Selection of Flagship Species and Their Use as Umbrellas in Bird Conservation: A Case Study in Lishui, Zhejiang Province, China.

The concept of flagship species is widely used in conservation biology. Flagship birds play a key role in raising conservation funds, increasing awareness of biodiversity conservation, and maintaining ecosystem services. This study selected flagship bird species in Lishui, Zhejiang Province, China, and assessed their conservation effectiveness and ability to serve as umbrella species. A regional bird survey program from 2019-2022 recorded 361 bird species in Lishui. This study constructed a framework of flagship species selection based on social, ecological, economic, and cultural criteria. The analytic hierarchy process-entropy weight method (AHP-EM) was used to rank the score of 361 bird species, and the MaxEnt model was used to analyze the suitable distribution areas of these species. Finally, 10 species, which covered the distribution sites of all 361 bird species, were selected as the flagship species of Lishui. The distribution areas covered all the nature reserves and the priority areas of biodiversity of Lishui, in which these 10 species can also serve as umbrella species to protect local biodiversity. The methodology and ideas in this study could provide insights into the application of conservation concepts at the local level, as well as suggest possible recommendations for local governments to select flagship species for conservation.

COVID-19 lockdown has indirect, non-equivalent effects on activity patterns of Reeves's Pheasant (Syrmaticus reevesii) and sympatric species.

The outbreak of the COVID-19 pandemic has brought massive shifts in human activities through a global blockade, directly affecting wildlife survival. However, the indirect impacts of changes in human activities are often easily overlooked. We conducted surveys of Reeves's Pheasant (Syrmaticus reevesii) and its sympatric species by camera traps in forest-type nature reserves in three different scenarios: pre-lockdown, lockdown and post-lockdown. An increase in livestock activities observed during the lockdown and post-lockdown period in our study area provided us an opportunity to investigate the indirect impact of the lockdown on wildlife. The pre-lockdown period was used as a baseline to compare any changes in trends of relative abundance index, activity patterns and temporal spacing of targeted species and livestock. During the lockdown period, the relative abundance index of livestock increased by 50% and there was an increase in daytime activity. Reeves's Pheasant showed avoidance responses to almost all sympatric species and livestock in three different periods, and the livestock avoidance level of Reeves's Pheasant during the lockdown period was significantly and positively correlated with the relative abundance index of livestock. Species-specific changes in activity patterns of study species were observed, with reduced daytime activities of Hog Badger and Raccoon Dog during and after the confinement periods. This study highlights the effect of the COVID-19 lockdown on the responses of wildlife by considering the changes in their temporal and spatial use before, during and after lockdown. The knowledge gained on wildlife during reduced human mobility because of the pandemic aids in understanding the effect of human disturbances and developing future conservation strategies in the shared space, to manage both wildlife and livestock.

Evolution of Avian Eye Size Is Associated with Habitat Openness, Food Type and Brain Size.

The eye is the primary sensory organ that obtains information from the ecological environments and specifically bridges the brain with the extra environment. However, the coevolutionary relationships between eye size and ecological factors, behaviours and brain size in birds remain poorly understood. Here, we investigate whether eye size evolution is associated with ecological factors (e.g., habitat openness, food type and foraging habitat), behaviours (e.g., migration and activity pattern) and brain size among 1274 avian species using phylogenetically controlled comparative analyses. Our results indicate that avian eye size is significantly associated with habitat openness, food type and brain size. Species living in dense habitats and consuming animals exhibit larger eye sizes compared to species living in open habitats and consuming plants, respectively. Large-brained birds tend to possess larger eyes. However, migration, foraging habitat and activity pattern were not found to be significantly associated with eye size in birds, except for nocturnal birds having longer axial lengths than diurnal ones. Collectively, our results suggest that avian eye size is primarily influenced by light availability, food need and cognitive ability.

Optimizing protected areas to boost the conservation of key protected wildlife in China.

