Lung ventilation in salamanders and the evolution of vertebrate air-breathing mechanisms

Functional analysis of lung ventilation in salamanders combined with historical analysis of respiratory pumps provides new perspectives on the evolution of breathing mechanisms in vertebrates. Lung ventilation in the aquatic salamander Necturus maculosus was examined by means of cineradiography, measurement of buccal and pleuroperitoneal cavity pressures, and electromyography of hypaxial musculature. In deoxygenated water Necturus periodically rises to the surface, opens its mouth, expands its buccal cavity to draw in fresh air, exhales air from the lungs, closes its mouth, and then compresses its buccal cavity and pumps air into the lungs. Thus Necturus produces only two buccal movements per breath: one expansion and one compression. Necturus shares the use of this two-stroke buccal pump with lungfishes, frogs and other salamanders. The ubiquitous use of this system by basal sarcopterygians is evidence that a two-stroke buccal pump is the primitive lung ventilation mechanism for sarcopterygian vertebrates. In contrast, basal actinopterygian fishes use a four-stroke buccal pump. In these fishes the buccal cavity expands to fill with expired air, compresses to expel the pulmonary air, expands to fill with fresh air, and then compresses for a second time to pump air into the lungs. Whether the sarcopterygian two-stroke buccal pump and the actinopterygian four-stroke buccal pump arose independently, whether both are derived from a single, primitive osteichthyian breathing mechanism, or whether one might be the primitive pattern and the other derived, cannot be determined. Although Necturus and lungfishes both use a two-stroke buccal pump, they differ in their expiration mechanics. Unlike a lungfish (Protopterus), Necturus exhales by contracting a portion of its hypaxial trunk musculature (the m. Iransversus abdominis) to increase pleuroperitoneal pressure. The occurrence of this same expiratory mechanism in amniotes is evidence that the use of hypaxial musculature for expiration, but not for inspiration, is a primitive tetrapod feature. From this observation we hypothesize that aspiration breathing may have evolved in two stages: initially, from pure buccal pumping to the use of trunk musculature for exhalation but not for inspiration (as in Necturus); and secondarily, to the use of trunk musculature for both exhalation and inhalation by costal aspiration (as in amniotes).     

Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders

Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light-strand replication and the nearby tRNA genes or the regions flanking the origin of heavy-strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and nontandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mitochondrial DNAs, up to 25% of the total length is composed of tandem duplications of noncoding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with the otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intramolecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.     

Evidence for the local evolution of mechanisms underlying limb regeneration in salamanders

The most extensive regenerative ability in adult vertebrates is found in the salamanders. Although it is often suggested that regeneration is an ancestral property for vertebrates, our studies on the cell-surface three-finger-protein Prod 1 provide clear evidence for the importance of local evolution of limb regeneration in salamanders. Prod 1 is implicated in both patterning and growth in the regeneration of limbs. It interacts with well-conserved proteins such as the epidermal growth-factor receptor and the anterior gradient protein that are widely expressed in phylogeny. A detailed analysis of the structure and sequence of Prod 1 in relation to other vertebrate three-finger proteins in mammals and zebra fish supports the view that it is a salamander-specific protein. This is the first example of a taxon-specific protein that is clearly implicated in the mechanisms of regeneration. We propose the hypothesis that regeneration depends on the activity of taxon-specific components in orchestrating a cellular machinery that is extensively conserved between regenerating and non-regenerating taxa. This hypothesis has significant implications for our outlook on regeneration in vertebrates, as well as for the strategies employed in extending regenerative ability in mammals.     

