bluuebunny/crossref_metadata_2025 huggingface dataset:
Dietary intake, nutritional status and rehabilitation outcomes of stroke patients in hospital
Authors: Nip W. F. R. , Perry L. , McLaren S. , Mackenzie A.
Published: May 2011

Background:  Nutrition affects rehabilitation through its influence on physical and mental functioning, although little attention has been paid to effects on rehabilitation outcomes. The present study aimed to describe nutritional status and food consumption in stroke patients within 2 weeks of hospital admission and before discharge, as well as to investigate the effects of nutritional and dietary factors on rehabilitation outcomes.

Methods:  One hundred patients from a consecutive cohort admitted to a metropolitan hospital with acute stroke were recruited and assessed by a single researcher, with 38 reassessed at discharge. Nutritional status was assessed using Mini‐Nutritional Assessment and anthropometric indices and dietary intake was assessed by 1‐day weighed dietary records. Rehabilitation outcomes were changes in Barthel index scores and the rehabilitation efficiency index.

Results:  Few (n = 9; 10%) consumed ≥100% of the estimated average requirement (EAR) for energy within 2 weeks of admission and 13 (33%) had energy intakes <50% of EAR before discharge. A small but increasing proportion (7% at admission, 13% at discharge) were identified as being malnourished across the inpatient stay. Younger age, lower Barthel index and a higher energy intake in the early stages of admission predicted the extent and rate of restoration of functional abilities by discharge (F = 7.503, P = 0.001; F = 14.558, P < 0.001).

Conclusions:  Given a general finding of nutritional deterioration identified for these patients, as well as the identification of energy intake as a modifiable influence on the extent and rate of recovery, there is clearly scope for the multidisciplinary development of nutritional support for stroke patients to improve rehabilitation outcomes.
The value of DNA sequence data for studying landscape genetics
Authors: BOHONAK ANDREW J. , VANDERGAST AMY G.
Published: May 2011

In a recent Opinion article in Molecular Ecology, Wang (2010) emphasizes the fact that current patterns of genetic differentiation among populations reflect processes that have acted over temporal scales ranging from contemporary to ancient. He draws a sharp distinction between the fields of phylogeography (as the study of historical processes) and landscape genetics (which he restricts to very recent processes). Wang characterizes DNA sequence data as being inappropriate for the study of contemporary population processes and further states that studies which only include mitochondrial DNA or chloroplast DNA data cannot be considered part of landscape genetics. In this response, we clarify the generally accepted view that DNA sequence data can be analysed with methods that separate contemporary and historical processes. To illustrate this point, we summarize the study of Vandergast et al. (2007), which Wang mischaracterizes as being confused in terms of temporal scale. Although additional focus should be placed on the important issue of correct data interpretation, we disagree strongly with the implication that contemporary and historic processes cannot be separated in the analyses of DNA sequence data.
Choosing appropriate genetic markers and analytical methods for testing landscape genetic hypotheses
Authors: WANG IAN J.
Published: May 2011

Landscape genetics and phylogeography both examine population‐level microevolutionary processes, such as population structure and gene flow, in the context of environmental and geographic variation. They differ in terms of the spatial and temporal scales they typically investigate, meaning that different genetic markers and analytical methods are better suited for testing the different hypotheses typically posed by each discipline. In a recent comment, Bohonak & Vandergast (2011) argue that I overlooked the value of mtDNA for landscape genetics in an article I published last year in Molecular Ecology (Wang 2010) and that a gap between landscape genetics and phylogeography, which I outlined, does not exist. Here, I clarify several points in my original article and summarize the commonly held viewpoint that different genetic markers are appropriate for drawing inferences at different temporal scales.
Depressive symptoms and quality of life in people with age‐ related macular degeneration
Authors: Mathew Remy Sheena , Delbaere Kim , Lord Stephen R , Beaumont Paul , Vaegan  , Madigan Michele C
Published: May 2011

Citation information: Mathew RS, Delbaere K, Lord SR, Beaumont P, Vaegan & Madigan MC. Depressive symptoms and quality of life in people with age‐ related macular degeneration. Ophthalmic Physiol Opt 2011, 31, 375–380. doi: 10.1111/j.1475‐1313.2011.00848.x

Purpose:  To examine quality of life and associated factors in people with Age‐Related Macular Degeneration (AMD).

Methods:  One hundred and forty‐five AMD participants (mean age 78.0 ± 7.7 years) and 104 age‐ and gender‐ matched controls (mean age 78.1 ± 5.8 years) comprised the study populations for this case‐control study. Depressive symptoms were measured with the Goldberg Anxiety and Depression (GAD) scale; general health and daily functioning was assessed with the Medical Outcomes Study Short Form 36 (SF‐36) and questions relating to assistance required for daily living activities.

Results:  People with AMD performed more poorly than controls on the GAD depression scale, and physical functioning subscale of SF‐36. 44.4% of people with AMD had clinically significant depressive symptoms compared to 17.5% of controls (p < 0.001). Multiple regression analysis revealed that AMD was independently associated with depressive symptoms and a path model indicated that AMD led to depressive symptoms both directly and indirectly via reduced general health and social functioning.

