Complex genetic diseases: controversy over the Croesus code

The polarization of views on how best to exploit new information from the Human Genome Project for medicine reflects our ignorance of the genetic architecture underlying common diseases: are susceptibility alleles common or rare, neutral or deleterious, few or many? Single-nucleotide polymorphism (SNP) technology is almost in place to dissect such diseases and to create a personalized medicine, but success is critically dependent on the biology and "Nature to be commanded must be obeyed" (Francis Bacon, 1620, Novum Organum).     

The role of soil bacterial community during winter fallow period in the incidence of tobacco bacterial wilt disease

Applied Microbiology and Biotechnology - Bacterial wilt, caused by Ralstonia solanacearum, occurs occasionally during tobacco planting and potentially brings huge economic losses in affected areas....     

The controversy over the minimum quantum requirement for oxygen evolution

During the early- to mid-twentieth century, a bitter controversy raged among researchers on photosynthesis regarding the minimum number of light quanta required for the evolution of one molecule of oxygen. From 1923 until his death in 1970, Otto Warburg insisted that this value was about three or four quanta. Beginning in the late 1930s, Robert Emerson and others on the opposing side consistently obtained a value of 8–12 quanta. Warburg changed the protocols of his experiments, sometimes in unexplained ways, yet he almost always arrived at a value of four or less, except eight in carbonate/bicarbonate buffer, which he dismissed as “unphysiological”. This paper is largely an abbreviated form of the detailed story on the minimum quantum requirement of photosynthesis, as told by Nickelsen and Govindjee (The maximum quantum yield controversy: Otto Warburg and the “Midwest-Gang”, 2011); we provide here a scientific thread, leaving out the voluminous private correspondence among the principal players that Nickelsen and Govindjee (2011) examined in conjunction with their analysis of the principals’ published papers. We explore the development and course of the controversy and the ultimate resolution in favor of Emerson’s result as the phenomenon of the two-light-reaction, two-pigment-system scheme of photosynthesis came to be understood. In addition, we include a brief discussion of the discovery by Otto Warburg of the requirement for bicarbonate in the Hill reaction.     

Implications of imaginal-size variation over the flight period in stoneflies (Plecoptera)

In the present study, the decrease in the mean size of specimens over the species flight period in Plecoptera (12 species, 5 families) was analysed, revealing a significant decrease in the adult mean size, for both males and female, in almost all the species without an extended flight-period pattern. Some of the data show that, in addition to temperature, other regulatory factors must govern these variations. Data support the explanation previously proposed for other insect groups that the individuals with appropriate development emerge at the beginning of the flight period or slightly afterwards, when environmental conditions are suitable, whereas individuals with suboptimal size emerge later trying to increase in size but under pressure to emerge during a specific period of the year. Nevertheless, our data suggest that maximum size does not necessarily coincide with the peak flight period (maximum reproductive possibility).     

Talented but lazy. The height-school premium among Cracow’s schoolboys in the interwar period

This study finds that a positive association between stature and academic performance measured by the grades for various subjects, the height-school premium, was present in a historical sample of 147 school boys attending a gymnasium (public secondary school) in Cracow, Poland, between the wars. This effect persists when controlling for a set of demographic and socio-economic variables, though the strength of the relationship is modest (0.018 higher average grade for Polish, 0.014 for mathematics, 0.016 for art, and 0.013 for the combined subjects with each centimetre of height). The differences found between the magnitude and significance of the height-premium in different school subjects could be a marker of unequal association between stature, and cognitive, social, and physical skills, suggesting at least a partial role of cognitive ability in this relationship. However, the effect visible at the school level is not consistent between different teachers of the same subjects, hence the mechanism behind the height-school premium in the analysed population to a large extent relied on the subjective judgment of the teachers, who could reward social skills but also discriminate against shorter students.     

The generation of variation in bacterial genomes

In the context of a general overview of molecular mechanisms of microbial evolution, several genetic systems known to either promote or restrain the generation of genetic variations are discussed. Particular attention is given to functions involved in DNA rearrangements and DNA acquisition. Sporadic actions by a variety of such systems influencing genetic stability in either way result in a level of genetic plasticity which is tolerable to the overall wealth of microbial populations but which allows for evolutionary change needed for a steady adaptation to variable selective forces. Although these evolutionarily relevant biological functions are encoded by the genome of each individual, their actions are exerted to some degree randomly in rare individuals and are therefore seemingly nondeterministic and become manifest at the population level.     

Shame,reputation and Egypt's lovers: A controversy over the nation's image

This paper addresses aspects of contemporary Egyptian nationalism by focusing on reactions within Egypt to a BBC‐produced documentary dealing with the life of a lower class Cairene woman. In particular, it explores how the notions of honor, shame and reputation are central to the construction and expression of this nationalistic voice, and how the concern over “Egypt's image” involves a contest over who is to represent the nation. This article argues that the contemporary nationalistic voice, championed by the urban middle classes, expresses an ambivalent attitude to both “the West” and “the Egyptian people”, and that it necessarily involves the hiding and undermining of subordinate social groups.     

