Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

Effects of Hydrostatic Pressure on Carcinogenic Properties of Epithelia

The relationship between chronic inflammation and cancer is well known. The inflammation increases the permeability of blood vessels and consequently elevates pressure in the interstitial tissues. However, there have been only a few reports on the effects of hydrostatic pressure on cultured cells, and the relationship between elevated hydrostatic pressure and cell properties related to malignant tumors is less well understood. Therefore, we investigated the effects of hydrostatic pressure on the cultured epithelial cells seeded on permeable filters. Surprisingly, hydrostatic pressure from basal to apical side induced epithelial stratification in Madin-Darby canine kidney (MDCK) I and Caco-2 cells, and cavities with microvilli and tight junctions around their surfaces were formed within the multi-layered epithelia. The hydrostatic pressure gradient also promoted cell proliferation, suppressed cell apoptosis, and increased transepithelial ion permeability. The inhibition of protein kinase A (PKA) promoted epithelial stratification by the hydrostatic pressure whereas the activation of PKA led to suppressed epithelial stratification. These results indicate the role of the hydrostatic pressure gradient in the regulation of various epithelial cell functions. The findings in this study may provide clues for the development of a novel strategy for the treatment of the carcinoma.     

R-prime plasmids from Bradyrhizobium japonicum and Rhizobium fredii

The formation of R-prime plasmids was selected in crosses involving soybean microsymbionts with genomic Tn5 insertions and carrying plasmid pJB3JI (with one IS2) copy as donors and Escherichia coli HB101 as recipient. Whereas the parent plasmid was 60 kb, recombinant plasmids between 76 kb and 121 kb were obtained. Restriction and Southern analyses confirmed the mobilization of Tn5 on four R-primes from Bradyrhizobium japonicum I-110 and on an R-prime plasmid from Rhizobium fredii HH303. The largest R-prime plasmid was obtained from the rescue of two symbiotically defective R. fredii mutant strains that required adenosine.Non-standard abbreviation TDP transposon donor pool Scientific article number A-4728 and contribution number 7724 of the Maryland Agricultural Experiment Station     

Immunolocalization of β-1-4-galactan and its relationship with lignin distribution in developing compression wood of Cryptomeria japonica

Compression wood (CW) contains higher quantities of β-1-4-galactan than does normal wood (NW). However, the physiological roles and ultrastructural distribution of β-1-4-galactan during CW formation are still not well understood. The present work investigated deposition of β-1-4-galactan in differentiating tracheids of Cryptomeria japonica during CW formation using an immunological probe (LM5) combined with immunomicroscopy. Our immunolabeling studies clearly showed that differences in the distribution of β-1-4-galactan between NW (and opposite wood, OW) and CW are initiated during the formation of the S₁ layer. At this stage, CW was strongly labeled in the S₁ layer, whereas no label was observed in the S₁ layer of NW and OW. Immunogold labeling showed that β-1-4-galactan in the S₁ layer of CW tracheids significantly decreased during the formation of the S₂ layer. Most β-1-4-galactan labeling was present in the outer S₂ region in mature CW tracheids, and was absent in the inner S₂ layer that contained helical cavities in the cell wall. In addition, delignified CW tracheids showed significantly more labeling of β-1-4-galactan in the secondary cell wall, suggesting that lignin is likely to mask β-1-4-galactan epitopes. The study clearly showed that β-1-4-galactan in CW was mainly deposited in the outer portion of the secondary cell wall, indicating that its distribution may be spatially consistent with lignin distribution in CW tracheids of Cryptomeria japonica.     

New records for prehistoric introduction of Neotropical mammals to the West Indies: evidence from Carriacou,Lesser Antilles

