bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased gelling agent concentration promotes somatic embryo maturation in hybrid larch (Larix×eurolepsis): a 2‐DE proteomic analysis
Authors: Teyssier Caroline , Grondin Cécile , Bonhomme Ludovic , Lomenech Anne‐Marie , Vallance Michel , Morabito Domenico , Label Philippe , Lelu‐Walter Marie‐Anne
Published: October 2010

An integrated physiological and proteomic approach was used to investigate the effects of high gellan gum concentration in the medium during maturation of somatic embryos (SE) of hybrid larch, by comparing embryos incubated in media with a high gellan gum concentration (8 g l−1) and the standard concentration (4 g l−1) after 1, 3, 6 and 8 weeks of maturation. Because of the reduced availability of water in the 8 g l−1 medium, the cultured embryos had a lower osmotic water potential (Ψπ) and water contents, but higher dry weights (DWs), at 8 weeks compared with embryos cultured on the standard medium. The high gellan gum concentration induced a desiccation that is characteristic in zygotic embryo maturation. Total soluble proteins were extracted from SE with trichloroacetic acid (TCA)–acetone after 1 and 8 weeks of maturation on media with 4 and 8 g l−1 of gellan gum, and separated by two‐dimensional gel electrophoresis (2‐DE) at pH 4–7. More than 1100 proteins were reproducibly detected on each gel. At 1 and 8 weeks respectively, the abundances of 62 and 49 spots detected in analyses of embryos matured at the two gellan gum concentrations, significantly differed. Among 62 significantly differing spots at 1 week of maturation, the corresponding proteins of 56 were reliably identified by liquid chromatography‐mass spectrometry/mass spectrometry (LC‐MS/MS), and were found to be mainly involved in ‘carbohydrate metabolism’, ‘genetic information processing’ or ‘environmental information processing’ according to kegg taxonomy. Both physiological parameters and the proteins identified suggested that the embryos were stressed when they were cultured on 4 g l−1 of gellan gum.
Ecophysiology of photosynthesis in bryophytes: major roles for oxygen photoreduction and non‐photochemical quenching?
Authors: Proctor Michael C. F. , Smirnoff Nicholas
Published: October 2010

CO2 fixation in mosses saturates at moderate irradiances. Relative electron transport rate (RETR) inferred from chlorophyll fluorescence saturates at similar irradiance in shade species (e.g. Plagiomnium undulatum, Trichocolea tomentella), but many species of unshaded habitats (e.g. Andreaea rothii, Schistidium apocarpum, Sphagnum spp. and Frullania dilatata) show non‐saturating RETR at high irradiance, with high non‐photochemical quenching (NPQ). In P. undulatum and S. apocarpum, experiments in different gas mixtures showed O2 and CO2 as interchangeable electron sinks. Nitrogen + saturating CO2 gave high RETR and depressed NPQ. In S. apocarpum, glycolaldehyde (inhibiting photosynthesis and photorespiration) depressed RETR in air more at low than at high irradiance; in CO2‐free air RETR was maintained at all irradiances. Non‐saturating electron flow was not suppressed in ambient CO2 with 1% O2. The results indicate high capacity for oxygen photoreduction when CO2 assimilation is limited. Non‐saturating light‐dependent H2O2 production, insensitive to glycolaldehyde, suggests that electron transport is supported by oxygen photoreduction, perhaps via the Mehler‐peroxidase reaction. Consistent with this, mosses were highly tolerant to paraquat, which generates superoxide at photosystem I (PSI). Protection against excess excitation energy in mosses involves high capacity for photosynthetic electron transport to oxygen and high NPQ, activated at high irradiance, alongside high reactive oxygen species (ROS) tolerance.
Effects of meals with different glycaemic index on postprandial blood glucose response in patients with Type 1 diabetes treated with continuous subcutaneous insulin infusion
Authors: Parillo M. , Annuzzi G. , Rivellese A. A. , Bozzetto L. , Alessandrini R. , Riccardi G. , Capaldo B.
Published: October 2010

Diabet. Med. 28, 227–229 (2011)

Objective  To evaluate the impact of high‐glycaemic index and low‐glycaemic index meals on postprandial blood glucose in patients with Type 1 diabetes treated with continuous subcutaneous insulin infusion.

Methods  Sixteen patients with Type 1 diabetes under continuous subcutaneous insulin infusion treatment, age 36 ± 0.5 years (mean ± sem), HbA1c 7.6 ± 0.2% (56 ± 1.1 mmol/mol), consumed two test meals with an identical macronutrient composition, but with a different glycaemic index: 59 vs. 90. Blood glucose was checked before the test meal and every 30 min thereafter for 180 min. The same preprandial insulin dose was administered on the two occasions.

Results  Blood glucose concentrations following the low‐glycaemic index meal were significantly lower than those of the high‐glycaemic index meal (P < 0.05 to P < 0.01). The blood glucose area under the curve after the low‐glycaemic index meal was 20% lower than after the high‐glycaemic meal (P = 0.006).

