bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficacy of Photodynamic Therapy on Inflammatory Signs and Two Selected Periodontopathogenic Species in a Beagle Dog Model
Authors: Sigusch Bernd W. , Pfitzner Anne , Albrecht Volker , Glockmann Eike
Published: July 2005

Background: Current research aims to find alternatives to conventional methods for suppressing periodontopathogenic bacteria. Photodynamic therapy (PDT) could be a suitable treatment procedure of periodontal infections.

Methods: In the present study, the PDT method was tested with two photosensitizers, chlorine e6 and BLC1010, in an experiment on beagle dogs. The animals were infected with Porphyromonas gingivalis (Pg) and Fusobacterium nucleatum (Fn) in all subgingival areas. After infection, we observed clinical signs of gingival inflammation, including an increase of redness and bleeding on probing. Microbiological monitoring before and after treatment was performed using polymerase chain reaction (PCR). PDT was conducted with a diode laser with a wavelength of 662 nm using a power of 0.5 W and the photosensitizers.

Results: The PDT procedure carried out with either of the photosensitizers caused a significant reduction in the clinical inflammation signs of redness and BOP, compared to the controls (laser only and no treatment). Furthermore, PDT with chlorine e6 caused a significant reduction in P. gingivalis‐infected sites, whereas there was a lack in suppression after PDT with BLC1010. F. nucleatum could hardly be reduced with chlorine e6, and only to a certain extent with BLC 1010 and laser only. In the control groups, the Pg‐infected test sites did not change.

Conclusions: This study demonstrated that the photodynamic therapy using photosensitizer and a 662 nm laser light source is distinctly advantageous in reducing the periodontal signs of redness and bleeding on probing. The procedure also appears to significantly suppress P. gingivalis. J Periodontol 2005;76:1100‐1105.
Bisphosphonate Therapy Improves the Outcome of Conventional Periodontal Treatment: Results of a 12‐Month, Randomized, Placebo‐Controlled Study
Authors: Lane Nancy , Armitage Gary C. , Loomer Peter , Hsieh Susan , Majumdar Sharmila , Wang H.‐Y. , Jeffcoat Marjorie , Munoz Thelma
Published: July 2005

Background: Bone loss in periodontitis results from inflammatory reactions that stimulate osteoclastic bone resorption. Bisphosphonates inhibit bone resorption and increase bone mass. This study evaluated the effect of bisphosphonate therapy as an adjunct to non‐surgical periodontal treatment in patients with moderate to severe chronic periodontitis.

Methods: Patients were randomized (2:1) to one of two bisphosphonate therapies or placebo for 1 year. All patients received non‐surgical periodontal treatment (scaling, root planing) and periodontal maintenance therapy every 3 months. Clinical assessments at baseline and 6 and 12 months included clinical attachment level (CAL), probing depth (PD), and bleeding on probing (BOP). Periodontal bone mass was assessed by dental radiographs at baseline and 12 months using fractal analysis and digital subtraction radiography (DSR).

Results: Seventy patients were randomized, 43 to the bisphosphonate group and 27 to the placebo group. Bisphosphonate therapy significantly improved CAL, PD, and BOP relative to the placebo group during the 6‐ to 12‐month period (CAL, P = 0.0002; PD, P = 0.0156; BOP, P = 0.0079). There was no difference in the change in periodontal bone mass between the bisphosphonate and placebo groups as measured by fractal analysis and DSR.

Conclusion: These data suggest that bisphosphonate treatment improves the clinical outcome of non‐surgical periodontal therapy and may be an appropriate adjunctive treatment to preserve periodontal bone mass. J Periodontol 2005;76:1113‐1122.
Tetracycline at Subcytotoxic Levels Inhibits Matrix Metalloproteinase‐2 and ‐9 But Does Not Remove the Smear Layer
Authors: Wang Yao , Morlandt Anthony B. , Xu Xiaoping , Carnes David L. , Chen Zhihua , Steffensen Bjorn
Published: July 2005

Background: The antibacterial and anticollagenolytic properties of tetracycline (TCN) are valuable in periodontal therapy, and TCN treatment can remove the smear layer following root instrumentation. However, recent reports pointing to cytotoxic effects of several acids prompted this study to define TCN concentrations that are anticollagenolytic and remove the smear layer, but have low cytotoxicity.

Methods: Human gingival (hGF) and periodontal ligament (hPDL) cells were treated short‐ (3 minutes) or long‐term (24 hours) with TCN to determine concentrations yielding 50% (TD50) and 90% (TD10) cell survival. Activity assays measured TCN concentrations with half‐maximal inhibition (IC50) of matrix metalloproteinase‐ 2 and ‐9 (MMP‐2 and ‐9). Finally, we analyzed the effects of TCN with high (75 mg/ml) or low (1 mg/ml) cytotoxicity on the smear layer by scanning electron microscopy (SEM).

Results: The TD50 for TCN after short‐term treatment was 4 mg/ml for both hGF and hPDL. Ninety percent of the cells survived 0.2 mg/ml. With long‐term treatment, the TD50 for hGF and hPDL was 70 and 30 µg/ml, respectively, and the TD10 was 20 and 5 µg/ml. HGF and hPDL recovered from the 3‐minute treatment with 1 mg/ml, but not from concentrations exceeding 3 and 9 mg/ml, respectively. The IC50 was 25 µg/ml for both MMP‐2 and MMP‐9. Whereas 75 mg/ml TCN removed the smear layer, 1 mg/ml TCN had no effects.