Conclusion:  Psychological and functional outcome measures are reduced in people with AMD. Earlier recognition and treatment of depressive symptoms in people with AMD may be crucial to maintaining quality of life in this group.
Early transcriptional pattern of angiogenesis induced by EGCG treatment in cervical tumour cells
Authors: Tudoran Oana , Soritau Olga , Balacescu Ovidiu , Balacescu Loredana , Braicu Cornelia , Rus Meda , Gherman Claudia , Virag Piroska , Irimie Florin , Berindan‐Neagoe Ioana
Published: May 2011

The major green tea polyphenol (‐)‐epigallocatechin‐3‐gallate (EGCG) has been shown to exhibit antitumour activities in several tumour models. One of the possible mechanisms by which EGCG can inhibit cancer progression is through the modulation of angiogenesis signalling cascade. The tumour cells’ ability to tightly adhere to endothelium is a very important process in the metastatic process, because once disseminated into the bloodstream the tumour cells must re‐establish adhesive connections to endothelium in order to extravasate into the target tissues. In this study, we investigated the anti‐angiogenic effects of EGCG treatment (10 μM) on human cervical tumour cells (HeLa) by evaluating the changes in the expression pattern of 84 genes known to be involved in the angiogenesis process. Transcriptional analysis revealed 11 genes to be differentially expressed and was further validated by measuring the induced biological effects. Our results show that EGCG treatment not only leads to the down‐regulation of genes involved in the stimulation of proliferation, adhesion and motility as well as invasion processes, but also to the up‐regulation of several genes known to have antagonist effects. We observed reduced proliferation rates, adhesion and spreading ability as well as invasiveness of HeLa tumour cells upon treatment, which suggest that EGCG might be an important anti‐angiogenic therapeutic approach in cervical cancers.
Differential LEF1 and TCF4 expression is involved in melanoma cell phenotype switching
Authors: Eichhoff Ossia M. , Weeraratna Ashani , Zipser Marie C. , Denat Laurence , Widmer Daniel S. , Xu Mai , Kriegl Lydia , Kirchner Thomas , Larue Lionel , Dummer Reinhard , Hoek Keith S.
Published: May 2011

Recent observations suggest that melanoma cells drive disease progression by switching back and forth between phenotypic states of proliferation and invasion. Phenotype switching has been linked to changes in Wnt signalling, and we therefore looked for cell phenotype‐specific differences in the levels and activity of β‐catenin and its LEF/TCF co‐factors. We found that while cytosolic β‐catenin distribution is phenotype‐specific (membrane‐associated in proliferative cells and cytosolic in invasive cells), its nuclear distribution and activity is not. Instead, the expression patterns of two β‐catenin co‐factors, LEF1 and TCF4, are both phenotype‐specific and inversely correlated. LEF1 is preferentially expressed by differentiated/proliferative phenotype cells and TCF4 by dedifferentiated/invasive phenotype cells. Knock‐down experiments confirmed that these co‐factors are important for the phenotype‐specific expression of M‐MITF, WNT5A and other genes and that LEF1 suppresses TCF4 expression independently of β‐catenin. Our data show that melanoma cell phenotype switching behaviour is regulated by differential LEF1/TCF4 activity.
Meta-Analysis and Functional Validation of Nutritional Requirements of Solventogenic Clostridia Growing under Butanol Stress Conditions and Coutilization ofd-Glucose andd-Xylose
Authors: Heluane Humberto , Evans Matthew R. , Dagher Sue F. , Bruno-Bárcena José M.
Published: May 2011

Recent advances in systems biology, omics, and computational studies allow us to carry out data mining for improving biofuel production bioprocesses. Of particular interest are bioprocesses that center on microbial capabilities to biotransform both the hexose and pentose fractions present in crop residues. This called for a systematic exploration of the components of the media to obtain higher-density cultures and more-productive fermentation operations than are currently found. By using a meta-analysis approach of the transcriptional responses to butanol stress, we identified the nutritional requirements of solvent-tolerant strainClostridium beijerinckiiSA-1 (ATCC 35702). The nutritional requirements identified were later validated using the chemostat pulse-and-shift technique.C. beijerinckiiSA-1 was cultivated in a two-stage single-feed-stream continuous production system to test the proposed validated medium formulation, and the coutilization ofd-glucose andd-xylose was evaluated by taking advantage of the well-known ability of solventogenic clostridia to utilize a large variety of carbon sources such as mono-, oligo-, and polysaccharides containing pentose and hexose sugars. Our results indicated thatC. beijerinckiiSA-1 was able to coferment hexose/pentose sugar mixtures in the absence of a glucose repression effect. In addition, our analysis suggests that the solvent and acid resistance mechanisms found in this strain are differentially regulated compared to strain NRRL B-527 and are outlined as the basis of the analysis toward optimizing butanol production.
Engineering Escherichia coli BL21(DE3) Derivative Strains To Minimize E. coli Protein Contamination after Purification by Immobilized Metal Affinity Chromatography
Authors: Robichon Carine , Luo Jianying , Causey Thomas B. , Benner Jack S. , Samuelson James C.
Published: May 2011