Conclusions  Our data show that meals with the same carbohydrate content but a different glycaemic index produce clinically significant differences in postprandial blood glucose.
Reducing PEX13 Expression Ameliorates Physiological Defects of Late‐Acting Peroxin Mutants
Authors: Ratzel Sarah E. , Lingard Matthew J. , Woodward Andrew W. , Bartel Bonnie
Published: October 2010

Proteins are targeted to the peroxisome matrix via processes that are mechanistically distinct from those used by other organelles. Protein entry into peroxisomes requires peroxin (PEX) proteins, including early‐acting receptor (e.g. PEX5) and docking peroxins (e.g. PEX13 and PEX14) and late‐acting PEX5‐recycling peroxins (e.g. PEX4 and PEX6). We examined genetic interactions among Arabidopsis peroxin mutants and found that the weak pex13‐1 allele had deleterious effects when combined with pex5‐1 and pex14‐2, which are defective in early‐acting peroxins, as shown by reduced matrix protein import and enhanced physiological defects. In contrast, combining pex13‐1 with pex4‐1 or pex6‐1, which are defective in late‐acting peroxins, unexpectedly ameliorated mutant growth defects. Matrix protein import remained impaired in pex4‐1 pex13‐1 and pex6‐1 pex13‐1, suggesting that the partial suppression of pex4‐1 and pex6‐1 physiological defects by a weak pex13 allele may result from restoring the balance between import and export of PEX5 or other proteins that are retrotranslocated from the peroxisome with the assistance of PEX4 and PEX6. Our results suggest that symptoms caused by pex mutants defective in late‐acting peroxins may result not only from defects in matrix protein import but also from inefficient removal of PEX5 from the peroxisomal membrane following cargo delivery.
An Interactive Science Blog at UCF for High School Science Students
Authors: Paredes Jesus , del Barco Enrique
Published: October 2010

High school physics students are often capable of, and commonly interested in, understanding natural phenomena beyond those described in their textbooks. In order to supplement the shortage of topics covered in their physics courses, many students turn to popular scientific books, journals, and other media. There, they discover a plethora of topics that scientists are yet to understand or even explore. Although many high school students have this keen interest in science, very few are aware of actual research opportunities. Quite often, these students decide that the stuff that they really want to do is exclusive to universities and national labs, which appear to them as vast unknown universes. Unfortunately, since professional researchers and high school science teachers rarely communicate, no one bridges this gap for the students.
Discrepant Events: A Challenge to Students' Intuition
Authors: González-Espada Wilson J. , Birriel Jennifer , Birriel Ignacio
Published: October 2010

Studies on cognitive aspects of science education, especially how students achieve conceptual change, have been a focus of interest for many years.1 Researchers of student learning and conceptual change have developed several easily applicable teaching strategies. One of these strategies is known as discrepant events. Discrepant events are very powerful ways to stimulate interest, motivate students to challenge their covert science misconceptions, and promote higher-order thinking skills. The key point is that directly challenging students' naive ideas will lead to more quality science learning going on in the classroom. In this paper, we summarize the research-based role of discrepant events in conceptual change and we share several highly successful discrepant events we use in our own classes.
Gravity, Time, and Lagrangians
Authors: Huggins Elisha
Published: October 2010

Feynman mentioned to us that he understood a topic in physics if he could explain it to a college freshman, a high school student, or a dinner guest. Here we will discuss two topics that took us a while to get to that level. One is the relationship between gravity and time. The other is the minus sign that appears in the Lagrangian. (Why would one subtract potential energy from kinetic energy?) In this paper we discuss a thought experiment that relates gravity and time. Then we use a Feynman thought experiment to explain the minus sign in the Lagrangian. Our surprise was that these two topics are related.
The Statistical Interpretation of Entropy: An Activity
Authors: Timberlake Todd
Published: October 2010

The second law of thermodynamics, which states that the entropy of an isolated macroscopic system can increase but will not decrease, is a cornerstone of modern physics. Ludwig Boltzmann argued that the second law arises from the motion of the atoms that compose the system. Boltzmann's statistical mechanics provides deep insight into the functioning of the second law and also provided evidence for the existence of atoms at a time when many scientists (like Ernst Mach and Wilhelm Ostwald) were skeptical.1
A Mathematics Entrance Exam for General (Non-Majors) Physics
Authors: Chediak Alex
Published: October 2010

In a previous issue of The Physics Teacher, John Hubisz explained how a mathematics background check has been used at three different colleges to determine the appropriate physics sequence for incoming students.1 Based on their performance, students are placed into either calculus-based physics (CBP), algebra-trig physics (ATP), or a year of conceptual physics (CP). By placing the mathematically less-prepared students into either ATP or CP, Hubisz notes, higher success rates in CBP have been observed.
“Apparent Weight”: A Concept that Is Confusing and Unnecessary
Authors: Bartlett Albert A.
Published: October 2010

Two recent articles make prominent use of the concept of “apparent weight.”1,2 The concept of “apparent weight” leads to two confusing inconsistencies. We need to know that with very little change in our representations, we can give our students an improved understanding of “weight” without ever having to invent the appealing but confusing concept of “apparent weight.”
Global Warming: Lessons from Ozone Depletion
Authors: Hobson Art
Published: October 2010

My teaching and textbook1 have always covered many physics-related social issues, including stratospheric ozone depletion and global warming. The ozone saga is an inspiring good-news story that's instructive for solving the similar but bigger problem of global warming. Thus, as soon as students in my physics literacy course at the University of Arkansas have developed a conceptual understanding of energy and of electromagnetism, including the electromagnetic spectrum, I devote a lecture (and a textbook section) to ozone depletion and another lecture (and section) to global warming. Humankind came together in 1986 and quickly solved, to the extent that humans can solve it, ozone depletion. We could do the same with global warming, but we haven't and as yet there's no sign that we will. The parallel between the ozone and global warming cases, and the difference in outcomes, are striking and instructive.
Careers in Patent Law for Physics Majors
Authors: Oliver Douglas L.
Published: October 2010