To meet the challenge of biodiversity loss and reach the targets of the proposed Post-2020 Global Biodiversity Framework, the Chinese government updated the list of national key protected wildlife in 2021 and has been continually expanding the protected areas (PAs). However, the status of protected wildlife in PAs remains unclear. In this study, we conducted a national assessment of the status of protected wildlife and suggested an optimization plan to overcome these shortcomings. From 1988 to 2021, the number of protected species almost doubled, and the area of PAs increased by 2.4 times, covering over 92.8% of the protected species. Nonetheless, 70.8% of the protected species are still not effectively protected by PAs, with some having less than 10% of their habitat included in PAs. Despite the significant addition of amphibians and reptiles to the latest protection list, they are the fewest species and are the least covered by PAs compared with birds and mammals. To fix these gaps, we systematically optimized the current PAs network by adding another 10.0% of China's land area as PAs, which resulted in 37.6% coverage of protected species' habitats in PAs. In addition, 26 priority areas were identified. Our research aimed to identify gaps in current conservation policies and suggest optimization solutions to facilitate wildlife conservation planning in China. In general, updating the list of key protected wildlife species and systematically optimizing PA networks are essential and applicable to other countries facing biodiversity loss.

PhaGAA: an integrated web server platform for phage genome annotation and analysis.

MOTIVATION: Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. Accordingly, comprehensive and user-friendly platforms for phage genome annotation are needed. RESULTS: Here, we propose PhaGAA, an online integrated platform for phage genome annotation and analysis. By incorporating several annotation tools, PhaGAA is constructed to annotate the prophage genome at DNA and protein levels and provide the analytical results. Furthermore, PhaGAA could mine and annotate phage genomes from bacterial genome or metagenome. In summary, PhaGAA will be a useful resource for experimental biologists and help advance the phage synthetic biology in basic and application research. AVAILABILITY AND IMPLEMENTATION: PhaGAA is freely available at http://phage.xialab.info/.

Effects of Livestock Grazing on Spatio-Temporal Patterns and Behaviour of Reeves's Pheasant Syrmaticus reevesii.

Protected areas are seeing an increase in anthropogenic disturbances in the world. Previous studies have demonstrated the impact of livestock grazing and human presence on the habitat use of birds, whereas little is known about the effect of free-ranging livestock on bird behaviour. Reeves's Pheasant (Syrmaticus reevesii) is endemic to China and has been threatened by habitat loss and fragmentation, illegal logging, and human disturbance over the past 20 years. Based on camera trapping in the Liankangshan National Nature Reserve (LKS) and the Zhonghuashan Birds Provincial Nature Reserve (ZHS), we explore the effects of livestock grazing and human activities on the spatio-temporal distribution and behavioural patterns of Reeves's Pheasant. Livestock does not appear to affect habitat use by the pheasant but changes its behavioural patterns. In addition, pheasants in areas with livestock foraged mostly during the early morning, while in areas without livestock, they foraged at dusk. Therefore, the study concludes that livestock intensity in nature reserves may have reduced pheasant suitability through altered patterns of vigilance and foraging behaviour.

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Oil and its pollutants, which enter environment through natural oil seepage and many human activities, have considerable impacts on birds. We summarized the research advances in how oil pollutants influence birds and the cleaning technology of polluted birds and their habitats. The toxicity and destruction to feather structure are the major impacts of oil pollution on birds. Oil pollution can lead to birds' death, and also produce many chronic harms, including causing hemolytic anemia, reducing their immunity, disrupting thermal insulation and waterproo-fing performance of feather. It is an important way to reduce the impacts of oil pollution on birds by timely cleaning up the oil in bird habitats as well as carrying out the clean and repair work to the polluted birds. As a big oil-consuming country, China has been left behind by foreign countries in the studies of the effects of oil pollution on birds. More attention should be paid on the short-term and long-term impacts of oil pollution on birds and the cleaning and remediation technologies of the polluted birds and their habitats.

Sex-Specific Movement Responses of Reeves's Pheasant to Human Disturbance: Importance of Body Characteristics and Reproductive Behavior.