Ecotypes and the controversy over stages in the formation of new species

Recent interest in the role of ecology in species formation has led to renewed discussion of the stages in the process of speciation. Although attempts to classify the stages in the process of species formation date back at least as far as Alfred Russel Wallace, one of the most intense debates on the subject occurred among botanists during the mid‐20th Century. The present review outlines the progression of the historical debate about stages in the evolution of species, which was instigated by the genecological classification scheme of Göte Turesson in the 1920s, championed in the mid‐century by Jens Clausen, and then brought under harsh scrutiny by many in the 1960s and 1970s. At the heart of the controversy is the question of whether speciation occurs rapidly on a local scale or gradually through the formation of geographically widespread ecotypes that evolve as precursors to species. A corollary to this debate is the question of whether speciation is reversible and, if so, how does it become irreversible? A third wave of interest in stages in the process of speciation is currently underway, thus making a modern historical narrative of the debate important. Both contemporary and past evolutionary biologists have argued that viewing speciation as being composed of stages can free researchers from concerns over species definitions and focus attention on the mechanisms involved in the process. How speciation becomes irreversible and whether ecogeographically isolated ecotypes are integral to this process remain as important unresolved issues. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 241–257.     

Changes in susceptibility to bacterial endotoxin and infection during the early postnatal period in rats

1. (1)
   На крысятах различного возраста (1, 5, 10 и 15-днeвных) тeстировали токсичность инактивированного штамма Salmonella paratyphi B. B тeчeниe пeрвых 2 вeдeль жизни чувствитeльность крыс044F;т к эндотоксичeскому дeйствию этого микроба повышаeтся приблизитeльно в 7 раз. Это повышeнная чувствитeльность сохраняeтся и во взрослом состоянии.     
   
   

Individual variation in field metabolic rate of kittiwakes (Rissa tridactyla) during the chick-rearing period

Field metabolic rate (FMR), using the doubly labelled water (DLW) method, was measured in free-ranging adult kittiwakes (Rissa tridactyla) early and late in the chick-rearing period at Svalbard, Norway. Individual variation in FMR was analysed by comparing FMR with body mass, sex, nest attendance, chick age, brood size, and basal metabolic rate (BMR). Mean FMR of kittiwakes during the chick-rearing period was 27.0+/-0.9 (SE) W kg(-1), while the individual variation (calculated as coefficient of variation [CV]) in FMR was 24%. Sex, time spent away from the nest, age of the chicks, and brood size contributed significantly to FMR and explained 65% of the variation in FMR. The FMR increased by 32% from early until late in the chick-rearing period. This occurred simultaneously with an increase in the time spent away from the nest. In 15 of 20 pairs, one of the mates had 15% or higher (mean of the 15 pairs, 22%+/-8%) FMR (W kg(-1)) than their partner, even though the mates spent equal amounts of time away from the nest. This indicates an intrapair conflict in FMR. The variation in total FMR of pairs was 40% less than the individual variation, and total FMR of pairs increased with age of the chicks. This indicates that the mates adjust their energy expenditure within a relatively constant FMR determined by the energy needs of the chicks. Individual variation in FMR could not be explained by variation in body mass or BMR. BMR measured late in the chick-rearing period was 26% lower than previous measurements of BMR from the prebreeding and incubation periods. The increase in FMR and simultaneous decrease in BMR caused a 40% increase in metabolic intensity (FMR/BMR) of kittiwakes during the chick-rearing period. It is suggested that the metabolic intensity is not a proper measure of the metabolic load in seabirds.     

Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth

The objective of this study was to determine whether host, compartment, or environmental specific factors play an important role in the establishment of the intestinal microflora in broiler chickens during growth. This objective was addressed using a 16S rDNA approach. PCR-amplicons from the V6 to V8 regions of the 16S rDNA of intestinal samples were separated by denaturing gradient gel electrophoresis (DGGE). The number of bands in all intestinal compartments increased when broilers grew older, indicating that the dominant bacterial community becomes more complex when chickens age. Each chicken had a unique banding pattern for all locations in the intestinal tract, irrespective of the age of chickens. This suggests that host-related factors affect the establishment of the dominant bacterial community. Banding patterns of intestinal compartments within one chicken were different from each other for broilers older than 4 days, except for both ceca which were highly similar. In 4-day-old broilers, banding patterns from crop, duodenum, and ileum were very similar. We conclude that (unknown) host specific factors play an important role in the development of the intestinal bacterial community in each broiler chicken. Furthermore, compartment-specific factors play an important role in the bacterial development of each intestinal compartment within one chicken.     

荒漠冻融期积雪变化对生物结皮甲烷通量的影响

温带荒漠积雪覆盖是土壤含水量增加的重要方式,在冻融期带来丰富的水分变化。全球气候变化导致温带荒漠积雪深度时空格局发生改变,从而影响荒漠生态系统温室气体的通量。生物结皮在维持荒漠生态系统结构和功能的稳定具有非常重要的作用,但对环境的变化较为敏感,尤其是降水变化。然而,目前有关冻融期不同积雪条件下生物结皮温室气体通量的研究十分匮乏。CH₄是重要的温室气体,选择古尔班通古特沙漠藓和地衣2种类型生物结皮为研究对象,以裸沙为对照,设置增雪、自然降雪(对照)和除雪三种处理,通过静态箱-气相色谱法,探究CH₄通量在冻融期的变化特征。结果表明：冻融期多数情况下积雪处理和结皮类型对CH₄通量影响不显著。荒漠生物结皮对CH₄整体表现为吸收作用,是荒漠生态系统CH₄重要的“汇”。两种结皮类型及裸沙CH₄的吸收速率呈现为地衣结皮(-10.12μg m^-2 h^-1)>藓结皮(-1.73μg m^-2 h^...     

BIGSdb: Scalable analysis of bacterial genome variation at the population level

Background  

The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner.