bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct roles of haptoglobin-related protein and apolipoprotein L-I in trypanolysis by human serum
Authors: Vanhollebeke Benoit , Nielsen Marianne J. , Watanabe Yoshihisa , Truc Philippe , Vanhamme Luc , Nakajima Kazunori , Moestrup Soren K. , Pays Etienne
Published: February 2007

Apolipoprotein L-I (apoL-I) is a human high-density lipoprotein (HDL) component able to kill
Trypanosoma brucei brucei
by forming anion-selective pores in the lysosomal membrane of the parasite. Another HDL component, haptoglobin-related protein (Hpr), has been suggested as an additional toxin required for full trypanolytic activity of normal human serum. We recently reported the case of a human lacking apoL-I (apoL-I
−/−
HS) as the result of frameshift mutations in both
apoL-I
alleles. Here, we show that this serum, devoid of any trypanolytic activity, exhibits normal concentrations of HDL-bound Hpr. Conversely, the serum of individuals with normal HDL-bound apoL-I but who lack Hpr and haptoglobin [Hp(r)
−/−
HS] as the result of gene deletion (anhaptoglobinemia) exhibited phenotypically normal but delayed trypanolytic activity. The trypanolytic properties of Hp(r)
−/−
HS were mimicked by free recombinant apoL-I, whereas recombinant Hpr did not affect trypanosomes. The lysis delay observed with either Hp(r)
−/−
HS or recombinant apoL-I could entirely be attributed to a defect in the uptake of the lytic components. Thus, apoL-I is responsible for the trypanolytic activity of normal human serum, whereas Hpr allows fast uptake of the carrier HDL particles, presumably through their binding to an Hp/Hpr surface receptor of the parasite.
c-Myb is required for progenitor cell homeostasis in colonic crypts
Authors: Malaterre Jordane , Carpinelli Marina , Ernst Matthias , Alexander Warren , Cooke Michael , Sutton Susan , Dworkin Sebastian , Heath Joan K. , Frampton Jon , McArthur Grant , Clevers Hans , Hilton Douglas , Mantamadiotis Theo , Ramsay Robert G.
Published: February 2007

The colonic crypt is the functional unit of the colon mucosa with a central role in ion and water reabsorption. Under steady-state conditions, the distal colonic crypt harbors a single stem cell at its base that gives rise to highly proliferative progenitor cells that differentiate into columnar, goblet, and endocrine cells. The role of c-Myb in crypt homeostasis has not been elucidated. Here we have studied three genetically distinct hypomorphicc-mybmutant mouse strains, all of which show reduced colonic crypt size. The mutations target the key domains of the transcription factor: the DNA binding, transactivation, and negative regulatory domains.In vivoproliferation and cell cycle marker studies suggest that these mice have a progenitor cell proliferation defect mediated in part by reducedCyclin E1expression. To independently assess the extent to whichc-mybis required for colonic crypt homeostasis we also generated a novel tissue-specific mouse model to allow the deletion ofc-mybin adult colon, and using these mice we show that c-Myb is required for crypt integrity, normal differentiation, and steady-state proliferation.
Chlorination of lignin by ubiquitous fungi has a likely role in global organochlorine production
Authors: Ortiz-Bermúdez Patricia , Hirth Kolby C. , Srebotnik Ewald , Hammel Kenneth E.
Published: February 2007

Soils and decayed plant litter contain significant quantities of chlorinated aromatic polymers that have a natural but largely unknown origin. We used cupric oxide ligninolysis coupled with gas chromatography/mass spectrometry to show thatCurvularia inaequalis, a widely distributed litter ascomycete, chlorinated the aromatic rings of lignin in wood that it was degrading. In aspen wood decayed for 24 weeks, two chlorolignin fragments, 5-chlorovanillin and 2-chlorosyringaldehyde, were each found at ≈10 μg/g of wood (dry weight). These levels resemble those of similar structures generally found in unpolluted environmental samples. Fractionation of the extractable proteins followed by tandem mass spectrometric analysis showed that the colonized wood contained a previously describedC. inaequalischloroperoxidase that very likely catalyzed lignin chlorination. Chlorolignin produced by this route and humus derived from it are probably significant components of the global chlorine cycle because chloroperoxidase-producing fungi are ubiquitous in decaying lignocellulose and lignin is the earth's most abundant aromatic substance.
Prospects for fungus identification usingCO1DNA barcodes, withPenicilliumas a test case
Authors: Seifert Keith A. , Samson Robert A. , deWaard Jeremy R. , Houbraken Jos , Lévesque C. André , Moncalvo Jean-Marc , Louis-Seize Gerry , Hebert Paul D. N.
Published: March 2007

DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochromecoxidase 1 (CO1) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence divergences in this gene region for 38 fungal taxa with fullCO1sequences. Because these results suggested thatCO1could be effective in species recognition, we designed primers for a 545-bp fragment ofCO1and generated sequences for multiple strains from 58 species ofPenicilliumsubgenusPenicilliumand 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370Penicilliumstrains. Representatives from 38 of 58 species formed cohesive assemblages with distinctCO1sequences, and all cases of sequence sharing involved known species complexes.CO1sequence divergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or β-tubulin sequences (BenA).CO1divergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values forBenA(14.4%). Although the latter gene delivered higher taxonomic resolution, the amplification and alignment ofCO1was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.
Molecular diagnosis of pituitary adenoma predisposition caused by aryl hydrocarbon receptor-interacting protein gene mutations
Authors: Georgitsi Marianthi , Raitila Anniina , Karhu Auli , Tuppurainen Karoliina , Mäkinen Markus J. , Vierimaa Outi , Paschke Ralf , Saeger Wolfgang , van der Luijt Rob B. , Sane Timo , Robledo Mercedes , De Menis Ernesto , Weil Robert J. , Wasik Anna , Zielinski Grzegorz , Lucewicz Olga , Lubinski Jan , Launonen Virpi , Vahteristo Pia , Aaltonen Lauri A.
Published: March 2007

