bluuebunny/crossref_metadata_2025 huggingface dataset:
Poly(3-Hydroxybutyrate) Biosynthesis in the Biofilm of
Alcaligenes eutrophus
, Using Glucose Enzymatically Released from Pulp Fiber Sludge
Authors: Zhang Songping , Norrlöw Olof , Wawrzynczyk Joanna , Dey Estera Szwajcer
Published: November 2004

Glucose, enzymatically released from pulp fiber sludge, was combined with inorganic salts and used as a growth medium for
Alcaligenes eutrophus
, a gram-negative strain producing poly(3-hydroxybutyrate) (PHB). By controlling the concentrations of the inorganic salts in the growth medium, almost 78% of the cell mass was converted to pure PHB. Efforts were made to find conditions for bacterial growth in the form of a biofilm on a cheap and reusable carrier. A number of positively charged carriers were tested, and the anion exchanger DEAE-Sephadex A-25 was chosen as a microcarrier for packed-bed biofilm cultures of
A. eutrophus.
Conditions for attachment, growth, and detachment were established. Biofilm formation on the microcarrier is strongly dependent on the ionic strength of the attachment medium. In order to achieve formation of the biofilm and its recovery from the microcarrier, the ionic strengths of the attachment and the detachment media were varied. Low ionic strength was tested for attachment, and high ionic strength was tested for detachment. Although biofilm formation in the packed-bed reactor is limited, the volumetric yield of cells based on the void volume of the packed bed is comparable with the batch culture yield.
Interaction and Transmission of Two
Borrelia burgdorferi
Sensu Stricto Strains in a Tick-Rodent Maintenance System
Authors: Derdáková Markéta , Dudiòák Vladimír , Brei Brandon , Brownstein John S. , Schwartz Ira , Fish Durland
Published: November 2004

In the northeastern United States, the Lyme disease agent,
Borrelia burgdorferi
sensu stricto, is maintained by enzoonotic transmission, cycling between white-footed mice (
Peromyscus leucopus
) and black-legged ticks (
Ixodes scapularis
).
B. burgdorferi
sensu stricto is genetically variable and has been divided into three major genotypes based on 16S-23S ribosomal DNA spacer (RST) analysis. To better understand how genetic differences in
B. burgdorferi
sensu stricto may influence transmission dynamics in nature, we investigated the interaction between an RST1 and an RST3 strain in a laboratory system with
P. leucopus
mice and
I. scapularis
ticks. Two groups of mice were infected with either BL206 (RST1) or B348 (RST3). Two weeks later, experimental mice were challenged with the opposite strain, while control mice were challenged with the same strain as that used for the primary infection. The transmission of BL206 and B348 from infected mice was then determined by xenodiagnosis with uninfected larval ticks at weekly intervals for 42 days. Mice in both experimental groups were permissive for infection with the second strain and were able to transmit both strains to the xenodiagnostic ticks. However, the overall transmission efficiencies of BL206 and B348 were significantly different. BL206 was more efficiently transmitted than B348 to xenodiagnostic ticks. Significantly fewer double infections than expected were detected in xenodiagnostic ticks. The results suggest that some
B. burgdorferi
sensu stricto strains, such as BL206, may be preferentially maintained in transmission cycles between ticks and white-footed mice. Other strains, such as B348, may be more effectively maintained in different tick-vertebrate transmission cycles.
Engineering of Chimeric Class II Polyhydroxyalkanoate Synthases
Authors: Niamsiri Nuttawee , Delamarre Soazig C. , Kim Young-Rok , Batt Carl A.
Published: November 2004

PHA synthase is a key enzyme involved in the biosynthesis of polyhydroxyalkanoates (PHAs). Using a combinatorial genetic strategy to create unique chimeric class II PHA synthases, we have obtained a number of novel chimeras which display improved catalytic properties. To engineer the chimeric PHA synthases, we constructed a synthetic
phaC
gene from
Pseudomonas oleovorans
(
phaC1

Po

) that was devoid of an internal 540-bp fragment. Randomly amplified PCR products (created with primers based on conserved
phaC
sequences flanking the deleted internal fragment) were generated using genomic DNA isolated from soil and were substituted for the 540-bp internal region. The chimeric genes were expressed in a PHA-negative strain of
Ralstonia eutropha
, PHB
−
4 (DSM 541). Out of 1,478 recombinant clones screened for PHA production, we obtained five different chimeric
phaC1

Po

genes that produced more PHA than the native
phaC1

Po

. Chimeras S1-71, S4-8, S5-58, S3-69, and S3-44 exhibited 1.3-, 1.4-, 2.0-, 2.1-, and 3.0-fold-increased levels of in vivo activity, respectively. All of the mutants mediated the synthesis of PHAs with a slightly increased molar fraction of 3-hydroxyoctanoate; however, the weight-average molecular weights (
M
w
) of the PHAs in all cases remained almost the same. Based upon DNA sequence analyses, the various
phaC
fragments appear to have originated from
Pseudomonas fluorescens
and
Pseudomonas aureofaciens
. The amino acid sequence analyses showed that the chimeric proteins had 17 to 20 amino acid differences from the wild-type phaC1
Po
, and these differences were clustered in the same positions in the five chimeric clones. A threading model of PhaC1
Po
, developed based on homology of the enzyme to the
Burkholderia glumae
lipase, suggested that the amino acid substitutions found in the active chimeras were located mostly on the protein model surface. Thus, our combinatorial genetic engineering strategy proved to be broadly useful for improving the catalytic activities of PHA synthase enzymes.
Visualization of Differential Gene Expression by Improved Cyan Fluorescent Protein and Yellow Fluorescent Protein Production in
Bacillus subtilis
Authors: Veening Jan-Willem , Smits Wiep Klaas , Hamoen Leendert W. , Jongbloed Jan D. H. , Kuipers Oscar P.
Published: November 2004

