bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome‐specific introgression between wheat and its wild relative Aegilops triuncialis
Authors: Parisod C. , Definod C. , Sarr A. , Arrigo N. , Felber F.
Published: December 2012

Introgression of sequences from crop species in wild relatives is of fundamental and practical concern. Here, we address gene flow between cultivated wheat and its widespread polyploid relative, Aegilops triuncialis, using 12 EST‐SSR markers mapped on wheat chromosomes. The presence of wheat diagnostic alleles in natural populations of the barbed goatgrass growing in proximity to cultivated fields highlights that substantial gene flow occurred when both species coexisted. Furthermore, loci from the A subgenome of wheat were significantly less introgressed than sequences from other subgenomes, indicating differential introgression into Ae. triuncialis. Gene flow between such species sharing nonhomeologous chromosomes addresses the evolutionary outcomes of hybridization and may be important for efficient gene containment.
Heritability of male attractiveness persists despite evidence for unreliable sexual signals in Drosophila simulans
Authors: Ingleby F. C. , Hunt J. , Hosken D. J.
Published: December 2012

Sexual signals can be used to attract mates, but to be honest indicators of signaller quality they need to convey information reliably. However, environmental variation and genotype‐by‐environment (G × E) interactions have the potential to compromise the reliability of sexual signals. Here, we test the reliability of cuticular hydrocarbons (CHCs) as signals of heritable aspects of male attractiveness in Drosophila simulans. We examined the heritability of male attractiveness and a measure of the difference between fathers' and sons' CHC profiles across dietary and temperature environments. Our results show that environmental heterogeneity disrupts the similarity of some components of father and son CHC profile. However, overall male attractiveness is heritable within and across environments, so that sire attractiveness is a good predictor of son attractiveness even with environmental heterogeneity. This suggests that although some male CHC signals are unreliable, attractive genotypes retain their attractiveness across environments on average.
Disturbed eating behaviours and thoughts in Australian adolescents with type 1 diabetes
Authors: d'Emden Helen , Holden Libby , McDermott Brett , Harris Mark , Gibbons Kristen , Gledhill Anne , Cotterill Andrew
Published: December 2012

Aim

To describe the presence and type of disturbed eating behaviours and thoughts in a combined male/female Australian sample of adolescents with type 1 diabetes, and examine the association of eating behaviours and thoughts with glycaemic control as evidenced by high glycosylated haemoglobin levels (HbA1c).

Methods

In this cross‐sectional descriptive study, 124 adolescents aged 13–18 years were invited to complete three self‐administered questionnaires. The Youth Eating Disorder Examination Questionnaire (YEDE‐Q) and the Eating Disorder Inventory −3 Risk Composite (EDI‐3RC) assessed risk for an eating disorder. The third questionnaire, the Strengths and Difficulties Questionnaire (SDQ) assessed emotional and behavioural concerns. Clinical data were collected from the medical records, routine clinic appointments and the adolescent.

Results

Any disturbed eating behaviour was reported by approximately one‐third of participants (32.3%) and was common in females and males (37.9% vs. 25.9%). Binge eating (17.7%), driven exercise (13.0%) and dietary restraint (8.9%) were the most common disturbed eating behaviours, although restraint was not evident in males. Insulin manipulation/omission (5.6%), vomiting (3.3%), laxative (0.8%) or diuretic use (0.8%) were less common. Regression analysis showed a significant association between HbA1c and more disturbed eating behaviours and thoughts which remained significant when adjusted for confounders.

Conclusions

High rates of disturbed eating behaviours and thoughts were seen in this Australian sample of adolescents with type 1 diabetes. High scores on both eating disorder measures were associated with poorer glycaemic control. These results highlight the need to screen for disordered eating in adolescents with type 1 diabetes.
Association between sleep and behavioural problems among children with enuresis
Authors: Abou‐Khadra Maha K , Amin Omnia R , Ahmed Dalia
Published: December 2012

Aim

This study was conducted to describe sleep problems in a sample of children with enuresis and to investigate the association between sleep and behavioural problems.

Methods

In this cross‐sectional study, 100 children with enuresis were recruited from paediatric enuresis clinic. The children's sleep problems and behaviours were assessed by the Children's Sleep Habits Questionnaire and Child Behaviour checklist.

Results

The most frequently reported sleep problems were in daytime sleepiness, bedtime resistance and sleep anxiety subscales. Children with T‐scores ≥ 60 in internalising, externalising and total behavioural problems had higher scores on daytime sleepiness subscale and total score than children with T‐scores < 60. Multivariate logistic regression analysis revealed that daytime sleepiness subscale was significantly related to behavioural disturbances.

Conclusions

Sleep problems are common among this sample of children with enuresis, and the presence of sleep disturbance such as daytime sleepiness could explain the association between enuresis and disturbed daytime behaviour.
Cancer in Australian Aboriginal children: Room for improvement
Authors: Rotte Laura , Hansford Jordan , Kirby Maria , Osborn Michael , Suppiah Ram , Ritchie Petra , Tapp Heather , Rice Michael , Revesz Tamas
Published: December 2012

Aim

The study aims to analyse clinical data and outcome in Aboriginal and non‐Aboriginal children with cancer.

Methods

This is a retrospective case‐note review of biological features, treatment outcome and survival in Aboriginal and non‐Aboriginal children with a malignancy who were treated at the Women's and Children's Hospital, a tertiary referral hospital, from January 1997 through March 2011. Two separate analyses were performed: firstly, for each Aboriginal patient comparisons were made with two age, sex and diagnosis‐matched control patients; then secondly, results for the Aboriginal group of patients were compared with the whole non‐Aboriginal group of patients.

