Secondary structure of Ac-Alan_n-LysH+^+ polyalanine peptides (nn=5,10,15) in vacuo: Helical or not?

The polyalanine-based peptide series Ac-Ala_n-LysH+ (n=5-20) is a prime example that a secondary structure motif which is well-known from the solution phase (here: helices) can be formed in vacuo. We here revisit this conclusion for n=5,10,15, using density-functional theory (van der Waals corrected generalized gradient approximation), and gas-phase infrared vibrational spectroscopy. For the longer molecules (n=10,15) \alpha-helical models provide good qualitative agreement (theory vs. experiment) already in the harmonic approximation. For n=5, the lowest energy conformer is not a simple helix, but competes closely with \alpha-helical motifs at 300K. Close agreement between infrared spectra from experiment and ab initio molecular dynamics (including anharmonic effects) supports our findings.Comment: 4 pages, 4 figures, Submitted to JPC Letter

Radically Rethinking Agriculture for the 21st Century

Population growth, arable land and fresh water limits, and climate change have profound implications for the ability of agriculture to meet this century’s demands for food, feed, fiber, and fuel while reducing the environmental impact of their production. Success depends on the acceptance and use of contemporary molecular techniques, as well as the increasing development of farming systems that use saline water and integrate nutrient flows

Plasma cholesterol levels and brain development in preterm newborns.

BackgroundTo assess whether postnatal plasma cholesterol levels are associated with microstructural and macrostructural regional brain development in preterm newborns.MethodsSixty preterm newborns (born 24-32 weeks gestational age) were assessed using MRI studies soon after birth and again at term-equivalent age. Blood samples were obtained within 7 days of each MRI scan to analyze for plasma cholesterol and lathosterol (a marker of endogenous cholesterol synthesis) levels. Outcomes were assessed at 3 years using the Bayley Scales of Infant Development, Third Edition.ResultsEarly plasma lathosterol levels were associated with increased axial and radial diffusivities and increased volume of the subcortical white matter. Early plasma cholesterol levels were associated with increased volume of the cerebellum. Early plasma lathosterol levels were associated with a 2-point decrease in motor scores at 3 years.ConclusionsHigher early endogenous cholesterol synthesis is associated with worse microstructural measures and larger volumes in the subcortical white matter that may signify regional edema and worse motor outcomes. Higher early cholesterol is associated with improved cerebellar volumes. Further work is needed to better understand how the balance of cholesterol supply and endogenous synthesis impacts preterm brain development, especially if these may be modifiable factors to improve outcomes

Breeding season concerns and response to forest management: can forest management produce more breeding birds?.

Cerulean Warblers (Setophaga cerulea), one of the fastest declining avian species in North America, are associated with heterogeneous canopies in mature hardwood forests. However, the age of most second and third-growth forests in eastern North American is not sufficient for natural tree mortality to maintain structurally diverse canopies. Previous research suggests that forest management through timber harvest also may create conditions suitable as Cerulean Warbler breeding habitat. We conducted a multistate study that examined Cerulean Warbler response to varying degrees of canopy disturbance created by operational timber harvest. Specifically, 3 harvest treatments and an un-harvested reference plot were replicated on 7 study areas in 4 Appalachian states in 2005-2010. We compared pre-harvest and four years post-harvest demographic response of Cerulean Warblers. Over all study areas, Cerulean Warbler territory density remained stable in un-harvested reference plots and increased significantly the first year post-harvest on intermediate harvest plots. By year 3 post-harvest, territory density remained significantly greater for intermediate harvest than reference plots, and marginally greater for light and heavy harvests than reference plots. However, un-harvested reference plots had greater nest survival than most harvest treatments. The one exception was nest survival between reference plots and the intermediate harvest on the northern study areas did not differ. Our results indicate that intermediate harvests likely benefit Cerulean Warblers in some portions of the species’ breeding range. However, additional research is needed to better examine fitness consequences of timber harvests and to estimate population-level implications. In particular, does the greater number of nesting individuals, particularly in intermediate harvests, compensate for lower nesting success? Until researchers provide such insight, we recommend management decisions be based on local conditions, particularly in forests where Cerulean Warbler populations are high

Rare coding SNP in DZIP1 gene associated with late-onset sporadic Parkinson's disease

