Crystal Structures of the Human and Fungal Cytosolic Leucyl-tRNA Synthetase Editing Domains: A Structural Basis for the Rational Design of Antifungal Benzoxaboroles

Leucyl-tRNA synthetase (LeuRS) specifically links leucine to the 3′ end of tRNA^leu isoacceptors. The overall accuracy of the two-step aminoacylation reaction is enhanced by an editing domain that hydrolyzes mischarged tRNAs, notably ile-tRNA^leu. We present crystal structures of the editing domain from two eukaryotic cytosolic LeuRS: human and fungal pathogen Candida albicans. In comparison with previous structures of the editing domain from bacterial and archeal kingdoms, these structures show that the LeuRS editing domain has a conserved structural core containing the active site for hydrolysis, with distinct bacterial, archeal, or eukaryotic specific peripheral insertions. It was recently shown that the benzoxaborole antifungal compound AN2690 (5-fluoro-1,3-dihydro-1-hydroxy-1,2-benzoxaborole) inhibits LeuRS by forming a covalent adduct with the 3′ adenosine of tRNA^leu at the editing site, thus locking the enzyme in an inactive conformation. To provide a structural basis for enhancing the specificity of these benzoxaborole antifungals, we determined the structure at 2.2 Å resolution of the C. albicans editing domain in complex with a related compound, AN3018 (6-(ethylamino)-5-fluorobenzo[c][1,2]oxaborol-1(3H)-ol), using AMP as a surrogate for the 3′ adenosine of tRNA^leu. The interactions between the AN3018-AMP adduct and C. albicans LeuRS are similar to those previously observed for bacterial LeuRS with the AN2690 adduct, with an additional hydrogen bond to the extra ethylamine group. However, compared to bacteria, eukaryotic cytosolic LeuRS editing domains contain an extra helix that closes over the active site, largely burying the adduct and providing additional direct and water-mediated contacts. Small differences between the human domain and the fungal domain could be exploited to enhance fungal specificity.     

Competition theory,evolution, and the concept of an ecological niche

This article examines some of the main tenets of competition theory in light of the theory of evolution and the concept of an ecological niche. The principle of competitive exclusion and the related assumption that communities exist at competitive equilibrium - fundamental parts of many competition theories and models - may be violated if non-equilibrium conditions exist in natural communities or are incorporated into competition models. Furthermore, these two basic tenets of competition theory are not compatible with the theory of evolution. Variation in ecologically significant environmental factors and non-equilibrium in population numbers should occur in most natural communities, and such changes have important effects on community relations, niche overlap, and the evolution of ecosystems. Ecologists should view competition as a process occurring within a complexdynamic system, and should be wary of theoretical positions built upon simple laboratory experiments or simplistic mathematical models.In considering the relationship between niche overlap and competition, niche overlap should not be taken as a sufficient condition for competition; many factors may prevent or diminish competition between populations with similar resource utilization patterns. The typically opposing forces of intraspecific and interspecific competition need to be simultaneously considered, for it is the balance between them that in large part determines niche boundaries.     

Diffusion Tensor Metrics as Biomarkers in Alzheimer's Disease

Background

Although diffusion tensor imaging has been a major research focus for Alzheimer’s disease in recent years, it remains unclear whether it has sufficient stability to have biomarker potential. To date, frequently inconsistent results have been reported, though lack of standardisation in acquisition and analysis make such discrepancies difficult to interpret. There is also, at present, little knowledge of how the biometric properties of diffusion tensor imaging might evolve in the course of Alzheimer’s disease.

Methods

The biomarker question was addressed in this study by adopting a standardised protocol both for the whole brain (tract-based spatial statistics), and for a region of interest: the midline corpus callosum. In order to study the evolution of tensor changes, cross-sectional data from very mild (N = 21) and mild (N = 22) Alzheimer’s disease patients were examined as well as a longitudinal cohort (N = 16) that had been rescanned at 12 months.