Pituitary adenomas are common neoplasms of the anterior pituitary gland. Germ-line mutations in the aryl hydrocarbon receptor-interacting protein (
AIP
) gene cause pituitary adenoma predisposition (PAP), a recent discovery based on genetic studies in Northern Finland. In this population, a founder mutation explained a significant proportion of all acromegaly cases. Typically, PAP patients were of a young age at diagnosis but did not display a strong family history of pituitary adenomas. To evaluate the role of
AIP
in pituitary adenoma susceptibility in other populations and to gain insight into patient selection for molecular screening of the condition, we investigated the possible contribution of
AIP
mutations in pituitary tumorigenesis in patients from Europe and the United States. A total of 460 patients were investigated by
AIP
sequencing: young acromegaly patients, unselected acromegaly patients, unselected pituitary adenoma patients, and endocrine neoplasia-predisposition patients who were negative for
MEN1
mutations. Nine
AIP
mutations were identified. Because many of the patients displayed no family history of pituitary adenomas, detection of the condition appears challenging. Feasibility of AIP immunohistochemistry (IHC) as a prescreening tool was tested in 50 adenomas: 12
AIP
mutation-positive versus 38 mutation-negative pituitary tumors. AIP IHC staining levels proved to be a useful predictor of
AIP
status, with 75% sensitivity and 95% specificity for germ-line mutations.
AIP
contributes to PAP in all studied populations. AIP IHC, followed by genetic counseling and possible
AIP
mutation analysis in IHC-negative cases, a procedure similar to the diagnostics of the Lynch syndrome, appears feasible in identification of PAP.
Virus-specific CD8+ T cells accumulate near sensory nerve endings in genital skin during subclinical HSV-2 reactivation
Authors: Zhu Jia , Koelle David M. , Cao Jianhong , Vazquez Julio , Huang Meei Li , Hladik Florian , Wald Anna , Corey Lawrence
Published: February 2007

Cytotoxic CD8+ T cells play a critical role in controlling herpes simplex virus (HSV) infection and reactivation. However, little is known about the spatiotemporal dynamics of CD8+ T cells during HSV lesion evolution or about their involvement in immune surveillance after lesion resolution. Using quantum dot–conjugated peptide–major histocompatibility complex multimers, we investigated the in vivo localization of HSV-2–specific CD8+ T cells in sequential biopsies of human genital skin during acute, resolving, and healed stages of HSV-2 reactivation. Our studies revealed that functionally active CD8+ T cells selectively infiltrated to the site of viral reactivation. After lesion healing in concert with complete reepithelialization and loss of HSV DNA from skin biopsies, HSV-2–specific CD8+ T cells persisted for more than two months at the dermal–epidermal junction, adjacent to peripheral nerve endings. In two out of the six sequentially studied individuals, HSV-2 DNA reappeared in clinically and histologically normal–appearing skin. Detection of viral DNA was accompanied by increased numbers of both HSV-specific and total CD8+ T cells in the dermis. These findings indicate that the frequency and clinical course of HSV-2 reactivation in humans is influenced by virus-specific CD8+ T cells that persist in peripheral mucosa and genital skin after resolution of herpes lesions.
Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager
Authors: Shah Anuj R. , Singhal Mudita , Klicker Kyle R. , Stephan Eric G. , Wiley H. Steven , Waters Katrina M.
Published: February 2007

Summary: The Bioinformatics Resource Manager (BRM) is a software environment that provides the user with data management, retrieval and integration capabilities. Designed in collaboration with biologists, BRM simplifies mundane analysis tasks of merging microarray and proteomic data across platforms, facilitates integration of users’ data with functional annotation and interaction data from public sources and provides connectivity to visual analytic tools through reformatting of the data for easy import or dynamic launching capability. BRM is developed using Java™ and other open-source technologies for free distribution.

Availability: BRM, sample data sets and a user manual can be downloaded from http://www.sysbio.org/dataresources/brm.stm

Contact:  anuj.shah@pnl.gov, brm@pnl.gov
The Navigation‐Controlled Drill in Temporal Bone Surgery: A Feasibility Study
Authors: Strauss Gero , Koulechov Kirill , Hofer Mathias , Dittrich Elmar , Grunert Ronny , Moeckel Hendrick , Müller Eva , Korb Werner , Trantakis Christos , Schulz Thomas , Meixensberger Juergen , Dietz Andreas , Lueth Tim
Published: March 2007

Background: This study examines the feasibility of a navigation‐controlled (NC) drill for surgery on the petrosal bone in an experimental environment. According to the principle of NC, the drill is to be switched off automatically once the borders of the workspace are exceeded during a mastoidectomy.

