In this 2006 volume John Murray investigates the ecological processes that control the distribution, abundance and species diversity of benthic foraminifera in environments ranging from marsh to the deepest ocean. To interpret the fossil record it is necessary to have an understanding of the ecology of modern foraminifera and the processes operating after death leading to burial and fossilisation. This book presents the ecological background required to explain how fossil forms are used in dating rocks and reconstructing past environmental features including changes of sea level. It demonstrates how living foraminifera can be used to monitor modern-day environmental change. Ecology and Applications of Benthic Foraminifera presents a comprehensive and global coverage of the subject using all the available literature. It is supported by a website hosting a large database of additional ecological information (www.cambridge.org/0521828392) and will form an important reference for academic researchers and graduate students in Earth and Environmental Sciences.

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Our previous studies demonstrated that fluorescent early endocytic vesicles prepared from rat liver after injection of Texas red asialoorosomucoid contain asialoglycoprotein and its receptor and move and undergo fission along microtubules using kinesin I and KIFC2, with Rab4 regulating KIFC2 activity (J. Cell Sci. 116, 2749, 2003). In the current study, procedures to prepare fluorescent late endocytic vesicles were devised. In addition, flow cytometry was utilized to prepare highly purified fluorescent endocytic vesicles, permitting validation of microscopy-based experiments as well as direct biochemical analysis. These studies revealed that late vesicles bound to and moved along microtubules, but in contrast to early vesicles, did not undergo fission. As compared with early vesicles, late vesicles had reduced association with receptor, Rab4, and kinesin I but were highly associated with dynein, Rab7, dynactin, and KIF3A. Dynein and KIF3A antibodies inhibited late vesicle motility, whereas kinesin I and KIFC2 antibodies had no effect. Dynamitin antibodies prevented the association of late vesicles with microtubules. These results indicate that acquisition and exchange of specific motor and regulatory proteins characterizes and may regulate the transition of early to late endocytic vesicles. Flow cytometric purification should ultimately facilitate detailed proteomic analysis and mapping of endocytic vesicle-associated proteins.

We have previously used the asialoglycoprotein receptor system to elucidate the pathway of hepatocytic processing of ligands such as asialoorosomucoid (ASOR). These studies suggested that endocytic vesicles bind to and travel along microtubules under the control of molecular motors such as cytoplasmic dynein. We now report reconstitution of this process in vitro with the use of a microscope assay to observe the interaction of early endocytic vesicles containing fluorescent ASOR with fluorescent microtubules. We find that ASOR-containing endosomes bind to microtubules and translocate along them in the presence of ATP. This represents the first time that mammalian endosomes containing a well-characterized ligand have been directly observed to translocate on microtubules in vitro. The endosome movement does not require cytosol or exogenous motor protein, is oscillatory, and is directed toward the plus and minus ends at equal frequencies. We also observe endosomes being stretched in opposite directions along microtubules, suggesting that microtubules could provide a mechanical basis for endocytic sorting events. The movement of endosomes in vitro is consistent with the hypothesis that microtubules actively participate in the sorting and distribution of endocytic contents.

Non-vital staining, especially with rose Bengal, has been widely used in ecological studies to differentiate between the tests of dead (unstained) foraminifera from those presumed to be living at the time of collection (stained). Doubts have been expressed about staining methods because of the possibility that dead individuals may retain undecayed protoplasm for weeks or months after death; when stained, such individuals would be recorded as living. To assess the importance of such false positives, it is necessary to examine rates of mortality, and the modes of generation of empty tests, i.e., whether due to reproduction, growth stages (leaving empty tests during growth) or death. It can be argued that reproduction, ontogeny, and death through predation lead to tests devoid of protoplasm. Whereas reproduction may affect only a small proportion of the population of each species (due to high pre-reproductive mortality), predation in oxygenated environments may be responsible for the major part of that pre-reproductive mortality. In oxygenated environments, disease or adverse environmental conditions are most likely to lead to dead individuals having tests containing protoplasm. In dysaerobic/anoxic environments, predation by macrofauna may be excluded, so foraminifera die through other causes and thus more tests with dead protoplasm may be potentially available for staining. Therefore, for most other environments, the problem of staining dead individuals is almost certainly overstated. Furthermore, from comparative studies, it seems that the most commonly used technique (staining with rose Bengal) is as reliable as others. Now that new vital staining techniques, especially the use of fluorescent probes, are being introduced, it is timely for further objective comparative studies of all techniques to be made in order to evaluate data already gathered and to develop the best strategies for future ecological studies according to whether they are fieldbased or experimental.

