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Depth profile techniques for U--Pb geochronology and rare earth element (REE) geochemistry were conducted on unpolished, Archean zircon with metasomatic rims from metasedimentary rocks within the Horseshoe Lake greenstone belt, western Superior Province, Canada. These zircon crystals are shown to have isotopically distinct rims (typically 100 million years younger than the cores. The [.sup.207]Pb/[.sup.206]Pb rim ages can be temporally correlated with regional magmatism and with a later, potentially Au-bearing, hydrothermal event synchronous with greenschist-facies metamorphism and regional deformation. Notably, the zircons do not record evidence of local ca. 2741-2715 Ma magmatism manifested by the emplacement of a quartz--feldspar porphyry dike swarm. Laser ablation--inductively coupled plasma--mass spectrometry (LA--ICP--MS) REE depth profile analyses on the same unpolished zircon show that the rims are commonly characterized by low Th/U ratios, elevated Hf, and variable REE concentrations in comparison with the interior of the grains. The variations in rim and core chemistry suggest that these elements, along with common Pb, were mobilized by fluids and interacted with zircon in the metasediments, resulting in the production of the metasomatic rims. In summary, this paper shows that depth profiling techniques applied to unpolished zircon can be useful to elucidate the tectonic, and potentially metallogenic, history of a complex Archean terrane. Des méthodes d'analyse des profils de concentrations en fonction de la profondeur pour la géochronologie U--Pb et la géochimie des terres rares ont été utilisées sur des zircons archéens non polis à bordures métasomatiques provenant de roches métasédimentaires de la ceinture de roches vertes de Horseshoe Lake de la partie ouest de la province du Supérieur (Canada). Il est démontré que ces cristaux de zircon ont des bordures (épaisseur typique 100 millions d'années plus jeunes que les coeurs. Les âges [.sup.207]Pb/[.sup.206]Pb de bordures peuvent être corrélés dans le temps à un magmatisme régional et un subséquent événement hydrothermal possiblement aurifère synchrone d'un métamorphisme au faciès des schistes verts et d'une déformation régionale. Les zircons ne présentent notamment aucun indice du magmatisme local vers 2741-2715 Ma dont témoigne la mise en place d'un essaim de dykes de porphyre quartzofeldspathique. Des analyses de profils de concentrations des terres rares par spectrométrie de masse avec plasma à couplage inductif jumelé à l'ablation par laser (LA--ICP--MS) sur les mêmes zircons non polis montrent que les bordures sont souvent caractérisées par des rapports Th/U faibles, des concentrations élevées de Hf et des concentrations de terres rares variables par rapport à l'intérieur des grains. Les variations de la chimie des bordures et des coeurs donnent à penser que ces éléments, ainsi que le plomb élémentaire, ont été mobilisés par des fluides et ont interagi avec les zircons dans les métasédiments, produisant ainsi les bordures métasomatiques. L'article démontre que les méthodes d'analyse des profils de concentration en fonction de la profondeur appliquées a des zircons non polis peuvent être utiles pour élucider l'évolution tectonique et possiblement métallogénique d'un terrane archéen complexe. [Traduit par la Rédaction], Introduction Despite 30 years of mineral exploration and several provincial survey publications outlining the local stratigraphy of the Horseshoe Lake greenstone belt (HLGB; Carruthers 1961; Jensen 1987, 1989; Talbot 1996), [...]

De nombreux pays, à travers le monde, investissent des moyens colossaux pour prendre part aux compétions internationales du football en vue de remporter le trophée et la République Démocratique du Congo n’en fait pas exception. Fort malheureusement, pour ce dernier pays, les résultats demeurent mitigés depuis de longues années. Eu égard à ce qui précède, la présente étude préconise la suspension de la participation de la RDC pour une durée de deux ans aux compétitions africaines et internationales en vue de mieux se réorganiser à l’interne en mettant, sur pied, une politique claire et précise pour un nouvel élan.