Results

In the first analysis, Aboriginal children had a significantly higher ‘remoteness index’ (6.14 vs. 0.95; P < 0.001) and were less likely to be enrolled on clinical trials. Survival analysis of the Aboriginal patients and their matched controls showed a trend towards inferior overall survival for the Indigenous children (P = 0.066). In the second analysis, Aboriginal children tended to have a higher proportion of leukaemias and lymphomas and had an overrepresentation of acute myeloid leukaemia (AML) (P = 0.009). The mean age among Aboriginal children with AML and lymphoma was lower (AML: 3.5 vs. 8 years, P = 0.065; lymphoma: 7.5 vs. 11.9 years, P = 0.01). A higher proportion of Aboriginal children died (P = 0.004).

Conclusions

Aboriginal children present with a somewhat different pattern of cancer, are less likely to be enrolled on studies and seem to have increased mortality. There is a need for improvement in study enrolment, treatment delivery, care coordination and suitably supported residential facilities.
Developmental and behavioural characteristics of children enrolled in a child protection pre‐school
Authors: McDonald Jenny L , Milne Susan , Knight Jenny , Webster Vana
Published: December 2012

Aim

The study aims to describe the developmental and behavioural difficulties in pre‐school children who have experienced maltreatment and/or neglect

Methods

A retrospective medical file audit of all children assessed at the Cottage Family Care Centre, a child protection pre‐school, between April 2004 and June 2010. Demographic characteristics, parent and teacher reports, and clinical and developmental assessment results were collated and analysed.

Results

The average age of the 55 children assessed was 36.3 months (ranging from 14 to 55.3 months). Fifty‐five per cent were male and 65% were from disadvantaged families. A significant developmental delay in at least one domain and or a significant behavioural problem was identified in 91% of assessments. Overall (or global) delay was found in 38% and this was significantly more likely in girls (P = 0.03). Emotional and/or behavioural difficulties were reported in 85% of children. Internalising problem behaviours were more common than externalising problems. A diagnosis of an autism spectrum disorder was made in four children. In the six review assessments, regression was identified in three children.

Conclusions

Children who have experienced maltreatment and/or neglect may present with developmental delays and behavioural problems. Language delays and internalising problems are characteristic. There are many features in common with primary developmental disorders. The presence of fearfulness and hypervigilance may provide a clue to diagnosis.
Factors determining vaccine uptake in Western Australian adolescents
Authors: Mak Donna B , Bulsara Max K , Wrate Megan J , Carcione Dale , Chantry Melissa , Efller Paul V
Published: December 2012

Aim

Adolescence is the final opportunity for a large‐scale immunisation programme before adulthood. The Western Australian (WA) school‐based vaccination programme provides Year 7 students with free vaccination against hepatitis B virus (HBV); diphtheria, tetanus and pertussis (dTpa); varicella zoster virus (VZV); and human papilloma virus (HPV). We aimed to identify factors determining consent form return and vaccination uptake.

Methods

Data were collected via a statewide, web‐based database in 2009 and 2010. Proportions of students who returned a vaccine consent form, and completed HBV and HPV multi‐dose courses and dTpa and VZV vaccination were determined. Factors associated with these outcomes were identified with multivariate analysis using logistic regression, accounting for clustering by school.

Results

In 2010, 92.8% of WA Year 7 students returned a vaccination consent form and 85.3%, 74.3%, 66.7.0% and 26.4% completed their adolescent vaccination(s) against dTpa, HPV (females only), HBV and VZV, respectively. Consent form return and dTpa vaccination uptake improved between 2009 and 2010. Independent and consistently negative associations were observed between outcome variables (consent form return and vaccine uptake) and male gender, geographically remote schools, government schools and schools in the most socio‐economically disadvantaged areas. Both HBV and HPV course completion were higher in Catholic than government schools, and the same in government and independent schools.

Conclusion

To effectively maximise vaccination coverage, the WA school‐based adolescent vaccination programme must specifically target male students and schools in the most disadvantaged and remote areas.
Glacial cycles as an allopatric speciation pump in north‐easternAmerican freshwater fishes
Authors: April Julien , Hanner Robert H. , Dion‐Côté Anne‐Marie , Bernatchez Louis
Published: December 2012

Allopatric speciation may be the principal mechanism generating new species. Yet, it remains difficult to judge the generality of this process because few studies have provided evidence that geographic isolation has triggered the development of reproductive isolation over multiple species of a regional fauna. Here, we first combine results from new empirical data sets (7 taxa) and published literature (9 taxa) to show that the easternGreatLakes drainage represents a multispecies suture zone for glacial lineages of freshwater fishes with variable levels of genetic divergence. Second, we performed amplified fragment length polymorphism analyses among four pairs of lineages. Results indicate that lineages with relatively deep levels of mtDNA5′COI(barcode) sequence divergence (>2%) developed strong reproductive barriers, while lineages with lower levels of divergence show weaker reproductive isolation when found in sympatry. This suggests that a threshold of 2% sequence divergence at mtDNAcould be used as a first step to flag cryptic species in North American freshwater fishes. By describing different levels of divergence and reproductive isolation in different co‐occurring fishes, we offer strong evidence that allopatric speciation has contributed significantly to the diversification of north‐eastern American freshwater fishes and confirm that Pleistocene glacial cycles can be viewed as a ‘speciation pump’ that played a predominant role in generating biodiversity.
Crossing the uncrossable: novel trans‐valley biogeographic patterns revealed in the genetic history of low‐dispersal mygalomorph spiders (Antrodiaetidae,Antrodiaetus) from California
Authors: Hedin Marshal , Starrett James , Hayashi Cheryl
Published: December 2012

