bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paenibacillus polymyxa
Invades Plant Roots and Forms Biofilms
Authors: Timmusk Salme , Grantcharova Nina , Wagner E. Gerhart H. 
Published: November 2005

ABSTRACT

Paenibacillus polymyxa
is a plant growth-promoting rhizobacterium with a broad host range, but so far the use of this organism as a biocontrol agent has not been very efficient. In previous work we showed that this bacterium protects
Arabidopsis thaliana
against pathogens and abiotic stress (S. Timmusk and E. G. H. Wagner, Mol. Plant-Microbe Interact.
12:
951-959, 1999; S. Timmusk, P. van West, N. A. R. Gow, and E. G. H. Wagner, p. 1-28,
in Mechanism of action of the plant growth promoting bacterium Paenibacillus polymyxa
, 2003). Here, we studied colonization of plant roots by a natural isolate of
P. polymyxa
which had been tagged with a plasmid-borne
gfp
gene. Fluorescence microscopy and electron scanning microscopy indicated that the bacteria colonized predominantly the root tip, where they formed biofilms. Accumulation of bacteria was observed in the intercellular spaces outside the vascular cylinder. Systemic spreading did not occur, as indicated by the absence of bacteria in aerial tissues. Studies were performed in both a gnotobiotic system and a soil system. The fact that similar observations were made in both systems suggests that colonization by this bacterium can be studied in a more defined system. Problems associated with green fluorescent protein tagging of natural isolates and deleterious effects of the plant growth-promoting bacteria are discussed.
Three Stages of a Biofilm Community Developing at the Liquid-Liquid Interface between Polychlorinated Biphenyls and Water
Authors: Macedo Alexandre José , Kuhlicke Ute , Neu Thomas R. , Timmis Kenneth N. , Abraham Wolf-Rainer 
Published: November 2005

ABSTRACT

Soil contaminated with polychlorinated biphenyls (PCB) was used as an inoculum to grow a complex biofilm community on PCB oil (Aroclor 1242) on a substratum (Permanox). The biofilm was monitored for 31 days by confocal laser scanning microscopy, community fingerprinting using single-strand conformational polymorphism (SSCP), amplicons of the 16S rRNA genes, and chemical analyses of the PCB congeners. SSCP analysis of the young biofilm revealed a rather diverse microbial community with species of the genera
Herbaspirillum
and
Bradyrhizobium
as dominant members. The biofilm developing on the PCB droplets displayed pronounced stages of PCB degradation and biofilm development not described before from pure-culture experiments. The first step was the colonization of the substratum while the PCB oil was hardly populated. When a certain density of bacteria was reached on the Permanox, the PCB was colonized, but soon the degradation of the congeners was markedly reduced and many cells were damaged, as seen by LIVE/DEAD staining. Finally, the biofilm formed aggregates and invaded the PCB oil, showing lower numbers of damaged cells than before and a dramatic increase in PCB degradation. This sequence of biofilm formation is understood as a maturation process prior to PCB oil colonization. This is followed by a thin biofilm on the PCB droplet, an aggregation process forming pockets in the PCB, and finally an invasion of the biofilm into the PCB oil. Only the mature biofilm showed degradation of pentachlorinated PCB congeners, which may be reductively dechlorinated and the resulting trichlorobiphenyls then aerobically metabolized.
Enzymatic and Genetic Characterization of Carbon and Energy Metabolisms by Deep-Sea Hydrothermal Chemolithoautotrophic Isolates ofEpsilonproteobacteria
Authors: Takai Ken , Campbell Barbara J. , Cary S. Craig , Suzuki Masae , Oida Hanako , Nunoura Takuro , Hirayama Hisako , Nakagawa Satoshi , Suzuki Yohey , Inagaki Fumio , Horikoshi Koki 
Published: November 2005