An important question that many undergraduate physics students ask is, “What can one do with a physics degree?” Of course there are many answers to this question. Often a general reference to becoming a lawyer is given as a possible answer. This paper is intended to explain the field of patent law and how a physics degree can lead to an interesting and potentially lucrative career as a patent examiner, a patent agent, or a patent attorney. This information may be of interest to physics students as well as those who recruit or counsel physics students.
Measuring the Specific Heat of Metals by Cooling
Authors: Dittrich William , Minkin Leonid , Shapovalov Alexander S.
Published: October 2010

Three in one? Yes, three standard undergraduate thermodynamics experiments in one, not an oval can of lubricating oil. Previously it has been shown that the PASCO scientific1 apparatus for measuring coefficients of thermal expansion of metals can also be used to illustrate Newton's law of cooling in the same experiment.2 Now it will be shown that by cooling geometrically identical metallic samples and measuring their surface temperature change as a function of time, the specific heat of metals can be found by the method of comparison. This technique is simple to implement using the PASCO equipment for measuring the coefficients of thermal expansion of metals. A slight variation on this method was used in the Moscow State University students' laboratory for measuring temperature dependence of specific heat of copper over a large temperature range. As a result of this method, three experiments can be undertaken simultaneously to measure:

1) the coefficient of thermal expansion (α);

2) the time constant in Newton's law of cooling (H); and

3) the specific heatof metals (C).
Gender Effects of Computer Use in a Conceptual Physics Lab Course
Authors: Van Domelen Dave
Published: October 2010

It's always hard to know what to expect when bringing computers into an educational setting, as things are always changing. Student skills with computers are different today than they were 10 years ago, and 20 years ago almost counts as an alien world. Still, one hopes that some of these changes result in positive trends, such as student attitudes toward the use of computers in the classroom. During the course of the Wandering Interactive Lecture Demonstration Project,1 we've seen a notable gender gap in some aspects of the previous experience of students, and worried that it might impact their learning. So we administered a number of surveys to see if we were right to be worried.
Magnetostatics Analysis, Design, and Construction of a Loudspeaker
Authors: Galeriu Calin
Published: October 2010

Making a loudspeaker is a very rewarding hands-on activity that can be used to teach about electro-magnetism and sound waves. Several loudspeaker designs have been described in this magazine.1–4 The simplest loudspeaker4 has only a magnet, a coil, and three plastic cups. The simpler devices3,4 require a powerful amplified output, e.g., from a boom box. The more complex devices1,2 can operate using the smaller electric current from a CD player earphone output. Unfortunately, the procedure to make a more efficient loudspeaker is lengthy and less recommended to some high school students, involving a hot glue gun, a safety razor, five-minute epoxy, etc. Our loudspeaker, a variation of Heller's,2 is both simple in construction and efficient in operation. An analysis of the magnetic field distribution helped us in the design of this loudspeaker.
The Collapse of the I-35W Bridge in Minneapolis
Authors: Feldman Bernard J.
Published: October 2010

On Wednesday, Aug. 1, 2007, at 6:05 p.m. (during evening rush hour), the I-35W bridge across the Mississippi River in Minneapolis collapsed, killing 13 people and injuring 145. At the time of the collapse, repair work was in progress on the deck of the bridge, resulting in an additional 287 tons of construction material and equipment being on the bridge deck. This paper will present an analysis of a simple but similar bridge structure, using only Newton's second law. This analysis can give some insights into the cause of the collapse. This paper is the third of a series on bridge collapses, the first two being on the Tacoma Narrows Bridge1 and the Nimitz Freeway.2
Teaching Standard Deviation by Building from Student Invention
Authors: Day James , Nakahara Hiroko , Bonn Doug
Published: October 2010

First-year physics laboratories are often driven by a mix of goals that includes the illustration or discovery of basic physics principles and a myriad of technical skills involving specific equipment, data analysis, and report writing. The sheer number of such goals seems guaranteed to produce cognitive overload, even when highly detailed “cookbook” instructions are given. Recent studies indicate that this approach leaves students with a poor conceptual understanding of one of the most important features of laboratory physics and of the real world of science, in general: the development of an understanding of the nature of measurement and its attendant uncertainty1. While students might be able to reproduce certain technical manipulations of data, as novice thinkers they lack the mental scaffolding that allows an expert to organize and apply this knowledge.2,3 Our goal is to put novices on the path to expertise, so that they will be able to transfer their knowledge to novel situations.
Simple System to Measure the Earth's Magnetic Field
Authors: Akoglu R. , Halilsoy M. , Mazharimousavi S. Habib
Published: October 2010

Our aim in this proposal is to use Faraday's law of induction as a simple lecture demonstration to measure the Earths magnetic field (B). This will also enable the students to learn about how electric power is generated from rotational motion. Obviously the idea is not original, yet it may be attractive in the sense that no sophisticated devices are used. All the equipment needed is available in an elementary physics laboratory and is displayed in Fig. 1. The square wooden coil and handmade belt system to rotate the coil may require some craftsmanship; once made, it can be used for years. Using a compass, we first orient the table parallel to the direction of the Earth's horizontal component of B field. This is necessary to maximize the Earth's field which can suppress the noise effects as much as possible. It is preferable to minimize also any environmental effects by conducting the experiment away from power lines, if possible of course.
A potpourri of practical (or not) projectiles
Authors: Riendeau Diane
Published: October 2010