L’Administration Publique en République Démocratique du Congo suscite des commentaires les plus divers. Le constat général traduit par des propos stéréotypés est que rien ne va. Le malaise observé au sein de cette Administration Publique ne date pas de nos jours, mais plutôt de plusieurs décennies derrière nous. Il remonte bien évidemment à l’époque coloniale. En vue d’une Administration Publique de développement en République Démocratique du Congo, plusieurs réformes ont été initiées, mais sans résultats optimaux. La mise en place des structures standards au sein de l’Administration Publique congolaise qui présente un caractère innovant et prometteur ne peut être une stratégie de réussite que si et seulement si certains préalables sont respectés notamment : le respect rigoureux des textes à la matière, le recrutement objectif des animateurs qui ne sera pas seulement réservé aux seuls fonctionnaires de l’Etat mais aussi aux énarques (ENA) ; et l’accompagnement tous azimuts pour une retraite paisible des fonctionnaires de l’Etat.

Melanoma is a highly immunogenic malignancy with an elevated mutational burden, diffuse lymphocytic infiltration, and one of the highest response rates to immune checkpoint inhibitors (ICIs). However, over half of all late-stage patients treated with ICIs will either not respond or develop progressive disease. Spatial imaging technologies are being increasingly used to study the melanoma tumor microenvironment (TME). The goal of such studies is to understand the complex interplay between the stroma, melanoma cells, and immune cell-types as well as their association with treatment response. Investigators seeking a better understanding of the role of cell location within the TME and the importance of spatial expression of biomarkers are increasingly turning to highly multiplexed imaging approaches to more accurately measure immune infiltration as well as to quantify receptor-ligand interactions (such as PD-1 and PD-L1) and cell-cell contacts. CyTOF-IMC (Cytometry by Time of Flight - Imaging Mass Cytometry) has enabled high-dimensional profiling of melanomas, allowing researchers to identify complex cellular subpopulations and immune cell interactions with unprecedented resolution. Other spatial imaging technologies, such as multiplexed immunofluorescence and spatial transcriptomics, have revealed distinct patterns of immune cell infiltration, highlighting the importance of spatial relationships, and their impact in modulating immunotherapy responses. Overall, spatial imaging technologies are just beginning to transform our understanding of melanoma biology, providing new avenues for biomarker discovery and therapeutic development. These technologies hold great promise for advancing personalized medicine to improve patient outcomes in melanoma and other solid malignancies., (© 2023. The Author(s).)

Dimethandrolone undecanoate (DMAU), an oral investigational male hormonal contraceptive, is a prodrug that is rapidly converted to its active metabolite, dimethandrolone (DMA). Poor and variable oral bioavailability of DMA after DMAU dosing is a critical challenge to develop it as an oral drug. The objective of our study was to elucidate the mechanisms of variable pharmacokinetics of DMA. We first identified DMA metabolites formed in vitro and in vivo in human hepatocyte incubation and serum samples following oral DMAU administration in men, respectively. The metabolite identification study revealed two metabolites, DMA-glucuronide (DMA-G; major) and the androstenedione analog of DMA (minor), in the hepatocyte incubations. After oral DMAU administration, only DMA-G was detected in serum, which was >100-fold compared with DMA levels, supporting glucuronidation as the major elimination mechanism for DMA. Next, 13 clinically relevant UDP-glucuronosyltransferase (UGT) enzymes were tested for their involvement in DMA-G formation, which revealed a major role of UDP-glucuronosyltransferase 2B17 (UGT2B17) isoform with a smaller contribution of UGT1A9 in DMA-G formation. These data were confirmed by dramatically higher DMA glucuronidation rates (>200- and sevenfold) in the high versus the null UGT2B17-expressing human intestinal and liver microsomes, respectively. Since human UGT2B17 is a highly variable enzyme with a 20%-80% gene deletion frequency, the in vitro data suggest a major role of UGT2B17 polymorphism on the first-pass metabolism of DMA. Further, considering DMA is a selective and sensitive UGT2B17 substrate, it could be used as a clinical probe of UGT2B17 activity. SIGNIFICANCE STATEMENT: Dimethandrolone (DMA) is an active metabolite of dimethandrolone undecanoate (DMAU), an investigational male hormonal contraceptive. Previous studies have indicated poor and inconsistent bioavailability of DMAU following oral administration. This study found that UDP-glucuronosyltransferase 2B17-mediated high intestinal first-pass metabolism is the key mechanism of variable DMA bioavailability., (U.S. Government Work not Protected by U.S. Copyright.)