ABSTRACTThe carbon and energy metabolisms of a variety of cultured chemolithoautotrophicEpsilonproteobacteriafrom deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. All theEpsilonproteobacteriatested had all three key reductive tricarboxylic acid (rTCA) cycle enzymatic activities—ATP-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase—while they had no ribulose 1,5-bisphosphate carboxylase (RubisCO) activity, the key enzyme in the Calvin-Benson cycle. These results paralleled the successful amplification of the key rTCA cycle genesaclB,porAB, andoorABand the lack of success at amplifying the form I and II RubisCO genes,cbbLandcbbM. The combination of enzymatic and genetic analyses demonstrates that theEpsilonproteobacteriatested use the rTCA cycle for carbon assimilation. The energy metabolisms of deep-seaEpsilonproteobacteriawere also well specified by the enzymatic and genetic characterization: hydrogen-oxidizing strains had evident soluble acceptor:methyl viologen hydrogenase activity and hydrogen uptake hydrogenase genes (hynoperon), while sulfur-oxidizing strains lacked both the enzyme activity and the genes. Although the energy metabolism of reduced sulfur compounds was not genetically analyzed and was not fully clarified, sulfur-oxidizingEpsilonproteobacteriashowed enzyme activity of a potential sulfite:acceptor oxidoreductase for a direct oxidation pathway to sulfate but no activity of AMP-dependent adenosine 5′-phosphate sulfate reductase for a indirect oxidation pathway. No activity of thiosulfate-oxidizing enzymes was detected. The enzymatic and genetic characteristics described here were consistent with cellular carbon and energy metabolisms and suggest that molecular tools may have great potential for in situ elucidation of the ecophysiological roles of deep-seaEpsilonproteobacteria.
Catalyzed Reported Deposition-Fluorescence In Situ Hybridization Protocol To Evaluate Phagotrophy in Mixotrophic Protists
Authors: Medina-Sánchez Juan M. , Felip Marisol , Casamayor Emilio O. 
Published: November 2005

ABSTRACT

We describe a catalyzed reported deposition-fluorescence in situ hybridization (CARD-FISH) protocol particularly suited to assess the phagotrophy of mixotrophic protists on prokaryotes, since it maintains cell and plastid integrity, avoids cell loss and egestion of prey, and allows visualization of labeled prey against plastid autofluorescence. This protocol, which includes steps such as Lugol's-formaldehyde-thiosulfate fixation, agarose cell attachment, cell wall permeabilization with lysozyme plus achromopeptidase, and signal amplification with Alexa-Fluor 488, allowed us to detect almost 100% of planktonic prokaryotes (
Bacteria
and
Archaea
) and, for the first time, to show archaeal cells ingested by mixotrophic protists.
Investigation of
Oscillatoria spongeliae
-Dominated Bacterial Communities in Four Dictyoceratid Sponges
Authors: Ridley Christian P. , John Faulkner D. , Haygood Margo G. 
Published: November 2005

ABSTRACT

Certain species of marine sponges in the order
Dictyoceratida
harbor large populations of the cyanobacterial symbiont
Oscillatoria spongeliae
in the mesohyl (interior) of the sponge. We show that in four of these sponge species (
Lamellodysidea herbacea
,
Lamellodysidea chlorea
,
Lendenfeldia chondrodes
, and
Phyllospongia papyracea
) from Palau there is a consistent community of α-proteobacteria in addition to
O. spongeliae
that fall within the
Rhodobacter
group based on 16S rRNA gene analysis. Some of the α-proteobacteria in
Lendenfeldia chondrodes
and
P. papyracea
but not in the
Lamellodysidea
spp. contained site-specific insertions in the 16S rRNA gene. Reverse transcription-PCR experiments demonstrated that the largest insertion found in this study (63 bp) is present in the mature rRNA.
Lendenfeldia chondrodes
was the only sponge found to have another cyanobacterium in the tissue, a
Synechocystis
sp. We found that the
Synechocystis
sp. was present in both the pinacoderm (surface epithelial tissue) and mesohyl, in contrast to
O. spongeliae
, which was only found in the mesohyl through the use of specific fluorescence in situ hybridization experiments. Of the four sponge species, only
P. papyracea
was found to contain a significant number of γ-proteobacteria. These results demonstrate that
O. spongeliae
-dominated bacterial communities in different sponge species can vary considerably and increase our understanding of the bacterial communities found in marine invertebrates.
Diversity, Localization, and Physiological Properties of Filamentous Microbes Belonging toChloroflexiSubphylum I in Mesophilic and Thermophilic Methanogenic Sludge Granules
Authors: Yamada Takeshi , Sekiguchi Yuji , Imachi Hiroyuki , Kamagata Yoichi , Ohashi Akiyoshi , Harada Hideki 
Published: November 2005

