Genomic insight into the nocturnal adaptation of the black-crowned night heron (Nycticorax nycticorax).

BACKGROUND: The black-crowned night heron (Nycticorax nycticorax) is an ardeid bird successfully adapted to the nocturnal environment. Previous studies had indicated that the eyes of the night herons have evolved several specialized morphological traits favoring nocturnal vision. However, the molecular mechanisms of the nocturnal vision adaptation of night herons remained inattentions. In this study, the whole genome of N. nycticorax was sequenced and comparative analyses were performed on the vision-related and olfactory receptor (OR) genes to understand the molecular mechanisms of the visual and olfactory adaptation of night herons. RESULTS: The results indicated that a number of vision genes were under positive or relaxed selection in N. nycticorax, whereas a number of other vision genes were under relaxed or intensified selection in the boat-billed heron (Cochlearius cochlearius), which suggested that the two species adapt to nocturnality with different genetic mechanisms. The different selections acting on vision genes are probably associated with the enlargement of eye size and the enhancement of visual sensitivity in night herons. The analyses on olfactory receptor (OR) genes indicated that the total number of OR genes in the genomes of N. nycticorax and C. cochlearius were about half those in the little egret (Egretta garzetta), whereas the diversity of their OR genes was not remarkably different. Additionally, the number of expressed OR genes in the transcriptomes of N. nycticorax was also fewer than that in E. garzetta. These results suggest a reduced olfactory capability in night herons compared with E. garzetta. CONCLUSIONS: Our results provided evidence that several vision genes of the night herons were subjected to different natural selections, which can contribute to a better understanding of the genetic mechanisms of visual adaptions of the night heron. In addition, the finding of the reduced number of total and expressed OR genes in night herons may reflect a trade-off between olfaction and vision.

Particle actuation by rotating magnetic fields in microchannels: a numerical study.

Magnetic particles confined in microchannels can be actuated to perform translation motion using a rotating magnetic field, but their actuation in such a situation is not yet well understood. Here, the actuation of a ferromagnetic particle confined in square microchannels is studied using immersed-boundary lattice Boltzmann simulations. In wide channels, when a sphere is positioned close to a side wall but away from channel corners, it experiences a modest hydrodynamic actuation force parallel to the channel walls. This force decreases as the sphere is shifted toward the bottom wall but the opposite trend is found when the channel is narrow. When the sphere is positioned midway between the top and bottom channel walls, the actuation force decreases as the channel width decreases and can reverse its direction. These phenomena are elucidated by studying the flow and pressure fields in the channel-particle system and by analyzing the viscous and pressure components of the hydrodynamic force acting on different parts of the sphere.

Magnetic Actuation of Surface Walkers: The Effects of Confinement and Inertia.

Driven by a magnetic field, the rotation of a particle near a wall can be rectified into a net translation. The particles thus actuated, or surface walkers, are a kind of active colloid that finds application in biology and microfluidics. Here, we investigate the motion of spherical surface walkers confined between two walls using simulations based on the immersed-boundary lattice Boltzmann method. The degree of confinement and the nature of the confining walls (slip vs no-slip) significantly affect a particle's translational speed and can even reverse its translational direction. When the rotational Reynolds number Reω is larger than 1, inertia effects reduce the critical frequency of the magnetic field, beyond which the sphere can no longer follow the external rotating field. The reduction of the critical frequency is especially pronounced when the sphere is confined near a no-slip wall. As Reω increases beyond 1, even when the sphere can still rotate in the synchronous regime, its translational Reynolds number ReT no longer increases linearly with Reω and even decreases when Reω exceeds ∼10.

Comparative transcriptomic analysis of two important life stages of Angiostrongylus cantonensis: fifth-stage larvae and female adults.

The mechanisms involved in the fast growth of Angiostrongylus cantonensis from fifth-stage larvae (L5) to female adults and how L5 breaks through the blood-brain barrier in a permissive host remain unclear. In this work, we compared the transcriptomes of these two life stages to identify the main factors involved in the rapid growth and transition to adulthood. RNA samples from the two stages were sequenced and assembled de novo. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of 1,346 differentially expressed genes between L5 and female adults was then undertaken. Based on a combination of analytical results and developmental characteristics, we suggest that A. cantonensis synthesizes a large amount of cuticle in L5 to allow body dilatation in the rapid growth period. Products that are degraded via the lysosomal pathway may provide sufficient raw materials for cuticle production. In addition, metallopeptidases may play a key role in parasite penetration of the blood-brain barrier during migration from the brain. Overall, these results indicate that the profiles of each transcriptome are tailored to the need for survival in each developmental stage.

