rarely has an inducer or a receptor gene acquired a new partner.*In most lineages,the genes are contiguous on the chromosome and retain their pairwise functional relationship, indicating that most gene partners have shared histories.*This process, termed diffusion sensing by Rosemary Redfield,could allow the cells to regulate the secretion of effectors, such as degradative enzymes, antibiotics, surfactants, and siderophores, to minimize losses to extracellular diffusion.说明基因活化因子在基因片段上具体结合位点的常用句型*LuxR binds to an inverted repeat referred to as the lux box,which is centered at -42.5 from the transcriptional start site, and makes contact with the RNA polymerase to stimulate the expression of the luxI CDABE genes.*Transcriptional activation by LuxR-type proteins requires cis-acting DNA elements, normally referred to as lux-type boxes.The typical lux-type box is an 18-to 22-bp inverted-repeat sequence centered at about -40 from the transcriptional start site.A putative ribosomal binding site(AGGTAA)was located 6 bp upstream of the ATG start codon.(这段话是中国人写的)*Opines secreted by crown gall tumors bind a receptor protein, AccR or OccR, depending on the strain.*The opine-receptor protein combination initiates the transcription of traR by either rinduction(OccR) or derepression(AccR).*However, with the identification of AHLs with long acyl chains, the idea that all AHLs are freely diffusible has come into question.*Studies of A.tumefaciens have suggested that TraR,on binding the AHL signal, undergoes a conformational change, dimerizes, and activates transcription.*A strain of Variovorax paradoxus was isolated from soil based on its ability to utilize AHLs as the sole source of energy and nitrogen, an activity that could disrupt the signaling process.*Many of the other nodulation genes determine the nature of the substitutions at the terminal residues and the structure of the acy lchain, both important features that play a role in determining host specificity.*Rosemeyer etal. Provided evidence that R.etli produced a long-chain AHL, related to(= similar to) the R.leguminosarum small.*Moreover, mutations in cinI and cinR , while(虽然) causing no readily observable defect in nodulation , resulted in decreased nitrogen fixation as well as abnormal symbiosome development.*Disruption of the sin system correlates with a delay in the appearance of nitrogen-fixing nodules, as well as with an over-all decrease in thenumber of pink nodules, suggesting a role for quorum sensing in establishing a successful symbiosis with medicag osativa.*NwsB then induces nolA, which in turn induces nodD2, leading to repression of the nod genes.*We identified the traI gene, which is required for AAI production, and found it to be homologous to the V. fischeri luxI gene.* Strain HF-1was related to the Pseudomonas sp.lineage, and closely clustered with two strains, P.plecogloscida FPC951T (Gen Bank accession no.AB009457) and P.putida MT4T (Gen Bank accession no.AB180734), having sequence identities of 98.0 and 97.8%, respectively.*The growth and nicotine degradation of strain HF-1 were optimal at an initial pH of 6.5–7.5 under 30 ◦C,150rpm, but were slow at an initial pH of 6 or between pH8.0 and 8.5, and were weak or even inexistent at an initial pH of 5.5 and over pH9.0 .*In the two media, the growth patterns of the isolate were very similar within the initial 13h of incubation;thereafter, however, they were better in the medium without(NH4)2SO4 than in the other medium.*The arithmetic mean of pH in culture media（补充说明：two nicotine media）in the above test was observed during incubation, and it showed that pH values lay between 7.38 and 7.69, with tiny change in the twonicotine media, and between 7.36 and 7.71 in the maltose medium.*The degradation rate of nicotine by the isolate corresponded to (与后者紧密联系) its growth rate.*Liquid culture and plate colonies of strain HF-1 in the media containing nicotine became virescent after growth, but not in media without nicotine, such as LB and maltose media.*Arthrobacter nicotinovorans isolated from the storage of tobacco leaves was capable of metabolizing nicotine and converting to yellow pigments, and then continuously turning to carmine after a certain period.*The degradation rate of nicotine by the isolate corresponded to its growth rate.*The isolate grew well in the nicotine medium, in which nicotine could be degraded almost completely during a period of 25 h of incubation with stable pH.*However, its growth and degradation of nicotine were inhibited by the sharp drop in pH from 6.4 to about 4.6in culture media during the transformation of nicotine.