The distinguishable cyan and yellow fluorescent proteins (CFP and YFP) enable the simultaneous in vivo visualization of different promoter activities. Here, we report new cloning vectors for the construction of
cfp
and
yfp
fusions in
Bacillus subtilis
. By extending the N-terminal portions of previously described CFP and YFP variants, 20- to 70-fold-improved fluorescent-protein production was achieved. Probably, the addition of sequences encoding the first eight amino acids of the N-terminal part of ComGA of
B. subtilis
overcomes the slow translation initiation that is provoked by the eukaryotic codon bias present in the original
cfp
and
yfp
genes. Using these new vectors, we demonstrate that, within an isogenic population of sporulating
B. subtilis
cells, expression of the
abrB
and
spoIIA
genes is distinct in individual cells.
Saccharomyces cerevisiae
Engineered for Xylose Metabolism Exhibits a Respiratory Response
Authors: Jin Yong-Su , Laplaza Jose M. , Jeffries Thomas W.
Published: November 2004

Native strains of
Saccharomyces cerevisiae
do not assimilate xylose.
S. cerevisiae
engineered for
d
-xylose utilization through the heterologous expression of genes for aldose reductase (
XYL1
), xylitol dehydrogenase (
XYL2
), and
d
-xylulokinase (
XYL3
or
XKS1
) produce only limited amounts of ethanol in xylose medium. In recombinant
S. cerevisiae
expressing
XYL1
,
XYL2
, and
XYL3
, mRNA transcript levels for glycolytic, fermentative, and pentose phosphate enzymes did not change significantly on glucose or xylose under aeration or oxygen limitation. However, expression of genes encoding the tricarboxylic acid cycle, respiration enzymes (
HXK1
,
ADH2
,
COX13
,
NDI1
, and
NDE1
), and regulatory proteins (
HAP4
and
MTH1
) increased significantly when cells were cultivated on xylose, and the genes for respiration were even more elevated under oxygen limitation. These results suggest that recombinant
S. cerevisiae
does not recognize xylose as a fermentable carbon source and that respiratory proteins are induced in response to cytosolic redox imbalance; however, lower sugar uptake and growth rates on xylose might also induce transcripts for respiration. A petite respiration-deficient mutant (ρ°) of the engineered strain produced more ethanol and accumulated less xylitol from xylose. It formed characteristic colonies on glucose, but it did not grow on xylose. These results are consistent with the higher respiratory activity of recombinant
S. cerevisiae
when growing on xylose and with its inability to grow on xylose under anaerobic conditions.
Identification of Common Subpopulations of Non-Sorbitol-Fermenting, β-Glucuronidase-Negative
Escherichia coli
O157:H7 from Bovine Production Environments and Human Clinical Samples
Authors: Yang Zhijie , Kovar Joy , Kim Jaehyoung , Nietfeldt Joseph , Smith David R. , Moxley Rodney A. , Olson Michael E. , Fey Paul D. , Benson Andrew K.
Published: November 2004

Non-sorbitol-fermenting, β-glucuronidase-negative
Escherichia coli
O157:H7 strains are regarded as a clone complex, and populations from different geographical locations are believed to share a recent common ancestor. Despite their relatedness, high-resolution genotyping methods can detect significant genome variation among different populations. Phylogenetic analysis of high-resolution genotyping data from these strains has shown that subpopulations from geographically unlinked continents can be divided into two primary phylogenetic lineages, termed lineage I and lineage II, and limited studies of the distribution of these lineages suggest there could be differences in their propensity to cause disease in humans or to be transmitted to humans. Because the genotyping methods necessary to discriminate the two lineages are tedious and subjective, these methods are not particularly suited for studying the large sets of strains that are required to systematically evaluate the ecology and transmission characteristics of these lineages. To overcome this limitation, we have developed a lineage-specific polymorphism assay (LSPA) that can readily distinguish between the lineage I and lineage II subpopulations. In the studies reported here, we describe the development of a six-marker test (LSPA-6) and its validation in a side-by-side comparison with octamer-based genome scanning. Analysis of over 1,400 O157:H7 strains with the LSPA-6 demonstrated that five genotypes comprise over 91% of the strains, suggesting that these subpopulations may be widespread.
Relationship of
Vibrio
Species Infection and Elevated Temperatures to Yellow Blotch/Band Disease in Caribbean Corals
Authors: Cervino James M. , Hayes Raymond L. , Polson Shawn W. , Polson Sara C. , Goreau Thomas J. , Martinez Robert J. , Smith Garriet W.
Published: November 2004

The bacterial and temperature factors leading to yellow blotch/band disease (YBD), which affects the major reef-building Caribbean corals
Montastrea
spp., have been investigated. Groups of bacteria isolated from affected corals and inoculated onto healthy corals caused disease signs similar to those of YBD. The 16S rRNA genes from these bacteria were sequenced and found to correspond to four
Vibrio
spp. Elevating the water temperature notably increased the rate of spread of YBD on inoculated corals and induced greater coral mortality. YBD-infected corals held at elevated water temperatures had 50% lower zooxanthella densities, 80% lower division rates, and a 75% decrease in chlorophyll
a
and
c
2
pigments compared with controls. Histological sections indicated that the algal pyrenoid was fragmented into separate segments, along with a reconfiguration and swelling of the zooxanthellae, as well as vacuolization. YBD does not appear to produce the same physiological response formerly observed in corals undergoing temperature-related bleaching. Evidence indicates that YBD affects primarily the symbiotic algae rather than coral tissue.
Long-Chain
N
-Acyltyrosine Synthases from Environmental DNA
Authors: Brady Sean F. , Chao Carol J. , Clardy Jon
Published: November 2004

