bluuebunny/crossref_metadata_2025 huggingface dataset:
Nutrigenomics: a case study in the measurement of insect response to nutritional quality
Authors: Coudron Thomas A. , Yocum George D. , Brandt Sandra L.
Published: September 2006

Recent developments in the area of nutrigenomics hold the promise of providing valuable information about the impact of nutrition on a wide range of biochemical parameters by investigating how nutrition alters global gene expression patterns. Our goal is to use a nutrigenomics approach to identify insect molecular markers that could be used as early indicators of insect responses to different nutritional sources. Such molecular markers could be chosen for degree of expression and evaluated for suitability as nutritional biomarkers by examining developmental and generational expression. Ideal markers would be highly expressed, manifested in the first generation within one developmental stage, and consistent over many generations. Our objective for the current study was to illustrate the potential discovery of molecular markers using Perillus bioculatus (F.) (Heteroptera: Pentatomidae), when reared on an optimal vs. suboptimal diet, and analyze the presence of differentially expressed genes resulting from those treatments. In this paper we present preliminary results of microarray and subtractive hybridization experiments that represent the feasibility of using nutrigenomics to assist in analyzing insect responses to nutritional changes and dietary quality with the intent of stimulating further studies in this area.
Correlation of p16 and pRb expression with HPV detection in Bowen’s disease
Authors: Willman Joseph H. , Heinz David , Golitz Loren E. , Shroyer Kenneth R.
Published: September 2006

Background:  Bowen’s disease is a form of cutaneous squamous cell carcinoma which may be caused by ultraviolet radiation, human papilloma virus (HPV) infection, or other causes. Although p16 over‐expression is a surrogate marker of HPV E7‐mediated catabolism of pRb in premalignant and malignant lesions of the cervical mucosa, the correlation of p16 and pRb expression with HPV detection in Bowen’s disease has not been well characterized.

Methods:  A retrospective study on formalin‐fixed tissues was performed. Immunohistochemistry for p16 and pRb was performed on 32 cases. DNA was successfully extracted from 20 cases, and polymerase chain reaction was performed to amplify a highly conserved region of the HPV L1 open reading frame.

Results:  Twenty‐eight of 32 (88%) cases showed strong diffuse staining for p16 but were negative for pRb; two of 32 cases (6%) were negative for p16 but were diffusely positive for pRb; one case was strongly positive for both p16 and pRb, and one case was negative for both p16 and pRb. Three of 20 cases (15%) contained HPV DNA. All three of these cases showed strong p16 expression and lack of pRb staining.

Conclusions:  Most cases of Bowen’s disease strongly express p16 but not pRb. In contrast to HPV‐associated lesions of the cervical mucosa, p16 overexpression in cutaneous Bowen’s disease appears to be unrelated to HPV status. The p16 overexpression in Bowen’s disease may reflect disruption of the G1/S checkpoint, resulting in unregulated cell cycle progression.
Pediatric primary cutaneous marginal zone lymphoma: in association with chronic antihistamine use
Authors: Sroa Novie , Magro Cynthia M.
Published: September 2006

Abstract:  Primary cutaneous marginal zone lymphoma of the mucosa‐associated lymphoid tissue predominantly occurs in adults and is rare in children. There have been no prior reports of this lymphoma occurring in American children. We present a case of a 15‐year‐old male with a history of atopic diathesis and chronic use of antihistamine agents who presented with an asymptomatic lesion on his left forearm of 6 months duration. Because histopathological and immunohistochemical studies were compatible with marginal zone lymphoma, and the patient had no associated extracutaneous disease, the diagnosis of primary cutaneous marginal zone lymphoma was rendered. Based on the patient’s past medical history prior to appearance of lesion, it was postulated that the development of lymphoma was associated with the ingestion of antihistamines and further propagated by his underlying atopic diathesis.
Cutaneous mixed tumor with lipomatous stroma
Authors: Vicioso Luis , Gallego Elena , Sanz Andrés
Published: September 2006

Aim:  Mixed tumors are usually composed of two components, one epithelial and the other mesenchymal. The latter component is commonly myxoid or myxochondroid; a massively lipomatous stroma is very unusual. To date, only two cases of mixed tumor of the skin have been reported with this type of stroma.

Methods and results:  We report the case of a 61‐year‐old man with a mixed tumor situated on the hand, an unusual site for these tumors, with over 90% of the tumor composed of adipose tissue. The tumor was a well‐circumscribed, 4.5‐cm mass, with the gross appearance of a lipoma. The lipomatous stroma contained nests and ribbons of epithelial cells, with occasional tubular structures, surrounded by a scarce amount of fibromyxoid tissue. Immunohistochemical study showed findings similar to those seen in classic mixed tumors.

Conclusion:  Together with a few other cases in the skin and parotid gland, this report shows how massive adipose differentiation can arise in a mixed tumor of the skin.
An unusual presentation of periocular Merkel cell carcinoma
Authors: Leibovitch Igal , Davis Garry , Huilgol Shyamala C. , Crompton John , James Craig L. , Selva Dinesh
Published: September 2006

Aim:  Merkel cell carcinoma (MCC) is an uncommon but potentially aggressive tumor. We describe a rare presentation of MMC of the upper lid.

