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In food processing environments, various microorganisms can adhere and aggregate on the surface of equipment, resulting in the formation of multispecies biofilms. Complex interactions among microorganisms may affect the formation of multispecies biofilms and resistance to disinfectants, which are food safety and quality concerns. This article reviews the various interactions among microorganisms in multispecies biofilms, including competitive, cooperative, and neutral interactions. Then, the preliminary mechanisms underlying the formation of multispecies biofilms are discussed in relation to factors, such as quorum-sensing signal molecules, extracellular polymeric substances, and biofilm-regulated genes. Finally, the resistance mechanisms of common contaminating microorganisms to disinfectants in food processing environments are also summarized. This review is expected to facilitate a better understanding of interspecies interactions and provide some implications for the control of multispecies biofilms in food processing. HIGHLIGHTS

Pantothenic acid is an essential metabolite found throughout all branches of life. Although the enzymes responsible for pantothenic biosynthesis have been characterized, those leading to its biodegradation remain poorly understood. In the study described herein, we showed that use of a "genomic enzymology" strategy enabled identification of four biodegradation pathway genes, which were then confirmed by using kinetic analysis of the purified recombinant enzymes encoded in Ochrobactrum anthropi. The reconstituted pathway converts pantothenic acid to β-alanine and (R)-pantoate, and then (R)-pantoate to aldopentoate, which is transformed to (R)-3,3-dimethylmalate and hence to α-ketoisovalerate. The pathway genes are common to Proteobacterial genomes in which they are not colocated.

Salmonella enterica is a prominent foodborne pathogen, including diverse serotypes that are prolific biofilm formers. Its ability to form biofilm can be affected by multiple environmental factors. In this study, the effect of salinity on biofilm formation by S. enterica was evaluated by using two recently isolated strains of Salmonella serotypes Enteritidis and Newport. Although supplementing the growth medium with a low concentration (0.5 to 2%) of sodium chloride (NaCl) slightly enhanced biofilm formation for the strain S. enterica serovar Enteritidis 110, it sharply reduced or abolished biofilm formation by the strain S. enterica serovar Newport 193. This differential effect of salinity on S. enterica strains of different serotypes was poorly correlated with inhibition of planktonic growth but strongly correlated with cell motility. Examining genes known to affect biofilm formation showed that the expression of adrA, csgD, and fliC, which encode proteins required for surface adhesion and cell motility, was significantly downregulated with salinity increase in Salmonella Newport 193 but not in Salmonella Enteritidis 110. Therefore, it is plausible that the differential effect of salinity on biofilm formation by Salmonella Enteritidis 110 and Salmonella Newport 193 resulted from the differential regulation to genes required for cell adherence and motility.

1-Deoxy-D-sorbitol, the 1-deoxy analogue of D-sorbitol, has been detected in human urine as well as in natural herbs and spices. Although there are sporadic reports about 1-deoxy-D-sorbitol dehydrogenase, the complete catabolic pathway of 1-deoxy-D-sorbitol remains unsolved. Informed by the promiscuous activities of fructose-6-phosphate aldolase (FSA) which is involved in the sorbitol (glucitol) utilization (gut) operon and guided by the large scale bioinformatics analysis, we predicted and then experimentally verified the gut operon encoded by Bacillus licheniformis ATCC14580 is responsible for the catabolism of both D-sorbitol and 1-deoxy-D-sorbitol by in vitro activity assays of pathway enzymes, in vivo growth phenotypes, and transcriptomic studies. Moreover, the phylogenetic distribution analysis suggests that the D-sorbitol and 1-deoxy-D-sorbitol catabolic gene cluster is mostly conserved in members of Firmicutes phylum.

Lysozyme acts as a kind of cationic antimicrobial protein and effectively hydrolyzes bacterial peptidoglycan to have a bactericidal effect, which also plays an important role in protecting eggs from microbial contamination. Dermacoccus abyssi HZAU 226, a Gram-positive bacterium isolated from spoiled eggs, has egg white and lysozyme tolerance, but its survival mechanism is unknown, especially from a transcriptomics point of view. In this study, the high lysozyme tolerance of D. abyssi HZAU 226 was characterized by three independent experiments, and then the Illumina RNA-seq was used to compare the transcriptional profiles of this strain in Luria&ndash, Bertani (LB) medium with and without 5 mg/mL lysozyme to identify differentially expressed genes (DEGs), 1024 DEGs were identified by expression analysis, including 544 up-regulated genes and 480 down-regulated genes in response to lysozyme treatment. The functional annotation analysis results of DEGs showed that these genes were mainly involved in glutathione biosynthesis and metabolism, ion transport, energy metabolism pathways, and peptidoglycan biosynthesis. This study is the first report of bacterial-related lysozyme RNA-seq, and our results help in understanding the lysozyme-tolerance mechanism of bacteria from a new perspective and provide transcriptome resources for subsequent research in related fields.