Findings and Significance

The results revealed that increased axial and mean diffusivity are the first abnormalities to occur and that the first region to develop such significant differences was mesial parietal/splenial white matter; these metrics, however, remained relatively static with advancing disease indicating they are suitable as ‘state-specific’ markers. In contrast, increased radial diffusivity, and therefore decreased fractional anisotropy–though less detectable early–became increasingly abnormal with disease progression, and, in the splenium of the corpus callosum, correlated significantly with dementia severity; these metrics therefore appear ‘stage-specific’ and would be ideal for monitoring disease progression. In addition, the cross-sectional and longitudinal analyses showed that the progressive abnormalities in radial diffusivity and fractional anisotropy always occurred in areas that had first shown an increase in axial and mean diffusivity. Given that the former two metrics correlate with dementia severity, but the latter two did not, it would appear that increased axial diffusivity represents an upstream event that precedes neuronal loss.     

To be an intra‐guild predator or a cannibal: is prey quality decisive?

Abstract.  1. Many cannibalistic species are also intra-guild predators. Such predators will often face the decision whether to consume a conspecific or a heterospecific prey from the same guild. This decision may depend on the relative quality and abundance of the prey but also on other factors such as relatedness by descent, prey-specific defence and the probability of the victim harbouring shared diseases.
2. Here, intra-guild interactions among two cannibalistic species of predatory mites, Iphiseius degenerans and Neoseiulus cucumeris (Acari: Phytoseiidae) that belong to closely related genera were studied.
3. Individuals of I. degenerans were offered a diet of conspecifics or heterospecifics. Because I. degenerans is capable of recognising kin individuals from non-kin, and they were exclusively offered conspecifics that were either distantly related or non-kin, it was expected that it would not refrain from cannibalising for reasons of possible relatedness.
4. When corrected for numbers of victims eaten, survival, and juvenile development of predators fed with intra-guild prey was higher than that of cannibals. This was probably caused by a higher quality of heterospecific victims, even though conspecific victims were larger and therefore potentially contained more food. This led to the prediction that the predators should strongly prefer heterospecific prey. This was indeed borne out in independent choice experiments. Thus, the choice of predators between heterospecific and conspecific prey is not only affected by avoidance of consuming conspecifics, but also by relative prey quality.     

Life mode of in situ Conularia in a Middle Devonian epibole

Abstract: Exceptionally abundant specimens of Conularia aff. desiderata Hall occur in multiple marine obrution deposits, in a single sixth‐order parasequence composed of argillaceous and silty very fine sandstone, in the Otsego Member of the Mount Marion Formation (Middle Devonian, Givetian) in eastern New York State, USA. Associated fossils consist mostly of rhynchonelliform brachiopods but also include bivalve molluscs, orthoconic nautiloids, linguliform brachiopods and gastropods. Many of the brachiopods, bivalve molluscs and conulariids have been buried in situ. Conulariids buried in situ are oriented with their aperture facing obliquely upward and with their long axis inclined at up to 87 degree to bedding. Most specimens are solitary, but some occur in V‐like pairs or in radial clusters consisting of three specimens, with the component specimens being about equally long or (less frequently) substantially different in length. The compacted apical end of Conularia buried in situ generally rests upon argillaceous sandstone. With one possible exception, none of the examined specimens terminates in a schott (apical wall), and internal schotts appear to be absent. The apical ends of specimens in V‐like pairs and radial clusters show no direct evidence of interconnection of their periderms. The apical, middle or apertural region of some inclined specimens abuts or is in close lateral proximity to a recumbent conulariid or to one or more spiriferid brachiopods, some of which have been buried in their original life orientation. The azimuthal bearings of Conularia and nautiloid long axes and the directions in which conulariids open are nonrandom, with conulariids being preferentially aligned between 350 and 50 degree and with their apertural end facing north‐east, and nautiloids being preferentially aligned between 30 and 70 degree. Otsego Member Conularia were erect or semi‐erect, epifaunal or partially infaunal animals, the apical end of which rested upon very fine bottom sediment. The origin of V‐like pairs and radial clusters remains enigmatic, but it is probable that production of schotts was not a regular feature of this animal’s life history. Finally, conulariids and associated fauna were occasionally smothered by distal storm deposits, under the influence of relatively weak bottom currents.     

