Genome Assembly of Pyrocephalus nanus: A Step Toward the Genetic Conservation of the Endangered Little Vermilion Flycatcher of the Galapagos Islands

Incredibly powerful whole genome studies of conservation genetics, evolution, and biogeography become possible for non-model organisms when reference genomes are available. Here, we report the sequence and assembly of the whole genome of the little vermilion flycatcher (Pyrocephalus nanus; family Tyrannidae), which is an endemic, endangered, and declining species of the Galapagos Islands. Using PacBio HiFi reads to assemble long contigs and Hi-C reads for scaffolding, we assembled a genome of 1.07 Gb comprising 267 contigs in 152 scaffolds, scaffold N50 74 M, contig N50 17.8 M, with 98.9% assigned to candidate chromosomal sequences and 99.72% of the BUSCO passeriformes 10,844 single-copy orthologs present. In addition, we used the novel HiFiMiTie pipeline to fully assemble and verify all portions of the mitochondrial genome from HiFi reads, obtaining a mitogenome of 17,151 bases, containing 13 protein-coding genes, 22 tRNAs, 2 rRNAs, two control regions, and a unique structure of control region duplication and repeats. These genomes will be a critical tool for much-needed studies of phylogenetics, population genetics, biogeography, and conservation genetics of Pyrocephalus and related genera. This genome and other studies that use it will be able to provide recommendations for conservation management, taxonomic improvement, and to understand the evolution and diversification of this genus within the Galapagos Islands.

High-Quality, Chromosome-Level Reference Genomes of the Viviparous Caribbean Skinks Spondylurus nitidus and S. culebrae

New World mabuyine skinks are a diverse radiation of morphologically cryptic lizards with unique reproductive biologies. Recent studies examining population-level data (morphological, ecological, and genomic) have uncovered novel biodiversity and phenotypes, including the description of dozens of new species and insights into the evolution of their highly complex placental structures. Beyond the potential for this diverse group to serve as a model for the evolution of viviparity in lizards, much of the taxonomic diversity is concentrated in regions experiencing increasing environmental instability from climate and anthropogenic change. Consequently, a better understanding of genome structure and diversity will be an important tool in the adaptive management and conservation of this group. Skinks endemic to Caribbean islands are particularly vulnerable to global change with several species already considered likely extinct and several remaining species either endangered or threatened. Combining PacBio long-read sequencing, Hi-C, and RNAseq data, here we present the first genomic resources for this group by describing new chromosome-level reference genomes for the Puerto Rican Skink Spondylurus nitidus and the Culebra Skink S. culebrae. Results indicate two high quality genomes, both ∼1.4 Gb, assembled nearly telomere to telomere with complete mitochondrion assembly and annotation.

How the Easter Egg Weevils Got Their Spots: Phylogenomics Reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae)

The evolutionary origins of mimicry in the Easter Egg weevil, Pachyrhynchus, have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Müllerian mimicry, or mimicry in which two or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns in Pachyrhynchus, this genus presents one of the best opportunities to study the evolution of both perfect and imperfect mimicry. We analyzed more than 10,000 UCE loci using a novel partitioning strategy to resolve the relationships of closely related species in the genus. Our results indicate that many of the mimetic color patterns observed in sympatric species are due to convergent evolution. We suggest that this convergence is driven by positive frequency-dependent selection.

Chromosome-level genome assembly of the bioluminescent cardinalfish Siphamia tubifer, an emerging model for symbiosis research

The bioluminescent symbiosis involving the sea urchin cardinalfish Siphamia tubifer and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate model for the study of microbial symbiosis. However, little genetic data are available for the host, limiting the scope of research that can be implemented with this association. We present a chromosome-level genome assembly for S. tubifer using a combination of PacBio HiFi sequencing and Hi–C technologies. The final assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO score of 99%. A comparison of the S. tubifer genome to that of another nonluminous species of cardinalfish revealed a high degree of synteny, whereas a comparison to a more distant relative in the sister order Gobiiformes revealed the fusion of two chromosomes in the cardinalfish genomes. The complete mitogenome of S. tubifer was also assembled, and an inversion in the vertebrate WANCY tRNA genes as well as heteroplasmy in the length of the control region were discovered. A phylogenetic analysis based on whole the mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, highlighting the potential role of the bioluminescent symbiosis in the initial divergence of Siphamia. This high-quality reference genome will provide novel opportunities for the bioluminescent S. tubifer–P. mandapamensis association to be used as a model for symbiosis research.

Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens

Phylogenomics via ultraconserved elements (UCEs) has led to improved phylogenetic reconstructions across the tree of life. However, inadvertently incorporating non‐targeted DNA into the UCE marker design will lead to misinformation being incorporated into subsequent analyses. To date, the effectiveness of basic metagenomic filtering strategies has not been assessed in arthropods. Designing markers from museum specimens requires careful consideration of methods due to the high levels of microbial contamination typically found in such specimens. We investigate if contaminant sequences are carried forward into a UCE marker set we developed from insect museum specimens using a standard bioinformatics pipeline. We find that the methods currently employed by most researchers do not exclude contamination from the final set of targets. Lastly, we highlight several paths forward for reducing contamination in UCE marker design.

The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.

An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)

Among vertebrates, turtles have many unique characteristics providing biologists with opportunities to study novel evolutionary innovations and processes. We present here a high-quality, partially phased, and chromosome-level Red-Eared Slider (Trachemys scripta elegans, TSE) genome as a reference for future research on turtle and tetrapod evolution. This TSE assembly is 2.269 Gb in length, has one of the highest scaffold N50 and N90 values of any published turtle genome to date (N50 = 129.68 Mb and N90 = 19 Mb), and has a total of 28,415 annotated genes. We introduce synteny analyses using BUSCO single-copy orthologs, which reveal two chromosome fusion events accounting for differences in chromosome counts between emydids and other cryptodire turtles and reveal many fission/fusion events for birds, crocodiles, and snakes relative to TSE. This annotated chromosome-level genome will provide an important reference genome for future studies on turtle, vertebrate, and chromosome evolution.

Correction: Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils

[This corrects the article DOI: 10.1371/journal.pone.0188044.].

Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils

Weevils (Curculionoidea) comprise one of the most diverse groups of organisms on earth. There is hardly a vascular plant or plant part without its own species of weevil feeding on it and weevil species diversity is greater than the number of fishes, birds, reptiles, amphibians and mammals combined. Here, we employ ultraconserved elements (UCEs) designed for beetles and a novel partitioning strategy of loci to help resolve phylogenetic relationships within the radiation of Australasian smurf-weevils (Eupholini). Despite being emblematic of the New Guinea fauna, no previous phylogenetic studies have been conducted on the Eupholini. In addition to a comprehensive collection of fresh specimens, we supplement our taxon sampling with museum specimens, and this study is the first target enrichment phylogenomic dataset incorporating beetle specimens from museum collections. We use both concatenated and species tree analyses to examine the relationships and taxonomy of this group. For species tree analyses we present a novel partitioning strategy to better model the molecular evolutionary process in UCEs. We found that the current taxonomy is problematic, largely grouping species on the basis of similar color patterns. Finally, our results show that most loci required multiple partitions for nucleotide rate substitution, suggesting that single partitions may not be the optimal partitioning strategy to accommodate rate heterogeneity for UCE loci.

Mutations in topoisomerase genes of fluoroquinolone-resistant salmonellae in Hong Kong

A total of 88 salmonella isolates (72 clinical isolates for which the ciprofloxacin MIC was >0.06 microg/ml, 15 isolates for which the ciprofloxacin MIC was < or =0.06 microg/ml, and Salmonella enterica serotype Typhimurium ATCC 13311) were studied for the presence of genetic alterations in four quinolone resistance genes, gyrA, gyrB, parC, and parE, by multiplex PCR amplimer conformation analysis. The genetic alterations were confirmed by direct nucleotide sequencing. A considerable number of strains had a mutation in parC, the first to be reported in salmonellae. Seven of the isolates sensitive to 0.06 micro g of ciprofloxacin per ml had a novel mutation at codon 57 of parC (Tyr57-->Ser) which was also found in 29 isolates for which ciprofloxacin MICs were >0.06 micro g/ml. Thirty-two isolates had a single gyrA mutation (Ser83-->Phe, Ser83-->Tyr, Asp87-->Asn, Asp87-->Tyr, or Asp87-->Gly), 34 had both a gyrA mutation and a parC mutation (29 isolates with a parC mutation of Tyr57-->Ser and 5 isolates with a parC mutation of Ser80-->Arg). Six isolates which were isolated recently (from 1998 to 2001) were resistant to 4 micro g of ciprofloxacin per ml. Two of these isolates had double gyrA mutations (Ser83-->Phe and Asp87-->Asn) and a parC mutation (Ser80-->Arg) (MICs, 8 to 32 microg/ml), and four of these isolates had double gyrA mutations (Ser83-->Phe and Asp87-->Gly), one parC mutation (Ser80-->Arg), and one parE mutation (Ser458-->Pro) (MICs, 16 to 64 micro g/ml). All six of these isolates and those with a Ser80-->Arg parC mutation were S. enterica serotype Typhimurium. One S. enterica serotype Typhi isolate harbored a single gyrA mutation (Ser83-->Phe), and an S. enterica serotype Paratyphi A isolate harbored a gyrA mutation (Ser83-->Tyr) and a parC mutation (Tyr57-->Ser); both of these isolates had decreased susceptibilities to the fluoroquinolones. The MICs of ciprofloxacin, levofloxacin, and sparfloxacin were in general the lowest of those of the six fluoroquinolones tested. Isolates with a single gyrA mutation were less resistant to fluoroquinolones than those with an additional parC mutation (Tyr57-->Ser or Ser80-->Arg), while those with double gyrA mutations were more resistant.

