bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘Downstream’ effects on the predicate in Functional Grammar clause derivations
Authors: CORNISH FRANCIS 
Published: October 2002

The article deals with the dynamic, retroactive effects within a clause derivation of
various ‘downstream’ specifications (that is, at subsequent levels in the derivation)
on the semantic structure and aspectual character of the predicator at the ‘nuclear’,
‘core’ and ‘extended’ predication layers within standard Functional Grammar
(Dik 1997a) – specifically, the insertion of given types of argument expressions within the predicate frame and the adjunction of certain semantically marked types of level 1 and level 2 satellites. A third type of retroactive effect is produced via the assignment or otherwise of the pragmatic function ‘Focus’ to the syntactic exponent of a predicate, which results in the singling out of a given part of the latter's semantic structure to act as a predicator.All these dynamic, retroactive effects on a predicator and the structures it projects assume
a semantically transparent underlying predicate structure on which to operate; yet in the
standard FG model, no such structure is available via the predicate frame, which forms the initial
structure for the derivation of a clause. The article demonstrates the drawbacks of the strict
separation of meaning definitions (lexical semantics) and predicate frames (semantically-based
syntax) within FG in terms, precisely, of the perspicuous mapping between syntax and semantics.
It proposes a semantically transparent alternative to the standard predicate frame, based on
Pustejovsky's (1995) ‘Generative Lexicon’ approach to lexico-semantic structure.
A Modern Tool for Classical Plant Growth Analysis
Authors: HUNT R. , CAUSTON D. R. , SHIPLEY B. , ASKEW A. P. 
Published: September 2002

Abstract
We present an all‐inclusive software tool for dealing with the essential core of mathematical and statistical calculations in plant growth analysis. The tool calculates up to six of the most fundamental growth parameters according to a purely ‘classical’ approach across one harvest‐interval. All of the estimates carry standard errors and 95 % confidence limits. The tool is written in Microsoft® Excel 2000 and is available free of charge for use in teaching and research from supplementary data.
Functional Expression of Enterobacterial O-Polysaccharide Biosynthesis Enzymes in
Bacillus subtilis
Authors: Schäffer Christina , Wugeditsch Thomas , Messner Paul , Whitfield Chris 
Published: September 2002

ABSTRACT

The expression of heterologous bacterial glycosyltransferases is of interest for potential application in the emerging field of carbohydrate engineering in gram-positive organisms. To assess the feasibility of using enzymes from gram-negative bacteria, the functional expression of the genes
wbaP
(formerly
rfbP
),
wecA
(formerly
rfe
), and
wbbO
(formerly
rfbF
) from enterobacterial lipopolysaccharide O-polysaccharide biosynthesis pathways was examined in
Bacillus subtilis
. WbaP and WecA are initiation enzymes for O-polysaccharide formation, catalyzing the transfer of galactosyl 1-phosphate from UDP-galactose and
N
-acetylglucosaminyl 1-phosphate from UDP-
N
-acetylglucosamine, respectively, to undecaprenylphosphate. The WecA product (undecaprenylpyrophosphoryl GlcNAc) is used as an acceptor to which the bifunctional
wbbO
gene product sequentially adds a galactopyranose and a galactofuranose residue from the corresponding UDP sugars to form a lipid-linked trisaccharide. Genes were cloned into the shuttle vectors pRB374 and pAW10. In
B. subtilis
hosts, the genes were effectively transcribed under the
vegII
promoter control of pRB374, but the plasmids were susceptible to rearrangements and deletion. In contrast, pAW10-based constructs, in which genes were cloned downstream of the
tet
resistance cassette, were stable but yielded lower levels of enzyme activity. In vitro glycosyltransferase assays were performed in
Escherichia coli
and
B. subtilis
, using membrane preparations as sources of enzymes and endogenous undecaprenylphosphate as an acceptor. Incorporation of radioactivity from UDP-α-
d
-
14
C-sugar into reaction products verified the functionality of WbaP, WecA, and WbbO in either host. Enzyme activities in
B. subtilis
varied between 20 and 75% of those measured in
E. coli.
Isolation and Characterization of a Freeze-Tolerant Diploid Derivative of an Industrial Baker's Yeast Strain and Its Use in Frozen Doughs
Authors: Teunissen Aloys , Dumortier Françoise , Gorwa Marie-Françoise , Bauer Jürgen , Tanghe An , Loïez Annie , Smet Peter , Van Dijck Patrick , Thevelein Johan M. 
Published: September 2002

