The Pakaru ‘Pipeline’: Māori and Pasifika Pathways within the Academy

We examine the academic ‘pipeline’ for Māori and Pasifika graduates and illustrate the chronic under-representation of Māori and Pasifika in permanent academic positions in New Zealand universities. We identify areas within higher education where significant opportunities are being lost for the recruitment and retention of Māori and Pasifika. The narratives of Māori and Pasifika post-doctoral researchers, research associates and professional teaching fellows provide further insight into the advantages and disadvantages of these positions. Lastly, we propose a Pacific alternative metaphor ‘Pacific Navigation of Academic Pathways’ based on Pacific navigation, as opposed to the more commonly used term ‘pipeline’, in order to capture the nuances of Pasifika and Māori experiences

The Pakaru ‘Pipeline’: Māori and Pasifika Pathways within the Academy

We examine the academic ‘pipeline’ for Māori and Pasifika graduates and illustrate the chronic under-representation of Māori and Pasifika in permanent academic positions in New Zealand universities. We identify areas within higher education where significant opportunities are being lost for the recruitment and retention of Māori and Pasifika. The narratives of Māori and Pasifika post-doctoral researchers, research associates and professional teaching fellows provide further insight into the advantages and disadvantages of these positions. Lastly, we propose a Pacific alternative metaphor ‘Pacific Navigation of Academic Pathways’ based on Pacific navigation, as opposed to the more commonly used term ‘pipeline’, in order to capture the nuances of Pasifika and Māori experiences

The effects of velocity and nitrate on Phormidium accrual cycles: a stream mesocosm experiment

Proliferations of benthic cyanobacteria in the genus Phormidium are a global concern because of their increasing prevalence and ability to produce harmful toxins. Most studies have been observational and have linked physicochemical variables to Phormidium cover measured at the reach scale. Authors of these studies have alluded to nutrients and flow as key factors in accrual. Our goal was to use an experimental approach to examine how changes in velocity and NO₃⁻ concentrations influence Phormidium accrual. We hypothesized that: 1) Phormidium biomass accrual would be positively correlated with stream velocity; 2) biomass accrual would be positively related to NO₃⁻ concentration, which would have a stronger effect during early accrual; 3) an NO₃⁻ ✕ velocity interaction would arise from saturation of accrual at high NO₃⁻ and high velocity; and 4) the probability of detachment would increase with decreasing velocity. We assessed mat expansion, biomass (as phycoerythrin and chlorophyll a [Chl a] concentrations, and biovolume), and algal assemblage composition in flow-through channel mesocosms for 16 d. We crossed 2 velocity treatments (0.1 and 0.2 m/s, slow and fast, respectively) with 3 NO₃⁻ treatments (0.02, 0.1, and 0.4 mg/L, ambient, medium, and high, respectively). Velocity was positively correlated with all measures of Phormidium biomass, but patch expansion rates increased at similar rates across all treatments. NO₃⁻ had no effect during early accrual, but phycoerythrin concentrations increased with increasing NO₃⁻ in fast-velocity treatments. At the end of the experiment, patch size was greater in the high-velocity treatments because of a greater number of partial or full patch detachments in slow-velocity treatments. These results suggest that NO₃⁻ concentrations do not affect Phormidium expansion and detachment, but may be important during colonization (not investigated), and that mat expansion occurs at a similar rate regardless of velocity, but termination of accrual cycles occurs earlier in slow velocities

Comprehensive molecular characterization of gastric adenocarcinoma

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive breast cancer. Here, we comprehensively profiled 817 breast tumors, including 127 ILC, 490 ductal (IDC), and 88 mixed IDC/ILC. Besides E-cadherin loss, the best known ILC genetic hallmark, we identified mutations targeting PTEN, TBX3 and FOXA1 as ILC enriched features. PTEN loss associated with increased AKT phosphorylation, which was highest in ILC among all breast cancer subtypes. Spatially clustered FOXA1 mutations correlated with increased FOXA1 expression and activity. Conversely, GATA3 mutations and high expression characterized Luminal A IDC, suggesting differential modulation of ER activity in ILC and IDC. Proliferation and immune-related signatures determined three ILC transcriptional subtypes associated with survival differences. Mixed IDC/ILC cases were molecularly classified as ILC-like and IDC-like revealing no true hybrid features. This multidimensional molecular atlas sheds new light on the genetic bases of ILC and provides potential clinical options