Human disturbance has a strong impact on the movement of wild animals. However, it remains unclear how the movement patterns of the Reeves's Pheasant (Syrmaticus reevesii) respond to human disturbance in human-dominated landscapes. We tracked the movement of 40 adult individual Reeves's Pheasants during the breeding season, and used the dynamic Brownian bridge motion model and kernel density estimation to analyze the diurnal movement patterns of Reeves's Pheasants and their response to human presence. We analyzed the paths of Reeves's Pheasants based on a partial least squares path model, considering habitat conditions, body characteristics, and reproductive behaviors. We found that males had two clear diurnal movement peaks, whereas reproductive and non-reproductive females did not show such movement peaks. Males shifted their movement peaks to earlier times in the day to avoid the presence peaks of humans. The correlation between human-modified habitat and the movement intensity of Reeves's Pheasant differed between sexes. For males, the distance to forest paths had a positive correlation with their movement intensity through affecting body conditions. For females, the distance to forest paths and farmland had a negative correlation with their movement intensity through affecting habitat conditions and reproductive behaviors. Our study provides a scientific basis for the protection of the Reeves's Pheasant and other related terrestrial forest-dwelling birds.

Objective vestibular function changes in children following cochlear implantation.

BACKGROUND: To date, systematically objective evaluations of vestibular function in children with cochlear implantation (CI) have been conducted sparsely, especially in children with large vestibular aqueduct syndrome (LVAS). OBJECTIVE: Our goal was to investigate the function of all five vestibular end-organs pre- and post-cochlear implantation in children with LVAS and normal CT. METHODS: In this retrospective cohort study, 34 children (age 4-17 years) with bilateral profound sensorineural hearing loss (SNHL) undergoing unilateral CI were included. Participants included 18 (52.9%) children with LVAS. Objective modalities to evaluate vestibular function included the caloric test, cervical vestibular-evoked myogenic potentials (cVEMP), ocular vestibular-evoked myogenic potentials (oVEMP), and video head impulse test (vHIT). All measurements were performed before surgery and 9 months after surgery. RESULTS: Mean age at CI was 8.1±3.7 years. Caloric testing showed hypofunction in 38.2% of cases before implantation and in 50% after (p > 0.05). We found a significant increase of overall abnormality rate in cVEMP and oVEMP from pre- to post-CI (p < 0.05). In all three semicircular canals tested by vHIT, there were no statistically significant mean gain changes (p > 0.05). Higher deterioration rates in cVEMP (53.3%) and oVEMP (52.0%) after surgery were observed (p < 0.05). In children with LVAS, cVEMP revealed a higher deterioration rate than superior semicircular canal (SSC) and posterior semicircular canal (PSC) (p < 0.05). In children with normal CT, the deterioration rates in VEMPs were both higher than those in vHIT (p < 0.05). CONCLUSIONS: In general, the otolith organs were the most affected peripheral vestibular sensors in children after cochlear implantation. The variations in otolith function influenced by CI were different between children with LVAS and normal CT. We recommend the use of this vestibular function test battery for children with cochlear implantation.

Response of Reeves's Pheasants Distribution to Human Infrastructure in the Dabie Mountains over the Last 20 Years.

Human infrastructure development drives habitat loss and fragmentation worldwide. In China, over the last 20 years, rapid infrastructure development impacted the habitats of endangered species. To facilitate conservation efforts, studies of how human infrastructure affects the distribution of Reeves's pheasant (Syrmaticus reevesii), an endangered species by the International Union for Conservation of Nature (IUCN) and a nationally protected species in China, are critically needed. We assessed how the distribution of Reeves's pheasant was impacted by human infrastructure development over the past 20 years in the Dabie Mountains, the main distribution range of the species. We surveyed Reeves's pheasants by direct sightings and indirect evidence through line transects which were randomly distributed in the Dabie Mountains from 2001 to 2002 and 2018 to 2019. We evaluated the variation of the roads and buildings in these areas in the last 20 years, and then modeled the relationship of the distribution of this pheasant with the road and building data from 2000 and 2017. Human infrastructure became more extensively distributed throughout the Dabie Mountains during the period, with all lands within 10 km of a road or a building. The distribution of Reeves's pheasants became closer to the buildings and roads and there was a significantly positive relationship between the occurrence of Reeves's pheasants and the distance to the nearest buildings and roads in 2018-2019. These results suggest that the increased density of buildings and roads in the Dabie Mountains may have caused negative effects on Reeves's pheasants.