ABSTRACTWe previously reported that the thermophilic filamentous anaerobeAnaerolinea thermophila, which is the first cultured representative of subphylum I of the bacterial phylumChloroflexi, not only was one of the predominant constituents of thermophilic sludge granules but also was a causative agent of filamentous sludge bulking in a thermophilic (55°C) upflow anaerobic sludge blanket (UASB) reactor in which high-strength organic wastewater was treated (Y. Sekiguchi, H. Takahashi, Y. Kamagata, A. Ohashi, and H. Harada, Appl. Environ. Microbiol. 67:5740-5749, 2001). To further elucidate the ecology and function ofAnaerolinea-type filamentous microbes in UASB sludge granules, we surveyed the diversity, distribution, and physiological properties ofChloroflexisubphylum I microbes residing in UASB granules. Five different types of mesophilic and thermophilic UASB sludge were used to analyze theChloroflexisubphylum I populations. 16S rRNA gene cloning-based analyses using a 16S rRNA gene-targetedChloroflexi-specific PCR primer set revealed that all clonal sequences were affiliated with theChloroflexisubphylum I group and that a number of different phylotypes were present in each clone library, suggesting the ubiquity and vast genetic diversity of these populations in UASB sludge granules. Subsequent fluorescence in situ hybridization (FISH) of the three different types of mesophilic sludge granules using aChloroflexi-specific probe suggested that all probe-reactive cells had a filamentous morphology and were widely distributed within the sludge granules. The FISH observations also indicated that theChloroflexisubphylum I bacteria were not always the predominant populations within mesophilic sludge granules, in contrast to thermophilic sludge granules. We isolated two mesophilic strains and one thermophilic strain belonging to theChloroflexisubphylum I group. The physiological properties of these isolates suggested that these populations may contribute to the degradation of carbohydrates and other cellular components, such as amino acids, in the bioreactors.
Design, Validation, and Application of a Seven-Strain
Staphylococcus aureus
PCR Product Microarray for Comparative Genomics
Authors: Witney Adam A. , Marsden Gemma L. , Holden Matthew T. G. , Stabler Richard A. , Husain Sarah E. , Vass J. Keith , Butcher Philip D. , Hinds Jason , Lindsay Jodi A. 
Published: November 2005

ABSTRACT

Bacterial comparative genomics has been revolutionized by microarrays, but the power of any microarray is dependent on the number and diversity of gene reporters it contains.
Staphylococcus aureus
is an important human pathogen causing a wide range of invasive and toxin-mediated diseases, and more than 20% of the genome of any isolate consists of variable genes. Seven whole-genome sequences of
S. aureus
are available, and we exploited this rare opportunity to design, build, and validate a comprehensive, nonredundant PCR product microarray carrying reporters that represent every predicted open reading frame (3,623 probes). Such a comprehensive microarray necessitated a novel design strategy. Validation with the seven sequenced strains showed correct identification of 93.9% of genes present or absent/divergent but was dependent on the method of analysis chosen. Microarray data were highly reproducible, reducing the need for many replicate slides. Interpretation of microarray data was enhanced by focusing on the major areas of variation—the presence or absence of mobile genetic elements (MGEs). We compiled “composite genomes” of every individual MGE and visualized their distribution. This allowed the sensitive discrimination of related isolates, including the first clear description of how isolates of the same clone of epidemic methicillin-resistant
S. aureus
differ substantially in their carriage of MGEs. These MGEs carry virulence and resistance genes, suggesting differences in pathogenic potential. The novel methods of design and interpretation of data generated from this microarray will enable further studies of
S. aureus
evolution, epidemiology, and pathogenesis.
Sulfate-Reducing Bacteria in Floating Macrophyte Rhizospheres from an Amazonian Floodplain Lake in Bolivia and Their Association with Hg Methylation
Authors: Achá Darío , Iñiguez Volga , Roulet Marc , Guimarães Jean Remy Davée , Luna Ruddy , Alanoca Lucia , Sanchez Samanta 
Published: November 2005

ABSTRACT

Five subgroups of sulfate-reducing bacteria (SRB) were detected by PCR in three macrophyte rhizospheres (
Polygonum densiflorum
,
Hymenachne donacifolia
, and
Ludwigia helminthorriza
) and three subgroups in
Eichhornia crassipes
from La Granja, a floodplain lake from the upper Madeira basin. The SRB community varied according to the macrophyte species but with different degrees of association with their roots. The rhizosphere of the C
4
plant
Polygonum densiflorum
had higher frequencies of SRB subgroups as well as higher mercury methylation potentials (27.5 to 36.1%) and carbon (16.06 ± 5.40%), nitrogen (2.03 ± 0.64%), Hg (94.50 ± 6.86 ng Hg g
−1
), and methylmercury (8.25 ± 1.45 ng Hg g
−1
) contents than the rhizosphere of the C
3
plant
Eichhornia crassipes
. Mercury methylation in
Polygonum densiflorum
and
Eichhornia crassipes
was reduced when SRB metabolism was inhibited by sodium molybdate.
On-Probe Sample Pretreatment for Direct Analysis of Lipids in Gram-Positive Bacterial Cells by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry
Authors: Ishida Yasuyuki , Kitagawa Kuniyuki , Nakayama Akihito , Ohtani Hajime 
Published: November 2005