Conclusions: Tetracycline has significant cytotoxicity on periodontal cells. Since non‐cytotoxic concentrations of TCN inhibited MMP‐2 and ‐9 but had no effects on the smear layer, TCN is not recommended for root surface treatment. J Periodontol 2005;76: 1129‐1139.
Expression of Activated Transcription Factor Nuclear Factor‐κB in Periodontally Diseased Tissues
Authors: Ambili R. , Santhi W.S. , Janam Prasanthila , Nandakumar K. , Pillai M. Radhakrishna
Published: July 2005

Background: Chronic periodontitis is an inflammatory disease found mainly in adults. Little is known about molecular level changes associated with host response in this condition. Nuclear factor‐κB (NF‐κB) is a transcription factor implicated in immune and inflammatory responses. NF‐κB activation has also been reported to be associated with many chronic inflammatory diseases. The purpose of this paper was to compare the nuclear and cytoplasmic expression of NF‐κB transcription factor (p50/p65) and cytoplasmic expression of IκB in periodontal tissues of periodontitis patients and controls.

Methods: Twenty patients with chronic periodontitis and 20 healthy controls were included in the study. Gingival tissues taken during extraction were processed for immunohistochemical staining and evaluation.

Results: Nuclear (activated) p50 was found in 90% of periodontal patient tissues compared to only 30% of healthy tissues. A more significant result was obtained with p65 (75% versus 5%). Intense cytoplasmic immunoreactivity was also observed in periodontitis tissues. IκB, the inhibitor of NF‐κB, was expressed only in 5% of periodontally diseased tissues.

Conclusion: Activation of NF‐κB (p50/p65) is significant in periodontally diseased tissues, suggesting the potential of inhibitors of NF‐κB in managing periodontitis. J Periodontol 2005;76:1148‐1153.
Forty‐Eight–Month Periodontal Attachment Loss Incidence in a Population‐Based Cohort Study: Role of Baseline Status, Incident Tooth Loss, and Specific Behavioral Factors
Authors: Gilbert Gregg H. , Shelton Brent J. , Fisher Monica A.
Published: July 2005

Background: The objectives of this study were to: 1) test hypotheses that behavioral factors, baseline clinical status, and incident tooth loss are significantly associated with attachment loss incidence (ALI) and 2) quantify the effect of incident tooth loss on conclusions made about ALI.

Methods: The Florida Dental Care Study was a prospective study of persons ≥45 years old. In‐person interviews and examinations were conducted at baseline and 48 months, with telephone interviews in between.

Results: Of 560 persons with baseline and 48‐month examinations, 22% of persons and 1.8% of teeth had ALI. This was highest among persons with no dental visit during follow‐up (person‐level incidence of 46%; 5.0% tooth‐level incidence). Statistically significant covariates in a multivariable regression of ALI were: losing a tooth due to periodontal reasons after baseline, but before the 48‐month examination; not receiving a dental cleaning; and baseline factors (worst attachment level of ≥7 mm, not flossing, a molar tooth, current smoker).

Conclusions: A substantial percentage of persons experienced ALI. Baseline attachment level and behavioral factors were significantly associated with ALI. Persons with incident tooth loss were also at increased risk for ALI, and teeth lost during follow‐up had worse baseline attachment level. Had these teeth not been lost before the final examination, the ALI estimate could only have been higher. These findings demonstrate that those at greatest risk for ALI are least likely to enter the dental care system, and among those who do, one health outcome (tooth loss) can affect conclusions made about the incidence of another (ALI). J Periodontol 2005;76:1161‐1170.
Receptor for Advanced Glycation End Product (RAGE) Upregulation in Human Gingival Fibroblasts Incubated With Nornicotine
Authors: Katz Joseph , Caudle Robert M. , Bhattacharyya Indraneel , Stewart Carol M. , Cohen Donald M.
Published: July 2005

Background: Clinical and epidemiological data strongly support a link between smoking and periodontal disease. The mechanism by which smoking contributes to the destruction of periodontal tissue is not clear and cannot be attributed solely to the vasoconstrictive effects of nicotine. Our hypothesis is that nornicotine, a metabolite of nicotine, upregulates the expression of the receptor for the advanced glycation end products (RAGE) in the gingiva of smokers and triggers the proinflammatory effects of AGE by stimulating the secretion of cytokines and reactive oxygen species which directly cause destruction of the periodontal apparatus.

Methods: Human gingival cells grown in tissue culture were exposed to 1 µM nornicotine for 72 hours. Following the nornicotine pretreatment, some of the cells were also treated with AGE that was generated with nornicotine for 48 hours and another group was continued on nornicotine only for 48 hours. Control cells that were not exposed to either nornicotine or AGE were also cultured. The cells were harvested and RNA was extracted for reverse transcription‐polymerase chain reaction (RT‐PCR) and RAGE mRNA was amplified.

