Climate change in our backyards: the reshuffling of North America's winter bird communities

Much of the recent changes in North American climate have occurred during the winter months, and as result, overwintering birds represent important sentinels of anthropogenic climate change. While there is mounting evidence that bird populations are responding to a warming climate (e.g., poleward shifts) questions remain as to whether these species‐specific responses are resulting in community‐wide changes. Here, we test the hypothesis that a changing winter climate should favor the formation of winter bird communities dominated by warm‐adapted species. To do this, we quantified changes in community composition using a functional index – the Community Temperature Index (CTI) – which measures the balance between low‐ and high‐temperature dwelling species in a community. Using data from Project FeederWatch, an international citizen science program, we quantified spatiotemporal changes in winter bird communities (n = 38 bird species) across eastern North America and tested the influence of changes in winter minimum temperature over a 22‐year period. We implemented a jackknife analysis to identify those species most influential in driving changes at the community level and the population dynamics (e.g., extinction or colonization) responsible for these community changes. Since 1990, we found that the winter bird community structure has changed with communities increasingly composed of warm‐adapted species. This reshuffling of winter bird communities was strongest in southerly latitudes and driven primarily by local increases in abundance and regional patterns of colonization by southerly birds. CTI tracked patterns of changing winter temperature at different temporal scales ranging from 1 to 35 years. We conclude that a shifting winter climate has provided an opportunity for smaller, southerly distributed species to colonize new regions and promote the formation of unique winter bird assemblages throughout eastern North America.     

Coupling Input‐Output Tables with Macro‐Life Cycle Assessment to Assess Worldwide Impacts of Biofuels Transport Policies

Many countries see biofuels as a replacement to fossil fuels to mitigate climate change. Nevertheless, some concerns remain about the overall benefits of biofuels policies. More comprehensive tools seem required to evaluate indirect effects of biofuel policies. This article proposes a method to evaluate large‐scale biofuel policies that is based on life cycle assessment (LCA), environmental extensions of input‐output (I‐O) tables, and a general equilibrium model. The method enables the assessment of indirect environmental effects of biofuels policies, including land‐use changes (LUCs), in the context of economic and demographic growth. The method is illustrated with a case study involving two scenarios. The first one describes the evolution of the world economy from 2006 to 2020 under business as usual (BAU) conditions (including demographic and dietary preferences changes), and the second integrates biofuel policies in the United States and the European Union (EU). Results show that the biofuel scenario, originally designed to mitigate climate change, results in more greenhouse gas emissions when compared to the BAU scenario. This is mainly due to emissions associated with global LUCs. The case study shows that the method enables a broader consideration for environmental effects of biofuel policies than usual LCA: Global economic variations calculated by a general equilibrium economic model and LUC emissions can be evaluated. More work is needed, however, to include new biofuel production technologies and reduce the uncertainty of the method.     

Cytology is useful in breast screening: results and long-term follow-up of the Singapore Breast Screening Pilot Project

OBJECTIVE: The Singapore Breast Screening Pilot Project (SBSPP) was embarked upon (1994-1997) to determine if mammography was useful in early breast cancer detection among Asian women. PATIENTS AND MEASUREMENTS: Of 28 231 women screened, fine needle aspiration cytology (FNAC) was performed in 232 individuals as part of the triple assessment. RESULTS: Absolute and complete sensitivities for the diagnosis of carcinoma were 46.7% and 82.2%, respectively, based on the results of FNAC. Specificity was 63.3%. The inadequate rate was 31%. Five women who were considered cancer-free on triple assessment and, in two cases open diagnostic biopsy during the SBSPP, subsequently developed breast cancer after a median follow-up of 6 years. CONCLUSION: Although our FNAC results compared relatively well with international standards, they reflect a small cohort, and may face additional difficulties in a larger programme.     

Synthetic genome engineering forging new frontiers for wine yeast

Over the past 15 years, the seismic shifts caused by the convergence of biomolecular, chemical, physical, mathematical, and computational sciences alongside cutting-edge developments in information technology and engineering have erupted into a new field of scientific endeavor dubbed Synthetic Biology. Recent rapid advances in high-throughput DNA sequencing and DNA synthesis techniques are enabling the design and construction of new biological parts (genes), devices (gene networks) and modules (biosynthetic pathways), and the redesign of biological systems (cells and organisms) for useful purposes. In 2014, the budding yeast Saccharomyces cerevisiae became the first eukaryotic cell to be equipped with a fully functional synthetic chromosome. This was achieved following the synthesis of the first viral (poliovirus in 2002 and bacteriophage Phi-X174 in 2003) and bacterial (Mycoplasma genitalium in 2008 and Mycoplasma mycoides in 2010) genomes, and less than two decades after revealing the full genome sequence of a laboratory (S288c in 1996) and wine (AWRI1631 in 2008) yeast strain. A large international project – the Synthetic Yeast Genome (Sc2.0) Project – is now underway to synthesize all 16 chromosomes (～12?Mb carrying ～6000 genes) of the sequenced S288c laboratory strain by 2018. If successful, S. cerevisiae will become the first eukaryote to cross the horizon of in silico design of complex cells through de novo synthesis, reshuffling, and editing of genomes. In the meantime, yeasts are being used as cell factories for the semi-synthetic production of high-value compounds, such as the potent antimalarial artemisinin, and food ingredients, such as resveratrol, vanillin, stevia, nootkatone, and saffron. As a continuum of previously genetically engineered industrially important yeast strains, precision genome engineering is bound to also impact the study and development of wine yeast strains supercharged with synthetic DNA. The first taste of what the future holds is the de novo production of the raspberry ketone aroma compound, 4-[4-hydroxyphenyl]butan-2-one, in a wine yeast strain (AWRI1631), which was recently achieved via metabolic pathway engineering and synthetic enzyme fusion. A peek over the horizon is revealing that the future of “Wine Yeast 2.0” is already here. Therefore, this article seeks to help prepare the wine industry – an industry rich in history and tradition on the one hand, and innovation on the other – for the inevitable intersection of the ancient art practiced by winemakers and the inventive science of pioneering “synthetic genomicists”. It would be prudent to proactively engage all stakeholders – researchers, industry practitioners, policymakers, regulators, commentators, and consumers – in a meaningful dialog about the potential challenges and opportunities emanating from Synthetic Biology. To capitalize on the new vistas of synthetic yeast genomics, this paper presents wine yeast research in a fresh context, raises important questions and proposes new directions.     

