bluuebunny/crossref_metadata_2025 huggingface dataset:
Orientation within the Exosporium and Structural Stability of the Collagen-Like Glycoprotein BclA of
Bacillus anthracis
Authors: Boydston Jeremy A. , Chen Ping , Steichen Christopher T. , Turnbough Charles L.
Published: July 2005

Bacillus anthracis
spores, which cause anthrax, are enclosed by an exosporium consisting of a basal layer and an external hair-like nap. The filaments of the nap are composed of BclA, a glycoprotein containing distinct N-terminal (NTD) and C-terminal (CTD) domains separated by an extended collagen-like central region. In this study, we used immunogold electron microscopy to show that the CTD of BclA forms the distal end of each filament of the hair-like nap, indicating that the NTD is attached to the basal layer. Ten randomly chosen anti-BclA monoclonal antibodies, raised against spores or exosporium, reacted with the CTD, consistent with its exterior location. We showed that recombinant BclA (rBclA), encoded by the
B. anthracis
Sterne strain and synthesized in
Escherichia coli
, forms a collagen-like triple helix as judged by collagenase sensitivity and circular dichroism spectroscopy. In contrast, native BclA in spores was resistant to collagenase digestion. Thermal denaturation studies showed that the collagen-like region of rBclA exhibited a melting temperature (
T

m

) of 37°C, like mammalian collagen. However, rBclA trimers exhibited
T

m

values of 84°C and 95°C in buffer with and without sodium dodecyl sulfate, respectively. CTD trimers exhibited the same
T

m

values, indicating that the high temperature and detergent resistances of rBclA were due to strong CTD interactions. We observed that CTD trimers are resistant to many proteases and readily form large crystalline sheets. Structural data indicate that the CTD is composed of multiple beta strands. Taken together, our results suggest that BclA and particularly its CTD form a rugged shield around the spore.
Staphylococcus aureus
Develops an Alternative,
ica-
Independent Biofilm in the Absence of the
arlRS
Two-Component System
Authors: Toledo-Arana Alejandro , Merino Nekane , Vergara-Irigaray Marta , Débarbouillé Michel , Penadés José R. , Lasa Iñigo
Published: July 2005

The biofilm formation capacity of
Staphylococcus aureus
clinical isolates is considered an important virulence factor for the establishment of chronic infections. Environmental conditions affect the biofilm formation capacity of
S. aureus
, indicating the existence of positive and negative regulators of the process. The majority of the screening procedures for identifying genes involved in biofilm development have been focused on genes whose presence is essential for the process. In this report, we have used random transposon mutagenesis and systematic disruption of all
S. aureus
two-component systems to identify negative regulators of
S. aureus
biofilm development in a chemically defined medium (
H
ussain-
H
astings-
W
hite
m
odified medium [HHWm]). The results of both approaches coincided in that they identified
arlRS
as a repressor of biofilm development under both steady-state and flow conditions. The
arlRS
mutant exhibited an increased initial attachment as well as increased accumulation of poly-
N
-acetylglucosamine (PNAG). However, the biofilm formation of the
arlRS
mutant was not affected when the
icaADBC
operon was deleted, indicating that PNAG is not an essential compound of the biofilm matrix produced in HHWm. Disruption of the major autolysin gene,
atl
, did not produce any effect on the biofilm phenotype of an
arlRS
mutant. Epistatic experiments with global regulators involved in staphylococcal-biofilm formation indicated that
sarA
deletion abolished, whereas
agr
deletion reinforced, the biofilm development promoted by the
arlRS
mutation.
Identification and Characterization of a Novel Adhesin Unique to Oral Fusobacteria
Authors: Han Yiping W. , Ikegami Akihiko , Rajanna Chythanya , Kawsar Hameem I. , Zhou Yun , Li Mei , Sojar Hakimuddin T. , Genco Robert J. , Kuramitsu Howard K. , Deng Cheri X.
Published: July 2005

Fusobacterium nucleatum
is a gram-negative anaerobe that is prevalent in periodontal disease and infections of different parts of the body. The organism has remarkable adherence properties, binding to partners ranging from eukaryotic and prokaryotic cells to extracellular macromolecules. Understanding its adherence is important for understanding the pathogenesis of
F. nucleatum
. In this study, a novel adhesin, FadA (
Fusobacterium ad
hesin
A
), was demonstrated to bind to the surface proteins of the oral mucosal KB cells. FadA is composed of 129 amino acid (aa) residues, including an 18-aa signal peptide, with calculated molecular masses of 13.6 kDa for the intact form and 12.6 kDa for the secreted form. It is highly conserved among
F. nucleatum
,
Fusobacterium periodonticum
, and
Fusobacterium simiae
, the three most closely related oral species, but is absent in the nonoral species, including
Fusobacterium gonidiaformans
,
Fusobacterium mortiferum
,
Fusobacterium naviforme
,
Fusobacterium russii
, and
Fusobacterium ulcerans
. In addition to FadA,
F. nucleatum
ATCC 25586 and ATCC 49256 also encode two paralogues, FN1529 and FNV2159, each sharing 31% identity with FadA. A double-crossover
fadA
deletion mutant,
F. nucleatum
12230-US1, was constructed by utilizing a novel sonoporation procedure. The mutant had a slightly slower growth rate, yet its binding to KB and Chinese hamster ovarian cells was reduced by 70 to 80% compared to that of the wild type, indicating that FadA plays an important role in fusobacterial colonization in the host. Furthermore, due to its uniqueness to oral
Fusobacterium
species,
fadA
may be used as a marker to detect orally related fusobacteria.
F. nucleatum
isolated from other parts of the body may originate from the oral cavity.
Induction of the MexXY Efflux Pump in
Pseudomonas aeruginosa
Is Dependent on Drug-Ribosome Interaction
Authors: Jeannot Katy , Sobel Mara L. , El Garch Farid , Poole Keith , Plésiat Patrick
Published: July 2005