Antrodiaetus riversiis a dispersal‐limited, habitat‐specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. Here, we build upon prior phylogeographic research using a much larger geographic sample and include additional nuclear genes, providing more detailed biogeographic insights throughout the range of this complex. Of particular interest is the uncovering of unexpected and replicated trans‐valley biogeographic patterns, where in two separate genetic clades western haplotypes in the California south Coast Ranges are phylogenetically closely related to eastern haplotypes from central and northern Sierran foothills. In both instances, these trans‐valley phylogenetic patterns are strongly supported by multiple genes. These western and eastern populations are currently separated by the Central Valley, a well‐recognized modern‐day and historical biogeographic barrier in California. For one clade, the directionality is clearly northeast to southwest, and all available evidence is consistent with a jump dispersal event estimated at 1.2–1.3 Ma. During this time period, paleogeographic data indicate that northern Sierran rivers emptied to the ocean in the south Coast Ranges, rather than at the San Francisco Bay. For the other trans‐valley clade genetic evidence is less conclusive regarding the mechanism and directionality of biogeographic exchange, although the estimated timeframe is similar (approximately 1.8 Ma). Despite the large number of biogeographic studies previously conducted in central California, to the best of our knowledge no prior studies have discussed or revealed a northern Sierran to south Coast Range biogeographic connection. This uniqueness may reflect the low‐dispersal biology of mygalomorph spiders, where ‘post‐event’ gene exchange rarely erases historical biogeographic signal.
Polymorphism pattern at a miniature inverted‐repeat transposable element locus downstream of the domestication gene Teosinte‐branched1 in wild and domesticated pearl millet
Authors: Dussert Y. , Remigereau M.‐S. , Fontaine M. C. , Snirc A. , Lakis G. , Stoeckel S. , Langin T. , Sarr A. , Robert T.
Published: December 2012

Unravelling the mechanisms involved in adaptation to understand plant morphological evolution is a challenging goal. For crop species, identification of molecular causal polymorphisms involved in domestication traits is central to this issue. Pearl millet, a domesticated grass mostly found in semi‐arid areas of Africa and India, is an interesting model to address this topic: the domesticated form shares common derived phenotypes with some other cereals such as a decreased ability to develop basal and axillary branches in comparison with the wild phenotype. Two recent studies have shown that the orthologue of the maize gene Teosinte‐Branched1 in pearl millet (PgTb1) was probably involved in branching evolution during domestication and that a miniature inverted‐repeat transposable element (MITE) of the Tuareg family was inserted in the 3′ untranslated region of PgTb1. For a set of 35 wild and domesticated populations, we compared the polymorphism patterns at this MITE and at microsatellite loci. The Tuareg insertion was nearly absent in the wild populations, whereas a strong longitudinal frequency cline was observed in the domesticated populations. The geographical pattern revealed by neutral microsatellite loci clearly demonstrated that isolation by distance does not account for the existence of this cline. However, comparison of population differentiation at the microsatellite and the MITE loci and analyses of the nucleotide polymorphism pattern in the downstream region of PgTb1 did not show evidence that the cline at the MITE locus has been shaped by selection, suggesting the implication of a neutral process. Alternative hypotheses are discussed.
Review: The long‐term consequences of microglial activation following acute traumatic brain injury
Authors: Smith C.
Published: December 2012

The brain is vulnerable to a number of acute insults, with traumatic brain injury being among the commonest. Neuroinflammation is a common response to acute injury and microglial activation is a key component of the inflammatory response. In the acute and subacute phase it is likely that this response is protective and forms an important part of the normal tissue reaction. However, there is considerable literature demonstrating an association between acute traumatic brain injury to the brain and subsequent cognitive decline. This article will review the epidemiological literature relating to both single and repetitive head injury. It will focus on the neuropathological features associated with long‐term complications of a single blunt force head injury, repetitive head injury and blast head injury, with particular reference to chronic traumatic encephalopathy, including dementia pugilistica. Neuroinflammation has been postulated as a key mechanism linking acute traumatic brain injury with subsequent neurodegenerative disease, and this review will consider the response to injury in the acute phase and how this may be detrimental in the longer term, and discuss potential genetic factors which may influence this cellular response. Finally, this article will consider future directions for research and potential future therapies.
Interaction structures formed in the psychodynamic therapy of five patients with borderline personality disorder in crisis
Authors: Goodman Geoff , Edwards Keiha , Chung Hyewon
Published: December 2012

Objectives

To identify interaction structures (i.e., patterns of reciprocal interaction) that characterize the treatments of patients with borderline personality disorder (BPD) in crisis.

Design

A 6‐month naturalistic psychotherapy process and outcome study in which interaction structures were correlated with outcome data.

Methods

Five BPD patients in crisis participated in 6 months of three‐times‐per‐week psychodynamic therapy. Patients completed a measure of psychological distress every week. One hundred and twenty‐seven sessions were audiotaped and coded using the Psychotherapy Process Q‐Set.

Results

Four interaction structures were identified: (1) collaborative relationship with supportive, reassuring therapist (IS1), (2) therapist empathic attunement (IS2), (3) erotized therapeutic relationship (IS3) and (4) directive therapist with compliant patient (IS4). The magnitude of these four interaction structures varied within and between the five therapist–patient dyads over time. Interaction structures correlations with time were inversely proportional to interaction structures correlations with distress levels. IS2 was correlated with two different outcomes in patient 3's and patient 5's treatments – a positive outcome for patient 3's treatment and a negative outcome for patient 5's treatment.

Conclusions

An effective treatment model for BPD patients in crisis needs to promote the emergence of empathically attuned interactions as well as supportive and directive interventions as dictated by the patient's individual needs. These treatments require flexibility to accommodate the patient's unique presentation in crisis. The therapeutic dyad senses which interaction structures to increase or decrease over time to reduce the patient's distress.

