Ciliary subcompartments: how are they established and what are their functions?

Cilia are conserved subcellular organelles with diverse sensory and developmental roles. Recently, they have emerged as crucial organelles whose dysfunction causes a wide spectrum of disorders called ciliopathies. Recent studies on the pathological mechanisms underlying ciliopathies showed that the ciliary compartment is further divided into subdomains with specific roles in the biogenesis, maintenance and function of cilia. Several conserved sets of molecules that play specific roles in each subcompartment have been discovered. Here we review recent progress on our understanding of ciliary subcompartments, especially focusing on the molecules required for their structure and/or function. [BMB Reports 2015; 48(7): 380-387]     

How many membrane proteins are there?

One of the basic issues that arises in functional genomics is the ability to predict the subcellular location of proteins that are deduced from gene and genome sequencing. In particular, one would like to be able to readily specify those proteins that are soluble and those that are inserted in a membrane. Traditional methods of distinguishing between these two locations have relied on extensive, time-consuming biochemical studies. The alternative approach has been to make inferences based on a visual search of the amino acid sequences of presumed gene products for stretches of hydrophobic amino acids. This numerical, sequence-based approach is usually seen as a first approximation pending more reliable biochemical data. The recent availability of large and complete sequence data sets for several organisms allows us to determine just how accurate such a numerical approach could be, and to attempt to minimize and quantify the error involved. We have optimized a statistical approach to protein location determination. Using our approach, we have determined that surprisingly few proteins are misallocated using the numerical method. We also examine the biological implications of the success of this technique.     

Therefore,what are recombination proteins there for?

The order of discovery can have a profound effect upon the way in which we think about the function of a gene. In E. coli, recA is nearly essential for cell survival in the presence of DNA damage. However, recA was originally identified, as a gene required to obtain recombinant DNA molecules in conjugating bacteria. As a result, it has been frequently assumed that recA promotes the survival of bacteria containing DNA damage by recombination in which DNA strand exchanges occur. We now know that several of the processes that interact with or are controlled by recA, such as excision repair and translesion synthesis, operate to ensure that DNA replication occurs processively without strand exchanges. Yet the view persists in the literature that recA functions primarily to promote recombination during DNA repair. With the benefit of hindsight and more than three decades of additional research, we reexamine some of the classical experiments that established the concept of DNA repair by recombination, and we consider the possibilities that recombination is not an efficient mechanism for rescuing damaged cells, and that recA may be important for maintaining processive replication in a manner that does not generally promote recombination.     

How many species are there?

How many species are there is a question receiving more attention from biologists and reasons for this are suggested. Different methods of answering this question are examined and include: counting all species; extrapolations from known faunas and regions; extrapolations from samples; methods using ecological models; censusing taxonomists' views. Most of these methods indicate that global totals of 5 to 15 million species are reasonable. The implications of much higher estimates of 30 million species or more are examined, particularly the question of where these millions of species might be found.     

How many birds are there?

Attempts to assess the magnitude of global biodiversity have focused on estimating species richness. However, this is but one component of biodiversity, and others, such as numbers of individuals or biomass, are at least as poorly known and just as important to quantify. Here, we use a variety of methods to estimate the global number of individuals for a single taxon, birds. The different methods yield surprisingly consistent estimates of a global bird population of between 200 billion and 400 billion individuals (1 billion=109). We discuss some of the implications of this figure.     

Nuclear targeting of proteins: how many different signals?

The nuclear import of proteins into the cell nucleus involves the recognition of a nuclear localization signal sequence, borne by the protein to be transported, by complex molecules called importins, that will subsequently mediate the crossing over of the nuclear envelope. The most frequently encountered signal sequence is made up of short stretches of basic amino acid residues and is recognized by importins alpha and/or beta. Other signal sequences have been described, and some have been shown to mediate the association with importins other than importin alpha or beta. Recently, approaches have been developed that allow the cloning, on a functional basis, of sequences able to specify the nuclear localization of proteins. A variety of peptidic motifs of limited size which do not contain previously described signal sequences were isolated in such assays. It reveals that the spectrum of sequences that are able to target a protein to the cell nucleus may be wider than currently expected. It will probably also lead to the identification of novel target sequences for importins and will demonstrate the implication of additional members of this family of proteins in nuclear transport.     