ABSTRACT
On-probe sample pretreatment using trifluoroacetic acid as an additional reagent enabled the direct detection of phospholipids in whole bacteria by means of matrix-assisted laser desorption ionization mass spectrometry for not only gram-negative organisms but also gram-positive ones with a thicker peptidoglycan layer.
Cutinase-Like Enzyme from the Yeast
Cryptococcus
sp. Strain S-2 Hydrolyzes Polylactic Acid and Other Biodegradable Plastics
Authors: Masaki Kazuo , Kamini Numbi Ramudu , Ikeda Hiroko , Iefuji Haruyuki 
Published: November 2005

ABSTRACT

A purified lipase from the yeast
Cryptococcus
sp. strain S-2 exhibited remote homology to proteins belonging to the cutinase family rather than to lipases. This enzyme could effectively degrade the high-molecular-weight compound polylactic acid, as well as other biodegradable plastics, including polybutylene succinate, poly (ε-caprolactone), and poly(3-hydroxybutyrate).
Modeling Bacteriocin Resistance and Inactivation of
Listeria innocua
LMG 13568 by
Lactobacillus sakei
CTC 494 under Sausage Fermentation Conditions
Authors: Leroy Frédéric , Lievens Kristoff , De Vuyst Luc 
Published: November 2005

ABSTRACT

In mixed cultures, bacteriocin production by the sausage isolate
Lactobacillus sakei
CTC 494 rapidly inactivated sensitive
Listeria innocua
LMG 13568 cells, even at low bacteriocin activity levels. A small fraction of the listerial population was bacteriocin resistant. However, sausage fermentation conditions inhibited regrowth of resistant cells.
Representational Difference Analysis and Real-Time PCR for Strain-Specific Quantification of
Lactobacillus sobrius
sp. nov
Authors: Konstantinov Sergey R. , Smidt Hauke , de Vos Willem M. 
Published: November 2005

ABSTRACT

Lactobacillus sobrius
sp. nov., which was recently isolated from the intestine of weaning piglets, has potential probiotic properties. To follow the fate of
L. sobrius
strain 001
T
in dietary interventions, a novel and strain-specific quantitative detection procedure was developed. This procedure was based on the isolation of specific genomic fragments from the type strain by representational difference analysis and their detection by real-time PCR. The described strain-specific quantification approach may be used in studies aimed at tracking bacterial strains added to specific environments.
Heterogeneity of Putative Surface Layer Proteins in
Lactobacillus helveticus
Authors: Gatti Monica , Rossetti Lia , Fornasari Maria Emanuela , Lazzi Camilla , Giraffa Giorgio , Neviani Erasmo 
Published: November 2005

ABSTRACT

The S-layer-encoding genes of 21
Lactobacillus helveticus
strains were characterized. Phylogenetic analysis based on the identified S-layer genes revealed two main clusters, one which includes a sequence similar to that of the
slpH1
gene of
L. helveticus
CNRZ 892 and a second cluster which includes genes similar to that of
prtY
. These results were further confirmed by Southern blot hybridization. This study demonstrates S-layer gene variability in the species
L. helveticus
.
Metagenomic Analysis of the Microbial Community at Zodletone Spring (Oklahoma): Insights into the Genome of a Member of the Novel Candidate Division OD1
Authors: Elshahed Mostafa S. , Najar Fares Z. , Aycock Mandy , Qu Chunmei , Roe Bruce A. , Krumholz Lee R. 
Published: November 2005

ABSTRACT
A metagenomic library was constructed from the anaerobic sediments of a mesophilic sulfur spring. Thirty-five bacterial 16S rRNA gene-containing clones were identified in this library. Analysis of a genomic fragment belonging to candidate division OD1 provided useful insights into the physiology and biochemistry of this novel, yet-uncultured candidate division.
Bacteriocin (Mutacin) Production by
Streptococcus mutans
Genome Sequence Reference Strain UA159: Elucidation of the Antimicrobial Repertoire by Genetic Dissection
Authors: Hale John D. F. , Ting Yi-Tian , Jack Ralph W. , Tagg John R. , Heng Nicholas C. K. 
Published: November 2005

ABSTRACT

Streptococcus mutans
UA159, the genome sequence reference strain, exhibits nonlantibiotic mutacin activity. In this study, bioinformatic and mutational analyses were employed to demonstrate that the antimicrobial repertoire of strain UA159 includes mutacin IV (specified by the
nlm
locus) and a newly identified bacteriocin, mutacin V (encoded by SMU.1914c).
Trichosporon
Species Isolated from Guano Samples Obtained from Bat-Inhabited Caves in Japan
Authors: Sugita Takashi , Kikuchi Ken , Makimura Koichi , Urata Kensaku , Someya Takashi , Kamei Katsuhiko , Niimi Masakazu , Uehara Yoshimasa 
Published: November 2005