Although combination BRAF/MEK inhibition has produced significant survival benefits for BRAF p.V600 mutant melanomas, targeted therapies approved for BRAF non-p.V600 mutant melanomas remain limited. Through the analysis of 772 cutaneous melanoma exomes, we reveal that BRAF non-p.V600 mutations co-occurs more frequently with NF1 loss, but not with oncogenic NRAS mutations, than expected by chance. We present cell signaling data, which demonstrate that BRAF non-p.V600 mutants can signal as monomers and dimers within an NF1 loss context. Concordantly, BRAF inhibitors that inhibit both monomeric and dimeric BRAF synergize with MEK inhibition to significantly reduce cell viability in vitro and tumor growth in vivo in BRAF non-p.V600 mutant melanomas with co-occurring NF1 loss-of-function mutations. Our data suggest that patients harboring BRAF non-p.V600 mutant melanomas may benefit from current FDA-approved BRAF/MEK inhibitor combination therapy currently reserved for BRAF p.V600 mutant patients., Competing Interests: Declaration of interests I.R.W. reports grants from Canadian Institutes of Health Research (grant #PJT-152975), the Melanoma Research Alliance (grant #412429), and the Canada Research Chairs Program. I.R.W. also reports collaboration with KEW, Inc. outside the submitted work. T.P. has received funding from Novartis and Roche and has also received honoraria from and has been on advisory boards for Novartis, BMS, Merck, Sunpharma, Sanofi, and Pfizer., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Melanoma is an immunogenic cancer with a high response rate to immune checkpoint inhibitors (ICIs). It harbors a high mutation burden compared with other cancers and, as a result, has abundant tumor-infiltrating lymphocytes (TILs) within its microenvironment. However, understanding the complex interplay between the stroma, tumor cells, and distinct TIL subsets remains a substantial challenge in immune oncology. To properly study this interplay, quantifying spatial relationships of multiple cell types within the tumor microenvironment is crucial. To address this, we used cytometry time-of-flight (CyTOF) imaging mass cytometry (IMC) to simultaneously quantify the expression of 35 protein markers, characterizing the microenvironment of 5 benign nevi and 67 melanomas. We profiled more than 220,000 individual cells to identify melanoma, lymphocyte subsets, macrophage/monocyte, and stromal cell populations, allowing for in-depth spatial quantification of the melanoma microenvironment. We found that within pretreatment melanomas, the abundance of proliferating antigen-experienced cytotoxic T cells (CD8 + CD45RO + Ki67 + ) and the proximity of antigen-experienced cytotoxic T cells to melanoma cells were associated with positive response to ICIs. Our study highlights the potential of multiplexed single-cell technology to quantify spatial cell-cell interactions within the tumor microenvironment to understand immune therapy responses.

Purpose: Next-generation sequencing studies and CRISPR-Cas9 screens have established mutations in the IFNγ-JAK-STAT pathway as an immune checkpoint inhibitor (ICI) resistance mechanism in a subset of patients with melanoma. We hypothesized ICI resistance mutations in the IFNγ pathway would simultaneously render melanomas susceptible to oncolytic virus (OV) therapy., Experimental Design: Cytotoxicity experiments were performed with a number of OVs on a matched melanoma cell line pair generated from a baseline biopsy and a progressing lesion with complete JAK2 loss from a patient that relapsed on anti-PD-1 therapy, in melanoma lines following JAK1/2 RNA interference (RNAi) and pharmacologic inhibition and in Jak2 knockout (KO) B16-F10 mouse melanomas. Furthermore, we estimated the frequency of genetic alterations in the IFNγ-JAK-STAT pathway in human melanomas., Results: The melanoma line from an anti-PD-1 progressing lesion was 7- and 22-fold more sensitive to the modified OVs, herpes simplex virus 1 (HSV1-dICP0) and vesicular stomatitis virus (VSV-Δ51), respectively, compared with the line from the baseline biopsy. RNAi, JAK1/2 inhibitor studies, and in vivo studies of Jak2 KOs B16-F10 melanomas revealed a significant increase in VSV-Δ51 sensitivity with JAK/STAT pathway inhibition. Our analysis of The Cancer Genome Atlas data estimated that approximately 11% of ICI-naïve cutaneous melanomas have alterations in IFNγ pathway genes that may confer OV susceptibility., Conclusions: We provide mechanistic support for the use of OVs as a precision medicine strategy for both salvage therapy in ICI-resistant and first-line treatment in melanomas with IFNγ-JAK-STAT pathway mutations. Our study also supports JAK inhibitor-OV combination therapy for treatment-naïve melanomas without IFN signaling defects. See related commentary by Kaufman, p. 3278 ., (©2021 American Association for Cancer Research.)