The heterologous expression of DNA extracted directly from environmental samples (environmental DNA [eDNA]) in easily cultured hosts provides access to natural products produced by previously inaccessible microorganisms. When eDNA cosmid libraries were screened in
Escherichia coli
for antibacterially active clones, long-chain
N
-acyltyrosine-producing clones were found in every eDNA library. These apparently common natural products have not been previously described from screening extracts of cultured bacteria for biologically active natural products. Of the 11 long-chain
N
-acyl amino acid synthases (NASs) that were characterized, 10 are unique sequences. A predicted protein of previously unknown function from
Nitrosomonas europaea
, a gram-negative nitrifying beta-proteobacterium, is 14 to 37% identical to eDNA NASs. When cloned into
E. coli
, this open reading frame confers the production of long-chain
N
-acyltyrosines to the host and is therefore the first NAS from a cultured bacterium to be functionally characterized. Understanding the role that long-chain
N
-acyl amino acids play in soil microbial communities should now be feasible with the identification of a cultured organism that has the genetic capacity to produce these compounds.
Electric Current-Induced Detachment of
Staphylococcus epidermidis
Biofilms from Surgical Stainless Steel
Authors: van der Borden Arnout J. , van der Werf Hester , van der Mei Henny C. , Busscher Henk J.
Published: November 2004

Biomaterial-centered infections of orthopedic percutaneous implants are serious complications which can ultimately lead to osteomyelitis, with devastating effects on bone and surrounding tissues, especially since the biofilm mode of growth offers protection against antibiotics and since removal frequently is the only ultimate solution. Recently, it was demonstrated that as a possible pathway to prevent infections of percutaneous stainless steel implants, electric currents of 60 to 100 μA were effective at stimulating the detachment of initially adhering staphylococci from surgical stainless steel. However, initially adhering bacteria are known to adhere more reversibly than bacteria growing in the later stages of biofilm formation. Hence, the aim of this study was to examine whether a growing
Staphylococcus epidermidis
biofilm can be stimulated to detach from surgical stainless steel by the use of electric currents. In separate experiments, four currents, i.e., 60 and 100 μA of direct current (DC) and 60 and 100 μA of block current (50% duty cycle, 1 Hz), were applied for 360 min to stimulate the detachment of an
S. epidermidis
biofilm that had grown for 200 min. A 100-μA DC yielded 78% detachment, whereas a 100-μA block current under the same experimental conditions yielded only 31% detachment. The same trend was found for 60 μA, with 37% detachment for a DC and 24% for a block current. Bacteria remaining on the surface after the current application were less viable than they were prior to the current application, as demonstrated by confocal laser scanning microscopy. In conclusion, these results suggest that DCs are preferred for curing infections.
Indole-Diterpene Gene Cluster fromAspergillus flavus
Authors: Zhang Shuguang , Monahan Brendon J. , Tkacz Jan S. , Scott Barry
Published: November 2004

Aflatrem is a potent tremorgenic mycotoxin produced by the soil fungusAspergillus flavusand is a member of a large structurally diverse group of secondary metabolites known as indole-diterpenes. By using degenerate primers for conserved domains of fungal geranylgeranyl diphosphate synthases, we cloned two genes,atmGandggsA(an apparent pseudogene), fromA. flavus. Adjacent toatmGare two other genes,atmCandatmM. These three genes have 64 to 70% amino acid sequence similarity and conserved synteny with a cluster of orthologous genes,paxG,paxC, andpaxM, fromPenicillium paxilliwhich are required for indole-diterpene biosynthesis.atmG,atmC, andatmMare coordinately expressed, with transcript levels dramatically increasing at the onset of aflatrem biosynthesis. A genomic copy ofatmMcan complement apaxMdeletion mutant ofP. paxilli, demonstrating thatatmMis a functional homolog ofpaxM. Thus,atmG,atmC, andatmMare necessary, but not sufficient, for aflatrem biosynthesis byA. flavus. This provides the first genetic evidence for the biosynthetic pathway of aflatrem inA. flavus.
Evaluation of the LIVE/DEAD
Bac
Light Kit for Detection of Extremophilic Archaea and Visualization of Microorganisms in Environmental Hypersaline Samples
Authors: Leuko Stefan , Legat Andrea , Fendrihan Sergiu , Stan-Lotter Helga
Published: November 2004

Extremophilic archaea were stained with the LIVE/DEAD
Bac
Light kit under conditions of high ionic strength and over a pH range of 2.0 to 9.3. The reliability of the kit was tested with haloarchaea following permeabilization of the cells. Microorganisms in hypersaline environmental samples were detectable with the kit, which suggests its potential application to future extraterrestrial halites.
Degradation of a Nonylphenol Single Isomer by
Sphingomonas
sp. Strain TTNP3 Leads to a Hydroxylation-Induced Migration Product
Authors: Corvini P. F. X. , Meesters R. J. W. , Schäffer A. , Schröder H. F. , Vinken R. , Hollender J.
Published: November 2004

Sphingomonas
sp. strain TTNP3 degrades 4(3′,5′-dimethyl-3′-heptyl)-phenol and unidentified metabolites that were described previously. The chromatographic analyses of the synthesized reference compound and the metabolites led to their identification as 2(3′,5′-dimethyl-3′-heptyl)-1,4-benzenediol. This finding indicates that the nonylphenol metabolism of this bacterium involves unconventional degradation pathways where an NIH shift mechanism occurs.
Detection and Enumeration of
Vibrio vulnificus
in Oysters from Two Estuaries along the Southwest Coast of India, Using Molecular Methods
Authors: Parvathi Ammini , Kumar H. Sanath , Karunasagar Indrani , Karunasagar Iddya
Published: November 2004

