Increased area of a highly suitable host crop increases herbivore pressure in intensified agricultural landscapes

Landscape simplification associated with agricultural intensification has important effects on economically important arthropods. The declining cover of natural and semi-natural habitats, in particular, has been shown to reduce natural-enemy attack of crop pests, but also in some cases reduced crop colonization by such pests. In this study, we examined the influence of changes in two elements of landscape composition, natural grassland cover and cover of a highly suitable crop host, on infestation by a generalist insect pest in wheat, and parasitism of this pest by its dominant natural enemies. Surprisingly, we found no significant influences of increasing natural grassland habitat, at either local or landscape scales, on infestation by the wheat stem sawfly, Cephus cinctus, or parasitism of this pest by the native parasitoid wasps, Bracon cephiand Bracon lissogaster. In contrast, we found significant increases in levels of C. cinctus infestation with increasing wheat cover at the landscape scale. This pattern was consistent across six study regions spanning three states in the northern Great Plains of North America, despite large differences in cropping systems and pest population densities across regions. Regional variation in pest infestation was best explained by long-term averages in precipitation, with higher C. cinctus infestation rates found in drier regions. Results suggest that landscape-mediated variation in pest pressure in this system is better explained by a direct response of pest insects to increasing cover of a highly suitable crop rather than an indirect response via reductions in natural enemies as natural habitat declines. The implication is that habitat diversification at the landscape scale could play a role in suppressing agricultural pest populations via reductions in area of suitable crop hosts

Building new twenty-first century medical school libraries from the ground up: challenges, experiences, and lessons learned

The twenty-first century library at a newly opened medical school often differs from those at traditional medical schools. One obvious difference is that the new medical school library tends to be a born-digital library, meaning that the library collection is almost exclusively digital. However, the unique issues related to building a library at a new medical school are not limited to online collections. A unique start-up culture is prevalent, of which newly appointed directors and other library and medical school leaders need to be aware. This special paper provides an overview of best practices experienced in building new medical school libraries from the ground up. The focus is on the key areas faced in a start-up environment, such as budgeting for online collections, space planning, staffing, medical informatics instruction, and library-specific accreditation issues for both allopathic and osteopathic institutions

Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD): Exome sequencing of trios, monozygotic twins and tumours

BACKGROUND: Rapid-onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD) is thought to be a genetic disease caused by de novo mutations, though causative mutations have yet to be identified. We searched for de novo coding mutations among a carefully-diagnosed and clinically homogeneous cohort of 35 ROHHAD patients. METHODS: We sequenced the exomes of seven ROHHAD trios, plus tumours from four of these patients and the unaffected monozygotic (MZ) twin of one (discovery cohort), to identify constitutional and somatic de novo sequence variants. We further analyzed this exome data to search for candidate genes under autosomal dominant and recessive models, and to identify structural variations. Candidate genes were tested by exome or Sanger sequencing in a replication cohort of 28 ROHHAD singletons. RESULTS: The analysis of the trio-based exomes found 13 de novo variants. However, no two patients had de novo variants in the same gene, and additional patient exomes and mutation analysis in the replication cohort did not provide strong genetic evidence to implicate any of these sequence variants in ROHHAD. Somatic comparisons revealed no coding differences between any blood and tumour samples, or between the two discordant MZ twins. Neither autosomal dominant nor recessive analysis yielded candidate genes for ROHHAD, and we did not identify any potentially causative structural variations. CONCLUSIONS: Clinical exome sequencing is highly unlikely to be a useful diagnostic test in patients with true ROHHAD. As ROHHAD has a high risk for fatality if not properly managed, it remains imperative to expand the search for non-exomic genetic risk factors, as well as to investigate other possible mechanisms of disease. In so doing, we will be able to confirm objectively the ROHHAD diagnosis and to contribute to our understanding of obesity, respiratory control, hypothalamic function, and autonomic regulation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13023-015-0314-x) contains supplementary material, which is available to authorized users

Guidelines for Genome-Scale Analysis of Biological Rhythms

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Guidelines for Genome-Scale Analysis of Biological Rhythms

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding ‘big data’ that is conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them

An Examination of Discrimination Under the Pennsylvania Civil Service Act

This article, which is written for the general practitioner, examines the 1963 amendment to the Civil Service Act, which amendment prohibits discrimination. The amendment is analyzed in detail and the advantages and disadvantages of construing it broadly are considered. Traditional forms of discrimination are reviewed, but in addition, certain non-traditional forms of discrimination which have evolved in civil service law because of employees\u27 restricted appeal rights are also discussed. The article also examines constitutional questions which have arisen under the amendment, and other forums in which aggrieved individuals may litigate their claims