What have we learnt from community-acquired infections in Hong Kong?

This study was initiated throughout Hong Kong, to reveal the characteristics of community-acquired infections. All specimens collected by general practitioners from infected patients were followed prospectively, and those that were culture-positive were analysed. Four thousand seven hundred and forty-one specimens were collected from 3977 patients by 89 doctors from July 2000 to October 2001. The most common specimens were throat swabs (33%), urine (26%) and sputa (16%). The average culture-positive rate was 28%. The most common organisms were Escherichia coli (18%), beta-haemolytic streptococci (15%) and Staphylococcus aureus (12%). Fluoroquinolone resistance was relatively high (up to 35%) in organisms commonly causing urinary tract infection (E. coli, Proteus and Morganella). Although none of the pneumococci was resistant to penicillin 1 mg/L, the proportion with intermediate resistance (0.1-1 mg/L) was alarming (81%). There were three strains of methicillin-resistant S. aureus. A decrease in ampicillin resistance but a high prevalence of macrolide resistance were noted in Haemophilus influenzae. All Neisseria gonorrhoeae isolates were resistant to penicillin, up to 79% to the fluoroquinolones, 15% to spectinomycin, but all were susceptible to ceftriaxone. Respiratory pathogens (Streptococcus pneumoniae, beta-haemolytic streptococci and H. influenzae) were relatively susceptible to the newer fluoroquinolones (0-2%, 0.5-6% and 2% resistant, respectively) or third-generation cephalosporins (0-2% resistant). The distribution of organisms and their antibiotic resistance varied over time. Thus frequent surveillance is needed to provide information on the drugs of choice for different infections.

Results of fixation of clavicle alone in managing floating shoulder

AIM OF STUDY

A retrospective review on the outcomes of four floating shoulder, ipsilateral scapular neck and clavicular fractures, treated with open reduction and internal fixation of the clavicle alone using plate and screws.

METHODS

All patients were evaluated by interview, physical examination and radiological examination at an average follow up period of 3.3 years (range: 2-4 years). Functional outcomes were rated using Rowe's score.

RESULTS

Radiological union of both fractures occurred at an average of 2.8 months (range: 8-12 weeks). Excellent result was seen in three cases and good in one.

CONCLUSION

Plating of clavicle alone restored stability of shoulder and allowed early range of motion exercises. All cases gained good and excellent function.

Trucut needle biopsy through superior orbital fissure for the diagnosis of rabies

Necropsy diagnosis of rabies can be done by taking a brain biopsy specimen with a trucut needle inserted through the superior orbital fissure into the cranial cavity. This technique reduces the number of personnel who require post-exposure prophylaxis and avoids full necropsy if the deceased's relatives are opposed.

Disconnection of a venous Port-A-Cath followed by embolization after saline flush: rare case report

A 77-year-old man presented with painful swelling of his Port-A-Cath insertion site soon after flushing with normal saline. No discomfort or abnormality was found during the saline flush. A chest roentgenogram showed that the disconnected catheter had separated from the disc and was absent from its original location. The disconnected catheter was found embolized, by chest roentgenogram and CT scan, to the right atrium and hepatic vein. The patient was treated successfully with an X-ray guided extraction of the catheter. The possibility of catheter disconnection with embolization should be considered and a chest roentgenogram performed immediately in cases of rapid swelling of subcutaneous tissue around the port chamber after fluid infusion.

