The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster

Jingwei (jgw) is the first gene found to be of sufficiently recent origin in Drosophila to offer insights into the origin of a gene. While its chimerical gene structure was partially resolved as including a retrosequence of alcohol dehydrogenase (ADH:), the structure of its non-ADH: parental gene, the donor of the N-terminal domain of jgw, is unclear. We characterized this non-ADH: parental locus, yellow emperor (ymp), by cloning it, mapping it onto the polytene chromosomes, sequencing the entire locus, and examining its expression patterns in Drosophila melanogaster. We show that ymp is located in the 96-E region; the N-terminal domain of ymp has donated the non-ADH: portion of jgw via a duplication. The similar 5' portions of the gene and its regulatory sequences give rise to similar testis-specific expression patterns in ymp and jgw in Drosophila teissieri. Furthermore, between-species comparison of ymp revealed purifying selection in the protein sequence, suggesting a functional constraint in ymp. While the structure of ymp provides clear information for the molecular origin of the new gene jgw, it unexpectedly casts a new light on the concept of genes. We found, for the first time, that the single locus of the ymp gene encompasses three major molecular mechanisms determining structure of eukaryotic genes: (1) the 5' exons of ymp are involved in an exon-shuffling event that has created the portion recruited by jgw; (2) using alternative cleavage sites and alternative splicing sites, the 3' exon groups of ymp produce two proteins with nonhomologous C-terminal domains, both exclusively in the testis; and (3) in the opposite strand of the third intron of ymp is an essential gene, musashi (msi), which encodes an RNA-binding protein. The composite gene structure of ymp manifests the complexity of the gene concept, which should be considered in genomic research, e.g., gene finding.     

The problem of the gene

During the early 20th century the diverse practices of genetics were unified by the concept of the gene. This classical gene was simultaneously a unit of structure, function, mutation, and recombination. Starting in the 1940s, however, the classical gene began to fragment. Today when we speak of a gene for some malady, a regulatory gene, a structural gene, or a gene frequency, it is entirely possible that we are deploying different gene concepts even though we are using the same term. The problem of the gene addresses the fragmentation of the classical gene concept by asking to what extent a comprehensive and unifying gene concept is possible or desirable. Fully comprehensive gene concepts seem untenable today, but, within different disciplinary domains, unifying, but non-comprehensive, gene concepts can be epistemically worthwhile. The problem of the gene persists, however, not because of its epistemic value, but because of its political value. Using both the arguments for newly proposed gene concepts and the historical dispute over the classical gene, I argue that the desirability of gene concepts rests in part on the political ramifications of their deployment and contestation.     

Effects of cell culture techniques on gene expression and cholesterol efflux in primary bovine mammary epithelial cells derived from milk and tissue

Primary bovine mammary epithelial cells (pbMEC) are often used in cell culture to study metabolic and inflammatory processes in the udder of dairy cows. The most common source is udder tissue from biopsy or after slaughter. However, it is also possible to culture them from milk, which is non-invasive, repeatable and yields less contamination with fibroblasts. Generally, not much is known about the influence of cell origin and cell culture techniques such as cryopreservation on pbMEC functionality. Cells were extracted from milk and udder tissue to evaluate if milk-derived pbMEC are a suitable alternative to tissue-derived pbMEC and to test what influence cryopreservation has. The cells were cultivated for three passages and stored in liquid nitrogen. The relative gene expression of the five target genes kappa-casein, lingual antimicrobial peptide (LAP), lactoferrin, lysozyme (LYZ1) and the prolactin receptor normalised with keratin 8 showed a tendency to decrease in the tissue cultures, but not in the milk-derived cultures, suggesting a greater influence of the cultivation process on tissue-derived cells, freezing lowered expression levels in both cultures. Overall expression of LAP and LYZ1 tended to be higher in milk cells. Cholesterol efflux was measured to compare passages one to seven in milk-derived cells. Passage number did not alter the efflux rate (p????0.05). We showed for the first time that the extraction of pbMEC from milk can be a suitable alternative to tissue extraction.     

Multi-gene engineering: simultaneous expression and knockdown of six genes off a single platform

Increases in our understanding of gene function have greatly expanded the repertoire of possible genetic interventions at our disposal with the consequence that many genetic engineering applications require multiple manipulations in which target genes can be both overexpressed and silenced in a simple and co-ordinated manner. Using synthetic introns as a source of encoding short-interfering RNA (siRNA), we demonstrate that it is possible to simultaneously express both a transgene and siRNA from a single polymerase (Pol) II promoter. By encoding siRNA as an intron between two protein domains requiring successful splicing for functionality, it was possible to demonstrate that splicing was occurring, that the coding genes (exonic transgenes) resulted in functional protein, and that the spliced siRNA-containing lariat was capable of modulating expression of a separate target gene. We subsequently extended this concept to develop pTRIDENT-based multi-cistronic vectors that were capable of co-ordinated expression of up to three siRNAs and three transgenes off a single genetic platform. Such multi-gene engineering technology, enabling concomitant transgene overexpression and target gene knockdown, should be useful for therapeutic, biopharmaceutical production, and basic research applications.     

