“整合物种概念”和“分化路上的物种”

已有的各个物种概念对物种的认识类似盲人摸象, 只包含了物种的某一个方面; 而一个分化后期的成熟物种应涵盖了所有的物种概念。但是, 尚未到达分化后期的物种往往又已开始新一轮的物种分化; 自然中存在的多数“物种”处于分化路上。这种循环往复连续分化产生的物种, 存在种间生殖隔离不彻底、基因流频繁发生、网状进化突出等现象。此外, 对于不同的物种对, 最早开始分化的基因以及不同物种概念所要求的条件的分化顺序不是统一的, 而是随机的。定义一个适合所有“分化路上的物种”概念存在较大困难。但是, 应采用尽可能多的物种概念来界定分化路上的物种、发表新种和进行分类处理; 也应承认种间可能广泛存在不完全的生殖隔离和有限的基因流, 即有不属于两个物种群体的杂交或回交个体的存在。这样划分的物种比只依据一个物种概念认定的物种具有更高的客观性和科学性。     

Validation of a spatial agent-based model for Taenia solium transmission (“CystiAgent”) against a large prospective trial of control strategies in northern Peru

BackgroundThe pork tapeworm (Taenia solium) is a parasitic helminth that imposes a major health and economic burden on poor rural populations around the world. As recognized by the World Health Organization, a key barrier for achieving control of T. solium is the lack of an accurate and validated simulation model with which to study transmission and evaluate available control and elimination strategies. CystiAgent is a spatially-explicit agent based model for T. solium that is unique among T. solium models in its ability to represent key spatial and environmental features of transmission and simulate spatially targeted interventions, such as ring strategy.Methods/Principal findingsWe validated CystiAgent against results from the Ring Strategy Trial (RST)–a large cluster-randomized trial conducted in northern Peru that evaluated six unique interventions for T. solium control in 23 villages. For the validation, each intervention strategy was replicated in CystiAgent, and the simulated prevalences of human taeniasis, porcine cysticercosis, and porcine seroincidence were compared against prevalence estimates from the trial. Results showed that CystiAgent produced declines in transmission in response to each of the six intervention strategies, but overestimated the effect of interventions in the majority of villages; simulated prevalences for human taenasis and porcine cysticercosis at the end of the trial were a median of 0.53 and 5.0 percentages points less than prevalence observed at the end of the trial, respectively.Conclusions/SignificanceThe validation of CystiAgent represented an important step towards developing an accurate and reliable T. solium transmission model that can be deployed to fill critical gaps in our understanding of T. solium transmission and control. To improve model accuracy, future versions would benefit from improved data on pig immunity and resistance, field effectiveness of anti-helminthic treatment, and factors driving spatial clustering of T. solium infections including dispersion and contact with T. solium eggs in the environment.     

Sporulation of the “Thermophilic Anaerobes.”

A reasonable degree of synchrony in the sporulation of Clostridium thermosaccharolyticum 3814 was obtained by using three 10% transfers of 8-hr cultures in a medium containing 0.5% L-arabinose, 0.5% peptone, 0.5% yeast extract, and Gc minerals. Sporulation was stimulated by L-arabinose and L-xylose, but was repressed by glucose, mannose, fructose, and D-pentoses. Sporulating cells were long and thin, whereas repressed cells were shorter and thicker. The optimal pH for sporulation was in the range of pH 5.0 to 5.5. As sporulation continued, the accumulated acetate decreased. Label studies indicated that a significant amount of acetate-2-C¹⁴ was incorporated into the spore lipid. The calcium, phosphorus, and dipicolinic acid (DPA) concentrations on a dry weight basis were 2.55, 2.60, and 7.25%, respectively. The molar ratio of Ca-DPA was 1.47.     

An Italian survey on “palliative intent” radiotherapy

BackgroundThe aim of this paper is to provide a comprehensive overview of the scenario on radiotherapy (RT) delivered with palliative intent in Italy.Materials and methodsA structured online questionnaire was submitted to Italian radiation oncologists in order to explore the clinical practice in different areas of palliation, namely: bone, lung, brain, liver, and emergencies suitable to RT.Results209 radiation oncologists took part in the study. Stereotactic body irradiation was found to be the preferred technique in lung and liver metastases, whereas 3D conformal RT was registered as the technique of choice for bone and brain metastases. The majority (98%) of participants stated to treat mainly radiotherapy emergencies with 3D conformal RT at doses ranging from 25 to 50 Gy. Re-irradiation is delivered by the majority of respondents, whereas post-treatment follow-up is done only by 51.4% of them.ConclusionsThis nationwide study highlights some heterogeneity among Italian radiation oncologists regarding treatment and follow-up of metastatic cancer patients.     

An assessment of terminology for intraspecific diversity in fishes,with a focus on “ecotypes” and “life histories”

Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., “PST”), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life‐history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life‐history traits. Life history is generally used in organismal‐ and ecology‐based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic‐ and evolution‐based journals. “Satellite species” is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life‐history components of ISD are not well understood, a conservative approach would be to call them phenotypes.

The terminology used to describe intraspecific diversity is varied and often used ambiguously. “Ecotype” was originally used to describe patterns in genes and ecology, and recent studies employing this term tend to report a genetic basis in ISD. By contrast, “life history” describes biological parameters that affect demography, and this term tends to be used in organismal‐ and ecology‐based journals.     

