Working through polytomies: Auklets revisited

Polytomies, or phylogenetic “bushes”, are the result of a series of internodes occurring in a short period of evolutionary time (which can result in data that do not contain enough information), or data that have too much homoplasy to resolve a bifurcating branching pattern. In this study we used the Aethia auklet polytomy to explore the effectiveness of different methods for resolving polytomies: mitochondrial DNA gene choice, number of individuals per species sampled, model of molecular evolution, and AFLP loci. We recovered a fully-resolved phylogeny using NADH dehydrogenase subunit 2 (ND2) sequence data under two different Bayesian models. We were able to corroborate this tree under one model with an expanded mtDNA dataset. Effectiveness of additional intraspecific sampling varied with node, and fully 20% of the subsampled datasets failed to return a congruent phylogeny when we sampled only one or two individuals per species. We did not recover a resolved phylogeny using AFLP data. Conflict in the AFLP dataset showed that nearly all possible relationships were supported at low levels of confidence, suggesting that either AFLPs are not useful at the genetic depth of the Aethia auklet radiation (7–9% divergent in the mtDNA ND2 gene), perhaps resulting in too much homoplasy, or that the Aethia auklets have experienced incomplete lineage sorting at many nuclear loci.     

假说检验和科学方法

本文的意图是让研究者审视研究方法,并在研究设计中充分使用假说检验,并在选择模式物种时充分理解其自然史.我们的总前提是,按照"强推论"(指假定拒绝某一假说而不是支持某一偏爱假说)的逻辑,科学能够进展得更快、更可观、更有确定性.我们强调并提供了符合逻辑的一系列步骤,即确定科学问题或确定具有未知生物学意义的问题;列出所有可靠的、能解释所观察现象的假说,每个假说列出其可检验的、可证明其无根据的预测;然后是符合预测检验的实验或研究设计.我们也强调,模式物种对于解决科学的理论问题以及得出推论是很重要的.本文所展示的不是新思想,只是提醒研究者要注意遵循的基本研究途径.     

Lambda excision revisited: testing a model for synapsis of prophage ends

Excision of lambda prophage was reexamined to test a model for prophage end synapsis. The model proposes that, during in situ prophage replication, following induction, the diverging replication forks are held together. Consequently, prophage DNA is spooled through the replication machinery, drawing the prophage ends together and facilitating synapsis. The model predicts that excision will be slowed if in situ lambda replication is inhibited, and the predicted low rate of excision of a nonreplicating prophage was observed after thermoinduction. However, excision was rapid if additional Int protein was supplied or if the temperature was reduced after induction, showing that (i) Int is partially thermosensitive for excision at 42 degrees C and (ii) in situ replication is not required for rapid excision, a finding that is inconsistent with the model.     

Manipulating flux through plant metabolic pathways

The past two years have seen a marked increase in patent applications for novel methods of altering the level and spectrum of commercially important products in plants. Results from these studies have proven surprising, showing that in many cases those enzymes traditionally thought of as flux-controlling have no impact on product formation when they are directly altered by genetic manipulation. In many cases, successful induction of increased flux throughout an entire pathway has been achieved by targeting one of the terminal enzymes in the pathway.     

The multiple functions of the thiol-based electron flow pathways of Escherichia coli: Eternal concepts revisited

Electron flow via thiols is a theme with many variations in all kingdoms of life. The favourable physichochemical properties of the redox active couple of two cysteines placed in the optimised environment of the thioredoxin fold allow for two electron transfers in between top biological reductants and ultimate oxidants. The reduction of ribonucleotide reductases by thioredoxin and thioredoxin reductase of Escherichia coli (E. coli) was one of the first pathways to be elucidated. Diverse functions such as protein folding in the periplasm, maturation of respiratory enzymes, detoxification of hydrogen peroxide and prevention of oxidative damage may be based on two electron transfers via thiols. A growing field is the relation of thiol reducing pathways and the interaction of E. coli with different organisms. This concept combined with the sequencing of the genomes of different bacteria may allow for the identification of fine differences in the systems employing thiols for electron flow between pathogens and their corresponding mammalian hosts. The emerging possibility is the development of novel antibiotics.     