This study was conducted to understand the seasonal distribution of
Vibrio vulnificus
in oysters from two estuaries and the effect of environmental factors on the abundance of
V. vulnificus
in tropical waters.
V. vulnificus
was detected in 56.6% of the samples tested by colony hybridization with an alkaline phosphatase-labeled oligonucleotide probe (VV-AP), and the counts ranged from <10/g during the summer months to 10
3
/g in the monsoon season at both sites. The density of
V. vulnificus
appeared to be controlled more by salinity than by temperature. A nested PCR used in this study detected
V. vulnificus
in 85% of the samples following 18 h of enrichment in alkaline peptone water.
ON THE BIOLOGICAL ELEMENT SPECTRUM IN ORGANISMS
Authors: TANG REN-HUAN
Published: November 2004

A definition of biological essential elements was proposed. Their origin and function in human body were discussed. An excellent strain Sl of Tetrahymena, a kind of ciliates, has been used in this study to observe both stimulation or nutritious and toxic inhibition effects of elements located in s block, p block, d block, and f block in the periodic table, some regularity between the biological effects of these elements and their positions in the periodic table has been obtained. It is shown that a “spectrum of biological element equilibrium”, which exists in organism, can be exhibited in the periodic table designed in the three-dimensional space, if the abundance of biological elements or/and their bioavailability is used as the third z axis, a vertical line to the plane of the periodic table, and then the biological element spectrum shows that the exchanges of matter and energy between organism and surface environment of the earth have reached the dynamic equilibrium state. It seems that not only physical and chemical properties of different elements and compounds, but also their biological properties to a certain extent can be shown in the developed periodic table.
LIGHT ION-INDUCED L-SHELL IONIZATION OF HIGH-Z ELEMENTS
Authors: PERILLO E. , CUZZOCREA P. , DE CESARE N. , SPADACCINI G. , VIGILANTE M.
Published: November 2004

L-shell X-ray production cross sections for selected heavy elements (Tl, Pb, Bi), of interest in BIO-PIXE analyses, have been measured by proton and 7 Li ion impact in the energy range 0.8–2.6 MeV and 1.8–3.3 MeV respectively. Further, production cross sections for 7 Li ion impact on Au between 1.0 and 2.4 MeV have been measured. L-subshell ionization cross sections have been extracted and arranged, together with similar results from other laboratories, in an analysis aiming at testing the performance of various theoretical approximations in the description of the ionization process. The disagreement observed at low values of the reduced velocity parameter ξ R L between the data and the predictions of the ECPSSR model is significantly reduced by using a United Atom approximation in the treatment of the binding correction, suggested by our group (ECPSSR-UA). The remaining discrepancies, mostly for the L 1-subshell, are almost completely removed by replacing the screened hydrogenlike wave functions with the more realistic Dirac-Hartree-Slater ones. In the case of 7 Li ions, especially for L 2-subshell, also a more refined Coulomb deflection correction and more sophisticated coupled channel calculations are needed.
USE OF HIGH-RESOLUTION X-RAY SPECTROMETER FOR THE STUDY OF CHEMICAL EFFECTS IN X-RAY SPECTRA
Authors: BUDNAR M. , KAVČIČ M. , TADIĆ T. , BOGDANOVIĆ I. , JAKŠIĆ M. , DESNICA U.
Published: November 2004

In the contribution the high-resolution X-ray spectrometer, originally constructed for the atomic physics research, is presented. Test measurements of Lβ and Lγ intensity ratios on In and Te compounds were performed. The applicability of the spectrometer for detection of chemical effects in X-ray spectra of compounds is discussed.
INVESTIGATION OF VACANCY DISTRIBUTION IN C+−B, C+−N, C+−Be andC+−O ION-ATOM COLLISIONS
Authors: Xia Zonghuang , Wang Demin , Wu Shigang
Published: November 2004

The mechanism of vacancy distribution in C +− B , C +− N , C +− Be , and C +− O ion-atom collision process is studied in this paper based on molecular orbital theory. It translates intensity ratio of X-ray and Auger decay in ion-atom collision process.
HIGH RESOLUTION PIXE USING CRYSTAL SPECTROMETER COMBINED WITH POSITION SENSITIVE DETECTORS
Authors: MAEDA KUNIKO , HAMANAKA HIROMI , HASEGAWA KEN-ICHI
Published: November 2004

We describe characteristics of high-resolution, wavelength-dispersive crystal spectrometers equipped with a different type of position sensitive X-ray detectors: PSPC, CCD, IP and MCP. Utilities of these position sensitive spectrometers in PIXE experiments are demonstrated by referring several recent topics of elemental analysis, chemical state analysis and a study on sample charging.
SAMPLE PREPARATION METHOD USING A MICROTOME FOR BIOLOGICAL SPECIMENS
Authors: FUTATSUGAWA S. , HATAKEYAMA S. , SAITOU Y. , SERA K.
Published: November 2004

The preparation of a biological sample using a microtome cryostat was attempted. The biological specimen was previously frozen with a freezing compound and an optimum section thickness was cut for PIXE analysis. First, bovine liver powder which was made into a paste with indium solution as an internal standard was prepared using the sectioning method. The concentrations of trace elements including volatile elements in the sample were determined and agreed with the certified values. Next, a mouse liver was prepared using the sectioning method. A polyphenylene sulfide (PPS) film containing a constant areal density of sulfur was used as a backing material for quantitative analysis. The concentrations of trace elements in a mouse liver prepared using the sectioning method were compared with those using the ordinary nitric acid method. The concentrations of some volatile elements were determined only in the sample obtained using the sectioning method. The preparation method using a microtome cryostat can be used to prepare a biological sample for PIXE analysis.
USE OF Si-PIN PHOTODIODE X-RAY DETECTOR FOR PIXE
Authors: INOUE J. , IWASAKI S. , MUROZONO K. , ISHII K. , MATSUYAMA S.
Published: November 2004

