Provisional classifications v standard avian sequences: heuristics and communication in ornithology

The past decades have been exciting ones for ornithologists interested in avian macrosystematics with many new ideas being proposed for consideration and further study. But this excitement should not blind ornithologists to the important distinction between the provisional classifications proposed by specialists in macrosystematics, no matter how convincing they may appear at first glance, and the standard sequence needed to maintain optimal communication among all students of avian biologists. An excellent standard sequence for Recent birds exists in Peters' Check-list . We urge that all ornithologists, authors and editors use this sequence until the time arrives, as it undoubtedly will, when enough is known about avian relationships to permit agreement on a new and better standard sequence.     

Reconstructing Earth's Past Climates: The Hidden Secrets of Pollen

Palynology is the study of fossil pollen and spores, and these tiny grains can provide fundamental information about past climates on Earth. Among their many unique and useful properties, pollen and spores are composed of some of the most chemically resistant organic compounds found in nature. They are also produced in vast quantities and are unique to the specific plant from which they originate. All these features make them ideal to reconstruct past climates from both recent history as well as from the ancient past. The purpose of this activity is to get students familiar with palynology and how scientists study climate change. It is based on real palynological data acquired from Antarctic cores obtained recently from the ANDRILL and SHALDRIL drilling campaigns. In order for students to understand this research and its importance, they will separate and identify pollen and spores from a simulated core sample in which different species of plants are represented as different colors of glitter. Students will compare the types and abundance of pollen and spores found in each layer of the core sample and research the climate preferences of the types of plants recovered in order to reconstruct the past climates of Antarctica.     

The rising level of medical student debt: potential risk for a national default

At the turn of the 20th century, mostly as a result of the Flexner report, medical education changed dramatically by establishing a scientific basis for the study of medicine within the institutions of the major universities. There have been major and dramatic changes in medicine during the past 80 years that have improved medical education in the United States, but these changes have also placed major economic strains on students who have educational debts. If medicine is a social responsibility to the public, then the public should share the responsibility of identifying and supporting new approaches to funding and financially managing the teaching of future physicians. There is no universal solution because there are various approaches institutions may take to structure these financial responsibilities. This article describes trends in medical student educational debt, identifies the financial needs of medical students, and proposes ways of addressing those needs to avert a possible national financial crisis among medical students. We must invest in medical students because they will be the leaders we need to help care for our society and our own families in the next century.     

Studies on the molecular evolution of the Crocodylia: footprints in the sands of time

A reasonably large number of studies focusing on the molecular evolution of crocodilians have been completed during the past 100 years. Proteins were initially studied before DNA was known to carry the genetic information of cells and organisms, and were subsequently studied to infer changes at the DNA level. More recently, studies on the DNA itself have been completed. We have had the pleasure of taking part in or facilitating many studies conducted over the past 50 years, especially several of the earliest studies done using newly developed molecular techniques. We provide a review of the molecular genetic studies on crocodilians, summarizing the findings of these studies as well as the context in which they were undertaken. This review is a personal look at the history of molecular studies on the evolutionary biology of crocodilians. Our excuse for this focus is that our professors, our students and we have had the opportunity to be among the first to apply many new techniques to studies of crocodilians since 1950, when one of us (HCD) was a graduate student of Roland Coulson and Tom Hernandez. Although we will review much of the material in this subject area, we do not claim that it is complete. Instead, we focus our presentation on work in which we have participated or with which we are particularly familiar. We especially focus on materials relevant to the research presented at the 2(nd) International Crocodilian DNA Workshop, 7-9 November, 2001, at the San Diego Zoo. Thus, the following review also stands as a tribute to our mentors, students, and colleagues.     

Gender and the Publication Output of Graduate Students: A Case Study

We examine gender differences among the six PhD student cohorts 2004–2009 at the California Institute of Technology using a new dataset that includes information on trainees and their advisors and enables us to construct detailed measures of teams at the advisor level. We focus on the relationship between graduate student publications and: (1) their gender; (2) the gender of the advisor, (3) the gender pairing between the advisor and the student and (4) the gender composition of the team. We find that female graduate students co-author on average 8.5% fewer papers than men; that students writing with female advisors publish 7.7% more. Of particular note is that gender pairing matters: male students working with female advisors publish 10.0% more than male students working with male advisors; women students working with male advisors publish 8.5% less. There is no difference between the publishing patterns of male students working with male advisors and female students working with female advisors. The results persist and are magnified when we focus on the quality of the published articles, as measured by average Impact Factor, instead of number of articles. We find no evidence that the number of publications relates to the gender composition of the team. Although the gender effects are reasonably modest, past research on processes of positive feedback and cumulative advantage suggest that the difference will grow, not shrink, over the careers of these recent cohorts.     

