bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Statistical Control Charts to Analyze Data from Student Evaluations of Teaching
Authors: Marks and Neil B. , O'Connell Richard T. 
Published: December 2003

ABSTRACTIn this paper, a method for analyzing data from student evaluations of teaching is presented. The first step of the process requires development of a regression model for teacher's summary rating as a function of student's expected grade. Then, two‐sigma control charts for individual evaluation scores (section averages) and residuals from the regression model are used to identify both excellent and poor outcomes. The performance of an individual whose scores are out of control on both charts cannot be explained by expected grade and therefore is worthy of note.
TradeSmith: An Exercise to Demonstrate the Illusion of Control in Decision Making
Authors: Martz Ben , Neil Thomas C. , Biscaccianti Alessandro 
Published: December 2003

ABSTRACTResource allocation decisions are a fundamental class of problems common throughout a business and therefore are found throughout business school curricula. Entrepreneurs must allocate capital, financiers must allocation cash, and production managers must create the best mix of multiple‐use resources. Within this context, a business school's curriculum, instructional materials, and learning processes must consider the implications of individual decision making. Our traditional instructional content and delivery methods may effectively teach how to set up a decision “problem” and how to obtain an optimal answer. Yet, we may not be teaching a key underlying factor: that entrepreneurs, managers, and future leaders appear to have implicit cognitive biases, which discount information and skew individual decision making. The results of this study demonstrate that a phenomenon known as the “illusion of control” presents a fundamental challenge to the efficacy of formalized educational programs on decision making. TradeSmith was designed as a problem‐based learning exercise to elicit for the illusion of control in a basic, resource allocation, decision environment. The subjects in this study demonstrate a decision‐making pattern consistent with the “illusion of control” phenomenon. Finally, by revealing individuals' implicit design‐making paradigms, TradeSmith helps them experience key issues for managerial decision making.
Physiological and Community Responses of EstablishedGrassland Bacterial Populations to WaterStress
Authors: Griffiths Robert I. , Whiteley Andrew S. , O'Donnell Anthony G. , Bailey Mark J. 
Published: December 2003

ABSTRACT
The
effects of water stress upon the diversity and culturable activity of
bacterial communities in the rhizosphere of an established upland
grassland soil have been investigated. Intact monoliths were subjected
to different watering regimens over a 2-month period to study community
adaptation to moisture limitation and subsequent response to stress
alleviation following rewetting. Genetic diversity was analyzed with
16S-based denaturing gradient gel electrophoresis (DGGE) of total
soil-extracted DNA (rRNA genes) and RNA (rRNA transcripts) in an
attempt to discriminate between total and active communities.
Physiological response was monitored by plate counts, total counts, and
BIOLOG-GN2 substrate utilization analyses. Controlled soil drying
decreased the total number of CFU on all the media tested and also
decreased the substrate utilization response. Following rewetting of
dried soil, culture-based analyses indicated physiological recovery of
the microbial population by the end of the experiment. In contrast,
DGGE analyses of community 16S rRNA genes, rRNA transcripts and
cultured communities did not reveal any changes relating to the
moisture regimens, despite the observed physiological effects. We
conclude that the imposed moisture regimen modulated the physiological
status of the bacterial community and that bacterial communities in
this soil are resistant to water stress. Further, we highlight the need
for a reexamination of rRNA transcript-based molecular profiling
techniques as a means of describing the active component of soil
bacterial
communities.
Cloning, Expression, and Cell Surface Localization of
Paenibacillus
sp. Strain W-61 Xylanase 5, a Multidomain Xylanase
Authors: Ito Yasuko , Tomita Toshio , Roy Narayan , Nakano Akito , Sugawara-Tomita Noriko , Watanabe Seiji , Okai Naoko , Abe Naoki , Kamio Yoshiyuki 
Published: December 2003