Recombinant His-tagged proteins expressed in
Escherichia coli
and purified by immobilized metal affinity chromatography (IMAC) are commonly coeluted with native
E. coli
proteins, especially if the recombinant protein is expressed at a low level. The
E. coli
contaminants display high affinity to divalent nickel or cobalt ions, mainly due to the presence of clustered histidine residues or biologically relevant metal binding sites. To improve the final purity of expressed His-tagged protein, we engineered
E. coli
BL21(DE3) expression strains in which the most recurring contaminants are either expressed with an alternative tag or mutated to decrease their affinity to divalent cations. The current study presents the design, engineering, and characterization of two
E. coli
BL21(DE3) derivatives, NiCo21(DE3) and NiCo22(DE3), which express the endogenous proteins SlyD, Can, ArnA, and (optionally) AceE fused at their C terminus to a chitin binding domain (CBD) and the protein GlmS, with six surface histidines replaced by alanines. We show that each
E. coli
CBD-tagged protein remains active and can be efficiently eliminated from an IMAC elution fraction using a chitin column flowthrough step, while the modification of GlmS results in loss of affinity for nickel-containing resin. The “NiCo” strains uniquely complement existing methods for improving the purity of recombinant His-tagged protein.
Monitoring the Wet-Heat Inactivation Dynamics of Single Spores of Bacillus Species by Using Raman Tweezers, Differential Interference Contrast Microscopy, and Nucleic Acid Dye Fluorescence Microscopy
Authors: Zhang Pengfei , Kong Lingbo , Wang Guiwen , Setlow Peter , Li Yong-qing
Published: May 2011

Dynamic processes during wet-heat treatment of individual spores of
Bacillus cereus
,
Bacillus megaterium
, and
Bacillus subtilis
at 80 to 90°C were investigated using dual-trap Raman spectroscopy, differential interference contrast (DIC) microscopy, and nucleic acid stain (SYTO 16) fluorescence microscopy. During spore wet-heat treatment, while the spores' 1:1 chelate of Ca
2+
with dipicolinic acid (CaDPA) was released rapidly at a highly variable time
T
lag
, the levels of spore nucleic acids remained nearly unchanged, and the
T
lag
times for individual spores from the same preparation were increased somewhat as spore levels of CaDPA increased. The brightness of the spores' DIC image decreased by ∼50% in parallel with CaDPA release, and there was no spore cortex hydrolysis observed. The lateral diameters of the spores' DIC image and SYTO 16 fluorescence image also decreased in parallel with CaDPA release. The SYTO 16 fluorescence intensity began to increase during wet-heat treatment at a time before
T
lag
and reached maximum at a time slightly later than
T
release
. However, the fluorescence intensities of wet-heat-inactivated spores were ∼15-fold lower than those of nutrient-germinated spores, and this low SYTO 16 fluorescence intensity may be due in part to the low permeability of the dormant spores' inner membranes to SYTO 16 and in part to nucleic acid denaturation during the wet-heat treatment.
Influence of the Drilling Mud Formulation Process on the Bacterial Communities in Thermogenic Natural Gas Wells of the Barnett Shale
Authors: Struchtemeyer Christopher G. , Davis James P. , Elshahed Mostafa S.
Published: May 2011

The Barnett Shale in north central Texas contains natural gas generated by high temperatures (120 to 150°C) during the Mississippian Period (300 to 350 million years ago). In spite of the thermogenic origin of this gas, biogenic sulfide production and microbiologically induced corrosion have been observed at several natural gas wells in this formation. It was hypothesized that microorganisms in drilling muds were responsible for these deleterious effects. Here we collected drilling water and drilling mud samples from seven wells in the Barnett Shale during the drilling process. Using quantitative real-time PCR and microbial enumerations, we show that the addition of mud components to drilling water increased total bacterial numbers, as well as the numbers of culturable aerobic heterotrophs, acid producers, and sulfate reducers. The addition of sterile drilling muds to microcosms that contained drilling water stimulated sulfide production. Pyrosequencing-based phylogenetic surveys of the microbial communities in drilling waters and drilling muds showed a marked transition from typical freshwater communities to less diverse communities dominated by
Firmicutes
and
Gammaproteobacteria
. The community shifts observed reflected changes in temperature, pH, oxygen availability, and concentrations of sulfate, sulfonate, and carbon additives associated with the mud formulation process. Finally, several of the phylotypes observed in drilling muds belonged to lineages that were thought to be indigenous to marine and terrestrial fossil fuel formations. Our results suggest a possible alternative exogenous origin of such phylotypes via enrichment and introduction to oil and natural gas reservoirs during the drilling process.
Lectin Microarray Reveals Binding Profiles of Lactobacillus casei Strains in a Comprehensive Analysis of Bacterial Cell Wall Polysaccharides
Authors: Yasuda Emi , Tateno Hiroaki , Hirabarashi Jun , Iino Tohru , Sako Tomoyuki
Published: May 2011

We previously showed a pivotal role of the polysaccharide (PS) moiety in the cell wall of the
Lactobacillus casei
strain Shirota (YIT 9029) as a possible immune modulator (E. Yasuda M. Serata, and T. Sako, Appl. Environ. Microbiol. 74:4746-4755, 2008). To distinguish PS structures on the bacterial cell surface of individual strains in relation to their activities, it would be useful to have a rapid and high-throughput methodology. Recently, a new technique called lectin microarray was developed for rapid profiling of glycosylation in eukaryotic polymers and cell surfaces. Here, we report on the development of a simple and sensitive method based on this technology for direct analysis of intact bacterial cell surface glycomes. The method involves labeling bacterial cells with SYTOX Orange before incubation with the lectin microarray. After washing, bound cells are directly detected using an evanescent-field fluorescence scanner in a liquid phase. Using this method, we compared the cell surface glycomes from 16 different strains of
L. casei
. The patterns of lectin-binding affinity of most strains were found to be unique. There appears to be two types of lectin-binding profiles: the first is characterized by a few lectins, and the other is characterized by multiple lectins with different specificities. We also showed a dramatic change in the lectin-binding profile of a YIT 9029 derivative with a mutation in the
cps1C
gene, encoding a putative glycosyltransferase. In conclusion, the developed technique provided a novel strategy for rapid profiling and, more importantly, differentiating numerous bacterial strains with relevance to the biological functions of PS.
Phylogenetic and Functional Analysis of Aspergillus fumigatus MGTC, a Fungal Protein Homologous to a Bacterial Virulence Factor
Authors: Gastebois Amandine , Blanc Potard Anne-Beatrice , Gribaldo Simonetta , Beau Rémi , Latgé Jean Paul , Mouyna Isabelle
Published: May 2011