MexXY is an inducible efflux system that contributes to the natural resistance of
Pseudomonas aeruginosa
to antibiotics. Experiments involving real-time PCR after reverse transcription in reference strain PAO1 showed concentration-dependent induction of gene
mexY
by various ribosome inhibitors (e.g., chloramphenicol, tetracycline, macrolides, and aminoglycosides) but not by antibiotics acting on other cellular targets (e.g., β-lactams, fluoroquinolones). Confirming a functional link between the efflux system and the translational machinery, ribosome protection by plasmid-encoded proteins TetO and ErmBP increased the resistance of a Δ
mexAB-oprM
mutant of PAO1 to tetracycline and erythromycin, respectively, as well as the concentrations of both drugs required to induce
mexY
. Furthermore, spontaneous mutations resulting in specific resistance to dihydrostreptomycin or spectinomycin also raised the minimal drug concentration for
mexXY
induction in strain PAO1. While strongly upregulated in a PAO1 mutant defective in gene
mexZ
(which codes for a putative repressor of operon
mexXY
), gene
mexY
remained inducible by agents such as tetracycline, chloramphenicol, and spectinomycin, suggesting additional regulatory loci for
mexXY
. Altogether, these data demonstrate physiological interplays between MexXY and the ribosome and are suggestive of an alternative function for MexXY beyond antibiotic efflux.
Mutation of the
priA
Gene of
Neisseria gonorrhoeae
Affects DNA Transformation and DNA Repair
Authors: Kline Kimberly A. , Seifert H. Steven
Published: July 2005

In
Escherichia coli
, PriA is central to the restart of chromosomal replication when replication fork progression is disrupted and is also involved in homologous recombination and DNA repair. To investigate the role of PriA in recombination and repair in
Neisseria gonorrhoeae
, we identified, cloned, and insertionally inactivated the gonococcal
priA
homologue. The
priA
mutant showed a growth deficiency and decreased DNA repair capability and was completely for deficient in DNA transformation compared to the isogenic parental strain. The
priA
mutant was also more sensitive to the oxidative damaging agents H
2
O
2
and cumene hydroperoxide compared to the parental strain. These phenotypes were complemented by supplying a functional copy of
priA
elsewhere in the chromosome. The
N. gonorrhoeae priA
mutant showed no alteration in the frequency of pilin antigenic variation. We conclude that PriA participates in DNA repair and DNA transformation processes but not in pilin antigenic variation.
Cationic Antimicrobial Peptide Resistance in
Neisseria meningitidis
Authors: Tzeng Yih-Ling , Ambrose Karita D. , Zughaier Susu , Zhou Xiaoliu , Miller Yoon K. , Shafer William M. , Stephens David S.
Published: July 2005

Cationic antimicrobial peptides (CAMPs) are important components of the innate host defense system against microbial infections and microbial products. However, the human pathogen
Neisseria meningitidis
is intrinsically highly resistant to CAMPs, such as polymyxin B (PxB) (MIC ≥ 512 μg/ml). To ascertain the mechanisms by which meningococci resist PxB, mutants that displayed increased sensitivity (≥4-fold) to PxB were identified from a library of mariner transposon mutants generated in a meningococcal strain, NMB. Surprisingly, more than half of the initial PxB-sensitive mutants had insertions within the
mtrCDE
operon, which encodes proteins forming a multidrug efflux pump. Additional PxB-sensitive mariner mutants were identified from a second round of transposon mutagenesis performed in an
mtr
efflux pump-deficient background. Further, a mutation in
lptA
, the phosphoethanolamine (PEA) transferase responsible for modification of the lipid A head groups, was identified to cause the highest sensitivity to PxB. Mutations within the
mtrD
or
lptA
genes also increased meningococcal susceptibility to two structurally unrelated CAMPs, human LL-37 and protegrin-1. Consistently, PxB neutralized inflammatory responses elicited by the
lptA
mutant lipooligosaccharide more efficiently than those induced by wild-type lipooligosaccharide.
mariner
mutants with increased resistance to PxB were also identified in NMB background and found to contain insertions within the
pilMNOPQ
operon involved in pilin biogenesis. Taken together, these data indicated that meningococci utilize multiple mechanisms including the action of the MtrC-MtrD-MtrE efflux pump and lipid A modification as well as the type IV pilin secretion system to modulate levels of CAMP resistance. The modification of meningococcal lipid A head groups with PEA also prevents neutralization of the biological effects of endotoxin by CAMP.
Mosaic Nature of theWolbachiaSurface Protein
Authors: Baldo Laura , Lo Nathan , Werren John H.
Published: July 2005

