Magnetospirillum bellicus sp. nov., a Novel Dissimilatory Perchlorate-Reducing Alphaproteobacterium Isolated from a Bioelectrical Reactor

Previously isolated dissimilatory perchlorate-reducing bacteria (DPRB) have been primarily affiliated with the Betaproteobacteria. Enrichments from the cathodic chamber of a bioelectrical reactor (BER) inoculated from creek water in Berkeley, CA, yielded a novel organism most closely related to a previously described strain, WD (99% 16S rRNA gene identity). Strain VDY^T has 96% 16S rRNA gene identity to both Magnetospirillum gryphiswaldense and Magnetospirillum magnetotacticum, and along with strain WD, distinguishes a clade of perchlorate-reducing Magnetospirillum species in the Alphaproteobacteria. In spite of the phylogenetic location of VDY^T, attempted PCR for the key magnetosome formation genes mamI and mamL was negative. Strain VDY^T was motile, non-spore forming, and, in addition to perchlorate, could use oxygen, chlorate, nitrate, nitrite, and nitrous oxide as alternative electron acceptors with acetate as the electron donor. Transient chlorate accumulation occurred during respiration of perchlorate. The organism made use of fermentation end products, such as acetate and ethanol, as carbon sources and electron donors for heterotrophic growth, and in addition, strain VDY^T could grow chemolithotrophically with hydrogen serving as the electron donor. VDY^T contains a copy of the RuBisCo cbbM gene, which was expressed under autotrophic but not heterotrophic conditions. DNA-DNA hybridization with strain WD confirmed VDY^T as a separate species (46.2% identity), and the name Magnetospirillum bellicus sp. nov. (DSM 21662, ATCC BAA-1730) is proposed.Dissimilatory perchlorate-reducing bacteria (DPRB) use perchlorate as a terminal electron acceptor during respiration, reducing it completely to chloride. As a consequence, bioremediation of perchlorate has been identified as the most effective means of treating this harmful contaminant (10), which, due to historically unregulated release into the environment, has become widespread (13, 20, 41). Fortunately, DPRB are ubiquitous and can be readily isolated from a variety of environments (1, 10, 11, 39, 44), and a key gene in the pathway, the chlorite dismutase (cld) gene, has been broadly detected (6). Much has been revealed about the biochemistry and genetics of microbial perchlorate reduction through the study of several model organisms, including Dechloromonas aromatica and Dechloromonas agitata, by a variety of groups (5, 6, 8, 9, 17, 28, 29, 34, 35, 38, 47, 51, 56, 57).Less is known about the variation in physiology between these organisms or the evolution of the perchlorate reduction metabolism, highlighting a need for further isolation and characterization of pure cultures. The lack of congruence between phylogenetic trees of cld and the 16S rRNA gene among tested DPRB suggests that the metabolism may be the result of horizontal gene transfer (6). Given that various elements of the pathway may be mobile, it is not unreasonable to expect that organisms with a wide phylogenetic diversity could acquire the ability to reduce perchlorate. As more varied enrichment conditions are tested (2, 39), sometimes as a result of novel bioreactor development for perchlorate treatment (38, 40, 45), the true phylogenetic diversity of DPRB is becoming apparent, supporting the hypothesis that the metabolism may be widespread within the tree of life, similar to other respiratory processes, such as the reduction of sulfate, Fe(III), and nitrate.Although perchlorate has been primarily regarded as an anthropogenic contaminant, a variety of studies have indicated that perchlorate occurs naturally (29-31, 34), which provides a possible explanation for the selective pressure behind the evolution of perchlorate reduction genes. As more is understood about the chlorine redox cycle on earth, knowledge about the diversity of organisms capable of interacting with the various oxyanions of chlorine is becoming more important. Here, we report the characterization of a unique DPRB in the Alphaproteobacteria. Strain VDY^T was isolated from the surface of a working electrode in an active perchlorate-reducing bioelectrical reactor (BER) that was inoculated with water from Strawberry Creek on the University of California, Berkeley, campus (40). This is only the second described DPRB in the Alphaproteobacteria, the other being the closely related strain WD (26), and these strains compose a unique clade of perchlorate-reducing organisms in the genus Magnetospirillum.     