Materials and Methods: The registration is based on an optical navigation system with navigation software (MiMed). As surgery engine, the Unidrive‐system (Karl Storz GmbH & CO. Kg, Tuttlingen, Germany) was integrated. The definition of the workspace was performed manually in axial computed tomography (CT) slices of the petrosal bone phantom. The mastoidectomy on the model was accomplished in three runs with 10 trial surgeons altogether (5 experienced [exp.] in otologic (ear) surgery, 5 inexperienced [nonexp.]). During each run, the following were logged: the total length of time for the procedure as well as the number and extent of injuries to the risk structures (facial nerve, horizontal semicircular canal, sigmoid sinus). The resultant petrosal bone cavities were measured on the CT.

Results: The time for the segmentation of the workspace for the mastoidectomy amounted to 17 minutes. The mean value of the drilling (e.g., milling) performance ranges from 6.61 mm3/s (group 1 [nonexp. + NC]), 9.62 mm3/s (group 2 [exp. w/o NC]), to 10.08 mm3/s (group 3 [exp. + NC]). The relative deviation to the segmented volume amounts to +7.4% (794.3 mm3) for group 1, –39.9% for group 2, and –34% (3,647.0 mm3) for group 3. In the groups with NC guidance of the drill, no damage to a risk structure could be logged. In the group of exp. ear surgeons without NC assistance, one injury to the facial nerve in the petrosal bone phantom occurred.

Discussion: The results that follow prove the fundamental feasibility of an NC drill for surgery of the petrosal bone using the example of the simple mastoidectomy in the laboratory test. When using NC, tissue resection is faster, more precise, and has fewer related complications than the same procedure without. The results offer a very promising basis for the introduction of a newly conceived system to the procedure of NC surgery on the petrosal bone. The device configuration used here was originally conceived for NC guidance of a shaver in functional endoscopic sinus surgery. Individual errors will have to be mitigated through the new version of the control unit presently in development.
Medium‐Term Symptom Outcomes After Paranasal Sinus Surgery in Children and Young Adults With Cystic Fibrosis
Authors: Keck Tilman , Rozsasi Ajnacska
Published: March 2007

Objective: To determine the effectiveness of paranasal sinus surgery (PSS) for individual symptoms and recurrence of nasal polyposis in children and young adults with cystic fibrosis and chronic rhinosinusitis (CRS).

Design: Nonrandomized, prospective, clinical trial.

Intervention: Children and young adults with medically refractory CRS were examined before and after PSS. The extend of nasal polyposis was graded endoscopically and on computed tomography images. The severity of symptoms of CRS was recorded on a 6‐point Likert scale by the investigator.

Results: In 26 patients, a complete rhinosinusitis symptom score (RSS) before and after surgery was available. The mean follow‐up time after surgery was 23 months. Postoperatively, no polyp recurrence was seen in eight patients (of 26 patients). An improved polyp score was found in 14 patients. In four patients, polyp recurrence to the same extent as before surgery was seen. The mean RSS was significantly improved after surgery. Before surgery, “nasal obstruction” was the most common complaint. “Headache” was the second most common complaint before PSS. After PSS, although improved, “headache” was the most common complaint. During further follow‐up, in two patients, endocranial complications caused by recurrent frontal mucopyoceles (1 frontal abscess, 1 subacute meningitis) were observed. After transfrontal revision surgery, both patients recovered without neurologic damage.

Conclusions: Even in cases of polyp recurrence, PSS provides significant symptom relief for nasal and facial symptoms associated with CRS. The symptom “headache” requires special attention because it improves least after surgery and may indicate recurrence of frontoethmoidal mucopyoceles or endocranial complication of CRS.
Microvascular Flap Reconstruction by Otolaryngologists: Prevalence, Postoperative Care, and Monitoring Techniques
Authors: Spiegel Jeffrey H. , Polat Julia K.
Published: March 2007

Background/Objectives: Microvascular “free flap” transplants have become the preferred method of reconstruction for a great variety of complicated head and neck defects. As recently as 10 years ago, having a microvascular surgeon within a department of otolaryngology was the exception rather than the rule, whereas it is our impression that today most academic programs have one or more microvascularly trained head and neck surgeons. Among microvascular surgeons, postoperative care and management regimens vary greatly. Through informal conversations, we discerned that some surgeons take a very aggressive approach to monitoring, perhaps including prolonged stays in an intensive care setting with implanted Doppler devices to monitor flap blood flow and intravenous administration of dextran or other pharmaceutical projects. Others report that patients are quickly discharged from the hospital after just aspirin and subcutaneous heparin for a few days. Some physicians perform “flap checks” hourly, whereas others have residents check only once daily.

Design/Methods: We surveyed academic otolaryngology–head and neck surgery departments that sponsor residency programs in the United States to 1) determine the prevalence of microvascular trained otolaryngologists within training programs and 2) assess variations in postoperative and monitoring regimens.

Results: We found that on average, 12.2% of otolaryngologists per department perform free flap transplants, and 71.6% of microvascular trained surgeons continue to do free flaps. The surgeons self reported a 96.4% average success rate and a 6.88% return rate to the operating room for complications. Monitoring methods used included flap color (used by 79.4% of surgeons), Doppler signal (79.4%), pin prick and bleeding rate (67.6%), capillary refill (61.8%), skin surface temperature (11.8%), and implanted Doppler (8.8%). Anticoagulants used included aspirin (used by 76.5% of microvascular surgeons), low‐molecular‐weight dextran (35.3%), and subcutaneous heparin (26.5%).

