bluuebunny/crossref_metadata_2025 huggingface dataset:
Economic Adversity and Criminal Behaviour: Rethinking Youth Unemployment and Crime
Authors: Polk Kenneth , White Rob
Published: January 2011

This paper argues that in order to understand the impact of youth unemployment on crime it is necessary to specify the particular social location and meaning of contemporary economic adversity. A starting point is an analysis of the collapse of the youth labour market. This has created high levels of youth unemployment, has dramatically worsened the educational situation of those who seek to leave school without high level qualifications, and has had major consequences for the income available to young people. These forms of economic adversity have direct impacts on the social lives of the early school leavers, and create a number of possible friction points with adults, such as conflicts over public space recognisable as the ‘mall problem’. We argue that there are particular forms of economic adversity which impact upon specific groups of young people, and these in turn may have consequences in terms of higher levels of recorded youth crime.
White-Collars and Black Sheep: A Twenty-Year Criminological Follow-Up of White-Collar Ex-Offenders
Authors: Soothill Keith , Francis Brian , Escarela Gabriel
Published: January 2011

This paper describes a further analysis of the outcome of a twenty-year criminological follow-up of a consecutive series of 348 male ex-offenders seeking white-collar employment who were offered the services of a specialist employment agency (APEX) in the early 1970s. This analysis shows the value of a more sophisticated statistical analysis which combines survival analysis with smoothing models: this provides new insights into the theoretical understanding of the data. There is evidence that remaining in contact with the organisation, irrespective of whether a suitable job is found, benefits those with around four to twelve previous convictions.
Pre-trial withdrawals: Trial, bargain, or pseudo-bargain?
Authors: Douglas Roger
Published: January 2011

An analysis of the correlates of pre-trial withdrawals in Melbourne magistrates' court cases suggests that withdrawals are largely a reponse to plea and to whether defendants were legally represented. Where defendants were willing to plead guilty to remaining charges, withdrawals appear to have been more likely where the prosecution case was weak. Although pre-trial withdrawals appear to be the outcome of a bargaining process, the value of withdrawals appears to be limited, especially in their impact on sentence.

In many US jurisdictions, cases are frequently disposed of by a decision by the prosecutor to withdraw the charges against the defendant. In other cases, some charges are withdrawn and others reduced. In some cases withdrawals reflect no more than an assessment by the prosecutor that the case should not proceed. The complainant may want the charges withdrawn. Key witnesses may be unavailable. However, withdrawals are frequently a response to some type of negotiation. Sometimes the negotiation may involve a process analogous to trial and the defence may succeed in persuading the prosecutor that the prosecution case is so weak that it would be a waste of time to take it to trial. Often the bargain involves an agreement whereby the defendant pleads guilty to some charges in exchange for the withdrawal of others. In some cases the bargain may be a genuine one, but in others, bargaining may represent “pseudo-bargaining”: charges may be withdrawn, but the sentence the defendant receives may in fact be identical to what he would have received had no charges been withdrawn.

In Australia, charge withdrawal is far less widespread than is the case in many American jurisdictions, but it nonetheless takes place. This study represents an examination of the correlates of charge withdrawal in six Melbourne magistrates' courts.

For methodological reason it has not been possible to examine the determinants of charge withdrawals in cases where all charges were withdrawn. However, these are the exceptions. Charge withdrawal usually involves withdrawal of only some of the charges which make up magistrates' court cases, and it is possible to explore the correlates of withdrawals in these cases.

I shall be arguing that charge withdrawal bears a rather complex relationship to the strength of the prosecution case, but is strongly related to plea and representation and in such a way as to suggest that withdrawals are the result of a bargaining process. However, the benefits of pre-trial withdrawals appear to be largely illusory. Defendants who fail to benefit from pre-trial withdrawals sometimes benefit from post-conviction withdrawals. Sentence appears to be unaffected by whether or not charges have been withdrawn.
A Supplement
Authors:   Lawfull Authority
Published: January 2011

A SUPPLEMENT or, Addendum made unto a Treatise lately publish'd, touching the Reformation of the Ecclesiasticall Calendar of the Church of England, Wherein are set forth divers new Arguments, and Refutations, whereby may be set at Rest the Doubts of the more timid Churchmen, and the Pretensions answered, of such as have rashly endeavoured to promote Opinions contrary to the Sense and Tenour of the Treatise aforesaid, which Treatise was expressly Commanded and Allowed
Theological Optimism in the Films of Frank Capra
Authors: Brown Stephen J.
Published: January 2011

