16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer)

CB was supported on a Daphne Jackson Fellowship sponsored by Natural Environmental Research Council (www.nerc.ac.uk) and the University of Edinburgh via the Daphne Jackson Trust. Field collections were supported by the National Science Foundation (www.nsf.gov) grant number OCE-1261519 to ADR and JSF.Uncovering the complexities of trophic and metabolic interactions among microorganisms is essential for the understanding of marine biogeochemical cycling and modelling climate-driven ecosystem shifts. High-throughput DNA sequencing methods provide valuable tools for examining these complex interactions, although this remains challenging, as many microorganisms are difficult to isolate, identify and culture. We use two species of planktonic foraminifera from the climatically susceptible, palaeoceanographically important genus Neogloboquadrina, as ideal test microorganisms for the application of 16S rRNA gene metabarcoding. Neogloboquadrina dutertrei and Neogloboquadrina incompta were collected from the California Current and subjected to either 16S rRNA gene metabarcoding, fluorescence microscopy, or transmission electron microscopy (TEM) to investigate their species-specific trophic interactions and potential symbiotic associations. 53–99% of 16S rRNA gene sequences recovered from two specimens of N. dutertrei were assigned to a single operational taxonomic unit (OTU) from a chloroplast of the phylum Stramenopile. TEM observations confirmed the presence of numerous intact coccoid algae within the host cell, consistent with algal symbionts. Based on sequence data and observed ultrastructure, we taxonomically assign the putative algal symbionts to Pelagophyceae and not Chrysophyceae, as previously reported in this species. In addition, our data shows that N. dutertrei feeds on protists within particulate organic matter (POM), but not on bacteria as a major food source. In total contrast, of OTUs recovered from three N. incompta specimens, 83–95% were assigned to bacterial classes Alteromonadales and Vibrionales of the order Gammaproteobacteria. TEM demonstrates that these bacteria are a food source, not putative symbionts. Contrary to the current view that non-spinose foraminifera are predominantly herbivorous, neither N. dutertrei nor N. incompta contained significant numbers of phytoplankton OTUs. We present an alternative view of their trophic interactions and discuss these results within the context of modelling global planktonic foraminiferal abundances in response to high-latitude climate change.Publisher PDFPeer reviewe

Assessing performance on the Montreal Cognitive Assessment (MoCA) in experienced cochlear implant users: use of alternative scoring guidelines.

Although research suggests a relationship between hearing impairment and cognitive decline in older adults, nuances of this relationship remain unclear. This uncertainty could be attributed to verbal administration of standardized cognitive measures to hearing-impaired (HI) individuals. Various strategies for testing HI populations have been suggested. We tested the efficacy of applying alternative scoring methods that systematically removed auditory-based items on the Montreal Cognitive Assessment (MoCA) in 27 cochlear implant patients. We calculated the original MoCA score and three alternative scores. The first alternative removed items from the Attention and Language sections; the second alternative removed the Delayed Recall task, and the third alternative removed the Attention, Language, and Delayed Recall items. QoL was assessed using the Glasgow Benefit Inventory and Nijmegen Cochlear Implant Questionnaire. Results indicate a significant difference in MoCA scores with two alternative scoring methods. The second alternative MoCA score related to self-reported performance on the GBI

Performance on the standard and hearing-impaired Montreal Cognitive Assessment in cochlear implant users.

OBJECTIVES: Commonly used cognitive screening tools were not originally developed for patients with hearing loss (HL) and rely heavily on the ability to hear the instructions and test stimuli. Recently, the Montreal Cognitive Assessment (MoCA) was modified for use with hearing-impaired populations (ie, HI-MoCA). In order to investigate the clinical utility of the HI-MoCA, we assessed performance between the standard MoCA and HI-MoCA among postlingually deafened cochlear implant (CI) users. METHODS: We administered the standard MoCA and HI-MoCA to 21 CI users and compared their performance. We assessed differences in pass/fail status when items from the attention and language sections and the delayed recall task were removed. RESULTS: There was no significant difference in performance between the standard MoCA and HI-MoCA. Participants scored higher on both test versions when the delayed recall task was removed. Participants also performed better on the delayed recall task on the HI-MoCA than on the standard MoCA. CONCLUSIONS: While our findings suggest that the modality of presentation for the MoCA does not influence overall performance for postlingually deafened CI users, visual presentation of stimuli impacted performance on delayed recall. Furthermore, irrespective of presentation modality, our participants scored higher on both MoCA versions when the delayed recall task was removed. Clinically, modifications to the presentation of the MoCA might not be necessary for CI users; however, clinicians should be aware that the delayed recall task is inherently harder for these patients