Influence of Cochlear Implantation on Vestibular Function in Children With an Enlarged Vestibular Aqueduct.

Background: Cochlear implantation (CI) is becoming increasingly used in the rehabilitation of hearing-impaired patients. Children with an enlarged vestibular aqueduct (EVA) need CI for severe or profound hearing loss, with excellent outcomes in hearing rehabilitation. However, vestibular function influenced by CI in children with EVA has not been clarified. We compared the characteristics of vestibular function in implanted children with EVA and those with a normal cochlea. Methods: In this retrospective case-control study, 16 children with large vestibular aqueduct syndrome (LVAS) and 16 children with a normal cochlea were recruited as the Study and Control Group, respectively. All children (mean age, 10.3 ± 4.4 years) had bilateral profound sensorineural hearing loss (SNHL) and normal pre-operative vestibular functions and underwent unilateral CI. Otolith and canal functions were assessed before CI and 12 months thereafter. Cervical vestibular-evoked myogenic potential (cVEMP), ocular vestibular-evoked myogenic potential (oVEMP), and video head impulse test (vHIT) were evaluated. Results: Full insertion of the electrode array was achieved in all the cases. Preoperatively, no significant differences in parameters in cVEMP between the Study and Control Group were revealed (p > 0.05). In pre-operative oVEMP, shorter N1 latencies (p = 0.012), shorter P1 latencies (p = 0.01), and higher amplitudes (p = 0.001) were found in the Study than in the Control Group. The Study Group had shorter P1 latency in cVEMP (p = 0.033), and had lower amplitude in oVEMP after implantation (p = 0.03). Statistically significant differences were not found in VOR gains of all three semicircular canals before and after surgery (p > 0.05). VEMP results revealed that the Control Group had significantly lower deterioration rates after CI (p < 0.05). The surgical approach and electrode array had no statistically significant influence on the VEMP results (p > 0.05). Conclusion: oVEMP parameters differed between children with EVA and children with a normal cochlea before surgery. Systematic evaluations before and after CI showed that otolith function was affected, but all three semicircular canals functions were essentially undamaged after implantation. In contrast to subjects with a normal cochlea, children with EVA are more likely to preserve their saccular and utricular functions after CI surgery. Possible mechanisms include less pressure-related damage, a reduced effect in terms of the air-bone gap (ABG), or more sensitivity to acoustic stimulation.

How do Snow Partridge (Lerwa lerwa) and Tibetan Snowcock (Tetraogallus tibetanus) coexist in sympatry under high-elevation conditions on the Qinghai-Tibetan Plateau?

The Qinghai-Tibetan Plateau (QTP) has the highest elevations of all biodiversity hotspots. Difficulties involved in fieldwork at high elevations cause challenges in researching mechanisms facilitating species coexistence. Herein, we investigated Snow Partridge (Lerwa lerwa) and Tibetan Snowcock (Tetraogallus tibetanus), the only two endemic Galliformes on the QTP, to understand species coexistence patterns and determine how they live in sympatry for the first time. We assembled occurrence data, estimated habitat suitability differences and the underlying factors between two species at different scales using ecological niche models. Niche overlap tests were used to investigate whether niche differences between these species allow for their coexistence. We found that elevation was the most important factor determining habitat suitability for both species. At the meso-scale, two species have similar ecological niches with their suitable habitats lying predominantly along ridge crests. However, ridge crests were more influential for habitat suitability by L. lerwa than for that of T. tibetanus because the latter species ranges further afield than ridge crests. Thus, differences in habitat suitability between these species lead to habitat partitioning, which allows stable coexistence. At the macro-scale, temperature and precipitation were major factors influencing habitat suitability differences between these species. Tetraogallus tibetanus extended into the hinterland of the QTP and occurred at higher elevations, where colder and drier alpine conditions are commonplace. Conversely, L. lerwa occurred along the southeastern margin of the QTP with a lower snow line, an area prone to rainy and humid habitats. Niche overlap analysis showed that habitat suitability differences between these species are not driven by niche differentiation. We concluded that the coexistence of these two pheasants under high-elevation conditions could be an adaption to different alpine conditions.