Characterization of a non-classical MHC class II gene in the vulnerable Chinese egret (Egretta eulophotes).

Genes of the major histocompatibility complex (MHC) are valuable makers of adaptive genetic variation in evolutionary ecology research, yet the non-classical MHC genes remain largely unstudied in wild vertebrates. In this study, we have characterized the non-classical MHC class II gene, Egeu-DAB4, in the vulnerable Chinese egret (Ciconiiformes, Ardeidae, Egretta eulophotes). Gene expression analyses showed that Egeu-DAB4 gene had a restricted tissue expression pattern, being expressed in seven examined tissues including the liver, heart, kidney, esophagus, stomach, gallbladder, and intestine, but not in muscle. With respect to polymorphism, only one allele of exon 2 was obtained from Egeu-DAB4 using asymmetric PCR, indicating that Egeu-DAB4 is genetically monomorphic in exon 2. Comparative analyses showed that Egeu-DAB4 had an unusual sequence, with amino acid differences suggesting that its function may differ from those of classical MHC genes. Egeu-DAB4 gene was only found in 30.56-36.56 % of examined Chinese egret individuals. Phylogenetic analysis showed a closer relationship between Egeu-DAB4 and the DAB2 genes in nine other ardeid species. These new findings provide a foundation for further studies to clarify the immunogenetics of non-classical MHC class II gene in the vulnerable Chinese egret and other ciconiiform birds.

The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements.

BACKGROUND: The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds. RESULTS: The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea. CONCLUSIONS: The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.

Immunolocalization and developmental expression patterns of two cathepsin B proteases (AC-cathB-1, -2) of Angiostrongylus cantonensis.

In this study we have investigated the anatomic sites of expression and developmental expression patterns of two cathepsin B-like cysteine proteases (AC-cathB-1, -2) of Angiostrongylus cantonensis. The immunolocalization results revealed that native AC-cathBs were found present in the L1 and L3 larvae, female and male adults, and the AC-cathBs were localized mainly on the digestive tract of A. cantonensis and expressed at varied levels and in different patterns in the internal tissues according to their developmental stage. Consistent with the infective stage of L3 is a much more intense staining of AC-cathBs in the esophagus compared with the intestine. In contrast to L3, more abundant signals were located to the intestine of adults, suggesting that nutrition digestion likely to be the main function of the protease at this point. AC-cathBs fluorescent signals were present in excretory pore, excretory tube in lateral cords, and muscular esophagus of larvae, further supported the AC-cathB-1, -2 likely to be released by A. cantonensis as excretory/secretory products. Additionally, only the protein AC-cathB-2 was detected in the reproductive system, especially in the wall of vas deferens, uterus, and oviduct of the parasites, whether the AC-cathB-2 has some function in germ cells development and maturation need to be further characterized. Although the anatomic sites and expression patterns were different in larvae and adults and the corresponding function might not the same, AC-cathB-1 and -2 involved in the host-parasite interaction in addition to digestive function.

Dissociative photoionization of ß-pinene: an experimental and theoretical study.

We investigated the photoionization and dissociation photoionization of the ß-pinene molecular using time-of-flight mass spectrometry with a tunable vacuum ultraviolet source in the region from 8.00eV to 15.50eV. The experimental ionization energy (IE) value is 8.60eV using electron impact as the ionization source which is not in good agreement with theoretical value (8.41 eV) with a G3MP2 method. We obtained the accurate IE of ß-pinene (8.45 ± 0.03eV) derived from the efficiency spectrum which is in good agreement with the theoretical value (8.38eV) of the CBS-QB3 method. We elucidated the dissociation pathways of primary fragment ions from the ß-pinene cation on the basis of experimental observations in combination with theoretical calculations. Most of the dissociation pathways occur via a rearrangement reaction prior to dissociation. We also determined the structures of the transition states and intermediates for those isomerization processes.