Methods:  A 63‐year‐old male presented with a 3‐month history of right upper lid fullness. Examination revealed a large multinodular mass protruding into the conjunctival aspect of the eyelid. An enlarged right submandibular lymph node was also noted.

Results:  An incisional biopsy was suggestive of MCC. Staged surgical excision with rapid paraffin sections was performed. The tumor cells were seen invading the tarsal plate and adjacent to the palpebral conjunctiva but not into the epidermis. MCC was confirmed using immunohistochemical stains and neuroendocrine markers (cytokeratins Cam 5.2, AE1/3, CK20, chromogranin, synaptophysin, and Leu 7). The lymph node biopsy was also confirmed as metastatic MCC. The patient was treated with postsurgical chemotherapy and radiotherapy, with no recurrence during a 6 months follow‐up period.

Conclusion:  Although uncommon, periocular MCC may present as an atypical conjunctival multinodular mass.
Parathyroid hormone modifies human periodontal ligament cell proliferation and survival in vitro
Authors: Lossdörfer S. , Götz W. , Jäger A.
Published: September 2006

Background and Objective:  Periodontal ligament (PDL) cells show traits that are typical of osteoblasts, such as osteoblastic marker gene expression and the ability to respond to parathyroid hormone (PTH) stimulation in an osteoblast‐like manner with respect to differentiation and local factor production. In the present study, we hypothesized that human PDL cells might respond to PTH stimulation with changes in proliferation and cell survival and thereby provide another mechanism by which PTH might affect the reparative potential of PDL cells. We speculated that the maturation state of the cells and the mode of PTH(1‐34) administration would have an impact on the cellular response.

Material and Methods:  PDL cells were challenged with PTH(1‐34) intermittently or continuously at different maturation states. Cell number, 5‐bromo‐2‐deoxyuridine (BrdU) incorporation, DNA fragmentation, nitric oxide production and the duration of the PTH(1‐34) effect were determined.

Results:  Intermittent PTH(1‐34) treatment of preconfluent cells caused a significant increase in proliferation and DNA fragmentation, whereas in more mature cells, proliferation was less enhanced while apoptosis was more pronounced than in immature cells. Continuous PTH(1‐34) exposure did not alter proliferation in any maturation state but increased DNA fragmentation in preconfluent cells. PTH(1‐34) prevented etoposide‐induced apoptosis after 6 h but no longer after 24 h. Nitric oxide production was unaffected.

Conclusion:  These results indicate that human PDL cells respond to PTH(1‐34) with changes in proliferative and apoptotic signaling in a maturation‐state‐dependent manner. Besides changes in local factor production, these findings provide a further possible mechanism to support the idea that PDL cells possess the potential to be involved in the regulation of dental hard tissue repair.
Areca nut extracts reduce the intracellular reactive oxygen species and release of myeloperoxidase by human polymorphonuclear leukocytes
Authors: Lai Y.‐L. , Lin J.‐C. , Yang S.‐F. , Liu T.‐Y. , Hung S.‐L.
Published: September 2006

Background and Objective:  Polymorphonuclear leukocytes (PMN) represent the first line of host defense. Areca nut extract inhibits the bactericidal activity of, and the release of superoxide anion (O2– ) by, PMN. This study investigated the effects of areca nut extract on the intracellular production of reactive oxygen species (ROS) and on the extracellular release of lysosomal enzyme, myeloperoxidase (MPO), by PMN. The effects of arecoline, a principal component of areca nut, were also examined.

Material and Methods:  Human PMN were treated with various concentrations of areca nut extract or arecoline followed by treatment with Hanks' balanced salt solution, with or without cytochalasin B and fMet‐Leu‐Phe (CB/fMLP). The viability of PMN was determined using propidium iodide staining and flow cytometry. The presence of intracellular ROS was determined using 2′,7′‐dichlorofluorescin diacetate and fluorometry. MPO release was determined using a substrate assay.

Results:  Areca nut extract (25 and 50 µg/ml) significantly decreased the viability of PMN. The intracellular levels of ROS and the extracellular release of MPO were induced in PMN by CB/fMLP. Exposure of PMN to areca nut extract (up to 25 µg/ml) or to arecoline (up to 2 mg/ml) did not directly affect the levels of ROS and MPO activity. However, under conditions that did not affect the viability of PMN, the ability of CB/fMLP to trigger production of intracellular ROS and release of MPO in human PMN was significantly suppressed by areca nut extract and arecoline.

Conclusion:  Areca nut impaired the activation of PMN by CB/fMLP that might decrease the effectiveness of PMN in the host defense. Alternatively, exposure of PMN to areca nut extract could decrease the capacity of PMN to damage tissues.
The Truth In Lending Act and Variable-Rate Mortgages and Balloon Notes
Authors: Landers Jonathan M. , Chandler Cathleen
Published: September 2006

To own one's own home has long been at the heart of the American dream. Despite the considerable recent attention to new and nontraditional modes of living–in planned communities, town houses, communes, condominiums, and cooperatives–and although some social reformers and intellectuals have criticized conventional modes of living, owning a home and “cooking hamburgers over a charcoal fire” remain a dominant part of the middle class ethos.
Echinococcus granulosus in northern Queensland
Authors: BANKS DJD , COPEMAN DB , SKERRATT LF
Published: September 2006

Objective  To provide information on possible ecological determinants of infection with Echinococcus granulosus in a beef pastoral area of northern Queensland.

