Particle‐attached microorganism oxidation of ammonia in a hypereutrophic urban river

To elucidate the importance and mechanisms of particle‐attached microorganisms on ammonia oxidation, we conducted a controlled simulation experiment with samples collected from the Shunao River, an ammonia‐rich hypereutrophic urban river in eastern China. The effects of particle concentration, ammonia concentration, organic carbon source and concentration, dissolved oxygen concentration, and pH were investigated on ammonia transformation rate (ammonia removal rate and NO₂^? + NO₃^? accumulation rate) and abundance of particle‐attached ammonia‐oxidizing bacteria (AOB) and archaea (AOA). All these factors significantly influenced ammonia transformation rates. Our results provided direct evidence that microorganisms attached on riverine suspended particles were associated with ammonia oxidation. Sequencing revealed that the AOA genus Nitrososphaera, and the AOB genus Nitrosomonas were the most dominant in particle‐attached ammonia‐oxidizing microbial communities. Further analysis showed that AOB communities had higher species richness and diversity compared with AOA communities. Additionally, AOB amoA genes were ~10–100 times more abundant than AOA amoA genes, and AOB abundance was more strongly correlated with ammonia transformation rates than AOA abundance in most experiments, indicating that particle‐attached AOB were more important than AOA in the hypereutrophic urban river. This study adds to our knowledge of particle‐attached microorganism oxidation of ammonia.     

A subgroup of spinocerebellar ataxias defective in DNA damage responses

A subgroup of human autosomal recessive ataxias is also characterized by disturbances of eye movement or oculomotor apraxia. These include ataxia telangiectasia (A-T); ataxia telangiectasia like disorder (ATLD); ataxia oculomotor apraxia type 1 (AOA1) and ataxia oculomotor apraxia type 2 (AOA2). What appears to be emerging is that all of these have in common some form of defect in DNA damage response which could account for the neurodegenerative changes seen in these disorders. We describe here sensitivity to DNA damaging agents in AOA1 and evidence that these cells have a defect in single strand break repair. Comparison is made with what appears to be a novel form of AOA (AOA3) which also shows sensitivity to agents that lead to single strand breaks in DNA as well as a reduced capacity to repair these breaks. AOA3 cells are defective in the DNA damage-induced p53 response. This defect can be overcome by incubation with the mdm2 antagonists, nutlins, but combined treatment with nutlins and DNA damage does not enhance the response. We also show that AOA3 cells are deficient in p73 activation after DNA damage. These data provide further evidence that different forms of AOA have in common a reduced capacity to cope with damage to DNA, which may account for the neurodegeneration observed in these syndromes.     

Justice and rule of law failure in Haiti: A view from the Shanties

Since 1995, significant investments have been made in justice reform initiatives in Haiti. The results, however, have been meager. Drawing upon data from a longitudinal study conducted in Cité Soleil between 2008 and 2011, this article illuminates the short-sightedness of top-down reforms that fail to meet the demands of the population, leaving them to fend for themselves. In the absence of a viable justice system Cité Soleil residents have resorted to alternative, and at times pathological, measures to exact some level of “justice”. In this article, we contend that an empirically grounded base of knowledge of the demand side of justice and the promotion of trust-building strategies that engage the active participation of citizens in the country are necessary to enact and sustain justice and rule of law reform. Such an approach will create a venue to channel civil society's demands, build political will and facilitate coordination between stakeholders and Haitian society for self-sustained rule of law institutions and long-term peace building in Haiti.     

Ataxia-ocular motor apraxia syndrome: an investigation of cellular radiosensitivity of patients and their families.

Although ataxia-ocular motor apraxia (AOA) has been described as a disease entity mimicking ataxia telangiectasia (AT), no radiobiological studies have been carried out on cells from patients with AOA to find their possible relationship to AT. In the present study, cultured fibroblasts from three patients with AOA and their asymptomatic relatives (parents and sibs) were, therefore, compared with those from a classical AT homozygote, an AT heterozygote, and four healthy subjects for cell survival after acute and chronic irradiation. While a moderately increased cellular sensitivity (compared to normal) was observed in two AOA patients and most of their relatives, the degree of their radiosensitivity was quite different from that of the AT homozygote after both acute and chronic irradiation. One AOA patient exhibited increased cellular sensitivity similar to that of a classical AT homozygote up to 4% survival level after chronic irradiation but not after acute irradiation. A comparison of peripheral blood lymphocytes from two AOA patients, an AT homozygote, and two normal controls for spontaneous and (acute) radiation induced chromosomal breaks also failed to show any similarity between AOA and AT. These data support the notion that AOA is different from classical AT, and may represent a distinct disease entity controlled by specific gene(s), or compound heterozygotes involving different AT genes promoting the manifestation of AOA characteristics.     