Conclusions: Microvascular training has become commonplace in otolaryngology–head and neck surgery training programs, with more than one in eight of these academic physicians reporting microvascular training. There was no self‐reported difference in flap failure rates on the basis of postoperative care and monitoring regimen. The results of this survey suggest that a simplified consensus postoperative regimen can be recommended.
Cold Dissection Versus Coblation‐Assisted Adenotonsillectomy in Children
Authors: Shapiro Nina L. , Bhattacharyya Neil
Published: March 2007

Objective: To compare intraoperative efficiency and postoperative recovery between cold dissection adenotonsillectomy (CDA) and coblation‐assisted adenotonsillectomy (CAA).

Methods: A prospective, randomized, single‐blind trial of pediatric patients aged 2 to 16 years undergoing adenotonsillectomy was conducted. Patients were randomized to undergo either CDA or CAA. Measured intraoperative parameters included surgical duration and intraoperative blood loss. Measured postoperative parameters included a 14 day caregiver questionnaire that recorded a daily pain rating using the Wong‐Baker FACES pain scale, pain medication use, days to return to a normal diet, and days to return to a normal caregiver routine. Postoperative complications were also recorded. Intraoperative and postoperative measures were statistically compared between groups.

Results: Forty‐six children with a mean age of 6.7 years (23 CDA and 23 CAA) were randomized and completed the study. Mean age and sex distributions were similar between groups (P > .05). Surgical times were significantly shorter for the CAA group versus the CDA group (11.2 min vs. 17.0 min, P < .001). Intraoperative blood loss was statistically lower for both the adenoidectomy and tonsillectomy portions of the procedure for the CAA group versus the CDA group (P < .001 and P < .001, respectively). There was no statistically significant difference in reported daily pain scores between groups (P = .296, analysis of variance). Both groups returned to normal diet (P = .982), and caregivers returned to their normal routine on similar postoperative days (P = .631).

Conclusions: CAA offers better operative speed and intraoperative hemostasis as compared with CDA. However, CAA does not result in poorer postoperative pain scores or recoveries despite these intraoperative advantages.
Evaluation of Radiofrequency Thermal Ablation Results in Inferior Turbinate Hypertrophies by Magnetic Resonance Imaging
Authors: Sapci Tarik , Usta Canan , Evcimik M Fatih , Bozkurt Ziya , Aygun Elcin , Karavus Ahmet , Peker Mustafa
Published: March 2007

Objectives: Nasal obstruction caused by inferior turbinate hypertrophies is one of the most frequent problems in otolaryngology. Treatment of this disease may involve medical and surgical methods. Thermal ablation with radiofrequency energy has become quite popular in the recent years as one of the surgical methods used when medical therapy is not adequate.

Study Design: Prospective, clinical trial.

Methods: Thermal ablation with radiofrequency energy was used in this study on the inferior turbinates of 21 patients who had nasal obstruction caused by inferior turbinate hypertrophy only. The results were evaluated subjectively by preoperative and postoperative patient‐ and physician‐assigned visual analogue scales and objectively by magnetic resonance imaging (MRI) investigation.

Results: By the end of the postoperative week 10, 64.76% recovery was detected according to the patient evaluation, and 40.75% recovery was detected according to the physician evaluation. Measurement of the average volumes of the inferior turbinates by MRI revealed a 8.70% postoperative reduction. The most significant change was detected in the anterior‐posterior length measurement performed in the axial plane.

Conclusions: These results suggest that thermal ablation with radiofrequency energy is an easily applied, efficient, and reliable technique in treatment of the inferior turbinate hypertrophy, and that anterior‐posterior length measurement in the axial section of the inferior turbinate by MRI, which is thought as an objective evaluation method, could be an efficient diagnostic tool in detecting the efficiency of radiofrequency on inferior turbinate.
Concurrent Cetuximab and Bevacizumab Therapy in a Murine Orthotopic Model of Anaplastic Thyroid Carcinoma
Authors: Prichard Christopher N. , Kim Seungwon , Yazici Yasmin D. , Doan Dao D. , Jasser Samar A. , Mandal Mahitosh , Myers Jeffrey N.
Published: March 2007

Objective: To evaluate the therapeutic efficacy of bevacizumab and cetuximab, alone and in combination, in an orthotopic model of anaplastic thyroid carcinoma (ATC) in athymic nude mice.

Study Design and Setting: This was a randomized, controlled in vivo study.

Materials and Methods: The ATC cell line, ARO, was used to establish orthotopic xenografts of ATC in athymic nude mice. Mice were randomized to therapy for 4 weeks in one of four treatment groups: placebo, cetuximab, bevacizumab, or the combination of cetuximab and bevacizumab. A second study compared the antitumor efficacy of the cetuximab‐bevacizumab combination with doxorubicin. In both studies, tumor volumes on completion were measured and compared. Immunohistochemical analysis was performed with antiCD31 and antiproliferating cell nuclear antigen (PCNA) antibodies to assess the in vivo mechanisms of action of these agents.

Results: Cetuximab decreased the production of vascular endothelial growth factor by ATC cell lines in vitro. Mean tumor volumes for the control, bevacizumab, cetuximab, and combination groups at the end of the in vivo study were 291, 213, 94, and 42 mm3, respectively. The differences in mean tumor volume for the control versus treatment groups were statistically significant. Immunohistochemical analysis showed decreased microvessel density and PCNA positivity in the treatment groups. In the doxorubicin comparison study, mean tumor volumes for control, doxorubicin, and combination antibody treatment groups were 175, 162, and 22 mm3, respectively.