Do Parental Feeding Rate and Feeding Synchrony Affect Nest Survival in a Songbird?

Nest predation risk is an important factor that may promote the evolution of adaptive parental reproductive strategies in animals. In altricial birds, where parents feed their offspring at the nest for a period of time, parent birds must balance the benefit from increased nest visits and the cost from increased nest predation resulting from their nest visits being detected by predators. Empirical evidence has shown a relationship between parental nest visits and nest predation risks, and parents have been found to be able to reduce the chance of being detected by predators by synchronizing their feeding visits while maintaining feeding rate unchanged. However, it remains poorly understood whether the relationships are universal to all species. We investigated whether nest survival is correlated with parental feeding rate and feeding synchrony in the silver-throated tit (Aegithalos glaucogularis), a songbird endemic to China. We found that parental feeding rate varied by brood size, nestling age and the time during the day, but feeding synchrony was unrelated to the above factors. Moreover, we showed no effect of parental feeding rate or synchrony on nest survival. The failure to find a relationship between parental feeding synchrony and nest survival seems exceptional because it is contrary to findings of previous studies. While there was likely a publication bias regarding previous studies, it is also possible that the evolution of feeding synchrony in different species has different explanations, or the complexity of the predator community and other factors affecting nest survival need to be considered in the analyses.

Influence factors of dental anxiety in patients with impacted third molar extractions and its correlation with postoperative pain: a prospective study

BACKGROUND: To explore the prevalence of dental anxiety (DA) in patients with third molar extractions and its influence factors and the correlation between DA levels and postoperative pain. MATERIAL AND METHODS: A prospective and descriptive clinical study was performed. All patients who underwent the impacted third molar extraction from October 2017 to February 2019 were enrolled. DA levels were assessed by virtue of the modified dental anxiety scale (MDAS) and pain was assessed with a visual analog scale (VAS). RESULTS: A total of 150 patients were investigated and 136 valid questionnaires were retrieved, with an effective rate of 90.7%. The independent sample t-test and ANOVA results showed that the anxiety level of patients with the third molar extractions was statistically different in gender, teeth extraction experience and self-assessment oral health status. Multiple linear regression analysis with DA as a dependent variable showed that gender and teeth extraction experience were independent factors influencing DA in patients with third molar extractions. Pearson's test showed that there was a significant correlation between DA level in patients and the postoperative pain on the first day (r = 0.542, p = 0.000). CONCLUSIONS: For patients (females, poor oral hygiene and no teeth extraction experience), surgeon should pay more attention to DA of such patients and take measures to reduce the anxiety when removing the third molars. Furthermore, surgeon can recommend oral administration ibuprofen sustained release capsules after surgery

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Improve the roles of nature reserves in conservation of endangered pheasant in a highly urbanized region.

Nature reserves play an extraordinarily important role in conserving animal populations and their habitats. However, landscape change and unreasonable zoning designations often render these protected areas inadequate. Therefore, regular evaluation of the efficacy of protected lands is critical for maintaining and improving management strategies. Using species distribution models and GAP analysis, we assessed the changes in suitable habitat for the Brown Eared-pheasant (Crossoptilon mantchuricum) in two Chinese nature reserves between 1995 and 2013. Our results showed that the habitat suitability of Brown Eared-pheasant has changed dramatically during this period, and fragmentation analyses showed an increase in concentration area and decrease in patch area. In particular, our findings show that the national nature reserves need to adjust their ranges to ensure the conservation of this flagship species. Our study further provides a new viewpoint for evaluating the efficacy of protected lands, particularly in highly urbanized regions where conservation goals must be balanced with changing landscapes.

