A de novo interstitial deletion of 8p11.2 including ANK1 identified in a patient with spherocytosis, psychomotor developmental delay, and distinctive facial features

The contiguous gene syndrome involving 8p11.2 is recognized as a combined phenotype of both Kallmann syndrome and hereditary spherocytosis, because the genes responsible for these 2 clinical entities, the fibroblast growth factor receptor 1 (FGFR1) and ankyrin 1 (ANK1) genes, respectively, are located in this region within a distance of 3.2Mb. We identified a 3.7Mb deletion of 8p11.2 in a 19-month-old female patient with hereditary spherocytosis. The identified deletion included ANK1, but not FGFR1, which is consistent with the absence of any phenotype or laboratory findings of Kallmann syndrome. Compared with the previous studies, the deletion identified in this study was located on the proximal end of 8p, indicating a pure interstitial deletion of 8p11.21. This patient exhibited mild developmental delay and distinctive facial findings in addition to hereditary spherocytosis. Thus, some of the genes included in the deleted region would be related to these symptoms.     

Competition in chemostat-type equations with two habitats

Competition on a model with nutrient recycling is considered. The model is based on a chemostat-type equation which is used to study population dynamics of microorganisms. The model consists of four organisms competing for a limiting nutrient. Nutrient is supplied both from the in-flow of medium and a recycling with delay, the latter is generated from dead organisms by bacterial decomposition. This paper shows that the model undergoes a Hopf bifurcation through a critical value of time delay when the in-flow is small. Coexistence of four organisms competing for one limiting nutrient is indicated by numerical simulation results.     

Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses,plasmids, and more

Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes that characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores the memory of previous exposure. Our protocol can infer CRISPR-targeted sequences, including viruses, plasmids, and previously uncharacterized elements, and predict their hosts using unassembled short-read metagenomic sequencing data. By analyzing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences, which are likely complete circular genomes. The sequences included 2,154 tailed-phage genomes, together with 257 complete crAssphage genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 56 genomes of Inoviridae species, and 95 previously uncharacterized circular small genomes that have no reliably predicted protein-coding gene. We predicted the host(s) of approximately 70% of the discovered genomes at the taxonomic level of phylum by linking protospacers to taxonomically assigned CRISPR direct repeats. These results demonstrate that our protocol is efficient for de novo inference of CRISPR-targeted sequences and their host prediction.     

Validation study of assay method for DE-310, a novel polymer-bound camptothecin derivative, and the free drug in mouse plasma by liquid chromatography with fluorimetric detection

DE-310 is a macromolecular carrier conjugate containing an anti-tumor camptothecin derivative, DX-8951, which is conjugated to a water-soluble polymer via a peptide spacer. Assay methods have been developed for the determination of a polymer-bonded DX-8951 conjugate, DX-8951, and Glycyl-DX-8951 (G-DX-8951) in mouse plasma. Free DX-8951 and Glycyl-DX-8951 were extracted from plasma by protein precipitation and analyzed by HPLC (Method I). Conjugated DX-8951 was extracted by protein precipitation and digested by using a thermolysin. The productive compound was analyzed by HPLC (Method II). The lower limits of quantitation of DX-8951, Glycyl-DX-8951, and Conjugated DX-8951 were 0.60, and 0.77 ng/ml and 3.45 microg/ml (as DX-8951 equivalent). These two methods showed satisfactory sensitivity, precision, accuracy, recovery, and selectivity.     

Effective DNA extraction method for fragment analysis using capillary sequencer of the kelp, Saccharina

Deoxyribonucleic acid (DNA) fragment analysis can become an effective tool to study genetic differences between species and individuals on saccharinan kelp from which the little genetic diversity has been reported. Here, extraction methods of DNA suitable for use in analysis with a capillary sequencer is examined on Saccharina japonica var. diabolica which contains abundant polysaccharide. When amplified fragment length polymorphism was performed using genomic DNA extracted by seven different methods: (1) commercial kit, (2) original cetyl trimethylammonium bromide (CTAB) method, (3)–(5) three types of modified CTAB method, (6) modified sodium dodecyl sulfate (SDS) method, (7) combination of CTAB method and SDS method, a high reproducible peak that was suitable for analysis was noticeable in the electropherogram in the experiment with the last combination method (7). It is considered that the pretreatment washing of polysaccharide and the subsequent purification for protein and ribonucleic acid in SDS method and for polysaccharide in CTAB method are effective to obtain the high-purity DNA.     