Practitioner Points

Unique constellations of four different interaction structures characterized the treatments of five BPD patients in crisis, which provide practitioners with a finite range of expectations in their therapeutic interactions with such patients.

Practitioners need to implement intervention strategies with BPD patients in crisis tailored to the unique characteristics of each patient rather than strategies designed for all patients. Being empathic attuned, supportive or directive in treatment with BPD patients in crisis depends on the nature of the therapeutic dyad at any given moment in time.

Practitioners need to be flexible enough to change intervention strategies when they seem to be increasing distress in BPD patients in crisis.
Divorce and Death: A Case Study for Health Psychology
Authors: Sbarra David A. , Hasselmo Karen , Nojopranoto Widyasita
Published: December 2012

Marital separation and divorce are associated with increased risk for early death, and the magnitude of this association rivals that of many well‐established public health factors. In the case of divorce, however, the mechanisms explaining precisely why and how some people are at risk for early death remain unclear. This paper reviews what is known about the association between divorce and risk for all‐cause mortality, then discusses four emerging themes: the biological intermediaries linking divorce to pathophysiology and disease onset, moving beyond the statistical mean, focusing research on the diathesis‐stress model, and studying how opportunity foreclosures may place people on a trajectory toward poor distal health outcomes. These ideas are grounded in a set of public lay commentaries about the association between divorce and death; in this way, the paper seeks to integrate current research ideas with how the general public thinks about divorce and its correlates. Although this paper focuses on divorce, many of the emerging themes are applicable to the study of psychosocial stress and health more generally. Therefore, the study of divorce and death provides a good case study for health psychology and considers new questions that can be pursued in a variety of research areas.
Applied Social Psychology: A Critical Theoretical Perspective
Authors: McDonald Matthew , Bubna‐Litic David
Published: December 2012

The purpose of this analysis is to review, through a critical theoretical lens, social psychology applied to work and organisations. In our reading of the applied social psychological literature four key issues emerged. These include the valorisation of a positivist epistemology, an owner/management perspective on workplace issues, a focus on intra‐psychic variables or internal mental states when accounting for organisational problems, and the ignoring of moral and ethical commitments in determining workplace research and practice. Each of these issues is then further analysed in light of insights from the field of Critical Management Studies. This alternative approach to organisational behaviour points to the ways in which applied social psychological theory and practice have the potential to disadvantage workers.
B‐cell lymphoma with plasmacytoid differentiation, atypical cytoplasmic inclusions, and secondary leukemia in a dog
Authors: Kol A. , Christopher M.M. , Skorupski K.A. , Tokarz D. , Vernau W.
Published: December 2012

A 7‐year‐old male castrated Jack Russell Terrier was presented to the oncology service at the University of California–Davis Veterinary Medical Teaching Hospital for evaluation of suspected lymphoma. The dog had several enlarged lymph nodes and moderate lymphocytosis. Aspirates of an enlarged inguinal lymph node contained a bimorphic population of large immature lymphocytes and smaller cells with plasmacytoid features. Both cell types often contained a single large cytoplasmic inclusion that varied from clear to pale pink to sky blue. Cytologic changes were interpreted as most consistent with lymphoid neoplasia. Based on the predominantly mature cell morphology and some morphologic heterogeneity, the peripheral lymphocytosis was interpreted as most likely reactive in nature. However, the immunophenotype of the cells (CD20+, CD21+, CD79a+, MUM‐1+, and MHCII+) and clonality assays showed that tissue and blood lymphocytes were neoplastic B cells with clonal identity despite their different morphologic appearances. The cytoplasmic inclusions were positive with periodic acid‐Schiff and were immunoreactive for IgM and IgG. By transmission electron microscopy, inclusions consisted of aberrant rough endoplasmic reticulum; a few small Russell bodies were also noted. A final diagnosis of high‐grade B‐cell lymphoma with plasmacytoid differentiation, atypical cytoplasmic inclusions, and secondary leukemia was made. Chemotherapy was initiated, but the dog was euthanized due to severe and uncontrolled seizures 9 months after the initial diagnosis. This case extends the morphologic repertoire of canine plasmacytoid neoplasms and emphasizes their continuum with multicentric lymphoma. This case also demonstrates the need for advanced diagnostic techniques in establishing blood involvement in lymphoma in some instances.
Assessment of wastewater treatment technologies: life cycle approach
Authors: Kalbar Pradip P. , Karmakar Subhankar , Asolekar Shyam R.
Published: December 2012

Four municipal wastewater treatment plants (WWTPs) in India based on different technologies are compared by conducting Life Cycle Assessment (LCA) using field data. CML 2 baseline 2000 methodology is adopted in which eight impact categories are considered. SBRs ranked highest in energy consumption and global warming potential (GWP) but also produced the best effluent with respect to organics and nutrients. Constructed wetlands have negligible energy consumption and negative GWP because of carbon sequestration in the macrophytes. Emissions associated with electricity production required to operate the WWTPs, emissions to water from treated effluent and heavy metal emissions from waste sludge applied to land are identified as main contributors for overall environmental impacts of WWTPs. This comparison of technologies suggests that results from LCA can be used as indicators in a multicriteria decision‐making framework along with other sustainability indicators.
Inactivation of enveloped and non‐enveloped viruses in the process of chemical treatment and gamma irradiation of bovine‐derived grafting materials
Authors: Lee Kwang‐Il , Lee Jung‐Soo , Jung Hong‐Hee , Lee Hwa‐Yong , Moon Seong‐Hwan , Kang Kyoung‐Tak , Shim Young‐Bock , Jang Ju‐Woong
Published: December 2012

Lee K‐I, Lee J‐S, Jung H‐H, Lee H‐Y, Moon S‐H, Kang K‐T, Shim Y‐B, Jang J‐W. Inactivation of enveloped and non‐enveloped viruses in the process of chemical treatment and gamma irradiation of bovine‐derived grafting materials. Xenotransplantation 2012; 19: 365–369. © 2012 John Wiley & Sons A/S.