High aspect ratio features in silicon have broad applications in micro-electro-mechanical systems, microfluidic control and advanced packaging. This structure is usually fabricated by Bosch process, and the corresponding scallop should be controlled. Obtaining large scallop size seems easier than that of small scallop, however, it is a big challenge to obtain uniform large scallop. Herein, by using dry etching system, we demonstrate a novel high aspect ratio silicon trench with scallop size uniformly larger than 300 nm in both single crystal silicon and polycrystalline silicon. Additionally, the difference between single crystal silicon etching and polycrystalline silicon etching is compared. This work is beneficial to understanding the silicon etching mechanism in Bosch process and has potential applications in microelectronic and microfluidic devices.

Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind d-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for d-apiose with eleven previously unknown reactions. The new enzymes include d-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible ( http://efi.igb.illinois.edu/efi-est/ ), so similar ‘genomic enzymology’ strategies for discovering novel pathways can be used by the community. A bioinformatic strategy beginning with solute-binding proteins involved in sugar transport led to the functional annotation of four previously unknown catabolic pathways of the branched pentose d-apiose.

The resistance of food-borne pathogens to many unfavorable environments after the formation of microbial aggregates is significantly enhanced, which is an important reason for the continuous pathogen contamination. Ralstonia insidiosa can induce the food-borne pathogens to form larger multi-species suspended aggregates, but its formation mechanism is unknown, especially from a transcriptomics point of view. In this study, the condition of forming suspended aggregates by Listeria monocytogenes was investigated, and then, Illumina RNA-seq was used to compare the transcription profiles of L. monocytogenes in floating state and suspended aggregates to identify differentially expressed genes (DEGs): 511 DEGs were identified by expression analysis, including 273 up-regulated genes and 238 down-regulated genes. The functional annotation analysis results of DEGs showed that these genes were mainly involved in two-component system, phosphotransferase system, flagellar assembly, ABC transporter, glycolysis/gluconeogenesis. This study is the first report of suspended aggregates RNA-seq, and our results are of great significance to further exploring the resistance mechanism of L. monocytogenes to adverse environment and the control of pathogenic microorganisms.

Egg spoilage is a microecological phenomenon, involving several specific spoilage microorganisms, that is affected by numerous factors. The specific biological characteristics of egg spoilage microorganisms are particularly significant for their survival in eggs. This research focusses on the specific biological characteristics of 24 spoilage bacteria isolated from eggs. Their protease activities, alkalinity tolerance, egg white and lysozyme tolerance, and survival rates in egg whites were analysed. The results showed that the strains of Bacillus spp. had the strongest protease activity, the strains of Staphylococcus spp. had the strongest alkaline pH tolerance, and most of the spoilage bacteria could tolerate an egg white or lysozyme environment. Notably, the survival rate test of egg whites showed that only the strains of Dermacoccus spp. could survive and grow in egg whites. This study of the specific biological characteristics of spoilage microorganisms in eggs aims to extend eggs’ shelf life and provide theoretical guidance for controlling spoilage microorganisms during storage.

The broad synthetic utility of labile enol esters demands efficient methods for the stereo- and regioselective synthesis of both Z and E isomers. The available synthetic methods dominated by metal catalysis cannot meet the challenge. We wish to report a metal-free organocatalytic divergent approach to both E and Z isomers of enol esters from the same reactant pools with the same catalytic system. A process involves an amine-catalyzed conjugate addition of carboxylic acids to ynals, which triggers a rearrangement leading to enol esters. The reaction proceeds highly regio- and stereoselectively. Simple manipulation of reaction temperatures enabled us to produce Z isomers at 0 °C (Z:E (15–20):1), whereas E isomers were produced at 30 °C (E:Z (15–20):1). Furthermore, the mild reaction conditions accommodate a broad array of densely functionalized carboxylic acids for the process, including complex biologically relevant structures and ynals. Therefore, synthetically valued, structurally diverse enol esters are...

