prevalence of bacteria and parasites in white ibis in egypt. | a field survey was conducted to evaluate the prevalence of bacterial infections among free-living white ibis (nipponia nippon) in which 92 bacterial isolates were recovered from 193 different internal organs of 55 apparently healthy ibis. escherichia coli and salmonella spp. were isolated at rates of 43.6% and 14.5%, respectively. the other bacterial pathogens isolated were shigella spp. (34.5%), enterobacter spp. (21.8%) citrobacter spp. (18.1%), klebsiella pneumonia (16.3), staphylococcus aure ... | 2010 | 20857378 |
reduced dependence of crested ibis on winter-flooded rice fields: implications for their conservation. | the crested ibis nipponia nippon was once thought to be extinct in the wild until seven birds were discovered in a remote mountain village in china in 1981. studies suggested that winter-flooded rice fields play an essential role in nest site selection by the crested ibis and hence in their survival. considerable efforts were therefore made to conserve the winter-flooded rice fields, but these have caused conflicts between the agricultural and conservation communities. the population and geograp ... | 2014 | 24874870 |
[establishment of cell lines derived from skin biopsies of crested ibis (nipponia nippon) and their biological characteristics]. | the crested ibis is among the rarest and most endangered species worldwide. to preserve its genetic resources and conveniently provide materials for biological research, we successfully established two cell lines from biopsies of a male and female adult crested ibis. the cultured cells from both specimens had typical fibroblast morphology. immunofluorescence staining revealed that the cultured cells strongly expressed the marker of smooth muscle specific α-actin, clearly indicating the cells wer ... | 2012 | 23266978 |
insight into the mechanism of reproductive dysfunction caused by neonicotinoid pesticides. | neonicotinoids, which were developed in the 1990 s as an insecticide having selective toxicity, were later found to cause reproductive abnormalities in experimental animals. in japan there is an attempt to preserve endangered animals, including the japanese crested ibis, and there is a question of whether neonicotinoids affect the reproduction of this bird, since they are used in its habitat. hence, we investigated whether the daily oral administration of the neonicotinoid clothianidin (ctd) has ... | 2014 | 25177026 |
the first report of a pelecaniformes defensin cluster: characterization of β-defensin genes in the crested ibis based on bac libraries. | defensins play a key role in the innate immunity of various organisms. detailed genomic studies of the defensin cluster have only been reported in a limited number of birds. herein, we present the first characterization of defensins in a pelecaniformes species, the crested ibis (nipponia nippon), which is one of the most endangered birds in the world. we constructed bacterial artificial chromosome libraries, including a 4d-pcr library and a reverse-4d library, which provide at least 40 equivalen ... | 2014 | 25372018 |
genomic organization of the crested ibis mhc provides new insight into ancestral avian mhc structure. | the major histocompatibility complex (mhc) plays an important role in immune response. avian mhcs are not well characterized, only reporting highly compact galliformes mhcs and extensively fragmented zebra finch mhc. we report the first genomic structure of an endangered pelecaniformes (crested ibis) mhc containing 54 genes in three regions spanning ~500 kb. in contrast to the loose bg (26 loci within 265 kb) and class i (11 within 150) genomic structures, the core region is condensed (17 within ... | 2015 | 25608659 |
decline of traditional rice farming constrains the recovery of the endangered asian crested ibis (nipponia nippon). | traditional agriculture benefits a rich diversity of plants and animals. the winter-flooded rice fields in the qinling mountains, china, are the last refuge for the endangered asian crested ibis (nipponia nippon), and intensive efforts have been made to protect this anthropogenic habitat. analyses of multi-temporal satellite data indicate that winter-flooded rice fields have been continuously reduced across the current range of crested ibis during the past two decades. the rate of loss of these ... | 2015 | 25851484 |
genetics and evolution of plumage color in crested ibis: analysis of the melanocortin-1 receptor (mc1r). | the melanocortin-1-recepter gene (mc1r), an important regulator in melanin synthesis, may cause different plumage color patterns in birds: gain-of-function mutations lead to the synthesis of eumelanin, whereas loss-of-function mutations help to generate pheomelanin synthesis. we had chosen mc1r as a candidate gene for the depigmentation of crested ibis, cloned and sequenced the crested ibis mc1r gene the first time. the crested ibis mc1r sequence, highly conserved with other birds during evoluti ... | 2015 | 26314199 |