Background:  Xenografts, unlike other grafting products, cannot be commercialized unless they conform to stringent safety regulations. Particularly with bovine‐derived materials, it is essential to remove viruses and inactivate infectious factors because of the possibility that raw materials are imbrued with infectious viruses. The removal of the characteristics of infectious viruses from the bovine bone grafting materials need to be proved and inactivation process should satisfy the management provision of the Food and Drug Administration (FDA). To date, while most virus inactivation studies were performed in human allograft tissues, there have been almost no studies on bovine bone.

Methods:  To evaluate the efficacy of virus inactivation after treatment of bovine bone with 70% ethanol, 4% sodium hydroxide, and gamma irradiation, we selected a variety of experimental model viruses that are known to be associated with bone pathogenesis, including bovine parvovirus (BPV), bovine herpes virus (BHV), bovine viral diarrhea virus (BVDV), and bovine parainfluenza‐3 virus (BPIV‐3). The cumulative virus log clearance factor or cumulative virus log reduction factor for the manufacturing process was obtained by calculating the sum of the individual virus log clearance factors or log reduction factors determined for individual process steps with different physicochemical methods.

Results:  The cumulative log clearance factors achieved by three different virus inactivation processes were as follows: BPV ≥17.73, BHV ≥20.53, BVDV ≥19.00, and BPIV‐3 ≥16.27. On the other hand, the cumulative log reduction factors achieved were as follows: BPV ≥16.95, BHV ≥20.22, BVDV ≥19.27, and BPIV‐3 ≥15.58.

Conclusions:  Treatment with 70% ethanol, 4% sodium hydroxide, or gamma irradiation was found to be very effective in virus inactivation, since all viruses were at undetectable levels during each process. We have no doubt that application of this established process to bovine bone graft manufacture will be effective and essential.
Genome Sequence of Francisella tularensis subspecies holarctica Strain FSC200, Isolated from a Child with Tularemia
Authors: Svensson Kerstin , Sjödin Andreas , Byström Mona , Granberg Malin , Brittnacher Mitchell J. , Rohmer Laurence , Jacobs Michael A. , Sims-Day Elizabeth H. , Levy Ruth , Zhou Yang , Hayden Hillary S. , Lim Regina , Chang Jean , Guenthener Donald , Kang Allison , Haugen Eric , Gillett Will , Kaul Rajinder , Forsman Mats , Larsson Pär , Johansson Anders
Published: December 2012

Here we report the complete, accurate 1.89-Mb genome sequence of
Francisella tularensis
subsp.
holarctica
strain FSC200, isolated in 1998 in the Swedish municipality Ljusdal, which is in an area where tularemia is highly endemic. This genome is important because strain FSC200 has been extensively used for functional and genetic studies of
Francisella
and is well-characterized.
Revised Sequence and Annotation of the Rhodobacter sphaeroides 2.4.1 Genome
Authors: Kontur Wayne S. , Schackwitz Wendy S. , Ivanova Natalia , Martin Joel , LaButti Kurt , Deshpande Shweta , Tice Hope N. , Pennacchio Christa , Sodergren Erica , Weinstock George M. , Noguera Daniel R. , Donohue Timothy J.
Published: December 2012

The DNA sequences of chromosomes I and II of
Rhodobacter sphaeroides
strain 2.4.1 have been revised, and the annotation of the entire genomic sequence, including both chromosomes and the five plasmids, has been updated. Errors in the originally published sequence have been corrected, and ∼11% of the coding regions in the original sequence have been affected by the revised annotation.
Complete Genome Sequence of Brucella melitensis 133, an Isolate of Biovar 1 of Sequence Type 32
Authors: Ke Yuehua , Zhen Qing , Li Tiefeng , Wang Yufei , Yuan Xitong , Xu Jie , Huang Liuyu , Wang Dali , Song Hongbin , Chen Zeliang
Published: December 2012

Brucellosis is highly epidemic in China. Of the six classical species,
Brucella melitensis
and biovar 1 are the most represented species and biovar that cause human brucellosis in China. Here, we report the genome sequence of
Brucella melitensis
strain 133, a strain of biovar 1 of sequence type 32.
Genome Sequence of Brucella melitensis Strain 128, an Isolate of Biovar 3 of Sequence Type 8
Authors: Li Tiefeng , Yuan Xitong , Ding Jiabo , Zhen Qing , Ke Yuehua , Wang Yufei , Huang Liuyu , Mao Kairong , Chen Zeliang , Wang Dali
Published: December 2012

Brucella melitensis
is the most common
Brucella
species causing human brucellosis.
B. melitensis
is divided into 3 biovars. Here, we report the complete genome sequence of
B. melitensis
strain 128, a strain of biovar 3 of sequence type 8, which is prevalent in China.
Full Genome Sequences of All Nine Chlamydia psittaci Genotype Reference Strains
Authors: Van Lent Sarah , Piet Jurgen R. , Beeckman Delphine , van der Ende Arie , Van Nieuwerburgh Filip , Bavoil Patrik , Myers Garry , Vanrompay Daisy , Pannekoek Yvonne
Published: December 2012

Chlamydia psittaci
primarily infects birds, but zoonotic transmission occurs in people in close contact with infected birds. The clinical outcome ranges from inapparent disease to pneumonia. Here we report the genome sequences of all 9
Chlamydia psittaci
genotype reference strains.
Draft Genome Sequence of Methanobacterium formicicum DSM 3637, an Archaebacterium Isolated from the Methane Producer Amoeba Pelomyxa palustris
Authors: Gutiérrez Gabriel
Published: December 2012