Background: The neutrophil-to-lymphocyte ratio (NLR) is a measure of systemic inflammation and a prognostic factor for multiple malignancies. This study assesses the value of the NLR as an independent prognostic marker in triple-negative breast cancer (TNBC) and explores the association between dynamic NLR changes and patient outcomes., Methods: The study retrospectively analyzed a prospectively maintained database including patients 18 to 80 years old with TNBC treated at the authors' institution between 2006 to 2016. Clinical and demographic data were collected, including blood test results and treatments received. Age at diagnosis, stage of disease, and NLR scores were tested for association with overall and disease-free survival in uni- and multivariate Cox models., Results: The inclusion criteria were met by 329 women with a median age of 58. Most of the patients had early-stage disease (30.1% with stage 1 and 47% with stage 2 malignancy). An NLR higher than 2.84 at diagnosis was associated with decreased overall survival (hazard ratio [HR], 1.8; 95% confidence interval [CI], 1.023-3.176), whereas an NLR higher than 7.82 at any time during the follow-up period was a strong predictor of 5-year mortality (HR, 10.76; 95% CI, 4.193-26.58), independent of age or stage of disease. Patients who experienced recurrence had a higher NLR than their counterparts during the 6 months before recurrence. The NLR also significantly rose during the final 18 months of life (p < 0.01)., Conclusion: The NLR is an important prognostic marker in TNBC, both at diagnosis and during the course of the disease. Moreover, dynamic changes in NLR strongly correlate with disease recurrence and the time of death.

The high background tumor mutation burden in cutaneous melanoma limits the ability to identify significantly mutated genes (SMGs) that drive this cancer. To address this, we performed a mutation significance study of over 1,000 melanoma exomes, combined with a multi-omic analysis of 470 cases from The Cancer Genome Atlas. We discovered several SMGs with co-occurring loss-of-heterozygosity and loss-of-function mutations, including PBRM1, PLXNC1 and PRKAR1A, which encodes a protein kinase A holoenzyme subunit. Deconvolution of bulk tumor transcriptomes into cancer, immune and stromal components revealed a melanoma-intrinsic oxidative phosphorylation signature associated with protein kinase A pathway alterations. We also identified SMGs on the X chromosome, including the RNA helicase DDX3X, whose loss-of-function mutations were exclusively observed in males. Finally, we found that tumor mutation burden and immune infiltration contain complementary information on survival of patients with melanoma. In summary, our multi-omic analysis provides insights into melanoma etiology and supports contribution of specific mutations to the sex bias observed in this cancer., (© 2020. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Background: The p66ShcA redox protein is the longest isoform of the Shc1 gene and is variably expressed in breast cancers. In response to a variety of stress stimuli, p66ShcA becomes phosphorylated on serine 36, which allows it to translocate from the cytoplasm to the mitochondria where it stimulates the formation of reactive oxygen species (ROS). Conflicting studies suggest both pro- and anti-tumorigenic functions for p66ShcA, which prompted us to examine the contribution of tumor cell-intrinsic functions of p66ShcA during breast cancer metastasis., Methods: We tested whether p66ShcA impacts the lung-metastatic ability of breast cancer cells. Breast cancer cells characteristic of the ErbB2+/luminal (NIC) or basal (4T1) subtypes were engineered to overexpress p66ShcA. In addition, lung-metastatic 4T1 variants (4T1-537) were engineered to lack endogenous p66ShcA via Crispr/Cas9 genomic editing. p66ShcA null cells were then reconstituted with wild-type p66ShcA or a mutant (S36A) that cannot translocate to the mitochondria, thereby lacking the ability to stimulate mitochondrial-dependent ROS production. These cells were tested for their ability to form spontaneous metastases from the primary site or seed and colonize the lung in experimental (tail vein) metastasis assays. These cells were further characterized with respect to their migration rates, focal adhesion dynamics, and resistance to anoikis in vitro. Finally, their ability to survive in circulation and seed the lungs of mice was assessed in vivo., Results: We show that p66ShcA increases the lung-metastatic potential of breast cancer cells by augmenting their ability to navigate each stage of the metastatic cascade. A non-phosphorylatable p66ShcA-S36A mutant, which cannot translocate to the mitochondria, still potentiated breast cancer cell migration, lung colonization, and growth of secondary lung metastases. However, breast cancer cell survival in the circulation uniquely required an intact p66ShcA S36 phosphorylation site., Conclusion: This study provides the first evidence that both mitochondrial and non-mitochondrial p66ShcA pools collaborate in breast cancer cells to promote their maximal metastatic fitness.