the size of winter-flooded paddy fields no longer limits the foraging habitat use of the endangered crested ibis (nipponia nippon) in winter. | paddy fields have traditionally been viewed as the key foraging habitats for the endangered crested ibis (nipponia nippon). with the population of this species now increasing, its distribution has expanded to both lowland areas and outside the nature reserve. however, little is known about the current foraging habitat preferences of these birds, especially during winter. in this research, a total of 54 used sites and 50 unused sites were investigated during winter from december 2011 to january 2 ... | 2016 | 27498793 |
signatures of crested ibis mhc revealed by recombination screening and short-reads assembly strategy. | whole-genome shotgun (wgs) sequencing has become a routine method in genome research over the past decade. however, the assembly of highly polymorphic regions in wgs projects remains a challenge, especially for large genomes. employing bac library constructing, pcr screening and sanger sequencing, traditional strategy is laborious and expensive, which hampers research on polymorphic genomic regions. as one of the most highly polymorphic regions, the major histocompatibility complex (mhc) plays a ... | 2016 | 27997612 |
unusual sleeping site selection by southern bamboo lemurs. | selection of sleeping sites has consequences for individual fitness. non-human primates often bias their selection towards arboreal sites, and the lemurs of madagascar typically rest/sleep in trees, tree holes, and/or constructed nests. three non-mutually exclusive hypotheses to explain sleeping site selection include protection from predators, avoidance of parasitic vectors, and improved thermoregulation. here, we examine these hypotheses for the unusual sleeping site selections by the southern ... | 2016 | 26860934 |
identification of novel genetic markers and evaluation of genetic structure in a population of japanese crested ibis. | japanese population of the japanese crested ibis nipponia nippon was founded by five individuals gifted from the people's republic of china. in order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross-amplification. of these, only three primer pairs were useful for the genetic markers. additionally, we sequenced allelic pcr products of these three markers together with 10 markers previous ... | 2014 | 24330458 |
proteomic analysis of nipponia nippon (id#162). | we investigated the proteome of a female crested ibis (nipponia nippon, id#162) that died on march 10, 2010 at the sado japanese crested ibis conservation center. protein preparations from the brain, trachea, liver, heart, lung, proventriculus, muscular stomach, small intestine, duodenum, ovary and neck muscle were subjected to in-solution shotgun mass spectrometry (ms)/ms analyses using an ltq orbitrap xl mass spectrometer. a search of the national center for biotechnology information gallus ga ... | 2014 | 24961376 |
improved molecular assay for sex identification of the endangered crested ibis (nipponia nippon) based on the chd1 gene and a sex-linked microsatellite locus. | sex identification of monomorphic birds, especially endangered avian species, is essential for ecological study and biodiversity conservation. in this study, two popular primer sets of 2550f/2718r and p2/p8, which were designed to amplify different fragments of chromodomain-helicase-dna binding protein 1 (chd1) genes mapped on both z and w chromosomes in birds, were used to identify for the first time the sex of individuals of the endangered species crested ibis (nipponia nippon) in a large numb ... | 2013 | 24004080 |
genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. | nearly one-quarter of all avian species is either threatened or nearly threatened. of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. one of the previously most critically-endangered is the crested ibis, nipponia nippon. once widespread across north-east asia, by 1981 only seven individuals from two breeding pairs remained in the wild. the recovering crested ibis populations thus provide an excellent example for conservation genomics since every individu ... | 2014 | 25496777 |
structure and polymorphisms of the major histocompatibility complex in the oriental stork, ciconia boyciana. | the major histocompatibility complex (mhc) is highly polymorphic and plays a central role in the vertebrate immune system. despite its functional consistency, the mhc genomic structure differs substantially among organisms. in birds, the mhcs of galliformes and the japanese crested ibis (pelecaniformes) are well-characterized, but information about other avian mhcs remains scarce. the oriental stork (ciconia boyciana, order ciconiiformes) is a large endangered migrant. the current japanese popul ... | 2017 | 28211522 |