Si-PIN photodiode type detector is one of the X-ray detectors which have recently shown significant improvement in resolution of FWHM of 250 eV at 5.9 keV which is worse only by 130 eV than that of a conventional type Si(Li) detector. The remarkable advantages of the SPINP detector are high operability with the thermoelectric cooling system and low voltage bias, and small volume including the preamplifier system. It is found that SPINP detector is applicable to the X-ray spectrometry and also PIXE in the X-ray energy range below about 15 keV with a reasonable efficiency. The pattern analysis method is feasible to analysis such bad resolution spectra obtained with this detector. Some techniques related to the Si-PIN photodiode type detector in Bio-PIXE are discussed.
Carbonized Treatment of Biological Samples for High Beam Current PIXE - its advantages and problems -
Authors: KOHNO M. , YOSHIDA K. , MORITANI K. , NORIZAWA K. , NAITO M. , KITAO K. , ENAMI K. , MAEDA H. , KASAJIMA H. , TAKADA J.
Published: November 2004

Trace elements in ancient Chinese ink, ancient Chinese paper of sutras, ancient Japanese paper of manuscripts, modem Japanese paper and some plants were analyzed by PIXE. Part of these samples were carbonized at 400°C in vacuum of several torrs. These carbonized biological samples were able to resist very high current of 2 MeV He + (500 nA/mm 2 on target) for more than 30 minutes. The observation indicates that the carbonized samples save the measuring time by using high beam current. But mercury and sulfur contained in red Chinese ink on the paper were lost through the carbonization and lead in the same sample was lost by heating up during the measurement on condition that it was irradiated by 2 MeV He + (50 nA/mm 2 to 230 nA/mm 2). A small part of iron was gradually lost on the same condition. Under 230 nA/mm 2, a small portion of calcium was lost but no portion of chromium was lost.
ADVANCES OF NUCLEAR MICROPROBES AND THEIR APPLICATIONS
Authors: ZHU JIEQING , LI XIAOLIN
Published: November 2004

This paper reviews the recent progress of the nuclear microprobe technology in both micro-analysis and micro-imaging. Some features of the nuclear microprobe facilities established at the Shanghai Institute of Nuclear Research and Fudan University are described Four examples of recent applications are enclosed to show the potentialities of the technique for a variety of scientific studies.
PIXE AND ITS APPLICATIONS TO BIOLOGICAL SAMPLES: PRESENT STATUS
Authors: ALDAPE F. , FLORES M. J.
Published: November 2004

Throughout this century, industrialized society has seriously affected the ecology by introducing huge amounts of pollutants into the atmosphere as well as marine and soil environments. On the other hand, it is known that these pollutants, in excess of certain levels of concentration, not only put at risk the life of living beings but may also cause the extinction of some species. It is therefore of basic importance to substantially increase quantitative determinations of trace element concentrations in biological specimens in order to assess the effects of pollutants. It is in this field that PIXE plays a key role in these studies, where its unique analytical properties are decisive. Moreover, since the importance of these research has been recognized in many countries, many scientists have been encouraged to continue or initiate new research programmes aimed to solve the worldwide pollution problem. This document presents an overview of those papers reporting the application of PIXE analysis to biological samples during this last decade of the XX century and recounts the number of PIXE laboratories dedicating their efforts to find the clues of the biological effects of the presence of pollutants introduced in living beings. Sample preparation methods, different kinds of samples under study and the use of complementary analytical techniques are also ilustrated.
PIXE Analysis of Fish Otoliths: Application to Fish Stock Discrimination
Authors: ARAI NOBUAKI , SAKAMOTO WATARU , TATENO KOJI , YOSHIDA KOJI
Published: November 2004

PIXE was adopted to analyze trace elements in otoliths of Japanese flounder to discriminate among several local fish stocks. The otoliths were removed from samples caught at five different sea areas along with the coast of the Sea of Japan: Akita, Ishikawa, Kyoto (2 stations), and Fukuoka. Besides calcium as main component, strontium, manganese, and zinc were detected. Especially Sr concentrations were different among 4 areas except between 2 stations in Kyoto. It suggested that the fish in the 2 stations in Kyoto were the same stock differed to the others.
THE VOLATILE CHARACTER OF TRACE ELEMENTS IN BIOMEDICAL SAMPLES AND GUM TISSUE ANALYSES
Authors: MAETZ MISCHA , RIEGER PETER , STEIN KIRSTEN , TRAXEL KURT
Published: November 2004

During PIXE analyses of biomedical samples often great damage of the sample occurs. This damage is always combined with mass loss and strong alterations of the initial structure. The loss of mass can be explained by the loss of volatile elements, mainly the major elements Hydrogen, Carbon, Nitrogen, and Oxygen. This results in a charge dependency of the element contents and has to be corrected during the data reduction. Here we describe measurements of different samples that monitor the mass loss and the charge dependency of the trace element concentrations. A model was developed to give the correct concentrations after the PIXE analyses. Additionally first results of PIXE analyses of gum tissue are reported. They give direct hints for amalgam residues inside the tissue in pathologically altered areas.
LEAD CONTENTS IN BLOOD SAMPLES OF A CHILDREN POPULATION OF MEXICO CITY RELATED TO LEVELS OF AIRBORNE LEAD DETERMINED BY PIXE
Authors: URIBE-HERNÁNDEZ R. , PÉREZ-ZAPATA A.J. , FLORES M. J. , ALDAPE F. , HERNÁNDEZ-MÉNDEZ B.
Published: November 2004