Pilocytic astrocytoma (PA) is emerging as a tumor entity with dysregulated RAS/RAF/MEK/ERK signaling. In this study, we report the identification of a novel recurrent BRAF insertion (p.V504&#95;R506dup) in five PA cases harboring exclusively this somatic tandem duplication. This recurrent alteration leads to an addition of three amino acids in the kinase domain of BRAF and has functional impact on activating MAPK phosphorylation. Importantly, we show that this mutation confers resistance to RAF inhibitors without changing effectiveness while downstream MEK inhibitors remain effective. Our results further emphasize the importance of BRAF alterations in PA and the need to characterize them in a given tumor as this can affect therapeutic strategies and their potential use as tumor marker in molecular diagnostics.

Competing Interests: Competing interests. The authors declare no competing interests

Purpose: Dual MAPK pathway inhibition (dMAPKi) with BRAF and MEK inhibitors improves survival in BRAF V600E/K mutant melanoma, but the efficacy of dMAPKi in non-V600 BRAF mutant tumors is poorly understood. We sought to characterize the responsiveness of class II (enhanced kinase activity, dimerization dependent) BRAF mutant melanoma to dMAPKi., Experimental Design: Tumors from patients with BRAF wild-type (WT), V600E (class I), and L597S (class II) metastatic melanoma were used to generate patient-derived xenografts (PDX). We assembled a panel of melanoma cell lines with class IIa (activation segment) or IIb (p-loop) mutations and compared these with WT or V600E/K BRAF mutant cells. Cell lines and PDXs were treated with BRAFi (vemurafenib, dabrafenib, encorafenib, and LY3009120), MEKi (cobimetinib, trametinib, and binimetinib), or the combination. We identified 2 patients with BRAF L597S metastatic melanoma who were treated with dMAPKi., Results: BRAFi impaired MAPK signaling and cell growth in class I and II BRAF mutant cells. dMAPKi was more effective than either single MAPKi at inhibiting cell growth in all class II BRAF mutant cells tested. dMAPKi caused tumor regression in two melanoma PDXs with class II BRAF mutations and prolonged survival of mice with class II BRAF mutant melanoma brain metastases. Two patients with BRAF L597S mutant melanoma clinically responded to dMAPKi., Conclusions: Class II BRAF mutant melanoma is growth inhibited by dMAPKi. Responses to dMAPKi have been observed in 2 patients with class II BRAF mutant melanoma. These data provide rationale for clinical investigation of dMAPKi in patients with class II BRAF mutant metastatic melanoma. See related commentary by Johnson and Dahlman, p. 6107 ., (©2018 American Association for Cancer Research.)

Recently, a new class of extrachromosomal circular DNA, called microDNA, was identified. They are on average 100 to 400 bp long and are derived from unique non-repetitive genomic regions with high gene density. MicroDNAs are thought to arise from DNA breaks associated with RNA metabolism or replication slippage. Given the paucity of information on this entirely novel phenomenon, we aimed to get an additional insight into microDNA features by performing the microDNA analysis in 20 independent human lymphoblastoid cell lines (LCLs) prior and after treatment with chemotherapeutic drugs. The results showed non-random genesis of microDNA clusters from the active regions of the genome. The size periodicity of 190 bp was observed, which matches DNA fragmentation typical for apoptotic cells. The chemotherapeutic drug-induced apoptosis of LCLs increased both number and size of clusters further suggesting that part of microDNAs could result from the programmed cell death. Interestingly, proportion of identified microDNA sequences has common loci of origin when compared between cell line experiments. While compatible with the original observation that microDNAs originate from a normal physiological process, obtained results imply complementary source of its production. Furthermore, non-random genesis of microDNAs depicted by redundancy between samples makes these entities possible candidates for new biomarker generation.