Paramutation: an encounter leaving a lasting impression

Paramutation is the result of heritable changes in gene expression that occur upon interaction between alleles. Whereas Mendelian rules, together with the concept of genetic transmission via the DNA sequence, can account for most inheritance in sexually propagating organisms, paramutation-like phenomena challenge the exclusiveness of Mendelian inheritance. Most paramutation-like phenomena have been observed in plants but there is increasing evidence for its occurrence in other organisms, including mammals. Our knowledge of the underlying mechanisms, which might involve RNA silencing, physical pairing of homologous chromosomal regions or both, is still limited. Here, we discuss the characteristics of different paramutation-like interactions in the light of arguments supporting each of these alternative mechanisms.     

Biodiversity Realism: Preserving the tree of life

Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the concept of “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata, this concept should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the ‘tree of life’.     

Identification of novel potent hydroxamic acid inhibitors of peptidyl deformylase and the importance of the hydroxamic acid functionality on inhibition

Peptidyl deformylase (PDF) is a metallo protease that catalyzes the removal of a formyl group from the N-termini of prokaryotic prepared polypeptides, an essential step in bacterial protein synthesis. Screening of our compound collection using Staphylococcus aureus PDF afforded a very potent inhibitor with an IC(50) in the low nanomolar range. Unfortunately, the compound that contains a hydroxamic acid did not exhibit antibacterial activity (MIC). In order to address the lack of activity in the MIC assay and to determine what portion of the molecule was responsible for binding to PDF, we prepared several analogues. This paper describes our findings that the hydroxamic acid functionality found in 1 is mainly responsible for the high affinity to PDF. In addition, we identified an alternative class of PDF inhibitors, the N-hydroxy urea 18, which has both PDF and antibacterial activity.     

It Takes All Kinds in Acoustic Communication: A New Perspective on the Song Overlapping Phenomenon

Over the last few decades, research into song overlapping produced many – often conflicting – interpretations of its function and culminated in the current debate about the usefulness of this concept. To avoid a deadlock in song overlapping research, we present a new approach to existing evidence and offer several novel hypotheses that might help enhance future experiments. Our analysis offers both a theoretical perspective and specific predictions of each testable hypothesis. We present a detailed analysis of important questions. First, what information does song overlapping convey (is it a signal of aggressive intent or of male quality)? Second, what evolutionary mechanism stabilizes honesty of song overlapping as a signal (is it an index signal, handicap, proximity risk, conventional signal or a modifier)? Additionally, we offer some alternative explanations of the phenomenon (song overlapping as a mask or an incidental phenomenon). We hope to encourage future researchers not only to gather high‐quality experimental data, but also to make more careful interpretations, as we believe that no all‐encompassing explanation of song overlapping will be formulated any time soon. Focused comparative approaches will be necessary, as song overlapping might have different functions in different species.     

Local renin-angiotensin systems: the unanswered questions

The concept of local renin-angiotensin systems has been introduced almost 20 years ago to explain the beneficial blood pressure-independent effects of ACE inhibitors and AT(1) receptor antagonists in cardiovascular diseases. In the past decade, research has focussed on the local effects of angiotensin II rather than on the mechanism(s) of its local generation. This review addresses several of the unanswered questions with regard to tissue angiotensin II generation, focussing in particular on the heart and vascular wall: (1) what is the origin of the renin that is required to generate angiotensin II locally, (2) where does tissue angiotensin generation occur (intra- versus extracellular), (3) what is the importance of alternative (non-renin, non-ACE) angiotensin-generating enzymes, (4) do ACE inhibitors and AT(1) receptor antagonists exert local effects that are renin-angiotensin system independent (thereby incorrectly leading to the conclusion that they interfere with the local generation or effects of angiotensin II), and (5) to what degree do differences in tissue angiotensin generation underlie the association between cardiovascular diseases and renin-angiotensin system gene polymorphisms?     