Optimism is a way of thinking and living which affirms on the one hand the capacity to improve oneself and the whole human condition, and on the other hand, claims that ultimate reality, being under the control of good rather than evil, supports, if not guarantees this improvement.
Comprehensive Airway Management of Neonatal Head and Neck Teratomas
Authors: Neidich Marci J. , Prager Jeremy D. , Clark Stacey L. , Elluru Ravindhra G.
Published: January 2011

Objectives

To determine the success of initial airway management and to characterize late airway‐related complications in patients with airway obstruction due to congenital head and neck teratomas

Study Design

Case series with chart review.

Setting

Tertiary airway referral institution.

Subjects and Methods

Review of consecutive patients with congenital head and neck teratomas from 1988 to 2010. Variables examined include initial airway stabilization at time of birth and perinatal airway management. Outcomes include short‐ and long‐term complications.

Results

Fourteen cases were reviewed. In 12 patients, initial airway management was accomplished on placental support with either intubation or tracheotomy. Two vaginal births required subsequent uncomplicated oral intubation within 24 hours. Nine patients required tracheotomy (3 within the delivery suite, 2 during mass excision on day of life 6 and 24, and the remaining 4 occurred at days 29, 32, 92, and 100). Five deaths occurred, 4 within several days of birth due to complications related to the cervical teratomas and 1 on day of life 32 due to an airway‐related complication. Follow‐up for surviving patients ranged from 1 month to 18 years. Long‐term airway complications ranged from vocal cord paralysis to stenosis requiring laryngotracheoplasty.

Conclusion

This study demonstrates that a multidisciplinary team and a standardized approach in the operating suite have led to successful initial airway stabilization. Furthermore, this study demonstrates the need for continued airway management after delivery. Reassessment of the airway after delivery and an airway management planning meeting with the multidisciplinary team may help decrease morbidity and mortality.
Comparison of Applicant Criteria and Program Expectations for Choosing Residency Programs in the Otolaryngology Match
Authors: Sharp Scott , Puscas Liana , Schwab Brian , Lee Walter T.
Published: January 2011

Objective

To evaluate criteria used by residency applicants in ranking otolaryngology residency programs and to compare applicant criteria with program expectations of ranking otolaryngology residency programs.

Study Design

Cross‐sectional survey.

Setting

2009 and 2010 match cycles.

Subjects and Methods

Program applicants and otolaryngology program directors.

Main Outcome Measures

Applicants were asked to rank the importance of 10 criteria in choosing a residency program (1 = criterion was of the utmost importance and 20 = not important at all). Program directors were asked to express expectations of how applicants should rank programs using those same criteria. The Mann‐Whitney U test was used to analyze responses between groups.

Results

Comprehensiveness of subspecialties and resident satisfaction were the most important criteria for both groups; salary, call schedule, and likelihood to rank the resident highly were least valued. Four criteria were significantly different between groups. Applicants significantly valued location (4.36 vs 8.9, P <. 0001) and call schedule (9.85 vs 12.73, P =. 002) more than program directors did. Program directors valued didactic schedule (6.1 vs 9.18, P <. 0001) and comprehensiveness of subspecialties (2.53 vs 3.02, P =. 007) more than applicants did. Forty‐one of 105 (39%) program directors completed the survey.

Conclusion

While applicants and program directors agree on the most and least important criteria for ranking residency programs, there are several significant differences in these criteria. This study provides insight on ranking criteria that may improve the resident match process and subsequent training experience. However, the ability to generalize the results is limited by the low response rate.
Analysis of Flap Tension in Surgical Rejuvenation of the Midface
Authors: Herrero Nicholas A. , Sherman Ethan G. , Adelson Robert T.
Published: January 2011

Objective

To determine the flap tension present for 2 different surgical approaches for midface lifts and whether a gingivobuccal incision for release of the midface periosteum will diminish the resultant load on the midface flap.

Study Design

Cadaver study.

Setting

Anatomy laboratory at the University of Florida.

