Human behavioral ecology and niche construction

We examine the relationship between niche construction theory (NCT) and human behavioral ecology (HBE), two branches of evolutionary science that are important sources of theory in archeology. We distinguish between formal models of niche construction as an evolutionary process, and uses of niche construction to refer to a kind of human behavior. Formal models from NCT examine how environmental modification can change the selection pressures that organisms face. In contrast, formal models from HBE predict behavior assuming people behave adaptively in their local setting, and can be used to predict when and why people engage in niche construction. We emphasize that HBE as a field is much broader than foraging theory and can incorporate social and cultural influences on decision‐making. We demonstrate how these approaches can be formally incorporated in a multi‐inheritance framework for evolutionary research, and argue that archeologists can best contribute to evolutionary theory by building and testing models that flexibly incorporate HBE and NCT elements.     

Genetic engineering in vivo using translocatable drug-resistance elements. New methods in bacterial genetics.

A number of translocatable drug-resistance elements have recently been described which are able to insert themselves into a large number of different sites in prokaryotic genomes. These elements cause recognizable mutations when insertion occurs within a structural gene or an operon. Drug-resistance elements are also associated with other kinds of illegitimate recombination events, notably deletions and inversions.This paper summarizes uses to which these properties of translocatable drugr-esistance elements can be put in genetic manipulations of bacteria. Translocatable drug-resistance elements are useful in isolation of mutants (even where the mutant phenotype is not easily scored), in the construction of strains and other genetic manipulations (even when selection is difficult or impossible), in localized mutagenesis, in chromosomal mapping, in construction of Hfr strains with known origin and direction of chromosome transfer, in complementation tests, in construction of new F′ plasmids, in construction of new specialized transducing phages, in isolation of deletions with one or both endpoints specified, in construction of gene and operon fusions, and in the selection and maintenance of chromosomal duplications. Experiments are described which illustrate many of these techniques.     

Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays

Efficient construction of BAC-based human artificial chromosomes (HACs) requires optimization of each key functional unit as well as development of techniques for the rapid and reliable manipulation of high-molecular weight BAC vectors. Here, we have created synthetic chromosome 17-derived alpha-satellite arrays, based on the 16-monomer repeat length typical of natural D17Z1 arrays, in which the consensus CENP-B box elements are either completely absent (0/16 monomers) or increased in density (16/16 monomers) compared to D17Z1 alpha-satellite (5/16 monomers). Using these vectors, we show that the presence of CENP-B box elements is a requirement for efficient de novo centromere formation and that increasing the density of CENP-B box elements may enhance the efficiency of de novo centromere formation. Furthermore, we have developed a novel, high-throughput methodology that permits the rapid conversion of any genomic BAC target into a HAC vector by transposon-mediated modification with synthetic alpha-satellite arrays and other key functional units. Taken together, these approaches offer the potential to significantly advance the utility of BAC-based HACs for functional annotation of the genome and for applications in gene transfer.     

转座子相关技术在微生物功能基因组研究中的应用

转座子是DNA插入因子的一种,是指能在基因组间或组内跳跃的DNA片段。转座子作为插入突变剂或分子标签已被广泛地应用于基因的分离和克隆,且因其独特的性质已成为发现新基因和基因功能分析的有效工具。这使得转座子无论是在单基因水平还是全基因组水平,都成为细菌、酵母和其他微生物研究的有力工具。简单而有效的体外转座反应可以对一些以往难以进行分析的顽固微生物进行转座诱变分析。而建立在转座子基础上的信号标签诱变技术和遗传足迹法的应用则发现了一些新的病原微生物毒力因子,从而可以更好地对这些病原微生物的致病机理进行阐述。这些再次说明转座子是微生物功能基因组研究中的有力工具。本文综述了转座子及其衍生载体介导的一些技术,并讨论其在微生物功能基因组研究中的应用。     

Life cycle assessment of construction materials: the influence of assumptions in end-of-life modelling

Purpose

The nature of end-of-life (EoL) processes is highly uncertain for constructions built today. This uncertainty is often neglected in life cycle assessments (LCAs) of construction materials. This paper tests how EoL assumptions influence LCA comparisons of two alternative roof construction elements: glue-laminated wooden beams and steel frames. The assumptions tested include the type of technology and the use of attributional or consequential modelling approaches.

