New Pliocene remains of Camelus grattardi (Mammalia,Camelidae) from the Shungura Formation,Lower Omo Valley,Ethiopia, and the evolution of African camels

Abstract

Camels are exceptionally rare in the Plio-Pleistocene fossil record of Africa, hindering attempts to understand the evolution of this family on the continent. Here we describe recently collected camel specimens from the Shungura Formation, Lower Omo Valley, Ethiopia, and attribute these remains to Camelus grattardi. The new specimens date to the late Pliocene (~3 to 2.6 Ma) and consist of three upper molars, one upper premolar, and two proximal metatarsals. The dental specimens confirm this species’ small P4 relative to its molars, a trait that differs significantly from all extant and fossil Old World camels. The metatarsals indicate that C. grattardi was similar in size to the living Bactrian camel, C. bactrianus. Phylogenetically, we find no suitable ancestor, sister, or descendant of the eastern African fossil camel, which suggests greater lineage diversity in Plio-Pleistocene Camelus than previously recognised. Microwear analyses suggest that C. grattardi was likely a mixed-feeder preferring browse, which is consistent with carbon isotopes of enamel from the Turkana Basin. A review of the fossil record of African camels suggests no clear paleoenvironmental association, as fossil camels occur in a range of environments from dry savannas with no permanent water bodies to closed woodlands along the paleo-Omo River.     

Enantiomers of 4-amino-3-fluorobutanoic acid as substrates for gamma-aminobutyric acid aminotransferase. Conformational probes for GABA binding

Gamma-aminobutyric acid aminotransferase (GABA-AT), a pyridoxal 5'-phosphate dependent enzyme, catalyzes the degradation of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) to succinic semialdehyde with concomitant conversion of pyridoxal 5'-phosphate (PLP) to pyridoxamine 5'-phosphate (PMP). The enzyme then catalyzes the conversion of alpha-ketoglutarate to the excitatory neurotransmitter L-glutamate. Racemic 4-amino-3-fluorobutanoic acid (3-F-GABA) was shown previously to act as a substrate for GABA-AT, not for transamination, but for HF elimination. Here we report studies of the reaction catalyzed by GABA-AT on (R)- and (S)-3-F-GABA. Neither enantiomer is a substrate for transamination. Very little elimination from the (S)-enantiomer was detected using a coupled enzyme assay; The rate of elimination of HF from the (R)-enantiomer is at least 10 times greater than that for the (S)-enantiomer. The (R)-enantiomer is about 20 times more efficient as a substrate for GABA-AT catalyzed HF elimination than GABA is a substrate for transamination. The (R)-enantiomer also inhibits the transamination of GABA 10 times more effectively than the (S)-enantiomer. Using a combination of computer modeling and the knowledge that vicinal C-F and C-NH3+ bonds have a strong preference to align gauche rather than anti to each other, it is concluded that on binding of free 3-F-GABA to GABA-AT the optimal conformation places the C-NH3+ and C-F bonds gauche in the (R)-enantiomer but anti in the (S)-enantiomer. Furthermore, the dynamic binding process and the bioactive conformation of GABA bound to GABA-AT have been inferred on the basis of the different biological behavior of the two enantiomers of 3-F-GABA when they bind to the enzyme. The present study suggests that the C-F bond can be utilized as a conformational probe to explore the dynamic binding process and provide insight into the bioactive conformation of substrates, which cannot be easily determined by other biophysical approaches.     

Analytical biochemistry of DNA–protein assemblies from crude cell extracts

Purification of specific DNA–protein complexes is a challenging task, as the involved interactions can be both electrostatic/H-bond and hydrophobic. The chromatographic stringency needed to obtain reasonable purifications uses salts and detergents. However, these components elicit the removal of proteins unspecifically bound to the chromatographic support itself, thus contaminating the purification products. In this work, a photocleavable linker connected the target oligonucleotidic sequence to the chromatographic beads so as to allow the irradiation-based release of the purified DNA–protein complexes off the beads. Our bioanalytical conditions were validated by purifying the tetracycline repressor protein onto a specific oligonucleotide. The purification factor was unprecedented, with a single contaminant. The robustness of our method was challenged by applying it to the purification of multiprotein assemblies forming onto DNA damage-mimicking oligonucleotides. The purified components were identified as well-known DNA repair proteins, and were shown to retain their enzymatic activities, as seen by monitoring DNA ligation products. Remarkably, kinase activities, also monitored, were found to be distinct on the beads and on the purified DNA–protein complexes, showing the benefits to uncouple the DNA–protein assemblies from the beads for a proper understanding of biochemical regulatory mechanisms involved in the DNA–protein assemblies.     

Analytical biochemistry of DNA--protein assemblies from crude cell extracts

Purification of specific DNA-protein complexes is a challenging task, as the involved interactions can be both electrostatic/H-bond and hydrophobic. The chromatographic stringency needed to obtain reasonable purifications uses salts and detergents. However, these components elicit the removal of proteins unspecifically bound to the chromatographic support itself, thus contaminating the purification products. In this work, a photocleavable linker connected the target oligonucleotidic sequence to the chromatographic beads so as to allow the irradiation-based release of the purified DNA-protein complexes off the beads. Our bioanalytical conditions were validated by purifying the tetracycline repressor protein onto a specific oligonucleotide. The purification factor was unprecedented, with a single contaminant. The robustness of our method was challenged by applying it to the purification of multiprotein assemblies forming onto DNA damage-mimicking oligonucleotides. The purified components were identified as well-known DNA repair proteins, and were shown to retain their enzymatic activities, as seen by monitoring DNA ligation products. Remarkably, kinase activities, also monitored, were found to be distinct on the beads and on the purified DNA-protein complexes, showing the benefits to uncouple the DNA-protein assemblies from the beads for a proper understanding of biochemical regulatory mechanisms involved in the DNA-protein assemblies.     