Results: The nornicotine‐treated cells increased their expression of RAGE by approximately 4‐fold (P <0.05, Student t test). These data suggest that nornicotine, a byproduct of cigarette smoke, can induce RAGE expression in gingival tissues. Therefore, our data support the hypothesis that RAGE potentially plays a significant role in the progression of periodontal disease exacerbated by smoking.

Conclusion: Nornicotine, AGE, and upregulation of RAGE may be involved in the pathogenesis of periodontal disease associated with smoking. J Periodontol 2005;76:1171‐1174.
Glycosylation Pattern and Cell Attachment‐Inhibiting Property of Human Salivary Mucins
Authors: Gabriel Matthias O. , Grünheid Thorsten , Zentner Andrej
Published: July 2005

Background: Whole human saliva (WHS) and its high molecular weight mucin constituent (Muc) inhibit fibroblast attachment and might influence periodontal and peri‐implant wound healing. The aim of this work was to study the potential role of glycosylation of Muc in fibroblast attachment‐inhibiting property and to examine in vitro the effect of WHS and Muc on epithelial cell attachment.

Methods: Muc was isolated from WHS by CsCl density gradient ultracentrifugation; covalently immobilized on polystyrene; and subjected to enzymic digestion by N‐glycanase, O‐glycanase, and sialidase, or chemical desulfation and periodate treatment. Wells of tissue culture microtiter plates were incubated with WHS, Muc, or buffer as control; suspensions of normal human oral keratinocytes, spontaneously immortalized human keratinocytes, or human gingival fibroblasts were applied; and cell attachment determined using methylene blue assay.

Results: While enzymic cleavage of N‐linked carbohydrates showed no effect, selective removal of O‐linked residues and sialic acid as well as desulfation and periodate oxidation resulted in statistically significant reduction of cell attachment‐inhibiting property of immobilized Muc. Significantly lower numbers of attached cells of each cell type were found in wells pretreated with WHS or Muc.

Conclusions: Inhibition of cell attachment may be mediated by the carbohydrate residues suggesting specific interactions between the salivary constituent and the cell surface. Exposure of root and implant surfaces to saliva during early wound healing events might influence healing by inhibiting surface colonization by oral keratinocytes and fibroblasts, and enhancing wound repair in the form of long junctional epithelium rather than regeneration. J Periodontol 2005;76:1175‐1181.
Interleukin‐1β–Induced Prostaglandin E2 Production by Human Gingival Fibroblasts Is Upregulated by Glycine
Authors: Rausch‐Fan Xiaohui , Ulm Christian , Jensen‐Jarolim Erika , Schedle Andreas , Boltz‐Nitulescu George , Rausch Wolf‐Dieter , Matejka Michael
Published: July 2005

Background: Human gingival fibroblasts (GFB) may produce prostaglandin E2 (PGE2) in response to proinflammatory cytokines. Elevated concentrations of glycine were previously found in periodontal pockets and saliva of periodontitis patients and, therefore, we aimed to study the influence of glycine on PGE2 production.

Methods: Human GFB were cultured in the presence of various concentrations of glycine and/or interleukin (IL)‐1β, tumor necrosis factor (TNF)‐α, and IL‐10 and their influence on PGE2 production was measured. The expression of cyclooxygenases (COX) was analyzed by Western blot and immunocytochemistry.

Results: The PGE2 production by IL‐1β‐stimulated GFB was significantly upregulated by glycine. The effect of glycine on IL‐ 1β‐induced cell proliferation and PGE2 production was concentration‐ dependent, reached a peak at 3 mM, and declined slowly at higher doses. The synthesis of PGE2 by human GFB cultured in the absence of glycine was significantly inhibited by IL‐10 and partially induced in cells cultured with glycine. Glycine had no effect on TNF‐α‐induced PGE2 production. The IL‐1β‐driven PGE2 synthesis was blocked by indomethacin, a COX‐1/COX‐2 inhibitor, and by COX‐2 inhibitor NS‐398. The expression of COX‐2 protein was slightly induced by glycine, more evidently by IL‐1β, and mostly enhanced by combined IL‐1β with glycine.

Conclusion: Since PGE2 is a potent stimulator of bone resorption, and production of PGE2 and COX‐2 protein is augmented by glycine, our results strongly suggest that glycine may be involved in the pathogenesis of periodontitis. J Periodontol 2005;76:1182‐1188.
Resistance of Human Periodontal Ligament Fibroblasts to the Cytolethal Distending Toxin of Actinobacillus actinomycetemcomitans
Authors: Kanno Fumio , Korostoff Jonathan , Volgina Alla , DiRienzo Joseph M.
Published: July 2005

Background: The cytolethal distending toxin (CDT) of Actinobacillus actinomycetemcomitans is a typical member of this Gram‐negative bacterium holotoxin family that targets a wide spectrum of eukarytotic cells, typically causing cell cycle arrest at either the G1 or G2/M phase of the cell cycle. In view of the possible role of the CDT as a prominent A. actinomycetemcomitans virulence factor in periodontal diseases, we have examined the effects of the toxin on primary cultures of human periodontal ligament fibroblasts (HPLF).

Methods: HPLF and an immortalized human gingival epithelial cell line, GMSM‐K, were exposed to recombinant A. actinomycetemcomitans CDT. Effects of the toxin on cell proliferation and cell cycle were assessed by a cell viability assay and flow cytometry, respectively. Double‐strand DNA damage was detected by pulsed field gel electrophoresis. Binding of the toxin and its individual subunits to HPLF was examined by immunofluorescence microscopy.

