A “Natural” Agglomerative Clustering Method for Biology

The authors consider that cluster analysis does not objectivize but represents the biologist's subjectivity as to (1) characters considered to be significant and to (2) the way of classification. The latter, however, in authors' opinion, must be specific to the field of application. To this effect some methods are suggested for biology. The methods originate in improvements or transformation of Buser and Baroni-Urbani's method, as well as Watanabe's method, and have the property of processing overall information with no loss or distortion. An agglomerative method which yields a necessarily unique result is suggested, being considered by the authors as a homologue of Watanabe's divisive method. The methods proposed are studied using examples logically constructed. These examples can provide from biology, especially from ecology.     

Highly efficient labeling of DNA polymerases by a binary system of photoaffinity reagents

A binary system of photoaffinity reagents was proposed earlier for highly efficient labeling of DNA polymerases by 5"-[³²P]DNA primers. In the present study we demonstrate the feasibility of this approach to increase the efficiency of DNA polymerase labeling. A photoactive 2,3,5,6-tetrafluoro-4-azidobenzoyl (FAB) group was incorporated at the 3"-end of 5"-[³²P]DNA primers synthesized by DNA polymerase or Tte in the presence of one of the dTTP analogs—FAB-4-dUTP, FAB-9-dUTP, or FAB-4-ddUTP. The reaction mixture was irradiated by light with wavelength of 334-365 nm (direct labeling) or 365-450 nm in the presence of photosensitizer, one of dTTP analogs containing a pyrene moiety, Pyr-6-dUTP or Pyr-8-dUTP. In the case of the binary system of photoaffinity reagents, a FAB group is activated by energy transfer from sensitizer localized in the dNTP-binding site of DNA polymerase in the triple complex, comprised by reagent, DNA polymerase, and Pyr-6(8)-dUTP. Direct activation of the FAB group under these conditions is negligible. The most efficient photolabeling of DNA polymerases was observed with a primer containing a FAB-4-dUMP group at the 3"-end, and Pyr-6-dUTP as a photosensitizer. Using 10-fold molar excess of photoreagent to DNA polymerase , the labeling efficiency was shown to achieve 60%, which is 2-fold higher than the efficiency of the direct DNA polymerase labeling under harsher conditions (334-365 nm).     

Marginal regression analysis of a multivariate binary response

We propose the use of the mean parameter for regression analysisof a multivariate binary response. We model the associationusing dependence ratios defined in terms of the mean parameter,the components of which are the joint success probabilitiesof all orders. This permits flexible modelling of higher-orderassociations, using maximum likelihood estimation. We reanalysetwo data sets, one with variable cluster size and the othera longitudinal data set with constant cluster size.     

The treatment of isolated genera

Problems presented by genera, or small groups of genera, which have been given family rank are reviewed, and the genera are divided into a number of categories according to the closeness of their affinity to other genera or families. Satellite genera that stand in close relation to families should be united with them. Binary families, that have been divided into two (or more) related families, should be re–united. Families connected by linking genera, should, logically, be united but practical considerations usually prevent this. Clusters of diverse but more or less distantly related genera present unusual problems, being treated either as several, often monogeneric families or as a loosely structured family. Truly isolated genera must be given family and often ordinal rank.     

Examples of non-trivial efficiency-balanced designs with b=v+1

This note provides examples of binary efficiency-balanced block designs with b=v+1, having no complete blocks, which are unequal-replicated and unequal-blocksized from a biometrical and agricultural standpoint.     

Cell division in baeocyte producing cyanobacteria

Summary An ultrastructural examination of cell division in two baeocyte producing cyanobacteria,Pleurocapsa minor andDermocarpa violaceae, reveals two distinct patterns of binary (transverse) fission. Septate binary fission, inPleurocapsa minor, involves centripetal synthesis and deposition of the mucopolymer cell wall layer (L 2). The ingrowth of the cytoplasmic membrane and L 1 cell wall layer, along with the synthesis of the L 2 cell wall layer, results in the formation of a prominent septum. Partitioning of the cell occurs by the constriction of the outer cell wall layers (L 3 and L 4) through the septum. InDermocarpa violaceae, constrictive binary fission occurs by the simultaneous ingrowth or constriction of the cytoplasmic membrane and all cell wall layers (L1, L2, L3, L4). Septate and constrictive binary fission may proceed symmetrically (medially) or asymmetrically (nonmedially). Multiple fission occurs regularly inDermocarpa violaceae and provides for a rapid means of reproduction when compared to binary fission. Successive radial and tangential divisions of the protoplast result in formation of many small daughter cells (baeocytes). The process of multiple fission is similar to septate binary fission with reduced septa being formed. However, constriction of the outer cell wall layers, through the septa, proceeds concurrently with septum formation.     