Donor‐specific tolerance induction in organ transplantation via mixed splenocytes chimerism

We have shown previously that donor‐derived splenocytes can replace recipients' bone marrow and induce donor‐specific tolerance (DST). We have also shown the usefulness of the chimeric state for the induction of DST. Further analysis of mixed splenocytes chimera, especially the role of each T cells in mixed splenocytes chimera, is indispensable issue for its clinical use. A chimeric state has been shown to achieve long‐term survival in major histocompatibility complex (MHC)‐mismatched grafts. The donor‐derived splenocytes can replace recipients' bone marrow and induce DST. The long‐term survival of allogeneic skin grafts was achieved without immunosuppressants. In this study we show the role of each T cell type in a splenocyte mixed chimera. This review provides a short summary of our original work, adding some supplemental interpretations. Mixed chimerism is thus considered an attractive approach for the induction of DST without the use of immunosuppressants. In this paper, we summarize some of the findings on mixed splenocyte chimeras and review mixed chimerism in recent organ transplantation.     

Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems

Thaumarchaeota have been recognized as the main drivers of aerobic ammonia oxidation in many ecosystems. However, little is known about the role of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in lacustrine ecosystems. In this study, the photic zone of three contrasted freshwater ecosystems located in France was sampled during two periods: winter homothermy (H) and summer thermal stratification (TS), to investigate the distribution of planktonic AOA and AOB. We showed that AOB were predominant in nutrient-rich ecosystems, whereas AOA dominated when ammonia concentrations were the lowest and during winter, which could provide a favorable environment for their growth. Moreover, analyses of archaeal libraries revealed the ubiquity of the thaumarchaeal I.1a clade associated with higher diversity of AOA in the most nutrient-poor lake. More generally, this work assesses the presence of AOA in lakes, but also highlights the existence of clades typically associated with lacustrine and hot spring ecosystems and specific ecological niches occupied by these microorganisms.     

Modeling startle eyeblink electromyogram to assess fear learning

Pavlovian fear conditioning is widely used as a laboratory model of associative learning in human and nonhuman species. In this model, an organism is trained to predict an aversive unconditioned stimulus from initially neutral events (conditioned stimuli, CS). In humans, fear memory is typically measured via conditioned autonomic responses or fear‐potentiated startle. For the latter, various analysis approaches have been developed, but a systematic comparison of competing methodologies is lacking. Here, we investigate the suitability of a model‐based approach to startle eyeblink analysis for assessment of fear memory, and compare this to extant analysis strategies. First, we build a psychophysiological model (PsPM) on a generic startle response. Then, we optimize and validate this PsPM on three independent fear‐conditioning data sets. We demonstrate that our model can robustly distinguish aversive (CS+) from nonaversive stimuli (CS‐, i.e., has high predictive validity). Importantly, our model‐based approach captures fear‐potentiated startle during fear retention as well as fear acquisition. Our results establish a PsPM‐based approach to assessment of fear‐potentiated startle, and qualify previous peak‐scoring methods. Our proposed model represents a generic startle response and can potentially be used beyond fear conditioning, for example, to quantify affective startle modulation or prepulse inhibition of the acoustic startle response.     

Analysis of Secondary Phenotype Involving the Interactive Effect of the Secondary Phenotype and Genetic Variants on the Primary Disease

A genome‐wide association (GWA) study is usually designed as a case‐control study, where the presence and absence of the primary disease define the cases and controls, respectively. Using the existing data from GWA studies, investigators are also trying to identify the association between genetic variants and secondary phenotypes, which are defined as traits associated with the primary disease. However, recent studies have shown that bias arises in the estimation of marker‐secondary phenotype association using originally collected data. We recently proposed a bias correction approach to accurately estimate the odds ratio (OR) for marker‐secondary phenotype association. In this communication, we further investigated whether our bias correction approach is robust for a scenario involving the interactive effect of the secondary phenotype and genetic variants on the primary disease. We found that in such a scenario, our bias correction approach also provides an accurate estimation of OR for marker‐secondary phenotype association. We investigated accuracy of our approach using simulation studies and showed that the approach better controlled for type I errors than the existing approaches. We also applied our bias correction approach to the real data analysis of association between an N‐acetyltransferase gene, NAT2, and smoking on the basis of colorectal adenoma data.     