Results: Viability of HPLF was not reduced following prolonged exposure to the CDT. There was no indication of cell cycle arrest or double‐strand DNA damage. GMSM‐K cells exhibited morphological alterations and a rapid decrease in cell viability within 6 and 12 hours, respectively, following exposure to the toxin for 5 minutes. These effects were dependent on toxin dose and age of the cultures and occurred more rapidly compared to CDT‐treated HeLa cells. CDT‐treated GMSM‐K cells displayed cell cycle arrest at the S phase of growth and double‐strand DNA damage was observed by 6 hours post‐intoxication. Holotoxin and the CdtA subunit were detected on the surface of both HPLF and epithelial cells.

Conclusions: These results demonstrate that HPLF are resistant to the cytotoxic effects of the A. actinomycetemcomitans CDT. The mechanism of resistance is not known but may be related to the inability of the toxin to cause DNA damage. The difference in sensitivities of HPLF and oral epithelial cells to the CDT has important implications for the role of this putative microbial virulence factor in periodontal pathogenesis. J Periodontol 2005;76:1189‐1201.
Detection of Subgingival Calculus With a Novel LED‐Based Optical Probe
Authors: Krause Felix , Braun Andreas , Jepsen Søren , Frentzen Matthias
Published: July 2005

Background: A recently introduced detection device is designed for objective subgingival calculus diagnosis. The aim of the present study was to assess the possibility of detecting subgingival calculus with this novel LED‐based optical probe in vitro.

Methods: Twenty extracted human teeth with calculus on the root surface were fixed on a translation stage. Measurements on the root surface were carried out in increments of 0.25 mm with an angulation of 0 to 10°, 45°, or 90° to the optical fiber. Teeth were covered either with sodium chloride (NaCl) or blood in order to determine the influence of ambient fluids. Successional areas of positive measurements were defined as “length of positive values” (LPV). The results were compared to the clinical and histological findings.

Results: Clinically and histologically apparent calculus on the root surface was accompanied by positive measurement values. A reduction of the angulation between probe and root surface resulted in shorter LPV when measurements were performed in blood (P<0.05) and longer LPV employing NaCl as the ambient fluid (P<0.05). For both blood and NaCl, sensitivity and/or specificity values decreased when using lower angulations.

Conclusion: The optical probe offers the possibility of subgingival calculus detection and may, therefore, be suited to determine the endpoint of root surface instrumentation during non‐surgical periodontal therapy. J Periodontol 2005;76:1202‐1206.
Periodontal Treatment in Severe Aplastic Anemia
Authors: Oyaizu Kosuke , Mineshiba Fumi , Mineshiba Junji , Takaya Hirokazu , Nishimura Fusanori , Tanimoto Ichiro , Arai Hideo , Takashiba Shogo
Published: July 2005

Background: Aplastic anemia (AA) is a rare hematologic disease characterized by hypo‐cellular bone marrow. The clinical features include fatigue, increased bruising, and gingival bleeding caused by anemia, leukopenia, and thrombocytopenia. A patient with AA is at high risk for infection because of leukopenia. The risk of systemic infection is especially high in AA patients with severe local infections, including periodontitis. Accordingly, periodontal treatment should include antibiotic prophylaxis to reduce the risk of systemic infection. However, treatment of periodontitis in the AA patient is significantly complicated by the bleeding disorder. We present a case report of the successful periodontal treatment of an AA patient with spontaneous gingival bleeding.

Methods: The patient was closely monitored for platelet and neutrophil counts before every treatment. The patient's platelet count was always under 10,000/µl. Therefore, it was necessary to increase platelet counts to over 25,000/µl by transfusion, after which subgingival scaling with anesthesia was performed. When the neutrophil count was less than 2,000/µl, local minocycline chemotherapy was applied to the pockets. Periodontal infection was monitored by detection of bacterial DNA and measurement of serum immunoglobulin (Ig) G titer against periodontal bacteria.

Results: Following the physical and chemical treatment, the gingival appearance improved dramatically and the spontaneous gingival bleeding disappeared. Moreover, the IgG titer against periodontal bacteria decreased to normal range and specific periodontal pathogens were no longer detectable in the tested pockets.

Conclusion: We believe that the treatment strategy in the present report provides new sight into treatment planning for severely medically compromised patients. J Periodontol 2005;76:1211‐1216.
Felodipine‐Influenced Gingival Enlargement in an Uncontrolled Type 2 Diabetic Patient
Authors: Fay Ann Adams , Satheesh Keerthana , Gapski Ricardo
Published: July 2005

Background: The potential of calcium channel blockers (CCBs) to induce gingival enlargement (GE) as well as the influence of diabetes mellitus on periodontal tissues has been well documented. This case report documents a conservative clinical approach to the management of felodipine‐influenced gingival enlargement and displays a clinical and histologic case of felodipine‐influenced GE in an undiagnosed type 2 diabetic patient.