Subjects and Methods

Twelve fresh‐frozen cadaver heads are subjected to a transblepharoplasty (TB) approach on one side of the cadaver head while a transtemporal (TT) approach is performed on the contralateral side. The tension (grams) generated by moving the midface flap a distance of 1.03 cm is recorded by a digital load cell. A gingivobuccal incision is made on each side to allow transoral periosteal release (TOPR) of the midface flap, and the experiment is repeated. Three trials are performed for each operation, and the average load is calculated. A paired t test is applied.

Results

The tension resulting from the TT approach (172 g) was not found to be significantly different from that of the TB approach (179 g; P =. 75). Significant differences in the resultant tension were not appreciated when comparing standard techniques to TT with TOPR (141.5 g; P =. 27) or for TB with TOPR (164.1 g; P =. 45).

Discussion

An experimental method is described for determining flap tension in facial rejuvenation surgery. No significant difference is found between flap tensions generated in the TB and TT approaches to the midface.
Introduction: change and continuity in recent family policies
Authors: Mätzke Margitta , Ostner Ilona
Published: January 2011

Families have become a focal point in debates of ‘new risks’ and much needed ‘new policies’ for Western welfare states. Family policy responses to the new challenges and even the goals associated with welfare policies designed to aid families have, however, varied across countries, and there is much uncertainty about the sources of this variation and the future development of the policy field. This special issue takes stock of recent developments in the field of family policy. It brings together a range of countries that, taken together, map the full spectrum of advanced industrial countries’ family policy dilemmas, responses, and intervening institutional and ideational variables. Its goal is to take a first step towards explaining the varied degrees and forms of family policy activism in mature welfare states of Western liberal democracies. The introduction to the special issue first sketches the changing nature and social roles of the family, as they evolved along with public law and welfare policies. It then presents family policy regimes which allow for a systematic account of possible intervening factors in the formulation of country-specific responses. Most importantly, the introduction provides a brief outline of plausible causal approaches to the question of family policy change and comments on their strengths and the potential hazards and describes how the papers assembled here may collectively contribute to a better understanding of what drives and shapes family policy development and how these potential causes are interrelated.
Continuity and consensus: governing families in Denmark
Authors: Abrahamson Peter
Published: January 2011

In Danish family policy, changes initiated by the present conservative-liberal government differ little from those proposed by the opposition. Recent changes are minor, but significant ones occurred in the 1960s, when childcare was universalized, and in the 1980s, when parental leave substituted maternal leave. These changes can be explained as adjustments to post-industrial conditions within a political culture relying on class compromises and a broad consensus informed by expert advice coming from civil servants and ad hoc policy commissions. The paper concludes that changes in Danish family policy reflect changing conditions for employment and the minding of children and that there has been a high degree of continuity and consensus about the change, as indicated by the strong increase in female labour market involvement.
Adaptive immunity to rhinoviruses: sex and age matter
Authors: Carroll Melanie L , Yerkovich Stephanie T , Pritchard Antonia L , Davies Janet M , Upham John W
Published: January 2011

Background

Rhinoviruses (RV) are key triggers in acute asthma exacerbations. Previous studies suggest that men suffer from infectious diseases more frequently and with greater severity than women. Additionally, the immune response to most infections and vaccinations decreases with age. Most immune function studies do not account for such differences, therefore the aim of this study was to determine if the immune response to rhinovirus varies with sex or age.

Methods

Blood mononuclear cells were isolated from 63 healthy individuals and grouped by sex and age (≤50 years old and ≥52 years old). Cells were cultured with rhinovirus 16 at a multiplicity of infection of 1. The chemokine IP-10 was measured at 24 h as an index of innate immunity while IFNγ and IL-13 were measured at 5 days as an index of adaptive immunity.

Results

Rhinovirus induced IFNγ and IL-13 was significantly higher in ≤50 year old women than in age matched men (p < 0.02 and p < 0.05) and ≥52 year old women (p < 0.02 and p > 0.005). There was no sex or age based difference in rhinovirus induced IP-10 expression. Both IFNγ and IL-13 were negatively correlated with age in women but not in men.

Conclusions

This study suggests that pre-menopausal women have a stronger adaptive immune response to rhinovirus infection than men and older people, though the mechanisms responsible for these differences remain to be determined. Our findings highlight the importance of gender and age balance in clinical studies and in the development of new treatments and vaccines.
Streptavidin-Binding Peptide (SBP)-tagged SMC2 allows single-step affinity fluorescence, blotting or purification of the condensin complex
Authors: Kim Ji Hun , Chang Tsz M , Graham Alison N , Andy Choo K H , Kalitsis Paul , Hudson Damien F
Published: January 2011

Background

Cell biologists face the need to rapidly analyse their proteins of interest in order to gain insight into their function. Often protein purification, cellular localisation and Western blot analyses can be multi-step processes, where protein is lost, activity is destroyed or effective antibodies have not yet been generated.