Methods

The study covers impact categories often considered in the construction industry: total and non-renewable primary energy demand, water depletion, global warming, eutrophication and photo-chemical oxidant creation. The following elements of the EoL processes are tested: energy source used in demolition, fuel type used for transportation to the disposal site, means of disposal and method for handling allocation problems of the EoL modelling. Two assumptions regarding technology development are tested: no development from today’s technologies and that today’s low-impact technologies have become representative for the average future technologies. For allocating environmental impacts of the waste handling to by-products (heat or recycled material), an attributional cut-off approach is compared with a consequential substitution approach. A scenario excluding all EoL processes is also considered.

Results and discussion

In all comparable scenarios, glulam beams have clear environmental benefits compared to steel frames, except for in a scenario in which steel frames are recycled and today’s average steel production is substituted, in which impacts are similar. The choice of methodological approach (attributional, consequential or fully disregarding EoL processes) does not seem to influence the relative performance of the compared construction elements. In absolute terms, four factors are shown to be critical for the results: whether EoL phases are considered at all, whether recycling or incineration is assumed in the disposal of glulam beams, whether a consequential or attributional approach is used in modelling the disposal processes and whether today’s average technology or a low-impact technology is assumed for the substituted technology.

Conclusions

The results suggest that EoL assumptions can be highly important for LCA comparisons of construction materials, particularly in absolute terms. Therefore, we recommend that EoL uncertainties are taken into consideration in any LCA of long-lived products. For the studied product type, LCA practitioners should particularly consider EoL assumptions regarding the means of disposal, the expected technology development of disposal processes and any substituted technology and the choice between attributional and consequential approaches.     

Fungal transposable elements: Generators of diversity and genetic tools

Representatives of several classes of transposable elements (TEs) have been characterized in a broad range of fungal species. The studies indicate that these elements are ancient and ubiquitous components of fungal genomes. Some of these elements have been shown to actively affect gene structure and function in several ways: inactivation of gene expression upon insertion, modification of the nucleotide sequence through excision, and probably by inducing extensive chromosomal rearrangements. The ability of TEs to generate a high degree of genetic diversity may therefore be important in the evolution of the fungal genome. TEs also have many potential applications in genetic research, including insertional mutagenesis and population fingerprinting, as well as gene transfer within and between species. All these genetic approaches are important as tools in studies of molecular biology and evolution of fungal species, many of which lack a functional sexual cycle.     

Spider Glue Proteins Have Distinct Architectures Compared with Traditional Spidroin Family Members

Adhesive spider glues are required to perform a variety of tasks, including web construction, prey capture, and locomotion. To date, little is known regarding the molecular and structural features of spider glue proteins, in particular bioadhesives that interconnect dragline or scaffolding silks during three-dimensional web construction. Here we use biochemical and structural approaches to identify and characterize two aggregate gland specific gene products, AgSF1 and AgSF2, and demonstrate that these proteins co-localize to the connection joints of both webs and wrapping silks spun from the black widow spider, Latrodectus hesperus. Protein architectures are markedly divergent between AgSF1 and AgSF2, as well as traditional spider silk fibroin family members, suggesting connection joints consist of a complex proteinaceous network. AgSF2 represents a nonglycosylated 40-kDa protein that has novel internal amino acid block repeats with the consensus sequence NVNVN embedded in a glycine-rich matrix. Analysis of the amino acid sequence of AgSF1 reveals pentameric QPGSG iterations that are similar to conserved modular elements within mammalian elastin, a rubber-like elastomeric protein that interfaces with collagen. Wet-spinning methodology using purified recombinant proteins show AgSF1 has the potential to self-assemble into fibers. X-ray fiber diffraction studies performed on these synthetic fibers reveal the presence of noncrystalline domains that resemble classical rubber networks. Collectively, these data support that the aggregate gland serves to extrude a protein mixture that contains substances that allow for the self-assembly of fiber-like structures that interface with dragline silks to mediate prey capture.     