Methods: At the initial examination, a medical consultation was requested and two incisional biopsies were taken for pathological evaluation. The patient was diagnosed with uncontrolled type 2 diabetes. Felodipine was withdrawn and the diabetes was controlled before dental treatment was initiated. The patient then underwent selective extractions and full‐mouth scaling and root planing as well as oral hygiene instructions. No surgical therapy was indicated.

Results: The histological results demonstrated the presence of elongated rete pegs; fibrous hyperplasia; a low‐grade chronic inflammatory infiltrate, predominantly consisting of lymphocytes; and collagen bundle groups randomly distributed. These features were similar to those present in other drug‐influenced GE. Clinical results have demonstrated almost complete resolution of GE after the withdrawal of felodipine and the control of diabetes. Further improvements were seen after scaling and root planing and oral hygiene instructions. No recurrences were noted 12 months after initial therapy.

Conclusions: This report demonstrated that the control of systemic factors seemed to have the most influence on success for this particular case. Since the control of diabetes was managed at the same time as the felodipine withdrawal, it remains difficult to speculate how these two factors impacted both the severity of the GE and the therapeutic results. More importantly, the conservative treatment rendered demonstrated the stability of periodontal status during maintenance phase and the avoidance of surgical interventions. J Periodontol 2005;76:1217‐1222.
Imprinting and epigenetics in mouse models and embryogenesis: understanding the requirement for both parental genomes
Authors: Mann Mellissa R. W.
Published: July 2005

Twenty years ago, elegant nuclear transplantation studies in the mouse demonstrated that both a maternal and a paternal genome are required to complete normal mammalian development. Since that time, further investigation of parthenogenetic and androgenetic embryos indicates that maternally and paternally expressed genes are required for proper development of both embryonic and extraembryonic lineages. Poor development of uniparental embryos is attributed to misregulation of multiple genes governed by genomic imprinting and imprinted X chromosome inactivation that act synergistically on growth, development, and viability. The most important of these genes likely have roles in cell proliferation and differentiation.
Variable expressivity and epigenetics
Authors: Blewitt Marnie E. , Whitelaw Emma
Published: July 2005

There is an increasing awareness that some genes do not behave in a strictly Mendelian fashion. In plants, flies, and mice, some alleles have been identified where the activity state varies among cells of the same cell type (termed variegation) and among genetically identical individuals (variable expressivity). We now know that this is the result of the stochastic establishment of differential epigenetic states at the locus. These states are set up during early development and are stably inherited for the life of the organism. While, in general, the states are cleared between generations, this is not always the case. Some alleles, now referred to as metastable epialleles, are not completely cleared from one generation to the next, resulting in a phenomenon termedtransgenerational epigenetic inheritance. One of the interesting questions that arises from these findings is whether this mechanism has been involved in the evolution of morphological traits.
Familial adenomatous polyposis
Authors: Hegde Madhuri R. , Richards C. Sue
Published: July 2005

Three cases of familial adenomatous polyposis (FAP) are presented to illustrate multiple genetic principles, including disease phenotype, mutational spectrum, and inheritance patterns. The first case represents the most common form, classical FAP consisting of thousands of polyps in an adolescent with a family history of colorectal cancer (CRC). Molecular analysis of the adenomatous polyposis gene (
APC
) using scanning and sequencing molecular methods reveals a novel insertion and deletion (indel) mutation on one allele, thus confirming the diagnosis and allowing targeted mutation analysis for at‐risk family members. The second case illustrates attenuated FAP (AFAP), presenting at a later age with fewer polyps, in an individual with a family history of CRC. In this case, a full gene deletion of one allele was identified during molecular analysis using various technologies. The implications of these findings are discussed along with genetic counseling and testing for at‐risk family members. The third example presents with a newborn diagnosed with Gardner syndrome and having no family history of FAP or CRC. Molecular analysis confirms the diagnosis and identifies a novel truncating nonsense mutation. Genetic testing and counseling implications for the family are discussed, including the possibility of gonadal mosaicism and de novo events. In all three cases, the molecular data are presented with a clinical interpretation. A discussion of inherited CRC and gene contributions, the clinical phenotypes of FAP and AFAP, the
APC
gene structure, types of mutations, gene function, molecular mechanisms, mutation analysis technologies, genetic counseling issues, and surveillance and treatment options are presented.
Gene transfer vectors as medicinal products: risks and benefits
Authors: Buchholz Christian J. , Cichutek Klaus
Published: July 2005

Gene transfer medicinal products (GT‐MPs) include a broad range of product types as for example, genetically modified somatic cells, viral and nonviral vectors, or carrier‐free nucleic acids used in humans for preventive, therapeutic, or in vivo diagnostic purposes. Treatment is targeted not only at inherited diseases but also at common disorders such as cancer, cardio‐vascular, and infectious diseases. About a thousand clinical trails using GT‐MPs are ongoing or have been completed worldwide, mainly performed in the United States and in the European Union. Up to now, however, only one GT‐MP has been licensed, licensing applications in the European Union are expected starting from 2005. In the European Union, marketing authorization for GT‐MPs is obtained following the centralized procedure via the European Medicines Evalution Agency (EMEA). Coordinated by the EMEA, experts from national authorities are reviewing applications and give scientific advice to pharmaceutical industry developing medicinal products. This article summarizes the various concepts and definitions of GT‐MPs, their state of development, clinical approaches, serious adverse events, and relevant regulatory documents and activities.
YAC
‐
STS
content mapping
Authors: Gosele Claudia , Zimdahl Heike , Hubner Norbert
Published: July 2005