MgtC is important for the survival of several bacterial pathogens in macrophages and for growth under magnesium limitation. Among eukaryotes, a gene homologous to
mgtC
was found only in the pathogenic fungus
Aspergillus fumigatus
. Our data show that the
A. fumigatus
MgtC (AfuMgtC) protein does not have the same function as the bacterial MgtC proteins.
Responses of Escherichia coli, Listeria monocytogenes, and Staphylococcus aureus to Simulated Food Processing Treatments, Determined Using Fluorescence-Activated Cell Sorting and Plate Counting
Authors: Kennedy Deirdre , Cronin Ultan P. , Wilkinson Martin G.
Published: May 2011

Three common food pathogenic microorganisms were exposed to treatments simulating those used in food processing. Treated cell suspensions were then analyzed for reduction in growth by plate counting. Flow cytometry (FCM) and fluorescence-activated cell sorting (FACS) were carried out on treated cells stained for membrane integrity (Syto 9/propidium iodide) or the presence of membrane potential [DiOC
2
(3)]. For each microbial species, representative cells from various subpopulations detected by FCM were sorted onto selective and nonselective agar and evaluated for growth and recovery rates. In general, treatments giving rise to the highest reductions in counts also had the greatest effects on cell membrane integrity and membrane potential. Overall, treatments that impacted cell membrane permeability did not necessarily have a comparable effect on membrane potential. In addition, some bacterial species with extensively damaged membranes, as detected by FCM, appeared to be able to replicate and grow after sorting. Growth of sorted cells from various subpopulations was not always reflected in plate counts, and in some cases the staining protocol may have rendered cells unculturable. Optimized FCM protocols generated a greater insight into the extent of the heterogeneous bacterial population responses to food control measures than did plate counts. This study underlined the requirement to use FACS to relate various cytometric profiles generated by various staining protocols with the ability of cells to grow on microbial agar plates. Such information is a prerequisite for more-widespread adoption of FCM as a routine microbiological analytical technique.
Combined Application of PCR-Based Functional Assays for the Detection of Aromatic-Compound-Degrading Anaerobes
Authors: Kuntze Kevin , Vogt Carsten , Richnow Hans-Hermann , Boll Matthias
Published: May 2011

To explore the reliability of assays that detect aromatic-compound-degrading anaerobes, a combination of three functional-gene-targeting assays was applied to microcosms from benzene-contaminated aquifers. Results of the assays were consistent and suggest that species related to the generaAzoarcusandGeobacterdominated benzene degradation at the individual sites.
FadD19 of Rhodococcus rhodochrous DSM43269, a Steroid-Coenzyme A Ligase Essential for Degradation of C-24 Branched Sterol Side Chains
Authors: Wilbrink M. H. , Petrusma M. , Dijkhuizen L. , van der Geize R.
Published: May 2011

The actinobacterial cholesterol catabolic gene cluster contains a subset of genes that encode β-oxidation enzymes with a putative role in sterol side chain degradation. We investigated the physiological roles of several genes, i.e.,
fadD17
,
fadD19
,
fadE26
,
fadE27
, and

ro04690
DSM43269

, by gene inactivation studies in mutant strain RG32 of
Rhodococcus rhodochrous
DSM43269. Mutant strain RG32 is devoid of 3-ketosteroid 9α-hydroxylase (KSH) activity and was constructed following the identification, cloning, and sequential inactivation of five
kshA
gene homologs in strain DSM43269. We show that mutant strain RG32 is fully blocked in steroid ring degradation but capable of selective sterol side chain degradation. Except for RG32Δ
fadD19
, none of the mutants constructed in RG32 revealed an aberrant phenotype on sterol side chain degradation compared to parent strain RG32. Deletion of
fadD19
in strain RG32 completely blocked side chain degradation of C-24 branched sterols but interestingly not that of cholesterol. The additional inactivation of
fadD17
in mutant RG32Δ
fadD19
also did not affect cholesterol side chain degradation. Heterologously expressed FadD19
DSM43269
nevertheless was active toward steroid-C
26
-oic acid substrates. Our data identified FadD19 as a steroid-coenzyme A (CoA) ligase with an essential
in vivo
role in the degradation of the side chains of C-24 branched-chain sterols. This paper reports the identification and characterization of a CoA ligase with an
in vivo
role in sterol side chain degradation. The high similarity (67%) between the FadD19
DSM43269
and FadD19
H37Rv
enzymes further suggests that FadD19
H37Rv
has an
in vivo
role in sterol metabolism of
Mycobacterium tuberculosis
H37Rv.
Goose-Type Lysozyme Inhibitor (PliG) Enhances Survival of Escherichia coli in Goose Egg Albumen
Authors: Vanderkelen Lise , Van Herreweghe Joris M. , Callewaert Lien , Michiels Chris W.
Published: May 2011

The goose-type lysozyme inhibitor PliG enhances the survival of
Escherichia coli
in goose but not in chicken egg white, which contains goose- and chicken-type lysozymes, respectively. These results indicate that both the type of host lysozyme and the type of bacterial lysozyme inhibitor may affect bacterium-host interactions.
Thalassospira sp. Isolated from the Oligotrophic Eastern Mediterranean Sea Exhibits Chemotaxis toward Inorganic Phosphate during Starvation
Authors: Hütz Annemarie , Schubert Karin , Overmann Jörg
Published: May 2011