Airborne lead has been considered for many years one of the main pollutants adversely affecting the health of human beings. Moreover, this problem becomes remarkably important in large urban areas such as Mexico City. In order to assess the influence of atmospheric airborne lead in a children population, a biological blood sampling was carried out from September 1992 to June 1993 taking 698 samples in children with ages ranging from a few weeks to thirteen years old. Lead contents in whole blood were determined using anode stripping voltammetry as analytical technique. At the same time, aerosol lead contents were determined by PIXE from samples taken twice a week (two samples per day) in a neighbour area. In 58 % of the samples, lead contents in blood was found over the maximum permissible level established by the Center for Disease Control (CDC) of the U.S.A. The biological sampling was correlated to levels of airborne lead as well as children age and date of sampling. General results of these comparisons are presented.
ELEMENTAL BALANCE IN SOY SAUCE
Authors: HARUYAMA YOICHI , SAITO MANABU , YOSHIDA KOJI
Published: November 2004

We have measured the elemental concentrations of soy sauce and its actual raw materials which are used in a certain soy sauce factory. In the present measurement, we measured de-fatted soybean, wheat and salt as raw materials and soy sauce and soy sauce waste as final products. Five kinds of elements, such as Mn, Fe, Cu. Zn and Br, were detected. We obtained elemental concentrations of them except for Mn in each materials. The measured elemental concentration in soy sauce agreed well each other with the calculated one within the experimental errors using the measured concentration in the raw mateials and their weight in actual producing process. Contrary to our expectation, it was found that wheat contributes to soy sauce bromine concentration dominantly in the present case.
ANALYSIS OF LIVER BIOPSY SAMPLES FOR Fe, Cu AND Zn USING PIXE
Authors: PEYROVAN H. , HATAMI P. , MANSOURIAN N. , SHOKOUHI F.
Published: November 2004

Proton Induced X-ray Emission analysis was applied to measure the concentration of Fe, Cu and Zn in liver biopsy samples with Wilson’s disease. Due to the small size of sample and non-conductive character of the material absolute measurement was not possible, therefore the ratio of elements such as Cu/Fe and Zn/Fe were determined. The comparison of these values obtained from normal liver samples helps the physicians to determine the stage of disease.
SIZE DISTRIBUTION AND SOLUBILITY OF 15 ELEMENTS IN ATMOSPHERIC AEROSOLS
Authors: KASAHARA M. , PARK J.H. , CHATANI S.
Published: November 2004

To investigate the physical and chemical characteristics of atmospheric aerosols, aerosol particles were sampled with classifying into 13 size ranges between 0.01 and 30µm. Collected aerosol particles were separated into the soluble and insoluble components. The concentrations of 15 elements in both components were determined by a PIXE analysis using a 2.0MeV-proton beam.

The mass size distribution of each element was illustrated in three types: mono-modal distribution having only one peak in the fine or coarse fraction and the bimodal distribution having one peak each in fine and coarse fractions. The mass mean diameter of 15 elements ranged between 0.62µm of S and 3.15µm of Fe. More than 85% of atmospheric aerosols consists of the lighter elements such as C, N, O, H and Al. The soluble component was dominant in the smaller size range and the insoluble component in the larger size range. Si, Ti and especially Fe existed in high insoluble state. Conversely, Ca, Zn, Br and especially S and Cl were dissolved in water.
RELATIONSHIP BETWEEN STATOLITHS AND ENVIRONMENTAL VARIABLES IN CEPHALOPOD
Authors: IKEDA Y. , ARAI N. , SAKAMOTO W. , KIDOKORO H. , YOSHIDA K.
Published: November 2004

The hard tissues of cephalopod, namely statoliths were analyzed with PIXE for the Japanese common squid Todarodes pacificus of the Sea of Japan origin in order to examine the relationship between the amount of trace elements in statoliths and environmental temperature of the squid habitat. Calcium, iron, zinc. copper and strontium were detected in the statoliths. Negative relationship was observed between Sr concentration in statoliths and environmental temperature. On the contrary to Sr, Fe and Zn concentration in statoliths related positively with environmental temperature. These observations revealed that the statoliths would be a useful thermometer for reconstructing the environmental temperature of cephalopod habitat as seen in the hard tissues of other marine organisms.
PIXE ANALYSIS VS. GRAVIMETRY TO MONITOR THE MASS CONCENTRATION OF ATMOSPHERIC AEROSOLS IN THE RESPIRABLE FRACTION
Authors: ROMO-KRÖGER C.M.
Published: November 2004

It is demonstrated in this work, that PIXE is a good mass indicator for suspended particles in urban environments. Results are presented for several samplings performed in urban and other environments in Chile and other countries. Aerosols were collected on filters operated by a Stacked Filter Unit (SFU) in the range of particles < 15 µ m (PM15) and < 10 µ m (PM10), mainly the respirable fraction. For samplings performed in downtown Santiago, the sum of the concentrations of the elements detected by PIXE correlated well with the indices of respirable suspended particles (RSP) measured by gravimetry. There was no high correlation for other samplings, near a crushing plant and near mineral storage. On the average, the sum of the PIXE results for Santiago’s aerosols represents about the 15% of the total mass collected in the respirable fraction. A measurement of collection efficiency for the 0.4 µm Nuclepore filter was performed by means of PIXE and gravimetry. These results were η PIXE =0.98 and η balance =0.96, for the PIXE and the gravimetric method.
ELEMENTS DISTRIBUTION IN KIDNEY OF RATS TREATED WITH CdCL2 BY MICRO-SXRF
Authors: LIU NIANQING , SHAO HANRU , LIU PENG , XU QING , PAN JUXIANG , WU YINGRONG , MA DONGXIN , ZHAO JINYUAN
Published: November 2004