Posture, gait and the ecological relevance of locomotor costs and energy-saving mechanisms in tetrapods

A reanalysis of locomotor data from functional, energetic, mechanical and ecological perspectives reveals that limb posture has major effects on limb biomechanics, energy-saving mechanisms and the costs of locomotion. Regressions of data coded by posture (crouched vs. erect) reveal nonlinear patterns in metabolic cost, limb muscle mass, effective mechanical advantage, and stride characteristics. In small crouched animals energy savings from spring and pendular mechanisms are inconsequential and thus the metabolic cost of locomotion is driven by muscle activation costs. Stride frequency appears to be the principal functional parameter related to the decreasing cost of locomotion in crouched animals. By contrast, the shift to erect limb postures invoked a series of correlated effects on the metabolic cost of locomotion: effective mechanical advantage increases, relative muscle masses decrease, metapodial limb segments elongate dramatically (as limbs shift from digitigrade to unguligrade designs) and biological springs increase in size and effectiveness. Each of these factors leads to decreases in the metabolic cost of locomotion in erect forms resulting from real and increasing contributions of pendular savings and spring savings. Comparisons of the relative costs and ecological relevance of different gaits reveal that running is cheaper than walking in smaller animals up to the size of dogs but running is more expensive than walking in horses. Animals do not necessarily use their cheapest gaits for their predominant locomotor activity. Therefore, locomotor costs are driven more by ecological relevance than by the need to optimize locomotor economy.     

Decoding mechanisms by which silent codon changes influence protein biogenesis and function

ScopeSynonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health.PurposeThis synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics.Physiological and medical relevanceUnderstanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies.     

陆地生态系统中低剂量毒物刺激作用及拟合模型研究进展

低剂量毒物刺激作用(hormesis)是在毒物剂量/效应关系中低剂量毒物可能表现出对生物生长的一种刺激作用.大量的实验数据表明毒物刺激作用发生的剂量低于未观察到毒性效应的剂量(NOAEL),毒物刺激作用的最大刺激效应一般是对照的130%～160%,是一种客观存在的剂量/反应现象.就毒物刺激作用的概念、机理、毒物刺激作用剂量/反应曲线的一些定量特点和模型的拟合等方面进行了综述,并用实例说明毒物刺激作用模型的最新拟合方法的应用,最后提出了目前毒物刺激作用研究中存在的问题及今后的研究方向.     

Next‐generation sequencing,FISH mapping and synteny‐based modeling reveal mechanisms of decreasing dysploidy in Cucumis

In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage‐specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1–AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian‐like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., 2009 , Nat. Genet. 41, 1275–1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia‐Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine‐scale understanding of the mechanisms of dysploid chromosome reduction that has not been achieved previously.     

Study of B72.3 combining sites by molecular modeling and site-directed mutagenesis

A B72.3 Fab/sTn(2) complex was modeled from the known structure of B72.3 Fab and the dimeric Tn-serine cluster (sTn(2)). In the complex model, the side chains of 15 heavy- and light-chain complementarity-determining region (CDR) residues and the main chains of two light-chain CDR residues contact the sTn(2) epitope. Among 15 CDR residues which contact sTn(2) in the model, two heavy-chain residues (Ser95 and Tyr97) and light-chain CDR residue (Tyr96) have been confirmed in a previous study. To test the accuracy of the computational model, further site-directed mutagenesis was performed by alanine scanning on the remaining 12 residues that are predicted in the model to have side-chain interactions with sTn(2). Of these 12 mutants, eight that are all from the heavy-chain (His32Ala, Ala33Leu, Tyr50Ala, Ser52Ala, Asn52Ala, Asp56Ala, Lys58Ala and Tyr96Ala) had significantly reduced sTn(2) affinities, and four consisting of three light-chain mutations (Asn32Ala, Trp92Ala and Thr94Ala) and one heavy-chain mutation (His35Ala) retained wild-type sTn(2) affinity. On the whole, this evidence suggests that the complex model, although not perfect, is correct in many of its features. In a more general vein, these results lend credibility to the computational modeling approach for the study of the molecular basis of antigen-antibody complexes.     