The eastern Mediterranean Sea represents an ultraoligotrophic environment where soluble phosphate limits the growth of bacterioplankton. Correspondingly, genes coding for high-affinity phosphate uptake systems and for organophosphonate utilization are highly prevalent in the plankton metagenome. Chemotaxis toward inorganic phosphate constitutes an alternative strategy to cope with phosphate limitation, but so far has only been demonstrated for two bacterial pathogens and an archaeon, and not in any free-living planktonic bacterium. In the present study, bacteria affiliated with the genus
Thalassospira
were found to constitute a regular, low-abundance member of the bacterioplankton that can be detected throughout the water column of the eastern Mediterranean Sea. A representative (strain EM) was isolated in pure culture and exhibited a strong positive chemotaxis toward inorganic phosphate that was induced exclusively in phosphate-starved cultures. Phosphate-depleted cells were 2-fold larger than in exponentially growing cultures, and 43% of the cells retained their motility even during prolonged starvation over 10 days. In addition,
Thalassospira
sp. strain EM was chemotactically attracted by complex substrates (yeast extract and peptone), amino acids, and 2-aminoethylphosphonate but not by sugar monomers. Similarly to the isolate from the eastern Mediterranean, chemotaxis toward phosphate was observed in starved cultures of the other two available isolates of the genus,
T. lucentensis
DSM 14000
T
and
T. profundimaris
WP0211
T
. Although
Thalassospira
sp. represents only up to 1.2% of the total bacterioplankton community in the water column of the eastern Mediterranean Sea, its chemotactic behavior potentially leads to an acceleration of nutrient cycling and may also explain the persistence of marine copiotrophs in this extremely nutrient-limited environment.
Dehydrogenase GRD1 Represents a Novel Component of the Cellulase Regulon in Trichoderma reesei (Hypocrea jecorina)
Authors: Schuster André , Kubicek Christian P. , Schmoll Monika
Published: May 2011

Trichoderma reesei
(
Hypocrea jecorina
) is nowadays the most important industrial producer of cellulase and hemicellulase enzymes, which are used for pretreatment of cellulosic biomass for biofuel production. In this study, we introduce a novel component, GRD1 (glucose-ribitol dehydrogenase 1), which shows enzymatic activity on cellobiose and positively influences cellulase gene transcription, expression, and extracellular endo-1,4-β-
d
-glucanase activity.
grd1
is differentially transcribed upon growth on cellulose and the induction of cellulase gene expression by sophorose. The transcription of
grd1
is coregulated with that of
cel7a
(
cbh1
) under inducing conditions. GRD1 is further involved in carbon source utilization on several carbon sources, such as those involved in lactose and
d
-galactose catabolism, in several cases in a light-dependent manner. We conclude that GRD1 represents a novel enhancer of cellulase gene expression, which by coregulation with the major cellulase may act via optimization of inducing mechanisms.
Shedding Light on Selenium Biomineralization: Proteins Associated with Bionanominerals
Authors: Lenz Markus , Kolvenbach Boris , Gygax Benjamin , Moes Suzette , Corvini Philippe F. X.
Published: May 2011

Selenium-reducing microorganisms produce elemental selenium nanoparticles with particular physicochemical properties due to an associated organic fraction. This study identified high-affinity proteins associated with such bionanominerals and with nonbiogenic elemental selenium. Proteins with an anticipated functional role in selenium reduction, such as a metalloid reductase, were found to be associated with nanoparticles formed by one selenium respirer,
Sulfurospirillum barnesii
.
Preferential Feeding by the Ciliates Chilodonella and Tetrahymena spp. and Effects of These Protozoa on Bacterial Biofilm Structure and Composition
Authors: Dopheide Andrew , Lear Gavin , Stott Rebecca , Lewis Gillian
Published: May 2011

Protozoa are important components of microbial food webs, but protozoan feeding preferences and their effects in the context of bacterial biofilms are not well understood. The feeding interactions of two contrasting ciliates, the free-swimming filter feeder
Tetrahymena
sp. and the surface-associated predator
Chilodonella
sp., were investigated using biofilm-forming bacteria genetically modified to express fluorescent proteins. According to microscopy, both ciliates readily consumed cells from both
Pseudomonas
costantinii
and
Serratia
plymuthica
biofilms. When offered a choice between spatially separated biofilms, each ciliate showed a preference for
P. costantinii
biofilms. Experiments with bacterial cell extracts indicated that both ciliates used dissolved chemical cues to locate biofilms.
Chilodonella
sp. evidently used bacterial chemical cues as a basis for preferential feeding decisions, but it was unclear whether
Tetrahymena
sp. did also. Confocal microscopy of live biofilms revealed that
Tetrahymena
sp. had a major impact on biofilm morphology, forming holes and channels throughout
S. plymuthica
biofilms and reducing
P. costantinii
biofilms to isolated, grazing-resistant microcolonies. Grazing by
Chilodonella
sp. resulted in the development of less-defined trails through
S. plymuthica
biofilms and caused
P. costantinii
biofilms to become homogeneous scatterings of cells. It was not clear whether the observed feeding preferences for spatially separated
P. costantinii
biofilms over
S. plymuthica
biofilms resulted in selective targeting of
P. costantinii
cells in mixed biofilms. Grazing of mixed biofilms resulted in the depletion of both types of bacteria, with
Tetrahymena
sp. having a larger impact than
Chilodonella
sp., and effects similar to those seen in grazed single-species biofilms.
Functional Characterization of a Mucus-Specific LPXTG Surface Adhesin from Probiotic Lactobacillus rhamnosus GG
Authors: von Ossowski Ingemar , Satokari Reetta , Reunanen Justus , Lebeer Sarah , De Keersmaecker Sigrid C. J. , Vanderleyden Jos , de Vos Willem M. , Palva Airi
Published: May 2011