Enolase of Angiostrongylus cantonensis: more likely a structural component?

The cloned enolase gene of Angiostrongylus cantonensis (AcEno) comprised 1,667 bp and encoded a peptide with 434 amino acid residues which lacked of a signal peptide but contained a transmembrane region, indicating that AcEno tends to be a structural component (intracellular or membrane protein). The real-time PCR revealed a meaningful difference in the expression level of AcEno in varied development stages. By immunolocalization, native AcEno was detected mainly in the cytoplasm in most tissues, such as parietal muscle, genital tracts, nerve ring, and alimentary canal where the energy consumption is high, but not as expected on the cuticle and hypodermis layer of the nematode. This suggests that the AcEno may be involved in a host of other biological functions, rather than a receptor of plasminogen or a component of excretory-secretory antigen. In addition, AcEno expressed alike in the nucleus, indicating that AcEno also involved in regulating the continuous growth and development of A. cantonensis in hosts. Despite of living in the vasculature at a certain stage of life cycle, AcEno was not localized in the outer surface of L3 and adults, indicating that A. cantonensis may have other virulence and immune evasion mechanisms.

Genomic insights into the endangered white-eared night heron (Gorsachius magnificus).

OBJECTIVES: A genome sequence of a threatened species can provide valuable genetic information that is important for improving the conservation strategies. The white-eared night heron (Gorsachius magnificus) is an endangered and poorly known ardeid bird. In order to support future studies on conservation genetics and evolutionary adaptation of this species, we have reported a de novo assembled and annotated whole-genome sequence of the G. magnificus. DATA DESCRIPTION: The final draft genome assembly of the G. magnificus was 1.19 Gb in size, with a contig N50 of 187.69 kb and a scaffold N50 of 7,338.28 kb. According to BUSCO analysis, the genome assembly contained 97.49% of the 8,338 genes in the Aves (odb10) dataset. Approximately 10.52% of the genome assembly was composed of repetitive sequences. A total of 14,613 protein-coding genes were predicted in the genome assembly, with functional annotations available for 14,611 genes. The genome assembly exhibited a heterozygosity rate of 0.49 heterozygosity per kilobase pair. This draft genome of G. magnificus provides valuable genomic resources for future studies on conservation and evolution.

Data-Driven Intelligent Manipulation of Particles in Microfluidics.

Automated manipulation of small particles using external (e.g., magnetic, electric and acoustic) fields has been an emerging technique widely used in different areas. The manipulation typically necessitates a reduced-order physical model characterizing the field-driven motion of particles in a complex environment. Such models are available only for highly idealized settings but are absent for a general scenario of particle manipulation typically involving complex nonlinear processes, which has limited its application. In this work, the authors present a data-driven architecture for controlling particles in microfluidics based on hydrodynamic manipulation. The architecture replaces the difficult-to-derive model by a generally trainable artificial neural network to describe the kinematics of particles, and subsequently identifies the optimal operations to manipulate particles. The authors successfully demonstrate a diverse set of particle manipulations in a numerically emulated microfluidic chamber, including targeted assembly of particles and subsequent navigation of the assembled cluster, simultaneous path planning for multiple particles, and steering one particle through obstacles. The approach achieves both spatial and temporal controllability of high precision for these settings. This achievement revolutionizes automated particle manipulation, showing the potential of data-driven approaches and machine learning in improving microfluidic technologies for enhanced flexibility and intelligence.

Cathepsin B-like and hemoglobin-type cysteine proteases: stage-specific gene expression in Angiostrongy cantonensis.

Three cysteine protease genes, cathepsin B-like enzyme gene 1, 2 (AC-cathB-1, AC-cathB-2) and hemoglobin-type cysteine protease gene (AC-hem) were isolated and described from Angiostrongylus cantonensis adult. The deduced amino acid sequence of Ac-cathB-1 and AC-cathB-2 contain all of the conserved regions of cathepsin B. AC-cathB-2 is similar to a host intrusion-related cysteine protease B from Parelaphostrongylus tenuis, and the AC-hem shares high similarity to legumain from Haemonchus contortus. AC-cathB-1 was expressed significantly higher in L1 as compared with AC-hem, the AC-cathB-2 followed; AC-cathB-2 transcripts in L3 were found increased rapidly and obviously abundant, suggesting that AC-cathB-1 and AC-cathB-2 may play an important role in intermediate and final host invasion, separately. The cysteine protease genes were more or less expressed in adult stage excepted for AC-cathB-2. As the AC-cathB-1 and AC-hem highly expressed in adult worms, suggesting AC-hem may activate AC-cathB-1 which involved in the host invasion and feeding process.