genome-wide snp and str discovery in the japanese crested ibis and genetic diversity among founders of the japanese population. | the japanese crested ibis is an internationally conserved, critically threatened bird. captive-breeding programs have been established to conserve this species in japan. since the current japanese population of crested ibis originates only from 5 founders donated by the chinese government, understanding the genetic diversity between them is critical for an effective population management. to discover genome-wide single nucleotide polymorphisms (snps) and short tandem repeats (strs) while obtaini ... | 2013 | 23991150 |
molecular cloning and biochemical analysis of tyrosinase from the crested ibis in china. | the crested ibis, one of the most endangered birds in the world, could benefit from research into its genetic diversity as a tool for conservation in the future. tyrosinase is thought to play a major role in the production of common yellow to black melanins in birds. we have cloned and sequenced four exons of the crested ibis tyrosinase gene and discovered that the amino acid sequence has high similarity to zebra finch tyrosinase (93 %), followed by chicken (91 %) and quail (91 %). some function ... | 2012 | 22990953 |
how much can we trust gps wildlife tracking? an assessment in semi-free-ranging crested ibis nipponia nippon. | gps tracking has been increasingly used for wildlife studies in recent decades, but its performance has not been fully assessed, especially for newly developed lightweight transmitters. we assessed the performance of eight gps transmitters developed in china by attaching them to crested ibises nipponia nippon confined to two acclimation cages mimicking real habitats. we calculated the distance between gps locations and the centroid of the cages as the positioning error, and used the 95% (95th pe ... | 2018 | 30065886 |
structure and polymorphism of the major histocompatibility complex class ii region in the japanese crested ibis, nipponia nippon. | the major histocompatibility complex (mhc) is a highly polymorphic genomic region that plays a central role in the immune system. despite its functional consistency, the genomic structure of the mhc differs substantially among organisms. in birds, the mhc-b structures of galliformes, including chickens, have been well characterized, but information about other avian mhcs remains sparse. the japanese crested ibis (nipponia nippon, pelecaniformes) is an internationally conserved, critically threat ... | 2014 | 25247679 |
prevalence of a septicemia disease in the crested ibis (nipponia nippon) in china. | this study investigated six cases of septicemia in young crested ibises (nipponia nippon). these birds all died with similar clinical signs, including sudden death, anorexia, diarrhea, and lameness. immediately after death, the birds were necropsied; a blood sample was taken from heart and tissues were sampled from liver, lung, spleen, peritoneal mucus, and feces for bacteriologic examination. anatomic observation showed that the main findings common to the sick birds were arthrocele, associated ... | 2007 | 17626495 |
major histocompatibility complex variation in the endangered crested ibis nipponia nippon and implications for reintroduction. | the major histocompatibility complex (mhc), with its extraordinary levels of genetic variation, is thought to be an essential aspect of the ability of an organism to recognize different parasites and pathogens. it has also been proposed to regulate reproductive processes in many aspects. here we examine the genetic variation of the second exon of the mhc class ii b genes of the crested ibis, an endangered species known to descend from just two breeding pairs rediscovered in 1981. only five allel ... | 2006 | 16648992 |
cloning of the genes for the pituitary glycoprotein hormone alpha and follicle-stimulating hormone beta subunits in the japanese crested ibis, nipponia nippon. | we have isolated a part of the gene for the pituitary glycoprotein hormone common alpha subunit (pghalpha) and the whole gene for the follicle-stimulating hormone beta subunit (fshbeta) in the japanese crested ibis (nipponia nippon), a critically endangered bird species in east asia. the nucleotide sequence of a part of the pghalpha gene (5026 bp) contained three exons holding the whole coding and 3' untranslated regions, but lacked a 5' untranslated region. its exon-intron structure was similar ... | 2003 | 12719648 |
cloning of the gene for the thyrotropin beta subunit in the japanese crested ibis, nipponia nippon. | we isolated a putative gene for the thyrotropin beta subunit (tshbeta) from two types of genomic libraries of the japanese crested ibis, nipponia nippon. exon-intron structure was deduced by comparing the determined sequence with those of tsh beta cdna of other birds. the deduced amino acid sequence shows extensive similarities to those of the other birds, which assures our assumption that the acquired nucleotide sequence represents the tshbeta gene. the assembled genomic fragment is 4192 bp in ... | 2003 | 12655183 |
