Challenges in identifying cancer genes by analysis of exome sequencing data.

Massively parallel sequencing has permitted an unprecedented examination of the cancer exome, leading to predictions that all genes important to cancer will soon be identified by genetic analysis of tumours. To examine this potential, here we evaluate the ability of state-of-the-art sequence analysis methods to specifically recover known cancer genes. While some cancer genes are identified by analysis of recurrence, spatial clustering or predicted impact of somatic mutations, many remain undetected due to lack of power to discriminate driver mutations from the background mutational load (13-60% recall of cancer genes impacted by somatic single-nucleotide variants, depending on the method). Cancer genes not detected by mutation recurrence also tend to be missed by all types of exome analysis. Nonetheless, these genes are implicated by other experiments such as functional genetic screens and expression profiling. These challenges are only partially addressed by increasing sample size and will likely hold even as greater numbers of tumours are analysed

Learning Styles of Farmers and Others Involved with the Maine Potato Industry

The article reports on the learning preferences of Maine Potato Industry representatives. Using the Gregorc Mind Styles™ approach to examine learning styles, we categorized potato farmers, university/government employees, allied industry personnel, and others involved in the potato industry into four learning styles: Concrete Sequential, Concrete Random, Abstract Sequential, and Abstract Random. The plurality of potato farmers were Concrete Sequential, while the plurality of university/government employees and allied industry personnel were Abstract Random. The difference in learning styles of the deliverers and the recipients of the information can result in poor communication and a less than optimum learning environment

Perceptions and Attitudes: Analyzing Opinion Leaders in Relation to Genetically Modified Foods

Controversial issues in agriculture arise, and it falls on opinion leaders to disseminate information to their networks and the public. Agriculturalists are often blamed for not taken consumers’ concerns into consideration. This study sought to add to previous research by identifying the current perceptions of Florida agricultural leaders toward GM food, what percentage of them identify as opinion leaders with respect to GM food, and what they identify as sources of information regarding GM food. Through an online survey, the trust and attitudes towards GM foods and science, of agricultural leaders who participated in the Wedgworth Leadership Institute, were measured as well as their sources and channels of information. By identifying opinion leaders and helping them understand how to create and disseminate effective agricultural messages, agricultural educators and communicators can reach consumers and reduce the current knowledge gap more successfully. The results of this study confirm previous literature which states that both “what one knows” and “who one knows” impacts the level of influence an opinion leader may have with their peers. Agricultural educators should work with both agricultural opinion leaders and communicators to identify current consumer perceptions and how to address any differences or concerns that arise in interactions

The Influence of Problem Solving Style on Team Dynamics When Building Consensus

Issues facing the agricultural and natural resource (ANR) sector can be contentious due to opposing viewpoints, with people working against one another rather than working together to come to consensus on what will benefit the industry as a whole. Without a consistent message, the ANR industry will struggle when trying to gain support from decision makers. Therefore, opinion leaders need the skills to bring individuals and organizations together when facing critical issues that require groups to reach consensus. Agricultural leadership programs can offer educational opportunities for individuals to build problem-solving and team-building skills that will enable them to lead discussions when facing current issues. Unfortunately, little is known about how opinion leaders in the ANR sector work together when facing critical issues or how diverse cognitive styles influence this process. This study explored how cognitive style influenced team dynamics while ANR opinion leaders built consensus around critical ANR issues. Results illustrated that grouping participants by cognitive style influenced how the teams progressed through the consensus building process. The findings and resulting recommendations can assist educators in being selective when assigning groups and developing team-building activities that will prepare ANR opinion leaders to lead cognitively-diverse teams when building consensus

Can Anyone Hear Us? An Exploration of Echo Chambers at a Land-Grant University

Faculty at land-grant universities are expected to engage in some form of Extension, or science communication, as part of the land-grant mission. However, critics have claimed these institutions are out of touch with their stakeholders’ needs and faculty mainly communicate with others in academia. This engagement with a homogenous group reflects the concepts of echo chambers, where people are only exposed to information that aligns with their beliefs and current knowledge and discredit opposing information. An explanatory mixed-methods design was used to understand land-grant faculty’s engagement in echo chambers. A survey was distributed to a census of tenure-track faculty in the University of Florida’s Institute of Food and Agricultural Sciences to understand respondents’ engagement in echo chambers. Follow-up interviews were conducted with 13 of the survey respondents to further explore their audiences and channels used in science communication to understand their engagement in echo chambers. Survey results indicated faculty did not necessarily participate in echo chambers, but they also did not contribute to an open communication network. However, the interviews found participants were interested in reaching new audiences yet struggled to communicate with stakeholders. The participants also reported wanting to find alternative channels to peer reviewed journals to help disseminate their work. The findings from this study indicated faculty contributed to a type of echo chamber, but rather than viewing their stakeholders’ opinions as false, they simply did not hear the opinions. Agricultural communicators should work with land-grant faculty administrators to identify appropriate audiences and channels for science communication

Associations between emotion recognition and autistic and callous-unemotional traits:differential effects of cueing to the eyes