Conclusions: Cetuximab and bevacizumab alone and in combination inhibit tumor growth and angiogenesis in an in vivo model of ATC. Also, this therapy was superior to doxorubicin therapy.
Bigger teeth for longer life? Longevity and molar height in two roe deer populations
Authors: Veiberg Vebjørn , Mysterud Atle , Gaillard Jean-Michel , Delorme Daniel , Laere Guy Van , Klein François
Published: February 2007

The role of tooth wear as a proximate cause of senescence in ruminants has recently been highlighted. There are two competing hypotheses to explain variation in tooth height and wear; the diet-quality hypothesis predicting increased wear in low-quality habitats, and the life-history hypothesis predicting molar height to be related to expected longevity. We compared tooth height and wear from roe deer of known age from two contrasting populations of roe deer (
Capreolus capreolus
) in France: Trois Fontaines (TF) with good habitat and shorter animal life expectancy and Chizé (CH) with poor habitat and longer animal life expectancy. There was no population difference in tooth wear, leading to rejection of the diet-quality hypothesis. However, despite their smaller body size, initial molar height for animals from CH was larger than for animals from TF. This provides the first evidence that variation in longevity between populations can lead to differences in molar height within a species.
A general framework for analysing diversity in science, technology and society
Authors: Stirling Andy
Published: February 2007

This paper addresses the scope for more integrated general analysis of diversity in science, technology and society. It proposes a framework recognizing three necessary but individually insufficient properties of diversity. Based on 10 quality criteria, it suggests a general quantitative non-parametric diversity heuristic. This allows the systematic exploration of diversity under different perspectives, including divergent conceptions of relevant attributes and contrasting weightings on different diversity properties. It is shown how this heuristic may be used to explore different possible trade-offs between diversity and other aspects of interest, including portfolio interactions. The resulting approach offers a way to be more systematic and transparent in the treatment of scientific and technological diversity in a range of fields, including conservation management, research governance, energy policy and sustainable innovation.
Shearing of fibrillar adhesive microstructure: friction and shear-related changes in pull-off force
Authors: Varenberg M , Gorb S
Published: February 2007

To characterize the effect of shearing on function of fibrillar adhesive microstructure, friction and shear-related changes in pull-off force of a biomimetic polyvinylsiloxane mushroom-shaped fibrillar adhesive microstructure were studied. In contrast to a control flat surface, which exhibited pronounced stick–slip motion accompanied with high friction, the fibrillar microstructure demonstrated a stable and smooth sliding with a friction coefficient approximately four times lower. The structured contact also manifested zero pull-off force in a sheared state, while the flat surface exhibited highly scattered and unreliable pull-off force when affected by contact shearing. It appears that the fibrillar microstructure can be used in applications where a total attachment force should be generated in a binary on/off state and, most surprisingly, is suitable to stabilize and minimize elastomer friction.
Seasonality and the persistence and invasion of measles
Authors: Conlan Andrew J.K , Grenfell Bryan T
Published: February 2007

The critical community size (CCS) for measles, which separates persistent from extinction-prone populations, is arguably the best understood stochastic threshold in ecology. Using simple models, we explore a relatively neglected relationship of how the CCS scales with birth rate. A predominantly positive relationship of persistence with birth rate is complicated by the accompanying dynamical transitions of the underlying deterministic process. We show that these transitions imply a lower CCS for high birth rate less developed countries and contrary to the experience in lower birth rate, industrial countries, the CCS may increase after vaccination. We also consider the evolutionary implications of the CCS for the origin of measles; this analysis explores how the deterministic and stochastic thresholds for invasion and persistence set limits on the mechanism by which this highly infectious pathogen could have successfully colonized its human host.
Altruism towards cousins
Authors: Jeon Joonghwan , Buss David M
Published: February 2007

Recent research on kin investment shows a matrilateral bias as a function of paternity uncertainty. Kin investment, however, is a special case of kin altruism. We thus hypothesize that psychological adaptations have evolved to regulate cousin-directed altruism according to predictably variable levels of paternity uncertainty in different categories of cousins. We develop a formal mathematical model that predicts that individuals should be most willing to act altruistically towards their mother's sister's (MoSis) children and least willing to act altruistically towards their father's brother's (FaBro) children. Altruism towards father's sister's (FaSis) and mother's brother's (MoBro) children are predicted to fall in between. An empirical study (N=195), assessing expressed altruistic proclivities, confirmed the predictions from the model. Participants expressed willingness-to-help following the descending order: (i) MoSis children, (ii) MoBro children, (iii) FaSis children, and (iv) FaBro children. The psychological variables of emotional closeness, empathic concern and contact frequency showed precisely the same pattern across distinct cousins, providing convergent confirmation of the model. The results support the hypothesis of cousin-specific adaptations sensitive to varying probabilities of paternity uncertainty.
Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov.
Authors: Nevin Kelly P. , Holmes Dawn E. , Woodard Trevor L. , Covalla Sean F. , Lovley Derek R.
Published: March 2007