ABSTRACT

We
have shown that a xylan-degrading bacterium, W-61, excretes multiple
xylanases, including xylanase 5 with a molecular mass of 140 kDa. Here,
we emend the previously used classification of the bacterium (i.e.,
Aeromonas caviae
W-61) to
Paenibacillus
sp. strain
W-61 on the basis of the nucleotide sequence of the 16S rRNA gene, and
we clone and express the
xyn5
gene encoding xylanase 5 (Xyn5)
in
Escherichia coli
and study the subcellular localization of
Xyn5.
xyn5
encodes 1,326 amino acid residues, including a
27-amino-acid signal sequence. Sequence analysis indicated that Xyn5
comprises two family 22 carbohydrate-binding modules (CBM), a family 10
catalytic domain of glycosyl hydrolases, a family 9 CBM, a domain
similar to the lysine-rich region of
Clostridium thermocellum
SdbA, and three S-layer-homologous (SLH) domains. Recombinant Xyn5
bound to a crystalline cellulose, Avicel PH-101, while an N-terminal
90-kDa fragment of Xyn5, which lacks the C-terminal half of the family
9 CBM, did not bind to Avicel PH-101. Xyn5 was cell bound, and the
cell-bound protein was digested by exogenous trypsin to produce
immunoreactive and xylanolytic fragments with molecular masses of 80
and 60 kDa. Xyn5 was exclusively distributed in the cell envelope
fraction consisting of a peptidoglycan-containing layer and an
associated S layer. Thus,
Paenibacillus
sp. strain W-61 Xyn5
is a cell surface-anchored modular xylanase possessing a functional
cellulose-binding module and SLH domains. Possible
cooperative action of multiple xylanases produced by strain W-61 is
discussed on the basis of the modular structure of
Xyn5.
Improvementof Foreign-Protein Production in
Aspergillus niger
var.
awamori
by Constitutive Induction of the Unfolded-ProteinResponse
Authors: Valkonen Mari , Ward Michael , Wang Huaming , Penttilä Merja , Saloheimo Markku 
Published: December 2003

ABSTRACT

Unfolded-protein
response (UPR) denotes the upregulation of endoplasmic reticulum
(ER)-resident chaperone and foldase genes and numerous
other genes involved in secretory functions during the accumulation of
unfolded proteins into the ER. Overexpression of individual foldases
and chaperones has been used in attempts to improve protein production
in different production systems. We describe here a novel strategy to
improve foreign-protein production. We show that the constitutive
induction of the UPR pathway in
Aspergillus niger
var.
awamori
can be achieved by expressing the activated form of
the transcription factor
hacA
. This induction enhances the
production of
Trametes versicolor
laccase by up to sevenfold
and of bovine preprochymosin by up to 2.8-fold in this biotechnically
important fungus. The regulatory range of UPR was studied by analyzing
the mRNA levels of novel
A. niger
var.
awamori
genes
involved in different secretory functions. This revealed both
similarities and differences to corresponding studies in
Saccharomyces
cerevisiae
.
Investigation of Protein Export in
Bifidobacteriumbreve
UCC2003
Authors: MacConaill Laura E. , Fitzgerald Gerald F. , van Sinderen Douwe 
Published: December 2003

ABSTRACT

The
molecular interactions between the bifidobacterial cell and its natural
environment, namely, the gastrointestinal tract of its host, are
particularly important in understanding the presumed positive effects
of
Bifidobacterium
on the health status of the host. In this
study an export-specific reporter system, designed for use in
gram-positive organisms and based on the use of the staphylococcal
nuclease (Nuc) as a reporter, was employed to identify exported
proteins in
Bifidobacterium breve
UCC2003. A
B. breve
genomic library of translational fusions to the Nuc-encoding gene
devoid of its own export signal was established in the shuttle vector
pFUN (I. Poquet, S. D. Ehrlich, and A. Gruss, J. Bacteriol.
180:
1904-1912, 1998) and screened for bifidobacterial
export signals. Sequence analysis of the fusion proteins obtained that
displayed a nuclease-producing phenotype in both
Lactococcus
lactis
and
B. breve
predicted the presence of a classical
signal peptide and/or single or multiple transmembrane domains, thus
indicating that some of the export signals in
B. breve
are
comparable to those used in
L. lactis
. Cell fractionation
studies, zymograms, nuclease assays, and Western blotting were employed
to confirm the function of the predicted signals and to determine the
location and activity of the exported fusion proteins in
B.
breve
and/or
L.
lactis
.
Identification and Distribution of Insertion Sequences of
Paracoccus solventivorans
Authors: Bartosik Dariusz , Szymanik Michal , Baj Jadwiga 
Published: December 2003