The goals of physical mapping are to provide (1) an ordered set of all the DNA of the chromosome (or genome), (2) accurate distances between a dense set of DNA markers, and (3) a set of DNA clones from which direct DNA sequencing can be done. High‐resolution physical mapping of a certain chromosomal interval or even the whole genome implies that large‐insert genomic clones with overlapping inserts are assembled and ordered according to their position in the genome. Physical mapping usually involves the construction of YAC, BAC, and/or BAC contigs. Ideally, a contig covers the defined chromosomal region or even an entire chromosome without gaps. Because of their large size, YACs have enabled the rapid construction of physical maps by ordered clone mapping and contig building. Conventional contig assembly is performed primarily by PCR assays (STS content mapping), by hybridization‐based techniques, or by restriction fingerprinting. The chromosomal location of a contig can be determined by anchoring it to genetic and radiation hybrid maps.

STS content mapping is a commonly used, robust, and effective technique, which is applicable to all kinds of cloning systems and has been employed for the physical mapping of the human and mouse genome (Hudson
et al.
,

; Nusbaum
et al.
,

). The disadvantages are that the isolation of endclones is laborious and often does not result in any suitable clone, a large number of preexisting evenly distributed STS markers is required, and the large number of primers required results in significant costs. The alternative strategy is based on the screening of large‐insert libraries spotted on high‐density gridded filters by hybridization. Subcloned genomic fragments, end sequences of genomic clones, oligonucleotides, or interrepeat sequences are mostly used as hybridization probes. This method allows the efficient screening of high genome coverage by a single hybridization. Hybridization‐based physical maps have been constructed, for example, of the human chromosome (Hattori
et al.
,

) and the mouse genome (Schalkwyk
et al.
,

).
Farm animals
Authors: Andersson Leif
Published: July 2005

Farm animal genomics will add to our basic understanding of genotype–phenotype relationships and may lead to important practical applications in agriculture and human medicine. Genetic studies of those traits that have been under strong artificial selection during the history of animal domestication are particularly interesting due to the enrichment of novel mutations in certain populations. The genomic tools and resources are accumulating rapidly for farm animals, as shown by the release of the first high‐quality draft genome sequence for a farm animal, the chicken, during 2004. The available genome resources and the strategies for mapping and molecular characterization of trait loci are reviewed. The power of farm animal genomics is illustrated by the successful identifications of the causative mutations for simple monogenic traits as well as some quantitative trait loci.
Bacterial pathogens of man
Authors: Parkhill Julian
Published: July 2005

Bacterial pathogens of man can be found in a number of different phylogenetic groups of bacteria, although their distribution amongst all the known genera of prokaryotes is somewhat patchy, and there is still a great deal of debate as to whether there are any pathogenic archaea. Genomic study of these pathogens has begun to identify some common themes amongst these organisms, but none that are truly universal, and has also served to underline the diversity of mechanisms utilized for virulence and host interaction. Comparative genomic analysis has also begun to indicate the different mechanisms by which these organisms may have evolved their specific interactions with the human host. Bacterial pathogenicity is not a discrete state, and these interactions can range from commensalism, where the disease outcome is accidental, through occasional, opportunistic pathogenicity in a generalist organism, to specialist pathogens that are dependent on the host. However, it is becoming increasingly clear that organisms can move between these categories over the course of evolution.
The nuclear genome of apicomplexan parasites
Authors: Ajioka James W. , Brooke‐Powell Elizabeth T. , Wan Kiew‐Lian
Published: July 2005

The Apicomplexa is a highly diverse phylum of parasitic protists that includes the causative agents of malaria and other important human and animal diseases. These unicellular pathogens have been shaped by a key evolutionary event: the secondary endosymbiosis of a single eukaryotic cell and photosynthetic algae. From this event and subsequent evolution, most species in the phylum retain a single mitochondrion and a plastid‐like organelle known as the apicoplast (seeThe organelles of Apicomplexan parasites). The reduced function of these organelles is mirrored by their highly compact genomes, where genes have been lost or transferred to the nucleus, making the nuclear genome a mosaic of former organellar genes embedded in chromosomal DNA from both endosymbionts. Natural selection on this basic cellular and genetic plan has led to a diversity of parasitic life cycles, each with adaptations that specify host range and mechanisms of transmission. Comparative genomics is beginning to reveal the similarities and differences between member species, enhancing our capability to treat and control the devastating diseases they cause.
NormalDNAsequence variations in humans
Authors: Kidd Kenneth K.
Published: July 2005

Within the past quarter century, researchers have been able to study variation directly in the human DNA sequence. Though almost all of the human DNA sequence is identical in all humans, the small fraction, less than 1%, that does vary is more than sufficient to make each independently conceived human genetically unique. Many types of normal variation exist, from differences in a single nucleotide to the presence or absence of blocks of DNA hundreds of nucleotides long. The distributions among populations of the variant forms can differ but overall, they are consistent with a pattern of human expansion from an origin in Africa to occupation of all major continents.
Evolutionary modeling in haplotype analysis
Authors: Donnelly Peter
Published: July 2005

