MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163-185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.

Use of a simple arm-raising test with a portable laser Doppler blood flow meter to detect dehydration

Using micro electromechanical systems (MEMS) technologies, the authors have developed the world’s smallest, lightest, and least power-consuming laser Doppler blood flow meter. Unlike commercial fibre-type blood flow instruments, the new blood flow meter is invulnerable to any movements of the person wearing it and has a wireless transmitter. Utilizing the characteristics of the blood flow meter, the authors attempted to detect dehydration by having a subject simply raise an arm (arm-raising test) with the flow meter attached to a fingertip. Healthy young volunteers (20 men and two women, mean age 22.9, age range 21–27 years) were instructed to perspire in a sauna until they became dehydrated. The target dewatering ratio was 2 per cent, which was calculated from the body weight measured using a weight scale. Four markers were compared: mean blood flow (MBF) before arm-raising, MBF during arm-raising, maximum amplitude (MA) of the pulse wave during arm-raising, and inclination of reflex (IR) wave calculated from the recorded blood flow data for the non-dehydrated (before sauna) and dehydrated (3 h after sauna) states in the arm-raising test. Each of the mean total markers (MBF during arm-raising, MA, and IR) was significantly lower ( P < 0.05) during the dehydrated state than the non-dehydrated. These results suggest that three markers could detect dehydration and the blood flow meter devised has the potential to be used as a portable device for detecting dehydration.

Coordination structures of Ca2+ and Mg2+ in Akazara scallop troponin C in solution. FTIR spectroscopy of side-chain COO- groups

FTIR spectroscopy has been applied to study the coordination structures of Mg2+ and Ca2+ ions bound in Akazara scallop troponin C (TnC), which contains only a single Ca2+ binding site. The region of the COO- antisymmetric stretch provides information about the coordination modes of COO- groups to the metal ions: bidentate, unidentate, or pseudo-bridging. Two bands were observed at 1584 and 1567 cm-1 in the apo state, whereas additional bands were observed at 1543 and 1601 cm-1 in the Ca2+-bound and Mg2+-bound states, respectively. The intensity of the band at 1567 cm-1 in the Mg2+-bound state was identical to that in the apo state. Therefore, the side-chain COO- group of Glu142 at the 12th position in the Ca2+-binding site coordinates to Ca2+ in the bidentate mode but does not interact with Mg2+ directly. A slight upshift of COO- antisymmetric stretch due to Asp side-chains was also observed upon Mg2+ and Ca2+ binding. This indicates that the COO- groups of Asp131 and Asp133 interact with both Ca2+ and Mg2+ in the pseudo-bridging mode. Therefore, the present study directly demonstrated that the coordination structure of Mg2+ was different from that of Ca2+ in the Ca2+-binding site. In contrast to vertebrate TnC, most of the secondary structures remained unchanged among apo, Mg2+-bound and Ca2+-bound states of Akazara scallop TnC, as spectral changes upon either Ca2+ or Mg2+ binding were very small in the infrared amide-I' region as well as in the CD spectra. Fluorescence spectroscopy indicated that the spectral changes upon Ca2+ binding were larger than that upon Mg2+ binding. Moreover, gel-filtration experiments indicated that the molecular sizes of TnC had the order apo TnC > Mg2+-bound TnC > Ca2+-bound TnC. These results suggest that the tertiary structures are different in the Ca2+- and Mg2+-bound states. The present study may provide direct evidence that the side-chain COO- groups in the Ca2+-binding site are directly involved in the functional on/off mechanism of the activation of Akazara scallop TnC.

Crystallization and preliminary X-ray diffraction studies of a 40 kDa calcium binding protein specifically expressed in plasmodia of Physarum polycephalum

A calcium binding protein with a molecular mass of 40 kDa (CBP40), the gene product of plasmodial-specific LAV1-2 of Physarum polycephalum, was crystallized in the presence of EDTA. The crystals diffracted X-rays up to a resolution of 3.0 A. They belonged to the trigonal space group, P3221 (or P3121), with unit cell dimensions of a = b = 64.4 A and c = 207.2 A. Ca2+-bound crystals were obtained by soaking in a CaCl2 solution, which gave diffraction data of similar quality. The Ca2+-soaked crystals belonged to the same space group as those crystallized in the presence of EDTA with unit cell dimensions of a = b = 64.4 A and c = 209.4 A.

Solution structure of midkine, a new heparin-binding growth factor

Midkine (MK) is a 13 kDa heparin-binding polypeptide which enhances neurite outgrowth, neuronal cell survival and plasminogen activator activity. MK is structurally divided into two domains, and most of the biological activities are located on the C-terminal domain. The solution structures of the two domains were determined by NMR. Both domains consist of three antiparallel beta-strands, but the C-terminal domain has a long flexible hairpin loop where a heparin-binding consensus sequence is located. Basic residues on the beta-sheet of the C-terminal domain form another heparin-binding site. Measurement of NMR signals in the presence of a heparin oligosaccharides verified that multiple amino acids in the two sites participated in heparin binding. The MK dimer has been shown to be the active form, giving signals to endothelial cells and probably to neuronal cells. We present a head-to-head dimer model of MK. The model was supported by the results of cross-linking experiments using transglutaminase. The dimer has a fused heparin-binding site at the dimer interface of the C-terminal domain, and the heparin-binding sites on MK fit the sulfate group clusters on heparin. These features are consistent with the proposed stronger heparin-binding activity and biological activity of the dimer.

Epidemiology of blindness and visual impairment in Vanuatu

A population-based survey of blindness was conducted in Vanuatu. Data were gathered on a sample of 3520 of the approximately 150,000 inhabitants of Vanuatu aged at least 6 years, in order to estimate the prevalence and causes of blindness among the whole population. An overall prevalence of blindness of 4.0 per 1000 was found, 85% of which was due to cataract, an avoidable cause of this disability.

Absorption of topical disodium cromoglycate and its preservatives by soft contact lenses

Disodium cromoglycate (2%) (DSCG) was administered four times daily for one month to 10 patients using extended wear contact lenses. The same regimen was also followed for five days by 25 patients using daily wear soft contact lenses. The contact lenses and their soaking solutions were collected at the end of the wearing period and analyzed for DSCG, benzalkonium chloride (BAK), 2-phenylethanol, and EDTA. The lens soaking solutions and eluates prepared from the lenses were tested. In the extended wear group, small amounts of DSCG were detected in both the eluates and the soaking solutions. In the daily wear group DSCG was detected in small amounts in the soaking solutions but not in the eluates. BAK, EDTA, and 2-phenylethanol were not detected in any of the eluates or soaking solutions. During the study, no side effects of DSCG were observed in any of the patients. In animal experiments, radioactive DSCG was applied once to a series of rabbit eyes. Four hours after administration of the labelled DSCG, the animals' tears, cornea, and aqueous humor were examined for DSCG. Of the instilled dose, approximately 0.2% was found in the cornea, and less than 0.04% was found in the aqueous humor. We conclude that commercial DSCG applied topically to contact lenses does not result in the accumulation of either the drug or its preservatives in lenses and that DSCG can be safely applied directly onto a worn contact lens.