Procedure  An ecological study was carried out on the prevalence and viability of infection with Echinococcus granulosus in definitive and potential intermediate hosts, and their predator prey relationships.

Seven adjacent extensive beef properties 100 km south of Townsville, that included areas of savannah, open woodland and dense closed scrub, were selected for the study. Infection with E granulosus in dingoes was determined at post mortem, and in domestic dogs by examining duodenal mucus after purging with arecoline hydrobromide. Cattle, wild pigs and macropods were examined at post mortem for viable hydatid cysts. The diet of dingoes was investigated by identifying the hair of prey species found in their stomach and colon, and that of domestic dogs by questioning their owners.

Results  Prevalence of hydatidosis in adult cattle ranged from 41% in animals from properties with large areas of dense closed scrub, to 3% on properties with little or no scrub. Hydatid cysts were found in 21.8% of black‐striped wallabies (Macropus dorsalis), 9.4% of feral pigs, 1.5% of wallaroos (Macropus robustus), and 1.4% of eastern grey kangaroos (Macropus giganteus). No rufous rat kangaroos (Aepyprymnus rufescens) or swamp wallabies (Wallabia bicolor) were infected. Most cysts in macropods were viable, whereas in pigs about half were viable and in cattle only 0.7% contained viable protoscoleces. Infection with E granulosus was detected in 76% of dingoes, whereas no infection was detected in domestic dogs in the study area.

Conclusions  It was concluded that the sylvatic cycle of E granulosus in the study area was maintained mainly through predation of black‐striped wallabies by dingoes, and that the verges of dense scrub were the main nidus of infection.
Detection of Anaplasma platys and Babesia canis vogeli and their impact on platelet numbers in free‐roaming dogs associated with remote Aboriginal communities in Australia
Authors: BROWN GK , CANFIELD PJ , DUNSTAN RH , ROBERTS TK , MARTIN AR , BROWN CS , IRVING R
Published: September 2006

Objective   To detect Anaplasma platys and Babesia canis vogeli infection, using polymerase chain reaction (PCR)‐based assays, in free‐roaming dogs associated with eight Aboriginal communities in remote areas of Australia and to determine the impact of infection through the assessment of platelet numbers.

Procedures   Blood samples from 215 dogs were screened by PCR for A platys and B canis vogeli using established genus‐specific DNA primers for the 16S and 18S rRNA genes respectively. Both A platys DNA and B canis vogeli DNA were confirmed from the screening PCR either by sequencing or by the use of species‐specific primers. Peripheral blood films from 92 of the 215 dogs were used to estimate platelet numbers through an indirect method.

Results   Of 215 dogs, 69 (32%) were positive for A platys, 22 (10%) for B canis vogeli and 24 (11%) for both. The two organisms were detected singularly and as coinfection in all communities. For the 92 dogs in which peripheral blood films were examined, the mean estimated platelet counts for the non‐infected dogs was 318 × 109/L, those infected with A platys alone was 256 × 109/L, those with B canis vogeli alone was 276 × 109/L and those infected with both parasites was 169 × 109/L. In young dogs, infection produced significantly decreased mean platelet counts when compared to uninfected dogs. Thrombocytopenia (< 200 × 109/L) was detected in 18 (51%) dogs infected with A platys alone, 3 (33%) dogs infected with B canis vogeli alone, 13 (72%) dogs coinfected, and 8 (27%) uninfected dogs.

Conclusions   A platys and B canis vogeli infection, either singularly or together, was widespread in free roaming dogs associated with remote Aboriginal communities in the Northern Territory and north‐western New South Wales. Moreover, both A platys and B canis vogeli infections were associated with a reduction in mean platelet numbers in dog populations, particularly in young dogs. The fact that 51% of dogs infected with A platys alone and 72% dogs coinfected were thrombocytopenic compared to 27% of uninfected dogs suggests that the organism alone or in combination with B canis vogeli has the potential to cause thrombocytopenia and perhaps contribute to a clinical bleeding disorder in infected dogs.
MRI findings of haematomyelia in a dog with spontaneous systemic haemorrhage
Authors: OKADA M , KOIE H , KITAGAWA M , KANAYAMA K , SATO T , YAMAMURA H , SAKAI T
Published: September 2006

A 7‐year‐old female cross‐breed dog was brought to Nihon University Animal Medical Center for investigation of tetraplegia. Lameness in the pelvic limbs, that had developed 2 weeks previously, had progressed to tetraplegia. On magnetic resonance imaging of the spinal cord, isointensity was detected from C2 to C4 and T12 to T13, isointensity and hyperintensity were intermingled from L3 to L4, and hyperintensity was detected from L5 to L7 by T1‐weighted imaging. On T2‐weighted imaging, hyperintensity was detected in all regions described above. The dog recovered from anaesthesia, but died during the day from systemic bleeding as the result of a coagulopathy of unknown aetiology. Histopathological examination revealed haematomyelia in these regions of the spinal cord. This is the first report of magnetic resonance imaging findings of haematomyelia in canine spontaneous systemic haemorrhage. It appeared that the differences in the findings of T1‐weighted imaging along the spinal regions reflected time‐lags in the occurrence of bleeding.
Testosterone increases lactate transport, monocarboxylate transporter (MCT) 1 and MCT4 in rat skeletal muscle
Authors: Enoki Taisuke , Yoshida Yuko , Lally James , Hatta Hideo , Bonen Arend
Published: September 2006