ABSTRACT
The routine production and storage of frozen doughs are still problematic. Although commercial baker's yeast is highly resistant to environmental stress conditions, it rapidly loses stress resistance during dough preparation due to the initiation of fermentation. As a result, the yeast loses gassing power significantly during storage of frozen doughs. We obtained freeze-tolerant mutants of polyploid industrial strains following screening for survival in doughs prepared with UV-mutagenized yeast and subjected to 200 freeze-thaw cycles. Two strains in the S47 background with a normal growth rate and the best freeze tolerance under laboratory conditions were selected for production in a 20-liter pilot fermentor. Before frozen storage, the AT25 mutant produced on the 20-liter pilot scale had a 10% higher gassing power capacity than the S47 strain, while the opposite was observed for cells produced under laboratory conditions. AT25 also retained more freeze tolerance during the initiation of fermentation in liquid cultures and more gassing power during storage of frozen doughs. Other industrially important properties (yield, growth rate, nitrogen assimilation, and phosphorus content) were very similar. AT25 had only half of the DNA content of S47, and its cell size was much smaller. Several diploid segregants of S47 had freeze tolerances similar to that of AT25 but inferior performance for other properties, while an AT25-derived tetraploid, TAT25, showed only slightly improved freeze tolerance compared to S47. When AT25 was cultured in a 20,000-liter fermentor under industrial conditions, it retained its superior performance and thus appears to be promising for use in frozen dough production. Our results also show that a diploid strain can perform at least as well as a tetraploid strain for commercial baker's yeast production and usage.
Isolation of Elemental Sulfur as a Self-Growth-Inhibiting Substance Produced by
Legionella pneumophila
Authors: Inoue Hiroaki , Kawano Genji , Nagasawa Hiromichi , Sakuda Shohei 
Published: September 2002

ABSTRACT

The addition of HP-20 resin to a medium could enhance the growth of
Legionella
species. Elemental sulfur was isolated as a self-growth-inhibiting substance produced endogenously by
Legionella pneumophila
from methanol extracts of the resins used to culture the bacterium. Elemental sulfur shows strong growth-inhibiting activity toward all
Legionella
species tested.
The Exopolyphosphatase Gene from
Sulfolobus solfataricus
: Characterization of the First Gene Found To Be Involved in Polyphosphate Metabolism in
Archaea
Authors: Cardona Silvia T. , Chávez Francisco P. , Jerez Carlos A. 
Published: September 2002

ABSTRACT

Inorganic polyphosphate (polyP) polymers are widely distributed in all kinds of organisms. Although the presence of polyP in members of the domain
Archaea
has been described, at present nothing is known about the enzymology of polyP metabolism or the genes involved in this domain. We have cloned, sequenced, and overexpressed an exopolyphosphatase (PPX) gene (
ppx
) from thermophilic
Sulfolobus solfataricus
. The gene codes for a functional PPX and possesses an open reading frame for 417 amino acids (calculated mass, 47.9 kDa). The purified recombinant PPX was highly active, degrading long-chain polyP (700 to 800 residues) in vitro at 50 to 60°C. The putative PPXs present in known archaeal genomes showed the highest similarity to yeast PPXs. In contrast, informatic analysis revealed that the deduced amino acid sequence of
S. solfataricus
PPX showed the highest similarity (25 to 45%) to sequences of members of the bacterial PPXs, possessing all of their conserved motifs. To our knowledge, this is the first report of an enzyme characterized to be involved in polyP metabolism in members of the
Archaea
.
Characterization and Implications of the Cell Surface Reactivity of
Calothrix
sp. Strain KC97
Authors: Phoenix V. R. , Martinez R. E. , Konhauser K. O. , Ferris F. G. 
Published: September 2002