Footedness predicts escape performance in a passerine bird.

Behavioral lateralization, which is associated with the functional lateralization of the two brain hemispheres, commonly exists in animals and can provide an individual with benefits such as enhanced cognition and dual tasking. Lateral bias in limb use, as a type of behavioral lateralization, occur in many species, but the reasons for the coexistence of left- and right-biased individuals in a population remain poorly understood. We examined the footedness of male yellow-bellied tits (Pardaliparus venustulus) when they used feet to clamp mealworms against a perch, and tested its association with other fitness-related behavioral traits (i.e., feeding efficiency, exploration tendency, and escape performance). We expected differently footed individuals to have respective advantages in these behaviors and thereby coexist ("respective advantage" hypothesis). We found their footedness repeatable, and there was no population-level bias. While no associations of feeding efficiency and exploration tendency with footedness were detected, the right-footed individuals were found to be harder to catch than the other individuals. Future studies need to investigate the reasons for the right-footed individuals' superior escape performance. Moreover, the escape advantage for being right-footed and the lack of population-level bias in footedness in male yellow-bellied tits suggest that the benefits related to left footedness also remain to be explored.

Consumer perceptions and reported wild and domestic meat and fish consumption behavior during the Ebola epidemic in Guinea, West Africa.

The handling, capturing, butchering, and transportation of wildmeat can increase the risk of zoonoses, including the Ebola virus disease (EVD). Guinea, West Africa, experienced a catastrophic outbreak of EVD between 2013 and 2016. This study aimed to understand local people's sources of information concerning EVD, their perceptions of potential wildlife carriers of EVD and their meat and fish consumption behavior during this period. A semi-structured questionnaire was administered to 332 participants in two urban centers (N = 209) and three villages (N = 123) between January 3 and March 30, 2015 in the prefecture of Lola in southeastern Guinea. Chi-square analyses revealed that, in rural areas, awareness missions represented the main source of information about EVD (94.3%), whereas in urban settings such missions (36.1%), as well as newspapers (31.6%) and radio (32.3%) were equally mentioned. Bats (30.1% and 79.4%), chimpanzees (16.3% and 48.8%) and monkeys (13.0% and 53.1%) were the most commonly cited potential agents of EVD in both rural and urban areas respectively, while the warthog (2.3% rural and 6.5% urban), crested porcupine (1.7% rural and 10.7% urban), duiker (1.19% rural and 2.6% urban) and the greater cane rat (1.1% rural and 9.5% urban) were also cited but to a lesser extent. However, 66.7% of rural respondents compared to only 17.2% in the urban area did not consider any of these species as potential carriers of the Ebola virus. Nonetheless, a fifth of our respondents reported not consuming any of these species altogether during the EVD outbreak. Among all seven faunal groups mentioned, a significant reduction in reported consumption during the Ebola outbreak was only noted for bats (before: 78.3% and during: 31.9%) and chimpanzees (before: 31.6% and during: 13.5%). Automatic Chi-Square Interaction Detection (CHAID) analysis revealed that the belief that bats or chimpanzees were associated with EVD or not had a significant effect respectively on their non-consumption or continued consumption. However, only 3.9% of respondents reported shifting to alternative protein sources such as domestic meat or fish specifically to avoid EVD. Only 10.8% reported consuming more domestic meat during the EVD outbreak compared with before; affordability and availability were the main reported reasons for why people did not consume more domestic meat and why two thirds reported consuming more fish. While increased domestic meat consumption was linked to the belief that duikers, the most commonly consumed wildmeat before the epidemic, were associated with EVD, increased fish consumption was not predicted by any EVD related factors. Our study revealed deep-rooted false beliefs among rural respondents and constraints when it comes to access to alternative protein sources such as domestic meat. Our findings emphasize the urgent need for greater consideration of the relationship between socio-economic context, food security, and public health.