Aim This paper investigates the prehistoric introduction of five mammalian taxa to Carriacou (Lesser Antilles) and refines the known anthropogenic ranges for these fauna in the pre‐Columbian West Indies. The importance of such records for understanding the region’s historical biogeography and ecology is considered. Location Carriacou Island, Grenada (12°28′ N, 61°26′ W). Methods Zooarchaeological assemblages from Carriacou’s earliest documented prehistoric sites, Grand Bay and Sabazan, were analysed, and exotic taxa were identified and quantified. The timing of introductions was established based on multiple radiocarbon assays, including three new accelerator mass spectrometry (AMS) direct dates obtained on the bone of exotic taxa. Source species and location(s) are considered and compared with known prehistoric records for the Caribbean to synthesize anthropogenic distributions for the pre‐Columbian period. The contexts of the zooarchaeological remains are evaluated to better understand the nature and purpose of introductions. Results Zooarchaeological investigation on Carriacou reveals the occurrence of multiple mammal introductions from South American between c. ad 700 and ad 1400. This paper presents the first records for guinea pig (Cavia sp.), armadillo (Dasypus sp.), peccary (Tayassu/Pecari sp.), opossum (Didelphis sp.) and agouti (Dasyprocta sp.) from the island. Human‐mediated transport of these taxa is indicated by their absence from the record prior to human settlement of Carriacou. Several translocated species are either rare or entirely unknown for the region, and overall West Indian distributions are temporally and spatially discontinuous. Archaeological contexts indicate that mammalian introductions arose from human subsistence needs, but other social factors may have shaped the dispersal of these fauna. Main conclusions The taxonomic combination and richness of Carriacou’s introduced fauna are unusual within the region. Importantly, the new records significantly improve the known pre‐Columbian geographic range for peccary, guinea pig and armadillo. Integrated with regional records, these data augment our understanding of the Caribbean’s historical biogeography, and have the potential to improve our understanding of human mobility and anthropogenic environmental impacts in the West Indies prior to the arrival of Europeans.     

Anti-Inflammatory Effects of Acupuncture Stimulation via the Vagus Nerve

Although acupuncture therapy is widely used in traditional Asian medicine for the treatment of diverse internal organ disorders, its underlying biological mechanisms are largely unknown. Here, we investigated the functional involvement of acupuncture stimulation (AS) in the regulation of inflammatory responses. TNF-α production in mouse serum, which was induced by lipopolysaccharide (LPS) administration, was decreased by manual acupuncture (MAC) at the zusanli acupoint (stomach36, ST36). In the spleen, TNF-α mRNA and protein levels were also downregulated by MAC and were recovered by using a splenic neurectomy and a vagotomy. c-Fos, which was induced in the nucleus tractus solitarius (NTS) and dorsal motor nucleus of the vagus nerve (DMV) by LPS and electroacupuncture (EAC), was further increased by focal administration of the AMPA receptor blocker CNQX and the purinergic receptor antagonist PPADS. TNF-α levels in the spleen were decreased by CNQX and PPADS treatments, implying the involvement of inhibitory neuronal activity in the DVC. In unanesthetized animals, both MAC and EAC generated c-Fos induction in the DVC neurons. However, MAC, but not EAC, was effective in decreasing splenic TNF-α production. These results suggest that the therapeutic effects of acupuncture may be mediated through vagal modulation of inflammatory responses in internal organs.     

Effect of Composition and Impurities on the Phosphorescence of Green-Emitting Alkaline Earth Aluminate Phosphor

Recent improvements to SrAl₂O₄:Eu²⁺, Dy³⁺ phosphors have enabled the use of luminescent hosts with a stable crystal structure and high physical and chemical stability, thus overcoming the bottleneck in the applicability of ZnS:Cu phosphors. However, enhancement of afterglow lifetime and brightness in SrAl₂O₄:Eu²⁺, Dy³⁺ phosphors remains a challenging task. Here, we have improved the afterglow characteristics in terms of persistence time and brightness by a systematic investigation of the composition of Eu-doped alkaline earth aluminate SrAl₂O₄:Eu²⁺, Dy³⁺ crystals. We found that a Dy³⁺/Eu²⁺ ratio of ~2.4 and ~0.935 mol Eu²⁺ (per mol of SrAl₂O₄) gave the brightest and longest emissions (11% and 9% increase for each). Doping with Si⁴⁺ also resulted in a slight increase in brightness up to ~15%. Doping with alkali metal or alkaline earth metal significantly enhanced the phosphorescence intensity. In particular, doping with 0.005 mol Li⁺ (per mol of SrAl₂O₄) alone boosted the phosphorescence intensity to 239% of the initial value, as compared to that observed for the non-doped crystal, while doping with 0.01 mol Mg²⁺ and 0.005 mol Li⁺ (per 1 mol SrAl₂O₄) boosted the phosphorescence intensity up to 313% of the initial value. The results of this investigation are expected to act as a guideline for the synthesis of bright and long persistent phosphors, and facilitate the development of persistent phosphors with afterglow characteristics superior to those of conventional phosphors.     

Secretion of Recombinant Pediocin PA-1 by Bifidobacterium longum, Using the Signal Sequence for Bifidobacterial α-Amylase

A recombinant DNA, encoding the chimeric protein of the signal sequence for bifidobacterial α-amylase mature pediocin PA-1, was introduced into Bifidobacterium longum MG1. Biologically active pediocin PA-1 was successfully secreted from the strain and showed bactericidal activity against Listeria monocytogenes and the same molecular mass as native pediocin PA-1.