Monitoring occurrence,extinction, and colonization probabilities for gibbon populations

All gibbon species (Family: Hylobatidae) are considered threatened with extinction and recognized on the International Union for Conservation of Nature Red List of Threatened Species. Because gibbons are one of the most threatened families of primates, monitoring their status is now critically important. Long-term monitoring programs applying occupancy approaches, in addition to assessing occurrence probability, improves understanding of other population parameters such as site extinction or colonization probabilities, which elucidate temporal and spatial changes and are therefore important for guiding conservation efforts. In this study, we used multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities for northern yellow-cheeked crested gibbon Nomascus annamensis in three adjacent protected areas in the Central Annamites mountain range, Vietnam. We collected data at 30 listening posts in 2012, 2014, and 2016 using the auditory point count method. Occurrence probabilities were highest in 2012 (0.74, confidence interval [CI]: 0.56–0.87) but slightly lower in 2014 (0.66, CI: 0.51–0.79) and 2016 (0.67, CI: 0.49–0.81). Extinction probabilities during the 2012–2014 and 2014–2016 intervals were 0.26 (0.14–0.44) and 0.25 (0.12–0.44), respectively. Colonization probabilities during 2012–2014 were 0.44 (0.19–0.73) and between 2014 and 2016 was 0.51 (0.26–0.75). Although local site extinctions have occurred, high recolonization probability helped to replenish the unoccupied sites and kept the occurrence probability stable. Long-term monitoring programs which use occurrence probability alone might not fully reveal the true dynamics of gibbon populations. We strongly recommend including multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities in long-term gibbon monitoring programs.     

Flexibility within the Rotor and Stators of the Vacuolar H+-ATPase

The V-ATPase is a membrane-bound protein complex which pumps protons across the membrane to generate a large proton motive force through the coupling of an ATP-driven 3-stroke rotary motor (V₁) to a multistroke proton pump (V_o). This is done with near 100% efficiency, which is achieved in part by flexibility within the central rotor axle and stator connections, allowing the system to flex to minimise the free energy loss of conformational changes during catalysis. We have used electron microscopy to reveal distinctive bending along the V-ATPase complex, leading to angular displacement of the V₁ domain relative to the V_o domain to a maximum of ~30°. This has been complemented by elastic network normal mode analysis that shows both flexing and twisting with the compliance being located in the rotor axle, stator filaments, or both. This study provides direct evidence of flexibility within the V-ATPase and by implication in related rotary ATPases, a feature predicted to be important for regulation and their high energetic efficiencies.     

Biodeterioration of Mayan buildings at uxmal and tulum,Mexico

Uxmal and Tulum are two important Mayan sites in the Yucatan peninsula. The buildings are mainly composed of limestone and grey/black discoloration is seen on exposed walls and copious greenish biofilms on inner walls. The principal microorganisms detected on interior walls at both Uxmal and Tulum were cyanobacteria; heterotrophic bacteria and filamentous fungi were also present. A dark‐pigmented mitosporic fungus and Bacillus cereus, both isolated from Uxmal, were shown to be acidogenic in laboratory cultures. Cyanobacteria belonging to rock‐degrading genera Synechocystis and Gloeocapsa were identified at both sites. Surface analysis previously showed that calcium ions were present in the biofilms on buildings at Uxmal and Tulum, suggesting the deposition of biosolubilized stone. Apart from their potential to degrade the substrate, the coccoid cyanobacteria supply organic nutrients for bacteria and fungi, which can produce organic acids, further increasing stone degradation.     

5,6-Dihydro-5-aza-2′-deoxycytidine potentiates the anti-HIV-1 activity of ribonucleotide reductase inhibitors

The nucleoside analog 5,6-dihydro-5-aza-2′-deoxycytidine (KP-1212) has been investigated as a first-in-class lethal mutagen of human immunodeficiency virus type-1 (HIV-1). Since a prodrug monotherapy did not reduce viral loads in Phase II clinical trials, we tested if ribonucleotide reductase inhibitors (RNRIs) combined with KP-1212 would improve antiviral activity. KP-1212 potentiated the activity of gemcitabine and resveratrol and simultaneously increased the viral mutant frequency. G-to-C mutations predominated with the KP-1212-resveratrol combination. These observations represent the first demonstration of a mild anti-HIV-1 mutagen potentiating the antiretroviral activity of RNRIs and encourage the clinical translation of enhanced viral mutagenesis in treating HIV-1 infection.     

Seasonal Variation in the Activity and Dietary Budgets of Cat Ba Langurs (<Emphasis Type="Italic">Trachypithecus poliocephalus</Emphasis>)

Primate activity budgets are dictated by food availability and distribution; thus primates living in seasonal environments must adapt their behaviors to accommodate fluctuations in resources. Cat Ba langurs (Trachypithecus poliocephalus), a Critically Endangered Asian colobine and a member of the limestone langur group (francoisi superspecies group within genus Trachypithecus), live only in fragmented and disturbed habitats on Cat Ba Island, northeastern Vietnam. This study aimed to assess the behaviors and diet of Cat Ba langurs by group, age, sex, and season. We predicted they would have high rates of inactivity and foraging, low rates of social behaviors, with seasonal variation that reflects an energy-maximizing strategy. We conducted behavioral observations through scan sampling over an 11-month period and found that Cat Ba langurs spent a significant portion of their day inactive (57 %) followed by foraging (18 %), socializing (13 %), locomoting (10 %), and engaging in “other” behaviors (2 %). Their diet was made up primarily of leaves (83 %) followed by flowers (8 %), fruit (6 %), and stems (3 %). We found groups to differ in diet and activity, which is likely owing to differences in demographics and home range between groups. Seasonally, the animals ate more leaves and spent more time foraging in the dry season than the wet season, suggesting that they are energy maximizers. Cat Ba langurs have activity and dietary budgets similar to those of other limestone langurs, and respond to a presumed seasonal fluctuation in food availability similarly.     