Decreased Porphyromonas gingivalis adhesion and improved biocompatibility on tetracycline-loaded TiO2 nanotubes: an in vitro study.

BACKGROUND: Titanium dioxide (TiO2) nanotubes are often used as carriers for loading materials such as drugs, proteins, and growth factors. MATERIALS AND METHODS: In this study, we loaded tetracycline onto TiO2 nanotubes to demonstrate its antibacterial properties and biocompatibility. The two-layered anodic TiO2 nanotubes with a honeycomb-like porous structure were fabricated by using a two-step anodization, and they were loaded with tetracycline by using a simplified lyophilization method and vacuum drying. Their physical properties, such as chemical compositions, wettability, and surface morphologies of the different samples, were observed and measured by X-ray photoelectron spectroscopy (XPS), contact angle measurement, and scanning electron microscopy (SEM). The in vitro growth behaviors of mouse bone marrow stromal cells (BMSCs) on these substrates were investigated. RESULTS: The TiO2 nanotube (NT) substrates and the tetracycline-loaded TiO2 nanotube (NT-T) substrates revealed a crucial potential for promoting the adhesion, proliferation, and differentiation of BMSCs. Similarly, the NT-T substrates displayed a sudden release of tetracycline in the first 15 minutes of their administration, and the release tended to be stable 90 minutes later. The antibacterial performances of the prepared substrates were assessed with Porphyromonas gingivalis. The result showed that NT and NT-T substrates had antibacterial capacities. CONCLUSION: Overall, this research provides a promising method with potential for clinical translation by allowing local slow release of antimicrobial compounds by loading them onto constructed nanotubes.

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population.

Accurate individual identification is required to estimate survival rates in avian populations. For endangered species, non-invasive methods of obtaining individual identification, such as using molted feathers as a source of DNA for microsatellite markers, are preferred because of less disturbance, easy sample preparation and high efficiency. With the availability of many avian genomes, a few pipelines isolating genome-wide microsatellites have been published, but it is still a challenge to isolate microsatellites from the reference genome efficiently. Here, we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome. We have identified over 95 000 microsatellite loci and established a system comprising 10 highly polymorphic markers (PIC value: 0.49-0.93, mean: 0.79) for an endangered species, saker falcon (Falco cherrug). These markers (except 1) were successfully amplified in 126 molted feathers, exhibiting high amplification success rates (83.9-99.7%), high quality index (0.90-0.97) and low allelic dropout rates (1-9.5%). To further assess the efficiency of this marker system in a population study, we identified individual sakers using these molted feathers (adult) and 146 plucked feathers (offspring). The use of parent and offspring samples enabled us to infer the genotype of missing samples (N = 28), and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers. Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.

Nest survival rate of Reeves's pheasant (Syrmaticus reevesii) based on artificial nest experiments.

To explore the nest survival rate of Reeves's pheasant(Syrmaticus reevesii) and the nest-site factors that affect it, we conducted artificial nest experiments with reference to natural nests at Dongzhai National Nature Reserve(DNNR), Henan Province and Pingjingguan, Hubei Province from April to June 2014 simulating the situation in its early and later breeding season. We also determined distance characteristics of the nest sites by ArcGIS 10.0. Nest survival models were constructed in Program MARK for data analysis. Results indicated that in the early breeding season, the apparent survival rate(ASR) in DNNR(52.4%) was significantly greater than that in Pingjingguan(13.5%), and the ASR in the later breeding season in DNNR(26.7%) was not indistinctively correlated with Pingjingguan(3.2%). The daily survival rate(DSR) in the later breeding season was 93.8% in DNNR and 92.0% in Pingjingguan, respectively. The DSRs were both negatively correlated with nest distance to forest edges and settlements. The DSR in Pingjingguan was positively correlated with nest distance to paths and negatively correlated with nest distance to water sources. However, the DSR in DNNR was negatively correlated with nest distance to paths but positively correlated with nest distance to water sources.