In spite of the wealth of clinical evidence supporting the health benefits of
Lactobacillus rhamnosus
GG in humans, there is still a lack of understanding of the molecular mechanisms behind its probiosis. Current knowledge suggests that the health-promoting effects of this probiotic strain might be partly dependent on its persistence in the intestine and adhesion to mucosal surfaces. Moreover,
L. rhamnosus
GG contains mucus-binding pili that might also explain the occupation of its ecological niche as a comparatively less stringent allochthonous intestine-dwelling bacterium. To uncover additional surface proteins involved in mucosal adhesion, we investigated the adherence properties of the only predicted protein (LGG_02337) in
L. rhamnosus
GG that exhibits homology with a known mucus-binding domain. We cloned a recombinant form of the gene for this putative mucus adhesin and established that the purified protein readily adheres to human intestinal mucus. We also showed that this mucus adhesin is visibly distributed throughout the cell surface and participates in the adhesive interaction between
L. rhamnosus
GG and mucus, although less prominently than the mucus-binding pili in this strain. Based on primary structural comparisons, we concluded that the current annotation of the LGG_02337 protein likely does not accurately reflect its predicted properties, and we propose that this mucus-specific adhesin be called the mucus-binding factor (MBF). Finally, we interpret our results to mean that
L. rhamnosus
GG MBF, as an active mucus-specific surface adhesin with a presumed ancillary involvement in pilus-mediated mucosal adhesion, plays a part in the adherent mechanisms during intestinal colonization by this probiotic.
Development of a Streptomyces venezuelae-Based Combinatorial Biosynthetic System for the Production of Glycosylated Derivatives of Doxorubicin and Its Biosynthetic Intermediates
Authors: Han Ah Reum , Park Je Won , Lee Mi Kyeong , Ban Yeon Hee , Yoo Young Ji , Kim Eun Ji , Kim Eunji , Kim Byung-Gee , Sohng Jae Kyung , Yoon Yeo Joon
Published: May 2011

Doxorubicin, one of the most widely used anticancer drugs, is composed of a tetracyclic polyketide aglycone andl-daunosamine as a deoxysugar moiety, which acts as an important determinant of its biological activity. This is exemplified by the fewer side effects of semisynthetic epirubicin (4′-epi-doxorubicin). An efficient combinatorial biosynthetic system that can convert the exogenous aglycone ε-rhodomycinone into diverse glycosylated derivatives of doxorubicin or its biosynthetic intermediates, rhodomycin D and daunorubicin, was developed through the use ofStreptomyces venezuelaemutants carrying plasmids that direct the biosynthesis of different nucleotide deoxysugars and their transfer onto aglycone, as well as the postglycosylation modifications. This system improved epirubicin production from ε-rhodomycinone by selecting a substrate flexible glycosyltransferase, AknS, which was able to transfer the unnatural sugar donors and a TDP-4-ketohexose reductase, AvrE, which efficiently supported the biosynthesis of TDP-4-epi-l-daunosamine. Furthermore, a range of doxorubicin analogs containing diverse deoxysugar moieties, seven of which are novel rhodomycin D derivatives, were generated. This provides new insights into the functions of deoxysugar biosynthetic enzymes and demonstrates the potential of theS. venezuelae-based combinatorial biosynthetic system as a simple biological tool for modifying structurally complex sugar moieties attached to anthracyclines as an alternative to chemical syntheses for improving anticancer agents.
Spatiotemporal Changes in the Structure and Composition of a Less-Abundant Bacterial Phylum (Planctomycetes) in Two Perialpine Lakes
Authors: Pollet Thomas , Tadonléké Rémy D. , Humbert Jean François
Published: May 2011

We used fingerprinting and cloning-sequencing to study the spatiotemporal dynamics and diversity of
Planctomycetes
in two perialpine lakes with contrasting environmental conditions.
Planctomycetes
, which are less-abundant bacteria in freshwater ecosystems, appeared to be structured in the same way as the entire bacterial community in these ecosystems. They were more diversified and displayed fewer temporal variations in the hypolimnia than in the epilimnia. Like the more-abundant bacterial groups in aquatic systems,
Planctomycetes
communities seem to be composed of a very small number of abundant and widespread operational taxonomic units (OTUs) and a large number of OTUs that are present at low abundance. This indicates that the concept of “abundant or core” and “rare” bacterial phylotypes could also be applied to less-abundant freshwater bacterial phyla. The richness and diversity of
Planctomycetes
were mainly driven by pH and were similar in both of the lakes studied, whereas the composition of the
Planctomycetes
community seemed to be determined by a combination of factors including temperature, pH, and nutrients. The relative abundances of the dominant OTUs varied over time and were differently associated with abiotic factors. Our findings demonstrate that less-abundant bacterial phyla, such as
Planctomycetes
, can display strong spatial and seasonal variations linked to environmental conditions and suggest that their functional role in the lakes studied might be attributable mainly to a small number of phylotypes and vary over space and time in the water column.
Selection Pressure Required for Long-Term Persistence of
bla
CMY-2
-Positive IncA/C Plasmids
Authors: Subbiah Murugan , Top Eva M. , Shah Devendra H. , Call Douglas R.
Published: May 2011