We present the first application of the hypothesis-rich mathematical theory to genome-wide association data. The Hamza et al. late-onset sporadic Parkinson's disease genome-wide association study dataset was analyzed. We found a rare, coding, non-synonymous SNP variant in the gene DZIP1 that confers increased susceptibility to Parkinson's disease. The association of DZIP1 with Parkinson's disease is consistent with a Parkinson's disease stem-cell ageing theory.Comment: 14 page

A transcriptome anatomy of human colorectal cancers

BACKGROUND: Accumulating databases in human genome research have enabled integrated genome-wide study on complicated diseases such as cancers. A practical approach is to mine a global transcriptome profile of disease from public database. New concepts of these diseases might emerge by landscaping this profile. METHODS: In this study, we clustered human colorectal normal mucosa (N), inflammatory bowel disease (IBD), adenoma (A) and cancer (T) related expression sequence tags (EST) into UniGenes via an in-house GetUni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM). Additionally, we downloaded UniGene based cDNA libraries of colon and analyzed them by Xprofiler to cross validate the efficiency of GetUni. Semi-quantitative RT-PCR was used to validate the expression of β-catenin and. 7 novel genes in colorectal cancers. RESULTS: The efficiency of GetUni was successfully validated by Xprofiler and RT-PCR. Genes in library N, IBD and A were all found in library T. A total of 14,879 genes were identified with 2,355 of them having at least 2 transcripts. Differences in gene enrichment among these libraries were statistically significant in 50 signal transduction pathways and Pfam protein domains by GOTM analysis P < 0.01 Hypergeometric Test). Genes in two metabolic pathways, ribosome and glycolysis, were more enriched in the expression profiles of A and IBD than in N and T. Seven transmembrane receptor superfamily genes were typically abundant in cancers. CONCLUSION: Colorectal cancers are genetically heterogeneous. Transcription variants are common in them. Aberrations of ribosome and glycolysis pathway might be early indicators of precursor lesions in colon cancers. The electronic gene expression profile could be used to highlight the integral molecular events in colorectal cancers

Financing U.S. Graduate Medical Education: A Policy Position Paper of the Alliance for Academic Internal Medicine and the American College of Physicians

In this position paper, the Alliance for Academic Internal Medicine and the American College of Physicians examine the state of graduate medical education (GME) financing in the United States and recent proposals to reform GME funding. They make a series of recommendations to reform the current funding system to better align GME with the needs of the nation's health care workforce. These recommendations include using Medicare GME funds to meet policy goals and to ensure an adequate supply of physicians, a proper specialty mix, and appropriate training sites; spreading the costs of financing GME across the health care system; evaluating the true cost of training a resident and establishing a single per-resident amount; increasing transparency and innovation; and ensuring that primary care residents receive training in well-functioning ambulatory settings that are financially supported for their training roles

(Same)-sex in the City: urbanisation and LGBTI rights expansion

Despite the notable successes of lesbian, gay, bisexual, transgender and intersex (LGBTI) activism in the region, individual European countries have varied considerably in the extent and speed with which they have adopted legislation to recognise the rights of their LGBTI citizens. Scholars have often turned to modernisation theory to explain these variable outcomes and argue that high levels of national wealth are an important factor in the success of LGBTI movements. Although the correlation between modernity, economic development and tolerance of LGBTI lifestyles is often treated as a truism in the literature, scholars have paid less attention to the precise mechanisms by which the complex processes associated with modernisation facilitate policy change. Drawing on the classic works of both modernisation theory and gay and lesbian history, we examine a less explored route by which modernisation leads to the expansion of LGBTI rights. Specifically, we posit that urbanisation facilitates the adoption of rights policies by strengthening LGBTI movements and enhancing their political effectiveness. To test this proposition, we use event history analysis and an original dataset that contains measures for institutional, cultural, economic and movement variables, as well as measures of urbanisation in 44 European countries between 1980 and 2015. Our findings support the contention that urbanisation has a strong effect on the formation of LGBTI movement organisations as well as the speed with which European states adopt both same‐sex union and anti‐discrimination legislation. The relationship between urbanisation and rights expansion persists even after controlling for a country's level of wealth, religious adherence and the influence of European institutions and norms