Inverted pyramids were fabricated through a method combining cesium chloride (CsCl) self-assembly technology and anisotropy corrosion of silicon solar cells. Ti film with nanoporous masks was formed by lift-off the CsCl nanoislands for the inverted pyramids. The pyramids were then formed by anisotropy corrosion of alkaline solution. The average diameter and morphology of the pyramids were controlled by varying the average diameter of CsCl nanoislands from 400 nm to 1.5 mu m and by varying the etching time of alkaline solution from 2 to 8 min. The inverted-pyramid texture could suppress reflection to below 10% at wavelengths from 400 to 1000 nm, which was much lower than that of planar wafer. A solar cell fabricated from the pyramids had higher short-circuit current density (J(sc)) and photovoltaic conversion efficiency (PCE) compared with those of planar solar cells for the good antireflection property. The solar cell showed a PCE of 15.25%, a J(sc) of 38.35 mA/cm(2), and an open-circuit voltage of 555.7 mV. (C) 2015 Elsevier Ltd. All rights reserved.

The genome of Labrenzia aggregata IAM 12614 encodes an uncharacterized member of the muconate lactonizing enzyme (MLE) subgroup of the enolase superfamily (UniProt ID A0NXQ8 ). The gene encoding A0NXQ8 is located between genes that encode members of the proline racemase superfamily, 4R-hydroxyproline 2-epimerase (UniProt ID A0NXQ7 ; 4HypE) and trans-3-hydroxy-l-proline dehydratase (UniProt ID A0NXQ9 ; t3LHypD). A0NXQ8 was screened with a library of proline analogues; two reactions were observed with cis-3-hydroxy-l-proline (c3LHyp), competing 2-epimerization to trans-3-hydroxy-d-proline (1,1-proton transfer) and dehydration to Δ(1)-pyrroline-2-carboxylate (β-elimination; c3LHyp dehydratase), with eventual total dehydration. The genome context encoding A0NXQ8 both (1) confirms its novel c3LHyp dehydratase function and (2) provides evidence for metabolic pathways that allow L. aggregata to utilize several isomeric 3- and 4-hydroxyprolines as sole carbon sources.

A simple fabrication technology for both nanoscrews and nanoholes by Cesium Chloride (CsCl) self-assembly lithography and dry etching on silicon substrates is demonstrated. The porous Al template ranging from 400 nm to 2 mu M average diameter is formed by lift-off the CsCl nanoislands in DI water as the ICP etching masks for nanoholes. Nanoscrews and nanoholes of desired height/depth from 1.2 to 4 mu m are obtained by this method. The reflectance of nanoscrew and nanohole structures can achieve below 5% from wavelength of 400 to 1000 am which is much lower than that of pyramid but the performance of pyramid solar cells is the best. Results show that the performance of nanoscrew and nanohole solar cells is strongly affected by some other factors such as surface passivation and electrode-contact property. Therefore, not only the antireflection advantage but also the surface passivation and improving the electrode-contact property should be considered together to improve nanostructure solar cells photovoltaic performance.

The silicon solar cell with selective pillars is fabricated by Cesium Chloride (CsCI) self-assembly lithography and UV-lithography. This solar cell has pillars selectively in the active area (i.e. emitter exposed to light) while keeping electrode area plain to overcome the problem of metal contacts on pillars' surface. CsCI self-assembly and dry etching are used to make silicon pillars only on the active silicon surface as antireflection layer for the solar cell. UV-lithography is used to provide the selective area for the silicon pillars fabrication and the pattern for electrode. Ti/Ag layer is deposited on the electrode pattern surface with the alignment shadow mask by thermal evaporation. The solar cell with selective pillars has the lower reflectivity below 5% in the spectral ranging from 400 to 1000 nm compared to the planar cell without antireflection coating, and it also has the better electrode contacts compared to the cell with pillars all over the entire front surface. The photovoltaic conversion efficiency (PCE) improves from 12.18% to 15.37% at the experiment condition. (C) 2014 Elsevier Ltd. All rights reserved.

A simple technology with cesium chloride (CsCl) self-assembly lithography and wet electrochemical etching is introduced to fabricate the wafer scale, disordered, well-aligned, and high aspect ratio silicon nanopillars. The original nano structures of CsCl islands with diameters of 500–2000 nm are formed by self-assembly and used as template of lift-off for the nanoporous gold film for wet electrochemical etching as the catalyst in etching solution of HF and H2O2. The average diameter of silicon nanopillars is determined by the CsCl nanoislands with 500–2000 nm, and the height of silicon nanopillars is mainly determined by the etching time in etching solution with 3–12 μm. The aspect ratio can achieve to 60. The solar cells with different height nanopillars are made for the research of photovoltaic conversion efficiency (PCE). The reflectance of the nanopillars with different height is measured from the wavelength of 400 to 1000 nm and the 9 μm height silicon nanopillars has the lowest one which is below 3%. The PCE shows the highest value of 14.19% at the condition of 3 μm height nanopillars and 12.18% of planar one with the same fabrication process.