lack of structural variation but extensive length polymorphisms and heteroplasmic length variations in the mitochondrial dna control region of highly inbred crested ibis, nipponia nippon. | the animal mitochondrial dna (mtdna) length polymorphism and heteroplasmy are accepted to be universal. here we report the lack of structural variation but the presence of length polymorphism as well as heteroplasmy in mtdna control region of an endangered avian species - the crested ibis (nipponia nippon). the complete control region was directly sequenced while the distribution pattern and inheritance of the length variations were examined using both direct sequencing and genotyping of the pcr ... | 2013 | 23805212 |
genetic diversity and structure in the sado captive population of the japanese crested ibis. | the japanese crested ibis nipponia nippon is a critically threatened bird. we assessed genetic diversity and structure in the sado captive population of the japanese crested ibis based on 24 and 50 microsatellite markers developed respectively for the same and related species. of a total of 74 loci, 19 showed polymorphisms in the five founder birds of the population, and therefore were useful for the analysis of genetic diversity and structure. genetic diversity measures, a, ne, he, hoand pic, o ... | 2013 | 23721466 |
effects of exposure to clothianidin on the reproductive system of male quails. | clothianidin (ctd) is a neonicotinoid developed in the 1990s as an insecticide having selective toxicity, but it was later found to cause reproductive abnormalities in rats through oxidative stress. there is an attempt to preserve endangered animals, including the japanese crested ibis, in japan. however, there is a concern that neonicotinoid affects the reproduction of this bird, since it is used in its habitat. ctd toxicity in the birds is poorly understood, so we investigated whether or not t ... | 2013 | 23358514 |
the w- and z-linked ee0.6 sequences used for molecular sexing of captive japanese crested ibis on sado island. | the japanese crested ibis nipponia nippon is a critically threatened bird. accurate sexing is necessary to perform effective management of captive breeding toward a national project for a tentative release of the japanese crested ibis on sado island. a pcr-based sexing method targeting a 0.6 kb ecori fragment (ee0.6) sequence on w chromosome with aws03 and usp3 primers has been developed for the japanese crested ibis. however, the primers were selected from the ee0.6 sequences from bird species ... | 2012 | 22250744 |
dna sexing of nipponia nippon by duplex polymerase chain reaction. | the aim of this study was to develop a rapid, simple, sensitive, and accurate duplex polymerase chain reaction (pcr) to sex nipponia nippon, a monomorphic bird. amplification by duplex pcr of a sex-related gene on the female chromosome and the 12s rrna gene yielded good results using genomic dna extracted from a feather follicle or the membranes of eggshell samples. to simplify the dna extraction procedure, a simple boiling method was used. our simple boiling dna extraction method produced simil ... | 2011 | 21967221 |
non-invasive sampling technique for dna extraction from captive japanese crested ibis on sado island. | the japanese crested ibis nipponia nippon is a critically threatened bird. the post-hatch eggs of the current captive population of this species on sado island have been stored at room temperature for the long-term. in this study, we investigated the suitability of the vascularized chorioallantois membrane from the eggs as a non-invasive dna source. using microsatellite loci developed for the japanese crested ibis, we performed three experiments for comparison of genotypes obtained among dna. fi ... | 2011 | 21794023 |
[determination of ca, mg, pb, cd, as and hg in the feather of japanese crested ibis]. | trace elements participate in many important life processes of japanese crested ibis. a method of simultaneous and direct determination of ca, mg, pb, cd, as and hg in the feather of japanese crested ibis by icp and hg-aas is reported. the results show that the method has good precision and accuracy. the recovery is 95%-105%. a long term track of trace elements contained in japanese crested ibis, particularly the collection and study of the data concerning harmful trace elements, is significant ... | 2007 | 18306809 |