Lateral gene transfer and recombination play important roles in the evolution of many parasitic bacteria. Here we investigate intragenic recombination inWolbachiabacteria, considered among the most abundant intracellular bacteria on earth. We conduct a detailed analysis of the patterns of variation and recombination within theWolbachiasurface protein, utilizing an extensive set of published and new sequences from five main supergroups ofWolbachia. Analysis of nucleotide and amino acid sequence variations confirms four hypervariable regions (HVRs), separated by regions under strong conservation. Comparison of shared polymorphisms reveals a complex mosaic structure of the gene, characterized by a clear intragenic recombining of segments among several distinct strains, whose major recombination effect is shuffling of a relatively conserved set of amino acid motifs within each of the four HVRs. Exchanges occurred both within and between the arthropod supergroups. Analyses based on phylogenetic methods and a specific recombination detection program (MAXCHI) significantly support this complex partitioning of the gene, indicating a chimeric origin ofwsp. Althoughwsphas been widely used to define macro- and microtaxonomy amongWolbachiastrains, these results clearly show that it is not suitable for this purpose. The role ofwspin bacterium-host interactions is currently unknown, but results presented here indicate that exchanges of HVR motifs are favored by natural selection. Identifying host proteins that interact withwspvariants should help reveal how these widespread bacterial parasites affect and evolve in response to the cellular environments of their invertebrate hosts.
Unusual Group II Introns in Bacteria of theBacillus cereusGroup
Authors: Tourasse Nicolas J. , Stabell Fredrik B. , Reiter Lillian , Kolstø Anne-Brit
Published: July 2005

A combination of sequence and structure analysis and reverse transcriptase PCR experiments was used to characterize the group II introns in the complete genomes of two strains of the pathogenBacillus cereus. WhileB. cereusATCC 14579 harbors a single intron element in the chromosome,B. cereusATCC 10987 contains three introns in the chromosome and four in its 208-kb pBc10987 plasmid. The most striking finding is the presence inB. cereusATCC 10987 of an intron [B.c.I2(a)] located on the reverse strand of a gene encoding a putative cell surface protein which appears to be correlated to strains of clinical origin. Because of the opposite orientation ofB.c.I2(a), the gene is disrupted. Even more striking is thatB.c.I2(a) splices out of an RNA transcript corresponding to the opposite DNA strand. All other intragenic introns studied here are inserted in the same orientation as their host genes and splice out of the mRNA in vivo, setting the flanking exons in frame. Noticeably,B.c.I3 inB. cereusATCC 10987 represents the first example of a group II intron entirely included within a conserved replication gene, namely, the α subunit of DNA polymerase III. Another striking finding is that the observed 3′ splice site ofB.c.I4 occurs 56 bp after the predicted end of the intron. This apparently unusual splicing mechanism may be related to structural irregularities in the 3′ terminus. Finally, we also show that the intergenic introns ofB. cereusATCC 10987 are transcribed with their upstream genes and do splice in vivo.
De Novo Alanine Synthesis by Bacteroids ofMesorhizobium lotiIs Not Required for Nitrogen Transfer in the Determinate Nodules ofLotus corniculatus
Authors: Kumar Shalini , Bourdès Alexandre , Poole Philip
Published: July 2005

Deletion of both alanine dehydrogenase genes (aldA) inMesorhizobium lotiresulted in the loss of AldA enzyme activity from cultured bacteria and bacteroids but had no effect on the symbiotic performance ofLotus corniculatusplants. Thus, neither indeterminate pea nodules nor determinateL. corniculatusnodules export alanine as the sole nitrogen secretion product.
Characterization of the
Vibrio cholerae vceCAB
Multiple-Drug Resistance Efflux Operon in
Escherichia coli
Authors: Woolley Robin C. , Vediyappan Govindsamy , Anderson Matthew , Lackey Melinda , Ramasubramanian Bhagavathi , Jiangping Bai , Borisova Tatyana , Colmer Jane A. , Hamood Abdul N. , McVay Catherine S. , Fralick Joe A.
Published: July 2005

Herein, we identify
vceC
as a component of a
vceCAB
operon, which codes for the
Vibrio cholerae
VceAB multiple-drug resistance (MDR) efflux pump, and
vceR
, which codes for a transcriptional autoregulatory protein that negatively regulates the expression of the
vceCAB
operon and is modulated by some of the substrates of this MDR efflux pump.
THE KEY ROLE OF LIQUIDITY FLUCTUATIONS IN DETERMINING LARGE PRICE CHANGES
Authors: LILLO FABRIZIO , DOYNE FARMER J.
Published: July 2005

Recent empirical analyses have shown that liquidity fluctuations are important for understanding large price changes of financial assets. These liquidity fluctuations are quantified by gaps in the order book, corresponding to blocks of adjacent price levels containing no quotes. Here we study the statistical properties of the state of the limit order book for 16 stocks traded at the London Stock Exchange (LSE). We show that the time series of the first three gaps are characterized by fat tails in the probability distribution and are described by long memory processes.
ION BEAM LITHOGRAPHY AND NANOFABRICATION: A REVIEW
Authors: WATT F. , BETTIOL A. A. , VAN KAN J. A. , TEO E. J. , BREESE M. B. H.
Published: July 2005

To overcome the diffraction constraints of traditional optical lithography, the next generation lithographies (NGLs) will utilize any one or more of EUV (extreme ultraviolet), X-ray, electron or ion beam technologies to produce sub-100 nm features. Perhaps the most under-developed and under-rated is the utilization of ions for lithographic purposes. All three ion beam techniques, FIB (Focused Ion Beam), Proton Beam Writing (p-beam writing) and Ion Projection Lithography (IPL) have now breached the technologically difficult 100 nm barrier, and are now capable of fabricating structures at the nanoscale. FIB, p-beam writing and IPL have the flexibility and potential to become leading contenders as NGLs.

The three ion beam techniques have widely different attributes, and as such have their own strengths, niche areas and application areas. The physical principles underlying ion beam interactions with materials are described, together with a comparison with other lithographic techniques (electron beam writing and EUV/X-ray lithography). IPL follows the traditional lines of lithography, utilizing large area masks through which a pattern is replicated in resist material which can be used to modify the near-surface properties. In IPL, the complete absence of diffraction effects coupled with ability to tailor the depth of ion penetration to suit the resist thickness or the depth of modification are prime characteristics of this technique, as is the ability to pattern a large area in a single brief irradiation exposure without any wet processing steps. p-beam writing and FIB are direct write (maskless) processes, which for a long time have been considered too slow for mass production. However, these two techniques may have some distinct advantages when used in combination with nanoimprinting and pattern transfer. FIB can produce master stamps in any material, and p-beam writing is ideal for producing three-dimensional high-aspect ratio metallic stamps of precise geometry. The transfer of large scale patterns using nanoimprinting represents a technique of high potential for the mass production of a new generation of high area, high density, low dimensional structures. Finally a cross section of applications are chosen to demonstrate the potential of these new generation ion beam nanolithographies.
POPS: A COMPUTATIONAL TOOL FOR MODELING AND PREDICTING PROTEASE SPECIFICITY
Authors: BOYD SARAH E. , PIKE ROBERT N. , RUDY GEORGE B. , WHISSTOCK JAMES C. , DE LA BANDA MARIA GARCIA
Published: July 2005

Proteases play a fundamental role in the control of intra- and extra-cellular processes by binding and cleaving specific amino acid sequences. Identifying these targets is extremely challenging. Current computational attempts to predict cleavage sites are limited, representing these amino acid sequences as patterns or frequency matrices. Here we present PoPS, a publicly accessible bioinformatics tool () that provides a novel method for building computational models of protease specificity, which while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user. PoPS specificity models can be used to predict and rank likely cleavages within a single substrate, and within entire proteomes. Other factors, such as the secondary or tertiary structure of the substrate, can be used to screen unlikely sites. Furthermore, the tool also provides facilities to infer, compare and test models, and to store them in a publicly accessible database.
PROFILE-BASED STRING KERNELS FOR REMOTE HOMOLOGY DETECTION AND MOTIF EXTRACTION
Authors: KUANG RUI , IE EUGENE , WANG KE , WANG KAI , SIDDIQI MAHIRA , FREUND YOAV , LESLIE CHRISTINA
Published: July 2005

We introduce novel profile-based string kernels for use with support vector machines (SVMs) for the problems of protein classification and remote homology detection. These kernels use probabilistic profiles, such as those produced by the PSI-BLAST algorithm, to define position-dependent mutation neighborhoods along protein sequences for inexact matching of k-length subsequences ("k-mers") in the data. By use of an efficient data structure, the kernels are fast to compute once the profiles have been obtained. For example, the time needed to run PSI-BLAST in order to build the profiles is significantly longer than both the kernel computation time and the SVM training time. We present remote homology detection experiments based on the SCOP database where we show that profile-based string kernels used with SVM classifiers strongly outperform all recently presented supervised SVM methods. We further examine how to incorporate predicted secondary structure information into the profile kernel to obtain a small but significant performance improvement. We also show how we can use the learned SVM classifier to extract "discriminative sequence motifs" — short regions of the original profile that contribute almost all the weight of the SVM classification score — and show that these discriminative motifs correspond to meaningful structural features in the protein data. The use of PSI-BLAST profiles can be seen as a semi-supervised learning technique, since PSI-BLAST leverages unlabeled data from a large sequence database to build more informative profiles. Recently presented "cluster kernels" give general semi-supervised methods for improving SVM protein classification performance. We show that our profile kernel results also outperform cluster kernels while providing much better scalability to large datasets.

Supplementary website:.
SUREGENE, A SCALABLE SYSTEM FOR AUTOMATED TERM DISAMBIGUATION OF GENE AND PROTEIN NAMES
Authors: PODOWSKI RAF M. , CLEARY JOHN G. , GONCHAROFF NICHOLAS T. , AMOUTZIAS GREGORY , HAYES WILLIAM S.
Published: July 2005

Researchers, hindered by a lack of standard gene and protein-naming conventions, endure long, sometimes fruitless, literature searches. A system that is able to automatically assign gene names to their LocusLink ID (LLID) in previously unseen MEDLINE abstracts is described. The system is based on supervised learning and builds a model for each LLID. The training sets for all LLIDs are extracted automatically from MEDLINE references in the LocusLink and SwissProt databases. A validation was done of the performance for all 20,546 human genes with LLIDs. Of these, 7344 produced good quality models (F-measure >0.7, nearly 60% of which were >0.9) and 13,202 did not, mainly due to insufficient numbers of known document references. A hand validation of MEDLINE documents for a set of 66 genes agreed well with the system's internal accuracy assessment. It is concluded that it is possible to achieve high quality gene disambiguation using scaleable automated techniques.
RECURRENCE TIME STATISTICS: VERSATILE TOOLS FOR GENOMIC DNA SEQUENCE ANALYSIS
Authors: CAO YINHE , TUNG WEN-WEN , GAO J. B. , QI YAN
Published: July 2005