We have examined the effects of administration of testosterone for 7 days on monocarboxylate transporter (MCT) 1 and MCT4 mRNAs and proteins in seven metabolically heterogeneous rat hindlimb muscles and in the heart. In addition, we also examined the effects of testosterone treatment on plasmalemmal MCT1 and MCT4, and lactate transport into giant sarcolemmal vesicles prepared from red and white hindlimb muscles and the heart. Testosterone did not alter MCT1 or MCT4 mRNA, except in the plantaris muscle. Testosterone increased MCT1 (20%–77%, P < 0.05) and MCT4 protein (29%–110%, P< 0.05) in five out of seven muscles examined. In contrast, in the heart MCT1 protein was not increased (P> 0.05), and MCT 4 mRNA and protein were not detected. There was no correlation between the testosterone‐induced increments in MCT1 and MCT4 proteins. Muscle fibre composition was not associated with testosterone‐induced increments in MCT1 protein. In contrast, there was a strong positive relationship between the testosterone‐induced increments in MCT4 protein and the fast‐twitch fibre composition of rat muscles. Lactate transport into giant sarcolemmal vesicles was increased in red (23%, P< 0.05) and white muscles (21%, P< 0.05), and in the heart (58%, P< 0.05) of testosterone‐treated animals (P< 0.05). However, plasmalemmal MCT1 protein (red, +40%, P< 0.05; white, +39%, P< 0.05) and plasmalemmal MCT4 protein (red, +25%, P< 0.05; white, +48%, P< 0.05) were increased only in skeletal muscle. In the heart, plasmalemmal MCT1 protein was reduced (−20%, P< 0.05). In conclusion, these studies have shown that testosterone induces an increase in both MCT1 and MCT4 proteins and their plasmalemmal content in skeletal muscle. However, the testosterone‐induced effect was tissue‐specific, as MCT1 protein expression was not altered in the heart. In the heart, the testosterone‐induced increase in lactate transport cannot be explained by changes in plasmalemmal MCT1 content, but in skeletal muscle the increase in the rate of lactate transport was associated with increases in plasmalemmal MCT1 and MCT4.
An Essential Role for LEDGF/p75 in HIV Integration
Authors: Llano Manuel , Saenz Dyana T. , Meehan Anne , Wongthida Phonphimon , Peretz Mary , Walker William H. , Teo Wulin , Poeschla Eric M.
Published: September 2006

Chromosomal integration enables human immunodeficiency virus (HIV) to establish a permanent reservoir that can be therapeutically suppressed but not eradicated. Participation of cellular proteins in this obligate replication step is poorly understood. We used intensified RNA interference and dominant-negative protein approaches to show that the cellular transcriptional coactivator lens epithelium–derived growth factor (LEDGF)/p75 (p75) is an essential HIV integration cofactor. The mechanism requires both linkages of a molecular tether that p75 forms between integrase and chromatin. Fractionally minute levels of endogenous p75 are sufficient to enable integration, showing that cellular factors that engage HIV after entry may elude identification in less intensive knockdowns. Perturbing the p75-integrase interaction may have therapeutic potential.
Rapid, Sensitive, and Discriminating Identification ofNaegleriaspp. by Real-Time PCR and Melting-Curve Analysis
Authors: Robinson Bret S. , Monis Paul T. , Dobson Phillip J.
Published: September 2006

The free-living amoeboflagellate genusNaegleriaincludes one pathogenic and two potentially pathogenic species (Naegleria fowleri,Naegleria italica, andNaegleria australiensis) plus numerous benign organisms. Monitoring of bathing water, water supplies, and cooling systems for these pathogens requires a timely and reliable method for identification, but current DNA sequence-based methods identify onlyN. fowlerior require full sequencing to identify other species in the genus. A novel closed-tube method for distinguishing thermophilicNaegleriaspecies is presented, using a single primer set and the DNA intercalating dye SYTO9 for real-time PCR and melting-curve analysis of the 5.8S ribosomal DNA gene and flanking noncoding spacers (ITS1, ITS2). Collection of DNA melting data at close temperature intervals produces highly informative melting curves with one or more recognizable melting peaks, readily distinguished for sevenNaegleriaspecies and the relatedWillaertia magna. Advantages over other methods used to identify these organisms include its comprehensiveness (encompassing all species tested to date), simplicity (no electrophoresis required to verify the product), and sensitivity (unambiguous identification from DNA equivalent to one cell). This approach should be applicable to a wide range of microorganisms of medical importance.
Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation
Authors: Brodie Eoin L. , DeSantis Todd Z. , Joyner Dominique C. , Baek Seung M. , Larsen Joern T. , Andersen Gary L. , Hazen Terry C. , Richardson Paul M. , Herman Donald J. , Tokunaga Tetsu K. , Wan Jiamin M. , Firestone Mary K.
Published: September 2006