Abstract. The machinery of eukaryotic protein synthesis is found in association with the actin cytoskeleton. A major component of this translational apparatus, which is involved in the shuttling of aa-tRNA, is the actinbinding protein elongation factor let (EF-let). To investigate the consequences for translation of the interaction of EF-let with F-actin, we have studied the effect of F-actin on the ability of EF-let to bind to aa-tRNA. We demonstrate that binding of EF-let:GTP to aatRNA is not pH sensitive with a constant binding affinity of ~0.2 ~M over the physiological range of pH. However, the sharp pH dependence of binding of EF-let to F-actin is sufficient to shift the binding of EFlet from F-actin to aa-tRNA as pH increases. The ability of EF-let to bind either F-actin or aa-tRNA in competition binding experiments is also consistent with the observation that EF-let's binding to F-actin and aatRNA is mutually exclusive. Two pH-sensitive actinbinding sequences in EF-let are identified and are predicted to overlap with the aa-tRNA-binding sites. Our results suggest that pH-regulated recruitment and release of EF-let from actin filaments in vivo will supply a high local concentration of EF-let to facilitate polypeptide elongation by the F-actin-associated translational apparatus.

Microtubule-mediated anterograde transport of herpes simplex virus (HSV) from the neuronal cell body to the axon terminal is crucial for the spread and transmission of the virus. It is therefore of central importance to identify the cellular and viral factors responsible for this trafficking event. In previous studies, we isolated HSV-containing cytoplasmic organelles from infected cells and showed that they represent the first and only destination for HSV capsids after they emerge from the nucleus. In the present study, we tested whether these cytoplasmic compartments were capable of microtubule-dependent traffic. Organelles containing green fluorescent protein-labeled HSV capsids were isolated and found to be able to bind rhodamine-labeled microtubules polymerized in vitro. Following the addition of ATP, the HSV-associated organelles trafficked along the microtubules, as visualized by time lapse microscopy in an imaging microchamber. The velocity and processivity of trafficking resembled those seen for neurotropic herpesvirus traffic in living axons. The use of motor-specific inhibitors indicated that traffic was predominantly kinesin mediated, consistent with the reconstitution of anterograde traffic. Immunocytochemical studies revealed that the majority of HSV-containing organelles attached to the microtubules contained the trans-Golgi network marker TGN46. This simple, minimal reconstitution of microtubule-mediated anterograde traffic should facilitate and complement molecular analysis of HSV egress in vivo.The herpes simplex virus (HSV) particle consists of a ϳ152-kb DNA genome contained within an icosahedral capsid. A complex layer of proteins termed tegument lies between the capsid and the viral envelope, a lipid bilayer obtained from a host cell cytoplasmic organelle that contains multiple membrane proteins, most of which are glycosylated. During infection, the envelope and host cell plasma membranes fuse, the capsid and associated tegument polypeptides enter the cytoplasm, and the capsid travels from the periphery of the cell to the vicinity of the nucleus via retrograde microtubular traffic by utilizing dynein motors (6,21,22,46,60,62,70). The DNA genome is replicated and transcribed in the nucleoplasm, and progeny capsids are assembled.Following the packaging of progeny procapsids with newly replicated viral genomes, the mature nucleocapsids undergo a round of envelopment and deenvelopment at the nuclear membranes (13, 57) and enter the cytoplasm. They then acquire their final, mature envelope by budding into a cytoplasmic organelle (7,9,26,30,37,48,53,57,63,67). In sensory neurons, capsids and/or enveloped particles utilize microtubule-mediated anterograde traffic to travel to the nerve terminal for subsequent release from the cell. A number of elegant ultrastructural and live-cell imaging studies using both herpes simplex virus and pseudorabies virus (PRV) have begun to define the kinetics and saltatory nature of this anterograde flow and the structural composition of the trafficking particles (4,1...