Here is reported the draft genome sequence of
Methanobacterium formicicum
DSM 3637, which was isolated from the methane-producing amoeba
Pelomyxa palustris
. This bacterium was determined to be an endosymbiont living in the cytoplasm of
P. palustris
and the source of methane; however, the global characteristics of its genome suggest a free-living lifestyle rather than an endosymbiotic one.
Genome Sequence and Comparative Genomics Analysis of a Vibrio cholerae O1 Strain Isolated from a Cholera Patient in Malaysia
Authors: Osama Abdulrazak , Gan Han Ming , Teh Cindy Shuan Ju , Yap Kien-Pong , Thong Kwai-Lin
Published: December 2012

The genome sequence analysis of a clinical
Vibrio cholerae
VC35 strain from an outbreak case in Malaysia indicates multiple genes involved in host adaptation and a novel Na
+
-driven multidrug efflux pump-coding gene in the genome of
Vibrio cholerae
with the highest similarity to VMA_001754 of
Vibrio mimicus
VMA223.
Genome Sequence of Moraxella catarrhalis RH4, an Isolate of Seroresistant Lineage
Authors: Zomer Aldert , de Vries Stefan P. W. , Riesbeck Kristian , Meinke Andreas L. , Hermans Peter W. M. , Bootsma Hester J.
Published: December 2012

Here we report the annotated genome sequence of
Moraxella catarrhalis
strain RH4, a seroresistant-lineage strain isolated from the blood of an infected patient. This genome sequence will allow us to gain further insight into the genetic diversity of clinical
M. catarrhalis
isolates and will facilitate study of
M. catarrhalis
pathogenesis.
Draft Genome Sequence of the Biocontrol Bacterium Bacillus amyloliquefaciens Strain M27
Authors: Lee Sang-Yeob , Kim Byung-Yong , Ahn Jae-Hyung , Song Jaekyeong , Seol Young-Joo , Kim Wan-Gyu , Weon Hang-Yeon
Published: December 2012

Bacillus amyloliquefaciens
strain M27 is a biocontrol agent with antagonistic activities against a wide range of fungal pathogens. Here we present the 3.86-Mb draft genome sequence of the bacterium with the aims of providing insights into the genomic basis of its antifungal mechanism and facilitating its application in the biocontrol of plant diseases.
Genome Sequence of an Alkane-Degrading Bacterium, Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment
Authors: Lai Qiliang , Shao Zongze
Published: December 2012

Alcanivorax pacificus
W11-5
T
was isolated from a pyrene-degrading consortium, enriched from the deep sea sediment of the Pacific Ocean. Strain W11-5
T
can degrade various
n
-alkanes. Here we report the draft genome of W11-5
T
and genes associated with alkane degradation.
Complete Genome Sequence of Acidovorax sp. Strain KKS102, a Polychlorinated-Biphenyl Degrader
Authors: Ohtsubo Yoshiyuki , Maruyama Fumito , Mitsui Hisayuki , Nagata Yuji , Tsuda Masataka
Published: December 2012

We report the complete genome sequence of
Acidovorax
sp. strain KKS102, a polychlorinated-biphenyl-degrading strain isolated from a soil sample in Tokyo. The genome contains a single circular 5,196,935-bp chromosome and no plasmids.
Genome Sequence of Idiomarina xiamenensis Type Strain 10-D-4
Authors: Lai Qiliang , Wang Liping , Wang Wanpeng , Shao Zongze
Published: December 2012

Idiomarina xiamenensis
strain 10-D-4
T
was isolated from an oil-degrading consortium enriched from surface seawater around the Xiamen island. Here, we present the draft genome of strain 10-D-4
T
, which contains 2,899,282 bp with a G+C content of 49.48% and contains 2,673 protein-coding genes and 43 tRNA genes.
Genome Sequence of Oceanibaculum indicum Type Strain P24
Authors: Lai Qiliang , Shao Zongze
Published: December 2012

Oceanibaculum indicum
type strain P24 was isolated from a polycyclic-aromatic-hydrocarbon-degrading consortium enriched from a deep-seawater sample collected from the Indian Ocean. Here we present the draft genome of strain P24
T
, which contains 3,952,792 bp with a G+C content of 65.5% and contains 3,755 protein-coding genes and 45 tRNAs.
Complete Genome Sequence of Bacillus thuringiensis Serovar Sichuansis Strain MC28
Authors: Guan Peng , Ai Peng , Dai Xiaojuan , Zhang Jing , Xu Lizhi , Zhu Jun , Li Qiao , Deng Qiming , Li Shuangcheng , Wang Shiquan , Liu Huannian , Wang Lingxia , Li Ping , Zheng Aiping
Published: December 2012

Bacillus thuringiensis
is an important microbial insecticide used in the control of agricultural pests. Here we report the finished, annotated genome sequence of
Bacillus thuringiensis
serovar Sichuansis strain MC28, which can form parasporal crystals consisting of Cry4Cc1, Cry30Fa1, Cry53Ab1, Cry54Aa1, Cry54Ab1, Cry68Aa1, Cry69Aa1, Cry69Aa2, Cry70Ba1, Cyt1Da1, and Cyt2Aa3. It is also highly toxic to lepidopterous and dipterous insects.
Genome Sequence of Borrelia afzelii Strain HLJ01, Isolated from a Patient in China
Authors: Jiang Bao-Gui , Zheng Yuan-Chun , Tong Yi-Gang , Jia Na , Huo Qiu-Bo , Fan Hang , Ni Xue-Bing , Ma Lan , Yang X. Frank , Jiang Jia-Fu , Cao Wu-Chun
Published: December 2012