Special thanks to Frank Noschese, John Jay High School, and Karen Boone, Hallettsville High School. If you have a favorite video, please send the link and a brief description to: Diane Riendeau at driendeau@dist113.org.
Connecting colors to flexible frequencies
Authors: Shaw Mike
Published: October 2010

Here is a simple way to reinforce the relationships among wavelength, frequency, and color in the visible light spectrum. All that is required is a 3-ft section of plastic or metal electric dryer venting hose, cans of red and violet spray paint, a couple of 5-in elastic bands, and a metric ruler.
High Diversity and Abundance of
Legionella
spp. in a Pristine River and Impact of Seasonal and Anthropogenic Effects
Authors: Parthuisot N. , West N. J. , Lebaron P. , Baudart J.
Published: October 2010

The diversity and dynamics of
Legionella
species along a French river watershed subject to different thermal and wastewater discharges during an annual cycle were assessed by 16S rRNA gene sequencing and by a fingerprint technique, single-strand conformation polymorphism. A high diversity of
Legionella
spp. was observed at all the sampling sites, and the dominant
Legionella
clusters identified were most closely related to uncultured bacteria. The monthly monitoring revealed that
Legionella
sp. diversity changes were linked only to season at the wastewater site whereas there was some evidence for anthropogenic effects on
Legionella
sp. diversity downstream of the thermal bath. Quantification of
Legionella pneumophila
and
Legionella
spp. by culture and quantitative PCR (qPCR) was performed. Whereas only
L. pneumophila
was quantified on culture media, the qPCR assay revealed that
Legionella
spp. were ubiquitous and abundant from the pristine source of the river to the downstream sampling sites. These results suggest that
Legionella
spp. may be present at significant concentrations in many more freshwater environments than previously thought, highlighting the need for further ecological studies and culturing efforts.
New Blue Pigment Produced by
Pantoea agglomerans
and Its Production Characteristics at Various Temperatures
Authors: Fujikawa Hiroshi , Akimoto Ryo
Published: October 2010

A bacterium capable of producing a deep blue pigment was isolated from the environment and identified as
Pantoea agglomerans
. The pigment production characteristics of the bacterium under various conditions were studied. The optimal agar plate ingredients for pigment production by the bacterium were first studied: the optimal ingredients were 5 g/liter glucose, 10 g/liter tryptic soy broth, and 40 g/liter glycerol at pH 6.4. Bacterial cells grew on the agar plate during the incubation, while the pigment spread into the agar plate, meaning that it is water soluble. Pigment production was affected by the initial cell density. Namely, at higher initial cell densities ranging from 10
6.3
to 10
8.2
CFU/cm
2
on the agar plate, faster pigment production was observed, but no blue pigment was produced at a very high initial density of 10
9.1
CFU/cm
2
. Thus, the cell population of 10
8.2
CFU/cm
2
was used for subsequent study. Although the bacterium was capable of growing at temperatures above and below 10°C, it could produce the pigment only at temperatures of ≥10°C. Moreover, the pigment production was faster at higher temperatures in the range of 10 to 20°C. Pigment production at various temperature patterns was well described by a new logistic model. These results suggested that the bacterium could be used in the development of a microbial temperature indicator for the low-temperature-storage management of foods and clinical materials. To our knowledge, there is no other
P. agglomerans
strain capable of producing a blue pigment and the pigment is a new one of microbial origin.
Multiple UniqueCryptosporidiumIsolates from Three Species of Ground Squirrels (Spermophilus beecheyi,S. beldingi, andS. lateralis) in California
Authors: Pereira Maria das Graças Cabral , Li Xunde , McCowan Brenda , Phillips Ralph L. , Atwill Edward R.
Published: October 2010

Phylogenetic analyses of the 18S small-subunit (SSU) rRNA andCryptosporidiumoocyst wall protein (COWP) genes indicate that multiple uniqueCryptosporidiumisolates are shed by separate species ofSpermophilusground squirrels (S. beecheyi,S. beldingi, andS. lateralis) throughout California, despite some squirrel populations' being geographically isolated. The data support our assertion thatSpermophilussquirrels shed novelCryptosporidiumspecies.
Modulation of
Pseudomonas aeruginosa
Biofilm Dispersal by a Cyclic-Di-GMP Phosphodiesterase with a Putative Hypoxia-Sensing Domain
Authors: An Shuwen , Wu Ji'en , Zhang Lian-Hui
Published: October 2010