The antimicrobial activity and beta-lactamase stability of cefpirome, a new fourth-generation cephalosporin in comparison with other agents

The antimicrobial activity of cefpirome was compared with amoxycillin/clavulanic acid, ampicillin/sulbactam, cefuroxime, ceftazidime, gentamicin and amikacin against 743 non-duplicate clinical isolates. MIC50 and MIC90 showed that the antibiotic was active against both Gram-negative and Gram-positive organisms. Cefpirome was highly active against most of the Enterobacteriaceae, including indole-positive Proteus spp., Aeromonas spp. (MIC < or = 1 mg/L) and Salmonella spp. (MIC < or = 0.5 mg/L). Neisseria gonorrhoeae and Haemophilus influenzae (including beta-lactamase producers) were all susceptible, with MIC less than 0.5 and 0.25 mg/L respectively. Cefpirome was more active than cefuroxime and ceftazidime against Campylobacter spp. (MIC < or = 2 mg/L), but less active than ceftazidime against Pseudomonas aeruginosa. Cefpirome was active against Streptococcus pneumoniae. Streptococcus bovis and coagulase-negative staphylococci (MIC < or = 0.5 mg/L) and methicillin-sensitive Staphylococcus aureus (MIC < or = 2 mg/L). Methicillin-resistant S. aureus, Gram-positive and Gram-negative anaerobes were resistant to cefpirome. The stability of cefpirome to TEM-1, TEM-2, PSE-1, SHV-1 and the chromosomal-mediated P99 and K-1 beta-lactamases was comparable to ceftazidime.

Unilateral piriformis syndrome in a patient with previous melanoma

Several years after undergoing surgery for a malignant melanoma on his left lower back, a 51 year old man developed intermittently severe pain in his left posterior thigh. Plain X-rays showed no abnormality, but computerized tomography and magnetic resonance imaging scans demonstrated an abnormal soft tissue mass in the left sciatic notch. Although a metastasis from the original melanoma was suspected, exploration of the suspicious area revealed only hypertrophy of the left piriformis muscle. This was due to regular gymnasium exercises designed to selectively build up the musculature of the left lower limb, which the patient had undertaken in the firm belief that it would help to prevent a recurrence of his left-sided melanoma. Complete relief of the unilateral piriformis syndrome was achieved by division of the hypertrophied piriformis muscle, thereby relieving the pressure on the left sciatic nerve as it passed through the greater sciatic foramen.

Pharmacokinetics of parenteral imipenem/cilastatin in patients on continuous ambulatory peritoneal dialysis

We investigated the pharmacokinetics of two intravenous (iv) dose regimens of imipenem/cilastatin in Chinese patients on chronic ambulatory peritoneal dialysis (CAPD), who had an average creatinine clearance of 3.2 ml/min/1.73 m2. Doses of 0.5 and 1.0 g produced mean peak serum imipenem concentrations of 30 and 70 mg/l respectively, about 60% of cilastatin. Peritoneal dialysis fluid (PDF) imipenem concentrations reached 20-30% of the serum peak 4-5 h after iv injection, and the lowest maximum PDF concentrations were 2 mg/l after the 0.5 g dose and 14 mg/l after 1.0 g. Thus both regimes produced PDF imipenem concentrations above the MICs of susceptible pathogens. The half-life of imipenem was 6.4 h and the plasma clearance 66 ml/min; serum and PDF imipenem were in equilibration after about 5 h. Cilastatin had a prolonged half-life of 19 h and a plasma clearance of 10 ml/min, and accumulated in both serum and PDF. With a 0.5 g dose, the pharmacokinetics of imipenem/cilastatin suggest that the combination may prove an effective treatment for peritonitis associated with CAPD.

Effect of tumour necrosis factor and lipid A on functional and structural vascular volume in solid murine tumours

Effects of recombinant tumour necrosis factor (TNF) on functional and structural vascular volumes in solid murine Meth A tumours were investigated by injection of Hoechst 33342 and staining for the vascular basement membrane component laminin, respectively. Systemic injection of 3 x 10(4) U TNF caused an initial increase in functional volume in the tumour, but a strong decrease from 1 to 48 h after treatment. Early effects of intralesional treatment were more moderate. Systemic injection of 10(4) U TNF or 0.3 or 3 micrograms lipid A caused a fall in functional volume at 4 h, but a recovery was seen at 24 h. This recovery did not occur after treatment with a combination of 10(4) U TNF and 0.3 micrograms lipid A. Structural vascular volume was not markedly reduced until 24 h after treatment with the high doses of the separate agents and the combination. All effects appeared generally more prominent in the tumour centre than in the borders. Data suggest that TNF induces initially an active hyperaemia that rapidly converts to passive hyperaemia. A prolonged disturbance of tumour blood supply is probably necessary for therapeutic activity. Breakdown of laminin in the vascular basement membrane may be a cause of loss of vascular integrity.