[research on the genetic polymorphism in crested ibis by rmapd]. | the genetic polymorphism of yangxian artificially reared 43 crested ibises (nipponia nippon) was firstly investigated by rmapd (random microsatellite amplify polymorphic dna) marker. the results showed that rmapd was more stable and polymorphic than rapd. 2147 bands were amplified by 12 pairs of primers,of which 93 bands had polymorphisms. the band sharing frequency and the genetic diversity index were 0.718 and 3.664, respectively, indicating that the genetic structure of crested ibis populatio ... | 2005 | 16378939 |
[determination of cu, zn, mn, ni, cr, fe and mo in the feather of japanese crested ibis by icp]. | a method of simultaneous and direct determination of cu, zn, mn, ni, cr, fe, mo in the feather of japanese crested ibis by icp is reported, with precision and accuracy. the recovery is 95%-104%. this method is also simple and rapid. | 2005 | 16128089 |
molecular cloning and functional characterization of duck tyk2. | tyrosine kinase 2 (tyk2), a member of janus kinase family, has been identified as a crucial protein in signal transduction initiated by interferons or interleukins in mammals. however, the function of avian tyk2 in innate immune response remains largely unknown. in this study, the full-length duck tyk2 (dutyk2) cdna was cloned for the first time, which encoded a putative protein of 1187 amino acid residues and showed the high sequence similarity with bald eagle, crested ibis, and white-tailed tr ... | 2020 | 31437526 |
phylogenetic and pathogenic analyses of two virulent newcastle disease viruses isolated from crested ibis (nipponia nippon) in china. | the crested ibis is one of the most endangered birds in the world, found only in shaanxi province in central china, and it has been reintroduced in sadogashima in japan. two newcastle disease virus (ndv) isolates were collected from sick crested ibises, and their pathogenic and phylogenetic characteristics were investigated. the results showed that they are virulent, with intracerebral pathogenicity indices of 1.46-1.83 and a mean time of death of 54.4-84.4 h. they shared the same virulent motif ... | 2013 | 23344613 |
deeply digging the interaction effect in multiple linear regressions using a fractional-power interaction term. | in multiple regression y ~ β0 + β1x1 + β2x2 + β3x1 x2 + ɛ., the interaction term is quantified as the product of x1 and x2. we developed fractional-power interaction regression (fpir), using βx1m x2n as the interaction term. the rationale of fpir is that the slopes of y-x1 regression along the x2 gradient are modeled using the nonlinear function (slope = β1 + β3mx1m-1 x2n), instead of the linear function (slope = β1 + β3x2) that regular regressions normally implement. the ranges of m and n are f ... | 2020 | 33072528 |
genomic characterisation of two virulent newcastle disease viruses isolated from crested ibis (nipponia nippon) in china. | this paper describes the complete genomic sequences of two virulent newcastle disease virus (ndv) isolates, shaanxi06 (prevalent genotype viid) and shaanxi10 (novel sub-genotype vii), from sick crested ibises. the genomes of both isolates were 15,192 nt long and consisted of six genes in the order of 3'-np-p-m-f-hn-l-5'. the genomes of the two isolates were highly similar to other reference ndv strains. however, some unique features were found in the hn protein of shaanxi06 and the f gene end of ... | 2014 | 25281014 |
transcriptome comparison reveals key components of nuptial plumage coloration in crested ibis. | nuptial plumage coloration is critical in the mating choice of the crested ibis. this species has a characteristic nuptial plumage that develops from the application of a black sticky substance, secreted by a patch of skin in the throat and neck region. we aimed to identify the genes regulating its coloring, by comparing skin transcriptomes between ibises during the breeding and nonbreeding seasons. in breeding season skins, key eumelanin synthesis genes, tyr, dct, and tyrp1 were upregulated. ty ... | 2020 | 32549189 |
trace elements exposure of endangered crested ibis (nipponia nippon) under in situ and ex situ conservations. | crested ibis (nipponia nippon), one of the rarest birds in the world, was almost extinct in the historically widespread areas partly due to the environmental pollution. therefore, non-invasive indicators of feather, eggshell, and excrement were used to investigate the exposure of this endangered bird to eleven trace elements in this study. the results indicated that crested ibises under in situ and ex situ conservations were diversely exposed to trace elements, with higher exposure levels of as, ... | 2019 | 31344541 |
seeing-good-gene-based mate choice: from genes to behavioural preferences. | although vertebrates have been reported to gain higher reproductive outputs by choosing mates, few studies have been conducted on threatened species. however, species recovery should benefit if natural mate choice could improve reproductive output (i.e. pair performance related to offspring number, such as increased clutch size, numbers of fertilized egg and fledglings). we assessed the evidence for major histocompatibility complex (mhc)-based mate preference in the endangered crested ibis (nipp ... | 2019 | 31332779 |