Reduction of soluble uranium U(VI) to less-soluble uranium U(IV) is a promising approach to minimize migration from contaminated aquifers. It is generally assumed that, under constant reducing conditions, U(IV) is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To determine if changes in microbial community composition were a factor in U(IV) reoxidation, we employed a high-density phylogenetic DNA microarray (16S microarray) containing 500,000 probes to monitor changes in bacterial populations during this remediation process. Comparison of the 16S microarray with clone libraries demonstrated successful detection and classification of most clone groups. Analysis of the most dynamic groups of 16S rRNA gene amplicons detected by the 16S microarray identified five clusters of bacterial subfamilies responding in a similar manner. This approach demonstrated that amplicons of known metal-reducing bacteria such as
Geothrix fermentans
(confirmed by quantitative PCR) and those within the
Geobacteraceae
were abundant during U(VI) reduction and did not decline during the U(IV) reoxidation phase. Significantly, it appears that the observed reoxidation of uranium under reducing conditions occurred despite elevated microbial activity and the consistent presence of metal-reducing bacteria. High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner.
Identification of a Diagnostic Marker To Detect Freshwater Cyanophages of Filamentous Cyanobacteria
Authors: Baker Andrea C. , Goddard Victoria J. , Davy Joanne , Schroeder Declan C. , Adams David G. , Wilson William H.
Published: September 2006

Cyanophages are viruses that infect the cyanobacteria, globally important photosynthetic microorganisms. Cyanophages are considered significant components of microbial communities, playing major roles in influencing host community diversity and primary productivity, terminating cyanobacterial water blooms, and influencing biogeochemical cycles. Cyanophages are ubiquitous in both marine and freshwater systems; however, the majority of molecular research has been biased toward the study of marine cyanophages. In this study, a diagnostic probe was developed to detect freshwater cyanophages in natural waters. Oligonucleotide PCR-based primers were designed to specifically amplify the major capsid protein gene from previously characterized freshwater cyanomyoviruses that are infectious to the filamentous, nitrogen-fixing cyanobacterial genera
Anabaena
and
Nostoc
. The primers were also successful in yielding PCR products from mixed virus communities concentrated from water samples collected from freshwater lakes in the United Kingdom. The probes are thought to provide a useful tool for the investigation of cyanophage diversity in freshwater environments.
Fiber-Optic Microarray for Simultaneous Detection of Multiple Harmful Algal Bloom Species
Authors: Ahn Soohyoun , Kulis David M. , Erdner Deana L. , Anderson Donald M. , Walt David R.
Published: September 2006

Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species
Alexandrium fundyense
,
Alexandrium ostenfeldii
, and
Pseudo-nitzschia australis
. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 μm) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.
Tick-Borne Rickettsial Pathogens in Ticks and Small Mammals in Korea
Authors: Kim Chul-Min , Yi Ying-Hua , Yu Do-Hyeon , Lee Mi-Jin , Cho Mae-Rim , Desai Atul R. , Shringi Smriti , Klein Terry A. , Kim Heung-Chul , Song Jin-Won , Baek Luck-Ju , Chong Sung-Tae , O'Guinn Monica L. , Lee John S. , Lee In-Yong , Park Jin-Ho , Foley Janet , Chae Joon-Seok
Published: September 2006

In order to investigate the prevalence of tick-borne infectious agents among ticks, ticks comprising five species from two genera (Hemaphysalisspp. andIxodesspp.) were screened using molecular techniques. Ticks (3,135) were collected from small wild-caught mammals or by dragging/flagging in the Republic of Korea (ROK) and were pooled into a total of 1,638 samples (1 to 27 ticks per pool). From the 1,638 tick samples, species-specific fragments ofAnaplasma phagocytophilum(1 sample),Anaplasma platys(52 samples),Ehrlichia chaffeensis(29 samples),Ehrlichia ewingii(2 samples),Ehrlichia canis(18 samples), andRickettsia rickettsii(28 samples) were amplified by PCR assay. Twenty-one pooled and individual tick samples had mixed infections of two (15 samples) or three (6 samples) pathogens. In addition, 424 spleen samples from small captured mammals (389 rodents, 33 insectivores, and 2 weasels) were screened for selected zoonotic pathogens. Species-specific DNA fragments ofA. phagocytophilum(110 samples),A. platys(68 samples),E. chaffeensis(8 samples),E. ewingii(26 samples),E. canis(51 samples), andRickettsiasp. (22 samples) were amplified by PCR assay. One hundred thirty small mammals had single infections, while 4, 14, and 21 striped field mice (Apodemus agrarius) had mixed infections of four, three, and two pathogens, respectively. Phylogenetic analysis based on nucleotide sequence comparison also revealed that Korean strains ofE. chaffeensisclustered closely with those from China and the United States, while theRickettsia(rOmpA) sequences clustered within a clade together with a Chinese strain. These results suggest that these agents should be considered in differential diagnosis while examining cases of acute febrile illnesses in humans as well as animals in the ROK.
Abundance of
narG
,
nirS
,
nirK
, and
nosZ
Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland
Authors: Kandeler Ellen , Deiglmayr Kathrin , Tscherko Dagmar , Bru David , Philippot Laurent
Published: September 2006

Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 × 10
5
to 8.9 × 10
5
copies per nanogram of DNA but smaller amounts of
narG
,
nirK
, and
nosZ
target molecules. Thus, numbers of
narG
,
nirK
,
nirS
, and
nosZ
copies per nanogram of DNA ranged from 2.1 × 10
3
to 2.6 × 10
4
, 7.4 × 10
2
to 1.4 × 10
3
, 2.5 × 10
2
to 6.4 × 10
3
, and 1.2 × 10
3
to 5.5 × 10
3
, respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of
narG
and
nirS
versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of
nirK
and
nosZ
genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of
nirK
and
nosZ
communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.
An Oxidoreductase Is Involved in Cercosporin Degradation by the Bacterium
Xanthomonas campestris
pv. zinniae
Authors: Taylor Tanya V. , Mitchell Thomas K. , Daub Margaret E.
Published: September 2006

The polyketide toxin cercosporin plays a key role in pathogenesis by fungal species of the genus
Cercospora
. The bacterium
Xanthomonas campestris
pv. zinniae is able to rapidly degrade this toxin. Growth of
X. campestris
pv. zinniae strains in cercosporin-containing medium leads to the breakdown of cercosporin and to the formation of xanosporic acid, a nontoxic breakdown product. Five non-cercosporin-degrading mutants of a strain that rapidly degrades cercosporin (XCZ-3) were generated by ethyl methanesulfonate mutagenesis and were then transformed with a genomic library from the wild-type strain. All five mutants were complemented with the same genomic clone, which encoded a putative transcriptional regulator and an oxidoreductase. Simultaneous expression of these two genes was necessary to complement the mutant phenotype. Sequence analysis of the mutants showed that all five mutants had point mutations in the oxidoreductase gene and no mutations in the regulator. Quantitative reverse transcription-PCR (RT-PCR) showed that the expression of both of these genes in the wild-type strain is upregulated after exposure to cercosporin. Both the oxidoreductase and transcriptional regulator genes were transformed into three non-cercosporin-degrading bacteria to determine if they are sufficient for cercosporin degradation. Quantitative RT-PCR analysis confirmed that the oxidoreductase was expressed in all transconjugants. However, none of the transconjugants were able to degrade cercosporin, suggesting that additional factors are required for cercosporin degradation. Further study of cercosporin degradation in
X. campestris
pv. zinniae may allow for the engineering of
Cercospora
-resistant plants by using a suite of genes.
Elucidation of the
hrp
Clusters of
Xanthomonas oryzae
pv. oryzicola That Control the Hypersensitive Response in Nonhost Tobacco and Pathogenicity in Susceptible Host Rice
Authors: Zou Li-fang , Wang Xing-ping , Xiang Yong , Zhang Bing , Li Yu-Rong , Xiao You-lun , Wang Jin-sheng , Walmsley Adrian R. , Chen Gong-you
Published: September 2006

Xanthomonas oryzae
pv. oryzicola, the cause of bacterial leaf streak in rice, possesses clusters of
hrp
genes that determine its ability to elicit a hypersensitive response (HR) in nonhost tobacco and pathogenicity in host rice. A 27-kb region of the genome of
X. oryzae
pv. oryzicola (RS105) was identified and sequenced, revealing 10
hrp
, 9
hrc
(
hrp
conserved), and 8
hpa
(
hrp
-associated) genes and 7 regulatory plant-inducible promoter boxes. While the region from
hpa2
to
hpaB
and the
hrpF
operon resembled the corresponding genes of other xanthomonads, the
hpaB
-
hrpF
region incorporated an
hrpE3
gene that was not present in
X. oryzae
pv. oryzae. We found that an
hrpF
mutant had lost the ability to elicit the HR in tobacco and pathogenicity in adult rice plants but still caused water-soaking symptoms in rice seedlings and that Hpa1 is an HR elicitor in nonhost tobacco whose expression is controlled by an
hrp
regulator, HrpX. Using an Hrp phenotype complementation test, we identified a small
hrp
cluster containing the
hrpG
and
hrpX
regulatory genes, which is separated from the core
hrp
cluster. In addition, we identified a gene,
prhA
(plant-regulated
hrp
), that played a key role in the Hrp phenotype of
X. oryzae
pv. oryzicola but was neither in the core
hrp
cluster nor in the
hrp
regulatory cluster. A
prhA
mutant failed to reduce the HR in tobacco and pathogenicity in rice but caused water-soaking symptoms in rice. This is the first report that
X. oryzae
pv. oryzicola possesses three separate DNA regions for HR induction in nonhost tobacco and pathogenicity in host rice, which will provide a fundamental base to understand pathogenicity determinants of
X. oryzae
pv. oryzicola compared with those of
X. oryzae
pv. oryzae.
Discrimination of Multiple
Dehalococcoides
Strains in a Trichloroethene Enrichment by Quantification of Their Reductive Dehalogenase Genes
Authors: Holmes Victor F. , He Jianzhong , Lee Patrick K. H. , Alvarez-Cohen Lisa
Published: September 2006