Kinetics and morphology of chemically induced popliteal lymph node reactions compared with antigen-, mitogen-, and graft-versus-host-reaction-induced responses

Changes in the popliteal lymph node (PLN) in mice evoked by a local graft-versus-host (GVH) reaction and by a single injection of various agents into the hind footpad were compared. The drug diphenylhydantoin induced similar weight changes in time as the GVH reaction. More vigorous and protracted reactions were induced by the drug nitrofurantoin and the contact sensitizer dinitrochlorobenzene, whereas the antigens lipopolysaccharide and sheep erythrocytes caused very moderate and short-lasting weight changes. Alterations of lymph node architecture upon injection of diphenylhydantoin resembled those observed during the GVH response. Some quantitative and qualitative differences were noted for nitrofurantoin, but clearly deviant morphological alterations were seen in response to lipopolysaccharide and sheep erythrocytes. The PLN reaction to dinitrochlorobenzene had features of both the GVH reaction and the antigen-induced responses. These findings support the concept that some drugs and chemicals may induce or exacerbate lymphoproliferative disorders by GVH-like mechanisms.

Rapid HPLC assay of fluoroquinolones in clinical specimens

A simple isocratic HPLC procedure was developed for the analysis of seven quinolones and their metabolites in clinical specimens. It is likely that this system can be used for the assay of many other quinolone compounds, but not for nalidixic acid and the ciprofloxacin metabolite sulpho-ciprofloxacin which appear to be adsorbed in the column. Sample preparation takes approximately 20 min, and HPLC analysis is completed within 15 min with a simple solvent system eluted on a reversed phase column. The procedure is rapid, sensitive and specific, and is a modification of an assay for chloramphenicol and beta-lactam antibiotics. This method is therefore particularly useful for clinical laboratories, since a single HPLC system can be used for assays of chloramphenicol, beta-lactams and quinolones.

Susceptibilities of Hong Kong isolates of multiply resistant Shigella spp. to 25 antimicrobial agents, including ampicillin plus sulbactam and new 4-quinolones

Seventy-two percent of 129 shigella isolates from two Hong Kong hospitals were Shigella flexneri. Twenty-six percent were S. sonnei, and there was only one isolate each of S. dysenteriae and S. boydii. Ninety-six percent of the isolates were resistant to two or more antibiotics, and up to 11 resistances were seen in a single isolate. Fifty-seven percent or more of these isolates were resistant to ampicillin, streptomycin, tetracycline, chloramphenicol, and sulfamethoxazole; and up to twenty-three percent were resistant to kanamycin, trimethoprim, trimethoprim-sulfamethoxazole, and gentamicin. All the isolates were susceptible to amikacin, nalidixic acid, and the newer 4-quinolone agents; and all but one were susceptible to the cephalosporins tested. Only three isolates remained resistant to ampicillin in the presence of sulbactam. Ampicillin plus sulbactam or the newer 4-quinolone agents may be alternatives for the treatment of severe infections caused by multiply resistant shigellas.

Comparative evaluation of the Abbott TDX, the Abbott ABA200, and the Syva LAB5000 for assay of serum gentamicin

Three automated chemical assays for serum gentamicin were compared for accuracy, reproducibility and cost. One method utilized fluorescence polarization (Abbott TDX), and the other two enzyme-multiplied immunoassay (Abbott ABA200, and the Syva Lab5000). All three systems produced a high degree of accuracy and reproducibility with spiked samples when the concentrations of gentamicin were within the range of 3.0-8.0 mg/l. However, with concentrations below 2.0 mg/l or above 8.0 mg/l, only the TDX system gave acceptable coefficients of variation and accurate recoveries. Similarly, excellent correlations were obtained between all three systems for assays of clinical specimens containing 2.0-8.0 mg/l gentamicin, but above and below this range, the correlations were poor except between TDX and Lab5000 within the range of 0.0-2.0 mg/l. The Abbott TDX was thus the most accurate and reproducible of the three systems for the assay of serum gentamicin in the critical concentrations below 2.0 mg/l and above 8.0 mg/l. The cost per assay by the Abbott TDX was US$4.57 compared with US$5.40 for the Abbott ABA200, and US$3.20 for the Syva Lab5000.