Multidrug resistance
bla
CMY-2
plasmids that confer resistance to expanded-spectrum cephalosporins have been found in multiple bacterial species collected from different hosts worldwide. The widespread distribution of
bla
CMY-2
plasmids may be driven by antibiotic use that selects for the dissemination and persistence of these plasmids. Alternatively, these plasmids may persist and spread in bacterial populations in the absence of selection pressure if a balance exists among conjugative transfer, segregation loss during cell division, and fitness cost to the host. We conducted a series of experiments (both
in vivo
and
in vitro
) to study these mechanisms for three
bla
CMY-2
plasmids, peH4H, pAR060302, and pAM04528. Results of filter mating experiments showed that the conjugation efficiency of
bla
CMY-2
plasmids is variable, from <10
−7
for pAM04528 and peH4H to ∼10
−3
for pAR060302. Neither peH4H nor pAM04528 was transferred from
Escherichia coli
strain DH10B, but peH4H was apparently mobilized by the coresident trimethoprim resistance-encoding plasmid pTmpR. Competition studies showed that carriage of
bla
CMY-2
plasmids imposed a measurable fitness cost on the host bacteria both
in vitro
(0.095 to 0.25) and
in vivo
(dairy calf model). Long-term passage experiments in the absence of antibiotics demonstrated that plasmids with limited antibiotic resistance phenotypes arose, but eventually drug-sensitive, plasmid-free clones dominated the populations. Given that plasmid decay or loss is inevitable, we infer that some level of selection is required for the long-term persistence of
bla
CMY-2
plasmids in bacterial populations.
Impact of Medicated Feed on the Development of Antimicrobial Resistance in Bacteria at Integrated Pig-Fish Farms in Vietnam
Authors: Dang Son Thi Thanh , Petersen Andreas , Van Truong Dung , Chu Huong Thi Thanh , Dalsgaard Anders
Published: May 2011

Integrated livestock-fish aquaculture utilizes animal excreta, urine, and feed leftovers as pond fertilizers to enhance the growth of plankton and other microorganisms eaten by the fish. However, antimicrobial-resistant bacteria may be transferred and develop in the pond due to selective pressure from antimicrobials present in animal feed, urine, and feces. In an experimental pig-fish farm located in periurban Hanoi, Vietnam, nine piglets were provided feed containing 5 μg of tetracycline (TET)/kg pig weight/day and 0.45 μg of enrofloxacin (ENR)/kg pig weight/day during the second and fourth (last) months of the experiment. The aim of this study was to determine the association between the provision of pig feed with antimicrobials and the development of antimicrobial resistance, as measured in a total of 520
Escherichia coli
and 634
Enterococcus
strains isolated from pig manure and water-sediment pond samples. MIC values for nalidixic acid (NAL) and ENR showed that
E. coli
and
Enterococcus
spp. overall exhibited significant higher frequencies of resistance toward NAL and ENR during the 2 months when pigs were administered feed with antimicrobials, with frequencies reaching 60 to 80% in both water-sediment and manure samples. TET resistance for both indicators was high (>80%) throughout the study period, which indicates that TET-resistant
E. coli
and
Enterococcus
spp. were present in the piglets before the initiation of the experiment. PCR-based identification showed similar relative occurrences of
Enterococcus faecium
,
Enterococcus faecalis
, and other
Enterococcus
spp. in the water-sediment and manure samples, suggesting that
Enterococcus
spp. isolated in the ponds originated mainly from the pig manure. The development of antimicrobial resistance in integrated animal husbandry-fish farms and possible transfers and the impact of such resistance on food safety and human health should be further assessed.
Effect of Lactobacillus fermentum on Beta2 Toxin Production by Clostridium perfringens
Authors: Allaart Janneke G. , van Asten Alphons J. A. M. , Vernooij Johannes C. M. , Gröne Andrea
Published: May 2011

Clostridium perfringens
, although a member of the normal gut flora, is also an important cause of intestinal disease in animals and, to a lesser extent, in humans. Disease is associated with the production of one or more toxins, and little is known about environmental influences on the production of these toxins. One of the health-promoting effects of lactic acid bacteria (LAB) is the establishment and maintenance of a low pH in the intestine since an acidic environment inhibits the growth of many potentially harmful bacteria. Here, the effect of the LAB
Lactobacillus fermentum
on beta2 toxin production by
C. perfringens
is described. Coculturing of
C. perfringens
with
L. fermentum
showed that under
in vitro
conditions,
L. fermentum
was capable of silencing beta2 toxin production by
C. perfringens
without influencing bacterial viability. The reduction in toxin production was shown to be most likely a result of the decline in pH. Quantitative PCR showed that the reduction in beta2 toxin production was due to a decrease in
cpb2
mRNA. These results suggest that in the intestine, the production of beta2 toxin by
C. perfringens
might be regulated by other members of the normal intestinal flora.
Planktonic versus Biofilm Catabolic Communities: Importance of the Biofilm for Species Selection and Pesticide Degradation
Authors: Verhagen Pieter , De Gelder Leen , Hoefman Sven , De Vos Paul , Boon Nico
Published: May 2011