*No reason could be provided for the stability of pH during transformation of nicotine by strain HF-1, related to the existence of phosphate buffer solution in media, which indicates that it might be different from the two Pseudomonas sp.strains mentioned above.*Genomic DNA of Pseudomonas sp. CTN-3 was prepared by a high-salt method and subjected to partial digestion with Sau3AI. Fractions containing approximately 2-to 4-kb DNA fragments were pooled（获取，产生）, ligated into the BamHI site of the plasmid pUC118,and transformed into competent Escherichia coli DH5.*Nucleotide sequence accession nnumbers. The nucleotide sequences of the chlorothalonil hydrolytic dehalogenasegenes were deposited in the Gen Bank database under accession numbers GQ292539 and GQ485642. *Site-directed mutagenesis. Mutagenesis of the enzyme was performed using rapid PCR site-directed mutagenesis.*Therefore, the conversion of chlorothalonil to 4-TPN-OH was a hydrolytic process, as opposed to an oxidative one.*The culture was plated periodically onto MM containing monocrotophos as sole carbon source and2.0%(w/v) purified agar.*the following conditions:5min of denaturation at 94,followed by 30cycles at 94 for 30s, 50 for 30s and 72 for 2min, with a final extension at 72 for10min.*The determined sequence was compared with those available in the GenBank database using the BLAST program.*Multiple alignments(多重比对)were carried out using CLUSTALX1.8.3, and phylogenesis was analysed using MEGA version 3.0 software.The distance was calculated using the Kimura two-parametermodel. An unrooted tree was built using the neighbour-joining method. The nucleotide sequence coding for the 16S rRNA gene of Paracoccus sp.M-1(1425bp) was deposited in the GenBank database with accession number DQ307757.*microbiologists can identify mechanisms by which bacteria degrade contaminants, either to detoxify their habitat or for use as food and energy sources.*The genome of this bacterium was found to comprise a 4.3 Mb chromosome (65.1% GC content) encoding 4,133 predicted coding sequences (CDSs), and two plasmids, one of 207 kb (57.6% GC content; 274 predicted CDSs) and another of 224 kb (63.1% GC content; 196 predicted CDSs).*Although this strain is related to nitrogen-fixing plant symbionts, it is a member of a branch of environmental isolates of Azoarcus that neither have nitrogen-fixation genes nor interact with plants.*This organism grows in pure culture, dechlorinating a wider repertoire of substrates than D. ethenogenes strain 195, including some trichlorobenzenes.*Both Dehalococcoides strains have nitrogen-fixation genes, leading the authors to propose that the ancestral strain was a nitrogen-fixing auto trop.*Pyrethroids differ from many other pesticides in that they contain oneto three chiral centers; the chirality may arise from the acid moiety, the alcohol moiety, or both.*For example, there was a preference in both bacterial and mammali an pyrethroid-hydrolyzing carboxylesterases for trans-permethrin over cis- permethrin,while the carboxylesterase from N.cincticeps Uhler preferred cis-permethrin over trans-permethrin*All chemicals were analytical grade and 98% pure.*However,chlorpyrifosis hydrolyzed almost 1,000-folds lower than the preferred substrate , paraoxon, by organophosphorus hydrolase(OPH), an enzyme that can degrade a broad range of organophosphate epesticides.*We have recently demonstrated that directed evolution can be used to Generate OPH variants with up to 25-fold improvement in hydrolysis of methyl parathion.*Variants were selected from two rounds of directed evolution based on the formation of clear haloes on Luria-Bertani plates overlaid with chlorpyrifos.*Unfortunately, the rates of hydrolysis by OPH differ dramatically for members of the family of OP compounds, ranging from hydrolysis at the diffusion-controlled limit for paraoxon( 这种物质可以很有效地被OPH 降解)to several orders of magnitude(若干个数量级) slower for malathion,chlorpyrifos, and VX.（reduce by severalfolds：减少了好几倍）*Directed evolution has recently been used to generate OPH variants with up to 25-fold improvements in hydrolysis of methyl parathion, a substrate that is hydrolyzed 30-fold less efficiently than paraoxon.*The addition of strain B-14 to soil with a low indigenous population of chlorpyrifos-degrading bacteria treated with chlorpyrifos resulted in a higher degradation rate than was observed in noninoculated soils.*Recently, there have been reports of organophosphate degradation genes with similar function but different sequences from the opd gene: for example, a methyl parathion-degrading Plesiomonas species had a DNA sequence quite different from those of the known opd genes.