Reclassification of the species Trichlorobacter thiogenes as Geobacter thiogenes comb. nov. is proposed on the basis of physiological traits and phylogenetic position. Characteristics additional to those provided in the original description revealed that the type strain (strain K1T=ATCC BAA-34T=JCM 14045T) has the ability to use Fe(III) as an electron acceptor for acetate oxidation and has an electron donor and acceptor profile typical of a Geobacter species, contains abundant c-type cytochromes, and has a temperature optimum of 30 °C and a pH optimum near pH 7.0; traits typical of members of the genus Geobacter. Phylogenetic analysis of nifD, recA, gyrB, rpoB, fusA and 16S rRNA genes further indicated that T. thiogenes falls within the Geobacter cluster of the family Geobacteraceae. Based on extensive phylogenetic evidence and the fact that T. thiogenes has the hallmark physiological characteristics of a Geobacter species, Trichlorobacter thiogenes should be reclassified as a member of the genus Geobacter.
Pseudoxanthomonas yeongjuensis sp. nov., isolated from soil cultivated with Korean ginseng
Authors: Yoo Seung-Hee , Weon Hang-Yeon , Kim Byung-Yong , Kim Jin-Ho , Baek Youn-Kyung , Kwon Soon-Wo , Go Seung-Joo , Stackebrandt Erko
Published: March 2007

A Gram-negative, strictly aerobic, non-spore-forming bacterium, motile by means of single polar flagellum and rod-shaped, designated strain GR12-1T, was isolated from soil of a ginseng field in Yeongju region, Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain is related to members of the genusPseudoxanthomonas, showing sequence similarity values ranged from 92.3 to 96.2 %. This organism grew at 5–33 °C, with optimum growth at 28 °C. Strain GR12-1Tgrew optimally in the presence of 0–2 % NaCl. The whole-cell fatty acid profile included iso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0, iso-C11 : 03-OH and iso-C17 : 0as major components. The only isoprenoid quinone was ubiquinone 8 (Q-8). The DNA G+C content was 63.4 mol%. On the basis of phenotypic, genetic and phylogenetic data, strain GR12-1Tshould be classified as a member of a novel species of the genusPseudoxanthomonas, for which the namePseudoxanthomonas yeongjuensissp. nov. is proposed, with strain GR12-1T(=KACC 11580T=DSM 18204T) as the type strain.
Pseudoruegeria aquimaris gen. nov., sp. nov., isolated from seawater of the East Sea in Korea
Authors: Yoon Jung-Hoon , Lee Soo-Young , Kang So-Jung , Lee Choong-Hwan , Oh Tae-Kwang
Published: March 2007

A Gram-negative, non-motile, rod-shaped bacterial strain, SW-255T, was isolated from seawater from Hwajinpo, on the coast of the East Sea, Korea, and subjected to a polyphasic taxonomic study. Strain SW-255T grew optimally at pH 7.0–8.0 and 37 °C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c as the major fatty acid. The DNA G+C content was 67.0 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain SW-255T is phylogenetically closely related to the genera Ruegeria and Silicibacter of the Alphaproteobacteria. The levels of 16S rRNA gene sequence similarity between strain SW-255T and the type strains of Ruegeria atlantica and two Silicibacter species were in the range 95.8–96.2 %. A phylogenetic tree based on gyrB sequences showed that strain SW-255T forms a distinct evolutionary lineage within the Alphaproteobacteria. Differential phenotypic properties, polar lipid profiles and DNA G+C contents, together with the phylogenetic distinctiveness, suggest that strain SW-255T should be distinguished from the members of the genera Ruegeria and Silicibacter. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain SW-255T represents a novel genus and species, for which the name Pseudoruegeria aquimaris gen. nov., sp. nov. is proposed. The type strain of Pseudoruegeria aquimaris is SW-255T (=KCTC 12737T=JCM 13603T).
Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing ‘signature’ fatty acids of type I methanotrophs
Authors: Dedysh Svetlana N. , Belova Svetlana E. , Bodelier Paul L. E. , Smirnova Ksenia V. , Khmelenina Valentina N. , Chidthaisong Amnat , Trotsenko Yuri A. , Liesack Werner , Dunfield Peter F.
Published: March 2007

A novel species is proposed for two strains of methanotrophic bacteria (H2T and Sakb1) isolated from an acidic (pH 4.3) Sphagnum peat bog lake (Teufelssee, Germany) and an acidic (pH 4.2) tropical forest soil (Thailand), respectively. Cells of strains H2T and Sakb1 were aerobic, Gram-negative, non-motile, straight or curved rods that were covered by large polysaccharide capsules and contained an intracytoplasmic membrane system typical of type II methanotrophs. They possessed both a particulate and a soluble methane monooxygenase and utilized the serine pathway for carbon assimilation. They were moderately acidophilic organisms capable of growth between pH 4.4 and 7.5 (optimum 5.8–6.2). The most unique characteristic of these strains was the phospholipid fatty acid profile. In addition to the signature fatty acid of type II methanotrophs (18 : 1ω8c), the cells also contained large amounts of what was previously considered to be a signature fatty acid of type I methanotrophs, 16 : 1ω8c. The DNA G+C contents of strains H2T and Sakb1 were 61.5 and 62.1 mol%, respectively. The 16S rRNA gene sequences possessed 96–98 % similarity to sequences of other type II methanotrophs in the genera Methylosinus and Methylocystis. 16S rRNA gene sequence and pmoA phylogeny demonstrated that the strains form a novel lineage within the genus Methylocystis. DNA–DNA hybridization values of strain H2T with Methylocystis parvus OBBPT and Methylocystis echinoides IMET 10491T were 18 and 25 %, respectively. Thus, it is proposed that these two strains represent a novel species, Methylocystis heyeri sp. nov. Strain H2T (=DSM 16984T=VKM B-2426T) is the type strain.
Halococcus qingdaonensis sp. nov., a halophilic archaeon isolated from a crude sea-salt sample
Authors: Wang Qian-fu , Li Wei , Yang Hai , Liu Yan-li , Cao Hai-hua , Dornmayr-Pfaffenhuemer Marion , Stan-Lotter Helga , Guo Guang-qin
Published: March 2007