Aim

To develop a method that simplifies the critical protein analytical steps of the laboratory researcher, leading to easy, efficient and rapid protein purification, cellular localisation and quantification.

Results

We have tagged the SMC2 subunit of the condensin complex with the Streptavidin-Binding Peptide (SBP), optimising and demonstrating the efficacious use of this tag for performing these protein analytical steps. Based on silver staining, and Western analysis, SBP delivered an outstanding specificity and purity of the condensin complex. We also developed a rapid and highly specific procedure to localise SBP-tagged proteins in cells in a single step procedure thus bypassing the need for using antibodies. Furthermore we have shown that the SBP tag can be used for isolating tagged proteins from chemically cross-linked cell populations for capturing DNA-protein interactions.

Conclusions

The small 38-amino acid synthetic SBP offers the potential to successfully perform all four critical analytical procedures as a single step and should have a general utility for the study of many proteins and protein complexes.
SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
Authors: Holm Kristian , Melum Espen , Franke Andre , Karlsen Tom H
Published: January 2011

Background

Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III) of 3.96 million single nucleotide polymorphisms (SNPs) in the same individuals are publicly available. We aimed to generate a user-friendly web based tool for visualization of the correlation between SNP genotypes within a specified genomic region and a gene of interest, which is also well-known as an expression quantitative trait locus (eQTL) analysis.

Results

SNPexp is implemented as a server-side script, and publicly available on this website: http://tinyurl.com/snpexp. Correlation between genotype and transcript expression levels are calculated by performing linear regression and the Wald test as implemented in PLINK and visualized using the UCSC Genome Browser. Validation of SNPexp using previously published eQTLs yielded comparable results.

Conclusions

SNPexp provides a convenient and platform-independent way to calculate and visualize the correlation between HapMap genotypes within a specified genetic region anywhere in the genome and gene expression levels. This allows for investigation of both cis and trans effects. The web interface and utilization of publicly available and widely used software resources makes it an attractive supplement to more advanced bioinformatic tools. For the advanced user the program can be used on a local computer on custom datasets.
Lack of α8 integrin leads to morphological changes in renal mesangial cells, but not in vascular smooth muscle cells
Authors: Marek Ines , Volkert Gudrun , Jahn Angelika , Fahlbusch Fabian , Zürn Christina , Özcan Zehra , Goppelt-Struebe Margarete , Hilgers Karl F , Rascher Wolfgang , Hartner Andrea
Published: January 2011

Background

Extracellular matrix receptors of the integrin family are known to regulate cell adhesion, shape and functions. The α8 integrin chain is expressed in glomerular mesangial cells and in vascular smooth muscle cells. Mice deficient for α8 integrin have structural alterations in glomeruli but not in renal arteries. For this reason we hypothesized that mesangial cells and vascular smooth muscle cells differ in their respective capacity to compensate for the lack of α8 integrin.

Results

Wild type and α8 integrin-deficient mesangial cells varied markedly in cell morphology and expression or localization of cytoskeletal molecules. In α8 integrin-deficient mesangial cells α-smooth muscle actin and CTGF were downregulated. In contrast, there were no comparable differences between α8 integrin-deficient and wild type vascular smooth muscle cells. Expression patterns of integrins were altered in α8 integrin-deficient mesangial cells compared to wild type mesangial cells, displaying a prominent overexpression of α2 and α6 integrins, while expression patterns of the these integrins were not different between wild type and α8 integrin-deficient vascular smooth muscle cells, respectively. Cell proliferation was augmented in α8 integrin-deficient mesangial cells, but not in vascular smooth muscle cells, compared to wild type cells.