Pre-B cell childhood acute lymphoblastic leukemia (pre-B cALL) is a heterogeneous disease involving many subtypes typically stratified using a combination of cytogenetic and molecular-based assays. These methods, although widely used, rely on the presence of known chromosomal translocations, which is a limiting factor. There is therefore a need for robust, sensitive, and specific molecular biomarkers unaffected by such limitations that would allow better risk stratification and consequently better clinical outcome. In this study we performed a transcriptome analysis of 56 pre-B cALL patients to identify expression signatures in different subtypes. In both protein-coding and long non-coding RNAs (lncRNA), we identified subtype-specific gene signatures distinguishing pre-B cALL subtypes, particularly in t(12;21) and hyperdiploid cases. The genes up-regulated in pre-B cALL subtypes were enriched in bivalent chromatin marks in their promoters. LncRNAs is a new and under-studied class of transcripts. The subtype-specific nature of lncRNAs suggests they may be suitable clinical biomarkers to guide risk stratification and targeted therapies in pre-B cALL patients.

The rules of engagement between zinc finger transcription factors and DNA have been partly defined by in vitro DNA-binding and structural studies, but less is known about how these rules apply in vivo. Here, we demonstrate how a missense mutation in the second zinc finger of Krüppel-like factor-1 (KLF1) leads to degenerate DNA-binding specificity in vivo, resulting in ectopic transcription and anemia in the Nan mouse model. We employed ChIP-seq and 4sU-RNA-seq to identify aberrant DNA-binding events genome wide and ectopic transcriptional consequences of this binding. We confirmed novel sequence specificity of the mutant recombinant zinc finger domain by performing biophysical measurements of in vitro DNA-binding affinity. Together, these results shed new light on the mechanisms by which missense mutations in DNA-binding domains of transcription factors can lead to autosomal dominant diseases.

Childhood acute lymphoblastic leukemia (cALL) is the most common pediatric cancer and, despite an 85% cure rate, still represents a major cause of disease-related death in children. Recent studies have implicated long non-coding RNAs (lncRNAs) in cALL etiology, progression, and treatment response. However, barring some exceptions little is known about the functional impact of lncRNAs on cancer biology, which limits their potential as potential therapeutic targets. We wanted to investigate the functional role of lncRNAs identified as specifically overexpressed in pre-B cALL by whole-transcriptome sequencing. Here we report five lncRNAs specifically upregulated in pre-B cALL that had significant impacts on cancer hallmark traits such as cell proliferation, migration, apoptosis, and treatment response. In particular, silencing of the RP11-137H2.4 lncRNA effectively restored normal glucocorticoid (GC) response in a GC-resistant pre-B cALL cell line and specifically modulated expression of members of both the NRAS/BRAF/NF-κB MAPK cascade and cell cycle pathways. Since GC form the cornerstone of cALL chemotherapy and resistance in cALL confers a dismal prognosis, characterizing RP11-137H2.4'sexact role and function in this process will be critical to the development of new therapeutic approaches to overcome GC resistance in children treated for cALL.

Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all three phylogenetic domains. Genome engineering technologies are now making it possible to rationally change the genetic code, offering resistance to viruses, genetic isolation from horizontal gene transfer, and prevention of environmental escape by genetically modified organisms. We discuss the biochemical, genetic, and technological challenges that must be overcome in order to engineer the genetic code., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

We detail gross and histopathological changes associated with infection by the eggs, larvae, and cuticular remnants of Unionicola sp. in the mantle, gill, and visceral mass of 25 Alabama creekmussels, Strophitus connasaugaensis, collected during May 2010 through July 2012 from 2 Alabama streams. A multitude (estimated mean intensity >100) of mite eggs and larvae typically infected mantle, gill, and visceral mass integument. Pathology associated with eggs (prevalence = 0.57) and larvae (prevalence = 0.39) typically consisted of localized distension of the infection site; a host response to these infections was indeterminate. However, larval mites embedded in suprabranchial connective tissues were typically encapsulated (prevalence = 0.89). Mite remnants (prevalence = 0.5) occurred in mantle, gill, visceral mass integument, foot, heart, pericardial gland, intestinal lamina propria, and were typically encapsulated. We speculate that S. connasaugaensis clears some infections but is recolonized by autoinfection or horizontal dispersal of mites in the stream. Noteworthy is that high-intensity infections seemingly do not markedly impact the histological picture of mussel tissues, indicating that mites are relatively benign symbionts that are of little concern to mussels under normal environmental conditions.

