Amoxicillin Haptenation of α-Enolase is Modulated by Active Site Occupancy and Acetylation

Allergic reactions to antibiotics are a major concern in the clinic. ß-lactam antibiotics are the class most frequently reported to cause hypersensitivity reactions. One of the mechanisms involved in this outcome is the modification of proteins by covalent binding of the drug (haptenation). Hence, interest in identifying the corresponding serum and cellular protein targets arises. Importantly, haptenation susceptibility and extent can be modulated by the context, including factors affecting protein conformation or the occurrence of other posttranslational modifications. We previously identified the glycolytic enzyme α-enolase as a target for haptenation by amoxicillin, both in cells and in the extracellular milieu. Here, we performed an in vitro study to analyze amoxicillin haptenation of α-enolase using gel-based and activity assays. Moreover, the possible interplay or interference between amoxicillin haptenation and acetylation of α-enolase was studied in 1D- and 2D-gels that showed decreased haptenation and displacement of the haptenation signal to lower pI spots after chemical acetylation of the protein, respectively. In addition, the peptide containing lysine 239 was identified by mass spectrometry as the amoxicillin target sequence on α-enolase, thus suggesting a selective haptenation under our conditions. The putative amoxicillin binding site and the surrounding interactions were investigated using the α-enolase crystal structure and molecular docking. Altogether, the results obtained provide the basis for the design of novel diagnostic tools or approaches in the study of amoxicillin-induced allergic reactions.

Half-Heusler-like compounds with wide continuous compositions and tunable p- to n-type semiconducting thermoelectrics

Half-Heusler and full-Heusler compounds were considered as independent phases with a natural composition gap. Here we report the discovery of TiRu1+xSb (x = 0.15 ~ 1.0) solid solution with wide homogeneity range and tunable p- to n-type semiconducting thermoelectrics, which bridges the composition gap between half- and full-Heusler phases. At the high-Ru end, strange glass-like thermal transport behavior with unusually low lattice thermal conductivity (~1.65 Wm−1K−1 at 340 K) is observed for TiRu1.8Sb, being the lowest among reported half-Heusler phases. In the composition range of 0.15 < x < 0.50, TiRu1+xSb shows abnormal semiconducting behaviors because tunning Ru composition results in band structure change and carrier-type variation simultaneously, which seemingly correlates with the localized d electrons. This work reveals the possibility of designing fascinating half-Heusler-like materials by manipulating the tetrahedral site occupancy, and also demonstrates the potential of tuning crystal and electronic structures simultaneously to realize intriguing physical properties.

Crystal structure of a dicationic PdII dimer containing a 2-[(diisopropylphosphanyl)methyl]quinoline-8-thiolate pincer ligand

A dicationic PdII dimer, bis{2-[(diisopropylphosphanyl)methyl]quinoline-8-thiolato}palladium(II) bis(hexafluoridoantimonate) dichloromethane monosolvate, [Pd2(C32H42N2P2S2)](SbF6)2·CH2Cl2, containing a 2-[(diisopropylphosphanyl)methyl]quinoline-8-thiolate pincer ligand, was isolated and its crystal structure determined. The title compound crystallizes in the orthorhombic space group Pbca. A dimeric structure is formed by bridging coordination of the S atoms. The geometry of the butterfly-shaped Pd2S2 core is bent, with a hinge angle of 108.0 (1)° and a short Pd...Pd distance of 2.8425 (7) Å. These values are the lowest measured compared to ten dicationic dimers with a Pd2S2 core featuring sulfur atoms embedded in a chelating ligand. One of the two hexafluoridoantimonate anions is disordered over two sets of positions with site-occupancy factors of 0.711 (5) and 0.289 (5). The crystal structure is stabilized by many C—H...F and C—H...π interactions, forming a supramolecular network.

Occupancy of wild southern pig-tailed macaques in intact and degraded forests in Peninsular Malaysia