Conclusions

Our findings suggest that α8 integrin deficiency has differential effects in mesangial cells and vascular smooth muscle cells. While the phenotype of vascular smooth muscle cells lacking α8 integrin is not altered, mesangial cells lacking α8 integrin differ considerably from wild type mesangial cells which might be a consequence of compensatory changes in the expression patterns of other integrins. This could result in glomerular changes in α8 integrin-deficient mice, while the vasculature is not affected in these mice.
Gene structure, transcripts and calciotropic effects of the PTH family of peptides in Xenopus and chicken
Authors: Pinheiro Pedro LC , Cardoso João CR , Gomes Ana S , Fuentes Juan , Power Deborah M , Canário Adelino VM
Published: January 2011

Background

Parathyroid hormone (PTH) and PTH-related peptide (PTHrP) belong to a family of endocrine factors that share a highly conserved N-terminal region (amino acids 1-34) and play key roles in calcium homeostasis, bone formation and skeletal development. Recently, PTH-like peptide (PTH-L) was identified in teleost fish raising questions about the evolution of these proteins. Although PTH and PTHrP have been intensively studied in mammals their function in other vertebrates is poorly documented. Amphibians and birds occupy unique phylogenetic positions, the former at the transition of aquatic to terrestrial life and the latter at the transition to homeothermy. Moreover, both organisms have characteristics indicative of a complex system in calcium regulation. This study investigated PTH family evolution in vertebrates with special emphasis on Xenopus and chicken.

Results

The PTH-L gene is present throughout the vertebrates with the exception of placental mammals. Gene structure of PTH and PTH-L seems to be conserved in vertebrates while PTHrP gene structure is divergent and has acquired new exons and alternative promoters. Splice variants of PTHrP and PTH-L are common in Xenopus and chicken and transcripts of the former have a widespread tissue distribution, although PTH-L is more restricted. PTH is widely expressed in fish tissue but from Xenopus to mammals becomes largely restricted to the parathyroid gland. The N-terminal (1-34) region of PTH, PTHrP and PTH-L in Xenopus and chicken share high sequence conservation and the capacity to modify calcium fluxes across epithelia suggesting a conserved role in calcium metabolism possibly via similar receptors.

Conclusions

The parathyroid hormone family contains 3 principal members, PTH, PTHrP and the recently identified PTH-L. In teleosts there are 5 genes which encode PTHrP (2), PTH (2) and PTH-L and in tetrapods there are 3 genes (PTHrP, PTH and PTH-L), the exception is placental mammals which have 2 genes and lack PTH-L. It is hypothesized that genes of the PTH family appeared at approximately the same time during the vertebrate radiation and evolved via gene duplication/deletion events. PTH-L was lost from the genome of eutherian mammals and PTH, which has a paracrine distribution in lower vertebrates, became the product of a specific endocrine tissue in Amphibia, the parathyroid gland. The PTHrP gene organisation diverged and became more complex in vertebrates and retained its widespread tissue distribution which is congruent with its paracrine nature.
Conservation, loss, and redeployment of Wnt ligands in protostomes: implications for understanding the evolution of segment formation
Authors: Janssen Ralf , Le Gouar Martine , Pechmann Matthias , Poulin Francis , Bolognesi Renata , Schwager Evelyn E , Hopfen Corinna , Colbourne John K , Budd Graham E , Brown Susan J , Prpic Nikola-Michael , Kosiol Carolin , Vervoort Michel , Damen Wim GM , Balavoine Guillaume , McGregor Alistair P
Published: January 2011

Background

The Wnt genes encode secreted glycoprotein ligands that regulate a wide range of developmental processes, including axis elongation and segmentation. There are thirteen subfamilies of Wnt genes in metazoans and this gene diversity appeared early in animal evolution. The loss of Wnt subfamilies appears to be common in insects, but little is known about the Wnt repertoire in other arthropods, and moreover the expression and function of these genes have only been investigated in a few protostomes outside the relatively Wnt-poor model species Drosophila melanogaster and Caenorhabditis elegans. To investigate the evolution of this important gene family more broadly in protostomes, we surveyed the Wnt gene diversity in the crustacean Daphnia pulex, the chelicerates Ixodes scapularis and Achaearanea tepidariorum, the myriapod Glomeris marginata and the annelid Platynereis dumerilii. We also characterised Wnt gene expression in the latter three species, and further investigated expression of these genes in the beetle Tribolium castaneum.