Bivariate binary data analysis with nonignorably missing outcomes

One of the objectives in the Northern Manhattan Stroke Study is to investigate the impact of stroke subtype on the functional status 2 years after the first ischemic stroke. A challenge in this analysis is that the functional status at 2 years after stroke is not completely observed. In this paper, we propose a method to handle nonignorably missing binary functional status when the baseline value and the covariates are completely observed. The proposed method consists of fitting four separate binary regression models: for the baseline outcome, the outcome 2 years after the stroke, the product of the previous two, and finally, the missingness indicator. We then conduct a sensitivity analysis by varying the assumptions about the third and the fourth binary regression models. Our method belongs to an imputation paradigm and can be an alternative to the weighting method of Rotnitzky and Robins (1997, Statistics in Medicine 16, 81-102). A jackknife variance estimate is proposed for the variance of the resulting estimate. The proposed analysis can be implemented using statistical software such as SAS.     

Measures of spatial heterogeneity for species occurrence or disease incidence with finite-counts

We propose two types of indices with finite-count correction to measure the spatial heterogeneity of binary characteristics of organisms, such as occurrence or non-occurrence of organisms and infected or non-infected plants. We consider the following two examples: plant occurrence in a grassland community, and yellow dwarf disease infection in a rice field. For the grassland community, N quadrats comprising n cells of equal area, were set at random sites in a grassland, and the occurrence of a given species A in each of n cells was recorded. For disease infection, N quadrats, each consisting of n rice plants, were set at random sites in a paddy field, and the number of plants infected with yellow dwarf virus in each quadrat were counted. In these examples, since the number of cells in a quadrat is finite, neither occurrence nor incidence increase infinitely, unlike the number of aphids on a maize leaf. The first category of index belongs to the mean : variance ratio type. The estimated index value for occurrence (or incidence) is the same as that for non-occurrence (or non-incidence). The second category belongs to the k-type of a negative binomial distribution. If some random plants die or recover from the disease then the expected value of the second type of index does not change. For n, the current indices approach the mean : variance ratio and the inverse of k in a negative binomial distribution, respectively. This indicates that these indices are suitable for binary data sets.     

Numerical evidence of heterogeneity and nanophases in a binary liquid confined at the nanoscale

Recent results suggest that a binary liquid that is usually homogeneous in the bulk phase can demix and form a core–shell organisation in a confined medium. In this work, we combine molecular dynamics and Monte Carlo simulations to verify this specific structure and to capture the driving force governing this possible segregation at the nanoscale.     

pBIN20: An Improved Binary Vector for shape Agrobacterium-mediated Transformation

We report the construction of a binary vector for Agrobacterium tumefaciens-mediated transformation, pBIN20, which contains a superlinker region located between the left and right Ti border sequences. This vector, derived from pBI121, simplifies the cloning of plant expression cassettes and has been used in our laboratory to create lines of transgenic BY-2 tobacco cells. This new vector contains more than 20 unique restriction sites as well as the nptII selectable marker gene within the Ti-DNA borders.     

Complete sequence of the binary vector Bin 19

Despite the widespread use of Bin 19 as a vector for plant transformation, detailed sequence information on its T-DNA region has only recently become available. We now show that the non-T-DNA region, like the T-DNA region, contains several superfluous insertions and find that some functional elements may not contain optimal sequences. Knowledge of the complete 11 777 bp sequence will aid in the construction of exceptionally efficient derivative vectors of approximately half this size. Precise knowledge of restriction sites and removal of unnecessary sequences will facilitate plasmid manipulations and plant transformation.     

Testing Significant Homogeneities Within Binary Information Strings

In a previous paper (Buser, 1982) a nonparametric test has been presented for deciding whether or not a binary coded taxonomic node is significantly homogeneous. In the following tables the corresponding critical values, both for the one and two tailed test, are given.     