While many anaerobic microbial communities are capable of reductively dechlorinating tetrachloroethene (PCE) and trichloroethene (TCE) to dichloroethene (DCE), vinyl chloride (VC), and finally ethene, the accumulation of the highly toxic intermediates,
cis
-DCE (cDCE) and VC, presents a challenge for bioremediation processes. Members of the genus
Dehalococcoides
are apparently solely responsible for dechlorination beyond DCE, but isolates of
Dehalococcoides
each metabolize only a subset of PCE dechlorination intermediates and the interactions among distinct
Dehalococcoides
strains that result in complete dechlorination are not well understood. Here we apply quantitative PCR to 16S rRNA and reductase gene sequences to discriminate and track
Dehalococcoides
strains in a TCE enrichment derived from soil taken from the Alameda Naval Air Station (ANAS) using a four-gene plasmid standard. This standard increased experimental accuracy such that 16S rRNA and summed reductase gene copy numbers matched to within 10%. The ANAS culture was found to contain only a single
Dehalococcoides
16S rRNA gene sequence, matching that of
D. ethenogenes
195, but both the
vcrA
and
tceA
reductive dehalogenase genes. Quantities of these two genes in the enrichment summed to the quantity of the
Dehalococcoides
16S rRNA gene. Further, between ANAS subcultures enriched on TCE, cDCE, or VC, the relative copy number of the two dehalogenases shifted 14-fold, indicating that the genes are present in two different
Dehalococcoides
strains. Comparison of cell yields in VC-, cDCE-, and TCE-enriched subcultures suggests that the
tceA
-containing strain is responsible for nearly all of the TCE and cDCE metabolism in ANAS, whereas the
vcrA
-containing strain is responsible for all of the VC metabolism.
Molecular Diversity, Cultivation, and Improved Detection by Fluorescent In Situ Hybridization of a Dominant Group of Human Gut Bacteria Related toRoseburiaspp. orEubacterium rectale
Authors: Aminov Rustam I. , Walker Alan W. , Duncan Sylvia H. , Harmsen Hermie J. M. , Welling Gjalt W. , Flint Harry J.
Published: September 2006

Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains ofRoseburiaandEubacterium rectalewith 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.
Composition and Metabolic Activities of Bacterial Biofilms Colonizing Food Residues in the Human Gut
Authors: Macfarlane Sandra , Macfarlane George T.
Published: September 2006

Bacteria growing in the human large intestine live in intimate association with the host and play an important role in host digestive processes, gut physiology, and metabolism. Fecal bacteria have been investigated extensively, but few studies have been done on biofilms that form on digestive wastes in the large bowel. The aims of this investigation were to investigate the composition and metabolic activities of bacterial communities that colonize the surfaces of food residues in fecal material, with respect to their role in the fermentation of complex carbohydrates. Fresh stools were obtained from 15 healthy donors, and food residues were separated by filtration. Adherent bacteria were removed by surfactant treatment for microbiological analysis and fermentation studies. Scanning electron microscopy and fluorescent in situ hybridization in conjunction with confocal laser scanning microscopy (CLSM) were used to visualize intact biofilms. Results showed that bacterial populations strongly adhering to particulate matter were phenotypically similar in composition to unattached communities, with bacteroides and bifidobacteria predominating. Biofilms comprised a mixture of living and dead bacteria, and CLSM showed that bifidobacteria in the biofilms occurred as isolated dispersed cells and in microcolonies near the interface with the substratum. Fermentation experiments with a variety of complex carbohydrates demonstrated that biofilm populations were more efficient in digesting polysaccharides, while nonadhering communities fermented oligosaccharides most rapidly. Acetate was the principal fermentation product formed by biofilm bacteria, whereas higher levels of butyrate were produced by nonadherent populations, showing that the two communities were metabolically distinct.
Quantification of the Effects of Salt Stress and Physiological State on Thermotolerance of
Bacillus cereus
ATCC 10987 and ATCC 14579
Authors: den Besten Heidy M. W. , Mataragas Marios , Moezelaar Roy , Abee Tjakko , Zwietering Marcel H.
Published: September 2006

The food-borne pathogen
Bacillus cereus
can acquire enhanced thermal resistance through multiple mechanisms. Two
Bacillus cereus
strains, ATCC 10987 and ATCC 14579, were used to quantify the effects of salt stress and physiological state on thermotolerance. Cultures were exposed to increasing concentrations of sodium chloride for 30 min, after which their thermotolerance was assessed at 50°C. Linear and nonlinear microbial survival models, which cover a wide range of known inactivation curvatures for vegetative cells, were fitted to the inactivation data and evaluated. Based on statistical indices and model characteristics, biphasic models with a shoulder were selected and used for quantification. Each model parameter reflected a survival characteristic, and both models were flexible, allowing a reduction of parameters when certain phenomena were not present. Both strains showed enhanced thermotolerance after preexposure to (non)lethal salt stress conditions in the exponential phase. The maximum adaptive stress response due to salt preexposure demonstrated for exponential-phase cells was comparable to the effect of physiological state on thermotolerance in both strains. However, the adaptive salt stress response was less pronounced for transition- and stationary-phase cells. The distinct tailing of strain ATCC 10987 was attributed to the presence of a subpopulation of spores. The existence of a stable heat-resistant subpopulation of vegetative cells could not be demonstrated for either of the strains. Quantification of the adaptive stress response might be instrumental in understanding adaptation mechanisms and will allow the food industry to develop more accurate and reliable stress-integrated predictive modeling to optimize minimal processing conditions.
Novel Intermediates of Acenaphthylene Degradation by
Rhizobium
sp. Strain CU-A1: Evidence for Naphthalene-1,8-Dicarboxylic Acid Metabolism
Authors: Poonthrigpun Siriwat , Pattaragulwanit Kobchai , Paengthai Sarunya , Kriangkripipat Thanyanuch , Juntongjin Kanchana , Thaniyavarn Suthep , Petsom Amorn , Pinphanichakarn Pairoh
Published: September 2006