*Use of pesticide-degrading microbial systems for removal of pollutants from the contaminated systems requires an understanding of ecological, physiological, and biochemical requirements of degrading organisms.*All isolates were shown to be the same species, as indicated by RFLP of the 16SrRNA gene and SDS-PAGE protein profiles.*The isolate selected for further study, strain B-14, showed greatest similarity to members of the order Enterobacteriales and in particular the E.asburiae.*All these organisms synthesize an enzyme called parathion hydrolase, and in each case the enzyme is encoded by a gene (opd) located on a large indigenous plasmid.*The opd gene is flanked upstream by an insertion sequence, ISFlsp1, that is a member of the IS21 family,and downstream by a Tn3-like element encoding a transposase and a resolvase.*Adjacent to opd but transcribed in the opposite direction is an open reading frame(orf 243) with the potential to encode an aromatic hydrolase Somewhat similar to Pseudomonas putida TodF.*sequencing of the opd genes showed that the nucleotide sequences of the Philippines and Texas isolates were 100% identical and that of the Indian isolate was 98% identical.*We also describe a novel gene , linked to opd , that is involved in the degradation of p-nitrophenol.*Although DDT levels have dropped since 1972,1990 levels in regional studies were still as much as 10 times higher than the chronic toxicity criterion established by the Environmental Protection Agency.*We constructed a strain of Pseudomonas putida that can efficiently degrade a model organophosphate, paraoxon, and use it as a carbon, energy, and phosphorus source.*This strain was engineered with the pnp operon from Pseudomonas sp.strainENV2030,which encodes enzymes that transform p-nitrophenol into b-ketoadipate, and with a synthetic operon encoding an organophosphate hydrolase(encoded by opd)from Flavobacterium sp.strainATCC27551,a phosphodiesterase (encoded by pde)from Delftiaacidovorans, and an alkaline phosphatase(encoded by phoA)from Pseudomonas aeruginosa HN854 under control of a constitutive promoter.*The initial hydrolysis of paraoxon by an organophosphate acid anhydrase(Opd from Flavobacterium sp.strainATCC27551)to p-nitrophenol(PNP) and diethyl phosphate (DEP) reduces the toxicity 100-fold.*In the environment, PNP is degraded by a few microorganisms, most notably Moraxella and Pseudomonas isolates.*Delftia acidovorans, one of the few organisms known to use DEP as a sole phosphorus source, produces a phosphodiesterase(Pde,encoded by the pde gene)that hydrolyzes phosphodiester bonds.*Expression of the gene, with the aid of an ative alkaline phosphatase(PhoA from Pseudomonas aeruginosa HN854),enabled Escherichia coli and the infectious organism P.aeruginosa to use DEP as a phosphate source.*Though there is no known single microorganism that is capable of hydrolyzing paraoxon and mineralizing its hydrolysis products as a source of carbon and phosphorus, such a strain not only would reduce the toxicity of the organophosphate but also would prevent the accumulation of potentially toxic hydrolysis products in the environment . *Today we can use the resources of synthetic biology to create a strainthat performs catabolic processes that have not been observed in nature. *Synthetic in origin, many organophosphates are persistent in the environment and resist degradation by naturally extant microorganisms. *The results show that, under the control of the P43 promoter,the mpd gene was continuously expressed throughout the exponential growth phase and into the late stationary phase.*However, a certain degree of MPH degradation was observed, indicating that the enzyme may be sensitive to an as-yet-uncharacterized protease produced by the host during the late stationary phase or to intracellular proteases released during cell lysis.*microorganisms are known to metabolize numerous pesticides in various formulation forms under mild conditions, acting on the aqueous andpossibly on the nonaqueous phase.*The hydroquinone pathway, preferentially found in gram-negative bacteria,was proposed for a Moraxella sp. in which PNP monooxygenase activity in the membrane fraction was found t oconvert PNP to hydroquinone*Based on the sequence similarities and the proposed PNP degradation pathway, it can be tentatively concluded that the genes involved in PNP degradation (pnpABCDEF) are tightly clustered(成簇排列).*The catA gene, encoding catechol 1,2-dioxygenase, which converts catechol to cis,cis-muconate, is not present in the two operons but is alsoregulated by both CatM and BenM。