Data that captures genetic variation at closely spaced markers in samples from a population is the result of various evolutionary and chance forces. Interpretation of such data is often aided by an understanding of these evolutionary processes, and statistical methods that explicitly model aspects of the evolutionary history, including coalescent‐based approaches, are often more powerful than available alternatives, even for applications such as disease gene mapping when the evolutionary processes are not of primary interest.
Finding and using haplotype blocks in candidate gene association studies
Authors: Stram Daniel O.
Published: July 2005

Recent discoveries (Daly
et al.
,

; Jeffreys
et al.
,

; Gabriel
et al.
,

) that there is considerable heterogeneity in the amount of linkage disequilibrium (LD) between single‐nucleotide polymorphism (SNP) markers over the genome and the implication that recombination rates themselves may also be considerably heterogeneous suggest specific analysis strategies for design and analysis of genetic association studies of disease. This article focuses upon the implications for such studies of the existence of well‐defined “haplotype blocks” covering much of the genome over which there is little evidence for recombination and within which there is limited haplotype diversity. The main topics addressed are:

SNP and haplotype discovery

Picking of haplotype‐tagging SNPs (ht SNPs) for large‐scale genotyping (e.g., in a case‐control study)

Testing and estimation of haplotype‐specific risk in a large‐scale case–control study.
Sample preparation for
MALDI
and electrospray
Authors: Langridge J. I. , Snel M.
Published: July 2005

The role of mass spectrometry in the analysis of biomolecules was revolutionized by the development of electrospray (ESI) and matrix‐assisted laser desorption/ionization (MALDI) ion sources. The advances made since then, in both source and mass analyzer design, have made modern mass spectrometers inherently sensitive instruments. The limiting factor for the detection of many biological compounds is not the instrumentation itself, but rather the preparation and presentation of the sample to the mass spectrometer. Sample preparation for MALDI is vital to obtaining good‐quality information. The level of contaminants, choice of matrix, and spotting technique used all contribute to the sensitivity and quality of the data required. By comparison, much of the sample preparation for ESI is done using HPLC coupled on‐line to the mass spectrometer. This provides a sensitive technique for the analysis of biomolecules, if performed on the micro‐ or nanoscale, and can be easily automated. High‐sensitivity work has also been performed using microcolumn separations prior to infusion‐based analysis using nanoelectrospray.
Separation‐independent approaches for protein expression profiling
Authors: Jenkins Rosalind E. , Pennington Stephen R.
Published: July 2005

The field of proteomics has expanded enormously in the last few years, but many of the methods used to investigate proteins are based on relatively old technologies such as two‐dimensional gel electrophoresis. While such approaches have been extremely useful in protein expression mapping, and still generate useful data today, global coverage of protein expression, activity, and protein interactions both temporally and spatially will require the continued development of higher‐throughput approaches. The analysis of gene expression has been revolutionized by the advent of DNA chip technology, and it is now becoming apparent that a similar approach would be invaluable for the analysis of the dynamic proteome. This article introduces the concept of protein and antibody chips and, by comparison with nucleic acid–based microarrays, highlights the practical issues to be addressed if this technology is to become widely applicable.
Getting the most out of protein family classification resources
Authors: Mulder Nicola J.
Published: July 2005

Protein family classification resources include the following protein signature and protein clustering databases: Pfam, PRINTS, PROSITE, ProDom, TIGRFAMs, SMART, PIR SuperFamily, SUPERFAMILY, and CluSTr. SCOP and CATH classify protein structures, and Merops, Transport Classification, and so on, are specialized protein family resources. All of them have their individual websites and databases available for searching, and are intuitive to use. Some of them are integrated into InterPro, which serves the data and software from a single source, and thus makes using the individual data and software quick and easy to access. All of them are represented in SRS (sequence retrieval system), which provides an interface for simple and complex queries and facilitates linking between results and new data. The resources are simple to use and include help pages for users.
Silicon and Silicon Alloys, Chemical and Metallurgical
Authors: Dosaj Vishu , Kroupa Michael , Bittar Reinaldo
Published: July 2005

Silicon is a low density element having nonmetallic characteristics. The production of silicon from silica is discussed as is silicon refining technology. The primary uses of silicon are in the chemical, aluminum, and electronics industries. Silicon is the chemical precursor of silicones, a versatile, fast‐growing market, and of advanced ceramics such as silicon nitride. Silicon forms an integral part of the aluminum parts industry; aluminum–silicon alloys are readily cast. Silicon is also important to aluminum production. Silicon forms alloys with a large number of metallic elements. Many of these alloys are of utmost importance to the production and refining of irons and steels. The most prevalent are the ferrosilicons, production of which is discussed.
Polyamides, Fibers
Authors: Anton Anthony , Baird Bennett R.
Published: July 2005