A Gram-negative, extremely halophilic, coccoid archaeal strain, CM5T, was isolated from a crude sea-salt sample collected near Qingdao, China. The organism grew optimally at 35–40 °C and pH 6.0 in the presence of 20 % (w/v) NaCl. Its colonies were red in colour and it could use glucose as a sole carbon source for growth. The 16S rRNA gene sequence of CM5Twas most closely related to those ofHalococcusspecies. Its pattern of antibiotic susceptibility was similar to those of other describedHalococcusspecies. Biochemical tests revealed no sign of H2S production or gelatin liquefaction. The main polar lipids of strain CM5Twere phosphatidylglycerol, phosphatidylglycerol methylphosphate and sulfated diglycosyl diether. No phosphatidylglycerol sulfate was present. The DNA G+C content of strain CM5Twas 61.2 mol% and it gave DNA–DNA reassociation values of 33.7, 57.1 and 29.6 %, respectively, withHalococcus salifodinaeDSM 8989T,Halococcus dombrowskiiDSM 14522TandHalococcus morrhuaeATCC 17082T. Based on its morphological and chemotaxonomic properties and phylogenetic analysis of 16S rRNA gene sequence data, we propose that CM5Tshould be classified within a novel species,Halococcus qingdaonensissp. nov., with strain CM5T(=CGMCC 1.4243T=JCM 13587T) as the type strain.
Pseudomonas knackmussii sp. nov.
Authors: Stolz Andreas , Busse Hans-Jürgen , Kämpfer Peter
Published: March 2007

The taxonomic position of Pseudomonas sp. B13T, isolated as a 3-chlorobenzoate-degrading organism and used for several groundbreaking studies on the enzymology and genetics of the degradative pathway for haloaromatic compounds, was studied in detail. The previously performed physiological studies, the detection of ubiquinone Q-9, the polyamine pattern with putrescine and spermidine as major polyamines, a fatty acid profile with C18 : 1
ω7c, summed feature 3 and C16 : 0 as quantitatively the most important constituents and the 16S rRNA gene sequence demonstrated that Pseudomonas sp. B13T indeed belongs to the genus Pseudomonas. The sequence of the Pseudomonas sp. B13T 16S rRNA gene demonstrated a high degree of similarity with that of Pseudomonas citronellolis DSM 50332T (98.9 %), Pseudomonas nitroreducens DSM 14399T (98.7 %), Pseudomonas jinjuensis DSM 16612T (98.1 %) and Pseudomonas multiresinivorans DSM 17553T (98.7 %). Thus it was shown that strain Pseudomonas sp. B13T can be distinguished from related species by the ability/inability to assimilate N-acetylgalactosamine, d-galactose, putrescine, trans-aconitate and mesaconate and some differences in the fatty acid profile. The positioning of Pseudomonas sp. B13T as a separate taxon was finally verified by DNA hybridization, which demonstrated less than 45 % DNA–DNA similarity between strain Pseudomonas sp. B13T and the reference strains. On the basis of these results, Pseudomonas sp. B13T represents a novel species for which the name Pseudomonas knackmussii sp. nov. is proposed. The type strain is B13T (=DSM 6978T=LMG 23759T).
Azospirillum canadense sp. nov., a nitrogen-fixing bacterium isolated from corn rhizosphere
Authors: Mehnaz Samina , Weselowski Brian , Lazarovits George
Published: March 2007

A free-living diazotrophic strain, DS2T, was isolated from corn rhizosphere. Polyphasic taxonomy was performed including morphological characterization, Biolog analysis, and 16S rRNA, cpn60 and nifH gene sequence analyses. 16S rRNA gene sequence analysis indicated that strain DS2T was closely related to the genus Azospirillum (96 % similarity). Chemotaxonomic characteristics (DNA G+C content 67.9 mol%; Q-10 quinone system; major fatty acid 18 : 1ω7c) were also similar to those of the genus Azospirillum. In all the analyses, including phenotypic characterization using Biolog analysis and comparison of cellular fatty acids, this isolate was found to be different from the closely related species Azospirillum lipoferum, Azospirillum oryzae and Azospirillum brasilense. On the basis of these results, a novel species is proposed for this nitrogen-fixing strain. The name Azospirillum canadense sp. nov. is suggested with the type strain DS2T (=NCCB 100108T=LMG 23617T).
Interactions between methamphetamine and environmental stress: role of oxidative stress, glutamate and mitochondrial dysfunction
Authors: Tata Despina A. , Yamamoto Bryan K.
Published: February 2007

Aims Methamphetamine is an amphetamine derivative that is abused increasingly world‐wide at an alarming rate over the last decade. Pre‐clinical and human studies have shown that methamphetamine is neurotoxic to brain dopamine and serotonin. Other lines of study indicate that stress enhances the vulnerability to drug abuse. The purpose of this review is to shed light on the biochemical similarities between methamphetamine and stress in an effort to highlight the possibility that prior exposure to stress may interact with methamphetamine to exacerbate neurotoxicity.

Methods A review of the literature on methamphetamine and stress was conducted that focused on the common neurotoxic and biochemical consequences of methamphetamine administration and stress exposure.