Permutation and Parametric Bootstrap Tests for Gene–Gene and Gene–Environment Interactions

Permutation tests are widely used in genomic research as a straightforward way to obtain reliable statistical inference without making strong distributional assumptions. However, in this paper we show that in genetic association studies it is not typically possible to construct exact permutation tests of gene‐gene or gene‐environment interaction hypotheses. We describe an alternative to the permutation approach in testing for interaction, a parametric bootstrap approach. Using simulations, we compare the finite‐sample properties of a few often‐used permutation tests and the parametric bootstrap. We consider interactions of an exposure with single and multiple polymorphisms. Finally, we address when permutation tests of interaction will be approximately valid in large samples for specific test statistics.     

A high‐content drug screening strategy to identify protein level modulators for genetic diseases: A proof‐of‐principle in autosomal dominant leukodystrophy

In genetic diseases, the most prevalent mechanism of pathogenicity is an altered expression of dosage‐sensitive genes. Drugs that restore physiological levels of these genes should be effective in treating the associated conditions. We developed a screening strategy, based on a bicistronic dual‐reporter vector, for identifying compounds that modulate protein levels, and used it in a pharmacological screening approach. To provide a proof‐of‐principle, we chose autosomal dominant leukodystrophy (ADLD), an ultra‐rare adult‐onset neurodegenerative disorder caused by lamin B1 (LMNB1) overexpression. We used a stable Chinese hamster ovary (CHO) cell line that simultaneously expresses an AcGFP reporter fused to LMNB1 and a Ds‐Red normalizer. Using high‐content imaging analysis, we screened a library of 717 biologically active compounds and approved drugs, and identified alvespimycin, an HSP90 inhibitor, as a positive hit. We confirmed that alvespimycin can reduce LMNB1 levels by 30%–80% in five different cell lines (fibroblasts, NIH3T3, CHO, COS‐7, and rat primary glial cells). In ADLD fibroblasts, alvespimycin reduced cytoplasmic LMNB1 by about 50%. We propose this approach for effectively identifying potential drugs for treating genetic diseases associated with deletions/duplications and paving the way toward Phase II clinical trials.     

Haplotype Misclassification Resulting from Statistical Reconstruction and Genotype Error,and Its Impact on Association Estimates

Haplotypes are an important concept for genetic association studies, but involve uncertainty due to statistical reconstruction from single nucleotide polymorphism (SNP) genotypes and genotype error. We developed a re‐sampling approach to quantify haplotype misclassification probabilities and implemented the MC‐SIMEX approach to tackle this as a 3 × 3 misclassification problem. Using a previously published approach as a benchmark for comparison, we evaluated the performance of our approach by simulations and exemplified it on real data from 15 SNPs of the APM1 gene. Misclassification due to reconstruction error was small for most, but notable for some, especially rarer haplotypes. Genotype error added misclassification to all haplotypes resulting in a non‐negligible drop in sensitivity. In our real data example, the bias of association estimates due to reconstruction error alone reached ?48.2% for a 1% genotype error, indicating that haplotype misclassification should not be ignored if high genotype error can be expected. Our 3 × 3 misclassification view of haplotype error adds a novel perspective to currently used methods based on genotype intensities and expected number of haplotype copies. Our findings give a sense of the impact of haplotype error under realistic scenarios and underscore the importance of high‐quality genotyping, in which case the bias in haplotype association estimates is negligible.     

A missense mutation in PIK3R5 gene in a family with ataxia and oculomotor apraxia

Autosomal recessive ataxias are heterogeneous group of disorders characterized by cerebellar atrophy and peripheral sensorimotor neuropathy. Molecular characterization of this group of disorders identified a number of genes contributing to these overlapping phenotypes. Ataxia with oculomotor apraxia type 2 (AOA2) is an autosomal recessive form of ataxia caused by mutations in the SETX gene. We report on a consanguineous family with autosomal recessive inheritance and clinical characteristics of AOA2, and no mutations in the SETX gene. We mapped the AOA locus in this family to chromosome 17p12-p13. Sequencing of all genes in the refined region identified a homozygous missense mutation in PIK3R5 that was absent in 477 normal controls. Our characterization of the PIK3R5 protein and findings suggest that it may play a role in the development of the cerebellum and vermis.     