ABSTRACT

Three
novel insertion sequences (ISs) (IS
Pso1
, IS
Pso2
, and
IS
Pso3
) of the soil bacterium
Paracoccus
solventivorans
DSM 11592 were identified by transposition into
entrapment vector pMEC1. IS
Pso1
(1,400 bp) carries one large
open reading frame (ORF) encoding a putative basic protein (with a DDE
motif conserved among transposases [Tnps] of elements
belonging to the IS
256
family) with the highest levels of
similarity with the hypothetical Tnps of
Rhodospirillum rubrum
and
Sphingopyxis macrogoltabida
. IS
Pso2
(832 bp)
appeared to be closely related to IS
Ppa2
of
Paracoccus
pantotrophus
DSM 11072 and IS
1248
of
Paracoccus
denitrificans
PdX22, both of which belong to the IS
427
group (IS
5
family). These elements contain two overlapping
ORFs and a putative frameshift motif (AAAAG) responsible for production
of a putative transframe Tnp. IS
Pso3
(1,286 bp) contains a
single ORF, whose putative product showed homology with Tnps of ISs
classified as members of a distinct subgroup of the IS
5
group
of the IS
5
family. The highest levels of similarity were
observed with IS
Ssp126
of
Sphingomonas
sp. and
IS
1169
of
Bacteroides fragilis
. Analysis of the
distribution of ISs of
P. solventivorans
revealed that
IS
Pso2
-like elements are the most widely spread of the
elements in nine species of the genus
Paracoccus
.
IS
Pso1
and IS
Pso3
are present in only a few
paracoccal strains, which suggests that they were acquired by lateral
transfer. Phylogenetic analysis of Tnps of the novel ISs and their
closest relatives showed their evolutionary relationships and possible
directions of lateral transfer between various bacterial
hosts.
Nitrate/NitriteAssimilation System of the Marine Picoplanktonic Cyanobacterium
Synechococcus
sp. Strain WH 8103: Effect of NitrogenSource and Availability on GeneExpression
Authors: Bird Clare , Wyman Michael 
Published: December 2003

ABSTRACT

The
genes encoding the structural components of the nitrate/nitrite
assimilation system of the oceanic cyanobacterium
Synechococcus
sp. strain WH 8103 were cloned and
characterized. The genes encoding nitrate reductase (
narB
) and
nitrite reductase (
nirA
) are clustered on the chromosome but
are organized in separate transcriptional units. Upstream of
narB
is a homologue of
nrtP
that encodes a
nitrate/nitrite-bispecific permease rather than the components of an
ABC-type nitrate transporter found in freshwater cyanobacteria.
Unusually, neither
nirA
nor
ntcA
(encoding a positive
transcription factor of genes subject to nitrogen control) were found
to be tightly regulated by ammonium. Furthermore, transcription of
glnA
(encoding glutamine synthetase) is up-regulated in
ammonium-grown cells, highlighting significant differences in nitrogen
control in this cyanobacterium. Nitrogen depletion led to the transient
up-regulation of
ntcA
,
nirA
,
nrtP
,
narB
, and
glnA
in what appears to be an
NtcA-dependent manner. The NtcA-like promoters found upstream of
nirA
,
nrtP
, and
narB
all differ in sequence
from the canonical NtcA promoter established for other cyanobacteria,
and in the case of
nirA
, the NtcA-like promoter was functional
only in cells deprived of combined nitrogen. The ecological
implications of these findings are discussed in the context of the
oligotrophic nature of oceanic surface waters in which
Synechococcus
spp.
thrive.
Carbon Source-Induced Modifications in the MycolicAcid Content and Cell Wall Permeability of
Rhodococcuserythropolis
E1
Authors: Sokolovská Ivana , Rozenberg Raoul , Riez Christophe , Rouxhet Paul G. , Agathos Spiros N. , Wattiau Pierre 
Published: December 2003