异源蛋白质相互作用数据整合算法的进展

蛋白质相互作用在生物学过程和细胞功能行使中起核心作用。高通量技术的应用结合计算机预测方法的发展,使得直接和间接来源的蛋白质相互作用数据得到了大规模的增加。如何系统地整合这些数据并从中提取有用的信息是一项挑战,这也促使了许多整合算法应运而生。本文综述了八种整合蛋白质相互作用数据源的方法：投票、支持向量机、朴素贝叶斯、逻辑斯蒂回归、决策树、随机森林、基于随机森林的k-近邻法以及混合属性分类等方法。     

A new binary system for photosensitized labeling of DNA polymerases in nuclear extract

A binary system of reagents was used for photosensitized labeling of proteins of bovine testis nuclear extract. A dUTP analog containing 4-azido-2,5-difluoro-3-chloropyridyl group (FAP-dUTP) was used for the first time as a component of the binary system, and a dUTP analog containing the pyrenyl group (Pyr-dUTP) was used as a photosensitizer. Photoaffinity labeling of proteins of nuclear extract was performed using the radioactively labeled DNA duplex with the photoreactive FAP group at the 3"-end of elongating DNA strand and analog of the deoxyribose phosphate residue (3-hydroxy-2-hydroxymethyltetrahydrofuran (F) 5"-phosphate) at the 5"-end of the nick. Such structure is formed by the action of nuclear extract enzymes from the initial DNA duplex containing a synthetic apurine/apyrimidine site and is a photoreactive analog of a long-patch base excision repair intermediate. UV-irradiation modified a limited number of proteins of the nuclear extract. As shown using specific antibodies, the new binary system of photoreagents increases the efficiency of DNA polymerase labeling.     

Studies on the binary and ternary complexes formed by a neurospora glutamate dehydrogenase and its substrates

The NADP⁺ specific glutamate dehydrogenase from wild-type $\text{Neurospora crassa}$ forms a stable binary complex with NADPH. This can combine with L-glutamate, α-ketoglutarate or the substrate analogue D-glutamate to form ternary complexes which can be distinguished by their different fluorescence properties. The affinity of the enzyme for NADPH diminishes with increases in pH or ionic strength of the solution. Experimental data obtained using modified glutamate dehydrogenases from mutant strains of $\text{N. crassa}$ suggest that the reduced-coenzyme binding sites observed fluorimetrically are the same as those observed by enzyme kinetics.     

Construction of small binary vectors forAgrobacterium-Mediated transformation in plants

Despite the popular use of theAgrobacterium-mediated method for transforming plants, only a very limited number of binary vectors are available. In addition, those binary vectors are rather inconvenient for plasmid manipulation because of their large size. Here, we report the construction of small binary vectors, pBmin1 and pBminGFP1, forAgrobacterium-mediated transformation. The sizes of pBmin1 and pBminGFP1 are approximately 5.0 kb and 6.5 kb, respectively. These vectors contain one kanamycin resistance gene, with a double promoter for expression in both bacteria and plant cells. Vector pBminGFP1 has the 35S-GFP chimeric gene as a reporter. These small binary vectors would greatly facilitate plasmid manipulation and plant transformation.     

新型喜树碱类抗癌药物的研究进展

喜树碱是1966年由喜树中分离而来的一种五环结构的生物碱,早期对其抗肿瘤活性的发现更是引发了科学家们对此类化合物极大的研究兴趣,现在已经证实喜树碱类化合物主要是通过抑制在DNA代谢过程中发挥重要作用的I型拓扑异构酶。但其自身因水溶性差、毒副作用强,在临床应用上易出现不良反应。半个世纪以来,国内外研究者在对其作用机制及构效关系的研究基础上,开发出了数以百计的喜树碱类衍生物,很多已经进入临床或临床前研究。但目前仅有两种喜树碱类的化合物拓扑替康和依立替康被美国FDA批准应用于临床上肿瘤的治疗。本文就已上市的喜树碱类化合物以及喜树碱类抗肿瘤药物开发的挑战进行了综述。     

The fixation probability of a beneficial allele in a population dividing by binary fission

We derive formulae for the fixation probability, P, of a rare benefical allele segregating in a population of fixed size which reproduces by binary fission, in terms of the selection coefficient for the beneficial allele, s. We find that an earlier result P 4s does not depend on the assumption of binary fission, but depends on an assumption about the ordering of events in the life cycle. We find that P 2s for mutations occurring during chromosome replication and P 2.8s for mutations occurring at random times between replication events.     

Influencing the direct formation of ‘Janus’ particles in molecular dynamics simulations

The binary nucleation of phase-separated Lennard-Jones clusters was analysed under various system conditions using molecular dynamics simulations. The modified potential model provides a simple gateway to observe non-wetting behaviour and imitates the more complex interactions of non-miscible substances. Thus, not only the transition from ideally mixed clusters to so-called ‘Janus’ particles, but also the structural aspects and dynamic formation processes of nanoscopic droplets are directly observable from the gas phase. Various shapes and sizes of these inhomogeneous clusters have been found via simple tuning of system parameters. From this analysis, we gained further insight into the direct formation of ‘Janus’ particles from the gas phase.