With the completion of the human and a few model organisms' genomes, and with the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time-based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or non-coding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. Our method requires approximately 6 · N byte memory and a computational time of N log N to extract all the repeat-related and periodic or quasi-periodic features from a sequence of length N without any prior knowledge on the consensus sequence of those features, hence enables us to carry out sequence analysis on the whole genomic scale by a PC.
DECISION TREE BASED INFORMATION INTEGRATION FOR AUTOMATED PROTEIN CLASSIFICATION
Authors: ÇAMOĞLU ORHAN , CAN TOLGA , SINGH AMBUJ K. , WANG YUAN-FANG
Published: July 2005

We propose a novel technique for automatically generating the SCOP classification of a protein structure with high accuracy. We achieve accurate classification by combining the decisions of multiple methods using the consensus of a committee (or an ensemble) classifier. Our technique, based on decision trees, is rooted in machine learning which shows that by judicially employing component classifiers, an ensemble classifier can be constructed to outperform its components. We use two sequence- and three structure-comparison tools as component classifiers. Given a protein structure and using the joint hypothesis, we first determine if the protein belongs to an existing category (family, superfamily, fold) in the SCOP hierarchy. For the proteins that are predicted as members of the existing categories, we compute their family-, superfamily-, andfold-level classifications using the consensus classifier. We show that we can significantly improve the classification accuracy compared to the individual component classifiers. In particular, we achieve error rates that are 3–12 times less than the individual classifiers' error rates at the family level, 1.5–4.5 times less at the superfamily level, and 1.1–2.4 times less at the fold level.
GENOME WIDE IDENTIFICATION OF DNA BINDING MOTIFS OF NodD-FACTOR IN SINORHIZOBIUM MELILOTI AND MESORHIZOBIUM LOTI
Authors: KHAN FEROZ , AGARWAL SHIPRA , MISHRA B. N.
Published: July 2005

NodD transcription factor is a regulatory protein of nitrogen fixing bacteria, which activates expression of nod genes participating in nodulation during interaction with its symbiont legumes. It's DNA binding motifs have been characterized and reported in Sinorhizobium meliloti and this pattern information has been used in our theoretical analyses to detect its novel regulated genes in genomes of S. meliloti and Mesorhizobium loti. M. loti, a symbiont to model legume plant Lotus japonicus, showed presence of these regulatory motifs in upstream sequences of nod and other functionally related genes. The methodology involved comparative potential weight matrix construction through GIBBS SAMPLER (RSAT) and MEME tools, using information of conserved upstream sequences of nine genes including nod and neighboring genes of both genomes possessing nod-box like motif. The resultant DNA consensus sequence had highly conserved nod-box like 17 bp long motif consensus sequence pattern for binding of detected NodD transcription factors as analyzed by homologous clustering method and therefore the genome wide predictions were considered highly accurate since confirmed by operon delineation method and the described methodology can be used in other nitrogen fixing bacteria to pursue the study in detail.
The role of surface geochemistry in the discovery of the Babel and Nebo magmatic nickel–copper–PGE deposits
Authors: Baker P.M. , Waugh R.S.
Published: July 2005

The inexpensive geochemical exploration technique based on broad-spaced deflation lag sampling played a key role in the discovery of the Babel and Nebo ortho-magmatic Ni–Cu–platinum group elements (PGE) deposits. An area of 1100 km
2
in the western Musgrave Block in central Australia was explored using deflation lag samples collected on a 1 km × 0.5 km grid. A total of 35 elements were determined using either inductively coupled plasma mass spectrometry (ICP-MS) or inductively coupled plasma optical emission spectrometry on a sample aliquot digested with mixed acid. The precious elements including Au, Pt and Pd were determined using a lead collection fire assay method with an ICP-MS determination. The multi-element analysis revealed two samples indicative of weathered Ni–Cu sulphides from among many stronger Ni or Cu and Pt anomalies. The most anomalous sample of the two contained concentrations of 566 ppm Ni, 950 ppm Cu and 27 ppb Pt.

The Babel deposit is a large low-grade disseminated deposit that reaches through thin sand cover to sub-crop locally. The Nebo deposit lies 2 km to the NE under a few metres of aeolian dune sand and is smaller, but contains a number of high grade massive sulphide pods. The discovery intersection for the Babel deposit was 148.9 m at 0.3% Ni, 0.42% Cu and 0.29 ppm Pt, Pd+Au and for the Nebo deposit 26.55 m at 2.45% Ni, 1.78% Cu, 0.09 % Co and 0.74 ppm Pt, Pd+Au.
Dispersion of gold in stream sediments in the Sungai Kuli region, Sabah, Malaysia
Authors: Fletcher W.K. , Muda J.
Published: July 2005

The distribution of Au in a Au-rich tributary of the Sungai Kuamut, Sabah, Malaysia, was studied initially by the authors in 1999 prior to disturbance of the tropical rain forest by logging. That study found: (i) a strong but extremely erratic Au anomaly with median values of 230 to 690 ppb in the fine and medium sand sized fractions from both cobble and gravel sites; and (ii) Au values typically <15 ppb in the −53 μm fraction. It was suggested that increased input of fine sediment into the stream after logging might substantially dilute and modify the Au anomaly. Logging of the drainage basin in 2000–2001 provided an opportunity to test this possibility.