We report here the genome sequence of
Borrelia afzelii
strain HLJ01, isolated from a patient with Lyme disease in China. It is the first report of the whole genome of a
B. burgdorferi
sensu lato isolate from a human in China.
Genome Sequence of the Bacteriocin-Producing Strain Lactococcus garvieae DCC43
Authors: Gabrielsen Christina , Brede Dag A. , Hernández Pablo E. , Nes Ingolf F. , Diep Dzung B.
Published: December 2012

This work describes the draft genome sequence of
Lactococcus garvieae
DCC43. The 2.2-Mb draft genome contains 2,227 predicted protein-coding genes, among which is a region encoding the bacteriocin garvicin ML. No antibiotic resistance genes or capsule-related virulence genes were identified. Two plasmid replication regions indicate that this strain likely contains plasmids. Comparative genomics suggests that this strain displays a high degree of sequence variation from the previously sequenced
L. garvieae
strains.
Genome Sequence of Clostridium tunisiense TJ, Isolated from Drain Sediment from a Pesticide Factory
Authors: Sun Lili , Wang Yu , Yu Chunyan , Zhao Yongqin , Gan Yinbo
Published: December 2012

Clostridium tunisiense
is a Gram-positive, obligate anaerobe that was first isolated in an anaerobic evironment under eutrophication. Here we report the first genome sequence of the
Clostridium tunisiense
TJ isolated from drain sediment of a pesticide factory in Tianjin, China. The genome is of great importance for both basic and application research.
Draft Genome Sequence of the Bean-Nodulating Sinorhizobium fredii Strain GR64
Authors: Torres Tejerizo Gonzalo , Lozano Luis , González Víctor , Bustos Patricia , Romero David , Brom Susana
Published: December 2012

Sinorhizobium fredii
GR64 is a peculiar strain that is able to effectively nodulate bean but not soybean, the common host of
S. fredii
. Here we present the draft genome of
S. fredii
GR64. This information will contribute to a better understanding of the symbiotic rhizobium-plant interaction and of rhizobial evolution.
Genome Sequence of Strain IMCC14465, Isolated from the East Sea, Belonging to the PS1 Clade of Alphaproteobacteria
Authors: Yang Seung-Jo , Kang Ilnam , Cho Jang-Cheon
Published: December 2012

Strain IMCC14465 was isolated from surface seawater of the East Sea using dilution-to-extinction culturing. Phylogenetic analysis indicated that the strain belongs to the PS1 clade, which is closely related to the OCS116 clade in the
Alphaproteobacteria
. Here, we report the genome sequence of IMCC14465, the first isolate of the PS1 clade.
Genome Sequence of Thalassospira profundimaris Type Strain WP0211
Authors: Lai Qiliang , Shao Zongze
Published: December 2012

Thalassospira profundimaris
WP0211
T
was isolated from a pyrene-degrading consortium, enriched from deep-sea sediment collected from the West Pacific Ocean. Here, we present the draft genome of strain WP0211
T
, which contains 4,380,232 bp with a G+C content of 55.19% and contains 4,040 protein-coding genes and 45 tRNAs.
Complete Genome Sequence of Clostridium sp. Strain BNL1100, a Cellulolytic Mesophile Isolated from Corn Stover
Authors: Li Luen-Luen , Taghavi Safiyh , Izquierdo Javier A. , van der Lelie Daniel
Published: December 2012

We present the full genome sequence of
Clostridium
sp. strain BNL1100, a Gram-positive, endospore-forming, lignocellulolytic bacterium isolated from a corn stover enrichment culture. The 4,613,747-bp genome of strain BNL1100 contains 4,025 putative protein-coding genes, of which 103 are glycoside hydrolases, the highest detected number in cluster III clostridia.
Draft Genome Sequence of Streptomyces sp. Strain SS, Which Produces a Series of Uridyl Peptide Antibiotic Sansanmycins
Authors: Wang Lifei , Xie Yunying , Li Qinglian , He Ning , Yao Entai , Xu Hongzhang , Yu Ying , Chen Ruxian , Hong Bin
Published: December 2012

Streptomyces
sp. SS produces a series of uridyl peptide antibiotic sansanmycins. Here, we present a draft genome sequence of
Streptomyces
sp. SS containing the biosynthetic gene cluster for the antibiotics. The identification of the biosynthetic gene cluster of sansanmycins may provide further insight into biosynthetic mechanisms for uridyl peptide antibiotics.
Genome Sequence of Nitratireductor indicus Type Strain C115
Authors: Lai Qiliang , Li Guizhen , Yu Zhiwei , Shao Zongze
Published: December 2012

Nitratireductor indicus
strain C115
T
was isolated from a crude-oil-degrading consortium enriched from deep seawater of the Indian Ocean. Here, we present the draft genome of strain C115
T
, which contains 4,992,479 bp with a G+C content of 60.8% and contains 4,825 protein-coding genes and 45 tRNA genes.
Genome Sequence of the Protease-Producing Bacterium Rheinheimera nanhaiensis E407-8
T
, Isolated from Deep-Sea Sediment of the South China Sea
Authors: Zhang Xi-Ying , Zhang Yan-Jiao , Qin Qi-Long , Xie Bin-Bin , Chen Xiu-Lan , Zhou Bai-Cheng , Zhang Yu-Zhong
Published: December 2012

The protease-producing bacterium E407-8
T
was isolated from deep-sea sediment of the South China Sea and has been identified recently as representing a new species,
Rheinheimera nanhaiensis
. The draft genome of
R. nanhaiensis
E407-8
T
consists of 3,987,205 bp and contains 3,730 predicated protein-coding genes, including 82 extracellular peptidase genes.
Genome Sequence of Bartonella rattaustraliani, a Bacterium Isolated from an Australian Rat
Authors: Merhej Vicky , Croce Olivier , Robert Catherine , Rolain Jean-Marc , Raoult Didier
Published: December 2012