Phylogenetic relationships of bolitoglossine salamanders: a demonstration of the effects of combining morphological and molecular data sets

We analyzed sequence data for 555 bp of the mitochondrial gene cytochrome b in plethodontid salamanders, taken from 18 ingroup (tribe Bolitoglossini) and 4 outgroup (tribe Plethodontini) taxa. There were 257 variable sites, of which 219 were phylogenetically informative. Sequence differences among taxa exceeded 20%, and there were up to 15% amino acid differences among the sequences. We also analyzed 37 morphological (including karyological) characters, taken from the literature. Data were analyzed separately and then combined using parsimony and likelihood approaches. There is little conflict between the morphological and DNA data, and that which occurs is at nodes that are weakly supported by one or both of the data sets. Treated separately, the morphological and DNA data provide strong support for some nodes but not for others. The combined data act synergistically so that good support is obtained for nearly all of the nodes in the tree. Recent divergences are supported by silent transitions, and older divergences are supported by a combination of morphological, karyological, DNA transversion, and amino acid changes. Eliminating silent changes from the DNA data improves the consistency index and improves some bootstrap and decay index values for several deeper branches in the tree. However, the combined data set with all characters included provides a better supported tree overall. Maximum likelihood and parsimony with all of the data give not only the same topology but also remarkably similar branch lengths. Results of this analysis support the monopoly of the supergenera Hydromantes and Batrachoseps, and of a sister group relationship of Batrachoseps and the supergenus Bolitoglossa (represented in this study one species of the genus Bolitoglossa).      

Analyzing and modeling of photobioreactors by combining first principles of physiology and hydrodynamics

Mixing in photobioreactors is known to enhance biomass productivity considerably, and flow dynamics play a significant role in the reactor's performance, as they determine the mixing and the cells' movement. In this work we focus on analyzing the effects of mixing and flow dynamics on the photobioreactor performance. Based on hydrodynamic findings from the CARPT(Computer Automated Radioactive Particle Tracking) technique, a possible mechanism for the interaction between the mixing and the physiology of photosynthesis is presented, and the effects of flow dynamics on light availability and light intensity fluctuation are discussed and quantitatively characterized. Furthermore, a dynamic modeling approach is developed for photobioreactor performance evaluation, which integrates first principles of photosynthesis, hydrodynamics, and irradiance distribution within the reactor. The results demonstrate the reliability and the possible applicability of this approach to commercially interesting microalgae/cyanobacteria culture systems.     

The neurobiology of depression--revisiting the serotonin hypothesis. I. Cellular and molecular mechanisms

The serotonin (5-HT) hypothesis of depression dates from the 1960s. It originally postulated that a deficit in brain serotonin, corrected by antidepressant drugs, was the origin of the illness. Nowadays, it is generally accepted that recurring mood disorders are brain diseases resulting from the combination, to various degrees, of genetic and other biological as well as environmental factors, evolving through the lifespan. All areas of neuroscience, from genes to behaviour, molecules to mind, and experimental to clinical, are actively engaged in attempts at elucidating the pathophysiology of depression and the mechanisms underlying the efficacy of antidepressant treatments. This first of two special issues of Philosophical Transactions B seeks to provide an overview of current developments in the field, with an emphasis on cellular and molecular mechanisms, and how their unravelling opens new perspectives for future research.     

Cellular, synaptic, network, and modulatory mechanisms involved in rhythm generation

The membrane properties and the synaptic interactions of individual neurons, as well as the interactions between neuronal networks, all contribute to the formation of the complex patterns of activity that underlie rhythmic motor patterns and slow-wave sleep rhythms. These properties and interactions are potential points of modulation for further refining network output. Recent work illustrates the range of these properties and interactions and suggests how they may be modulated.     

Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments

MOTIVATION: Two major bottlenecks in advancing comparative protein structure modeling are the efficient combination of multiple template structures and the generation of a correct input target-template alignment. RESULTS: A novel method, Multiple Mapping Method with Multiple Templates (M4T) is introduced that implements an algorithm to automatically select and combine Multiple Template structures (MT) and an alignment optimization protocol (Multiple Mapping Method, MMM). The MT module of M4T selects and combines multiple template structures through an iterative clustering approach that takes into account the 'unique' contribution of each template, their sequence similarity among themselves and to the target sequence, and their experimental resolution. MMM is a sequence-to-structure alignment method that optimally combines alternatively aligned regions according to their fit in the structural environment of the template structure. The resulting M4T alignment is used as input to a comparative modeling module. The performance of M4T has been benchmarked on CASP6 comparative modeling target sequences and on a larger independent test set, and showed favorable performance to current state of the art methods.     

Decoding common mechanisms of cellular genetic-epigenetic control in eukaryotes]

The mechanism of genetic epigenetic operation at genomic and chromosomic levels within the limits of imitation model of eucaryotic cellular compartment is postulated, this compartment including left and right operators. Probable pattern of interactions during reproduction, determination and expression of genes as a manifestation of genetic, epigenetic memory and memory of water is shown. A specific character and rate of transformations of nucleotides and proteins are realized through different operation mechanisms over hierarchic processes directed on the preservation of DNA in the line of cellular generations and also determining dynamics of the genome with DNA variations. The mechanism of programmed provision of genetic-epigenetic interaction lies in the ways of control, regulation, adaptation and modulation of nucleotides and proteins transformations which occur on the basis of specific (complementary, kinetic and tunnel effects) choice of directions, place, time and aim of nucleotide-nucleotide, nucleotide-protein, protein-nucleotide and protein-protein interactions.     

Transient hypermutability, chromothripsis and replication-based mechanisms in the generation of concurrent clustered mutations

Clustered mutations may be broadly defined as the presence of two or more mutations within a spatially localized genomic region on a single chromosome. Known instances vary in terms of both the number and type of the component mutations, ranging from two closely spaced point mutations to tens or even hundreds of genomic rearrangements. Although clustered mutations can represent the observable net result of independent lesions sequentially acquired over multiple cell cycles, they can also be generated in a simultaneous or quasi-simultaneous manner within a single cell cycle. This review focuses on those mechanisms known to underlie the latter type. Both gene conversion and transient hypermutability are capable of generating closely spaced multiple mutations. However, a recently described phenomenon in human cancer cells, known as ‘chromothripsis’, has provided convincing evidence that tens to hundreds of genomic rearrangements can sometimes be generated simultaneously via a single catastrophic event. The distinctive genomic features observed in the derivative chromosomes, together with the highly characteristic junction sequences, point to non-homologous end joining (NHEJ) as being the likely underlying mutational mechanism. By contrast, replication-based mechanisms such as microhomology-mediated break-induced replication (MMBIR) which involves serial replication slippage or serial template switching probably account for those complex genomic rearrangements that comprise multiple duplications and/or triplications.     

Transient hypermutability, chromothripsis and replication-based mechanisms in the generation of concurrent clustered mutations

Clustered mutations may be broadly defined as the presence of two or more mutations within a spatially localized genomic region on a single chromosome. Known instances vary in terms of both the number and type of the component mutations, ranging from two closely spaced point mutations to tens or even hundreds of genomic rearrangements. Although clustered mutations can represent the observable net result of independent lesions sequentially acquired over multiple cell cycles, they can also be generated in a simultaneous or quasi-simultaneous manner within a single cell cycle. This review focuses on those mechanisms known to underlie the latter type. Both gene conversion and transient hypermutability are capable of generating closely spaced multiple mutations. However, a recently described phenomenon in human cancer cells, known as 'chromothripsis', has provided convincing evidence that tens to hundreds of genomic rearrangements can sometimes be generated simultaneously via a single catastrophic event. The distinctive genomic features observed in the derivative chromosomes, together with the highly characteristic junction sequences, point to non-homologous end joining (NHEJ) as being the likely underlying mutational mechanism. By contrast, replication-based mechanisms such as microhomology-mediated break-induced replication (MMBIR) which involves serial replication slippage or serial template switching probably account for those complex genomic rearrangements that comprise multiple duplications and/or triplications.