The acenaphthylene-degrading bacterium
Rhizobium
sp. strain CU-A1 was isolated from petroleum-contaminated soil in Thailand. This strain was able to degrade 600 mg/liter acenaphthylene completely within three days. To elucidate the pathway for degradation of acenaphthylene, strain CU-A1 was mutagenized by transposon Tn
5
in order to obtain mutant strains deficient in acenaphthylene degradation. Metabolites produced from Tn
5
-induced mutant strains B1, B5, and A53 were purified by thin-layer chromatography and silica gel column chromatography and characterized by mass spectrometry. The results suggested that this strain cleaved the fused five-membered ring of acenaphthylene to form naphthalene-1,8-dicarboxylic acid via acenaphthenequinone. One carboxyl group of naphthalene-1,8-dicarboxylic acid was removed to form 1-naphthoic acid which was transformed into salicylic acid before metabolization to gentisic acid. This work is the first report of complete acenaphthylene degradation by a bacterial strain.
Relevance of the Endosymbiosis of
Blochmannia floridanus
and Carpenter Ants at Different Stages of the Life Cycle of the Host
Authors: Zientz Evelyn , Beyaert Ivo , Gross Roy , Feldhaar Heike
Published: September 2006

Expression of several genes possibly involved in the symbiotic relationship between the obligate intracellular endosymbiont
Blochmannia floridanus
and its ant host
Camponotus floridanus
was investigated at different developmental stages of the host by real-time quantitative PCR. These included a set of genes related to nitrogen metabolism (
ureC
,
ureF
,
glnA
, and
speB
) as well as genes involved in the synthesis of the aromatic amino acid tyrosine (
tyrA
,
aspC
, and
hisC
). The overall transcriptional activity of
Blochmannia
was found to be quite low during early developmental stages and to increase steadily with host age. However, a concerted peak of gene expression related to nitrogen recycling could be detected around the entire process of pupation, while expression of biosynthesis pathways for aromatic amino acids was elevated only during a short phase in pupation. These data suggest an important role of certain metabolic functions for the symbiotic interactions of the bacteria and an individual host organism in early phases of development. General relevance of
Blochmannia
for its ant host was tested in fostering experiments with worker groups of
Camponotus floridanus
, and their success in raising pupae from first-instar larvae was used as a fitness measure. Groups treated with antibiotics had a significantly reduced success in raising the brood in comparison to untreated control groups, indicating that the symbiosis is relevant for the development of the entire colony.
Cloning of the Novel Gene Encoding β-Agarase C from a Marine Bacterium,
Vibrio
sp. Strain PO-303, and Characterization of the Gene Product
Authors: Dong Jinhua , Hashikawa Shinnosuke , Konishi Takafumi , Tamaru Yutaka , Araki Toshiyoshi
Published: September 2006

The β-agarase C gene (
agaC
) of a marine bacterium,
Vibrio
sp. strain PO-303, consisted of 1,437 bp encoding 478 amino acid residues. β-Agarase C was identified as the first β-agarase that cannot hydrolyze neoagarooctaose and smaller neoagarooligosaccharides and was assigned to a novel glycoside hydrolase family.
Organotin Decomposition by Pyochelin, Secreted by
Pseudomonas aeruginosa
Even in an Iron-Sufficient Environment
Authors: Sun Guo-Xin , Zhou Wen-Qiang , Zhong Jian-Jiang
Published: September 2006

A triphenyltin (TPT)-decomposing strain,
Pseudomonas aeruginosa
CGMCC 1.860, was screened out. It secreted an unknown TPT-decomposing factor into the medium, later shown to be pyochelin, even in the presence of 100 μM iron. To our knowledge, this is the first report of organotin decomposition by pyochelin.
Effects of Chloromethanes on Growth of and Deletion of the
pce
Gene Cluster in Dehalorespiring
Desulfitobacterium hafniense
Strain Y51
Authors: Futagami Taiki , Yamaguchi Takehito , Nakayama Shun-ichi , Goto Masatoshi , Furukawa Kensuke
Published: September 2006

The dehalorespiring
Desulfitobacterium hafniense
strain Y51 efficiently dechlorinates tetrachloroethene (PCE) to
cis
-1,2-dichloroethene (
cis
-DCE) via trichloroethene by PceA reductive dehalogenase encoded by the
pceA
gene. In a previous study, we found that the significant growth inhibition of strain Y51 occurred in the presence of commercial
cis
-DCE. In this study, it turned out that the growth inhibition was caused by chloroform (CF) contamination of
cis
-DCE. Interestingly, CF did not affect the growth of PCE-nondechlorinating SD (small deletion) and LD (large deletion) variants, where the former fails to transcribe the
pceABC
genes caused by a deletion of the promoter and the latter lost the entire
pceABCT
gene cluster. Therefore, PCE-nondechlorinating variants, mostly LD variant, became predominant, and dechlorination activity was significantly reduced in the presence of CF. Moreover, such a growth inhibitory effect was also observed in the presence of carbon tetrachloride at 1 μM, but not carbon dichloride even at 1 mM.