A micro-scanning technique of SXRF (Synchrotron Radiation X-ray fluorescence) combined with multivariate statistical analysis was employed. The elements positional distribution in the kidney tissues of tree groups of Wistar rats (1, normal; 2, treated by CdCl 2; 3, Cd exposed rats treated with new complex) were obtained. The results show that Cd mainly distribute in the renal cortex of rat treated by CdCl 2. The level of Cd in the renal medulla is very low or not detectable. The elements measured in renal cortex of normal rat can be classified into two groups, Cu, Zn, Mn and Se belong to the same group. In acute CdCl 2 poisoning, Cd and Se have a very strong correlation, and the classification is different from normal renal cortex. After administration of a new chelator, Zn and Se have a very strong co-location and correlation, the classification of elements tend to return to normal distribution.
CONTINUUM X RAYS IN HIGHLY CHARGED ION-ATOM COLLISIONS
Authors: KAWATSURA K. , HASEGAWA T. , TERAZAWA N. , ARAI S. , SATAKA M. , NARAMOTO H. , KOMAKI K. , OOTUKA A.
Published: November 2004

Continuous X rays produced by highly charged heavy ion-atom collisions have been studied experimentally. 2–5.5 MeV/u F, Si, S and Cl ions with zero or one electron were bombarded with a thin gas target of H 2 and He. Emitted X-ray spectra were measured by using a Si(Li) X-ray detector at 90°. The characteristic X rays and radiative electron capture X rays were observed clearly, which were superimposed on the continuum X rays. The continuum X rays can be well explained by two types of radiative processes: mainly quasi-free electron bremsstrahlung (QFEB), and partly atomic bremsstrahlung (AB). It should be noticed that QFEB is predominant at low X-ray energy region and AB at high X-ray energy region in highly charged heavy ion-atom collision process.
STANDARD-FREE METHOD OF QUANTITATIVE ANALYSIS FOR BIO-SAMPLES
Authors: SERA K. , FUTATSUGAWA S. , MATSUDA K. , MIURA Y.
Published: November 2004

Internal Standard Method, which has been widely used for quantitative analysis of general bio-samples, requires certain skill in sample preparation since it sometimes accompanies a noticeable error due not only to inaccuracy of weight measurement both of a sample and of an internal standard but also to nonuniformity of the internal standard in the target. In this work, a standard-free method of quantitative analysis, based on the fact that the total yield of continuous x-rays from the sample approximately corresponds to effective weight of the sample, has been developed and applied to some typical bio-samples (NIST Bovine liver, a rat liver and a human serum). As a result, values of concentration obtained by the present method present good agreement with those obtained by the internal standard method. Further, in a case where target preparation is performed by unskilled person, the present method gives better results than those obtained by the internal standard method. It is also found that this method is applicable to almost all soft-tissue samples and, moreover, to targets prepared by a different method.
A PRECONCENTRATION TECHNIQUE FOR WATER ANALYSIS BY PIXE
Authors: YAMAZAKI H. , TANAKA M. , TSUTSUMI K. , ISHII K. , IWASAKI S. , MATSUYAMA S. , INOUE J. , MUROZONO K. , ORIHARA H.
Published: November 2004

The enrichment procedure of heavy metals ( Fe 3+, Co 2+, and Hg 2+) in water was examined in conjunction with in-air PIXE. The preconcentration step consisted of adsorption of dibenzyldithiocarbamate complexes of the metal ions onto dibenzylidene-D-sorbitol gels. The colloidal gels in solutions were then collected on a nuclepore membrane for direct irradiation by proton beams in a system of vertical beam type in-air PIXE. The amounts of the chemicals used in the enrichment were minimized to prepare thin target specimens with the homogeneous composition. The metal-recovery in the preconcentration step was confirmed to be quantitative in a wide range of the concentrations. The reproducibility and detection limit were shown and discussed for the present setup of PIXE analysis in our laboratory.
Loss of Elements in Ancient Red Chinese Ink on Japanese Paper through Proton-PIXE
Authors: KOHNO M. , YOSHIDA K. , MORITANI K. , NORIZAWA K. , NAITO M. , ENAMI K. , TAKADA J.
Published: November 2004

For the purpose of studying loss of elements through PIXE analysis, a target of modern Japanese paper with ancient red Chinese ink on was prepared and analyzed. Red Chinese ink includes mercury sulfide which has low melting point of 583 °C at 1 atm. In this study, two classes of 2 MeV proton beams of about 5 nA/mm 2 and 50 nA/mm 2 were used. A simple data taking system of multi-spectra was establised and X-ray spectra by proton-PIXE were consecutively obtained every 10 seconds for about 2 hours. The obtained multi-spectra were used for the loss of each element in the target. The results show that S, Hg and Pb in the target gradually decrease with time under 50 nA/mm 2 of a 2 MeV proton beam and the decreases start under about 25 nA/mm 2. These elements, however, don’t decrease under 5 nA/mm 2. Most of chlorine in modem Japanese paper was lost under 15 nA/mm 2.
Determination of Trace Elements in Mate using PIXE Analysis
Authors: YUKAWA MASAE , WATANABE YOSHITO , NISHIMURA YOSHIKAZU , WADA MASAHIRO
Published: November 2004