Results from sampling at gravel sites in 2001 show no dilution of Au values after logging. This is attributed to the occurrence of rainfall and flood events that counteracted dilution of the anomaly by releasing deeply buried Au and/or flushing excess fine sediment from the stream channel. It is concluded that the strength of Au anomalies in stream sediments is likely to fluctuate as a result of the interactions of rainfall events, stream discharge, and the effects of land disturbance on erosion.
Vertical ionic migration: mechanisms, soil anomalies, and sampling depth for mineral exploration
Authors: Mann A.W. , Birrell R.D. , Fedikow M.A.F. , de Souza H.A.F.
Published: July 2005

Field studies, in particular mobile metal ion analysis of soil samples taken over mineralization, suggest that subtle geochemical anomalies exist above mineral deposits which are demonstrably covered by allochthonous material such as glacial till. Empirical observations suggest that the anomalies are preferentially located 10 to 25 cm below the soil interface, comprise elements contained in ore, and are located directly above the mineralizing source. Laboratory experiments suggest that capillary rise and evaporation play an important part in determining the position of emplacement of ions in the soil profile: in nature, root-zone transpiration also plays a part in solute deposition/adsorption within the evapo-transpiration zone. The effects of downward-percolating water after rainfall events, as well as the upward force of capillary rise, are considered in a model which explains many of the features of ion emplacement in soils. Laboratory modelling also suggests that convection, perhaps due to the heat produced by oxidation of the deposit, may in some cases provide a mechanism for rapid ascension of ions beneath the water table.
Optimization of partial extraction chemistry for buffered acetate and hydroxylamine leaches
Authors: Dalrymple I.J. , Cohen D.R. , Gatehouse S.G.
Published: July 2005

The reaction conditions chosen for most partial geochemical extractions remain largely unjustified in terms of optimizing their ability to isolate element signatures related to the effects of mineralization. This study demonstrates the use of central composite designs to study the effects of variation in temperature, pH and reagent concentrations on metal extraction for a buffered acetate leach and a hydroxylamine leach. These designs have been used on nine soil samples from a traverse over porphyry Cu–Au mineralization in central NSW, Australia. For both leaches, metal extractability varies significantly with reaction conditions and the strongest responses to mineralization are generally provided under a very restricted range of digestion conditions. The optimum extraction conditions at Mandamah for the acetate leach are the low pH of the acetate buffer (3.76) and a high acetate concentration at any temperature. The optimum conditions at Mandamah for the hydroxylamine leach are pH = 0, T = 100°C and a moderate to high hydroxylamine concentration (although not for its ability to reduce metal oxides).
Rutile geochemistry as a guide to porphyry Cu–Au mineralization, Northparkes, New South Wales, Australia
Authors: Scott Keith M.
Published: July 2005

The textures and compositions of accessory minerals formed during hydrothermal alteration in porphyry Cu–Au deposits may reflect those processes. Furthermore, if the accessory minerals are stable during weathering processes, they should be able to be used as a guide to mineralization even when the sulphides have been destroyed by weathering. In the Northparkes district, central western NSW, Australia, several Cu–Au ore deposits occur as disseminated or veined sulphides associated with a number of quartz monzonite porphyries intruded into lower Palaeozoic K-rich trachyandesites. This paper reports results from 2000 analyses of rutile grains from 80 samples of rock and soil from around one of these deposits, the E26N porphyry Cu–Au deposit. Within 100 m of ore, rutile grains are larger (commonly with length × breadth >4000 μm
2
) than the grains further from ore (length × breadth <1500 μm
2
). The rutile grains closer to ore also are zoned and contain V-rich portions in which V contents are >0.2% (commonly >0.4%) whereas barren rutile generally contains <0.15% V. Niobium contents of >0.15% occur in rutile in the E26N ore zone and in an altered zone within an adjacent earlier intrusion. Thus, Nb in rutile is not as consistently related to mineralization as V in rutile. Vanadium- (and Nb-) rich rutile is present in both the saprolite and soils derived from mineralized rocks at the deposit. Thus, the V contents in rutile can be utilized as a guide to mineralization even in highly weathered material.
Indicator mineral methods in mineral exploration
Authors: McClenaghan M. Beth
Published: July 2005

Indicator minerals are mineral species that, when appearing as transported grains in clastic sediments, indicate the presence in bedrock of a specific type of mineralization, hydrothermal alteration or lithology. Their physical and chemical characteristics, including a relatively high density, facilitate their preservation and identification and allow them to be readily recovered at the parts per billion level from sample media such as till, stream sediments or soil producing large exploration targets. Another major advantage of indicator mineral methods is that grain morphology, surface textures or mineral chemistry may be examined to obtain information about transport distance and bedrock source. Indicator minerals have become an important exploration method in the past 20 years and now include suites for detecting a variety of ore deposit types including diamond, gold, Ni–Cu, PGE, porphyry Cu, massive sulphide, and tungsten deposits. One of the most significant events in the application of indicator mineral methods in the past 10 years was the explosion in diamond exploration activity in the glaciated terrain of Canada and the resultant changes in sampling and processing methods and improved understanding of kimberlite indicator minerals. At the same time, technological advances have led to increased sophistication of determining indicator mineral chemistry for all indicator minerals. This paper provides an overview of indicator mineral methods and their application in a variety of terrains in the past 20 years, focusing on gold and diamond exploration.
The use of quartz concentrate (acid-insoluble residue) as a sample medium in lithogeochemistry and regolith exploration studies: development of a method
Authors: van Moort J.C. , Pwa Aung
Published: July 2005