Background: Lung maturation is a late fetal developmental event in both mice and humans. Because of this, lung immaturity is a serious problem in premature infants. Disruption of genes for either the glucocorticoid receptor (Nr3c1) or the NFIB transcription factors results in perinatal lethality due to lung immaturity. In both knockouts, the phenotype includes excess cell proliferation, failure of saccularization and reduced expression of markers of epithelial differentiation. This similarity suggests that the two genes may co-regulate a specific set of genes essential for lung maturation., Results: We analyzed the roles of these two transcription factors in regulating transcription using ChIP-seq data for NFIB, and RNA expression data and motif analysis for both. Our new ChIP-seq data for NFIB in lung at E16.5 shows that NFIB binds to a NFI motif. This motif is over-represented in the promoters of genes that are under-expressed in Nfib-KO mice at E18.5, suggesting an activator role for NFIB. Using available microarray data from Nr3c1-KO mice, we further identified 52 genes that are under-expressed in both Nfib and Nr3c1 knockouts, an overlap which is 13.1 times larger than what would be expected by chance. Finally, we looked for enrichment of 738 recently published transcription factor motifs in the promoters of these putative target genes and found that the NFIB and glucocorticoid receptor motifs were among the most enriched, suggesting that a subset of these genes may be directly activated by Nfib and Nr3c1., Conclusions: Our data provide the first evidence for Nfib and Nr3c1 co-regulating genes related to lung maturation. They also establish that the in vivo DNA-binding specificity of NFIB is the same as previously seen in vitro, and highly similar to that of the other NFI-family members NFIA, NFIC and NFIX.

Approaches for regulatory element discovery from gene expression data usually rely on clustering algorithms to partition the data into clusters of co-expressed genes. Gene regulatory sequences are then mined to find overrepresented motifs in each cluster. However, this ad hoc partition rarely fits the biological reality. We propose a novel method called RED2 that avoids data clustering by estimating motif densities locally around each gene. We show that RED2 detects numerous motifs not detected by clustering-based approaches, and that most of these correspond to characterized motifs. RED2 can be accessed online through a user-friendly interface.

Plant cells are characterized by the presence of chloroplasts, membrane lipids of which contain up to ∼80% mono- and digalactosyldiacylglycerol (MGDG and DGDG). The synthesis of MGDG in the chloroplast envelope is essential for the biogenesis and function of photosynthetic membranes, is coordinated with lipid metabolism in other cell compartments and is regulated in response to environmental factors. Phenotypic analyses of Arabidopsis using the recently developed specific inhibitor called galvestine-1 complete previous analyses performed using various approaches, from enzymology, cell biology to genetics. This review details how this probe could be beneficial to study the lipid homeostasis system at the whole cell level and highlights connections between MGDG synthesis and Arabidopsis flower development.

Gene duplication is frequent within gene clusters and plays a fundamental role in evolution by providing a source of new genetic material upon which natural selection can act. Although classical phylogenetic inference methods provide some insight into the evolutionary history of a gene cluster, they are not sufficient alone to differentiate single- from multiple gene duplication events and to answer other questions regarding the nature and size of evolutionary events. In this paper, we present an algorithm allowing to infer a set of optimal evolutionary histories for a gene cluster in a single species, according to a general cost model involving variable length duplications (in tandem or inverted), deletions, and inversions. We applied our algorithm to the human olfactory receptor and protocadherin gene clusters, showing that the duplication size distribution differs significantly between the two gene families. The algorithm is available through a web interface at http://www-lbit.iro.umontreal.ca/DILTAG/.

This study aimed to demonstrate the sensitivity of virtual reality (VR)/motion tracking to detect global functional gait impairment resulting from an emulated knee disability as a prelude to describing mobility changes following lower limb injury/treatment. Participants walked in a figure-8 around two virtual posts placed 6m apart while viewing the computer-generated environment in a helmet-mounted display. Three-dimensional position and orientation of the participant's head were tracked and used to update the virtual scenes, measure walking path and speed, and control task parameters with real-time feedback. Participants walked with/without an emulated lower extremity disability (splint preventing normal knee flexion). Participants performed the task at self-selected Natural (NAT) speed providing a baseline measure of their turning speed and area. Turning speed and area were then in turn maintained fixed (controlled speed, CS; controlled path, CP) while the other variable was measured as a gait impairment indicator. Different adaptive strategies were used to cope with the emulated deficit during the NAT scenario: maintaining turning speed while altering path geometry; decreasing turning speed while maintaining path geometry; and combining the previous two strategies. This resulted, on average, in decreased turning speeds and increased turning areas. The CS and CP manipulations respectively generated even greater turning areas and more consistent speed decreases. The three subtests acted as intertwined filters enabling the detection of functional gait impairment in all subjects regardless of their adaptive strategies. This proof-of-concept study demonstrated how VR/motion tracking technology can be used to detect and quantitatively characterize global functional mobility impairment., (Copyright 2010 Elsevier B.V. All rights reserved.)