ABSTRACT

The cell surface reactivity of the cyanobacterium
Calothrix
sp. strain KC97, an isolate from the Krisuvik hot spring, Iceland, was investigated in terms of its proton binding behavior and charge characteristics by using acid-base titrations, electrophoretic mobility analysis, and transmission electron microscopy. Analysis of titration data with the linear programming optimization method showed that intact filaments were dominated by surface proton binding sites inferred to be carboxyl groups (acid dissociation constants [pK
a
] between 5.0 and 6.2) and amine groups (mean pK
a
of 8.9). Sheath material isolated by using lysozyme and sodium dodecyl sulfate generated pK
a
spectra similarly dominated by carboxyls (pK
a
of 4.6 to 6.1) and amines (pK
a
of 8.1 to 9.2). In both intact filaments and isolated sheath material, the lower ligand concentrations at mid-pK
a
values were ascribed to phosphoryl groups. Whole filaments and isolated sheath material displayed total reactive-site densities of 80.3 × 10
−5
and 12.3 × 10
−5
mol/g (dry mass) of cyanobacteria, respectively, implying that much of the surface reactivity of this microorganism is located on the cell wall and not the sheath. This is corroborated by electrophoretic mobility measurements that showed that the sheath has a net neutral charge at mid-pHs. In contrast, unsheathed cells exhibited a stronger negative-charge characteristic. Additionally, transmission electron microscopy analysis of ultrathin sections stained with heavy metals further demonstrated that most of the reactive binding sites are located upon the cell wall. Thus, the cell surface reactivity of
Calothrix
sp. strain KC97 can be described as a dual layer composed of a highly reactive cell wall enclosed within a poorly reactive sheath.
Bacterial Hemoglobins and Flavohemoglobins for Alleviation of Nitrosative Stress in
Escherichia coli
Authors: Frey Alexander D. , Farrés Judith , Bollinger Christian J. T. , Kallio Pauli T. 
Published: September 2002

ABSTRACT

Escherichia coli
MG1655 cells expressing novel bacterial hemoglobin and flavohemoglobin genes from a medium-copy-number plasmid were grown in shake flask cultures under nitrosative and oxidative stress.
E. coli
cells expressing these proteins display enhanced resistance against the NO
·
releaser sodium nitroprusside (SNP) relative to that of the control strain bearing the parental plasmid. Expression of bacterial hemoglobins originating from
Campylobacter jejuni
(CHb) and
Vitreoscilla
sp. (VHb) conferred resistance on SNP-challenged cells. In addition, it has been shown that NO
·
detoxification is also a common feature of flavohemoglobins originating from different taxonomic groups and can be transferred to a heterologous host. These observations have been confirmed in a specific in vitro NO
·
consumption assay. Protein extracts isolated from
E. coli
strains overexpressing flavohemoglobins consumed authentic NO
·
more readily than protein extracts from the wild-type strain. Oxidative challenge to the cells evoked nonuniform responses from the various cell cultures. Improved oxidative-stress-sustaining properties had also been observed when the flavohemoglobins from
E. coli
,
Klebsiella pneumoniae
,
Deinococcus radiodurans
, and
Pseudomonas aeruginosa
were expressed in
E. coli
.
Isolation and Identification of
Aspergillus fumigatus
Mycotoxins on Growth Medium and Some Building Materials
Authors: Nieminen Susanna M. , Kärki Riikka , Auriola Seppo , Toivola Mika , Laatsch Hartmut , Laatikainen Reino , Hyvärinen Anne , von Wright Atte 
Published: September 2002