LETTERS Response and resistance to MEK inhibition in leukaemias initiated by hyperactive Ras

The cascade comprising Raf, mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK) is a therapeutic target in human cancers with deregulated Ras signalling, which includes tumours that have inactivated the Nf1 tumour suppressor 1,2 . Nf1 encodes neurofibromin, a GTPaseactivating protein that terminates Ras signalling by stimulating hydrolysis of Ras-GTP. We compared the effects of inhibitors of MEK in a myeloproliferative disorder (MPD) initiated by inactivating Nf1 in mouse bone marrow and in acute myeloid leukaemias (AMLs) in which cooperating mutations were induced by retroviral insertional mutagenesis. Here we show that MEK inhibitors are ineffective in MPD, but induce objective regression of many Nf1-deficient AMLs. Drug resistance developed because of outgrowth of AML clones that were present before treatment. We cloned clone-specific retroviral integrations to identify candidate resistance genes including Rasgrp1, Rasgrp4 and Mapk14, which encodes p38a. Functional analysis implicated increased RasGRP1 levels and reduced p38 kinase activity in resistance to MEK inhibitors. This approach represents a robust strategy for identifying genes and pathways that modulate how primary cancer cells respond to targeted therapeutics and for probing mechanisms of de novo and acquired resistance. Aberrant Ras signalling contributes to the pathogenesis of myeloid malignancies and can result from acquired RAS mutations or from alternative genetic mechanisms that include FLT3 internal tandem duplications, the BCR-ABL fusion, PTPN11 mutations and NF1 inactivation (reviewed in ref. 3). Children with neurofibromatosis type 1 (NF1) have a 200-to 500-fold excess incidence of juvenile myelomonocytic leukaemia, an aggressive MPD characterized by leukocytosis, splenomegaly and tissue infiltration (reviewed in ref. 4). The bone marrows of affected patients frequently show loss of the normal parental NF1 allele and elevated ERK activity flox/flox pups to identify genes and pathways that might cooperate with Nf1 inactivation to induce progression of MPD to AML 3 . These mice developed acute leukaemia sooner and at a higher rate than control Mx1-Cre-negative littermates that retain normal Nf1 functio

Chromatin Remodeling Complexes Interact Dynamically with a Glucocorticoid Receptor–regulated Promoter

Brahma (BRM) and Brahma-related gene 1 (BRG1) are the ATP-dependent catalytic subunits of the SWI/SNF family of chromatin-remodeling complexes. These complexes are involved in essential processes such as cell cycle, growth, differentiation, and cancer. Using imaging approaches in a cell line that harbors tandem repeats of stably integrated copies of the steroid responsive MMTV-LTR (mouse mammary tumor virus–long terminal repeat), we show that BRG1 and BRM are recruited to the MMTV promoter in a hormone-dependent manner. The recruitment of BRG1 and BRM resulted in chromatin remodeling and decondensation of the MMTV repeat as demonstrated by an increase in the restriction enzyme accessibility and in the size of DNA fluorescence in situ hybridization (FISH) signals. This chromatin remodeling event was concomitant with an increased occupancy of RNA polymerase II and transcriptional activation at the MMTV promoter. The expression of ATPase-deficient forms of BRG1 (BRG1-K-R) or BRM (BRM-K-R) inhibited the remodeling of local and higher order MMTV chromatin structure and resulted in the attenuation of transcription. In vivo photobleaching experiments provided direct evidence that BRG1, BRG1-K-R, and BRM chromatin-remodeling complexes have distinct kinetic properties on the MMTV array, and they dynamically associate with and dissociate from MMTV chromatin in a manner dependent on hormone and a functional ATPase domain. Our data provide a kinetic and mechanistic basis for the BRG1 and BRM chromatin-remodeling complexes in regulating gene expression at a steroid hormone inducible promoter