Measure of similarity of amino acids or how to obtain the genetic code table from “nothing”

AbstractNature selects the genetic code table to have a minimum risk caused by a point mutation (a misprint in a text of nucleotide sequence). The purpose of this paper is to accurately formulate and verify this hypothesis. The “nothing” is 1.(1) the code table is a map: codon → amino acid;2.(2) the structure of amino acids in 3D-space is known

Net benefits of smallholder dairy cattle farms in Senegal can be significantly increased through the use of better dairy cattle breeds and improved management practices

Senegal, located in West Africa, is an example of a low-to middle-income country where the govern-ment has prioritized improving livestock production self-sufficiency, with a strong focus on dairy. Among other initiatives, the use of exotic dairy cattle has been promoted, despite no evidence for the potential liveli-hood benefits (or otherwise) to smallholder farmers on adopting the new genetics. The current work fills this evidence gap by performing a farm-level economic study comparing the keeping of different breed and cross-breed types of dairy cattle under different management levels. Data for the study were obtained by monitoring 220 smallholder dairy cattle farms, with a combined cattle population of about 3,000 animals, over an almost 2-yr period. Findings of the study suggest that the most net-beneficial and cost-beneficial dairy cattle enterprise that could be used by the smallholder farmers was to keep crossbred indigenous zebu by exotic Bos taurus animals under management standards that are consid-ered good compared with local standards. This dairy enterprise type was 7.4-fold more net beneficial and had a 1.4-fold more favorable cost-benefit ratio than the traditional system of keeping indigenous zebu animals under poor (low-input) management. Interestingly, the keeping of (near) pure B. taurus dairy cattle resulted in the highest milk yields and thus benefit from milk, but was not the most net beneficial due to the high costs of keeping these animals, particularly in terms of feed. We also found that increasing the managementlevel of any of the breed or cross-breed types under consideration, including the indigenous zebu animals, resulted in an increased net benefit of 2.2-to 2.9-fold. Results of this economic analysis are discussed as part of a broader trade-off analysis, resulting in recommendations to strengthen the Senegal dairy sector. The combined intervention of improved dairy cattle genetics and management is considered a promising intervention to improve livelihoods of the rural poor as well as livestock production self-sufficiency for Senegal; some other system constraints are addressed.Peer reviewe

Growth responses of Ailanthus altissima seedlings to SO2

Growth of Ailanthus altissima (Mill.) Swingle seedlings exposed to various levels of sulphur dioxide (SO2) was observed. Exposure for 1 or 2 weeks at 260 [mu]gm-3 (0[middle dot]1 ppm) or 520 [mu]g m-3 (0[middle dot]2 ppm) of SO2 significantly (p 2 concentration.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24357/1/0000626.pd

Importance of natural land cover for plant species’ conservation: a nationwide study in The Netherlands

Environmental Biolog

Quantifying heterogeneous responses of fish community size structure using novel combined statistical techniques

To understand changes in ecosystems, the appropriate scale at which to study them must be determined. Large marine ecosystems (LMEs) cover thousands of square kilometres and are a useful classification scheme for ecosystem monitoring and assessment. However, averaging across LMEs may obscure intricate dynamics within. The purpose of this study is to mathematically determine local and regional patterns of ecological change within an LME using empirical orthogonal functions (EOFs). After using EOFs to define regions with distinct patterns of change, a statistical model originating from control theory is applied (Nonlinear AutoRegressive Moving Average with eXogenous input – NARMAX) to assess potential drivers of change within these regions. We have selected spatial data sets (0.5° latitude × 1°longitude) of fish abundance from North Sea fisheries research surveys (spanning 1980–2008) as well as of temperature, oxygen, net primary production and a fishing pressure proxy, to which we apply the EOF and NARMAX methods. Two regions showed significant changes since 1980: the central North Sea displayed a decrease in community size structure which the NARMAX model suggested was linked to changes in fishing; and the Norwegian trench region displayed an increase in community size structure which, as indicated by NARMAX results, was primarily linked to changes in sea-bottom temperature. These regions were compared to an area of no change along the eastern Scottish coast where the model determined the community size structure was most strongly associated to net primary production. This study highlights the multifaceted effects of environmental change and fishing pressures in different regions of the North Sea. Furthermore, by highlighting this spatial heterogeneity in community size structure change, important local spatial dynamics are often overlooked when the North Sea is considered as a broad-scale, homogeneous ecosystem (as normally is the case within the political Marine Strategy Framework Directive)