Deforestation is a major threat to terrestrial tropical ecosystems, particularly in Southeast Asia where human activities have dramatic consequences for the survival of many species. However, responses of species to anthropogenic impact are highly variable. In order to establish effective conservation strategies, it is critical to determine a species’ ability to persist in degraded habitats. Here, we used camera trapping data to provide the first insights into the temporal and spatial distribution of southern pig-tailed macaques (Macaca nemestrina, listed as ‘Vulnerable’ by the IUCN) across intact and degraded forest habitats in Peninsular Malaysia, with a particular focus on the effects of clear-cutting and selective logging on macaque occupancy. Specifically, we found a 10% decline in macaque site occupancy in the highly degraded Pasoh Forest Reserve from 2013 to 2017. This may be strongly linked to the macaques’ sensitivity to intensive disturbance through clear-cutting, which significantly increased the probability that M. nemestrina became locally extinct at a previously occupied site. However, we found no clear relationship between moderate disturbance, i.e., selective logging, and the macaques’ local extinction probability or site occupancy in the Pasoh Forest Reserve and Belum-Temengor Forest Complex. Further, an identical age and sex structure of macaques in selectively logged and completely undisturbed habitat types within the Belum-Temengor Forest Complex indicated that the macaques did not show increased mortality or declining birth rates when exposed to selective logging. Overall, this suggests that low to moderately disturbed forests may still constitute valuable habitats that support viable populations of M. nemestrina, and thus need to be protected against further degradation. Our results emphasize the significance of population monitoring through camera trapping for understanding the ability of threatened species to cope with anthropogenic disturbance. This can inform species management plans and facilitate the development of effective conservation measures to protect biodiversity.

Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sub-lines.

Cultured cells are widely used in molecular biology despite poor understanding of how cell line genomes change in vitro over time. Previous work has shown that Drosophila cultured cells have a higher transposable element (TE) content than whole flies, but whether this increase in TE content resulted from an initial burst of transposition during cell line establishment or ongoing transposition in cell culture remains unclear. Here we sequence the genomes of 25 sub-lines of Drosophila S2 cells and show that TE insertions provide abundant markers for the phylogenetic reconstruction of diverse sub-lines in a model animal cell culture system. Analysis of DNA copy number evolution across S2 sub-lines revealed dramatically different patterns of genome organization that support the overall evolutionary history reconstructed using TE insertions. Analysis of TE insertion site occupancy and ancestral states support a model of ongoing transposition dominated by episodic activity of a small number of retrotransposon families. Our work demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, which may impact the reproducibility of experiments that do not control for sub-line identity.

Survival, predation, and behaviour of the Mahoenui giant wētā ('Deinacrida mahoenui': Anostostomatidae: Orthoptera)

<p>Introduced mammalian pests, such as rats (Rattus spp.), house mice (Mus musculus), brushtail possums (Trichosurus vulpecula), and European hedgehogs (Erinaceus europaeus), have been implicated in the suppression or extinction of many endemic invertebrate species in New Zealand, including the large-bodied giant wētā (Anostostomatidae: Deinacrida). The Mahoenui giant wētā (MGW; D. mahoenui) is the only lowland giant wētā species still naturally present on the mainland of New Zealand, where the last remaining individuals of the original population are currently restricted to an 187ha mainland reserve (Mahoenui Giant Wētā Scientific Reserve; MGWSR) in Mahoenui, western King Country. Having sought refuge in the introduced woody shrub, gorse (Ulex europaeus), these wētā have survived in the presence of introduced mammalian predators for almost six decades. However, due to natural succession, the reserve is gradually reverting to native bush and wētā monitoring data shows potential signs of population decline. Concerns for the species survival have been raised as it is unknown how wētā will cope in an altered habitat alongside mammalian predators. In chapter 2, we used 14-years’ of site-occupancy monitoring data to explore changes to the reserves’ gorse mosaic and MGW population. We additionally assessed the effect of abiotic covariates on MGW occupancy and detection probabilities in 2005 and 2018. Furthermore, we assessed mammalian pest population dynamics within the reserve over the past seven years. Significant changes to the reserve’s gorse mosaic were identified, whereby unbrowsed, tall bushes, which may provide less protection to wētā, are now dominant in 2018. Population trajectory analysis revealed the MGW population has decline since 2012. This result was consistent with naïve occupancy estimates and the increase in search time (0.3hrs/year) required to find wētā, suggesting the population is in a state of decline. Plot location was identified as an important covariate for predicting MGW occupancy in 2018, whereby plots in edge habitat, potentially being preferred or safer, had a higher occupancy probability. Mammalian pests (rats, house mice, brushtail possums, and European hedgehogs) appear to be present within the reserve year-round, populations peaking in summer and autumn. In chapter 3, we used radiotelemetry to explore MGW survival rates, movement patterns, and diurnal refuge use in gorse and native vegetation during summer (n=14), autumn (n=31), and spring (n=10). Survival rates, in relation to predation, revealed MGW inhabiting native vegetation were nine times more likely to be predated than those inhabiting gorse. This result suggests native species such as mahoe (Melicytus ramiflorus), and tree ferns (Dicksonia fibrosa and Cyathea spp.) do not provide good protection to MGW from mammalian predators. Assessment of movement behaviour revealed MGW move less in autumn (~3m/48hrs) compared to summer (~10m/48hrs) and spring (~8m/48hrs), and most commonly follow a movement pattern consistent with random-walk. Movement behaviour was also found to be temperature dependant, with both male and female MGW moving significantly further in warmer weather (>13.5°C). Radiotracked MGW were found to take refuge above 2.5m in the canopy of native vegetation, whereas in gorse habitat, wētā were most commonly found taking refuge between 0.62 – 2.38m in the denser foliage of unbrowsed gorse bushes. Furthermore, no radiotracked wētā were observed with another individual in autumn, compared to eight and 26 observations in summer and spring. In chapter 4, we attempted to identify potential mammalian predators of the MGW by analysing the stomach contents of ship rats (R. rattus; n=10), house mice (n=10), brushtail possums (n=5), and feral cats (Felis catus; n=2). Ship rats were identified as likely predators of MGW within the MGWSR. However, due to the limited number of stomachs and species analysed, further analysis is recommended. Collectively, these results provide an overview of the MGW reserve and population status, in addition to important ecological information that can be used to inform future management, monitoring, and translocation.</p>

