Building Interdisciplinary Skills and Mentorship Opportunities in a 2-Week Research Experience

ABSTRACT: A framework for a 2-wk summer research course is presented, with a mindset of discovery and self-advocacy that is interdisciplinary and inclusive. The foundations of the course are built upon 2 pillars: (a) a well-defined educational plan focused on cellular engineering, with a goal to instill an engineering mindset into the cell biology field; and (b) a tailored Dimensions of Mentoring policy, which uses a structured feedback system to define and strengthen mentor attributes and provide multiple opportunities for mentorship and mentorship training. Undergraduate and master’s student participants work with PhD students or postdoctoral/professor team leaders in small teams in discovery-based research projects. Multiple teams work in parallel during the 2-wk period and convene in course-wide meetings to share findings and give feedback. Working in small teams with multiple levels of peer and team lead mentoring, students experience advancement in research and technical skills. Participants also experience gains in their understanding of the overarching educational goals in cellular engineering and science communication skills through course-wide activities. The principles from the Dimensions of Mentoring were also effective, with mentors at different levels building strong inclusive teams, coaching practical skills, and promoting individual advocacy. Meeting basic needs, providing relatable role models, and prioritizing enjoyable team-building activities were found to be critical factors in providing inclusive and productive environments. Overall, participants report high satisfaction with a discovery-based interdisciplinary research experience because of a supported environment. This creation of a strong community benefits individual career development and contributes to sustainable research productivity

Climate change, water and agriculture in the Greater Mekong subregion

Climate change / Adaptation / Indicators / Water resource management / River basins / Water availability / Water quality / Groundwater / Fisheries / Ecosystems / Water power / Population growth / Land use / Biofuels / Sea level / South East Asia / Cambodia / Laos / Myanmar / Thailand / Vietnam / China / Greater Mekong Subregion / Yunnan Province

Scoping study on natural resources and climate change in Southeast Asia with a focus on agriculture. Final report

Climate change / Natural resources / Environmental effects / Agroecology / Agricultural production / Crops / Cropping systems / Farming systems / Livestock / Fisheries / Food security / Water management / Economic aspects / Rural poverty / Policy / Nutrient management / South East Asia / Cambodia / Laos / Thailand / Vietnam / Myanmar / China / Greater Mekong Subregion / Tonle Sap / Yunnan

Spermatogenesis-Specific Features of the Meiotic Program in Caenorhabditis elegans

In most sexually reproducing organisms, the fundamental process of meiosis is implemented concurrently with two differentiation programs that occur at different rates and generate distinct cell types, sperm and oocytes. However, little is known about how the meiotic program is influenced by such contrasting developmental programs. Here we present a detailed timeline of late meiotic prophase during spermatogenesis in Caenorhabditis elegans using cytological and molecular landmarks to interrelate changes in chromosome dynamics with germ cell cellularization, spindle formation, and cell cycle transitions. This analysis expands our understanding C. elegans spermatogenesis, as it identifies multiple spermatogenesis-specific features of the meiotic program and provides a framework for comparative studies. Post-pachytene chromatin of spermatocytes is distinct from that of oocytes in both composition and morphology. Strikingly, C. elegans spermatogenesis includes a previously undescribed karyosome stage, a common but poorly understood feature of meiosis in many organisms. We find that karyosome formation, in which chromosomes form a constricted mass within an intact nuclear envelope, follows desynapsis, involves a global down-regulation of transcription, and may support the sequential activation of multiple kinases that prepare spermatocytes for meiotic divisions. In spermatocytes, the presence of centrioles alters both the relative timing of meiotic spindle assembly and its ultimate structure. These microtubule differences are accompanied by differences in kinetochores, which connect microtubules to chromosomes. The sperm-specific features of meiosis revealed here illuminate how the underlying molecular machinery required for meiosis is differentially regulated in each sex

LAB-1 Targets PP1 and Restricts Aurora B Kinase upon Entrance into Meiosis to Promote Sister Chromatid Cohesion

Successful execution of the meiotic program depends on the timely establishment and removal of sister chromatid cohesion. LAB-1 has been proposed to act in the latter by preventing the premature removal of the meiosis-specific cohesin REC-8 at metaphase I in C. elegans, yet the mechanism and scope of LAB-1 function remained unknown. Here we identify an unexpected earlier role for LAB-1 in promoting the establishment of sister chromatid cohesion in prophase I. LAB-1 and REC-8 are both required for the chromosomal association of the cohesin complex subunit SMC-3. Depletion of lab-1 results in partial loss of sister chromatid cohesion in rec-8 and coh-4 coh-3 mutants and further enhanced chromatid dissociation in worms where all three kleisins are mutated. Moreover, lab-1 depletion results in increased Aurora B kinase (AIR-2) signals in early prophase I nuclei, coupled with a parallel decrease in signals for the PP1 homolog, GSP-2. Finally, LAB-1 directly interacts with GSP-1 and GSP-2. We propose that LAB-1 targets the PP1 homologs to the chromatin at the onset of meiosis I, thereby antagonizing AIR-2 and cooperating with the cohesin complex to promote sister chromatid association and normal progression of the meiotic program

Tracing the String: BMN correspondence at Finite J^2/N

Employing the string bit formalism of hep-th/0209215, we identify the basis transformation that relates BMN operators in N=4 gauge theory to string states in the dual string field theory at finite g_2=J^2/N. In this basis, the supercharge truncates at linear order in g_2, and the mixing amplitude between 1 and 2-string states precisely matches with the (corrected) answer of hep-th/0206073 for the 3-string amplitude in light-cone string field theory. Supersymmetry then predicts the order g_2^2 contact term in the string bit Hamiltonian. The resulting leading order mass renormalization of string states agrees with the recently computed shift in conformal dimension of BMN operators in the gauge theory.Comment: 11 pages, 1 figur

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment