Risk relationship between inflammatory bowel disease and urolithiasis: A two-sample Mendelian randomization study.

BACKGROUND: The causal genetic relationship between common parenteral manifestations of inflammatory bowel disease (IBD) and urolithiasis remains unclear because their timing is difficult to determine. This study investigated the causal genetic association between IBD and urolithiasis using Mendelian randomization (MR) based on data from large population-based genome-wide association studies (GWASs). METHODS: A two-sample MR analysis was performed to assess the potential relationship between IBD and urolithiasis. Specific single nucleotide polymorphism data were obtained from GWASs, including IBD (n = 59957) and its main subtypes, Crohn's disease (CD) (n = 40266) and ulcerative colitis (UC) (n = 45975). Summarized data on urolithiasis (n = 218792) were obtained from different GWAS studies. A random-effects model was analyzed using inverse-variance weighting, MR-Egger, and weighted medians. RESULTS: Genetic predisposition to IBD and the risk of urolithiasis were significantly associated [odds ratio (OR), 1.04 (95% confidence interval [CI], 1.00-.08), P = 0.01]. Consistently, the weighted median method yielded similar results [OR, 1.06 (95% CI, 1.00-1.12), P = 0.02]. The MR-Egger method also demonstrated comparable findings [OR, 1.02 (95% CI, 0.96-1.08), P = 0.45]. Both funnel plots and MR-Egger intercepts indicated no directional pleiotropic effects between IBD and urolithiasis. CD was strongly associated with it in its subtype analysis [OR, 1.04 (95% CI, 1.01-1.07), P = 0.01], and UC was also causally associated with urolithiasis, although the association was not significant [OR, 0.99 (95% CI, 0.95-1.03), P = 0.71]. CONCLUSION: A unidirectional positive causal correlation was identified between IBD and urolithiasis, with varying degrees of association observed among the different subtypes of IBD. Recognizing the increased incidence of urolithiasis in patients with IBD is crucial in clinical practice. Early detection and surveillance of IBD, improved patient awareness, adoption of preventive strategies, and promotion of collaborative efforts among healthcare providers regarding treatment methodologies are vital for improving patient outcomes.

AT-specific DNA visualization revisits the directionality of bacteriophage λ DNA ejection.

In this study, we specifically visualized DNA molecules at their AT base pairs after in vitro phage ejection. Our AT-specific visualization revealed that either end of the DNA molecule could be ejected first with a nearly 50% probability. This observation challenges the generally accepted theory of Last In First Out (LIFO), which states that the end of the phage λ DNA that enters the capsid last during phage packaging is the first to be ejected, and that both ends of the DNA are unable to move within the extremely condensed phage capsid. To support our observations, we conducted computer simulations that revealed that both ends of the DNA molecule are randomized, resulting in the observed near 50% probability. Additionally, we found that the length of the ejected DNA by LIFO was consistently longer than that by First In First Out (FIFO) during in vitro phage ejection. Our simulations attributed this difference in length to the stiffness difference of the remaining DNA within the phage capsid. In conclusion, this study demonstrates that a DNA molecule within an extremely dense phage capsid exhibits a degree of mobility, allowing it to switch ends during ejection.

Pyogranulomatous dermatitis with Enterococcus faecalis in a spotted seal (Phoca larga).

BACKGROUND: Cutaneous infections are important diseases in captive and free-ranging pinnipeds and are associated with various causative agents. Some special agents, such as fungi, morbillivirus and mycobacteria, can cause cutaneous specific granulomatous inflammation. OBJECTIVES: To identity the cause of chronic dermatitis in a spotted seal in an aquarium. METHODS: Herein, we analyze the clinical history and cutaneous samples of the spotted seal through differential diagnosis (histopathology, microorganism culture, special histochemical staining methods, PCR), and antibiotic susceptibility test. RESULTS: This is a rare pyogranulomatous dermatitis case caused by E. faecalis in a captive adult male spotted seal (Phoca largha) in an aquarium. CONCLUSIONS: We provide a meaningful approach to the diagnosis and treatment of bacterial dermatitis in pinnipeds.

DNA Visualization Using Fluorescent Proteins.

DNA binding fluorescent proteins are a powerful tool for single-molecule visualization. In this chapter, we discuss a protocol for the synthesis of DNA binding fluorescent proteins and visualization of single DNA molecules. This chapter includes stepwise methods for molecular cloning, reversible staining, two-color staining, sequence-specific staining, and microscopic visualization of single DNA molecules in a microfluidic device. This content will be useful for DNA characterization using DNA binding fluorescent proteins and its visualization at the single-molecule level.

Sarcoptic mange is an emerging threat to biodiversity in the Qinling Mountains in China.

Sarcoptic mange, a disease caused by the burrowing mite Sarcoptes scabiei, is globally endemic and an emerging threat to wildlife. Although many studies have shown that wildlife diseases play key roles in biodiversity conservation, knowledge about sarcoptic mange is still insufficient. In this study, we aim to improve the understanding of the impacts of sarcoptic mange on wildlife populations, the mechanisms involved in its eco-epidemiology and the associated risks to public and ecosystem health by investigating mass death events in gorals and serows in the Qinling Mountains. We conducted interviews with practitioners and local people in the central Qinling Mountains. From the same locations, we collected 24 cutaneous samples from various animals and surveillance data from infrared cameras. Pathological, parasitological and microbiological examinations of the samples were performed. Mite-induced cutaneous lesions, mites and eggs were observed in samples from dead gorals and one dead serow but not in other species. Molecular analysis confirmed the mites to be S. scabiei and shared the same cox 1 genotype. The data obtained from the interviews and infrared cameras indicated that the death of wildlife was related to sarcoptic mange infection and that there had been a decrease in the goral population since the outbreak of the disease. We confirmed that sarcoptic mange was the major cause of the mass death events and may have spread from the western to eastern Qinling Mountains. Based on our findings, we propose several protection strategies to help preserve biodiversity in the Qinling Mountains.

Feline herpesvirus infection and pathology in captive snow leopard.

Feline herpesvirus type 1 (FHV-1) is a common causative agent of domestic cats' rhinotracheitis in domestic cats, and it increasingly threatens wild felids worldwide. The endangered snow leopard (Panthera uncia) belongs to the family Felidae, and it is the top predator on the Tibetan Plateau. Here we report the identification and isolation of FHV-1 from three dead captive snow leopards that presented with sneezing and rhinorrhea. To explore the relationship between FHV-1 and their deaths, organs and nasal swabs were collected for histopathology, viral isolation and sequence analysis. The results revealed that all three snow leopards were infected with FHV-1. The first animal died primarily of cerebral infarction and secondary non-suppurative meningoencephalitis that was probably caused by FHV-1. The second animal died mainly of renal failure accompanied by interstitial pneumonia caused by FHV-1. The cause of death for the third animal was likely related to the concurrent reactivation of a latent FHV-1 infection. The gD and gE gene sequence alignment of the isolated FHV-1 isolate strain revealed that the virus likely originated from a domestic cat. It was found that FHV-1 infection can cause different lesions in snow leopards than in domestic cats and is associated with high risk of disease in wild felids. This suggests that there should be increased focus on protecting wild felids against FHV-1 infections originating from domestic cats.

A flagship species-based approach to efficient, cost-effective biodiversity conservation in the Qinling Mountains, China.

Prioritizing threatened species protection has been proposed as an efficient response to the global biodiversity crisis. We used in-situ conservation data to predict the potential habitat area of four flagship species: the giant panda (Ailuropoda melanoleuca), golden monkey (Rhinopithecus roxella quinlingensis), takin (Budorcas taxicolor bedfordi), and crested ibis (Nipponia nippon). We then designed systematic conservation planning schemes for various scenarios given species habitat preferences and anthropogenic activities and conducted a cost-effectiveness assessment. Broadly, the geographical distributions of suitable habitats for giant pandas, golden monkeys, and takins exhibited high spatial congruence (correlation coefficients of 0.59-0.90), and areas of high congruence were concentrated in the northern portion of the Qinling Mountains at high elevation (>1500 m). By contrast, the crested ibis was negatively correlated in space with its sympatric species (-0.47 to -0.29). Crested ibis habitats were clustered in the southern portion of the region at low elevation (<1500 m). A hypothetical conservation priority area (CPA) based on the giant panda, golden monkey, and takin included 39.64% of the Qinling Mountains and 100%, 99.99%, 99.59%, and 7.84% of the suitable habitats for giant pandas, golden monkeys, takins, and crested ibises, respectively. The same area included 99.07%, 70.87%, and 39.96% of the highly important areas for the ecosystem services of biodiversity conservation, water supply, and soil retention, respectively, and only 4.62%, 16.83%, and 13.4% of the area were associated with high-density residential area, impervious surfaces, and cropland, respectively. Therefore, we conclude that a CPA approach based on the specialist species could result in effective, low-cost biodiversity conservation in the Qinling Mountains. However, we note that existing protected areas account for only 26.52% of the CPA. We recommend that the main area of the proposed Qinling National Park should be based on the CPA developed here.

Shot-noise-limit performance of a weak-light phase readout system for intersatellite heterodyne interferometry.

A laser interferometer will be used in the spaceborne gravitational-wave detection missions to measure the inter-satellite optical pathlength variations. The phase readout system of the interferometer needs to be carefully designed and tested to accomplish a shot-noise-limited detection performance under the situation of pico-Watt level received lights. In this work, a scheme based on dual-tone acousto-optic diffraction is presented to verify the performance of the weak-light phase readout system. By optimizing the parameters of the photoreceiver and the local strong-light power, the signal-to-noise ratio of the beat-note signal is enhanced. Thanks to the scheme's common-mode noise rejections for the laser frequency noise, and the optical-path noise, etc., the differential phase noise has achieved a performance of 2×10-4 rad/Hz1/2, which is dominated by the weak-light (∼13 pW) shot noise above the frequencies of 2 mHz.

Experimental scheme and noise analysis of weak-light phase locked loop for large-scale intersatellite laser interferometer.

In the current space gravitational wave (GW) detection, satellites are separated by millions of kilometers. As a result, watts of laser from one satellite is attenuated to the picowatt level at the other end due to the Gaussian beam divergence and the finite aperture of the telescope. Establishing an effective interferometry with such weak-light is a major challenge. The key is to enhance the weak-light while preserving its phase information, which carries the actual GW signal. This can be accomplished by employing an optical phase-locked loop (PLL) to lock the phase of a local oscillator (LO) laser to the weak-light and then sending the power-amplified LO back to the interferometer on the other satellite. Although shot-noise-limited performance of the picowatt level weak-light PLL has been achieved for high frequencies, it remains elusive for frequencies below 0.1 Hz. Here, we propose a three-step experimental scheme to identify the main noise sources of the weak-light PLL, which turn out to be the low-frequency phase measurement noise, the weak-light shot noise, and the laser phase noise. In this paper, the first step experiment result shows that the out-loop phase noise can be suppressed to a level less than 6 × 10-6 rad/√Hz from 6 mHz to 1 Hz by first using the special pilot-tone technique in the PLL to directly reduce the sampling time jitter noise in the digital phasemeter. The out-loop phase noise is mainly limited by the signal amplitude variation and differential time jitter noise of the reference clock.

DNA binding fluorescent proteins as single-molecule probes.

DNA binding fluorescent proteins are useful probes for a broad range of biological applications. Fluorescent protein (FP)-tagging allows DNA binding proteins expressed within a living cell to be directly visualised, in real-time, to study DNA binding patterns and dynamics. Moreover, FP-tagged DNA binding proteins (FP-DBP) have allowed the imaging of single proteins bound to large elongated DNA molecules with a fluorescence microscope. Although there are numerous DNA binding proteins, only a small portion of them have been exploited to construct FP-DBPs to study molecular motion in a cell or in vitro single-molecule visualisation. Therefore, it would be informative to review FP-DBP for further development. Here, we summarise the design of FP-DBPs and their brightness, photostability, pKa, maturation rate, and binding affinity (Kd) characteristics. Then, we review the applications of FP-DBP in cells to study chromosome dynamics, DNA replication, transcription factors, DNA damage, and repair. Finally, we focus on single DNA molecule visualisation using FP-DBP.

Using unmanned aerial vehicles with thermal-image acquisition cameras for animal surveys: a case study on the Sichuan snub-nosed monkey in the Qinling Mountains.

Following significant developments in technology, alternative devices have been applied in fieldwork for animal and plant surveys. Thermal-image acquisition cameras installed on unmanned aerial vehicles (UAVs) have been used in animal surveys in the wilderness. This article demonstrates an example of how UAVs can be used in high mountainous regions, presenting a case study on the Sichuan snub-nosed monkey with a detection rate of 65.19% for positive individual identification. It also presents a model that can prospectively predict population size for a given animal species, which is based on combined initial work using UAVs and traditional surveys on the ground. A great potential advantage of UAVs is significantly shortening survey procedures, particularly for areas with high mountains and plateaus, such as the Himalayas, the Qinghai-Tibet Plateau, Hengduan Mountains, the Yunnan-Gui Plateau and Qinling Mountains in China, where carrying out a traditional survey is extremely difficult, so that species and population surveys, particularly for critically endangered animals, are largely absent. This lack of data has impacted the management of endangered animals as well as the formulation and amendment of conservation strategies.

Characteristics of heavy metal concentrations and risk assessment for giant pandas and their habitat in the Qinling Mountains, China.

High concentrations of heavy metals in the environment threaten the quality of ecosystems and the health of human beings and animals. Giant panda (Ailuropoda melanoleuca), which is endemic to China and a global conservation icon, has the largest density in the Qinling Mountains. This paper investigated the spatiotemporal variation of heavy metal concentrations in soil (N = 44) at the regional scale with three zones of urban areas, mountain edges, and central mountains, the temporal variation of heavy metal concentrations in three bamboo species (N = 19) and two types of feces (N = 10), and assessed the ecological risk and health risk for giant pandas and their habitat in the Qinling Mountains. The results showed that the median concentrations of studied eight heavy metals mercury (Hg), arsenic (As), copper (Cu), manganese (Mn), zinc (Zn), chromium (Cr), lead (Pb), and cadmium (Cd) in soil exceeded the background values of Shaanxi Province except Pb. The median concentrations of Hg, Zn, Cr, Pb, and Cd in bamboo surpassed the reference standard (RS) of national food safety limits in vegetables for human intake, but the concentration of Zn was within the nutrient range in the bamboo plants. Heavy metals were enriched more in feces of captive than the wild giant pandas, which illustrated either higher ingestion or lower digestibility for captive giant panda. Ecological risk assessment of soil by the geo-accumulation index (Igeo) and risk index (RI) showed strong pollution by Hg and moderate pollution by Cd. Health risk assessment by the hazard index (HI) showed a potential to strong risk for giant pandas exposed to Pb, As, and Hg. In addition, the concentrations of heavy metals in feces showed a higher exposure risk for captive giant pandas than wild giant pandas. We suggest that attention should be paid to and all effective measurements should be taken for reducing the emission of Hg, As, Pb, and Cd in the study area.

Molecular-Level Interactions between Engineered Materials and Cells.

Various recent experimental observations indicate that growing cells on engineered materials can alter their physiology, function, and fate. This finding suggests that better molecular-level understanding of the interactions between cells and materials may guide the design and construction of sophisticated artificial substrates, potentially enabling control of cells for use in various biomedical applications. In this review, we introduce recent research results that shed light on molecular events and mechanisms involved in the interactions between cells and materials. We discuss the development of materials with distinct physical, chemical, and biological features, cellular sensing of the engineered materials, transfer of the sensing information to the cell nucleus, subsequent changes in physical and chemical states of genomic DNA, and finally the resulting cellular behavior changes. Ongoing efforts to advance materials engineering and the cell-material interface will eventually expand the cell-based applications in therapies and tissue regenerations.

Blood transcriptomics of captive forest musk deer (Moschus berezovskii) and possible associations with the immune response to abscesses.

Forest musk deer (Moschus berezovskii; FMD) are both economically valuable and highly endangered. A problem for FMD captive breeding programs has been the susceptibility of FMD to abscesses. To investigate the mechanisms of abscess development in FMD, the blood transcriptomes of three purulent and three healthy individuals were generated. A total of ~39.68 Gb bases were generated using Illumina HiSeq 4000 sequencing technology and 77,752 unigenes were identified after assembling. All the unigenes were annotated, with 63,531 (81.71%) mapping to at least one database. Based on these functional annotations, 45,798 coding sequences (CDS) were detected, along with 12,697 simple sequence repeats (SSRs) and 65,536 single nucleotide polymorphisms (SNPs). A total of 113 unigenes were found to be differentially expressed between healthy and purulent individuals. Functional annotation indicated that most of these differentially expressed genes were involved in the regulation of immune system processes, particularly those associated with parasitic and bacterial infection pathways.

DNA Binding Peptide Directed Synthesis of Continuous DNA Nanowires for Analysis of Large DNA Molecules by Scanning Electron Microscope.

Synthesis of smooth and continuous DNA nanowires, preserving the original structure of native DNA, and allowing its analysis by scanning electron microscope (SEM), is demonstrated. Gold nanoparticles densely assembled on the DNA backbone via thiol-tagged DNA binding peptides work as seeds for metallization of DNA. This method allows whole analysis of DNA molecules with entangled 3D features.

Highway increases concentrations of toxic metals in giant panda habitat.

The Qinling panda subspecies (Ailuropoda melanoleuca qinlingensis) is highly endangered with fewer than 350 individuals inhabiting the Qinling Mountains. Previous studies have indicated that giant pandas are exposed to heavy metals, and a possible source is vehicle emission. The concentrations of Cu, Zn, Mn, Pb, Cr, Ni, Cd, Hg, and As in soil samples collected from sites along a major highway bisecting the panda's habitat were analyzed to investigate whether the highway was an important source of metal contamination. There were 11 sites along a 30-km stretch of the 108th National Highway, and at each site, soil samples were taken at four distances from the highway (0, 50, 100, and 300 m) and at three soil depths (0, 5, 10 cm). Concentrations of all metals except As exceeded background levels, and concentrations of Cu, Zn, Mn, Pb, and Cd decreased significantly with increasing distance from the highway. Geo-accumulation index indicated that topsoil next to the highway was moderately contaminated with Pb and Zn, whereas topsoil up to 300 m away from the highway was extremely contaminated with Cd. The potential ecological risk index demonstrated that this area was in a high degree of ecological hazards, which were also due to serious Cd contamination. And, the hazard quotient indicated that Cd, Pb, and Mn especially Cd could pose the health risk to giant pandas. Multivariate analyses demonstrated that the highway was the main source of Cd, Pb, and Zn and also put some influence on Mn. The study has confirmed that traffic does contaminate roadside soils and poses a potential threat to the health of pandas. This should not be ignored when the conservation and management of pandas is considered.

The application of the Internet of Things to animal ecology.

For ecologists, understanding the reaction of animals to environmental changes is critical. Using networked sensor technology to measure wildlife and environmental parameters can provide accurate, real-time and comprehensive data for monitoring, research and conservation of wildlife. This paper reviews: (i) conventional detection technology; (ii) concepts and applications of the Internet of Things (IoT) in animal ecology; and (iii) the advantages and disadvantages of IoT. The current theoretical limits of IoT in animal ecology are also discussed. Although IoT offers a new direction in animal ecological research, it still needs to be further explored and developed as a theoretical system and applied to the appropriate scientific frameworks for understanding animal ecology.

Large-scale genetic survey provides insights into the captive management and reintroduction of giant pandas.

The captive genetic management of threatened species strives to preserve genetic diversity and avoid inbreeding to ensure populations remain available, healthy, and viable for future reintroduction. Determining and responding to the genetic status of captive populations is therefore paramount to these programs. Here, we genotyped 19 microsatellite loci for 240 captive giant pandas (Ailuropoda melanoleuca) (∼64% of the captive population) from four breeding centers, Wolong (WL), Chengdu (CD), Louguantai (LGT), and Beijing (BJ), and analyzed 655 bp of mitochondrial DNA control region sequence for 220 of these animals. High levels of genetic diversity and low levels of inbreeding were estimated in the breeding centers, indicating that the captive population is genetically healthy and deliberate further genetic input from wild animals is unnecessary. However, the LGT population faces a higher risk of inbreeding, and significant genetic structure was detected among breeding centers, with LGT-CD and WL-BJ clustering separately. Based on these findings, we highlight that: 1) the LGT population should be managed as an independent captive population to resemble the genetic distinctness of their Qinling Mountain origins; 2) exchange between CD and WL should be encouraged because of similar wild founder sources; 3) the selection of captive individuals for reintroduction should consider their geographic origin, genetic background, and genetic contribution to wild populations; and 4) combining our molecular genetic data with existing pedigree data will better guide giant panda breeding and further reduce inbreeding into the future.

The bamboo-eating giant panda (Ailuropoda melanoleuca) has a sweet tooth: behavioral and molecular responses to compounds that taste sweet to humans.

A growing body of behavioral and genetic information indicates that taste perception and food sources are highly coordinated across many animal species. For example, sweet taste perception is thought to serve to detect and motivate consumption of simple sugars in plants that provide calories. Supporting this is the observation that most plant-eating mammals examined exhibit functional sweet perception, whereas many obligate carnivores have independently lost function of their sweet taste receptors and exhibit no avidity for simple sugars that humans describe as tasting sweet. As part of a larger effort to compare taste structure/function among species, we examined both the behavioral and the molecular nature of sweet taste in a plant-eating animal that does not consume plants with abundant simple sugars, the giant panda (Ailuropoda melanoleuca). We evaluated two competing hypotheses: as plant-eating mammals, they should have a well-developed sweet taste system; however, as animals that do not normally consume plants with simple sugars, they may have lost sweet taste function, as has occurred in strict carnivores. In behavioral tests, giant pandas avidly consumed most natural sugars and some but not all artificial sweeteners. Cell-based assays revealed similar patterns of sweet receptor responses toward many of the sweeteners. Using mixed pairs of human and giant panda sweet taste receptor units (hT1R2+gpT1R3 and gpT1R2+hT1R3) we identified regions of the sweet receptor that may account for behavioral differences in giant pandas versus humans toward various sugars and artificial sweeteners. Thus, despite the fact that the giant panda's main food, bamboo, is very low in simple sugars, the species has a marked preference for several compounds that taste sweet to humans. We consider possible explanations for retained sweet perception in this species, including the potential extra-oral functions of sweet taste receptors that may be required for animals that consume plants.

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation.

The panda lineage dates back to the late Miocene and ultimately leads to only one extant species, the giant panda (Ailuropoda melanoleuca). Although global climate change and anthropogenic disturbances are recognized to shape animal population demography their contribution to panda population dynamics remains largely unknown. We sequenced the whole genomes of 34 pandas at an average 4.7-fold coverage and used this data set together with the previously deep-sequenced panda genome to reconstruct a continuous demographic history of pandas from their origin to the present. We identify two population expansions, two bottlenecks and two divergences. Evidence indicated that, whereas global changes in climate were the primary drivers of population fluctuation for millions of years, human activities likely underlie recent population divergence and serious decline. We identified three distinct panda populations that show genetic adaptation to their environments. However, in all three populations, anthropogenic activities have negatively affected pandas for 3,000 years.