Use of minigene systems to dissect alternative splicing elements

Pre-mRNA splicing is an essential step for gene expression in higher eukaryotes. The splicing efficiency of individual exons is determined by multiple features involving gene architecture, a variety of cis-acting elements within the exons and flanking introns, and interactions with components of the basal splicing machinery (called the spliceosome) and auxiliary regulatory factors which transiently co-assemble with the spliceosome. Both alternative and constitutive exons are recognized by multiple weak protein:RNA interactions and different exons differ in the interactions which are determinative for exon usage. Alternative exons are often regulated according to cell-specific patterns and regulation is mediated by specific sets of cis-acting elements and trans-acting factors. Transient expression of minigenes is a commonly used in vivo assay to identify the intrinsic features of a gene that control exon usage, identify specific cis-acting elements that control usage of constitutive and alternative exons, identify cis-acting elements that control cell-specific usage of alternative exons, and once regulatory elements have been identified, to identify the trans-acting factors that bind to these elements and modulate splicing. This chapter describes approaches and strategies for using minigenes to define the cis-acting elements that determine splice site usage and to identify and characterize the trans-acting factors that bind to these elements and regulate alternative splicing.     

Conflicts between humans over wildlife management: on the diversity of stakeholder attitudes and implications for conflict management

Conflicts involving wildlife are, in essence, often conflicts between human parties with differing wildlife management objectives. However, the study and management of wildlife conflicts often focuses on the ecological context without addressing disagreements between people over these objectives. This research uses quantitative approaches to examine actors’ views on a complex wildlife-related conflict: a raptor of conservation concern that impacts on game-bird management. Four dominant elements of the debate emerged from initial semi-structured interviews: perceptions of conflict related issues; perceptions of each other; perceived barriers to consensus within the debate; and assessment of proposed practical management solutions. A quantitative survey that built on these elements demonstrates the degree to which perceptions differ between groups and how local variation in these elements may be obscured in a regional or national level debate. The findings emphasise the importance of understanding the social issues involved in wildlife related conflicts if management aims are to be agreed and achieved.     

Romping the cellular landscape: linear scaffolds for molecular recognition

Multivalent molecules with a precise array of recognition elements that interact with specific cell types are important for characterizing the topology of molecules on a cell surface. Applications ranging from the control of cellular signaling to drug delivery and tissue imaging rely on these surface-mapping molecules. Linear polymers provide a molecular scaffold that is advantageous for these types of applications and their synthesis can be amenable to the introduction of different recognition elements. Recently, advances have been made in the development of synthetic approaches for preparing linear polymeric substrates with highly controlled lengths and recognition element spacing.     

Role of nuclear analytical probe techniques in biological trace-element research

Many biomedical experiments require the qualitative and quantitative localization of trace elements with high sensitivity and good spatial resolution. The feasibility of measuring the chemical form of the elements, the time course of trace element metabolism, and conducting experiments in living biological systems are also important requirements for biological trace element research. Nuclear analytical techniques that employ ion or photon beams have grown in importance in the past decade and have led to several new experimental approaches. Some of the important features of these methods are reviewed here along with their role in trace element research. Examples of their use are given to illustrate potential for new research directions. It is emphasized that the effective application of these methods necessitates a closely integrated multidisciplinary scientific team.     