Pseudomonas aeruginosa
encodes many enzymes that are potentially associated with the synthesis or degradation of the widely conserved second messenger cyclic-di-GMP (c-di-GMP). In this study, we show that mutation of
rbdA
, which encodes a fusion protein consisting of PAS-PAC-GGDEF-EAL multidomains, results in decreased biofilm dispersal. RbdA contains a highly conserved GGDEF domain and EAL domain, which are involved in the synthesis and degradation of c-di-GMP, respectively. However,
in vivo
and
in vitro
analyses show that the full-length RbdA protein only displays phosphodiesterase activity, causing c-di-GMP degradation. Further analysis reveals that the GGDEF domain of RbdA plays a role in activating the phosphodiesterase activity of the EAL domain in the presence of GTP. Moreover, we show that deletion of the PAS domain or substitution of the key residues implicated in sensing low-oxygen stress abrogates the functionality of RbdA. Subsequent study showed that RbdA is involved in positive regulation of bacterial motility and production of rhamnolipids, which are associated with biofilm dispersal, and in negative regulation of production of exopolysaccharides, which are required for biofilm formation. These data indicate that the c-di-GMP-degrading regulatory protein RbdA promotes biofilm dispersal through its two-pronged effects on biofilm development, i.e., downregulating biofilm formation and upregulating production of the factors associated with biofilm dispersal.
Effect of Sulfadiazine-Contaminated Pig Manure on the Abundances of Genes and Transcripts Involved in Nitrogen Transformation in the Root-Rhizosphere Complexes of Maize and Clover
Authors: Ollivier Julien , Kleineidam Kristina , Reichel Rüdiger , Thiele-Bruhn Sören , Kotzerke Anja , Kindler Reimo , Wilke Berndt-Michael , Schloter Michael
Published: October 2010

The antibiotic sulfadiazine (SDZ) can enter the environment by application of manure from antibiotic-treated animals to arable soil. Because antibiotics are explicitly designed to target microorganisms, they likely affect microbes in the soil ecosystem, compromising important soil functions and disturbing processes in nutrient cycles. In a greenhouse experiment, we investigated the impact of sulfadiazine-contaminated pig manure on functional microbial communities involved in key processes of the nitrogen cycle in the root-rhizosphere complexes (RRCs) of maize (
Zea mays
) and clover (
Trifolium alexandrinum
). At both the gene and transcript level, we performed real-time PCR using
nifH
,
amoA
(in both ammonia-oxidizing bacteria and archaea),
nirK
,
nirS
, and
nosZ
as molecular markers for nitrogen fixation, nitrification, and denitrification. Sampling was performed 10, 20, and 30 days after the application. SDZ affected the abundance pattern of all investigated genes in the RRCs of both plant species (with stronger effects in the RRC of clover) 20 and 30 days after the addition. Surprisingly, effects on the transcript level were less pronounced, which might indicate that parts of the investigated functional groups were tolerant or resistant against SDZ or, as in the case of
nifH
and clover, have been protected by the nodules.
Antimicrobial Resistance of
Campylobacter
Isolates from Retail Meat in the United States between 2002 and 2007
Authors: Zhao S. , Young S. R. , Tong E. , Abbott J. W. , Womack N. , Friedman S. L. , McDermott P. F.
Published: October 2010

The emergence of antimicrobial resistance in
Campylobacter
spp. has been a growing public health concern globally. The objectives of this study were to determine the prevalence, antimicrobial susceptibility, and genetic relatedness of
Campylobacter
spp. recovered by the National Antimicrobial Resistance Monitoring System (NARMS) retail meat program. Retail meat samples (
n
= 24,566) from 10 U.S. states collected between 2002 and 2007, consisting of 6,138 chicken breast, 6,109 ground turkey, 6,171 ground beef, and 6,148 pork chop samples, were analyzed. A total of 2,258
Campylobacter
jejuni
, 925
Campylobacter
coli
, and 7
Campylobacter
lari
isolates were identified. Chicken breast samples showed the highest contamination rate (49.9%), followed by ground turkey (1.6%), whereas both pork chops and ground beef had <0.5% contamination. The most common resistance was to doxycycline/tetracycline (46.6%), followed by nalidixic acid (18.5%), ciprofloxacin (17.4%), azithromycin and erythromycin (2.8%), telithromycin (2.4%), clindamycin (2.2%), and gentamicin (<0.1%). In a subset of isolates tested, no resistance to meropenem and florfenicol was seen.
C. coli
isolates showed higher resistance rates to antimicrobials, with the exception of doxycycline/tetracycline, than those seen for C
. jejuni
. Pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 1,226 PFGE profiles among the 2,318 isolates, with many clones being widely dispersed throughout the 6-year sampling period.
Phylogenetic, Microbiological, and Glycoside Hydrolase Diversities within the Extremely Thermophilic, Plant Biomass-Degrading Genus
Caldicellulosiruptor
Authors: Blumer-Schuette Sara E. , Lewis Derrick L. , Kelly Robert M.
Published: October 2010

Phylogenetic, microbiological, and comparative genomic analyses were used to examine the diversity among members of the genus
Caldicellulosiruptor
, with an eye toward the capacity of these extremely thermophilic bacteria to degrade the complex carbohydrate content of plant biomass. Seven species from this genus (
C. saccharolyticus
,
C. bescii
,
C. hydrothermalis
,
C. owensensis
,
C. kronotskyensis
,
C. lactoaceticus
, and
C. kristjanssonii
) were compared on the basis of 16S rRNA gene phylogeny and cross-species DNA-DNA hybridization to a whole-genome
C. saccharolyticus
oligonucleotide microarray, revealing that
C. saccharolyticus
was the most divergent within this group. Growth physiology of the seven
Caldicellulosiruptor
species on a range of carbohydrates showed that, while all could be cultivated on acid-pretreated switchgrass, only
C. saccharolyticus
,
C. bescii
,
C. kronotskyensis
, and
C. lactoaceticus
were capable of hydrolyzing Whatman no. 1 filter paper. Two-dimensional gel electrophoresis of the secretomes from cells grown on microcrystalline cellulose revealed that the cellulolytic species also had diverse secretome fingerprints. The
C. saccharolyticus
secretome contained a prominent S-layer protein that appears in the cellulolytic
Caldicellulosiruptor
species, suggesting a possible role in cell-substrate interactions. Growth physiology also correlated with glycoside hydrolase (GH) and carbohydrate-binding module (CBM) inventories for the seven bacteria, as deduced from draft genome sequence information. These inventories indicated that the absence of a single GH and CBM family was responsible for diminished cellulolytic capacity. Overall, the genus
Caldicellulosiruptor
appears to contain more genomic and physiological diversity than previously reported, and this argues for continued efforts to isolate new members from high-temperature terrestrial biotopes.
Genetic Improvement of
Bacillus licheniformis
Strains for Efficient Deproteinization of Shrimp Shells and Production of High-Molecular-Mass Chitin and Chitosan
Authors: Hoffmann Kerstin , Daum Gabriele , Köster Marina , Kulicke Werner-Michael , Meyer-Rammes Heike , Bisping Bernward , Meinhardt Friedhelm
Published: October 2010

By targeted deletion of the polyglutamate operon (
pga
) in
Bacillus licheniformis
F11, a derivative form, F11.1 (Δ
pga
), was obtained that, along with lacking polyglutamate (PGA) formation, displayed enhanced proteolytic activities. The phenotypic properties were maintained in a strain in which the
chiBA
operon was additionally deleted: F11.4 (Δ
chiBA
Δ
pga
). These genetically modified strains, carrying the Δ
pga
deletion either alone (F11.1) or together with the Δ
chiBA
(F11.4) deletion, were used in fermentations (20-liter scale) aiming at the deproteinization of shrimp shells in order to obtain long-chain chitin. After chemical deacetylation, the resulting chitosan samples were analyzed by nuclear magnetic resonance spectroscopy, size exclusion chromatography, and viscometry and compared to a chitosan preparation that was produced in parallel by chemical methods by a commercial chitosan supplier (GSRmbH). Though faint lipid impurities were present in the fermented polysaccharides, the viscosity of the material produced with the double-deletion mutant F11.4 (Δ
pga
Δ
chiBA
) was higher than that of the chemically produced and commercially available samples (Cognis GmbH). Thus, enhanced proteolytic activities and a lack of chitinase activity render the double mutant F11.4 a powerful tool for the production of long-chain chitosan.
Purification and Characterization of an Active
N
-Acetylglucosaminyltransferase Enzyme Complex from Streptococci
Authors: Wu Ren , Zhou Meixian , Wu Hui
Published: October 2010

A new family of bacterial serine-rich repeat glycoproteins can function as adhesins required for biofilm formation and pathogenesis in streptococci and staphylococci. Biogenesis of these proteins depends on a gene cluster coding for glycosyltransferases and accessory secretion proteins. Previous studies show that Fap1, a member of this family from
Streptococcus parasanguinis
, can be glycosylated by a protein glycosylation complex in a recombinant heterogeneous host. Here we report a tandem affinity purification (TAP) approach used to isolate and study protein complexes from native streptococci. This method demonstrated that a putative glycosyltransferase (Gtf2), which is essential for Fap1 glycosylation, readily copurified with another glycosyltransferase (Gtf1) from native
S. parasanguinis
. This result and the similar isolation of a homologous two-protein complex from
Streptococcus pneumoniae
indicate the biological relevance of the complexes to the glycosylation in streptococci. Furthermore, novel
N
-acetylglucosaminyltransferase activity was discovered for the complexes. Optimal activity required heterodimer formation and appears to represent a novel type of glycosylation.
Growth and Virulence Properties of Biofilm-FormingSalmonellaentericaSerovar Typhimurium under Different Acidic Conditions
Authors: Xu Hua , Lee Hyeon-Yong , Ahn Juhee
Published: October 2010

This study was designed to characterize the viability and potential virulence of bofilm-formingSalmonellaentericaserovar Typhimurium under different pH levels, ranging from 5 to 7. The plate count method and real-time reverse transcription-PCR (RT-PCR) were used to evaluate the survival ofS.Typhimurium grown in Trypticase soy broth (TSB) adjusted to pH 5, 6, and 7 (TSB-5, TSB-6, and TSB-7, respectively) at 37°C for 10 days. In TSB-5 and TSB-6, the numbers of viable cells estimated by using the real-time RT-PCR were greater than the culturable counts enumerated by the plate count method. Reflectance micro-Fourier transform infrared (micro-FTIR) spectroscopy was used to evaluate the biochemical changes in biofilm cells. Considerable changes in chemical components were observed in the biofilm cells grown in TSB-5 and TSB-6 when compared to the cells grown in TSB-7. The enterotoxin production and invasive ability of planktonic and biofilmS.Typhimurium cells were inferred by the relative levels of expression ofstnandinvA. The levels of expression ofstnandinvAwere significantly increased in biofilmS.Typhimurium cells grown in TSB-5 (1.9-fold and 3.2-fold) and TSB-6 (2.1-fold and 22.3-fold) after 10 days of incubation. These results suggest that the biofilm-formingS. Typhimurium under different pH levels might change the virulence production and stress response mechanisms.
Distribution of Antimicrobial Resistance and Virulence Genes inEnterococcusspp. and Characterization of Isolates from Broiler Chickens
Authors: Diarra Moussa S. , Rempel Heidi , Champagne Julie , Masson Luke , Pritchard Jane , Topp Edward
Published: October 2010