genome resequencing reveals congenital causes of embryo and nestling death in crested ibis (nipponia nippon). | the crested ibis (nipponia nippon) is endangered worldwide. although a series of conservation measures have markedly increased the population size and distribution area of these birds, the high mortality of embryos and nestlings considerably decreases the survival potential of this bird species. high-throughput sequencing technology was utilized to compare whole genomes between ten samples from dead crested ibises (including six dead embryos and four dead nestlings aged 0-45 days) and 32 samples ... | 2019 | 31298688 |
genetic diversity and differentiation at structurally varying mhc haplotypes and microsatellites in bottlenecked populations of endangered crested ibis. | investigating adaptive potential and understanding the relative roles of selection and genetic drift in populations of endangered species are essential in conservation. major histocompatibility complex (mhc) genes characterized by spectacular polymorphism and fitness association have become valuable adaptive markers. herein we investigate the variation of all mhc class i and ii genes across seven populations of an endangered bird, the crested ibis, of which all current individuals are offspring ... | 2019 | 31027280 |
the genomic footprints of the fall and recovery of the crested ibis. | human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1-4]. however, factors such as outbreeding depression [5, 6] and a reduction in available genet ... | 2019 | 30639104 |
[influence of road on breeding habitat of nipponia nippon based on maxent model]. | quantitative study on effects of roads on suitable breeding habitats of wildlife is one of topics that need in-depth research in road ecology. crested ibis (nipponia nippon), a first class nationally protected bird species, is the species of interest in this research. using the maximum entropy models (maxent) in the species distribution model (sdm) toolbox of arcgis, autocorrelation of environmental variables were analyzed and environmental variables with r>0.8 were removed. ten environmental va ... | 2017 | 29741334 |
genetic analyses in the japanese captive population of japanese crested ibis (nipponia nippon) using pedigree information. | the japanese captive population of japanese crested ibis (nipponia nippon) was established using 5 founders derived from the chinese captive population. its size has increased rapidly, and the maintenance phase is about to start. thus, this study was designed to perform genetic analyses in this population with pedigree information, considering the adoption of mean kinship strategy as the breeding strategy suited to the maintenance phase. because the relationships among the 5 founders were unknow ... | 2016 | 32908357 |
ascaris spp. and capillaria caudinflata infections in captive-bred crested ibis (nipponia nippon) in china. | crested ibis (nipponia nippon), an endan gered native bird, was called the "precious stone" of oriental birds. n. nippon was considered a critically endangered species in the iucn red list of threatened species and a first-class national protected animal in china. the chinese government had exerted considerable effort to protect the n. nippon population. an effective approach to increase the number of these birds was captive breeding. however, several pathogens, including parasites, could jeopar ... | 2015 | 25486916 |
detection of chlamydia psittaci and chlamydia ibidis in the endangered crested ibis (nipponia nippon). | chlamydia spp. are a group of obligate intracellular pathogens causing a number of diseases in animals and humans. avian chlamydiosis (ac), caused by chlamydia psittaci (c. psittaci) as well as new emerging c. avium, c. gallinacea and c. ibidis, have been described in nearly 500 avian species worldwidely. the crested ibis (nipponia nippon) is a world endangered avian species with limited population and vulnerable for various infections. to get a better understanding of the prevalence of chlamydi ... | 2020 | 31910921 |
flexivirga lutea sp. nov., isolated from the faeces of a crested ibis, nipponia nippon, and emended description of the genus flexivirga. | a novel gram-staining-positive, aerobic, non-motile and coccus-shaped bacterium, designated strain tbs-100t, was isolated from the faeces of a crested ibis, nipponia nippon. the phylogenetic analysis based on the 16s rrna gene sequences showed that the closest relative of tbs-100t was flexivirga alba dsm 24460t with 97.11 % sequence similarity, and that strain tbs-100t belonged to the genus flexivirga. the optimum growth conditions for strain tbs-100t were 30 °c, at a ph of 7 and in the presence ... | 2016 | 27295948 |