The hologenome concept: we need to incorporate function

Are we in the midst of a paradigm change in biology and have animals and plants lost their individuality, i.e., are even so-called ‘typical’ organisms no longer organisms in their own right? Is the study of the holobiont—host plus its symbiotic microorganisms—no longer optional, but rather an obligatory path that must be taken for a comprehensive understanding of the ecology and evolution of the individual components that make up a holobiont? Or are associated microbes merely a component of their host’s environment, and the holobiont concept is just a beautiful idea that does not add much or anything to our understanding of evolution? This article explores different aspects of the concept of the holobiont. We focus on the aspect of functional integration, a central holobiont property, which is only rarely considered thoroughly. We conclude that the holobiont comes in degrees, i.e., we regard the property of being a holobiont as a continuous trait that we term holobiontness, and that holobiontness is differentiated in several dimensions. Although the holobiont represents yet another level of selection (different from classical individual or group selection because it acts on a system that is composed of multiple species), it depends on the grade of functional integration whether or not the holobiont concept helps to cast light on the various degrees of interactions between symbiotic partners.     

Insights into the interaction of high potency inhibitor IRC‐083864 with phosphatase CDC25

CDC25 phosphatases play a crucial role in cell cycle regulation. They have been found to be over‐expressed in various human tumours and to be valuable targets for cancer treatment. Here, we report the first model of binding of the most potent CDC25 inhibitor to date, the bis‐quinone IRC‐083864, into CDC25B obtained by combining molecular modeling and NMR studies. Our study provides new insights into key interactions of the catalytic site inhibitor and CDC25B in the absence of any available experimental structure of CDC25 with a bound catalytic site inhibitor. The docking model reveals that IRC‐083864 occupies both the active site and the inhibitor binding pocket of the CDC25B catalytic domain. NMR saturation transfer difference and WaterLOGSY data indicate the binding zones of the inhibitor and support the docking model. Probing interactions of analogues of the two quinone units of IRC‐083864 with CDC25B demonstrate that IRC‐083864 competes with each monomer. Proteins 2017; 85:593–601. © 2016 Wiley Periodicals, Inc.     

Distribution and ecology of the generalist lactic acid bacterium Carnobacterium maltaromaticum in different freshwater habitats: Metabolic and antagonistic abilities

We explored the distribution, metabolic and antagonistic activities of Carnobacterium maltaromaticum, isolated from freshwater locations in Denmark during winter or early spring. This species was widely distributed in such habitats although it was relatively rare in low pH locations. Isolates possessed a diverse metabolism, potentially enabling functional capacities independent of habitat. The intraspecies competition showed a relatively high degree of mostly low-intensity interactions, which overall were not correlated with phylogeny or location. Only a few isolates exhibited broad-spectrum inhibition activity, targeting species from other genera and families, including one isolate that exhibited a broad inhibitory activity due to H₂O₂ production. Bioinformatic analyses revealed that the frequency of bacteriocinogenic systems was low, and only one unmodified bacteriocin, piscicolin 126, correlated with phenotypic antagonistic activity. Furthermore, most potential bacteriocin gene complexes were not complete. Overall, this study showed C. maltaromaticum to be a generalist (nomadic) species with a constant presence in freshwater habitats, especially those with pH values >5. General metabolic properties did not suggest a strong degree of adaptation to the freshwater environment, and bacteriocin-mediated antagonistic activities appeared to play a minimal ecological role.     

Kite aerial photography: a low‐cost method for monitoring seabird colonies

Obtaining aerial high‐resolution images of bird nesting colonies using remote‐sensing technology such as satellite‐based remote sensing, manned aircraft, or Unmanned Aerial Vehicles might not be possible for many researchers due to financial constraints. Kite Aerial Photography (KAP) provides a possible low‐cost alternative. We collected digital images of ground‐nesting seabirds (i.e., cormorants and penguins) in two different ecosystems using a kite‐based platform equipped with consumer‐grade digital cameras with time‐lapse capability to obtain estimates of breeding population size. KAP proved to be an efficient method for acquiring high‐resolution aerial images. We obtained images of colonies of seabirds ranging in size from hundreds to several hundreds of thousands breeding pairs during flights lasting from a few minutes up to three hours, from flat to very steep areas, and in contrasted wind conditions (from 0.5 to 6 Beaufort force). KAP is an efficient low‐cost method for acquiring high‐resolution aerial images and an alternative to ground‐based censuses, especially useful in rugged areas.     

Dental Microwear Texture Analysis of Varswater Bovids and Early Pliocene Paleoenvironments of Langebaanweg,Western Cape Province,South Africa

The extensive early Pliocene mammalian assemblages at Langebaanweg hold the potential to provide important information about paleoenvironments of the southwestern tip of Africa, an area that today consititutes the Fynbos Biome. We here add to a growing body of literature on the paleoenviornments of the site with an examination of dental microwear textures of bovids from the Varswater Formation. Microwear texture analysis is a new, automated and repeatable approach that measures whole surfaces in three dimensions without observer error. A study of extant ruminants indicates that grazers have more anisotropic microwear surface textures, whereas browsers have more complex microwear surface textures. Fossil bovids recovered from the Muishond Fontein Pelletal Phosphorite Member vary in their microwear textures, with some taxa falling within the extant browser range, some closer to extant grazers, and others in between. These results are consistent with scenarios suggesting mosaic habitats including fynbos vegetation, some (probably C₃) grasses, and woodland elements when these fossils were accumulated.