Survival, predation, and behaviour of the Mahoenui giant wētā ('Deinacrida mahoenui': Anostostomatidae: Orthoptera)

<p>Introduced mammalian pests, such as rats (Rattus spp.), house mice (Mus musculus), brushtail possums (Trichosurus vulpecula), and European hedgehogs (Erinaceus europaeus), have been implicated in the suppression or extinction of many endemic invertebrate species in New Zealand, including the large-bodied giant wētā (Anostostomatidae: Deinacrida). The Mahoenui giant wētā (MGW; D. mahoenui) is the only lowland giant wētā species still naturally present on the mainland of New Zealand, where the last remaining individuals of the original population are currently restricted to an 187ha mainland reserve (Mahoenui Giant Wētā Scientific Reserve; MGWSR) in Mahoenui, western King Country. Having sought refuge in the introduced woody shrub, gorse (Ulex europaeus), these wētā have survived in the presence of introduced mammalian predators for almost six decades. However, due to natural succession, the reserve is gradually reverting to native bush and wētā monitoring data shows potential signs of population decline. Concerns for the species survival have been raised as it is unknown how wētā will cope in an altered habitat alongside mammalian predators. In chapter 2, we used 14-years’ of site-occupancy monitoring data to explore changes to the reserves’ gorse mosaic and MGW population. We additionally assessed the effect of abiotic covariates on MGW occupancy and detection probabilities in 2005 and 2018. Furthermore, we assessed mammalian pest population dynamics within the reserve over the past seven years. Significant changes to the reserve’s gorse mosaic were identified, whereby unbrowsed, tall bushes, which may provide less protection to wētā, are now dominant in 2018. Population trajectory analysis revealed the MGW population has decline since 2012. This result was consistent with naïve occupancy estimates and the increase in search time (0.3hrs/year) required to find wētā, suggesting the population is in a state of decline. Plot location was identified as an important covariate for predicting MGW occupancy in 2018, whereby plots in edge habitat, potentially being preferred or safer, had a higher occupancy probability. Mammalian pests (rats, house mice, brushtail possums, and European hedgehogs) appear to be present within the reserve year-round, populations peaking in summer and autumn. In chapter 3, we used radiotelemetry to explore MGW survival rates, movement patterns, and diurnal refuge use in gorse and native vegetation during summer (n=14), autumn (n=31), and spring (n=10). Survival rates, in relation to predation, revealed MGW inhabiting native vegetation were nine times more likely to be predated than those inhabiting gorse. This result suggests native species such as mahoe (Melicytus ramiflorus), and tree ferns (Dicksonia fibrosa and Cyathea spp.) do not provide good protection to MGW from mammalian predators. Assessment of movement behaviour revealed MGW move less in autumn (~3m/48hrs) compared to summer (~10m/48hrs) and spring (~8m/48hrs), and most commonly follow a movement pattern consistent with random-walk. Movement behaviour was also found to be temperature dependant, with both male and female MGW moving significantly further in warmer weather (>13.5°C). Radiotracked MGW were found to take refuge above 2.5m in the canopy of native vegetation, whereas in gorse habitat, wētā were most commonly found taking refuge between 0.62 – 2.38m in the denser foliage of unbrowsed gorse bushes. Furthermore, no radiotracked wētā were observed with another individual in autumn, compared to eight and 26 observations in summer and spring. In chapter 4, we attempted to identify potential mammalian predators of the MGW by analysing the stomach contents of ship rats (R. rattus; n=10), house mice (n=10), brushtail possums (n=5), and feral cats (Felis catus; n=2). Ship rats were identified as likely predators of MGW within the MGWSR. However, due to the limited number of stomachs and species analysed, further analysis is recommended. Collectively, these results provide an overview of the MGW reserve and population status, in addition to important ecological information that can be used to inform future management, monitoring, and translocation.</p>