A novel nonsense mutation in the APTX gene associated with delayed DNA single-strand break removal fails to enhance sensitivity to different genotoxic agents

APTX is the gene involved in ataxia with oculomotor apraxia type 1 (AOA1), a recessive disorder with early-onset cerebellar ataxia, oculomotor apraxia and peripheral neuropathy. The encoded protein, aprataxin, is a DNA repair protein processing the products of abortive ligations, 5'-adenylated DNA. We describe a novel nonsense mutation in APTX, c.892C>T (p.Gln298X), segregating in two AOA1 patients and leading to the loss of aprataxin protein in patient's cells. These cells, while exhibiting reduced catalase activity, are not hypersensitive to toxicity elicited by H(2)O(2) exposure at either physiologic or ice-bath temperature. On the other hand, the rate of repair of DNA single-strand-breaks (SSBs) induced in both conditions is always significantly slower in AOA1 cells. By using the alkylating agent methyl methane sulphonate (MMS) we confirmed the association of the APTX mutation with a DNA repair defect in the absence of detectable changes in susceptibility to toxicity. These results, while consistent with a role of aprataxin in the repair of SSBs induced by H(2)O(2), or MMS, demonstrate that other mechanisms may be recruited in AOA1 cells to complete the repair process, although at a slower rate. Lack of hypersensitivity to the oxidant, or MMS, also implies that delayed repair is not per se a lethal event.     

Experiences of oppression,liberation, and well‐being among Moroccans in Andalusia

This qualitative study explores the settlement experiences of Moroccan migrants living in Andalusia (southern Spain). Taking a liberation psychology approach, we focus on the roles that power relations, oppression, well‐being, and liberation play in the newcomers’ adaptation to the host country from a sociopolitical point of view. Based on grounded theory, we analyze the narratives of 28 Moroccan migrants across two different contexts within Andalusia; 15 participated in in‐depth interviews and 13 in 2 separate focus groups. A series of theoretical propositions emerged from the analysis, taking into account (a) conditions of oppression, (b) responses to conditions of oppression, and (c) the well‐being continuum. These interrelated dimensions were found to shape different migration trajectories, leading to either maintaining the unjust living conditions or choosing to confront them. In the latter case, migrants actively engaged in transformative civic actions promoting social justice and symmetrical power relations between the migrant and native‐born populations. The main contribution of this study is to value migrants by defining their migratory experiences and how, in their view, the liberation process is achieved.     

Leukocyte-modulating and antioxidant activity of blood serum and bronchoalveolar lavage fluid in the course of the decompression period of long crush syndrome

We studied leukocyte-modulating activity (LMA) and antioxidant activity (AOA) of blood serum and bronchoalveolar lavage fluid (BAL) in the course of a postcompression period of crush syndrome (CS) in rats. CS was modelled by compression of the left back leg of the animal with metal vice (compression area 5 cm2, duration 4 hours). In CS decompression, LMA of both the serum and BAL was high. On decompression day 1 there was a compensatory growth of serum and BAL AOA, its fall on day 3 and 7 and recovery by day 21. Calculation of the coefficient of LMA to AOA shows imbalance between pro- and antioxidant systems with development of oxidant stress. Thus, prevalence of blood and lung LMA over AOA on intermediate stages of CS may cause stimulation of destruction in hepatic and pulmonary tissues with development of inflammatory reaction.     

Novel PNKP mutation in siblings with ataxia-oculomotor apraxia type 4

The phenotypic and genetic spectrum of ataxia with oculomotor apraxia (AOA) disorders is rapidly evolving and new technologies such as genetic mapping using whole exome sequencing reveal subtle distinctions among the various subtypes. We report a novel PNKP mutation in two siblings with progressive ataxia, abnormal saccades, sensorimotor neuropathy and dystonia consistent with the AOA type 4 phenotype. Laboratory evaluation revealed hypoalbuminemia, hypercholesterolemia with elevated LDL, elevated IgE levels and normal α fetoprotein levels. Eye movement examination demonstrated a marked saccade initiation defect with profound hypometric horizontal saccades. Vertical saccades were also affected but less so. Also present were conspicuous thrusting head movements when attempting to change gaze, but rather than an apraxia these were an adaptive strategy to take advantage of an intact vestibulo-ocular reflex to carry the eyes to a new target of interest. This is demonstrated in accompanying videos.     