Characterization of the complete mitochondrial genome of Elanus caeruleus Desfontaines, 1789 (Accipitriformes: Accipitridae).

The complete mitochondrial genome of the Elanus caeruleus was sequenced via next-generation sequencing. The circular mitogenome is 18,898 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, a control region and a pseudo control region. The sequences (1210 bp) in the middle part of the two control regions are complete identical to each other. The gene order of the E. caeruleus mitogenome is identical to those of other Accipitridae species. The phylogenetic analysis indicated that E. caeruleus formed a basal lineage sister to other species within the Accipitridae family.

Anisakis pegreffii: a quantitative fluorescence PCR assay for detection in situ.

To facilitate improved diagnosis and detection of the third stage larva (L3) of Anisakis pegreffii from the Minnan-Taiwan bank fishing ground in Taiwan Strait, a real-time PCR method for the detection in situ and differentiation was developed to amplify a region of the second internal transcribed spacer (ITS-2) of this parasite. The real-time PCR assay was capable of detecting 1/3 of a single L3 in 30 mg of marine fish tissue, and also exhibited a high level of specificity for A. pegreffii, no fluorescence signals were observed in other five major larval anisakid species found in commercial marine fishes caught in this fishing ground.

How different freezing morphologies of impacting droplets form.

HYPOTHESIS: Freezing morphologies of impacting water droplets depend on the interaction between droplet spreading and solidification. The existing studies showed that the shape of frozen droplets mostly is of spherical cap with a singular tip, because of much shorter timescale of the droplet spreading than that of the solidification. Here, we create the experimental conditions of extended droplet spreading and greatly enhanced heat transfer for fast solidification, thereby allowing to study such droplet freezing process under the strong coupling of the droplet spreading and solidification. EXPERIMENTS: We design experiments that a room-temperature water droplet impacts on a subcooled superhydrophilic surface in an enclosure chamber filled with nitrogen gas. We thoroughly investigate the freezing processes of impacting droplets under the effects of impact velocity and substrate temperature. Both the droplet impact dynamics and solidification are studied with a high-speed camera. FINDINGS: We observed five different freezing morphologies which depend on the droplet impact velocity and substrate temperature. We found that the formation of diverse morphologies results from the competitive timescales related to droplet solidification and impact hydrodynamics. We also develop a phase diagram based on scaling analysis and show how freezing morphologies are controlled by droplet impact and freezing related timescales.

Multiple primer PCR for the identification of anisakid nematodes from Taiwan Strait.

There were six major larval anisakid species found in commercial marine fishes caught in the Minnan fishing ground in the Taiwan Strait: Anisakis physeteris, Anisakis pegreffii, Raphidascaris trichiuri, Contracaecum aduncum, Contracaecum muraenesoxi, Contracaecum sp. For rapid identification of the parasite species above, a single and a multiple primer PCR (multiplex PCR) method, using specific primers based on aligned sequences of the internal transcribed spacer ITS-1, 5.8S, and ITS-2 of nuclear ribosomal DNA, were jointly used for the rapid identification of these anisakid larvae. The primers yielded distinct PCR products for each of the anisakid nematodes, providing rapid and accurate tools for identifying anisakid nematodes with distinct geographical distribution.

ES proteins analysis of Angiostrongylus cantonensis: products of the potential parasitism genes?