Polyamide fibers are melt spun from linear semicrystalline thermoplastic polymers having recurring amide groups made from diamines and dicarboxylic acids or lactams. Poly(hexamethyleneadipamide), designated as nylon‐6,6, and poly(caprolactam), nylon‐6, account for 98% of the 4 million metric tons of the worldwide annual production of nylon fiber. The attributes of nylon such as high strength, durability, abrasion resistance, resilience, moderate hydrophilicity, ease of dyeability, and low specific gravity have been recognized since its introduction in 1938. Both the inherent properties and those properties that can be engineered into the fiber manufacturing and ultimately into the fabric in downstream mill processing combined with reasonable market pricing account for the diverse end uses and market longevity of nylon. Nylon fiber is offered in the forms of continuous flat and textured filaments, staple, tow and flock for hosiery, apparel, home, flooring, industrial and transportation fabric applications. The physical appearance, functionality, and end‐use performance of nylon fibers can be modified by incorporating additives, eg, delusterants, colorants, antioxidants, or antistats in the polymer, by designing a spinneret hole configuration to impart a desired luster, surface effect or specific dtex‐per‐filament, by spinning bicomponent or biconstituent fibers, and by chemically or mechanically treating the surface of the fiber or fabric.
Paper
Authors: Hubbe Martin A.
Published: July 2005

The process of paper formation involves dewatering an aqueous fibrous suspension, followed by drying. In most cases, the fibers are cellulosic, and paper’s strength is primarily due to hydrogen bond formation. The term paperboard is used in cases where the product is relatively thick and less flexible. In addition to fibers, modern paper often contains substantial amounts of minerals, such as calcium carbonate or kaolin clay. Other components, usually at lesser quantities, can include starch, modified starch products, synthetic polyelectrolytes, and a variety of other additives.

Though there is a tradition of hand‐made papermaking, going back almost two millennia, most modern paper is manufactured on large, highly automated machines. The fiber slurry is formed and dewatered on a continuous fabric screen or sandwiched between a pair of such screens. Though most of the water used in this process is recycled multiple times, the paper industry remains a major user of fresh water. Substantial gains have been achieved to minimize the loss of fibers and other solid components from the process. Likewise, progress has been achieved in reducing the amount of energy expended in the drying of paper, primarily through increases in the proportion of water that is removed by pressing, rather than evaporation.

After reviewing paper’s distinguishing characteristics and history, this article describes paper’s chemical composition, physical properties, preparation of the fibers, the use of chemical additives, formation, pressing, and drying of the sheet, coating and converting of paper, issues related to the environment and manufacturing efficiency, and a summary of common grades of paper and paperboard.
Phosphoric Acids and Phosphates
Authors: Gard David R. ,   Updated by Staff
Published: July 2005

Most commercial applications of phosphorus‐containing materials are based on phosphoric acids and the phosphates. Uses, other than as fertilizer, include applications in detergency, foods and food processing, dental materials, dentifrices, metal surface treatments, flame retardency, etc. Structures and properties of orthophosphoric acid and condensed phosphoric acids are presented. The manufacture of technical‐ and food‐grade phosphoric acids by thermal and wet acid purification processes, as well as some of the uses of the various phosphoric acids, are discussed.

The chemistry and properties of orthophosphates and condensed phosphates are presented. Emphasis is placed on alkali metal and calcium salts and their solution properties. Properties specific to condensed phosphate salts such as hydrolysis and metal ion complexation are outlined. Manufacturing schemes for the phosphates are described and attention is given to the control of product properties.
Quality
Authors: Silverstein Irwin
Published: July 2005

Quality in the chemical industry has come to encompass three areas: (
1
) quality control, (
2
) quality assurance, and, (
3
) quality systems. The importance of quality to the chemical industry is in its use as a competitive tool in domestic and international trade. Industrial quality in the late twentieth century emphasized competition with Japan due to Japanese quality improvement efforts. Quality in the twenty‐first century is driven by competition from low wage countries particularly in the Far East causing the need for our industries to reduce costs while maintaining or improving product quality. Quality improvement activities not only provide corporations with economic gain, but save jobs.

Quality control responsibilities involve issues, such as sampling plans, calibration, and replicate analyses. Statistical quality control and laboratory information management systems are often employed. Quality assurance, which encompasses quality control, covers such activities as employee training, quality system documentation, preparation and transfer of test methods, the application of the tools of quality, performing quality audits, and addressing customer complaints.

Different quality systems are compared. The corporate quality initiative for the beginning of this century is Six Sigma, while the product quality system Good Manufacturing Practices, the quality system ISO 9000 standard, and quality performance recognition by the Malcolm Baldrige National Quality Award are also widely used.
Microirrigation
Authors: Haman Dorota Z.
Published: July 2005

Microirrigation includes all methods of frequent water application, in small flow rates, on or below the soil surface. The terms drip, trickle, and spray irrigation have been supplanted by the term “microirrigation.” Microirrigation is usually characterized by (1) low water application rates, (2) high frequency of water application, (3) water applied near or into the root zone, (4) low pressure delivery system, and (5) delivery of fertilizers and other agricultural chemicals with irrigation water (fertigation and chemigation). Systems are classified by the types of emitter. These are drip, bubbler, spray jet, and microsprinkler. The system can also be subdivided into the point source emitters and line source emitters. In microirrigation systems, only a portion of the total field area is wetted. The goal is to only wet the root zone of the crop of interest. Microirrigation systems have many potential advantages compared to other irrigation methods, including very high potential efficiency of water application. Most of the advantages are related to the low rates of the system. Usually, microirrigation requires a higher management level than other irrigation systems. One of the biggest problems encountered under microirrigation is the clogging of the emitters.