Effects of age,size, and density on natural survival for an important coral reef fishery species,yellow tang, <Emphasis Type="Italic">Zebrasoma flavescens</Emphasis>

Hundreds of thousands of juvenile yellow tang, Zebrasoma flavescens, are caught each year in the state of Hawai’i (USA) for the live aquarium trade. As part of an extensive adaptive management strategy built around a network of protected areas, an emphasis was placed on understanding this important species’ life history. Multiple capture-mark-recapture techniques and a model selection approach to data analysis in Program MARK were used to estimate the effects of individual age and conspecific density on natural per-capita daily survival probabilities of yellow tang recruits (recently settled individuals, 30–50 mm total length) and the effects of body size and site on natural per-capita monthly survival probabilities for juveniles (58–127 mm total length). The models of recruit survival that included additive effects of density and age were best supported by the data and indicated an increase of survival with age and decrease of survival with increased conspecific density. At 1 day post-settlement, the model averaged daily per-capita survival probability ranged from 0.963 (95% CI: 0.932–0.981) at a low density of 0.1 recruits m⁻² to 0.848 (95% CI: 0.752–0.911) at a high density of 1.3 recruits m⁻². The best supported model of juvenile survival had no effect of fish length or site, with a constant monthly per-capita survival of 0.939 (95% CI: 0.925–0.950). Only about 1% of recruits may survive to adulthood when protected from fishing. These results can be used to better analyze and interpret data from protected area monitoring surveys and refine management practices. Continued long-term monitoring, combined with targeted life history studies and demographic modeling, is needed to further investigate the population level effects of fishing yellow tang juveniles.     

Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses,plasmids, and more

Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes that characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores the memory of previous exposure. Our protocol can infer CRISPR-targeted sequences, including viruses, plasmids, and previously uncharacterized elements, and predict their hosts using unassembled short-read metagenomic sequencing data. By analyzing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences, which are likely complete circular genomes. The sequences included 2,154 tailed-phage genomes, together with 257 complete crAssphage genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 56 genomes of Inoviridae species, and 95 previously uncharacterized circular small genomes that have no reliably predicted protein-coding gene. We predicted the host(s) of approximately 70% of the discovered genomes at the taxonomic level of phylum by linking protospacers to taxonomically assigned CRISPR direct repeats. These results demonstrate that our protocol is efficient for de novo inference of CRISPR-targeted sequences and their host prediction.     

FORAGING OF JUVENILE MONK SEALS AT FRENCH FRIGATE SHOALS, HAWAII

Emaciation and poor survivorship of juvenile Hawaiian monk seals at French Frigate Shoals atoll prompted a study of their foraging, using video camera technology ( crittercam ). Nine juveniles between the ages of 1 and 3 yr (six males, three females) were fitted with crittercam to identify their foraging habitat and feeding behavior. All feeding was directed at small (≤ 10 cm), cryptic, benthic prey. Older seals (ages 2 and 3), varied in their foraging intensity with most of their attention directed at shallow atoll depths (10–30 m). In contrast, the three yearlings focused all their feeding in the sand fields (50–100 m) on the atoll's outer slope. Bottom trawls were used to assess the prey abundance of the sand habitat and found 70% of the numerical catch was flounder ( Bothidae ). Extrapolating the yearlings' prey capture rate (0.13/min, derived from the crittercam video) over their total bottom time yielded an estimated 1–1.3 kg/day of flounder. The mean size of flounder (5 ± 1.7 cm) caught in the bottom trawls was close to the size at which larval flounder settle from the plankton (3 cm), suggesting that localized changes in oceanography could directly impact the seals' prey supply. Extensive use of sand communities by young seals may be the strongest link yet identified between juvenile survivorship and oceanographic dynamics.     

Capacitation of bovine spermatozoa by oviduct fluid

Oviduct fluid collected from chronically cannulated oviducts of heifers was evaluated for its effect on capacitation of bovine sperm in vitro. Capacitation was determined by the ability of sperm to fertilize bovine oocytes in vitro and to undergo an acrosome reaction (AR) upon exposure to lysophosphatidylcholine (LC). After incubation of sperm with 0-25% (v/v) estrual oviduct fluid (collected +/- 1 day from estrus) for 4 h, addition of LC (100 micrograms/ml) for an additional 0.25 h resulted in an increasing percentage of acrosome-reacted sperm as the concentration of oviduct fluid increased. Sperm incubated 4 h with 25% estrual oviduct fluid fertilized more oocytes than sperm incubated in medium alone (p less than 0.05) but was not different from sperm incubated with 10 micrograms/ml heparin (p greater than 0.05). Glucose inhibited the ability of LC to induce ARs in sperm incubated 4 h with heparin or estrual oviduct fluid. Incubation of sperm with 25% oviduct fluid collected at various days over the estrous cycle demonstrated that peak capacitating activity was found at estrus but was also present +/- 1 day from estrus. The active capacitating factor in oviduct fluid was found to be heat stable. In addition, when extraction procedures were applied in sequential order, oviduct fluid capacitating activity was resistant to protease digestion, precipitable by ethanol, size-excluded by Sephadex G-25, and destroyed by nitrous acid. These results suggest that a heparin-like glycosaminoglycan from the oviduct is a potential in vivo capacitating agent in the bovine.     

Cellular Mechanisms Controlling Caspase Activation and Function

Caspases are the primary drivers of apoptotic cell death, cleaving cellular proteins that are critical for dismantling the dying cell. Initially translated as inactive zymogenic precursors, caspases are activated in response to a variety of cell death stimuli. In addition to factors required for their direct activation (e.g., dimerizing adaptor proteins in the case of initiator caspases that lie at the apex of apoptotic signaling cascades), caspases are regulated by a variety of cellular factors in a myriad of physiological and pathological settings. For example, caspases may be modified posttranslationally (e.g., by phosphorylation or ubiquitylation) or through interaction of modulatory factors with either the zymogenic or active form of a caspase, altering its activation and/or activity. These regulatory events may inhibit or enhance enzymatic activity or may affect activity toward particular cellular substrates. Finally, there is emerging literature to suggest that caspases can participate in a variety of cellular processes unrelated to apoptotic cell death. In these settings, it is particularly important that caspases are maintained under stringent control to avoid inadvertent cell death. It is likely that continued examination of these processes will reveal new mechanisms of caspase regulation with implications well beyond control of apoptotic cell death.Apoptosis is a form of programmed cell death that eliminates individual cells within an organism while preserving the overall structure of surrounding tissue. Many of the prominent morphological features of apoptosis were first described in 1972 by Kerr, Wyllie, and Currie (Kerr et al. 1972). However, it was not until the mid-1990s that apoptosis was linked to the activation of the cysteine-dependent aspartate-driven proteases (caspases), which cleave key intracellular substrates to promote cell death (Cerretti et al. 1992; Nicholson et al. 1995; Alnemri et al. 1996; Liu et al. 1996; Thornberry and Lazebnik 1998). Given the critical role that caspases play in dismantling the cell during apoptosis, their activation and subsequent activity are highly regulated. Failure of a cell to properly modulate caspase activity can cause aberrant or untimely apoptotic cell death, potentially leading to carcinogenesis, autoimmunity, neurodegeneration, and immunodeficiency (Thompson 1995; Hanahan and Weinberg 2000; Yuan and Yankner 2000; Li and Yuan 2008).Caspases are synthesized within the cell as inactive zymogens that lack significant protease activity. Thus, caspases are, in essence, regulated from the moment of protein synthesis in that they are not activated until receipt of specific death stimuli (Earnshaw et al. 1999). The primary structure of a caspase is an amino-terminal prodomain and a carboxy-terminal protease domain, which contains the key catalytic cysteine residue. Caspases are categorized as initiator or effector caspases, based on their position in apoptotic signaling cascades. The initiator caspases (caspase-2, -8, -9, and -10) act apically in cell death pathways and all share long, structurally similar prodomains. This group of enzymes is activated through “induced proximity” when adaptor proteins interact with the prodomains and promote caspase dimerization (Boatright et al. 2003; Baliga et al. 2004; Pop et al. 2006; Riedl and Salvesen 2007; Wachmann et al. 2010). In contrast, the effector caspases (caspase-3, -6, and -7) have shorter prodomains and exist in the cell as preformed, but inactive, homodimers. Following cleavage mediated by an initiator caspase, effector caspases act directly on specific cellular substrates to dismantle the cell. Although many individual caspase substrates have been implicated in specific aspects of cellular destruction (e.g., lamin cleavage is required for the efficient packaging of nuclei into small membrane-bound vesicles), recent proteomic approaches have greatly expanded the known repertoire of proteolytic products generated during apoptosis (Van Damme et al. 2005; Dix et al. 2008; Mahrus et al. 2008). Further work will be needed to confirm these findings and to determine how (or if) all of these substrates participate in the apoptotic process (see Poreba et al. 2013), especially as new details emerge on the relationship between posttranslational modifications, like phosphorylation, and caspase cleavage (Dix et al. 2012).     

Evaluation of 2′-α-fluorine modified nucleoside phosphonates as potential inhibitors of HCV polymerase

Ribonucleoside phosphonate analogues containing 2′-α-fluoro modifications were synthesized and their potency evaluated against HCV RNA polymerase. The diphosphophosphonate (triphosphate equivalent) adenine and cytidine analogues displayed potent inhibition of the HCV polymerase in the range of 1.9–2.1 μM, but only modest cell-based activity in the HCV replicon. Pro-drugs of the parent nucleoside phosphonates improved the cell-based activity.     

Functions of the SLC36 transporter Pathetic in growth control

Neurons exhibit extreme diversity in size, but whether large neurons have specialized mechanisms to support their growth is largely unknown. Recently, we identified the SLC36 transporter Pathetic (Path) as a factor required for extreme dendrite growth in neurons. Path is broadly expressed, but only neurons with large dendrite arbors or small neurons that are forced to grow large require path for their growth. To gain insight into the basis of growth control by path, we generated additional alleles of path and further examined the apparent specificity of growth defects in path mutants. Here, we confirm our prior finding that loss of path function imposes an upper limit on neuron growth, and additionally report that path likely limits overall neurite length rather than dendrite length alone. Using a GFP knock-in allele of path, we identify additional tissues where path likely functions in nutrient sensing and possibly growth control. Finally, we demonstrate that path regulates translational capacity in a cell type that does not normally require path for growth, suggesting that path may confer robustness on growth programs by buffering translational output. Altogether, these studies suggest that Path is a nutrient sensor with widespread function in Drosophila.     

Learning to smell the roses: experience-dependent neural plasticity in human piriform and orbitofrontal cortices

It is widely presumed that odor quality is a direct outcome of odorant structure, but human studies indicate that molecular knowledge of an odorant is not always sufficient to predict odor quality. Indeed, the same olfactory input may generate different odor percepts depending on prior learning and experience. Combining functional magnetic resonance imaging with an olfactory paradigm of perceptual learning, we examined how sensory experience modifies odor perception and odor quality coding in the human brain. Prolonged exposure to a target odorant enhanced perceptual differentiation for odorants related in odor quality or functional group, an effect that was paralleled by learning-induced response increases in piriform cortex and orbitofrontal cortex (OFC). Critically, the magnitude of OFC activation predicted subsequent improvement in behavioral differentiation. Our findings suggest that neural representations of odor quality can be rapidly updated through mere perceptual experience, a mechanism that may underlie the development of odor perception.