Adapting Management of Marine Environments to a Changing Climate: A Checklist to Guide Reform and Assess Progress

Documented impacts of climate change on marine systems indicate widespread changes in many geographic regions and throughout all levels of the ocean’s food webs. Oceans provide the main source of animal protein for over a billion people, and contribute significantly to food security for billions more. Clearly, if we are to continue to derive these benefits, then the rate of adaptation in our human systems needs to at least keep pace with the rate of ecological change for these benefits to continue. An Australia-wide program of research into marine biodiversity and fisheries explored the opportunities for policy and management to respond to a changing climate. The research program spanned all Australian estuarine-nearshore and marine environments—tropical, subtropical, and temperate—and focused on two key marine sectors: biodiversity conservation and fisheries (commercial, recreational, and aquaculture). Key findings from across this strategic and extensive research investment were the need to foster resilience through habitat repair and protection, improve resource allocation strategies, fine-tune fisheries management systems, and enhance whole of government approaches and policies. Building on these findings, from a climate adaptation perspective, we generated a checklist of thirteen elements encompassing all project findings to assess and steer progress towards improving marine policy and management. These elements are grouped in three broad areas: preconditioning; future proofing; and transformational changes and opportunities. Arising from these elements is a suite of priority strategies that provide guidance for marine managers, policy practitioners, and stakeholders as they prepare for a future under climate change. As the research program encompassed a wide range of habitats and ecosystems, spanned a latitudinal range of over 30°, and considered a diversity of management systems and approaches, many of these elements and strategies will be applicable in a global context.     

Conjugation of plasminogen activators and fibrin-specific antibodies to improve thrombolytic therapeutic agents.

Here we have reviewed chemical and recombinant approaches to the construction of hybrid molecules that combine a "targeting" antibody and an "effector" enzyme activity. There are advantages and disadvantages to both chemical and recombinant methods, and one goal of this review has been to elucidate these so that the appropriate method can be used by those interested in using hybrid molecules to study questions of basic or therapeutic importance. The system studied in greatest detail has as its goal the targeting of a plasminogen activator to an occlusive intravascular thrombus. We have, therefore, used this system as an example of currently available approaches. Now that these methodologies have been studied and put into use, it is anticipated that this principle will be generalized both to other therapeutic applications, as well as to the design and construction of molecules that will allow more basic questions to be addressed.     

Discovery of regulatory elements in vertebrates through comparative genomics

We have analyzed issues of reliability in studies in which comparative genomic approaches have been applied to the discovery of regulatory elements at a genome-wide level in vertebrates. We point out some potential problems with such studies, including difficulties in accurately identifying orthologous promoter regions. Many of these subtle analytical problems have become apparent only when studying the more complex vertebrate genomes. By determining motif reliability, we compared existing tools when applied to the discovery of vertebrate regulatory elements. We then used a statistical clustering method to produce a computational catalog of high quality putative regulatory elements from vertebrates, some of which are widely conserved among vertebrates and many of which are novel regulatory elements. The results provide a glimpse into the wealth of information that comparative genomics can yield and suggest the need for further improvement of genome-wide comparative computational techniques.     

ULTRASTRUCTURAL CHANGES IN THE MITOTIC APPARATUS AT THE METAPHASE-TO-ANAPHASE TRANSITION

As the metaphase HeLa cell approaches anaphase, pericentriolar spindle tubules fragment and become encapsulated by a unit membrane. By early anaphase, the encapsulated forms appear to have expanded, giving rise to polar spherical aggregates. Some of these elements show ribosomes on their bounding membrane, and some of them localize on the condensed chromatin during reformation of the nuclear membrane. It thus is suggested that these elements are newly derived cisternae of the endoplasmic reticulum (ER). Similar transformations are seen in later anaphase in the interzonal region, and it may be that the ER serves as a storage depot for some fraction of depolymerized microtubules. The time and location of the pericentriolar transitions are consistent with their being intimately involved in the mechanics of chromosome separation.     

A Reporter Assay in Lamprey Embryos Reveals Both Functional Conservation and Elaboration of Vertebrate Enhancers

The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species.