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies

Development and Application of a Quantitative PCR Assay to Assess Genotype Dynamics and Anatoxin Content in <i>Microcoleus autumnalis</i>-Dominated Mats

Microcoleus is a filamentous cyanobacteria genus with a global distribution. Some species form thick, cohesive mats over large areas of the benthos in rivers and lakes. In New Zealand Microcoleus autumnalis is an anatoxin producer and benthic proliferations are occurring in an increasing number of rivers nationwide. Anatoxin content in M. autumnalis-dominated mats varies spatially and temporally, making understanding and managing proliferations difficult. In this study a M. autumnalis-specific TaqMan probe quantitative PCR (qPCR) assay targeting the anaC gene was developed. The assay was assessed against 26 non-M. autumnalis species. The assay had a detection range over seven orders of magnitude, with a limit of detection of 5.14 &#215; 10&#8722;8 ng &#956;L&#8722;1. The anaC assay and a cyanobacterial specific 16S rRNA qPCR were then used to determine toxic genotype proportions in 122 environmental samples collected from 19 sites on 10 rivers in New Zealand. Anatoxin contents of the samples were determined using LC-MS/MS and anatoxin quota per toxic cell calculated. The percentage of toxic cells ranged from 0 to 30.3%, with significant (p &lt; 0.05) differences among rivers. The anatoxin content in mats had a significant relationship with the percentage of toxic cells (R2 = 0.38, p &lt; 0.001), indicating that changes in anatoxin content in M. autumnalis-dominated mats are primarily related to the dominance of toxic strains. When applied to more extensive samples sets the assay will enable new insights into how biotic and abiotic parameters influence genotype composition, and if applied to RNA assist in understanding anatoxin production

Reach and mat scale differences in Microcoleus autumnalis (cyanobacterium) accrual along velocity and nitrate gradients in three New Zealand rivers

Proliferations of the toxic, mat-forming cyanobacterium Microcoleus autumnalis are an increasingly recognized problem in cobble-bed rivers worldwide. This study explored how flow and nutrient concentrations influence mat expansion. Microcoleus autumnalis was inoculated into cobbles placed in runs, riffles, and pools in three rivers with different nutrient conditions, and mat size was monitored over 21 days. The following hypotheses were tested: (i) mat expansion will reflect cover increases at the reach scale; (ii) biomass and cover will be highest in high-velocity habitats; and (iii) under similar velocities, nutrient concentrations will be more important than other abiotic and biotic variables in determining expansion rates. Mat expansion accurately reflected the increase in reach-scale cover, and expansion was most rapid at intermediate water velocities (0.25–0.45 m·s–1). Mats persisted the longest in riffles. Accrual cycles were terminated earlier in runs than in riffles, as high expansion rates resulted in patches reaching maximum mat size rapidly. Although M. autumnalis accrual differed among rivers, this was attributed to differences in shear stress and grazing pressure rather than nutrient concentrations.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The Pakaru ‘Pipeline’: Māori and Pasifika Pathways within the Academy

We examine the academic ‘pipeline’ for Māori and Pasifika graduates and illustrate the chronic under-representation of Māori and Pasifika in permanent academic positions in New Zealand universities. We identify areas within higher education where significant opportunities are being lost for the recruitment and retention of Māori and Pasifika. The narratives of Māori and Pasifika post-doctoral researchers, research associates and professional teaching fellows provide further insight into the advantages and disadvantages of these positions. Lastly, we propose a Pacific alternative metaphor ‘Pacific Navigation of Academic Pathways’ based on Pacific navigation, as opposed to the more commonly used term ‘pipeline’, in order to capture the nuances of Pasifika and Māori experiences