Biological physics in México

Biological and physical sciences possess a long-standing tradition of cooperativity as separate but related subfields of science. For some time, this cooperativity has been limited by their obvious differences in methods and views. Biological physics has recently experienced a kind of revival (or better a rebirth) due to the growth of molecular research on animate matter. New avenues for research have been opened for both theoretical and experimental physicists. Nevertheless, in order to better travel for such paths, the contemporary biological physicist should be armed with a set of specialized tools and methods but also with a new attitude toward multidisciplinarity. In this review article, we intend to somehow summarize what has been done in the past (in particular, as an example we will take a closer look at the Mexican case), to show some examples of fruitful investigations in the biological physics area and also to set a proposal of new curricula for physics students and professionals interested in applying their science to get a better understanding of the physical basis of biological function.     

Causing Physical Change to Create Art

The presentation involves students in a hands-on analysis of artifacts to create a time line of their local area's past societies. This exercise is more of a unit rather than a one-time activity. Procedures, ideas, and background for developing your own unit are presented in this article. The purpose of this unit is to engage students in applying the scientific method to archaeological research. Students will gain experience in designing and conducting their own investigations.     

Rodent models of genetic disease

The genetic study of rats and mice using natural variants, natural mutations, chemical or radiation induced mutations, engineered mutations and conditional engineered mutations has provided the tools for investigating the genetics of disease. The completion of the mouse genomic sequence and progress towards sequencing the rat genome in the past year will enable the molecular identification of quantitative trait loci and induced mutations. Sequence-based single nucleotide polymorphism discovery and a greater understanding of the haplotype structure of inbred strains is revitalising quantitative trait locus mapping and there are now plans for an ambitious eight-way recombinant inbred cross and renewed interest in existing resources such as heterogeneous stocks. In the past year there have been refinements to ENU mutagenesis approaches including balancer chromosomes and a new gene-driven approach.     

讨论课教学模式在生物化学教学中的优化

讨论课是在教师指导下以学生活动为主的教学形式,是第四军医大学生物化学与分子生物学教学的重要组成部分。近年来,适应我校的模块式教学改革需求,我们在以往的实践基础上,对生物化学讨论课的组织实施进行了系统优化,建立了科学合理的衡量标准和考核方式,实行及时有效的教学效果评估与反馈,实现了全面培养与提高学员的综合素质与能力,并充分促进了教学相长。因此,讨论课作为一种课堂教学新模式,是培养学员思维能力和综合素质、提高教学效果的有效方法和手段,值得进一步完善和推广。     

基于高性能服务器及网格技术的生物科研服务平台研究

为了解决生物科学方面的研究人员在使用生物研究软件工具中存在的“不知道、选不出、难学习和用不起”等问题,同时也为了能为生物类院校的师生提供教学辅助,利用网格技术在高性能服务器上,建立了一款服务于生物研究和教学的网上生物科研服务平台（Biological study service platform,BSP）。该平台包含“工具大全、工具论坛和web工作台”等三部分,拟分别从“找,学,用”三个方面彻底解决生物研究人员在使用生物研究软件工具中存在的问题,同时也为生物类的教师和学生提供了教与学平台。访问地址如下：http：//218．57．145．30：9999／biosp／。此外,该研究小组还将不断地更新和改进该平台,开发更多的自主应用软件,更好地服务生物科研工作。     

Another Look at the Medical “Generation Gap”—Second Triennial Survey of Attitudes of Medical Students and Recent Graduates

A 1969 survey of attitudes held by medical students and recent graduates was repeated in 1972, using the same samples of respondents and adding a new freshman group. Findings from both surveys showed that a “generation gap” existed on many issues.Furthermore, a comparison of the two studies suggested that two kinds of attitude change are occurring simultaneously. On some issues, the next generation of physicians will probably continue to differ from their predecessors. Perhaps the primary thread woven through this cluster of attitudes is that today''s medical students and young physicians perceive themselves as members of a larger structure for providing health care.However, many of the students'' attitudes held early in their medical careers appear to have been modified in the process of becoming physicians. It appears that medical education continues to convey many traditional professional values to students, and it seems likely that tomorrow''s physicians will retain a core of those values.     