Enterococci are now frequent causative agents of nosocomial infections. In this study, we analyzed the frequency and distribution of antibiotic resistance and virulence genotypes ofEnterococcusisolates from broiler chickens. Fecal and cecal samples from nine commercial poultry farms were collected to quantify total enterococci. Sixty-nine presumptive enterococci were isolated and identified by API 20 Strep, and their susceptibilities to antibiotics were determined. Genotypes were assessed through the use of a novel DNA microarray carrying 70 taxonomic, 17 virulence, and 174 antibiotic resistance gene probes. Total enterococcal counts were different from farm to farm and between sample sources (P< 0.01). Fifty-one (74%) of the isolates were identified asE. faecium, whereas nine (13%), seven (10%), and two (3%) isolates were identified asE. hirae,E. faecalis, andE. gallinarum, respectively. Multiple-antibiotic resistance was evident inE. faeciumandE. faecalisisolates. The most common multiple-antibiotic resistance phenotype was Bac Ery Tyl Lin Str Gen Tet Cip. Genes conferring resistance to aminoglycoside (aac,aacA-aphD,aadB,aphA,sat4), macrolide (ermA,ermB,ermAM,msrC), tetracycline (tetL,tetM,tetO), streptogramin (satG_vatE8), bacitracin (bcrR), and lincosamide (linB) antibiotics were detected in corresponding phenotypes. A range of 9 to 12 different virulence genes was found inE. faecalis, includingace,agg,agrBEfs(agrBgene ofE. faecalis),cad1, the cAM373 and cCF10 genes,cob,cpd1,cylAB,efaAEfs, andgelE. All sevenE. faecalisisolates were found to carry thegelEgene and to hydrolize gelatin and bile salts. Results from this study showed the presence of enterococci of public and environmental health concerns in broiler chicken farms and demonstrated the utility of a microarray to quickly and reliably analyze resistance and virulence genotypes ofEnterococcusspp.
Genotypic Diversity ofBorrelia burgdorferiStrains Detected inIxodes scapularisLarvae Collected from North American Songbirds
Authors: Brinkerhoff R. Jory , Bent Stephen J. , Folsom-O'Keefe Corrine M. , Tsao Kimberly , Hoen Anne Gatewood , Barbour Alan G. , Diuk-Wasser Maria A.
Published: October 2010

We genotypedBorrelia burgdorferistrains detected in larvae ofIxodes scapularisremoved from songbirds and compared them with those found in host-seekingI. scapularisnymphs sampled throughout the eastern United States. Birds are capable of transmitting most known genotypes, albeit at different frequencies than expected based on genotypes found among host-seeking nymphs.
Influence of the Composition of the Cellulolytic Flora on the Development of Hydrogenotrophic Microorganisms, Hydrogen Utilization, and Methane Production in the Rumens of Gnotobiotically Reared Lambs
Authors: Chaucheyras-Durand Frédérique , Masséglia Sébastien , Fonty Gérard , Forano Evelyne
Published: October 2010

We investigated the influence of the composition of the fibrolytic microbial community on the development and activities of hydrogen-utilizing microorganisms in the rumens of gnotobiotically reared lambs. Two groups of lambs were reared. The first group was inoculated with
Fibrobacter succinogenes
, a non-H
2
-producing species, as the main cellulolytic organism, and the second group was inoculated with
Ruminococcus albus
,
Ruminococcus flavefaciens
, and anaerobic fungi that produce hydrogen. The development of hydrogenotrophic bacterial communities, i.e., acetogens, fumarate and sulfate reducers, was monitored in the absence of methanogens and after inoculation of methanogens. Hydrogen production and utilization and methane production were measured in rumen content samples incubated
in vitro
in the presence of exogenous hydrogen (supplemented with fumarate or not supplemented with fumarate) or in the presence of ground alfalfa hay as a degradable substrate. Our results show that methane production was clearly reduced when the dominant fibrolytic species was a non-H
2
-producing species, such as
Fibrobacter succinogenes
, without significantly impairing fiber degradation and fermentations in the rumen. The addition of fumarate to the rumen contents stimulated H
2
utilization only by the ruminal microbiota inoculated with
F. succinogenes
, suggesting that these communities could play an important role in fumarate reduction
in vivo
.
Formation of Isobutene from 3-Hydroxy-3-Methylbutyrate by Diphosphomevalonate Decarboxylase
Authors: Gogerty David S. , Bobik Thomas A.
Published: October 2010