Quartz concentrates provide a general sample medium with low background concentration of minor and trace elements. They can be obtained from most rock types by hot nitric acid or aqua regia leach, sometimes supplemented by sulphuric acid leach. The concentrates consist of a mixture of primary quartz, secondary quartz resulting from wallrock alteration and insoluble minerals such as sericite and alkali feldspar. Multi-element analysis enables detection of even the weakest mineralization and wallrock alteration, as expressed mainly by Ba, Ca, Ge, K, Li, Mn, Na, Rb and Sr, in addition to Au, Pb, and Zn. Both wallrock alteration patterns and secondary dispersion trails remain preserved in the quartz concentrates, even in deeply weathered terrain. Results of 14 case histories of various types of gold and base metal deposits are compared.
Controls of element dispersion in aeolian sand and calcrete-dominated regolith associated with gold mineralization in the Kraaipan greenstone belt, South Africa
Authors: Okujeni C.D. , Ackon P. , Baugaard W. , Langa N.
Published: July 2005

This paper focuses on the geochemical controls and associated patterns of element dispersion in aeolian sand/calcrete regolith overlying the Goldridge Au mineralization in the Kraaipan greenstone belt, South Africa, and discusses possible sampling strategies.

Regolith in the Goldridge area consists of
in-situ
weathered basement rocks, overlain by a colluvium and valley-filled sedimentary sequence comprising carbonate-impregnated pebbly to coarse/medium-grained sands at the base, followed by an upper reworked friable/laminated calcrete. These units are unconformably overlain by a fine- to medium-grained ferruginized aeolian sand. The thickest and most laterally extensive regolith sequence occurs along major drainages. Broad valleys and deep channels permitted widespread development and preservation of thick colluvial and alluvial sediments, which were subsequently overlain by aeolian sand.

Gold shows variable dispersion patterns in aeolian sand, often with peak Au concentrations occurring in the central portions of the profile, coinciding with the transition zone between deep red and reddish-brown sands, that is geochemically characterized by a
c
. two-fold increase in the Fe/Mn ratio. The underlying calcite-rich laminated carbonate facies are accompanied by enhanced contents of CaO, MgO, Fe
2
O
3
, LOI, H
2
O
−
and a decrease in SiO
2
contents. The laminated calcretes are associated with the highest accumulation of Au in the entire regolith, whereas the calcrete-impregnated basal pebbly to sandy zone shows generally low but sporadically high Au content.

Results of multivariate analysis of geochemical data suggest an association of Au with Fe–Mn oxides/ oxyhydroxides in the upper zones of aeolian sand. Increased influence of ferricrete nodules and underlying calcrete in the distribution pattern of Au and associated base metals occurs with depth. The use of stacked or additive element plots (e.g Cu+Ni+Co+Mn) show patterns that reflect various rock types or lithologies concealed beneath aeolian sand.

The laminated to hardpan carbonate horizon and the basal zone of the aeolian sand horizon should therefore be sampled in exploration. An understanding of the spatial distribution of these regolith components is essential to maintain a consistent sample.
A Mitochondrial Paradigm of Metabolic and Degenerative Diseases, Aging, and Cancer: A Dawn for Evolutionary Medicine
Authors: Wallace Douglas C.
Published: July 2005

Life is the interplay between structure and energy, yet the role of energy deficiency in human disease has been poorly explored by modern medicine. Since the mitochondria use oxidative phosphorylation (OXPHOS) to convert dietary calories into usable energy, generating reactive oxygen species (ROS) as a toxic by-product, I hypothesize that mitochondrial dysfunction plays a central role in a wide range of age-related disorders and various forms of cancer. Because mitochondrial DNA (mtDNA) is present in thousands of copies per cell and encodes essential genes for energy production, I propose that the delayed-onset and progressive course of the age-related diseases results from the accumulation of somatic mutations in the mtDNAs of post-mitotic tissues. The tissue-specific manifestations of these diseases may result from the varying energetic roles and needs of the different tissues. The variation in the individual and regional predisposition to degenerative diseases and cancer may result from the interaction of modern dietary caloric intake and ancient mitochondrial genetic polymorphisms. Therefore the mitochondria provide a direct link between our environment and our genes and the mtDNA variants that permitted our forbears to energetically adapt to their ancestral homes are influencing our health today.
Topology in nonlinear extensions of hypernumbers
Authors: Burgin M. S.
Published: July 2005