ABSTRACT

Genotoxic and cytotoxic compounds were isolated and purified from the culture medium of an indoor air mold,
Aspergillus fumigatus
. One of these compounds was identified as gliotoxin, a known fungal secondary metabolite. Growth of
A. fumigatus
and gliotoxin production on some building materials were also studied. Strong growth of the mold and the presence of gliotoxin were detected on spruce wood, gypsum board, and chipboard under saturation conditions.
Glucose and Nutrient Concentrations Affect the Expression of a 104-Kilodalton
Listeria
Adhesion Protein in
Listeria monocytogenes
Authors: Jaradat Ziad W. , Bhunia Arun K. 
Published: September 2002

ABSTRACT

Growth media and environmental conditions influence the expression of adhesion and invasion proteins in
Listeria monocytogenes
. Here, the expression of the 104-kDa
Listeria
adhesion protein (LAP) was studied in nutrient-rich media (Trypticase soy broth [TSB] and brain heart infusion [BHI]), minimal medium (Luria-Bertani [LB]), or nutrient-deficient medium (peptone water [PW]) by immunoblotting, enzyme-linked immunosorbent assay (ELISA), and immunoelectron microscopy. Also, the effect of incorporating different concentrations of glucose on LAP expression was studied. Immunoblotting showed that LAP expression was at least twofold higher in LB medium than in TSB or BHI, while PW supported very poor cell growth and LAP expression. ELISA and immunoblotting results showed that higher concentrations of glucose (>1.6 g/liter) lowered the culture pH and suppressed LAP expression by more than 75%; however, the addition of K
2
HPO
4
reduced this effect.
L. monocytogenes
cells grown in LB media with lower concentrations of glucose showed higher adhesion to Caco-2 cells (3,716 and 4,186 cpm of attached bacteria for 0 and 0.2 g of glucose/liter, respectively), while
L. monocytogenes
cells grown in LB with higher glucose concentrations exhibited lower adhesion (2,126 and 2,221 cpm for 1.6 and 3.2 g of glucose/liter, respectively). A LAP-negative
L. monocytogenes
strain (A572) showed low adhesion profiles regardless of the amount of glucose added. Transmission electron microscopy revealed that LAP is localized mainly in the cytoplasm, with only a few molecules located on the cell surface. Growth in LB with high glucose (3.2 g/liter) showed the presence of only a few molecules in the cells, corroborating the results observed with ELISA or immunoblotting. In summary, nutrient-rich media and high concentrations of glucose suppressed LAP expression, which possibly is due to the changes in the pH of the media during growth from the accumulation of sugar fermentation by-products.
Inactivation of the Elongation Factor Tu by Mosquitocidal Toxin-Catalyzed Mono-ADP-Ribosylation
Authors: Schirmer Jörg , Wieden Hans-Joachim , Rodnina Marina V. , Aktories Klaus 
Published: September 2002

ABSTRACT

The mosquitocidal toxin (MTX) produced by
Bacillus sphaericus
strain SSII-1 is an ∼97-kDa single-chain toxin which contains a 27-kDa enzyme domain harboring ADP-ribosyltransferase activity and a 70-kDa putative binding domain. Due to cytotoxicity toward bacterial cells, the 27-kDa enzyme fragment cannot be produced in
Escherichia coli
expression systems. However, a nontoxic 32-kDa N-terminal truncation of MTX can be expressed in
E. coli
and subsequently cleaved to an active 27-kDa enzyme fragment. In vitro the 27-kDa enzyme fragment of MTX ADP-ribosylated numerous proteins in
E. coli
lysates, with dominant labeling of an ∼45-kDa protein. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry combined with peptide mapping identified this protein as the
E. coli
elongation factor Tu (EF-Tu). ADP ribosylation of purified EF-Tu prevented the formation of the stable ternary EF-Tuaminoacyl-tRNAGTP complex, whereas the binding of GTP to EF-Tu was not altered. The inactivation of EF-Tu by MTX-mediated ADP-ribosylation and the resulting inhibition of bacterial protein synthesis are likely to play important roles in the cytotoxicity of the 27-kDa enzyme fragment of MTX toward
E. coli
.
Diversity and Evolution of Hydrogenase Systems in Rhizobia
Authors: Baginsky Cecilia , Brito Belén , Imperial Juan , Palacios José-Manuel , Ruiz-Argüeso Tomás 
Published: September 2002