Results

We found that Daphnia and Platynereis both contain twelve Wnt subfamilies demonstrating that the common ancestors of arthropods, ecdysozoans and protostomes possessed all members of all Wnt subfamilies except Wnt3. Furthermore, although there is striking loss of Wnt genes in insects, other arthropods have maintained greater Wnt gene diversity. The expression of many Wnt genes overlap in segmentally reiterated patterns and in the segment addition zone, and while these patterns can be relatively conserved among arthropods and the annelid, there have also been changes in the expression of some Wnt genes in the course of protostome evolution. Nevertheless, our results strongly support the parasegment as the primary segmental unit in arthropods, and suggest further similarities between segmental and parasegmental regulation by Wnt genes in annelids and arthropods respectively.

Conclusions

Despite frequent losses of Wnt gene subfamilies in lineages such as insects, nematodes and leeches, most protostomes have probably maintained much of their ancestral repertoire of twelve Wnt genes. The maintenance of a large set of these ligands could be in part due to their combinatorial activity in various tissues rather than functional redundancy. The activity of such Wnt 'landscapes' as opposed to the function of individual ligands could explain the patterns of conservation and redeployment of these genes in important developmental processes across metazoans. This requires further analysis of the expression and function of these genes in a wider range of taxa.
454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher
Authors: Zagalska-Neubauer Magdalena , Babik Wiesław , Stuglik Michał , Gustafsson Lars , Cichoń Mariusz , Radwan Jacek
Published: January 2011

Background

Because of their functional significance, the Major Histocompatibility Complex (MHC) class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping.

Results

Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family.

Conclusions

454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective, genotyping of MHC systems of virtually any complexity.
Phylogenomic reconstruction of lactic acid bacteria: an update
Authors: Zhang Zhi-Gang , Ye Zhi-Qiang , Yu Li , Shi Peng
Published: January 2011

Background

Lactic acid bacteria (LAB) are important in the food industry for the production of fermented food products and in human health as commensals in the gut. However, the phylogenetic relationships among LAB species remain under intensive debate owing to disagreements among different data sets.

Results

We performed a phylogenetic analysis of LAB species based on 232 genes from 28 LAB genome sequences. Regardless of the tree-building methods used, combined analyses yielded an identical, well-resolved tree topology with strong supports for all nodes. The LAB species examined were divided into two groups. Group 1 included families Enterococcaceae and Streptococcaceae. Group 2 included families Lactobacillaceae and Leuconostocaceae. Within Group 2, the LAB species were divided into two clades. One clade comprised of the acidophilus complex of genus Lactobacillus and two other species, Lb. sakei and Lb. casei. In the acidophilus complex, Lb. delbrueckii separated first, while Lb. acidophilus/Lb. helveticus and Lb. gasseri/Lb. johnsonii were clustered into a sister group. The other clade within Group 2 consisted of the salivarius subgroup, including five species, Lb. salivarius, Lb. plantarum, Lb. brevis, Lb. reuteri, Lb. fermentum, and the genera Pediococcus, Oenococcus, and Leuconostoc. In this clade, Lb. salivarius was positioned most basally, followed by two clusters, one corresponding to Lb. plantarum/Lb. brevis pair and Pediococcus, and the other including Oenococcus/Leuconostoc pair and Lb. reuteri/Lb. fermentum pair. In addition, phylogenetic utility of the 232 genes was analyzed to identify those that may be more useful than others. The genes identified as useful were related to translation and ribosomal structure and biogenesis (TRSB), and a three-gene set comprising genes encoding ultra-violet resistance protein B (uvrB), DNA polymerase III (polC) and penicillin binding protein 2B (pbpB).

Conclusions

Our phylogenomic analyses provide important insights into the evolution and diversification of LAB species, and also revealed the phylogenetic utility of several genes. We infer that the occurrence of multiple, independent adaptation events in LAB species, have resulted in their occupation of various habitats. Further analyses of more genes from additional, representative LAB species are needed to reveal the molecular mechanisms underlying adaptation of LAB species to various environmental niches.
Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Authors: Lewis Richard A , Laing Emma , Allenby Nicholas , Bucca Giselda , Brenner Volker , Harrison Marcus , Kierzek Andrzej M , Smith Colin P
Published: January 2011

Background

Whilst being closely related to the model actinomyceteStreptomyces coelicolorA3(2),S. lividans66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density (one probe per gene) PCR-based spotted arrays. Here we use new experimentally optimised 104,000 × 60-mer probe arrays to characterize in detail the genomic differences between wild-typeS. lividans66, a derivative industrial strain, TK24, andS. coelicolorM145.