Role of the undergraduate student research assistant in the new millennium

In this study, we analyze the contribution of the undergraduate student who participates in the process of generating scientific data and developing a research project using Brazilian research as an example. Historically, undergraduate students have performed the critical role of research assistants in developing countries. This aspect has been underappreciated as a means of generating scientific data in Brazilian research facilities. Brazilian educational institutions are facing major age-related generational changes among the science faculty within the next 5-10 yr. A lack of adequate support for graduate students leads to a concern that undergraduates will not be interested in choosing research assistant programs and, subsequently, academic research careers. To remedy this situation it is important to focus on ways to encourage new research careers and enhance university-industry collaborations.     

A new method to reconstruct recombination events at a genomic scale

Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have fine-tuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 X-chromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation.     

What epidemiology has told us about risk factors and aetiopathogenesis in rheumatic diseases

This article will review how epidemiological studies have advanced our knowledge of both genetic and environmental risk factors for rheumatic diseases over the past decade. The major rheumatic diseases, including rheumatoid arthritis, juvenile idiopathic arthritis, psoriatic arthritis, ankylosing spondylitis, systemic lupus erythematosus, scleroderma, osteoarthritis, gout, and fibromyalgia, and chronic widespread pain, will be covered. Advances discussed will include how a number of large prospective studies have improved our knowledge of risk factors, including diet, obesity, hormones, and smoking. The change from small-scale association studies to genome-wide association studies using gene chips to reveal new genetic risk factors will also be reviewed.     

Multiplexed and microparticle-based analyses: quantitative tools for the large-scale analysis of biological systems.

While the term flow cytometry refers to the measurement of cells, the approach of making sensitive multiparameter optical measurements in a flowing sample stream is a very general analytical approach. The past few years have seen an explosion in the application of flow cytometry technology for molecular analysis and measurements using microparticles as solid supports. While microsphere-based molecular analyses using flow cytometry date back three decades, the need for highly parallel quantitative molecular measurements that has arisen from various genomic and proteomic advances has driven the development in particle encoding technology to enable highly multiplexed assays. Multiplexed particle-based immunoassays are now common place, and new assays to study genes, protein function, and molecular assembly. Numerous efforts are underway to extend the multiplexing capabilities of microparticle-based assays through new approaches to particle encoding and analyte reporting. The impact of these developments will be seen in the basic research and clinical laboratories, as well as in drug development.     

A bioinformatics approach to investigating developmental pathways in the kidney and other tissues.

Over the past few years, large amounts of data linking gene-expression (GE) patterns and other genetic data with the development of the mouse kidney have been published, and the next task will be to integrate these data with the molecular networks responsible for the emergence of the kidney phenotype. This paper discusses how a start to this task can be made by using the kidney database and its associated search tools, and shows how the data generated by such an approach can be used as a guide to future experimentation. Many of the events taking place as the kidney develops do, of course, also take place in other tissues and organisms and it will soon be possible to incorporate relevant information from these systems into analyses of kidney data as well as the new information from microarray technology. The key to success here will be the ability to access over the internet data from the textual and graphical databases for the mouse and other organisms now being established. In order to do this, informatic tools will be needed that will allow a user working with one database to query another. This paper also considers both the types of tools that will be necessary and the databases on which they will operate.     

Envisioning future strategies for vaccination against tuberculosis

The design of tuberculosis vaccines has entered a new era. Although several new vaccine candidates will pass Phase I clinical trials within the next year, I believe that the most effective vaccination strategy will be to combine different vaccine candidates and to use a prime-boost approach. This strategy, however, would require several years of iterative vaccine trials, unless the process is expedited by the identification of reliable biomarkers for assessing vaccine efficacy. In this Essay, I briefly summarize past and present attempts to develop a vaccine against tuberculosis, and I describe, using imagined scenarios, the tuberculosis vaccination schemes that might become available from a large repertoire of candidate schemes in the near and distant future.     

A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists

ABSTRACT. We have converted the hierarchically organized new higher level classification of eukaryotes with emphasis on the taxonomy of protists proposed by Adl et al. into an interactive and dynamic Java applet. The current version of the applet can be accessed via http://phylogenetics.bioapps.biozentrum.uni-wuerzburg.de/etv . We use the layout from a Degree-of-Interest tree (DOITree) that effectively displays all the taxonomic information as well as the phylogenetic relationships described in the original article by Adl et al. The tree was made using the Prefuse Toolkit for interactive information visualization. All browsers capable of using Java applets will be able to view the tree. The applet is freely available for scientists, teachers, and students.