Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies

Visuospatial working memory in intuitive geometry, and in academic achievement in geometry

A study was conducted on the involvement of visuospatial working memory (VSWM) in intuitive geometry and in school performance in geometry at secondary school. A total of 166 pupils were administered: (1) six VSWM tasks, comprising simple storage and complex span tasks; and (2) the intuitive geometry task devised by Dehaene, Izard, Pica, and Spelke (2006), which distinguishes between core, presumably innate, and culturally-mediated principles of geometry; and (3) a task measuring academic achievement in geometry. Path analysis models showed that some VSWM components support culturally-mediated principles of geometry, whereas no VSWM component is related to the core principles of geometry. A complex VSWM task requiring the manipulation of visual information as well as core and culturally-mediated principles of geometry directly predicted academic achievement in geometry. Our results are discussed in terms of the role of VSWM in learning geometry

When is working memory important for arithmetic?: the impact of strategy and age

Our ability to perform arithmetic relies heavily on working memory, the manipulation and maintenance of information in mind. Previous research has found that in adults, procedural strategies, particularly counting, rely on working memory to a greater extent than retrieval strategies. During childhood there are changes in the types of strategies employed, as well as an increase in the accuracy and efficiency of strategy execution. As such it seems likely that the role of working memory in arithmetic may also change, however children and adults have never been directly compared. This study used traditional dual-task methodology, with the addition of a control load condition, to investigate the extent to which working memory requirements for different arithmetic strategies change with age between 9-11 years, 12-14 years and young adulthood. We showed that both children and adults employ working memory when solving arithmetic problems, no matter what strategy they choose. This study highlights the importance of considering working memory in understanding the difficulties that some children and adults have with mathematics, as well as the need to include working memory in theoretical models of mathematical cognition

Verbal thinking and inner speech use in autism spectrum disorder

The extent to which cognition is verbally mediated in neurotypical individuals is the subject of debate in cognitive neuropsychology, as well as philosophy and psychology. Studying “verbal thinking” in developmental/neuropsychological disorders provides a valuable opportunity to inform theory building, as well as clinical practice. In this paper, we provide a comprehensive, critical review of such studies among individuals with autism spectrum disorder (ASD). ASD involves severe social-communication deficits and limitations in cognitive/behavioural flexibility. The prevailing view in the field is that neither cognition nor behaviour is mediated verbally in ASD, and that this contributes to diagnostic features. However, our review suggests that, on the contrary, most studies to date actually find that among people with ASD cognitive task performance is either a) mediated verbally in a typical fashion, or b) not mediated verbally, but at no obvious cost to overall task performance. Overall though, these studies have methodological limitations and thus clear-cut conclusions are not possible at this stage. The aim of the review is to take stock of existing empirical findings, as well as to help develop the directions for future research that will resolve the many outstanding issues in this field

Senescence-Associated Gene YPEL3 Is Downregulated in Human Colon Tumors

Background Previous work has demonstrated YPEL3 to be a growth-suppressive protein that acts through a pathway of cellular senescence. We set out to determine whether human colon tumors demonstrated downregulation of YPEL3. Methods We collected colon tumor samples with matched normal control samples and analyzed them forYPEL3 gene expression by reverse transcriptase–polymerase chain reaction and CpGhypermethylation of the YPEL3 promoter by base-specific polymerase chain reaction analysis. Colon cancer cell lines (Caco-2 and HCT116−/− p53) were used to assess YPEL3 gene expression after treatment with 5-azadeoxycytidine or trichostatin A. Results Reverse transcriptase–polymerase chain reaction analysis demonstrated a decrease in YPEL3expression in tumor samples when compared to their patient-matched normal tissue. We determined that DNA methylation of the YPEL3 promoter CpG island does not play a role in YPEL3regulation in human colon tumors or colon cancer cells lines, consistent with the inability of 5-azadeoxycytidine treatment to induce YPEL3 expression in colon cancer cell lines. In contrast, colon cell line results suggest that histone acetylation may play a role in YPEL3 regulation in colon cancer. Conclusions YPEL3 is preferentially downregulated in human colon adenocarcinomas. DNA hypermethylation does not appear to be the mechanism of YPEL3 downregulation in this subset of collected patient samples or in colon cell lines. Histone acetylation may be a relevant epigenetic modulator of YPEL3in colon adenocarcinomas. Future investigation of YPEL3 and its role in colon cancer signaling and development may lead to increased understanding and alternative treatment options for this disease

Senescence-Associated Gene \u3cem\u3eYPEL3\u3c/em\u3e Is Downregulated in Human Colon Tumors