The expressed sequence tags (ESTs) of Angiostrongylus cantonensis were analyzed in an attempt to gain further insight into its genomic expression patterns. A total of 1,277 ESTs of A. cantonensis were randomly downloaded from NCBI databank. ESTs were analyzed and annotated using Blastx. The result showed that there were 60 ESTs had no match to any of the proteins and gene sequences in the published databases, and 695 ESTs score more than 80. According to the function, the identified 695 ESTs could be grouped into 13 categories related to metabolism, cellular development, immune evasion, host-parasite interactions, and so on. Among them, 65 (9.4%) were proteases and protease inhibitors, represented 19 potential proteases and protease inhibitors genes; 42 (6.0%) were allergens or antigens, represented 15 potential antigens/allergens genes. Signal P analysis was applied to the 19 putative proteases and protease inhibitors and the 15 antigens/allergens protein sequences to identify the potential signal peptides and anchors. The result demonstrated that there were ten putative proteins had N-terminal signal peptides and three had signal anchors, these putative excretory/secretory proteins might be the products of potential parasitism genes which played an important role in the adaptation of A. cantonensis to a parasitism life. These parasitism genes and proteins identified are expected to become potential targets for future research on anti-A. cantonensis drugs; moreover, the resulting genetic information is useful in elucidating the mechanisms of parasitism of A. cantonensis.

Genetic diversity of toll-like receptor genes in the vulnerable Chinese egret (Egretta eulophotes).

Toll-like receptor (TLR) genes have recently been employed to assess genetic diversity, as they can be used to infer both demographic history and adaptation to environments with different pathogen pressure. Here, we sampled 120 individuals of the Chinese egret (Egretta eulophotes), a globally vulnerable species, from four breeding populations across China. We assessed the levels of genetic diversity, selection pressure, and population differentiation at seven TLR loci (TLR1LB, TLR2A, TLR3, TLR4, TLR5, TLR7, and TLR15). Using a variety of metrics (SNPs, heterozygosity, nucleotides, haplotypes), our analyses showed that genetic diversity was lower at 4 of the 7 TLR loci in the vulnerable Chinese egret compared to the more common little egret (Egretta garzetta). The selection test indicated TLRs, except for TLR5, were under purifying selection in TLR evolution, suggesting that low TLR genetic diversity in the Chinese egret may be caused by purifying selection. Moreover, analysis of molecular variance indicated low but significant population differentiation among four populations at all of the TLR loci in this egret. However, some comparisons based on fixation index analyses did not show significant population differentiation, and Bayesian clustering showed admixture. Our finding suggested that these four populations of the Chinese egret in China may be considered a single unit for conservation planning. These results, the new report of TLR genetic diversity in a long-distance migratory vulnerable Ardeid species, will provide fundamental TLR information for further studies on the conservation genetics of the Chinese egret and other Ardeids.

Axisymmetric lattice Boltzmann model for simulating the freezing process of a sessile water droplet with volume change.

Droplet freezing not only is of fundamental interest but also plays an important role in numerous natural and industrial processes. However, it is challenging to numerically simulate the droplet freezing process due to its involving a complex three-phase system with dynamic phase change and heat transfer. Here we propose an axisymmetric lattice Boltzmann (LB) model to simulate the freezing process of a sessile water droplet with consideration of droplet volume expansion. Combined with the multiphase flow LB model and the enthalpy thermal LB model, our proposed approach is applied to simulate the sessile water droplet freezing on both hydrophilic and hydrophobic surfaces at a fixed subcooled temperature. Through comparison with the experimental counterpart, the comparison results show that our axisymmetric LB model can satisfactorily describe such sessile droplet freezing processes. Moreover, we use both LB simulations and analytical models to study the effects of contact angle and volume expansion on the freezing time and the cone shape formed on the top of frozen droplets. The analytical models are obtained based on heat transfer and geometric analyses. Additionally, we show analytically and numerically that the freezing front-to-interface angle keeps nearly constant (smaller than 90°).

Signal sequence analysis of protein sequences from the filarial nematode parasite Brugia malayi and the evolution of secreted proteins in parasites.

Taking a genomic approach to characterize potential secreted products, we analyzed putative protein sequences from Brugia malayi whole-genome shotgun sequencing project. SignalP analysis was applied to predict protein sequences and to identify potential signal peptides and anchors. We randomly analyzed 552 sequences, of which 88 (15.9%) bear predicted signal sequence coding regions. Through comparisons of sequences with homologs from other species, we found that although some of the sequences with signal sequences have no homologs with others, there are almost the same amounts of the sequences with signals which are highly conserved. Considering the distribution of secretory proteins of B. malayi in three categories has not made big differences, and most of the homologues of free-living nematodes of these secretory proteins also contained either N-signal signal peptides or signal anchors; we speculated that secretory proteins may be in the same evolutional status as the non-secretory proteins.