Water transport through plant tissue: the apoplasm and symplasm pathways

A detailed quantitative analysis of water flow through the apoplasm and symplasm of plant tissue is presented. The analysis results in two coupled diffusion equations which describe water transport in the two pathways. Various parameters entering the analysis identify the physical properties of the tissue which control the transport process as the resistance to water flow per cell in the two parallel pathways, the resistance per cell between pathways, and the water capacity per cell in the two pathways. Values for the several resistances and water capacities are estimated from available data, and a model problem is solved wherein a sheet of tissue at an initial water potential of — δ bars is immersed in a container of water. The resulting solutions show that depending on the values assigned to the controlling parameters, local water potential equilibrium between each cell and its cell wall may or may not obtain. In the special case of local equilibrium (water potential in the symplasm and apoplasm pathways essentially equal), the transport process can be described by a single diffusion equation which is derived along with an expression for the tissue diffusivity. It is concluded that the weakest link in the analysis is the estimated value for the permeability of the plasmodesma membrane, and that a logical extension of the theory would be to include the effects of a diffusable solute.     

Protein secretion through autotransporter and two-partner pathways

Two distinct protein secretion pathways, the autotransporter (AT) and the two-partner secretion (TPS) pathways are characterized by their apparent simplicity. Both are devoted to the translocation across the outer membrane of mostly large proteins or protein domains. As implied by their name, AT proteins contain their own transporter domain, covalently attached to the C-terminal extremity of the secreted passenger domain, while TPS systems are composed of two separate proteins, with TpsA being the secreted protein and TpsB its specific transporter. In both pathways, the secreted proteins are exported in a Sec-dependent manner across the inner membrane, after which they cross the outer membrane with the help of their cognate transporters. The AT translocator domains and the TpsB proteins constitute distinct families of protein-translocating, outer membrane porins of Gram-negative bacteria. Both types of transporters insert into the outer membrane as beta-barrel proteins possibly forming oligomeric pores in the case of AT and serve as conduits for their cognate secreted proteins or domains across the outer membrane. Translocation appears to be folding-sensitive in both pathways, indicating that AT passenger domains and TpsA proteins cross the periplasm and the outer membrane in non-native conformations and fold progressively at the cell surface. A major difference between AT and TPS pathways arises from the manner by which specificity is established between the secreted protein and its transporter. In AT, the covalent link between the passenger and the translocator domains ensures the translocation of the former without the need for a specific molecular recognition between the two modules. In contrast, the TPS pathway has solved the question of specific recognition between the TpsA proteins and their transporters by the addition to the TpsA proteins of an N-proximal module, the conserved TPS domain, which represents a hallmark of the TPS pathway.     

Cellular pathways for viral transport through plasmodesmata

Plant viruses use plasmodesmata (PD) to spread infection between cells and systemically. Dependent on viral species, movement through PD can occur in virion or non-virion form, and requires different mechanisms for targeting and modification of the pore. These mechanisms are supported by viral movement proteins and by other virus-encoded factors that interact among themselves and with plant cellular components to facilitate virus movement in a coordinated and regulated fashion.     

Diagnostic difficulties in the interpretation of fine needle aspirates of salivary gland lesions: the problem revisited

Diagnostic difficulties in the interpretation of he needle aspirates of salivary gland lesions: the problem revisited
Cases of salivary gland lesions ( n =325), mainly neoplastic but including a small number of non-neoplastic lesions, investigated by fine needle aspiration (FNA) and with histological correlation, are reviewed. The review identified a number of differential diagnostic problems which are discussed in some detail. One false-positive and eight false-negative diagnoses had been made resulting in a 99.5% specificity and a 85.5% sensitivity. If type-specific diagnoses are made only when all defined diagnostic criteria are present and if any uncertainty is clearly conveyed to the clinician, FNA is a safe and accurate tool in the investigation of salivary gland lesions.