Results

The high coverage and specificity (detection of three nucleotide differences) of the new microarrays used has highlighted the macroscopic genomic differences between twoS. lividansstrains andS. coelicolor. In a series of case studies we have validated the microarray and have identified subtle changes in genomic structure which occur in the Asp-activating adenylation domains of CDA non-ribosomal peptide synthetase genes which provides evidence of gene shuffling between these domains. We also identify single nucleotide sequence inter-species differences which exist in the actinorhodin biosynthetic gene cluster. As the glyoxylate bypass is non-functional in bothS. lividansstrains due to the absence of the gene encoding isocitrate lyase it is likely that the ethylmalonyl-CoA pathway functions as the alternative mechanism for the assimilation of C2compounds.

Conclusions

This study provides evidence for widespread genetic recombination, rather than it being focussed at 'hotspots', suggesting that the previously proposed 'archipelago model' of genomic differences betweenS. coelicolorandS. lividansis unduly simplistic. The twoS. lividansstrains investigated differ considerably in genetic complement, with TK24 lacking 175 more genes than its wild-type parent when compared toS. coelicolor. Additionally, we confirm the presence ofbldBinS. lividansand deduce thatS. lividans66 and TK24, both deficient in the glyoxylate bypass, possess an alternative metabolic mechanism for the assimilation of C2compounds. Given that streptomycetes generally display high genetic instability it is envisaged that these high-density arrays will find application for rapid assessment of genome content (particularly amplifications/deletions) in mutational studies ofS. coelicolorand related species.
Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments
Authors: Sirota-Madi Alexandra , Olender Tsviya , Helman Yael , Ingham Colin , Brainis Ina , Roth Dalit , Hagi Efrat , Brodsky Leonid , Leshkowitz Dena , Galatenko Vladimir , Nikolaev Vladimir , Mugasimangalam Raja C , Bransburg-Zabary Sharron , Gutnick David L , Lancet Doron , Ben-Jacob Eshel
Published: January 2011

Background

The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium.

Results

The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289× coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes.

Conclusions

These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria.
A molecular inversion probe assay for detecting alternative splicing
Authors: Lin Shengrong , Wang Wenyi , Palm Curtis , Davis Ronald W , Juneau Kara
Published: January 2011

Absract

Background

A sensitive, high-throughput method for monitoring pre-mRNA splicing on a genomic scale is needed to understand the spectrum of alternatively spliced mRNA in human cells.

Results

We adapted Molecular Inversion Probes (MIPs), a padlock-probe based technology, for the multiplexed capture and quantitation of individual splice events in human tissues. Individual MIP capture probes can be quantified using either DNA microarrays or high-throughput sequencing, which permits independent assessment of each spliced junction. Using our methodology we successfully identified 100% of our positive controls and showed that there is a strong correlation between the data from our alternative splicing MIP (asMIP) assay and quantitative PCR.

Conclusion

The asMIP assay provides a sensitive, accurate and multiplexed means for measuring pre-mRNA splicing. Fully optimized, we estimate that the assay could accommodate a throughput of greater than 20,000 splice junctions in a single reaction. This would represent a significant improvement over existing technologies.
miRNeye: a microRNA expression atlas of the mouse eye
Authors: Karali Marianthi , Peluso Ivana , Gennarino Vincenzo A , Bilio Marchesa , Verde Roberta , Lago Giampiero , Dollé Pascal , Banfi Sandro
Published: January 2011

Background

MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution.

Results

In this report, we present the first comprehensive survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them. Next, we performed RNA ISH for over 220 miRNAs, including those showing the highest expression levels by microarray, and generated a high-resolution expression atlas of miRNAs in the developing and adult wild-type mouse eye, which is accessible in the form of a publicly available web database. We found that 122 miRNAs displayed restricted expression domains in the eye at different developmental stages, with the majority of them expressed in one or more cell layers of the neural retina.