Background: APOBEC3 (A3) proteins deaminate DNA cytosines and block the replication of retroviruses and retrotransposons. Each A3 gene encodes a protein with one or two conserved zinc-coordinating motifs (Z1, Z2 or Z3). The presence of one A3 gene in mice (Z2-Z3) and seven in humans, A3A-H (Z1a, Z2a-Z1b, Z2b, Z2c-Z2d, Z2e-Z2f, Z2g-Z1c, Z3), suggests extraordinary evolutionary flexibility. To gain insights into the mechanism and timing of A3 gene expansion and into the functional modularity of these genes, we analyzed the genomic sequences, expressed cDNAs and activities of the full A3 repertoire of three artiodactyl lineages: sheep, cattle and pigs., Results: Sheep and cattle have three A3 genes, A3Z1, A3Z2 and A3Z3, whereas pigs only have two, A3Z2 and A3Z3. A comparison between domestic and wild pigs indicated that A3Z1 was deleted in the pig lineage. In all three species, read-through transcription and alternative splicing also produced a catalytically active double domain A3Z2-Z3 protein that had a distinct cytoplasmic localization. Thus, the three A3 genes of sheep and cattle encode four conserved and active proteins. These data, together with phylogenetic analyses, indicated that a similar, functionally modular A3 repertoire existed in the common ancestor of artiodactyls and primates (i.e., the ancestor of placental mammals). This mammalian ancestor therefore possessed the minimal A3 gene set, Z1-Z2-Z3, required to evolve through a remarkable series of eight recombination events into the present day eleven Z domain human repertoire., Conclusion: The dynamic recombination-filled history of the mammalian A3 genes is consistent with the modular nature of the locus and a model in which most of these events (especially the expansions) were selected by ancient pathogenic retrovirus infections.

Tandemly arrayed genes (TAG) constitute a large fraction of most genomes and play important biological roles. They evolve through unequal recombination, which places duplicated genes next to the original ones (tandem duplications). Many algorithms have been proposed to infer a tandem duplication history for a TAG cluster. However, the presence of different transcriptional orientations in many clusters highlights the fact that processes such as inversions also contribute to their evolution. Moreover, existing algorithms are restricted to the study of TAGs evolution in a single species (only paralogous genes are considered). To circumvent these limitations, we consider an evolutionary model for TAGs involving duplication, gene loss, inversion, and speciation events. A general framework to infer ancestral gene orders that minimize the number of inversions in the whole evolutionary history is presented. At the methodological level, this paper integrates three approaches to genome evolution: the duplication tree reconstruction, the gene tree/species tree reconciliation theory, and the concept of inversion median used in order-based phylogeny reconstruction. An application on a cluster of olfactory receptor genes in four mammals is presented.

It is not known how the flexible protective zone maintained around oneself during locomotion (personal space or PS; see [Gérin-Lajoie M, Richards CL, McFadyen BJ. The negotiation of stationary and moving obstructions during walking: anticipatory locomotor adaptations and preservation of personal space. Motor Control 2005;9:242-69]) is modulated with walking speed, whether both sides of the PS are symmetrical, and whether the circumvention of physical and virtual obstructions elicit the same use of such PS. Personal space was measured in ten adults as they circumvented a cylindrical obstacle that was stationary within their path. Both left and right passes were performed at natural self-selected, slow and fast walking speeds. The same circumvention task was also performed at natural speeds in an immersive virtual environment (VE) replicating the same obstruction scenario. The shape and size of PS were maintained across walking speeds, and a smaller PS was generally observed on the dominant side. The general shape and lateral bias of the PS were preserved in the VE while its size was slightly increased. The systematic behavior across walking speeds and types of environment and the lateral bias suggest that PS is used to control navigation. This study deepens our understanding of normal adaptive walking behavior and has implications for the development of better tools for the assessment and retraining of locomotor capacity in different populations, from people with walking deficits to elite athletes. Since the PS behavior was shown to be robust in the VE used for this study, the virtual reality technology is proposed as a promising platform for the development of such assessment and retraining applications.