GENETICS OF SEX EXPRESSION IN FRAG ARIA SPECIES

Hermaphroditism is the normal mode of sex expression in diploid species of Fragaria (Rosaceae, 2n = 14, x = 7) with one known exception, gynodioecious F. vesca L. ssp. bracteata. The polyploid species of Fragaria are all trioecious. An extensive study involving appropriate hybridization, testcrossing, selling, and backcrossing revealed that the repression of sporangia and the inhibition of sporogenesis are controlled by a single gene (or a gene complex) with at least three alleles in the sporophytes of trioecious octoploid species (2n = 56, x = 7). A male suppressor (allele F) reduces microsporangia and represses microsporogenesis completely, but it allows normal development of the stigma, style, and ovary. A female suppressor (allele M), in the absence of modifier genes, inhibits megasporogenesis and drastically reduces the number of carpels and size of receptacles. The allele H, conferring perfect flowers at an early stage of flower organogenesis, acts as an inducer of microsporogenesis in females, but leaves both microand megasporangial development intact. At the sex locus, the F allele (femaleness) is dominant to H and M and the H allele (hermaphroditism) is dominant to M (maleness). Females are exclusively heterogametic (F/H or F/M), hermaphrodites may be homo- or heterogametic (H/H or H/M), and males are homogametic (M/M). The sex gene is expressed precisely in the genetic background of octoploid × diploid hybrids of Fragaria and their derivatives and in crosses with closely related hermaphroditic diploid Pontentilla glandulosa L. Gene dosage phenomena are absent. First generation progeny of colchi-decaploids (F/F, –/–) are exclusively female, but all generations thereafter segregate in a normal diploidized manner (1:1). Application of phytohormones alters sex expression to a limited extent.     

The architecture of gene regulatory variation across multiple human tissues: the MuTHER study

While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity in multiple primary tissues is not yet well understood. We explore in depth the role of cis-regulatory variation in three human tissues: lymphoblastoid cell lines (LCL), skin, and fat. The samples (156 LCL, 160 skin, 166 fat) were derived simultaneously from a subset of well-phenotyped healthy female twins of the MuTHER resource. We discover an abundance of cis-eQTLs in each tissue similar to previous estimates (858 or 4.7% of genes). In addition, we apply factor analysis (FA) to remove effects of latent variables, thus more than doubling the number of our discoveries (1,822 eQTL genes). The unique study design (Matched Co-Twin Analysis--MCTA) permits immediate replication of eQTLs using co-twins (93%-98%) and validation of the considerable gain in eQTL discovery after FA correction. We highlight the challenges of comparing eQTLs between tissues. After verifying previous significance threshold-based estimates of tissue-specificity, we show their limitations given their dependency on statistical power. We propose that continuous estimates of the proportion of tissue-shared signals and direct comparison of the magnitude of effect on the fold change in expression are essential properties that jointly provide a biologically realistic view of tissue-specificity. Under this framework we demonstrate that 30% of eQTLs are shared among the three tissues studied, while another 29% appear exclusively tissue-specific. However, even among the shared eQTLs, a substantial proportion (10%-20%) have significant differences in the magnitude of fold change between genotypic classes across tissues. Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits.     

Liver abscess as the presenting manifestation of chronic granulomatous disease

Chronic granulomatous disease (CGD) is a rare primary immunodeficiency disease, affecting phagocytic blood cells, which predispose patients to recurrent infectious complications. Herein, an 11-year-old girl is described who presented with liver abscess at the age of 9 years. Positive dihydrorhodamine (DHR) and nitrobluetetrazolium (NBT) tests confirmed the diagnosis of CGD for the patient. Anti-tuberculosis drugs and parenteral antibiotic therapy were started. Unusual visceral abscess and recurrent infections should be considered as an alarm for primary immunodeficiency diseases, while early diagnosis and appropriate treatment could prevent severe complications and even death in this group of patients.     

On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices

Statistical and biochemical studies have revealed non-random patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations, since it is known that when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, using altered forms of the fitness functions used in the prior studies, we have optimized the parameters involved in the calculation of the error minimizing property of the genetic code so that the genetic code outscores the random codes as much as possible. This work also compares two prominent matrices, the Mutation Matrix and Point Accepted Mutations 74-100 (PAM(74-100)). It has been resulted that the hypothetical properties of the coevolution theory of the genetic code are already considered in PAM(74-100), giving more evidence on the existence of bias towards the genetic code in this matrix. Furthermore, our results indicate that PAM(74-100) is biased towards the single base mistranslation occurrences in second codon position as well as the frequency of amino acids. Thus PAM(74-100) is not a suitable substitution matrix for the studies conducted on the evolution of the genetic code.     