ABSTRACT

Uptake hydrogenases allow rhizobia to recycle the hydrogen generated in the nitrogen fixation process within the legume nodule. Hydrogenase (
hup
) systems in
Bradyrhizobium japonicum
and
Rhizobium leguminosarum
bv. viciae show highly conserved sequence and gene organization, but important differences exist in regulation and in the presence of specific genes. We have undertaken the characterization of
hup
gene clusters from
Bradyrhizobium
sp. (
Lupinus
),
Bradyrhizobium
sp. (
Vigna
), and
Rhizobium tropici
and
Azorhizobium caulinodans
strains with the aim of defining the extent of diversity in
hup
gene composition and regulation in endosymbiotic bacteria. Genomic DNA hybridizations using
hupS
,
hupE
,
hupUV
,
hypB
, and
hoxA
probes showed a diversity of intraspecific
hup
profiles within
Bradyrhizobium
sp. (
Lupinus
) and
Bradyrhizobium
sp. (
Vigna
) strains and homogeneous intraspecific patterns within
R. tropici
and
A. caulinodans
strains. The analysis also revealed differences regarding the possession of hydrogenase regulatory genes. Phylogenetic analyses using partial sequences of
hupS
and
hupL
clustered
R. leguminosarum
and
R. tropici hup
sequences together with those from
B. japonicum
and
Bradyrhizobium
sp. (
Lupinus
) strains, suggesting a common origin. In contrast,
Bradyrhizobium
sp. (
Vigna
)
hup
sequences diverged from the rest of rhizobial sequences, which might indicate that those organisms have evolved independently and possibly have acquired the sequences by horizontal transfer from an unidentified source.
Ammonia Production by Ruminal Microorganisms and Enumeration, Isolation, and Characterization of Bacteria Capable of Growth on Peptides and Amino Acids from the Sheep Rumen
Authors: Eschenlauer S. C. P. , McKain N. , Walker N. D. , McEwan N. R. , Newbold C. J. , Wallace R. J. 
Published: September 2002

ABSTRACT

Excessive NH
3
production in the rumen is a major nutritional inefficiency in ruminant animals. Experiments were undertaken to compare the rates of NH
3
production from different substrates in ruminal fluid in vitro and to assess the role of asaccharolytic bacteria in NH
3
production. Ruminal fluid was taken from four rumen-fistulated sheep receiving a mixed hay-concentrate diet. The calculated rate of NH
3
production from Trypticase varied from 1.8 to 19.7 nmol mg of protein
−1
min
−1
depending on the substrate, its concentration, and the method used. Monensin (5 μM) inhibited NH
3
production from proteins, peptides, and amino acids by an average of 28% with substrate at 2 mg/ml, compared to 48% with substrate at 20 mg/ml (
P =
0.011). Of the total bacterial population, 1.4% grew on Trypticase alone, of which 93% was eliminated by 5 μM monensin. Many fewer bacteria (0.002% of the total) grew on amino acids alone. Nineteen isolates capable of growth on Trypticase were obtained from four sheep. 16S ribosomal DNA and traditional identification methods indicated the bacteria fell into six groups. All were sensitive to monensin, and all except one group (group III, similar to
Atopobium minutum
), produced NH
3
at >250 nmol min
−1
mg of protein
−1
, depending on the medium, as determined by a batch culture method. All isolates had exopeptidase activity, but only group III had an apparent dipeptidyl peptidase I activity. Groups I, II, and IV were most closely related to asaccharolytic ruminal and oral
Clostridium
and
Eubacterium
spp. Group V comprised one isolate, similar to
Desulfomonas piger
(formerly
Desulfovibrio pigra
). Group VI was 95% similar to
Acidaminococcus fermentans.
Growth of the
Atopobium
- and
Desulfomonas
-like isolates was enhanced by sugars, while growth of groups I, II, and V was significantly depressed by sugars. This study therefore demonstrates that different methodologies and different substrate concentrations provide an explanation for different apparent rates of ruminal NH
3
production reported in different studies and identifies a diverse range of hyper-ammonia-producing bacteria in the rumen of sheep.
Biofilm Dispersal of
Neisseria subflava
and Other Phylogenetically Diverse Oral Bacteria
Authors: Kaplan Jeffrey B. , Fine Daniel H. 
Published: September 2002