The Cultural Relics Distribution Characteristics Along the Canal Line and Appraisal of its Influence by the Middle Route Project for Water Transferring from South to North China

Assessments of the impacts of environmental hazards on ecological systems and human health have become a subject of ever-increasing importance. In this work, we extend current ecological hazard evaluation to the problem of protecting cultural relics from hazards attributable to the presence of a large-scale canal system being planned in China. The development and utilization of water resources must be closely combined with the preservation of cultural relics. The Middle Route Project for Water Transfer from South to North China (MRWT) is a current example. In this paper, the engineering background of this project is briefly introduced. The distribution of cultural relics related to it is also summarized in terms of different geographical divisions. An influence index E = f(L, δh, k, I, v, s) is introduced to measure the comprehensive effect of the canal on cultural relics. Because this function is really established at the preconstruction stage, it is treated by use of fuzzy mathematics. Each cultural relic has its own E value. Cultural relics with E values greater than 0.75 should be paid high attention, while those with E less than 0.5 may generally be ignored. What must be preserved through use of engineering measures are cultural relics with E values greater than 0.9. As to those cultural relics with E ranging between 0.5 and 0.75, whether they should be preserved with engineering controls depends upon practical circumstances specific to each relic.     

Drawing inferences about the coancestry coefficient

The coancestry coefficient, also known as the population structure parameter, is of great interest in population genetics. It can be thought of as the intraclass correlation of pairs of alleles within populations and it can serve as a measure of genetic distance between populations. For a general class of evolutionary models it determines the distribution of allele frequencies among populations. Under more restrictive models it can be regarded as the probability of identity by descent of any pair of alleles at a locus within a random mating population. In this paper we review estimation procedures that use the method of moments or are maximum likelihood under the assumption of normally distributed allele frequencies. We then consider the problem of testing hypotheses about this parameter. In addition to parametric and non-parametric bootstrap tests we present an asymptotically-distributed chi-square test. This test reduces to the contingency-table test for equal sample sizes across populations. Our new test appears to be more powerful than previous tests, especially for loci with multiple alleles. We apply our methods to HapMap SNP data to confirm that the coancestry coefficient for humans is strictly positive.     

Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes

Transmission distortion （TD） is a significant departure from Mendelian predictions of genes or chromosomes to offspring. While many biological processes have been implicated, there is still much to be understood about TD in humans. Here we present our findings from a genome-wide scan for evidence of TD using haplotype data of 60 trio families from the International HapMap Project. Fisher＇s exact test was applied to assess the extent of TD in 629,958 SNPs across the autosomes. Based on the empirical distribution of PFisher and further permutation tests, we identified 1,205 outlier loci and 224 candidate genes with TD. Using the PANTHER gene ontology database, we found 19 categories of biological processes with an enrichment of candidate genes. In particular, the “protein phosphorylation” category contained the largest number of candidates in both HapMap samples. Further analysis uncovered an intriguing non-synonymous change in PPPIR12B, a gene related to protein phosphorylation, which appears to influence the allele transmission from male parents in the YRI （Yoruba from Ibadan, Nigeria） population. Our findings also indicate an ethnicity-related property of TD signatures in HapMap samples and provide new clues for our understanding of TD in humans.     

Nuclear Energy in the Service of Biomedicine: The U.S. Atomic Energy Commission’s Radioisotope Program, 1946–1950

The widespread adoption of radioisotopes as tools in biomedical research and therapy became one of the major consequences of the “physicists’ war” for postwar life science. Scientists in the Manhattan Project, as part of their efforts to advocate for civilian uses of atomic energy after the war, proposed using infrastructure from the wartime bomb project to develop a government-run radioisotope distribution program. After the Atomic Energy Bill was passed and before the Atomic Energy Commission (AEC) was formally established, the Manhattan Project began shipping isotopes from Oak Ridge. Scientists and physicians put these reactor-produced isotopes to many of the same uses that had been pioneered with cyclotron-generated radioisotopes in the 1930s and early 1940s. The majority of early AEC shipments were radioiodine and radiophosphorus, employed to evaluate thyroid function, diagnose medical disorders, and irradiate tumors. Both researchers and politicians lauded radioisotopes publicly for their potential in curing diseases, particularly cancer. However, isotopes proved less successful than anticipated in treating cancer and more successful in medical diagnostics. On the research side, reactor-generated radioisotopes equipped biologists with new tools to trace molecular transformations from metabolic pathways to ecosystems. The U.S. government’s production and promotion of isotopes stimulated their consumption by scientists and physicians (both domestic and abroad), such that in the postwar period isotopes became routine elements of laboratory and clinical use. In the early postwar years, radioisotopes signified the government’s commitment to harness the␣atom for peace, particularly through contributions to biology, medicine, and agriculture.