Differential Sensitivity of “Old” versus “New” APOBEC3G to Human Immunodeficiency Virus Type 1 Vif

HIV-1 Vif counteracts the antiviral activity of APOBEC3G by inhibiting its encapsidation into virions. Here, we compared the relative sensitivity to Vif of APOBEC3G in stable HeLa cells containing APOBEC3G (HeLa-A3G cells) versus that of newly synthesized APOBEC3G. We observed that newly synthesized APOBEC3G was more sensitive to degradation than preexisting APOBEC3G. Nevertheless, preexisting and transiently expressed APOBEC3G were packaged with similar efficiencies into vif-deficient human immunodeficiency virus type 1 (HIV-1) virions, and Vif inhibited the encapsidation of both forms of APOBEC3G into HIV particles equally well. Our results suggest that HIV-1 Vif preferentially induces degradation of newly synthesized APOBEC3G but indiscriminately inhibits encapsidation of “old” and “new” APOBEC3G.     

Escherichia coli MazF Leads to the Simultaneous Selective Synthesis of Both “Death Proteins” and “Survival Proteins”

The Escherichia coli mazEF module is one of the most thoroughly studied toxin–antitoxin systems. mazF encodes a stable toxin, MazF, and mazE encodes a labile antitoxin, MazE, which prevents the lethal effect of MazF. MazF is an endoribonuclease that leads to the inhibition of protein synthesis by cleaving mRNAs at ACA sequences. Here, using 2D-gels, we show that in E. coli, although MazF induction leads to the inhibition of the synthesis of most proteins, the synthesis of an exclusive group of proteins, mostly smaller than about 20 kDa, is still permitted. We identified some of those small proteins by mass spectrometry. By deleting the genes encoding those proteins from the E. coli chromosome, we showed that they were required for the death of most of the cellular population. Under the same experimental conditions, which induce mazEF-mediated cell death, other such proteins were found to be required for the survival of a small sub-population of cells. Thus, MazF appears to be a regulator that induces downstream pathways leading to death of most of the population and the continued survival of a small sub-population, which will likely become the nucleus of a new population when growth conditions become less stressful.     

Genetic Control of “Flor” Formation by Saccharomyces

The results described indicate that in Saccharomyces sp. the formation of "flor" is under the control of a single Mendelian gene for which is proposed the symbol "Fl."     

Functional Brain Networks Develop from a “Local to Distributed” Organization

The mature human brain is organized into a collection of specialized functional networks that flexibly interact to support various cognitive functions. Studies of development often attempt to identify the organizing principles that guide the maturation of these functional networks. In this report, we combine resting state functional connectivity MRI (rs-fcMRI), graph analysis, community detection, and spring-embedding visualization techniques to analyze four separate networks defined in earlier studies. As we have previously reported, we find, across development, a trend toward ‘segregation’ (a general decrease in correlation strength) between regions close in anatomical space and ‘integration’ (an increased correlation strength) between selected regions distant in space. The generalization of these earlier trends across multiple networks suggests that this is a general developmental principle for changes in functional connectivity that would extend to large-scale graph theoretic analyses of large-scale brain networks. Communities in children are predominantly arranged by anatomical proximity, while communities in adults predominantly reflect functional relationships, as defined from adult fMRI studies. In sum, over development, the organization of multiple functional networks shifts from a local anatomical emphasis in children to a more “distributed” architecture in young adults. We argue that this “local to distributed” developmental characterization has important implications for understanding the development of neural systems underlying cognition. Further, graph metrics (e.g., clustering coefficients and average path lengths) are similar in child and adult graphs, with both showing “small-world”-like properties, while community detection by modularity optimization reveals stable communities within the graphs that are clearly different between young children and young adults. These observations suggest that early school age children and adults both have relatively efficient systems that may solve similar information processing problems in divergent ways.     

Growth of “Seeded” Cellulolytic Enrichment Cultures on Mesquite Wood

Eleven enrichment cultures were developed by a “seeded” enrichment culture technique, and one was developed by a simple enrichment technique. The seeded enrichment, the pure “seed,” and the simple enrichment cultures were compared during growth on mesquite wood, cotton, carboxymethylcellulose, and cellobiose. All of the enrichment cultures were cellulolytic and exceeded the pure seed cultures in mesquite wood hydrolysis and/or viable cell count. Yeast extract improved, but was not essential for, growth of the seeded enrichment cultures on carboxymethylcellulose. Two of the seeded enrichment cultures, CAD5 and CAD11, grew best at 37°C and pH 7.0 on mesquite wood. A 1.0% (wt/vol) wood concentration was optimum for their growth.     

Nonselective Incorporation into Sporangium of Either “Older” or “Younger” Chromosome of the Vegetative Cell During Sporulation in Bacillus cereus

Employing Bacillus cereus strain 2, we examined the fate of two chromosomes contained in vegetative cells in the course of sporulation. Cytological observations and quantitative estimation of deoxyribonucleic acid (DNA) confirmed the earlier observations that, during the course of sporulation, one of two chromosomes of the vegetative cell was incorporated into the sporangium and the other disappeared into the medium as the result of cell lysis. Log-phase cells, labeled completely with thymine-2-(14)C in the presence of deoxyadenosine, were cultured in the "cold" glucose-glutamate-glycine-salts medium, and culture samples, taken at intervals at successive generations, were subjected to sporulation in glutamate-salts medium. The percentage of radioactivity in the spores separated from each culture remained almost unchanged at nearly 50% and was independent of the number of generations of the preceding culture in the "cold" medium. This suggests that the selective incorporation into the sporangium of either the "older" or "younger" chromosome of a vegetative cell does not occur in the course of spore formation. Some examples of the selective and nonselective behavior of DNA molecules in cellular events in microorganisms are cited.     

Glucose-6-Phosphate Dehydrogenase from Escherichia coli and from a “High-Level” Mutant

Glucose-6-phosphate dehydrogenase has been purified to near homogeneity from wild-type Escherichia coli K-12 and from a mutant previously found to contain substantially more of the enzyme. The two enzymes are the same in all characteristics studied thus far: specific activity, kinetics, specificity, and subunit size.