Results Experimental findings of a large number of studies suggest that there are parallels between stress and methamphetamine with regard to their ability to increase glutamate release, produce a metabolic compromise and cause oxidative damage.

Conclusion A combination of methamphetamine administration and stress can act synergistically and/or additively to cause or augment toxicity in brain regions such as striatum and hippocampus.
‘Tweaking 12‐Step’: the potential role of 12‐Step self‐help group involvement in methamphetamine recovery
Authors: Donovan Dennis M. , Wells Elizabeth A.
Published: February 2007

Aims To determine from a review of the available literature the extent to which involvement in 12‐Step mutual support groups could play a role in the recovery process for individuals abusing or dependent on methamphetamine.

Method Review of the literature on outcomes associated with 12‐Step meeting attendance and involvement in 12‐Step activities among substance abusers, particularly those who abuse stimulants.

Results There are few if any data available on methamphetamine abusers and their use of 12‐Step approaches. Evidence derived from work with alcohol‐ and cocaine‐dependent individuals indicates that involvement in 12‐Step self‐help groups, both attending meetings and engaging in 12‐Step activities, is associated with reduced substance use and improved outcomes. Although involvement in 12‐Step fellowship improves outcome, many individuals do not engage on their own in 12‐Step activities, and there are high rates of dropout from such groups. There are a number of evidence‐based therapies available to assist clinicians in facilitating 12‐Step involvement; however, these have not been used with methamphetamine abusers. While there are some potential barriers to adopting manualized treatment interventions into clinical practice, the familiarity, in community‐based practice, of the 12‐Step approach may make this easier.

Conclusion More actively integrating 12‐Step approaches into the treatment process may provide low‐ or no‐cost options for methamphetamine abusers and increase the capacity for providing treatment. Further research and evaluation are necessary to determine the extent to which methamphetamine abusers do engage in 12‐Step self‐help programs, whether they prefer more general (e.g. Alcoholics Anonymous, Narcotics Anonymous, Cocaine Anonymous) or drug‐specific (e.g. Crystal Meth Anonymous) meetings, the rate of dropout and the outcomes associated with their involvement. Further, the efficacy of efforts to facilitate involvement of methamphetamine abusers in such 12‐Step groups needs to be determined.
Breed assignment of Italian cattle using biallelic AFLP®markers
Authors: Negrini R. , Milanesi E. , Colli L. , Pellecchia M. , Nicoloso L. , Crepaldi P. , Lenstra J. A. , Ajmone‐Marsan P.
Published: February 2007

The verification of the breed origin of animal products is relevant for food safety and authenticity. We assessed the suitability of AFLP molecular markers in the assignment of cattle individuals to their breed of origin. Three hundred and ninety‐six animals belonging to 16 cattle breeds genotyped with 141 AFLP markers were used as reference data set. Assignment was performed with likelihood (aflpop) and Bayesian (structure) methods. The Bayesian approach was superior to the likelihood algorithm with respect to (i) the correct assignment of simulated individuals to their breed of origin (93% vs. 81% respectively), (ii) the correct assignment of 44 sampled Romagnola animals (91% vs. 45% respectively) and (iii) the correct classification of animals belonging to a breed that was not included within the reference dataset. Thus, AFLP profiling in combination with the Bayesian approach seems a useful tool for breed assignment.
SHORT COMMUNICATION: MX1 exon 13 polymorphisms in broiler breeder chickens and associations with commercial traits
Authors: Livant E. J. , Avendano S. , McLeod S. , Ye X. , Lamont S. J. , Dekkers J. C. M. , Ewald S. J.
Published: February 2007

The Mx1 gene in mice is induced by type I interferons and is the major determinant of resistance to influenza virus and related orthomyxoviruses. It has been previously shown that a SNP in exon 13 of the chicken MX1 gene determines differential antiviral activity of the protein. We evaluated this SNP and two additional SNPs in elite broiler lines by PCR amplification and sequence analysis. Associations between MX1 exon 13 SNPs and several traits of economic interest were evaluated. Significant associations were found between the SNP determining antiviral activity and mortality in one line and leg defects in another line.
Reticulated platelets interfere with flow cytometric reticulocyte counts
Authors: IVORY K. , SARRIA B. , FAIRWEATHER‐TAIT S. J. , HUGHES D. A.
Published: February 2007

As part of an iron absorption study, we needed to accurately count reticulocytes in the peripheral blood of healthy human volunteers before measuring their enrichment with stable iron isotopes given in an oral dose. Recent studies have suggested the usefulness of reticulocyte counting by flow cytometry, through a combination of differential light scatter and measurement of the stoichiometric binding of thiazole orange (TO) to RNA within the maturing erythrocyte. Using this method we set out to improve the precision of our quantitative analysis by counting more cells, as reticulocytes normally comprise <2% of the red cell population. To ensure exclusion of other cell types, we identified WBCs and platelets with CD16+CD45− allophycocyanin and CD61− phycoerythrin, respectively. After removal of CD16+ CD45+ TO+ WBCs and CD61+ TO− platelets from analysis, the remaining cells were a combination of CD61− TO− erythrocytes, CD61− TO+ reticulocytes and CD61+ TO+ reticulated platelets. Reticulocyte counts were lower after exclusion of CD61+ TO+ cells from analysis. They were similarly lower when erythrocyte precursors were positively identified through their glycophorin A expression and TO uptake. We conclude that it is necessary to exclude reticulated platelets from flow cytometric reticulocyte analysis.