Mechanisms of biodiversity between Campylobacter sequence types in a flock of broiler–breeder chickens

Commercial poultry flocks frequently harbor the dangerous bacterial pathogen Campylobacter. As exclusion efforts frequently fail, there is interest in potential ecologically informed solutions. A long‐term study of Campylobacter sequence types was used to investigate the competitive framework of the Campylobacter metacommunity and understand how multiple sequence types simultaneously co‐occur in a flock of chickens. A combination of matrix and patch‐occupancy models was used to estimate parameters describing the competition, transmission, and mortality of each sequence type. It was found that Campylobacter sequence types form a strong hierarchical framework within a flock of chickens and occupied a broad spectrum of transmission–mortality trade‐offs. Upon further investigation of how biodiversity is thus maintained within the flock, it was found that the demographic capabilities of Campylobacter, such as mortality and transmission, could not explain the broad biodiversity of sequence types seen, suggesting that external factors such as host‐bird health and seasonality are important elements in maintaining biodiversity of Campylobacter sequence types.     

Mechanism of proteasome gate modulation by assembly chaperones Pba1 and Pba2

The active sites of the proteasome are housed within its central core particle (CP), a barrel-shaped chamber of four stacked heptameric rings, and access of substrates to the CP interior is mediated by gates at either axial end. These gates are constitutively closed and may be opened by the regulatory particle (RP), which binds the CP and facilitates substrate degradation. We recently showed that the heterodimeric CP assembly chaperones Pba1/2 also mediate gate opening through an unexpected structural arrangement that facilitates the insertion of the N terminus of Pba1 into the CP interior; however, the full mechanism of Pba1/2-mediated gate opening is unclear. Here, we report a detailed analysis of CP gate modulation by Pba1/2. The clustering of key residues at the interface between neighboring α-subunits is a critical feature of RP-mediated gate opening, and we find that Pba1/2 recapitulate this strategy. Unlike RP, which inserts at six α-subunit interfaces, Pba1/2 insert at only two α-subunit interfaces. Nevertheless, Pba1/2 are able to regulate six of the seven interfacial clusters, largely through direct interactions. The N terminus of Pba1 also physically interacts with the center of the gate, disrupting the intersubunit contacts that maintain the closed state. This novel mechanism of gate modulation appears to be unique to Pba1/2 and therefore likely occurs only during proteasome assembly. Our data suggest that release of Pba1/2 at the conclusion of assembly is what allows the nascent CP to assume its mature gate conformation, which is primarily closed, until activated by RP.     

Differential scanning calorimetry studies of intraembryonic freezing and cryoprotectant penetration in zebrafish (Danio rerio) embryos

Nucleation temperatures of intraembryonic water and cryoprotectant penetration in zebrafish embryos were studied using differential scanning calorimetry. The effects of embryo developmental stage, dechorionation, partial removal of yolk, cooling rate, and cryoprotectant treatment on the temperatures of intraembryonic freezing were investigated. Embryo stages were found to have a significant effect on the nucleation temperatures of intact embryos. Freeze onset temperatures of -11.9 +/- 1.5, -15.6 +/- 0.3, and -20.5 +/- 0.1 degrees C were obtained for intact embryos at 6-somite, prim-6, and high-pec stages, respectively. After dechorionation, the freeze onset temperatures of intraembryonic water shifted to significantly lower temperatures, being -23.5 +/- 0.8, -18.7 +/- 0.7, -24.9 +/- 0.8 degrees C for 6-somite, prim-6, and high-pec stages, respectively. Yolk-reduced high-pec stage embryos showed significantly lower nucleation temperatures with an average onset at -27.9 +/- 0.4 degrees C. The effect of cryoprotectant treatment on the nucleation temperatures of intraembryonic water varies among different embryo stages and different cryoprotectants. Thirty-minute treatment with 2 M methanol significantly decreased the nucleation temperatures of dechorionated 6-somite embryos whilst no temperature decrease was observed for prim-6 or yolk-reduced high-pec embryos. Thirty-minute exposure to 1 M propylene glycol did not significantly affect the nucleation temperatures of dechorionated 6-somite, prim-6, or yolk-reduced high-pec embryos. In order to increase the permeability of embryos to cryoprotectants, the yolk sacs of dechorionated embryos at 6-somite or prim-6 embryos were punctured with a sharp micro-needle before exposure to cryoprotectants. The punctured prim-6 embryos showed significantly lower temperatures of intraembryonic freezing after 30 min of exposure to 2 M methanol following the multi-punctures. The nucleation temperatures of punctured 6-somite or prim-6 embryos were also decreased significantly after exposure to 1 M propylene glycol for 30 min. These results suggested that in intact embryos, intraembryonic freezing appeared to be seeded by the external ice in the perivitelline fluid and that in dechorionated embryos (in the absence of external water) intraembryonic freezing was more likely a consequence of heterogeneous nucleation. Methanol was demonstrated to show a limited degree of penetration into prim-6 stage embryos, but it did not penetrate later-stage embryos such as prim-6 and yolk-reduced high-pec. No propylene glycol permeation was observed for embryos at all stages. However, multi-punctures of yolk resulted in the permeation of both cryoprotectants into prim-6 embryos and propylene glycol permeation into 6-somite embryos. These findings may have important implications in overcoming the problem associated with the low membrane permeability of zebrafish embryos to cryoprotectants.