Background Previous work has demonstrated YPEL3 to be a growth-suppressive protein that acts through a pathway of cellular senescence. We set out to determine whether human colon tumors demonstrated downregulation of YPEL3. Methods We collected colon tumor samples with matched normal control samples and analyzed them forYPEL3 gene expression by reverse transcriptase–polymerase chain reaction and CpG hypermethylation of the YPEL3 promoter by base-specific polymerase chain reaction analysis. Colon cancer cell lines (Caco-2 and HCT116−/− p53) were used to assess YPEL3 gene expression after treatment with 5-azadeoxycytidine or trichostatin A. Results Reverse transcriptase–polymerase chain reaction analysis demonstrated a decrease in YPEL3expression in tumor samples when compared to their patient-matched normal tissue. We determined that DNA methylation of the YPEL3 promoter CpG island does not play a role in YPEL3 regulation in human colon tumors or colon cancer cells lines, consistent with the inability of 5-azadeoxycytidine treatment to induce YPEL3 expression in colon cancer cell lines. In contrast, colon cell line results suggest that histone acetylation may play a role in YPEL3 regulation in colon cancer. Conclusions YPEL3 is preferentially downregulated in human colon adenocarcinomas. DNA hypermethylation does not appear to be the mechanism of YPEL3 downregulation in this subset of collected patient samples or in colon cell lines. Histone acetylation may be a relevant epigenetic modulator of YPEL3in colon adenocarcinomas. Future investigation of YPEL3 and its role in colon cancer signaling and development may lead to increased understanding and alternative treatment options for this disease

Senescence-Associated Gene YPEL3 Is Downregulated in Human Colon Tumors

Background Previous work has demonstrated YPEL3 to be a growth-suppressive protein that acts through a pathway of cellular senescence. We set out to determine whether human colon tumors demonstrated downregulation of YPEL3. Methods We collected colon tumor samples with matched normal control samples and analyzed them forYPEL3 gene expression by reverse transcriptase–polymerase chain reaction and CpGhypermethylation of the YPEL3 promoter by base-specific polymerase chain reaction analysis. Colon cancer cell lines (Caco-2 and HCT116−/− p53) were used to assess YPEL3 gene expression after treatment with 5-azadeoxycytidine or trichostatin A. Results Reverse transcriptase–polymerase chain reaction analysis demonstrated a decrease in YPEL3expression in tumor samples when compared to their patient-matched normal tissue. We determined that DNA methylation of the YPEL3 promoter CpG island does not play a role in YPEL3regulation in human colon tumors or colon cancer cells lines, consistent with the inability of 5-azadeoxycytidine treatment to induce YPEL3 expression in colon cancer cell lines. In contrast, colon cell line results suggest that histone acetylation may play a role in YPEL3 regulation in colon cancer. Conclusions YPEL3 is preferentially downregulated in human colon adenocarcinomas. DNA hypermethylation does not appear to be the mechanism of YPEL3 downregulation in this subset of collected patient samples or in colon cell lines. Histone acetylation may be a relevant epigenetic modulator of YPEL3in colon adenocarcinomas. Future investigation of YPEL3 and its role in colon cancer signaling and development may lead to increased understanding and alternative treatment options for this disease

Senescence-Associated Gene \u3cem\u3eYPEL3\u3c/em\u3e Is Downregulated in Human Colon Tumors

Background Previous work has demonstrated YPEL3 to be a growth-suppressive protein that acts through a pathway of cellular senescence. We set out to determine whether human colon tumors demonstrated downregulation of YPEL3. Methods We collected colon tumor samples with matched normal control samples and analyzed them forYPEL3 gene expression by reverse transcriptase–polymerase chain reaction and CpG hypermethylation of the YPEL3 promoter by base-specific polymerase chain reaction analysis. Colon cancer cell lines (Caco-2 and HCT116−/− p53) were used to assess YPEL3 gene expression after treatment with 5-azadeoxycytidine or trichostatin A. Results Reverse transcriptase–polymerase chain reaction analysis demonstrated a decrease in YPEL3expression in tumor samples when compared to their patient-matched normal tissue. We determined that DNA methylation of the YPEL3 promoter CpG island does not play a role in YPEL3 regulation in human colon tumors or colon cancer cells lines, consistent with the inability of 5-azadeoxycytidine treatment to induce YPEL3 expression in colon cancer cell lines. In contrast, colon cell line results suggest that histone acetylation may play a role in YPEL3 regulation in colon cancer. Conclusions YPEL3 is preferentially downregulated in human colon adenocarcinomas. DNA hypermethylation does not appear to be the mechanism of YPEL3 downregulation in this subset of collected patient samples or in colon cell lines. Histone acetylation may be a relevant epigenetic modulator of YPEL3in colon adenocarcinomas. Future investigation of YPEL3 and its role in colon cancer signaling and development may lead to increased understanding and alternative treatment options for this disease