Conclusions

This analysis revealed miRNAs with differential expression in ocular tissues and provided a detailed atlas of their tissue-specific distribution during development of the murine eye. The combination of the two approaches offers a valuable resource to decipher the contributions of specific miRNAs and miRNA clusters to the development of distinct ocular structures.
Accounting for multiple comparisons in a genome-wide association study (GWAS)
Authors: Johnson Randall C , Nelson George W , Troyer Jennifer L , Lautenberger James A , Kessing Bailey D , Winkler Cheryl A , O'Brien Stephen J
Published: January 2011

Background

As we enter an era when testing millions of SNPs in a single gene association study will become the standard, consideration of multiple comparisons is an essential part of determining statistical significance. Bonferroni adjustments can be made but are conservative due to the preponderance of linkage disequilibrium (LD) between genetic markers, and permutation testing is not always a viable option. Three major classes of corrections have been proposed to correct the dependent nature of genetic data in Bonferroni adjustments: permutation testing and related alternatives, principal components analysis (PCA), and analysis of blocks of LD across the genome. We consider seven implementations of these commonly used methods using data from 1514 European American participants genotyped for 700,078 SNPs in a GWAS for AIDS.

Results

A Bonferroni correction using the number of LD blocks found by the three algorithms implemented by Haploview resulted in an insufficiently conservative threshold, corresponding to a genome-wide significance level of α = 0.15 - 0.20. We observed a moderate increase in power when using PRESTO, SLIDE, and simpleℳ when compared with traditional Bonferroni methods for population data genotyped on the Affymetrix 6.0 platform in European Americans (α = 0.05 thresholds between 1 × 10-7and 7 × 10-8).

Conclusions

Correcting for the number of LD blocks resulted in an anti-conservative Bonferroni adjustment. SLIDE and simpleℳ are particularly useful when using a statistical test not handled in optimized permutation testing packages, and genome-wide corrected p-values using SLIDE, are much easier to interpret for consumers of GWAS studies.
Analysis of genomic differences among Clostridium botulinum type A1 strains
Authors: Fang Ping-Ke , Raphael Brian H , Maslanka Susan E , Cai Shuowei , Singh Bal Ram
Published: January 2011

Background

Type A1 Clostridium botulinum strains are a group of Gram-positive, spore-forming anaerobic bacteria that produce a genetically, biochemically, and biophysically indistinguishable 150 kD protein that causes botulism. The genomes of three type A1 C. botulinum strains have been sequenced and show a high degree of synteny. The purpose of this study was to characterize differences among these genomes and compare these differentiating features with two additional unsequenced strains used in previous studies.

Results

Several strategies were deployed in this report. First, University of Massachusetts Dartmouth laboratory Hall strain (UMASS strain) neurotoxin gene was amplified by PCR and sequenced; its sequence was aligned with the published ATCC 3502 Sanger Institute Hall strain and Allergan Hall strain neurotoxin gene regions. Sequence alignment showed that there was a synonymous single nucleotide polymorphism (SNP) in the region encoding the heavy chain between Allergan strain and ATCC 3502 and UMASS strains. Second, comparative genomic hybridization (CGH) demonstrated that the UMASS strain and a strain expected to be derived from ATCC 3502 in the Centers for Disease Control and Prevention (CDC) laboratory (ATCC 3502*) differed in gene content compared to the ATCC 3502 genome sequence published by the Sanger Institute. Third, alignment of the three sequenced C. botulinum type A1 strain genomes revealed the presence of four comparable blocks. Strains ATCC 3502 and ATCC 19397 share the same genome organization, while the organization of the blocks in strain Hall were switched. Lastly, PCR was designed to identify UMASS and ATCC 3502* strain genome organizations. The PCR results indicated that UMASS strain belonged to Hall type and ATCC 3502* strain was identical to ATCC 3502 (Sanger Institute) type.

Conclusions

Taken together, C. botulinum type A1 strains including Sanger Institute ATCC 3502, ATCC 3502*, ATCC 19397, Hall, Allergan, and UMASS strains demonstrate differences at the level of the neurotoxin gene sequence, in gene content, and in genome arrangement.
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley
Authors: Chutimanitsakun Yada , Nipper Rick W , Cuesta-Marcos Alfonso , Cistué Luis , Corey Ann , Filichkina Tanya , Johnson Eric A , Hayes Patrick M
Published: January 2011

Background

Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage map construction, employing barley as a model system. Using the published high density EST-based SNP map in the Oregon Wolfe Barley (OWB) mapping population as a reference, we created a RAD map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both maps for detection of quantitative trait loci (QTL).

Results

Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic map was constructed. The assembled RAD-only map consists of 445 markers with an average interval length of 5 cM, while an integrated map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total map lengths are comparable and the order of common markers is identical in both maps. The same large-effect QTL for reproductive fitness traits were detected with both maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley.

Conclusions

We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic maps and association mapping.