ABSTRACT

The
influence of the carbon source on cell wall properties was analyzed in
an efficient alkane-degrading strain of
Rhodococcus
erythropolis
(strain E1), with particular focus on the mycolic
acid content. A clear correlation was observed between the carbon
source and the mycolic acid profiles as estimated by high-performance
liquid chromatography and mass spectrometry. Two types of mycolic acid
patterns were observed after growth either on saturated linear alkanes
or on short-chain alkanoates. One type of pattern was characterized by
the lack of odd-numbered carbon chains and resulted from growth on
linear alkanes with even numbers of carbon atoms. The second type of
pattern was characterized by mycolic acids with both even- and
odd-numbered carbon chains and resulted from growth on compounds with
odd-numbered carbon chains, on branched alkanes, or on mixtures of
different compounds. Cellular short-chain fatty acids were twice as
abundant during growth on a branched alkane (pristane) as during growth
on acetate, while equal amounts of mycolic acids were found under both
conditions. More hydrocarbon-like compounds and less polysaccharide
were exposed at the cell wall surface during growth on alkanes.
Whatever the substrate, the cells had the same affinity for
aqueous-nonaqueous solvent interfaces. By contrast, bacteria displayed
completely opposite susceptibilities to hydrophilic and hydrophobic
antibiotics and were found to be strongly stained by hydrophobic dyes
after growth on pristane but not after growth on acetate. Taken
together, these data show that the cell wall composition of
R.
erythropolis
E1 is influenced by the nutritional regimen and that
the most marked effect is a radical change in cell wall
permeability.
Shigella dysenteriae
Type 1-SpecificBacteriophage from Environmental Waters inBangladesh
Authors: Faruque Shah M. , Chowdhury Nityananda , Khan Rasel , Hasan M. Rubayet , Nahar Jebun , Islam M. Johirul , Yamasaki Shinji , Ghosh A. N. , Nair G. Balakrish , Sack David A. 
Published: December 2003

ABSTRACT

Shigella
dysenteriae
type 1 is the causative agent of the most severe form
of bacillary dysentery, which occurs as epidemics in many developing
countries. We isolated a bacteriophage from surface water samples from
Bangladesh that specifically lyses strains of
S. dysenteriae
type 1. This phage, designated SF-9, belongs to the
Podoviridae
family and has a 41-kb double-stranded DNA genome.
Further screening of water samples for the prevalence of the phage
revealed 9 of 71 (12.6%) water samples which were positive for
the phage. These water samples were also positive in PCR assays for one
or more
S. dysenteriae
type 1-specific genes, including
ipaBCD
and
stx1
, and live
S. dysenteriae
type 1 was isolated from three phage-positive samples. The results of
this study suggest that phage SF-9 may have epidemiological
applications in tracing the presence of
S. dysenteriae
type 1
in environmental
waters.
Compatible Solutes Protect against Chaotrope(Ethanol)-Induced, Nonosmotic WaterStress
Authors: Hallsworth John E. , Prior Bernard A. , Nomura Yoshiyuki , Iwahara Masayoshi , Timmis Kenneth N. 
Published: December 2003

ABSTRACT

Water
stress is one of the major stresses experienced by cellular systems and
can take a number of distinct forms. In response to turgor-related
osmotic stress, cells produce compatible solutes that are macromolecule
protectants and also counteract the outflow of water from stressed
cells. In this report we show that the germination of conidia of
Aspergillus nidulans
, a sensitive indicator of water stress,
in the presence of ethanol is correlated with the intracellular
concentration of the compatible solutes glycerol and erythritol, which
protect against both osmotic and nonturgor forms of water
stress.
Role of Soil pH in the Development of EnhancedBiodegradation ofFenamiphos
Authors: Singh Brajesh K. , Walker Allan , Morgan J. Alun W. , Wright Denis J. 
Published: December 2003

ABSTRACT

Repeated
treatment with fenamiphos (ethyl 4-methylthio-
m
-tolyl
isopropylphosphoramidate) resulted in enhanced biodegradation of this
nematicide in two United Kingdom soils with a high pH (≥7.7).
In contrast, degradation of fenamiphos was slow in three acidic United
Kingdom soils (pH 4.7 to 6.7), and repeated treatments did not result
in enhanced biodegradation. Rapid degradation of fenamiphos was
observed in two Australian soils (pH 6.7 to 6.8) in which it was no
longer biologically active against plant nematodes. Enhanced degrading
capability was readily transferred from Australian soil to United
Kingdom soils, but only those with a high pH were able to maintain this
capability for extended periods of time. This result was confirmed by
fingerprinting bacterial communities by 16S rRNA gene profiling of
extracted DNA. Only United Kingdom soils with a high pH retained
bacterial DNA bands originating from the fenamiphos-degrading
Australian soil. A degrading consortium was enriched from the
Australian soil that utilized fenamiphos as a sole source of carbon.
The 16S rRNA banding pattern (determined by denaturing gradient gel
electrophoresis) from the isolated consortium migrated to the same
position as the bands from the Australian soil and those from the
enhanced United Kingdom soils in which the Australian soil had been
added. When the bands from the consortium and the soil were sequenced
and compared they showed between 97 and 100% sequence identity,
confirming that these groups of bacteria were involved in degrading
fenamiphos in the soils. The sequences obtained showed similarity to
those from the genera
Pseudomonas
,
Flavobacterium
,
and
Caulobacter
. In the Australian soils, two different
degradative pathways operated simultaneously: fenamiphos was converted
to fenamiphos sulfoxide (FSO), which was hydrolyzed to the
corresponding phenol (FSO-OH) or was hydrolyzed directly to fenamiphos
phenol. In the United Kingdom soils in which enhanced degradation had
been induced, fenamiphos was oxidized to FSO and then hydrolyzed to
FSO-OH, but direct conversion to fenamiphos phenol did not
occur.
Molecular Characterization of Community Structures and Sulfur Metabolism within Microbial Streamers in Japanese Hot Springs
Authors: Nakagawa Tatsunori , Fukui Manabu 
Published: December 2003