BackgroundAlthough autism and callous-unemotional (CU) traits are distinct conditions, both are associated with difficulties in emotion recognition. However, it is unknown whether the emotion recognition difficulties characteristic of autism and CU traits are driven by comparable underpinning mechanisms.MethodsWe tested whether cueing to the eyes improved emotion recognition in relation to autistic and CU traits in a heterogeneous sample of children enhanced for social, emotional and behavioural difficulties. Participants were 171 (n = 75 male) children aged 10–16 years with and without a diagnosis of autism (n = 99 autistic), who completed assessments of emotion recognition with and without cueing to the eyes. Parents completed the assessment of autistic and CU traits.ResultsAssociations between autistic and CU traits and emotion recognition accuracy were dependent upon gaze cueing. CU traits were associated with an overall decrease in emotion recognition in the uncued condition, but better fear recognition when cued to the eyes. Conversely, autistic traits were associated with decreased emotion recognition in the cued condition only, and no interactions between autistic traits and emotion were found.ConclusionsThe differential effect of cueing to the eyes in autistic and CU traits suggests different mechanisms underpin emotion recognition abilities. Results suggest interventions designed to promote looking to the eyes may be beneficial for children with CU traits, but not for children with autistic characteristics. Future developmental studies of autism and CU characteristics are required to better understand how different pathways lead to overlapping socio-cognitive profiles

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.

Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes, identifying a network of 193 noncoding loci in which mutations disrupt target gene expression. These 'somatic eQTLs' (expression quantitative trait loci) are frequently mutated in specific cancer tissues, and the majority can be validated in an independent cohort of 3,382 tumors. Among these, we find that the effects of noncoding mutations on DAAM1, MTG2 and HYI transcription are recapitulated in multiple cancer cell lines and that increasing DAAM1 expression leads to invasive cell migration. Collectively, the noncoding loci converge on a set of core pathways, permitting a classification of tumors into pathway-based subtypes. The somatic eQTL network is disrupted in 88% of tumors, suggesting widespread impact of noncoding mutations in cancer

Assessment of Diversity of Antimicrobial Resistance Phenotypes and Genotypes of \u3ci\u3eMannheimia haemolytica\u3c/i\u3e Isolates from Bovine Nasopharyngeal Swabs

The threat of bovine respiratory disease (BRD) for cattle operations is exacerbated by increasing prevalence of antimicrobial resistance (AMR) in Mannheimia haemolytica, a leading cause of BRD. Characterization of AMR in M. haemolytica by culture and susceptibility testing is complicated by uncertainty regarding the number of colonies that must be selected to accurately characterize AMR phenotypes (antibiograms) and genotypes in a culture. The study objective was to assess phenotypic and genotypic diversity of M. haemolytica isolates on nasopharyngeal swabs (NPS) from 28 cattle at risk for BRD or with BRD. NPS were swabbed onto five consecutive blood agar plates; after incubation up to 20 M. haemolytica colonies were selected per plate (up to 100 colonies per NPS). Phenotype was determined by measuring minimum inhibitory concentrations (MIC) for 11 antimicrobials and classifying isolates as resistant or not. Genotype was indirectly determined by matrix-assisted laser desorption/ionization time of flight mass spectroscopy (MALDI-TOF MS). NPS from 11 of 28 cattle yielded at least one M. haemolytica isolate; median (range) of isolates per NPS was 48 (1–94). NPS from seven cattle yielded one phenotype, 3 NPS yielded two, and 1 NPS yielded three; however, within a sample all phenotypic differences were due to only oneMIC dilution. On each NPS all M. haemolytica isolated were the same genotype; genotype 1 was isolated from three NPS and genotype two was isolated from eight. Diversity of M. haemolytica on bovine NPS was limited, suggesting that selection of few colonies might adequately identify relevant phenotypes and genotypes

Differential cargo mobilisation within Weibel-Palade bodies after transient fusion with the plasma membrane.

Inflammatory chemokines can be selectively released from Weibel-Palade bodies (WPBs) during kiss-and-run exocytosis. Such selectivity may arise from molecular size filtering by the fusion pore, however differential intra-WPB cargo re-mobilisation following fusion-induced structural changes within the WPB may also contribute to this process. To determine whether WPB cargo molecules are differentially re-mobilised, we applied FRAP to residual post-fusion WPB structures formed after transient exocytosis in which some or all of the fluorescent cargo was retained. Transient fusion resulted in WPB collapse from a rod to a spheroid shape accompanied by substantial swelling (>2 times by surface area) and membrane mixing between the WPB and plasma membranes. Post-fusion WPBs supported cumulative WPB exocytosis. To quantify diffusion inside rounded organelles we developed a method of FRAP analysis based on image moments. FRAP analysis showed that von Willebrand factor-EGFP (VWF-EGFP) and the VWF-propolypeptide-EGFP (Pro-EGFP) were immobile in post-fusion WPBs. Because Eotaxin-3-EGFP and ssEGFP (small soluble cargo proteins) were largely depleted from post-fusion WPBs, we studied these molecules in cells preincubated in the weak base NH4Cl which caused WPB alkalinisation and rounding similar to that produced by plasma membrane fusion. In these cells we found a dramatic increase in mobilities of Eotaxin-3-EGFP and ssEGFP that exceeded the resolution of our method (∼ 2.4 µm2/s mean). In contrast, the membrane mobilities of EGFP-CD63 and EGFP-Rab27A in post-fusion WPBs were unchanged, while P-selectin-EGFP acquired mobility. Our data suggest that selective re-mobilisation of chemokines during transient fusion contributes to selective chemokine secretion during transient WPB exocytosis. Selective secretion provides a mechanism to regulate intravascular inflammatory processes with reduced risk of thrombosis