Mate is a kind of tea popular in Central and South America. Trace elements contained in two types of Mate. green Mate and roast Mate. obtained from various districts were determined using PIXE technique comparing the results with those of other teas. Contents of Ca. Mn and Zn in Mate leaf were higher than those of the other tea leaves. Ca and Mn were exuded more easily from the Mate leaves than from the other tea leaves. Exudation amount of Zn was larger in the green Mate than in the roast Mate. It was suggested that Mate is a better supplier of trace elements than other teas.
PIXE ANALYSIS OF THE SERUM OF MICE ACQUIRED RADIORESISTANCE AFTER SMALL DOSE OF X-RAY IRRADIATION
Authors: YONEZAWA M. , MATSUDA Y. , NISHIYAMA F.
Published: November 2004

It is important for maintenance and understanding of health to make inquiries into the biological defence mechanisms. Yonezawa et al. came across an induction of yet unknown defence mechanisms in mice which acquired two types of radioresistance (decrease in bone-marrow death rate after midlethal exposure): one occured 2 weeks after preirradiation with 0.3–0.5 Gy and the other 2 months after 0.05–0.10 Gy of X-rays. To elucidate the acquired radioresistance induced after preirradiation with 0.5 Gy (in a shorter time case). recovery of blood cell counts after sublethal irradiation were measured in mice of ICR strain. Contrary to the common knowledge on radiation protection. recovery of blood cell counts of thrombocytes. leukocytes and erythrocytes after sublethal irradiation were not stimulated by the preirradiation. This study was planned to find some keys to elucidate the mechanism for the acquired radioresistance. Eleven elements. Cl. K. Ca. Cr. Mn. Fe. Ni. Cu. Zn. Se and Br. were analysed clearly in mice sera by PIXE.
COMPLEXITY AND REAL COMPUTATION: A MANIFESTO
Authors: BLUM LENORE , CUCKER FELIPE , SHUB MIKE , SMALE STEVE
Published: November 2004

Finding a natural meeting ground between the highly developed complexity theory of computer science — with its historical roots in logic and the discrete mathematics of the integers — and the traditional domain of real computation, the more eclectic less foundational field of numerical analysis — with its rich history and longstanding traditions in the continuous mathematics of analysis — presents a compelling challenge. Here we illustrate the issues and pose our perspective toward resolution.
CHAOTIC BEHAVIOR OF ORBITS CLOSE TO A HETEROCLINIC CONTOUR
Authors: BLÁZQUEZ M. , TUMA E.
Published: November 2004

We study the behavior of the solutions in a neighborhood of a closed contour formed by two heteroclinic connections to two equilibrium points of saddle-focus type. We consider both the three-dimensional case, as in the well-known Chua's circuit, as well as the infinite-dimensional case.
MULTI-PARAMETER CRITICALITY IN CHUA'S CIRCUIT AT PERIOD-DOUBLING TRANSITION TO CHAOS
Authors: KUZNETSOV A. P. , KUZNETSOV S. P. , SATAEV I. R. , CHUA L. O.
Published: November 2004

Investigation of non-Feigenbaum types of period-doubling universality is undertaken for a single Chua's circuit and for two systems with a unidirectional coupling. Some codimension-2 critical situations are found numerically that were known earlier for bimodal 1D maps. However, the simplest of them (tricritical) does not survive in a strict sense when the exact dynamical equations are used instead of the 1D map approximation. In coupled systems double Feigenbaum's point and bicritical behavior are found and studied. Scaling properties that are the same as in two logistic maps with a unidirectional coupling are illustrated.
THE TOPOLOGY OF BASIN BOUNDARIES IN A CLASS OF THREE-DIMENSIONAL DYNAMICAL SYSTEMS
Authors: KLEMM M. , BECKMANN P. E.
Published: November 2004

We will develop new methods to determine the topology of the basin boundary in a class of three-dimensional dynamical systems. One approach is to approximate the basin boundary by backward integration. Unfortunately, there are dynamical systems where it is hard to approximate the basin boundary by a numerical backward integration algorithm. We will introduce topological methods which will provide new information about the structure of the basin boundary. The topological invariants which we will use can be numerically computed.
TOPOLOGICAL WINDING NUMBERS FOR PERIOD-DOUBLING CASCADES
Authors: KNUDSEN CARSTEN
Published: November 2004

We define the topological winding number for unimodal maps that share the essential properties of that of winding numbers for forced oscillators exhibiting period-doubling cascades. It is demonstrated how this number can be computed for any of the periodic orbits in the first period-doubling cascade. The limiting winding number at the accumulation point of the first period-doubling cascade is also derived. It is shown that the limiting value for the winding number ω∞ can be computed as the Farey sum of any two neighbouring topological winding numbers in the period-doubling cascade. The derivations are all based on symbolic dynamics and simple combinatorics.
LINEAR TRANSPORT OF PARTICLES ON NETWORKS
Authors: BARLETTI LUIGI
Published: November 2004

We introduce a model of transport of particles in a network, which is represented by a connected graph with m vertices and n edges. Each edge represents a one-dimensional conductor of particles, whose behavior is described by means of a linear Boltzmann-like equation. In graph vertices, a system of linear boundary conditions is given which takes into account the exchanges of particles between the edges. The well-posedness of the initial value problem is studied into an abstract L1-like setting and the structure of the solution is given for simplest case of pure streaming transport.
SCATTERING OF PLANE WAVES FROM LAYERED MEDIA WITH A ROUGH INTERFACE
Authors: BJØRNØ LEIF , SUN SHAOBO
Published: November 2004

Scattering of acoustic plane waves from a multi-layer medium with a rough interface is studied theoretically and numerically in the present paper. The solution is based upon a multi-layer wave reflection model and a single rough interface scattering model. A Gaussian and random roughness is assumed for the rough interface. It turns out that the rms-height (h) and the correlation-length (L) of the rough interface are the two governing parameters for the scattered wave field. The scattered wave field is compared with the basic reflection pattern from a multi-layer model without interface roughnesses. The present model forms a good analogy to a layered seabed or a layered ice structure.