ABSTRACT

Community
structures of submerged microbial slime streamers (SMSS) in
sulfide-containing hot springs at 72 to 80°C at Nakabusa and
Yumata, Japan, were investigated by molecular analysis based on the 16S
rRNA gene. The SMSS were classified into two consortia; consortium I
occurred at lower levels of sulfide in the hot springs (less than 0.1
mM), and consortium II dominated when the sulfide levels were higher
(more than 0.1 mM). The dominant cell morphotypes in consortium I were
filamentous and small rod-shaped cells. The filamentous cells
hybridized with fluorescent oligonucleotide probes for the domain
Bacteria
, the domain
Archaea
, and the family
Aquificaceae
. Our analysis of the denaturing gradient gel
electrophoresis (DGGE) bands by using reverse transcription (RT)-PCR
amplification with two primer sets (Eub341-F with the GC clamp and
Univ907R for the
Bacteria
and Eub341-F with the GC clamp and
Arch915R) indicated that dominant bands were phylogenetically related
to microbes in the genus
Aquifex
. On the other hand,
consortium II was dominated by long, small, rod-shaped cells, which
hybridized with the oligonucleotide probe S-*-Tdes-0830-a-A-20
developed in this study for the majority of as-yet-uncultivated
microbes in the class
Thermodesulfobacteria
. The dominant DGGE
band obtained by PCR and RT-PCR was affiliated with the genus
Sulfurihydrogenibium
. Moreover, our analysis of dissimilatory
sulfite reductase (DSR) gene sequences retrieved from both consortia
revealed a high frequency of DSR genes corresponding to the DSR of
Thermodesulfobacteria
-like microorganisms. Using both sulfide
monitoring and
35
SO
4
2−
tracer
experiments, we observed microbial sulfide production and consumption
by SMSS, suggesting that there is in situ sulfide production by
as-yet-uncultivated
Thermodesulfobacteria
-like microbes and
there is in situ sulfide consumption by
Sulfurihydrogenibium
-like microbes within the SMSS in the
Nakabusa and Yumata hot
springs.
Linked Redox Precipitation of Sulfur and Seleniumunder Anaerobic Conditions by Sulfate-Reducing BacterialBiofilms
Authors: Hockin Simon L. , Gadd Geoffrey M. 
Published: December 2003

ABSTRACT

A
biofilm-forming strain of sulfate-reducing bacteria (SRB), isolated
from a naturally occurring mixed biofilm and identified by 16S rDNA
analysis as a strain of
Desulfomicrobium norvegicum
, rapidly
removed 200 μM selenite from solution during growth on lactate
and sulfate. Elemental selenium and elemental sulfur were precipitated
outside SRB cells. Precipitation occurred by an abiotic reaction with
bacterially generated sulfide. This appears to be a generalized ability
among SRB, arising from dissimilatory sulfide biogenesis, and can take
place under low redox conditions and in the dark. The reaction
represents a new means for the deposition of elemental sulfur by SRB
under such conditions. A combination of transmission electron
microscopy, environmental scanning electron microscopy, and cryostage
field emission scanning electron microscopy were used to reveal the
hydrated nature of SRB biofilms and to investigate the location of
deposited sulfur-selenium in relation to biofilm elements. When
pregrown SRB biofilms were exposed to a selenite-containing medium,
nanometer-sized selenium-sulfur granules were precipitated within the
biofilm matrix. Selenite was therefore shown to pass through the
biofilm matrix before reacting with bacterially generated sulfide. This
constitutes an efficient method for the removal of toxic concentrations
of selenite from solution. Implications for environmental cycling and
the fate of sulfur and selenium are discussed, and a general model for
the potential action of SRB in selenium transformations is
presented.