Yearly variation in recruitment and its effect on population dynamics inYoldia notabilis (Mollusca: Bivalvia), analyzed using projection matrix model

Long-term variation in recruitment was estimated by constructing projection matrices for a marine bivalve, Yoldia notabilis, at two stations in Otsuchi Bay, northeastern Japan, and the effects of its variation on population dynamics were examined using a simple matrix model. The matrix model was developed from the Leslie matrix, in which the population growth rate λ was expressed as a function of recruitment rate r₀. The equilibrium recruitment rate r_s, or the recruitment rate required to maintain population at constant size (λ=1), was expressed by the reciprocal of the reproductive value of a newly recruited individual. The estimates of r_s for the field population were lower at the shallower station than at the deeper station, reflecting higher survivorship and fecundity. Past recruitment rate estimated both by the field samplings for 3 years and by the back-calculation from the current age structure for over 10 years showed large yearly variation, ranging between 0 and 58.6×10⁻⁴. The estimates were larger than r_s, and hence, large enough to increase population size (λ>1) only in approximately one-third of the estimated years. This suggests that the population has been maintained by occasional successful recruitment occurring once every few years.     

Halteria grandinella: a rapid swimming ciliate with a high frequency of ciliary beating

A ciliated protozoan, Halteria grandinella, swam backward rapidly with a migration distance per second attaining 100 times the cell size. This high swimming velocity was accompanied by a high frequency of ciliary beating. Recordings with a high-speed digital video (10(3) frames/s) revealed that the frequency during forward and backward swimming was, respectively, 105 +/- 10 Hz and 260 +/- 30 Hz. These frequencies are the highest among cilia and flagella reported to date. Electron microscopic observation of the ciliary structure confirmed normal 9 + 2 arrangements of the axoneme except that cilia for migration are bundled into membranelles. Ciliary beating of saponin-treated cells was reactivated by the addition of Mg2+ -ATP, although the beating amplitude was smaller than that of intact cells. Kinetic analysis of the ATP-dependent increase of beating frequency revealed that the maximal frequency in the presence of free Ca2+ and 0.9 microM Ca2+ was approximately 60 and 110 Hz, respectively. A possible mechanism to increase beating frequency with Ca2+ is discussed.     

Effects of tropomyosin, troponin and Ca on the interaction between F-actin and heavy meromyosin

1. In the absence of ATP, H-meromyosin (heavy meromyosin) bound with the F-actin-tropomyosin-troponin complex up to the molar ratio of H-meromyosin to actin of 1:1, independently of the concentration of Ca²⁺.

2. In the presence of free Ca²⁺ above about 1 μM, with an increasing amount of H-meromyosin bound to a fixed amount of the F-actin-tropomyosin-troponin complex, the degree of flow birefringence decreased and the extinction angle increased. The minimum value of the birefringence and the maximum value of the extinction angle were found at the molar ratio of H-meromyosin to actin of 1:2. A further increase of bound H-meromyosin to actin restored both the degree of birefringence and the extinction angle to nearly the same level as the F-actin-tropomyosin-troponin complex only. In the absence of free Ca²⁺, the birefringence did not change with the binding of H-meromyosin.

3. This sensitivity of birefringence to the concentration of Ca²⁺ appeared only in the presence of tropomyosin and troponin. At a fixed ratio of H-meromyosin, actin and tropomyosin, the birefringence in the absence of Ca²⁺ increased with increasing amount of added troponin up to the weight ratio of troponin to actin of 1:6; whereas the birefringence in the presence of Ca²⁺ did not change.

4. At a fixed ratio of H-meromyosin to actin, the birefringence changed with increasing amount of tropomyosin added up to the weight ratio of tropomyosin to actin of 1:6; above this ratio, the birefringence was constant.

5. Subfragment S-1, prepared by the chymotryptic digestion of myosin, bound to F-actin, but the birefringence did not change even in the presence of tropomyosin and troponin.     

Human-Specific Adaptations in Vpu Conferring Anti-tetherin Activity Are Critical for Efficient Early HIV-1 Replication In Vivo

1. Download high-res image (235KB)
2. Download full-size image