Population genetic approaches to neurological disease: Parkinson's disease as an example

Parkinson's disease (PD) is a common, progressive, incurable disabling condition. The cause is unknown but over the past few years tremendous progress in our understanding of the genetic bases of this condition has been made. To date, this has almost exclusively come from the study of relatively rare Mendelian forms of the disease and there are no currently, widely accepted common variants known to increase susceptibility.The role that the "Mendelian" genes play in common sporadic forms of PD is unknown. Moreover, most studies in PD can really be described as candidate polymorphism studies rather than true and complete assessments of the genes themselves. We provide a model of how one might tackle some of these issues using Parkinson's disease as an illustration. One of the emerging hypotheses of gene environment interaction in Parkinson's disease is based on drug metabolizing (or xenobiotic) enzymes and their interaction with putative environmental toxins. This motivated us to describe a tagging approach for an extensive but not exhaustive list of 55 drug metabolizing enzyme genes. We use these data to illustrate the power, and some of the limitations of a haplotype tagging approach. We show that haplotype tagging is extremely efficient and works well with only a modest increase in effort through different populations. The tagging approach works much less well if the minor allele frequency is below 5%. However, it will now be possible using these tags to evaluate these genes comprehensively in PD and other neurodegenerative conditions.     

Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.     

Seoul Virus-Infected Rat Lung Endothelial Cells and Alveolar Macrophages Differ in Their Ability To Support Virus Replication and Induce Regulatory T Cell Phenotypes

Hantaviruses cause a persistent infection in reservoir hosts that is attributed to the upregulation of regulatory responses and downregulation of proinflammatory responses. To determine whether rat alveolar macrophages (AMs) and lung microvascular endothelial cells (LMVECs) support Seoul virus (SEOV) replication and contribute to the induction of an environment that polarizes CD4⁺ T cell differentiation toward a regulatory T (Treg) cell phenotype, cultured primary rat AMs and LMVECs were mock infected or infected with SEOV and analyzed for viral replication, cytokine and chemokine responses, and expression of cell surface markers that are related to T cell activation. Allogeneic CD4⁺ T cells were cocultured with SEOV-infected or mock-infected AMs or LMVECs and analyzed for helper T cell (i.e., Treg, Th17, Th1, and Th2) marker expression and Treg cell frequency. SEOV RNA and infectious particles in culture media were detected in both cell types, but at higher levels in LMVECs than in AMs postinfection. Expression of Ifnβ, Ccl5, and Cxcl10 and surface major histocompatibility complex class II (MHC-II) and MHC-I was not altered by SEOV infection in either cell type. SEOV infection significantly increased Tgfβ mRNA in AMs and the amount of programmed cell death 1 ligand 1 (PD-L1) in LMVECs. SEOV-infected LMVECs, but not AMs, induced a significant increase in Foxp3 expression and Treg cell frequency in allogeneic CD4⁺ T cells, which was virus replication and cell contact dependent. These data suggest that in addition to supporting viral replication, AMs and LMVECs play distinct roles in hantavirus persistence by creating a regulatory environment through increased Tgfβ, PD-L1, and Treg cell activity.     

Bio-effects and safety of low-intensity, low-frequency ultrasonic exposure

Low-frequency (LF) ultrasound (20-100 kHz) has a diverse set of industrial and medical applications. In fact, high power industrial applications of ultrasound mainly occupy this frequency range. This range is also used for various therapeutic medical applications including sonophoresis (ultrasonic transdermal drug delivery), dentistry, eye surgery, body contouring, the breaking of kidney stones and eliminating blood clots. While emerging LF applications such as ultrasonic drug delivery continue to be developed and undergo translation for human use, significant gaps exist in the coverage of safety standards for this frequency range. Accordingly, the need to understand the biological effects of LF ultrasound is becoming more important. This paper presents a broad overview of bio-effects and safety of LF ultrasound as an aid to minimize and control the risk of these effects. Its particular focus is at low intensities where bio-effects are initially observed. To generate a clear perspective of hazards in LF exposure, the mechanisms of bio-effects and the main differences in action at low and high frequencies are investigated and a survey of harmful effects of LF ultrasound at low intensities is presented. Mechanical and thermal indices are widely used in high frequency diagnostic applications as a means of indicating safety of ultrasonic exposure. The direct application of these indices at low frequencies needs careful investigation. In this work, using numerical simulations based on the mathematical and physical rationale behind the indices at high frequencies, it is observed that while thermal index (TI) can be used directly in the LF range, mechanical index (MI) seems to become less reliable at lower frequencies. Accordingly, an improved formulation for the MI is proposed for frequencies below 500 kHz.