Ancient and Recent Adaptive Evolution in the Antiviral TRIM22 Gene: Identification of a Single‐Nucleotide Polymorphism That Impacts TRIM22 Function

Tripartite motif protein 22 (TRIM22) is a novel interferon‐induced protein that potently inhibits the replication of evolutionarily diverse viruses, including HIV‐1. Altered TRIM22 expression is also associated with diseases, such as multiple sclerosis, cancer, and autoimmunity. The factors that influence TRIM22 expression and antiviral activity are largely unknown. In this study, we adopted an evolution‐guided functional approach to identify potential genetic determinants of TRIM22 function. Evolutionary analysis of TRIM22 from mammals spanning >100 million years demonstrated that TRIM22 evolution has been shaped by ancient and variable positive selection. We showed that positive selection is operating on multiple TRIM22 residues that cluster in putative functional regions and that some are predicted to be functionally damaging. Interestingly, the second most prevalent TRIM22 SNP in humans (rs1063303) is located at one of these positively selected sites. We showed that the frequency of rs1063303:G>C varies up to 10‐fold between ethnicities and that in some ethnicities SNP rs1063303:G>C is being actively maintained in the population. The SNP rs1063303:G>C variant also had an inverse functional impact where it increased TRIM22 expression and decreased the antiviral activity of TRIM22. Taken together, our data characterize the extensive genetic variation in TRIM22 and identify rs1063303:G>C as a highly prevalent SNP that influences its function.     

HDR‐del: A tool based on Hamming distance for prioritizing pathogenic chromosomal deletions in exome sequencing

High‐density oligonucleotide arrays have widely been used to detect pathogenic chromosomal deletions. In addition to high‐density oligonucleotide arrays, programs using whole‐exome sequencing have become available for estimating copy‐number variations using depth of coverage. Here, we propose a new statistical method, HDR‐del, to prioritize pathogenic chromosomal deletions based on Hamming distance in exome sequencing. In vcf (variant call format) files generated from exome sequencing, hemizygous chromosomal deletion regions lack heterozygous variants and lead to apparent long runs of homozygosity (ROH). In our Hamming distance ratio (HDR)‐del approach, we calculate the “difference” in heterozygous status between an affected individual and control individuals using the HDR over all candidate chromosomal deletion regions defined as ROH longer than 1Mbp. Using a suitable test statistic, which is expected to be large for a true pathogenic deletion region, we prioritize candidate chromosomal deletion regions based on this statistic. In our approach, we were able to considerably narrow down true pathogenic chromosomal deletion regions, which were confirmed by high‐density oligonucleotide arrays in four mitochondrial disease patients. Our HDR‐del approach represents an easy method for detecting chromosomal deletions.     

Aberrant spindle structures responsible for recurrent human metaphase I oocyte arrest with attempts to induce meiosis artificially

BACKGROUND In some couples, not all retrieved oocytes mature, even after prolonged in vitro culture. The underlying mechanisms are not known, although ionophore treatment may alleviate metaphase I (MI) arrest in some mouse strains. We attempted to induce first polar body (PB) extrusion and fertilization using assisted oocyte activation (AOA) after ICSI in maturation-resistant human MI oocytes. METHODS Four ICSI patients are described in this retrospective study. A pilot study tested the calcium ionophore ionomycin (10 μM) on donated MI oocytes from patients with a normal number of metaphase II (MII) oocytes. Subsequently, ionomycin was used to induce first PB extrusion in two patients showing maturation-resistant MI oocytes. AOA, by calcium injection and ionomycin exposure, was applied when mature oocytes were available. Oocytes were analysed by polarized microscopy and immunostaining. RESULTS Ionomycin induced the first PB extrusion in MI oocytes from patients with a normal number of retrieved MII oocytes, while extended in vitro culture failed to achieve the MII stage. Similarly, ionomycin induced first PB extrusion in one of two patients with recurrent maturation-resistant MI oocytes. Use of ICSI combined with AOA on MII oocytes matured in vitro or in vivo resulted in failed or abnormal fertilization with no further embryo cleavage potential. Highly abnormal spindle and chromosome configurations were observed in MI maturation-resistant oocytes, in contrast to control MI oocytes. CONCLUSIONS Ionophore induced first PB extrusion in MI oocytes from patients without maturation arrest but to a lower extent in maturation-resistant MI oocytes. Immunofluorescence staining and confocal analysis revealed, for the first time, highly abnormal spindle/chromosomal structures that may be responsible for this maturation arrest.