Interpreting ‘favourable conservation status’ for large carnivores in Europe: how many are needed and how many are wanted?

The EU Habitats Directive is a key biodiversity conservation instrument. It contains legal obligations for the 28 EU member states in order to safeguard a ‘favourable conservation status’ (FCS) for selected species and habitat types. The crucial FCS concept itself, however, remains subject to considerable confusion regarding its proper interpretation and operationalization, impairing the Directive’s effective implementation. Diminishing this confusion is the purpose of this review. It focuses specifically on large carnivores—wolf (Canis lupus), brown bear (Ursus arctos), Eurasian lynx (Lynx lynx) and wolverine (Gulo gulo). These pose particular challenges, given their low densities, transboundary populations, and human-wildlife conflict potential. Large carnivores are also the only species for which specific guidance has been adopted by the European Commission—and subsequently contested. Our methodology combines legal analysis with an understanding of the species’ ecology and associated social, economic and cultural dimensions. We analyze the methods and processes through which EU law is interpreted, implemented, and enforced, by member states, European Commission, and EU Court of Justice—which is the ultimate authority regarding EU law interpretation. On that basis, we engage three particularly complex interpretation questions which are also of great practical significance: (1) the appropriate scale to achieve FCS (national or transboundary population level); (2) the respective roles of demographic, genetic and ecological factors in determining FCS; and (3) the use of extinction versus carrying capacity as benchmark. Regarding these questions, we identify approaches that are workable and effective, as well as likely to be endorsed by the EU Court.     

Single-fiber myosin heavy chain polymorphism: how many patterns and what proportions?

Previous studies have reported the existence of skeletal muscle fibers that coexpress multiple myosin heavy chain isoforms. These surveys have usually been limited to studying the polymorphic profiles of skeletal muscle fibers from a limited number of muscles (i.e., usually <4). Additionally, few studies have considered the functional implications of polymorphism. Hence, the primary objective of this study was to survey a relatively large number of rat skeletal muscle/muscle regions and muscle fibers (n approximately 5,000) to test the hypothesis that polymorphic fibers represent a larger fraction of the total pool of fibers than do so-called monomorphic fibers, which express only one myosin heavy chain isoform. Additionally, we used Hill's statistical model of the force-velocity relationship to differentiate the functional consequences of single-fiber myosin heavy chain isoform distributions found in these muscles. The results demonstrate that most muscles and regions of rodent skeletal muscles contain large proportions of polymorphic fibers, with the exception of muscles such as the slow soleus muscle and white regions of fast muscles. Several muscles were also found to have polymorphic profiles that are not consistent with the I<-->IIA<-->IIX<-->IIB scheme of muscle plasticity. For instance, it was found that the diaphragm muscle normally contains I/IIX fibers. Functionally, the high degree of polymorphism may 1) represent a strategy for producing a spectrum of contractile properties that far exceeds that simply defined by the presence of four myosin heavy chain isoforms and 2) result in relatively small differences in function as defined by the force-velocity relationship.     

Sorting of proteins to storage vacuoles: how many mechanisms?

Vacuoles receive their proteins through the secretory pathway, this requires protein sorting signals and molecular machineries that, until recently, have been believed to be markedly distinct for lytic and storage vacuoles. However, new biochemical, morphological and genetic data indicate that the only known class of vacuolar sorting receptors, believed to be specific for lytic vacuoles, might also be involved in the sorting of certain storage proteins. Furthermore, storage vacuoles can have a complex multimembrane structure that is difficult to explain based on a single trafficking mechanism. A new array of possible molecular interactions is thus emerging that no longer supports a clear-cut distinction between the two types of vacuoles based on sorting signals and putative receptors.     