Isobutene is an important commercial chemical used for the synthesis of butyl rubber, terephthalic acid, specialty chemicals, and a gasoline performance additive known as alkylate. Currently, isobutene is produced from petroleum and hence is nonrenewable. Here, we report that the
Saccharomyces cerevisiae
mevalonate diphosphate decarboxylase (
Sc
MDD) can convert 3-hydroxy-3-methylbutyrate (3-HMB) to isobutene. Whole cells of
Escherichia coli
producing
Sc
MDD with an N-terminal 6×His tag (His
6
-
Sc
MDD) formed isobutene from 3-HMB at a rate of 154 pmol h
−1
g cells
−1
. In contrast, no isobutene was detected from control cells lacking
Sc
MDD. His
6
-
Sc
MDD was purified by nickel affinity chromatography and shown to produce isobutene from 3-HMB at a rate of 1.33 pmol min
−1
mg
−1
protein. Controls showed that both His
6
-
Sc
MDD and 3-HMB were required for detectable isobutene formation. Isobutene was identified by gas chromatography (GC) with flame ionization detection as well as by GC-mass spectrometry (MS).
Sc
MDD was subjected to error-prone PCR, and two improved variants were characterized,
Sc
MDD1 (I145F) and
Sc
MDD2 (R74H). Whole cells of
E. coli
producing
Sc
MDD1 and
Sc
MDD2 produced isobutene from 3-HMB at rates of 3,000 and 5,888 pmol h
−1
g cells
−1
, which are 19- and 38-fold increases compared to rates for cells producing His
6
-
Sc
MDD. This showed that genetic modifications can be used to increase the rate at which
Sc
MDD converts 3-HMB to isobutene. Because 3-HMB can be produced from
l
-leucine,
Sc
MDD has a potential application for the production of renewable isobutene. Moreover, isobutene is a gas, which might simplify its purification from a fermentation medium, substantially reducing production costs.
Ecophysiology of Fe-Cycling Bacteria in Acidic Sediments
Authors: Lu Shipeng , Gischkat Stefan , Reiche Marco , Akob Denise M. , Hallberg Kevin B. , Küsel Kirsten
Published: October 2010

Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their
in situ
functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the
Gammaproteobacteria
(an unknown
Dyella-
like genus and
Acidithiobacillus
-related strains) were obtained from the top acidic sediment zones (pH 2.8).
Firmicutes
strains (related to
Bacillus
and
Alicyclobacillus
) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the
Alphaproteobacteria
,
Acidocella
-related strains were only isolated from acidic zones, whereas
Acidiphilium
-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns.
Geobacter
-related clone sequences were only obtained from deep sediment zones, and
Geobacter
-specific quantitative PCR yielded 8 × 10
5
gene copy numbers. Isolates related to the
Acidobacterium
,
Acidocella
, and
Alicyclobacillus
genera and to the unknown
Dyella
-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratory-based studies that showed this trait to be widespread among acidophiles.
Inositol Catabolism, a Key Pathway in
Sinorhizobium meliloti
for Competitive Host Nodulation
Authors: Kohler Petra R. A. , Zheng Jasmine Y. , Schoffers Elke , Rossbach Silvia
Published: October 2010

The nitrogen-fixing symbiont of alfalfa,
Sinorhizobium meliloti
, is able to use
myo
-inositol as the sole carbon source. Putative inositol catabolism genes (
iolA
and
iolRCDEB
) have been identified in the
S. meliloti
genome based on their similarities with the
Bacillus subtilis iol
genes. In this study, functional mutational analysis revealed that the
iolA
and
iolCDEB
genes are required for growth not only with the
myo
-isomer but also for growth with
scyllo
- and
d
-
chiro
-inositol as the sole carbon source. An additional, hypothetical dehydrogenase of the IdhA/MocA/GFO family encoded by the
smc01163
gene was found to be essential for growth with
scyllo
-inositol, whereas the
idhA
-encoded
myo
-inositol dehydrogenase was responsible for the oxidation of
d
-
chiro
-inositol. The putative regulatory
iolR
gene, located upstream of
iolCDEB
, encodes a repressor of the
iol
genes, negatively regulating the activity of the
myo
- and the
scyllo
-inositol dehydrogenases. Mutants with insertions in the
iolA
,
smc01163
, and individual
iolRCDE
genes could not compete against the wild type in a nodule occupancy assay on alfalfa plants. Thus, a functional inositol catabolic pathway and its proper regulation are important nutritional or signaling factors in the
S. meliloti
-alfalfa symbiosis.
Promising Immunomodulatory Effects of Selected Strains of Dairy Propionibacteria as Evidenced
In Vitro
and
In Vivo
Authors: Foligné Benoît , Deutsch Stéphanie-Marie , Breton Jérôme , Cousin Fabien J. , Dewulf Joëlle , Samson Michel , Pot Bruno , Jan Gwénaël
Published: October 2010

Immunomodulatory properties of 10 dairy propionibacteria, analyzed on human peripheral blood mononuclear cells (PBMCs), revealed a highly strain-dependent induction of anti-inflammatory cytokine interleukin 10 (IL-10). Two selected strains of
Propionibacterium freudenreichii
showed a protective effect against two models of colitis in mice, suggesting a probiotic potential predicted by immune-based selection criteria for these cheese starter bacteria.
Abundance and Diversity of Archaeal Ammonia Oxidizers in a Coastal Groundwater System
Authors: Rogers Daniel R. , Casciotti Karen L.
Published: October 2010

Nitrification, the microbially catalyzed oxidation of ammonia to nitrate, is a key process in the nitrogen cycle. Archaea have been implicated in the first part of the nitrification pathway (oxidation of ammonia to nitrite), but the ecology and physiology of these organisms remain largely unknown. This work describes two different populations of sediment-associated ammonia-oxidizing archaea (AOA) in a coastal groundwater system in Cape Cod, MA. Sequence analysis of the ammonia monooxygenase subunit A gene (
amoA
) shows that one population of putative AOA inhabits the upper meter of the sediment, where they may experience frequent ventilation, with tidally driven overtopping and infiltration of bay water supplying dissolved oxygen, ammonium, and perhaps organic carbon. A genetically distinct population occurs deeper in the sediment, in a mixing zone between a nitrate- and oxygen-rich freshwater zone and a reduced, ammonium-bearing saltwater wedge. Both of these AOA populations are coincident with increases in the abundance of group I crenarchaeota 16S rRNA gene copies.