ABSTRACT

Yeasts from caves have rarely been examined. We examined yeasts collected from bat guano samples from 20 bat-inhabited limestone and volcanic caves located in 11 prefectures in Japan. Of ∼700 yeast-like colonies, nine
Trichosporon
species were recovered from 15 caves. Two of these were known species, and the remaining seven are potentially novel species, based on molecular phylogenetic analyses. In addition to
Trichosporon
species, identifiable strains of eight ascomycetous yeasts and one basidiomycetous yeast were recovered at frequencies of 5 to 35%. Our findings suggest that
Trichosporon
spp. are the major yeast species in bat guano in Japan and that bat guano is a potentially rich source of previously undescribed yeast species.
Human embryonic stem cell research debates: a Confucian argument
Authors: Tsai D F-C 
Published: November 2005

Human embryonic stem cell research can bring about major biomedical breakthroughs and thus contribute enormously to human welfare, yet it raises serious moral problems because it involves using human embryos for experiment. The “moral status of the human embryo” remains the core of such debates. Three different positions regarding the moral status of the human embryo can be categorised: the“all”position, the“none”position, and the“gradualist”position.The author proposes that the “gradualist” position is more plausible than the other two positions. Confucius’s moral principle ofjen, which proposes a unique theory of “love of gradation”, and the principle ofyi,which advocates “due treatment for persons”, are then explored. The author then argues that our moral obligations to do good to other living organisms, persons, and our families are different.Putting together the “gradualist” position on the human embryo, and Confucius’s theories of “love of gradation” and “due treatment for persons”, the author concludes that the early embryo has less ethical significance than the later fetus and adult human. The moral obligation we have toward persons is clearer and stronger than that which we have toward human embryos. Embryo research is justifiable if it brings enormous welfare to human persons that cannot be otherwise achieved. The “love of gradation” requires us, however, to extend love and respect towards other entities according to their different status. We should therefore be very cautious in using human embryos for research, acknowledging the gradualist nature of their moral status.
Les "anciens du peuple" et saül. Temps, espace et rite de passage dans Nombres xi et 1 Samuel x
Authors: Vartejanu-Joubert Madalina 
Published: November 2005

AbstractThis article analyses the cultural criteria of « time » and « space » as involving in the « rituel de passage » and the way they control its outcome. We focuse on two biblical passages, Numbers xi and 1 Samuel x, which both describe the accession of the individual to a new function and the anomalies related to this change of personnality. Reading in those texts the description of a « rituel de passgae » we interpret the mention of « prophecy » as representing the « ritual mark » through which the novice accomplishes his « rebrith ».
Genre disputes and communal accusatory laments: reflections on the genre of psalm lxxxix
Authors: Mitchell Matthew W. 
Published: November 2005

AbstractPsalm lxxxix has been the subject of numerous debates. Scholars have variously described it as a royal psalm, a lament, a prophetic complaint, or some combination of these genres. Genre designation is further complicated by the harsh tone of verses 39-52, traditionally explained as a redactional addition. This paper argues that Psalm lxxxix displays a marked unity through its use of covenantal, Davidic and symbolic language, and finds further clues to the psalm's genre in a Qûmran fragment (4Q236). Psalm lxxxix can still be defined as a "lament," but as fragment 4Q236 shows, it is an angry lament in which accusatory language serves as a unifying element rather than a redactional "seam".
Isaiah xxvii 7 and intertextual discourse about 'striking' in the book of Isaiah
Authors: Hibbard J. Todd 
Published: November 2005

AbstractIsaiah xxvii 7 is widely regarded as one of the most obscure verses in Isaiah xxiv-xxvii, one of the latest additions to the book. After briefly dealing with the verse's syntactical issues, this article seeks to address the question of the verse's meaning using an intertextual approach. I argue that the first half of the verse evokes other texts in Isaiah about "striking", a theme introduced in the first chapter (i 5-6) and developed through Isaiah. Understood as part of an inner-Isaianic textual development, the verse makes the point that Israel has not been struck like the one who struck it (Assyria). The second half of xxvii 7, which uses the idea of "killing", makes a more immediate intertextual connection with xxvi 21. The article concludes by noting that viewed against this intertextual backdrop, the verse offers a further elaboration of xxvii 2-5(6) which depict YHWH's vineyard.