Silicon micro-nano pillars are cost-efficiently integrated using twice cesium chloride (CsCl) islands lithography technique and dry etching for solar cell applications. The micro PMMA islands are fabricated by inductively coupled plasma (ICP) dry etching with micro CsCl islands as masks, and the nano CsCl islands with nano sizes then are made on the surface of micro PMMA islands and silicon. By ICP dry etching with the mask of micro PMMA islands and nano CsCl islands, the micro-nano silicon pillars are made and certain height micro pillars are randomly positioned between dense arrays of nano pillars with different morphologies by controlling etching conditions. With 300 nm depth p-n junction detected by secondary-ion mass spectrometry (SIMS), the micro pillars of the diameter about 1 μm form the core–shell p-n junction to maximize utility of p-n junction interface and enable efficient free carrier collection, and the nano tapered pillars of 150 nm diameter are used to decrease reflection by a graded-refractive-index. Compared to single micro or nano pillar arrayed cells, the co-integrated solar cell with micro and nano pillars demonstrates improved photovoltaic characteristic that is a photovoltaic conversion efficiency (PCE) of 15.35 % with a short circuit current density (J sc) of 38.40 mA/cm2 and an open circuit voltage (V oc) of 555.7 mV, which benefits from the advantages of micro-nano pillar structures and can be further improved upon process optimization.

Using a large-scale “genomic enzymology” approach, we (i) assigned novel ATP-dependent four-carbon acid sugar kinase functions to members of the DUF1537 protein family (domain of unknown function; Pfam families PF07005 and PF17042) and (ii) discovered novel catabolic pathways for d-threonate, l-threonate, and d-erythronate. The experimentally determined ligand specificities of several solute binding proteins (SBPs) for TRAP (tripartite ATP-independent permease) transporters for four-carbon acids, including d-erythronate and l-erythronate, were used to constrain the substrates for the catabolic pathways that degrade the SBP ligands to intermediates in central carbon metabolism. Sequence similarity networks and genome neighborhood networks were used to identify the enzyme components of the pathways. Conserved genome neighborhoods encoded SBPs as well as permease components of the TRAP transporters, members of the DUF1537 family, and a member of the 4-hydroxy-l-threonine 4-phosphate dehydrogenase (PdxA) oxidative decarboxylase, class II aldolase, or ribulose 1,5-bisphosphate carboxylase/oxygenase, large subunit (RuBisCO) superfamily. Because the characterized substrates of members of the PdxA, class II aldolase, and RuBisCO superfamilies are phosphorylated, we postulated that the members of the DUF1537 family are novel ATP-dependent kinases that participate in catabolic pathways for four-carbon acid sugars. We determined that (i) the DUF1537/PdxA pair participates in a pathway for the conversion of d-threonate to dihydroxyacetone phosphate and CO2 and (ii) the DUF1537/class II aldolase pair participates in pathways for the conversion of d-erythronate and l-threonate (epimers at carbon-3) to dihydroxyacetone phosphate and CO2. The physiological importance of these pathways was demonstrated in vivo by phenotypic and genetic analyses.

The title reaction proceeds via two different routes: the self-dimerization of two equivalents of the same aliphatic enal, and the hetero-dimerization of two distinct enals in a regio- and chemoselective manner using racemic diphenyl prolinol Tms ether as catalyst.

A matter of protection: The outcome of a divergent organocatalytic aza-Michael/aldol cascade process toward quinolines and 1,4-dihydroquinolines depends on the choice of the N-protecting group (see scheme; TEA = triethylamine, TMS = trimethylsilyl). Use of an electron-donating sulfonyl group results in an unanticipated aza-Michael/aldol/aromatization cascade to give polysubstituted quinolines (right). In contrast, chiral 1,4-dihydroquinolines are obtained with an electron-withdrawing sulfonyl group (left).

An unprecedented organocatalytic highly enantioselective cascade Michael-aldol reaction has been developed in high yields under mild reaction conditions. The "one-pot" process affords an efficient approach to the synthetically and biologically important chiral 4H-chromenes bearing a quaternary stereogenic center. The study significantly expands the scope of less explored organocatalytic iminium-allenamine chemistry.