ABSTRACT

Polystyrene petri dishes containing liquid medium were inoculated with single-cell suspensions of a fresh clinical isolate of
Neisseria subflava
and were incubated under conditions of low vibration.
N. subflava
colonies grew firmly attached to the surface of the dish, while the broth remained clear. Growing colonies released cells into the medium, resulting in the appearance of 10
2
to 10
4
small satellite colonies attached to the surface of the dish in an area adjacent to each mature colony after 24 h. Satellite colonies grew in patterns of streamers shaped like jets and flares emanating from mature colonies and pointing toward the center of the dish. This dispersal pattern evidently resulted from the surface translocation of detached biofilm cells by buoyancy-driven convection currents that were generated due to slight temperature gradients in the medium. Streamers of satellite colonies ranged from 2 to >40 mm in length. Satellite colonies in very long streamers were relatively uniform in size regardless of their distance from the mature colony, suggesting that mature colonies released single cells or small clusters of cells into the medium and that the detachment, surface translocation, and subsequent surface reattachment of released cells were a transitory process. Incubation of
N. subflava
single cells in a perfused biofilm fermentor resulted in a large spike of the number of CFU in the perfusate after 9.5 h of growth, consistent with a rapid release of cells into the medium. Biofilm colonies of several other phylogenetically diverse oral bacteria, including
Actinobacillus actinomycetemcomitans
,
Haemophilus aphrophilus
,
Streptococcus mitis
, and a prevalent but previously uncultured oral
Streptococcus
sp., exhibited similar temperature-dependent dispersal patterns in broth culture. This in vitro spreading phenotype could be a useful tool for studying biofilm dispersal in these and other nonflagellated bacteria and may have physiological relevance to biofilm dispersal in the oral cavity.
Mechanisms of Inactivation of Hepatitis A Virus by Chlorine
Authors: Li Jun Wen , Xin Zhong Tao , Wang Xin Wei , Zheng Jin Lai , Chao Fu Huan 
Published: September 2002

ABSTRACT
The study was intended to investigate the feasibility of reverse transcription-PCR (RT-PCR) for evaluation of the efficacy of inactivation of viruses in water and to elucidate the mechanisms of inactivation of hepatitis A virus (HAV) by chlorine. Cell culture, enzyme-linked immunosorbent assay, and long-overlap RT-PCR were used to detect the infectivity, antigenicity, and entire genome of HAV inactivated or destroyed by chlorine. The cell culture results revealed the complete inactivation of infectivity after 30 min of exposure to 10 or 20 mg of chlorine per liter and the highest level of sensitivity in the 5′ nontranslated regions (5′NTR), inactivation of which took as much time as the inactivation of infectivity of HAV by chlorine. However, antigenicity was not completely destroyed under these conditions. Some fractions in the coding region were resistant to chlorine. To determine the specific region of the 5′NTR lost, three segments of primers were redesigned to monitor the region from bp 1 to 1023 across the entire genome. It was shown that the sequence from bp 1 to 671 was the region most sensitive to chlorine. The results suggested that the inactivation of HAV by chlorine was due to the loss of the 5′NTR. It is believed that PCR can be used to assess the efficacy of disinfection of HAV by chlorine as well as to research the mechanisms of inactivation of viruses by disinfectants.