Bartonella rattaustraliani
is a facultative intracellular bacterium isolated from the blood of a
Rattus
sp. in Australia. The present study reports the draft genome of
B. rattaustraliani
strain AUST/NH4 (CSUR B609
T
).
Genome Sequence of Enterobacter sp. Strain SP1, an Endophytic Nitrogen-Fixing Bacterium Isolated from Sugarcane
Authors: Zhu Bo , Chen Mingyue , Lin Li , Yang Litao , Li Yangrui , An Qianli
Published: December 2012

Enterobacter
sp. strain SP1 is an endophytic nitrogen-fixing bacterium isolated from a sugarcane stem and can promote plant growth. The draft genome sequence of strain SP1 presented here will promote comparative genomic studies to determine the genetic background of interactions between endophytic enterobacteria and plants.
Stretching the limbs? Tonic spasms in multiple sclerosis
Authors: Andrade Carlos , Massano João , Guimarães Joana , Garrett Maria Carolina
Published: December 2012

A 23-year-old man with a clinically isolated syndrome (right optic neuritis) diagnosed 6 months before, presented with recurrent, brief, painful, stereotyped, involuntary posturing movements of the left upper limb. The neurological examination was otherwise unremarkable (except for right optic atrophy). Intravenous methylprednisolone was initiated; the paroxysms persisted and worsened 7 days later, as the left lower limb and hemiface became affected. A video-EEG showed no epileptiform activity despite the movements. Brain MRI revealed new lesions affecting the right pyramidal tract, contralateral to the clinical manifestations. Valproate was prescribed and the paroxysms were completely resolved 5 days later. Tonic spasms are classically, although infrequently, seen in multiple sclerosis, and may clinically resemble primary paroxysmal dyskinesias or even focal motor epileptic seizures.
Monophyly of some North American species ofRamalinaand inferred polyketide synthase gene function
Authors: Timsina Brinda A. , Stocker-Wörgötter E. , Piercey-Normore Michele D.
Published: December 2012

Ramalina thrausta (Ach.) Nyl., Ramalina roesleri (Hochst. Ex Schaerer) Hue, and Ramalina dilacerata (Hoffm.) Hoffm. are three common North American species that have not been placed in a phylogeny and are sympatric in their distribution leading to uncertainty about monophyly. Species characters include secondary metabolites (polyketides) in Ramalina that may be both hereditary and influenced by environmental conditions, but little is known about the function of polyketide synthase (PKS) genes. The main goal of this study was to examine the monophyly among some of the more common species in northern North America and secondarily to compare potential PKS gene function with the phylogeny. Nucleotide sequences of two genes, the internal transcribed spacer 1 of ribosomal DNA and the mitochondrial small subunit, were used to infer a phylogeny. Gene function was inferred from three PKS genes by the ratio of nonsynonymous to synonymous substitutions (dN:dS) ratios. Although seven species of Ramalina are highly supported in monophyletic clades, two other species form clusters with low support: Ramalina americana Hale is paraphyletic, and Ramalina pollinaria (Westr.) Ach. is polyphyletic. Three PKS genes were inferred to be functional but were not present in all samples. Functional PKS genes could enable adaptation to new habitats and facilitate species diversification.
Reply to the discussion of the reply by R.L. Romer and U. Kroner on “Geochemical signature of Ordovician Mn-rich sedimentary rocks on the Avalonian shelf” 1Appears in the Canadian Journal of Earth Sciences, 49(11): 1372–1377 [doi:10.1139/e2012-049].
Authors: Romer Rolf L. , Kroner Uwe
Published: December 2012

Romer and Kroner (2012) stated “the core of the Harlech Dome (i) in part is made up of Ordovician deposits and (ii) contains tectonic repetitions”. In their comment, Schofield et al. (this issue) distort this statement and state that (i) we claim the entire sedimentary sequence of the Harlech Dome is Ordovician and (ii) we misinterpreted their zircon data. We disagree. In our reply, we demonstrate that the argumentation of Schofield et al. (this issue) is driven by circular argumentation and that their use and interpretation of U–Pb zircon data is inadequate.
Discussion of the reply by R.L. Romer and U. Kroner on “Geochemical signature of Ordovician Mn-rich sedimentary rocks on the Avalonian shelf” 1Appears in Canadian Journal of Earth Sciences, 49(6): 775–780, 10.1139/e2012-006.
Authors: Schofield David I. , Waldron John W.F. , White Chris E. , Barr Sandra M.
Published: December 2012

In their article ‘Reply to the discussion by J.W.F. Waldron and C.E. White on “Geochemical signature of Ordovician Mn-rich sedimentary rocks on the Avalonian shelf”’, R.L. Romer and U. Kroner reinterpret geochronological data presented by J.W.F. Waldron, D.I. Schofield, C.E. White, and S.M. Barr to imply an Ordovician, not a Cambrian, depositional age for the succession of the Harlech Dome, North Wales, and Meguma Supergroup, Nova Scotia. However, an extensive history of biostratigraphic and geological survey data refutes this interpretation and shows that the rocks are unequivocally Cambrian. Waldron et al. used the U–Pb zircon laser-ablation – multicollector – inductively coupled plasma – mass spectrometry technique primarily to provide information on sediment provenance and not depositional age. Investigation of anomalously young 206Pb/238U ages showed evidence of Pb loss. These data provide little constraint on depositional age and cannot be used to infer that the Harlech Grits Group is Ordovician.