Ethanolamine, a major component of the cell membranes of bacteria and animals in the form of phosphatidylethanolamine, can be a source of carbon and/or nitrogen for many bacterial species. The cano...

A quinine thiourea promoted enantioselective Strecker reaction of cyclic ketoimines with TMSCN has been developed. The process affords new enantioenriched trifluoromethyl dihydroquinazolinones in high yields and with high enantioselectivities.

Synthetically and biologically important products are prepared effectively in a one-pot procedure.

High yields and enantioselectivities are obtained for substrates bearing a -CF3 function at C-4.

An unprecedented simple pyrrolidine catalyzed [4 + 1] annulation reaction of ynals with N-protected-2-aminophenols is reported. The utilization of the unique property and reactivity of the C≡C triple bond in ynals leads to two consecutive conjugate addition reactions at the same β-position with pyrrolidine via iminium activation. The powerful cascade process affords a new alternative approach to biologically and synthetically important benzoxazoles in high yields (83–95%).

Enantioenriched α-aminophosphate analogues (III) of the non-nucleoside reverse transcriptase inhibitor DPC-083 are readily obtained by an asymmetric hydrophosphonylation of quinazolinones (I).

The outcome of the aza-Michael/aldol cascade reaction of 2-aminobenzaldehydes or the corresponding ketones with ynals depends on the choice of the N-protecting group.

An organocatalytic enantioselective addition reaction of cyclic ketoimines with phosphites has been developed for the first time. The process, catalyzed by Soos' quinine thiourea, affords synthetically and medicinally interesting enantioenriched trifluoromethyl dihydroquinazolinones in high yields and with high enantioselectivities.

Polyene synthesis: An efficient approach to the total synthesis of polyene natural product dihydroxrulin (1) is described. A novel, mild, direct organocatalytic IBX-mediated dehydrogenation process of simple alcohols to enals has been developed, which serves as a key step in the synthesis (see scheme).

Even alkyl alkynals (IV) are converted with excellent enantioselectivities using higher catalyst loading and a longer reaction time.

Iminium catalysis, involving the transformation of iminium ions to enamines, has been extensively studied in the context of a number of organic processes. However, the reverse of this process involving conversion of enamines to iminium species has not been realized. Here, we describe a new transformation-'oxidative enamine catalysis'-in which direct oxidation of an enamine occurs to generate an iminium species. We show that the use of o-iodoxybenzoic acid as an oxidant in the presence of a secondary amine catalyst serves as effective system for promoting rapid conversion of enamines to iminium ions. The preparative power of this process has been demonstrated in the context of direct asymmetric β-functionalization of simple aldehydes. Moreover, a variety of enantioselective cascade transformations, including triple and quadruple cascades, have been developed for the 'one-pot' synthesis of versatile chiral building blocks and structural frameworks starting with simple aldehydes.

Nanotip arrays with high aspect ratio, which have attracted much attention due to their potential applications, have been fabricated by many methods. Dry etching combined with self-assembly masks is widely used because of the convenience of dry etching and high throughput of self-assembly. In this paper, we report a method combining Cesium Chloride (CsCl) self-assembly with inductively coupled plasma (ICP) dry etching to fabricate silicon nanotip arrays with high aspect ratio and silicon nanotip arrays with aspect ratio 15 have been achieved after optimization of all parameters.

Pyramids and nanoholes are integrated together to form a micro-nano-texture on silicon surface in order to suppress reflection for silicon solar cell application. The nanoholes are formed by inductively coupled plasma (ICP) dry etching employing a nanoporous aluminum (Al) mask which is fabricated by caesium chloride (CsCl) nanoislands lift-off technique. Reflection of less than 4% can be reached by pyramid-nanohole texture, which is much lower than that from pure pyramids or nanoholes texture. Higher short circuit current density (J(sc)) and photovoltaic conversion efficiency (PCE) are obtained for the solar cell with pyramid-nanohole texture due to its better antireflection. The average diameter and depth of the nanoholes affect the solar cell properties. The smaller and deeper nanoholes can suppress reflection a lot, but meanwhile, the formation of them means more crystal lattice defects generated from ICP etching. An optimized diameter of 800 nm and depth of 1 mu m for the nanoholes are obtained in our experiments to get the best photovoltaic performance that is a PCE of 14.89% with a J(sc) of 38.25 mA cm(-2) and an open circuit voltage (V-oc) of 544.8 mV.