Modern theory of dynamical systems is mostly based on nonlinear differential equations and operations. At the same time, the theory of hypernumbers and extrafunctions, a novel approach in functional analysis, has been limited to linear systems. In this paper, nonlinear structures are introduced in spaces of real and complex hypernumbers by extending the concept of a hypernumber. In such a way, linear algebras of extended hypernumbers are built. A special topology of conical neighborhoods in these algebras is introduced and studied. It is proved that the space of all extended real hypernumbers is Hausdorff. This provides uniqueness for limits what is very important for analysis of dynamical systems. It is also proved that construction of extended real
hypernumbers is defined by a definite invariance principle: the space of all extended real hypernumbers is the biggest Hausdorff factorization of the sequential extension of the space of all real numbers with the topology of conical neighborhoods. In addition,
this topology turns the set of all bounded extended real hypernumbers into a topological algebra. Other topologies in spaces of extended hypernumbers are considered.
Exploring the q‐Riemann zeta function and q‐Bernoulli polynomials
Authors: Kim T. , Ryoo C. S. , Jang L. C. , Rim S. H.
Published: July 2005

We study that the q‐Bernoulli polynomials, which were constructed by Kim, are analytic continued to βs(z). A new formula for the q‐Riemann zeta function ζq(s) due to Kim in terms of nested series of ζq(n) is derived. The new concept of dynamics of the zeros of analytic continued polynomials is introduced, and an interesting phenomenon of “scattering” of the zeros of βs(z) is observed. Following the idea of q‐zeta function due to Kim, we are going to use “Mathematica” to explore a formula for ζq(n).
An analytical formula for throughput of a production line withidentical stations and random failures
Authors: Blumenfeld Dennis E. , Li Jingshan
Published: July 2005

We derive a simple formula for the throughput (jobs produced per unit time) of a serial production line with workstations that are subject to random failures. The derivation is based on equations developed for a line flow model that takes into account the impact of finite buffers between workstations. The formula applies in the special case of a
line with identical workstations and buffers of equal size. It is a closed‐form expression that shows the mathematical relationships between the system parameters, and that can be used to gain basic insight into system behavior at the initial design stage.
Blockade of Endogenous Angiotensin-(1–7) in the Hypothalamic Paraventricular Nucleus Reduces Renal Sympathetic Tone
Authors: Gomes da Silva Ana Quênia , Sousa dos Santos Robson Augusto , Peliky Fontes Marco Antônio
Published: July 2005

In this study, we tested the hypothesis that angiotensin-(1–7) [Ang-(1–7)] acting in the neurons of paraventricular hypothalamic nucleus (PVN) contributes to the maintenance of sympathetic activity and blood pressure. For this purpose, the effects of microinjection of the A-779, the receptor Mas antagonist, into the PVN on mean arterial pressure (MAP), heart rate (HR), and renal sympathetic nerve activity (RSNA) were evaluated. In rats anesthetized with urethane (1.2 to 1.4 g/kg IP), bilateral microinjections of A-779 (0.1 nmol) into the PVN resulted in a selective and significant decrease in RSNA (−26±6% versus −2±3% vehicle; saline 0.9%). The magnitude of the decrease in RSNA produced by A-779 was comparable to that observed after microinjection of muscimol (1 nmol; −26±4%), a powerful neuronal inhibitor. A higher dose of A-779 (1 nmol) caused a reduction in RSNA (−21±4%) that was comparable in magnitude to the reduction observed with the lower dose. When compared with vehicle solution, no significant changes in MAP or HR were observed with both doses of A-779 tested. A decrease in RSNA was also observed after microinjections into the PVN of the angiotensin II type 2 (AT
2
) receptor antagonist PD123319 (1 nmol; −18±4%). Microinjections of the AT
1
antagonist losartan but not CV 11974 reduced MAP without changing RSNA. These results suggest that Ang-(1–7) Mas receptors and AT
2
receptors in the PVN neurons play a role in mediating the tonic maintenance of RSNA.
Role of Smoking in Global and Regional Cardiovascular Mortality
Authors: Ezzati Majid , Henley S. Jane , Thun Michael J. , Lopez Alan D.
Published: July 2005

Background—

Smoking is a major cause of cardiovascular disease mortality. There is little information on how it contributes to global and regional cause-specific mortality from cardiovascular diseases for which background risk varies because of other risks.

Method and Results—

We used data from the American Cancer Society’s Cancer Prevention Study II (CPS II) and the World Health Organization Global Burden of Disease mortality database to estimate smoking-attributable deaths from ischemic heart disease, cerebrovascular disease, and a cluster of other cardiovascular diseases for 14 epidemiological subregions of the world by age and sex. We used lung cancer mortality as an indirect marker for accumulated smoking hazard. CPS-II hazards were adjusted for important covariates. In the year 2000, an estimated 1.62 (95% CI, 1.27 to 2.04) million cardiovascular deaths in the world, 11% of total global cardiovascular deaths, were due to smoking. Of these, 1.17 million deaths were among men and 450 000 among women. There were 670 000 (95% CI, 440 000 to 920 000) smoking-attributable cardiovascular deaths in the developing world and 960 000 (95% CI, 770 000 to 1 200 000) in industrialized regions. Ischemic heart disease accounted for 54% of smoking-attributable cardiovascular mortality, followed by cerebrovascular disease (25%). There was variability across regions in the role of smoking as a cause of various cardiovascular diseases.

Conclusions—

More than 1 in every 10 cardiovascular deaths in the world in the year 2000 were attributable to smoking, demonstrating that it is an important preventable cause of cardiovascular mortality.