Just a hypothesis: a reply to Hanski

Hanski's critique of the habitat amount hypothesis (Hanski, 2015, Journal of Biogeography, 42 , 989–993) does not actually constitute a test of the hypothesis, but rather a series of arguments for why he suspects that it is not correct. But the habitat amount hypothesis is exactly that – a hypothesis. It will remain ‘just’ a hypothesis until it has been rigorously tested against empirical data. To facilitate such testing, in Fahrig (2013, Journal of Biogeography, 40 , 1649–1663) I presented specific, testable predictions of the hypothesis. Here, I reiterate the main tests needed, in the hope that some readers will be encouraged to carry them out. I appreciate this opportunity to emphasize that the habitat amount hypothesis needs to be tested against empirical data, and I look forward to seeing the results of such tests.     

REGgamma: a shortcut to destruction

Destruction of intact cellular proteins is largely orchestrated by ATP-dependent ubiquitination and subsequent degradation by the 26S proteasome. The REG-20S proteasome, however, only degrades short peptides. In this issue of Cell, challenge this notion by revealing that the proteasomal activator REGgamma directs degradation of the steroid receptor coactivator SRC-3 by the 20S proteasome in an ATP- and ubiquitin-independent manner.     

How to build a biofilm: a fungal perspective

Biofilms are differentiated masses of microbes that form on surfaces and are surrounded by an extracellular matrix. Fungal biofilms, especially those of the pathogen Candida albicans, are a cause of infections associated with medical devices. Such infections are particularly serious because biofilm cells are relatively resistant to many common antifungal agents. Several in vitro models have been used to elucidate the developmental stages and processes required for C. albicans biofilm formation, and recent studies have begun to define biofilm genetic control. It is clear that cell-substrate and cell-cell interactions, hyphal differentiation and extracellular matrix production are key steps in biofilm development. Drug resistance is acquired early in biofilm formation, and appears to be governed by different mechanisms in early and late biofilms. Quorum sensing might be an important factor in dispersal of biofilm cells. The past two years have seen the emergence of several genomic strategies to uncover global events in biofilm formation and directed studies to understand more specific events, such as hyphal formation, in the biofilm setting.     

Adhesion-mediated mechanosensitivity: a time to experiment, and a time to theorize

Adhesion-mediated signaling provides cells with information about multiple parameters of their microenvironment, including mechanical characteristics. Often, such signaling is based on a unique feature of adhesion structures: their ability to grow and strengthen when force is applied to them, either from within the cell or from the outside. Such adhesion reinforcement is characteristic of integrin-mediated cell-matrix adhesions, but may also operate in other types of adhesion structures. Though the amount of knowledge about adhesion-mediated signaling is growing rapidly, the mechanisms underlying force-dependent regulation of junction assembly are largely unknown. Experiments have been carried out that have started to uncover the major signaling pathways involved in the response of adhesion sites to force. Theoretical models have also been used to address the physical mechanisms underlying adhesion-mediated mechanosensing.     

Re-entry: a guide to success?

This article is based upon a former prisoner/parolee’s first hand account and analyzes some of the more obvious obstacles awaiting parolees when released from prison. Included is an examination of some basic resources the author considered necessary for successful re-entry. Potential conflicts between providing helpful resources and the status quo within the current Prison-Industrial Complex are also considered.     

WebPHYLIP: a web interface to PHYLIP

A web interface to PHYLIP (version 3.57 C) is implemented using CGI/Perl programming. It enables users to do phylogenetic analysis through the Internet.     

Biotelemetry: a mechanistic approach to ecology

Remote measurement of the physiology, behaviour and energetic status of free-living animals is made possible by a variety of techniques that we refer to collectively as 'biotelemetry'. This set of tools ranges from transmitters that send their signals to receivers up to a few kilometers away to those that send data to orbiting satellites and, more frequently, to devices that log data. They enable researchers to document, for long uninterrupted periods, how undisturbed organisms interact with each other and their environment in real time. In spite of advances enabling the monitoring of many physiological and behavioural variables across a range of taxa of various sizes, these devices have yet to be embraced widely by the ecological community. Our review suggests that this technology has immense potential for research in basic and applied animal ecology. Efforts to incorporate biotelemetry into broader ecological research programs should yield novel information that has been challenging to collect historically from free-ranging animals in their natural environments. Examples of research that would benefit from biotelemetry include the assessment of animal responses to different anthropogenic perturbations and the development of life-time energy budgets.     

Data standards: a call to action

Access to data is something that every molecular biologist takes for granted nowadays, but data alone is of little use unless it is made available in a useable form through the development and global uptake of data standards. The challenge of standards development has been taken up by grass-roots movements working within several different branches of the biomedical research community. Many of these initiatives are proving extremely successful; for example, the Gene Ontology, which provides a controlled vocabulary for describing the properties of gene products, the Microarray Gene Expression Data Society's standards for describing microarray experiments, and the emerging standards developed by the Proteomics Standards Initiative are gaining broad acceptance. Standards development now faces its greatest ever challenge--the integration of diverse data types to fulfill the goals of systems biology. Now is the time for the communities that are developing these standards, the funding bodies that have invested so heavily in high-throughput data generation, and the publishers of biomedical research papers to cooperate fully to make the goals of integrated data analysis a reality.     

Peptidomics: a logical sequel to proteomics

Rapid progress of separation techniques as well as methods of structural analysis provided conditions in the past decade for total screening of complex biologic mixtures for any given class of biomolecules. The present review updates the reader with the modern state of peptidomics, a chapter of chemical biology that deals with structure and biologic properties of sets of peptides present in biologic tissues, cells or fluids. Scope and limitations of currently employed experimental techniques are considered and the main results are outlined. Considerable attention will be afforded to the biologic role of peptides formed in vivo by proteolysis of nonspecialized precursor proteins with other well-defined functions. In conclusion, the connection is discussed between peptidomics and the much more mature and still closely related field of proteomics.