Chloropropham-degrading cultures were obtained from sludge and soil samples by using two different enrichment techniques: (i) planktonic enrichments in shaken liquid medium and (ii) biofilm enrichments on two types of solid matrixes (plastic chips and gravel). Denaturing gradient gel electrophoresis fingerprinting showed that planktonic and biofilm cultures had a different community composition depending on the presence and type of added solid matrix during enrichment. This was reflected in the unique chloropropham-degrading species that could be isolated from the different cultures. Planktonic and biofilm cultures also differed in chloropropham-degrading activity. With biofilm cultures, slower chloropropham removal was observed, but with less build-up of the toxic intermediate 3-chloroaniline. Disruption of the biofilm architecture resulted in degradation characteristics shifting toward those of the free suspensions, indicating the importance of a well-established biofilm structure for good performance. These results show that biofilm-mediated enrichment techniques can be used to select for pollutant-degrading microorganisms that like to proliferate in a biofilm and that cannot be isolated using conventional shaken-liquid procedures. Furthermore, the influence of the biofilm architecture on the pesticide degradation characteristics suggests that for bioaugmentation the use of biofilm catabolic communities might be a proficient alternative to using planktonic freely suspended cultures.
The Polyketide MPBD Initiates the SDF-1 Signaling Cascade That Coordinates Terminal Differentiation in Dictyostelium
Authors: Anjard Christophe , Su Yongxuan , Loomis William F.
Published: May 2011

Dictyostelium
uses a wide array of chemical signals to coordinate differentiation as it switches from a unicellular to a multicellular organism. MPBD, the product of the polyketide synthase encoded by
stlA
, regulates stalk and spore differentiation by rapidly stimulating the release of the phosphopeptide SDF-1. By analyzing specific mutants affected in MPBD or SDF-1 production, we delineated a signal transduction cascade through the membrane receptor CrlA coupled to Gα1, leading to the inhibition of GskA so that the precursor of SDF-1 is released. It is then processed by the extracellular protease of TagB on prestalk cells. SDF-1 apparently acts through the adenylyl cyclase ACG to activate the cyclic AMP (cAMP)-dependent protein kinase A (PKA) and trigger the production of more SDF-1. This signaling cascade shows similarities to the SDF-2 signaling pathway, which acts later to induce rapid spore encapsulation.
Age of Inoculum Strongly Influences Persister Frequency and Can Mask Effects of Mutations Implicated in Altered Persistence
Authors: Luidalepp Hannes , Jõers Arvi , Kaldalu Niilo , Tenson Tanel
Published: May 2011

The majority of cells transferred from stationary-phase culture into fresh medium resume growth quickly, while a few remain in a nongrowing state for longer. These temporarily nonproliferating bacteria are tolerant of several bactericidal antibiotics and constitute a main source of persisters. Several genes have been shown to influence the frequency of persisters in
Escherichia coli
, although the exact mechanism underlying persister formation is unknown. This study demonstrates that the frequency of persisters is highly dependent on the age of the inoculum and the medium in which it has been grown. The
hipA7
mutant had 1,000 times more persisters than the wild type when inocula were sampled from younger stationary-phase cultures. When started after a long stationary phase, the two displayed equal and elevated persister frequencies. The lower persister frequencies of
glpD
,
dnaJ
, and
surA
knockout strains were increased to the level of the wild type when inocula aged. The
mqsR
and
phoU
deletions showed decreased persister levels only when the inocula were from aged cultures, while
sucB
and
ygfA
deletions had decreased persister levels irrespective of the age of the inocula. A dependency on culture conditions underlines the notion that during screening for mutants with altered persister frequencies, the exact experimental details are of great importance. Unlike ampicillin and norfloxacin, which always leave a fraction of bacteria alive, amikacin killed all cells in the growth resumption experiment. It was concluded that the frequency of persisters depends on the conditions of inoculum cultivation, particularly its age, and the choice of antibiotic.
The xnp1 P2-Like Tail Synthesis Gene Cluster Encodes Xenorhabdicin and Is Required for Interspecies Competition
Authors: Morales-Soto Nydia , Forst Steven A.
Published: May 2011

Xenorhabdus nematophila
, the mutualistic bacterium of the nematode
Steinernema carpocapsae
, produces the R-type bacteriocin called xenorhabdicin, which is thought to confer a competitive advantage for growth in the insect host. We have identified a P2-like tail synthesis gene cluster (
xnp1
) that is required for xenorhabdicin production. The
xnp1
genes were expressed constitutively during growth and were induced by mitomycin C. Deletion of either the sheath (
xnpS1
) or fiber (
xnpH1
) genes eliminated xenorhabdicin production. Production of R-type bacteriocins in a host organism had not been shown previously. We show that xenorhabdicin is produced in the hemocoel of insects infected with the wild type but not with the Δ
xnpS1
deletion strain. Xenorhabdicin prepared from the wild-type strain killed the potential competitor
Photorhabdus luminescens
TT01.
P. luminescens
was eliminated during coculture with wild-type
X. nematophila
but not with the Δ
xnpS1
strain. Furthermore,
P. luminescens
inhibited reproduction of
S. carpocapsae
in insect larvae, while coinjection with wild-type
X. nematophila
, but not the Δ
xnpS1
, strain restored normal reproduction, demonstrating that xenorhabdicin was required for killing
P. luminescens
and protecting the nematode partner. Xenorhabdicin killed
X. nematophila
from
Steinernema anatoliense
, demonstrating for the first time that it possesses intraspecies activity. In addition, activity was variable against diverse strains of
Xenorhabdus
and
Photorhabdus
and was not correlated with phylogenetic distance. These findings are discussed in the context of the role of xenorhabdicin in the life cycle of the mutualistic bacterium
X. nematophila
.