Analytical glycobiology at high sensitivity: current approaches and directions

This review summarizes the analytical advances made during the last several years in the structural and quantitative determinations of glycoproteins in complex biological mixtures. The main analytical techniques used in the fields of glycomics and glycoproteomics involve different modes of mass spectrometry and their combinations with capillary separation methods such as microcolumn liquid chromatography and capillary electrophoresis. The need for high-sensitivity measurements have been emphasized in the oligosaccharide profiling used in the field of biomarker discovery through MALDI mass spectrometry. High-sensitivity profiling of both glycans and glycopeptides from biological fluids and tissue extracts has been aided significantly through lectin preconcentration and the uses of affinity chromatography.     

Transmission of stridulatory signals of the burrower bugs, Scaptocoris castanea and Scaptocoris carvalhoi (Heteroptera: Cydnidae) through the soil and soybean

Abstract.  Males and females of the burrower bug species Scaptocoris castanea Perty and Scaptocoris carvalhoi Becker emit stridulatory signals when on the roots of soybean. The substrate-borne components of the signal can be recorded on the plant but not on the surrounding soil surface. The stridulatory apparatus is composed of the tergal plectrum (lima) and the stridulitrum (stridulatory vein) on the underside of the hind wings. The male plectrum has one ridge and the female lima has 13 ridges. Stridulitra of different species differ in the length and in the number of teeth. Rubbing of plectrum (lima) ridges over the stridulitrum in one or both directions produces pulse trains. The velocity of signals that are recorded less than 0.5 cm from the bug is below 0.013 mm s⁻¹ on the soil and below 0.066 mm s⁻¹ on the leaf surface. Broadband spectra have a dominant frequency of less than 1 kHz and subdominant peaks extending up to 7 kHz. The dominant frequency of the stridulatory signal transmitted through a plant decreases together with the proportion of its higher frequency spectral components. Signals are attenuated for 3–9 dB cm⁻¹ when transmitted through the soil or soybean leaf and for approximately 1 dB cm⁻¹ when transmitted through soybean stem.     

N-linked glycan structures and their expressions change in the blood sera of ovarian cancer patients

Glycosylated proteins play important roles in a broad spectrum of biochemical and biological processes, and prior reports have suggested that changes in protein glycosylation occur during cancer initiation and progression. Ovarian cancer (OC) is a fatal malignancy, most commonly diagnosed after the development of metastases. Therefore, early detection of OC is key to improving survival. To this end, specific changes of the serum glycome have been proposed as possible biomarkers for different types of cancers. In this study, we extend this concept to OC. To characterize differences in total N-glycan levels, serum samples provided by 20 healthy control women were compared to those acquired from patients diagnosed with late-stage recurrent OC who were enrolled in an experimental treatment trial prior to receiving therapy (N=19) and one month later, prior to the second treatment cycle (N=11). Additionally, analyses of the N-glycans associated with IgG and characterization of the relative abundance levels of core vs outer-arm fucosylation were also performed. The N-linked glycomic profiles revealed increased abundances of tri- and tetra-branched structures with varying degrees of sialylation and fucosylation and an apparent decrease in the levels of "bisecting" glycans in OC samples compared to controls. Increased levels of a-galactosylation structures were observed on N-linked glycans derived from IgG, which were independent of the presence of fucose residues. Elevated levels of outer-arm fucosylation were also identified in the OC samples. These results allowed the control samples to be distinguished from the baseline ovarian cancer patients prior to receiving the experimental treatment. In some cases, the pre-treatment samples could be distinguished from the post-experimental treatment samples, as many of those patients showed a further progression of the disease.