The extended phenotype(s): a comparison with niche construction theory

While niche construction theory locates animal artefacts in their constructors’ environment, hence treating them as capable of exerting selective pressure on both the constructors and their descendants, the extended phenotype concept assimilates artefacts with their constructors’ genes. Analogous contrasts apply in the case of endoparasite and brood parasite genes influencing host behaviour. The explanatory power of these competing approaches are assessed by re-examining the core chapters of Richard Dawkins’ The Extended Phenotype. Because animal artefacts (chapter 11) have multiple evolutionary consequences for their constructors, the extra-body effects of a gene seemingly include feedback effects on multiple other genes, a result which is more consistent with niche construction theory than with selfish gene theory. In the case of endoparasite genes influencing host behaviour (chapter 12), Dawkins’ argument leaves out what appears to be the key explanatory component, namely the role of the host’s own bodily systems in making it possible for such genes to exist. For action at a distance (chapter 13), it is unclear whether the key genes have extended effects because they sit in the body of the manipulating organism, or alternatively do not have such effects because they sit in the body of its victim. It is argued that niche construction theory offers a superior explanation in all three cases, regardless of whether the extended phenotype concept is interpreted in selfish gene or selfish organism terms.     

Homology across inheritance systems

Recent work on inheritance systems can be divided into inclusive conceptions, according to which genetic and non-genetic inheritance are both involved in the development and transmission of nearly all animal behavioral traits, and more demanding conceptions of what it takes for non-genetic resources involved in development to qualify as a distinct inheritance system. It might be thought that, if a more stringent conception is adopted, homologies could not subsist across two distinct inheritance systems. Indeed, it is commonly assumed that homology relations cannot survive a shift between genetic and cultural inheritance systems, and substantial reliance has been placed on that assumption in debates over the phylogenetic origins of hominin behavioral traits, such as male-initiated intergroup aggression. However, in the homology literature it is widely accepted that a trait can be homologous—that is, inherited continuously in two different lineages from a single common ancestor—despite divergence in the mechanisms involved in the trait’s development in the two lineages. In this paper, we argue that even on an extremely stringent understanding of what it takes for developmental resources to form a separate inheritance system, homologies can nonetheless subsist across shifts between distinct inheritance systems. We argue that this result is a merit of this way of characterizing what it is to be an inheritance system, that it has implications for adjudicating between alternative accounts of homology, and that it offers an important cautionary lesson about how (not) to reason with the homology concept, particularly in the context of cultural species.     

The Ecosystem as a Multidimensional Concept: Meaning,Model, and Metaphor

The ecosystem is a fundamental ecological concept that is not as simple as it first appears. We explore three key dimensions of the concept that make it both complex and broadly useful—its basic definition, its application via models to concrete or specific situations, and its metaphorical connotations as used in general communication within the domain of science and with the public at large. Clarity in identifying what the dimensions are and how they are related can help to maintain the rigor of the concept for specific scientific uses while also allowing enough flexibility for its use in the integration of scientific principles, as well as in public discourse. This analysis of the ecosystem as a multidimensional concept is likely to be generalizable to other important concepts in ecology. Received 28 February 2001; accepted 5 September 2001.     

端粒维持研究进展

端粒是现代生物学的研究热点,与肿瘤发生、基因表达调控、衰老有着密切的关系。本综述介绍当前对端粒维持机理研究的进展。在端粒维持过程中有两类重要的蛋白：端粒相关蛋白和端粒酶。端粒相关蛋白是直接或间接与端粒结合的蛋白 ,在维持端粒稳定性方面有重要作用。端粒酶,特别是其催化亚基ｈＴＥＲＴ,在端粒延长过程中起着不可替代的作用,与细胞永生化和癌变密切相关。此外还介绍了在某些细胞中存在的不依赖端粒酶的端粒延长机     

Molecular evolution and phylogeny of the angiosperm ycf2 gene

Much of the recent progress in understanding angiosperm phylogeny has been achieved using multi-gene or plastid genome datasets. However, it is largely unclear what size of dataset is required to achieve suffi-cient resolution. The ycf2 gene is the largest plastid gene in angiosperms and it was used as part of multigene datasets in several earlier investigations into angiosperm relationships. In this study, we show that the ycf2 gene alone can provide a generally well-supported phylogeny that is consistent with those inferred from the most comprehensive multigene or plastid genome datasets. The phylogenetic signal of the ycf2 gene is likely de-rived from the combination of its long sequence length and low rate of nucleotide substitution. The ycf2 gene may provide a low-cost alternative to comprehensive multigene or genome datasets for investigating angiosperm relationships.     

Genome trees and the tree of life

Genome comparisons indicate that horizontal gene transfer and differential gene loss are major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the majority, of genes. The extent of these events casts doubt on the feasibility of constructing a 'Tree of Life', because the trees for different genes often tell different stories. However, alternative approaches to tree construction that attempt to determine tree topology on the basis of comparisons of complete gene sets seem to reveal a phylogenetic signal that supports the three-domain evolutionary scenario and suggests the possibility of delineation of previously undetected major clades of prokaryotes. If the validity of these whole-genome approaches to tree building is confirmed by analyses of numerous new genomes, which are currently being sequenced at an increasing rate, it would seem that the concept of a universal 'species' tree is still appropriate. However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution.