Jelly-falls historic and recent observations: a review to drive future research directions

The biological pump describes the transport of particulate matter from the sea surface to the ocean’s interior including the seabed. The contribution by gelatinous zooplankton bodies as particulate organic matter (POM) vectors (“jelly-falls”) has been neglected owing to technical and spatiotemporal sampling limitations. Here, we assess the existing evidence on jelly-falls from early ocean observations to present times. The seasonality of jelly-falls indicates that they mostly occur after periods of strong upwelling and/or spring blooms in temperate/subpolar zones and during late spring/early summer. A conceptual model helps to define a jelly-fall based on empirical and field observations of biogeochemical and ecological processes. We then compile and discuss existing strategic and observational oceanographic techniques that could be implemented to further jelly-falls research. Seabed video- and photography-based studies deliver the best results, and the correct use of fishing techniques, such as trawling, could provide comprehensive regional datasets. We conclude by considering the possibility of increased gelatinous biomasses in the future ocean induced by upper ocean processes favouring their populations, thus increasing jelly-POM downward transport. We suggest that this could provide a “natural compensation” for predicted losses in pelagic POM with respect to fuelling benthic ecosystems.     

Toward low-cost affinity reagents: lyophilized yeast-scFv probes specific for pathogen antigens

The generation of affinity reagents, usually monoclonal antibodies, remains a critical bottleneck in biomedical research and diagnostic test development. Recombinant antibody-like proteins such as scFv have yet to replace traditional monoclonal antibodies in antigen detection applications, in large part because of poor performance of scFv in solution. To address this limitation, we have developed assays that use whole yeast cells expressing scFv on their surfaces (yeast-scFv) in place of soluble purified scFv or traditional monoclonal antibodies. In this study, a nonimmune library of human scFv displayed on the surfaces of yeast cells was screened for clones that bind to recombinant cyst proteins of Entamoeba histolytica, an enteric pathogen of humans. Selected yeast-scFv clones were stabilized by lyophilization and used in detection assay formats in which the yeast-scFv served as solid support-bound monoclonal antibodies. Specific binding of antigen to the yeast-scFv was detected by staining with rabbit polyclonal antibodies. In flow cytometry-based assays, lyophilized yeast-scFv reagents retained full binding activity and specificity for their cognate antigens after 4 weeks of storage at room temperature in the absence of desiccants or stabilizers. Because flow cytometry is not available to all potential assay users, an immunofluorescence assay was also developed that detects antigen with similar sensitivity and specificity. Antigen-specific whole-cell yeast-scFv reagents can be selected from nonimmune libraries in 2-3 weeks, produced in vast quantities, and packaged in lyophilized form for extended shelf life. Lyophilized yeast-scFv show promise as low cost, renewable alternatives to monoclonal antibodies for diagnosis and research.     

In vitro induction of a trisomic of Agave tequilana Weber var. Azul (Agavaceae) by para-fluorophenylalanine treatment

The effect of para-fluorophenylalanine (PFP) on the production of trisomic plants of Agave tequilana Weber var. Azul produced through somatic embryogenesis was investigated. Normal diploid plants with 2n = 2x = 60 were obtained in the control treatment and with 4 mg L⁻¹ PFP exposure, while use of 8 and 12 mg L⁻¹ PFP led to production of trisomics with 2n = 2x = 61. Normal diploid plants showed a bimodal karyotype with five pairs of large chromosomes and 25 pairs of small chromosomes. Trisomic plants also had a bimodal karyotype with a group of three chromosomes in position five of the chromosome set. More than 13 homologous chromosome pairs exhibited structural changes. Differences in chromosome arm ratio (long arm/short arm) were also found in eight chromosome pairs; all these aberrations in the chromosome complement of trisomic plants were probably caused by inversions, deletions, and/or duplications produced by high concentrations of PFP. The gross chromosome structural changes and the presence of a single extra chromosome could have been induced by the effect of PFP on the mitotic spindle by inducing nondisjunction of sister chromatids, resulting in hyperploids (2n + x) and hypoploids (2n − x). Flow cytometric analysis of nuclear DNA content was performed using nuclei isolated from young leaves of normal and trisomic plants. The 2C DNA content of 8.635 pg (1Cx = 4,223 Mbp of trisomic plants was different (p < 0.001) than that of normal plants (2C DNA = 8.389 pg (1Cx = 4,102 Mbp). The difference in genome size was correlated with the large structural changes in the trisomic plant genomes.     

Future land use effects on the connectivity of protected area networks in southeastern Spain

Land-use change is a major driver of the global biodiversity crisis, mainly via the fragmentation and loss of natural habitat. Although land-use changes will accelerate to meet humankind's growing demand for agricultural products, conservation planning rarely considers future land uses and how they may affect the connectivity of ecological networks. Here, we integrate land-use models with landscape fragmentation and connectivity analyses, to assess the effects of past and future land-use changes on the connectivity of protected area networks for a highly dynamic region in southeast Spain. Our results show a continued geographical polarisation of land use, with agricultural intensification and urban development in the coastal areas, and the abandonment of traditional land use in the mountains (e.g., 1100 km² of natural vegetation are projected to be lost in coastal areas whereas 32 km² of natural vegetation would recover in interior areas from 1991 to 2015). As a result, coastal protected areas will experience increasing isolation. The connectivity analyses reveal that the two protected area networks in place in the study area, the European “Natura 2000” and the Andalusian “RENPA” networks, include many landscape connectors. However, we identify two areas that currently lack protection but contain several important patches for maintaining the region's habitat connectivity: the northwestern and the southwestern slopes of the Sierra Cabrera and Bédar protected area. Our results highlight the importance of considering future land-use trajectories in conservation planning to maintain connectivity at the regional scale, and to improve the resilience of conservation networks.     

Determinants of RNA-dependent RNA polymerase (in)fidelity revealed by kinetic analysis of the polymerase encoded by a foot-and-mouth disease virus mutant with reduced sensitivity to ribavirin

A mutant poliovirus (PV) encoding a change in its polymerase (3Dpol) at a site remote from the catalytic center (G64S) confers reduced sensitivity to ribavirin and forms a restricted quasispecies, because G64S 3Dpol is a high-fidelity enzyme. A foot-and-mouth disease virus (FMDV) mutant that encodes a change in the polymerase catalytic site (M296I) exhibits reduced sensitivity to ribavirin without restricting the viral quasispecies. In order to resolve this apparent paradox, we have established a minimal kinetic mechanism for nucleotide addition by wild-type (WT) FMDV 3Dpol that permits a direct comparison to PV 3Dpol as well as to FMDV 3Dpol derivatives. Rate constants for correct nucleotide addition were on par with those of PV 3Dpol, but apparent binding constants for correct nucleotides were higher than those observed for PV 3Dpol. The A-to-G transition frequency was calculated to be 1/20,000, which is quite similar to that calculated for PV 3Dpol. The analysis of FMDV M296I 3Dpol revealed a decrease in the calculated ribavirin incorporation frequency (1/8,000) relative to that (1/4,000) observed for the WT enzyme. Unexpectedly, the A-to-G transition frequency was higher (1/8,000) than that observed for the WT enzyme. Therefore, FMDV selected a polymerase that increases the frequency of the misincorporation of natural nucleotides while specifically decreasing the frequency of the incorporation of ribavirin nucleotide. These studies provide a mechanistic framework for understanding FMDV 3Dpol structure-function relationships, provide the first direct analysis of the fidelity of FMDV 3Dpol in vitro, identify the β9-α11 loop as a (in)fidelity determinant, and demonstrate that not all ribavirin-resistant mutants will encode high-fidelity polymerases.     

Effects of heterogeneous interaction strengths on food web complexity

Using a bioenergetic model we show that the pattern of foraging preferences greatly determines the complexity of the resulting food webs. By complexity we refer to the degree of richness of food-web architecture, measured in terms of some topological indicators (number of persistent species and links, connectance, link density, number of trophic levels, and frequency of weak links). The poorest food-web architecture is found for a mean-field scenario where all foraging preferences are assumed to be the same. Richer food webs appear when foraging preferences depend on the trophic position of species. Food-web complexity increases with the number of basal species. We also find a strong correlation between the complexity of a trophic module and the complexity of entire food webs with the same pattern of foraging preferences.     

The functions of the "Greeting Ceremony" among male mantled howlers (Alouatta palliata) on Agaltepec Island, Mexico

Nonhuman primates use greeting behaviors as nonaggressive communicatory signals in multiple social contexts. Adult male mantled howlers (Alouatta palliata) perform a ritual greeting that has been associated with bond-strengthening functions. The aim of this study is to explore the greeting patterns of male howlers living on Agaltepec Island, Mexico. Specifically, we analyzed the relationships between greetings and several individual, relational, and contextual variables, such as the expression of affiliation and agonism, dominance rank, age, kinship relationships, spatial organization, activity patterns, and subgrouping patterns. Greetings were more frequent between males with closer dominance ranks. Among those dyads that greeted at least once, dominant males initiated greetings more frequently than less-dominant males. On the other hand, more greetings were observed when one of the participants had recently returned to a subgroup and during locomotion. On the basis of these results, we propose that on Agaltepec greetings are a conflict management mechanism used between males of similar ranks. The fission-fusion social system of this group of howlers allows males with conflicting interests to remain separated, and greetings may reduce tension during fusion events.