Managing feral cats on a university's campuses: how many are there and is sterilization having an effect?

Worldwide domestic and feral cat (Felis catus) numbers have increased. Concerns regarding high populations of feral cats in urban areas include wildlife predation, public nuisance, and disease. This study aimed to estimate the size of the feral cat population on 5 campuses of the University of KwaZulu-Natal, South Africa, to determine whether sterilization has an effect and to make management recommendations. The study used both the total count and mark-recapture methods to estimate the feral cat population on each campus. The study chose a noninvasive method of taking photographs to "mark" individuals and record those who were sterilized. The study estimated a total of 186 cats on all campuses and density at 161 cats km(-2). There was a negative relationship between sterilization and numbers. Sites with higher sterilization showed a lower proportion of younger cats. At the average sterilization of 55%, the population, according to predictions, would remain stable at fecundity, survival, and immigration rates reported by cat caretakers. However, caretakers underestimated cat abundance by 7 ± 37 SD%. Caretakers' feral cat sterilization and feeding programs appear to provide a service to the university community. Key management recommendations were to increase sterilization to 90% to reduce the population over the long term and to raise funds to support the costs incurred by voluntary cat caretakers.     

SNARE complexes and neuroexocytosis: how many, how close?

Regulated secretion is an essential process in all eukaryotic cells. The release of molecules contained inside exocytic granules and synaptic vesicles is mediated by the assembly of a SNARE complex formed by the coil-coiling of three proteins: SNAP-25, syntaxin and VAMP/synaptobrevin. It seems that SNARE complexes assemble together in rosette-shaped super-complexes but there is controversy on the actual number (N) of copies of SNARE complexes that are necessary to mediate exocytosis. We discuss attempts to determine the value of N and suggest that N varies with the type of exocytic vesicles. In addition, we propose that the N value in neuroexocytosis can be estimated by the comparative use of different types of botulinum neurotoxins.     

How many species of Cladocera are there?

An estimation of the number of taxa within families, genera and local faunas of Cladocera reveals that only c. 129 species (17% of all known species) may be considered as sufficiently well described (valid species), and c. 146 as rather well described (fair species) but needing further study using modern methods of investigation. The status of all other species is vague. The families Chydoridae, Daphniidae and Sididae and genera Diaphanosoma, Daphnia, (including Daphniopsis), Megafenestra, Scapholeberis, Eurycercus, Chydorus, Ephemeroporus and Pleuroxus have been comparatively studied best. The largest number of valid species is known from Europe, North America, Australia and South America, and the smallest number from Africa. Presence of large number of vague species of Cladocera negatively affects faunistic, zoogeographic, and ecological studies of continental waters.Dedicated to the memory of Professor D. J. Frey     

Haldane's rule and its legacy: Why are there so many sterile males?

A general pattern of animal hybridization, known as Haldane's rule, is that the XY (ZW) sex is more severely affected in its viability or fertility than the XX (ZZ) sex. Recent evidence suggests that three different forces have shaped this pattern: (1) the X chromosome and autosomes are in greater disharmony in the XY sex; (2) evolution of hybrid male sterility is greatly accelerated, at least in species with XY males; and (3) maternal-zygotic incompatibility preferentially affects the viability of the XX sex. In species with XY males, the rapid evolution toward hybrid male sterility may be responsible for the bulk of observations pertaining to Haldane's rule. One interesting and testable hypothesis is that sexual selection drives this rapid evolution.     

Evolving endosomes: how many varieties and why?

The cell biologist's insight into endosomal diversity, in terms of both form and function, has increased dramatically in the past few years. This understanding has been promoted by the availability of powerful new techniques that allow imaging of both cargo and machinery in the endocytic process in real time, and by our ability to inhibit components of this machinery by RNA interference. The emerging picture from these studies is of a highly complex, dynamic and adaptable endosomal system that interacts at various points with the secretory system of the cell.