Nonequilibrium probe of paired electron pockets in the underdoped cuprates

We propose an experimental method that can be used generally to test whether the cuprate pseudogap involves precursor pairing that acts to gap out the Fermi surface. The proposal involves angular-resolved photoemission spectroscopy (ARPES) performed in the presence of a transport current driven through the sample. We illustrate this proposal with a specific model of the pseudogap that contains a phase-incoherent paired electron and unpaired hole Fermi surfaces. We show that even a weak current tilts the paired band and reveals parts of the previously gapped electron Fermi surface in ARPES if the binding energy is smaller but close to the pseudogap. Stronger currents can also reveal the Fermi surface through direct suppression of pairing. The proposed experiment is sufficiently general such that it can be used to reveal putative Fermi surfaces that have been reconstructed from other types of periodic order and are gapped out due to pairing. The observation of the predicted phenomena should help resolve the central question about the existence of pairs in the enigmatic pseudogap regime.Comment: 5 pages, 3 figures (published version

Northwest Pacific ice-rafted debris at 38°N reveals episodic ice-sheet change in late Quaternary Northeast Siberia

The ice-rafted-debris (IRD) record of the open Northwest Pacific points towards the existence of substantial glacial ice on the Northeast Siberian coast during the late Quaternary. However, the scale and timing of glaciation and de-glaciation remains controversial due to the dearth of both onshore and offshore records. Existing IRD data suggests at least one event of dynamic and abrupt change during mid-late Marine Isotope Stage (MIS 3) which mimics the massive collapse of the Laurentide ice sheet during Heinrich Events. It is uncertain whether other events of this magnitude occurred during the late Quaternary. Here we present a ∼160,000 yr IRD series, planktic foraminiferal counts and an age model, derived from a benthic δ18O curve, radiocarbon dates and tephrochronology, from core ODP 1207A (37.79°N, 162.75°E), revealing the presence of low but episodic flux of IRD. We conclude that glacial Northwest Pacific icebergs spread further south than previously thought, with icebergs emanating from Northeast Siberia being transported to the transition region between the subpolar and subtropical waters, south of the subarctic front during at least the Quaternary's last two glacial periods. The episodic nature of the 1207A IRD record during the last glacial, combined with coupled climate-iceberg modelling, suggests occasional times of much enhanced ice flux from the Kamchatka-Koryak coast, with other potential sources on the Sea of Okhotsk coast. These findings support the hypothesis of a variable but extensive ice mass during the last glacial over Northeast Siberia, particularly early in the last glacial period, behaving independently of North American and Eurasian ice masses. In strong contrast, IRD was absent during much of the penultimate glacial Marine Isotope Stage (MIS) 6 suggesting the possibility of very different Northeast Siberian ice coverage between the last two glacial periods

Mutations of the BRAF gene in human cancer

Cancers arise owing to the accumulation of mutations in critical genes that alter normal programmes of cell proliferation, differentiation and death. As the first stage of a systematic genome-wide screen for these genes, we have prioritized for analysis signalling pathways in which at least one gene is mutated in human cancer. The RAS RAF MEK ERK MAP kinase pathway mediates cellular responses to growth signals. RAS is mutated to an oncogenic form in about 15% of human cancer. The three RAF genes code for cytoplasmic serine/threonine kinases that are regulated by binding RAS. Here we report BRAF somatic missense mutations in 66% of malignant melanomas and at lower frequency in a wide range of human cancers. All mutations are within the kinase domain, with a single substitution (V599E) accounting for 80%. Mutated BRAF proteins have elevated kinase activity and are transforming in NIH3T3 cells. Furthermore, RAS function is not required for the growth of cancer cell lines with the V599E mutation. As BRAF is a serine/threonine kinase that is commonly activated by somatic point mutation in human cancer, it may provide new therapeutic opportunities in malignant melanoma

Continuous variable entanglement and quantum state teleportation between optical and macroscopic vibrational modes through radiation pressure

We study an isolated, perfectly reflecting, mirror illuminated by an intense laser pulse. We show that the resulting radiation pressure efficiently entangles a mirror vibrational mode with the two reflected optical sideband modes of the incident carrier beam. The entanglement of the resulting three-mode state is studied in detail and it is shown to be robust against the mirror mode temperature. We then show how this continuous variable entanglement can be profitably used to teleport an unknown quantum state of an optical mode onto the vibrational mode of the mirror.Comment: 18 pages, 10 figure