DeepSAGE—digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples

Digital transcriptomics with pyrophosphatase based ultra-high throughput DNA sequencing of di-tags provides high sensitivity and cost-effective gene expression profiling. Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE). We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato. The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest. Importantly, many transcripts were detected that cannot be matched to known genes, but is likely to be part of the abiotic stress-response in potato

The vaa locus of Mycoplasma hominis contains a divergent genetic islet encoding a putative membrane protein

BACKGROUND: The Mycoplasma hominis vaa gene encodes a highly variable, surface antigen involved in the adhesion to host cells. We have analysed the structure of the vaa locus to elucidate the genetic basis for variation of vaa. RESULTS: Mapping of vaa on existing physical maps of five M. hominis isolates by pulsed field gel electrophoresis revealed that vaa is located in a genomic region containing the majority of other characterized membrane protein genes of M. hominis. Sequencing of an 11 kb region containing the vaa locus of M. hominis isolate 132 showed the presence of conserved housekeeping genes at the borders of the region, uvrA upstream and the hitABL operon downstream to vaa. Analysis of 20 M. hominis isolates revealed that the vaa upstream region was conserved whereas the downstream region was highly variable. In isolate 132 this region contained an open reading frame (ORF) encoding a putative 160 kDa membrane protein. Homologous ORFs were present in half of the isolates, whereas this ORF, termed vmp (variable membrane protein), was deleted from the locus in the remaining isolates. Compellingly, the conserved upstream region and variable downstream region of vaa correlates with the genetic structure of vaa itself which consists of a conserved 5' end and a variable 3' end containing a variable number of exchangeable sequence cassettes. CONCLUSION: Our data demonstrate that the vaa locus contains a divergent genetic islet, and indicate pronounced intraspecies recombination. The high variability level of the locus indicate that it is a chromosomal 'hot spot', presumably important for sustaining diversity and a high adaptation potential of M. hominis

From cases to projects in problem-based medical education

Problem-based learning (PBL) based on patient cases has become a well-established worldwide educational approach in medical education. Recent studies indicate that case-based PBL when used throughout an entire curriculum may develop into a counter-productive routine for students as well as teachers. Consequently, there is a need to develop PBL approaches further allowing students to work with more ill-defined problems and alternative learning structures. In this paper, we argue that this can be realised by introducing project-PBL into the medical curriculum, as in the medical education at Aalborg University, Denmark. We outline organisations of case- and project- PBL in the medical curriculum and present an explorative study of 116 first and second year students’ experiences working in the two settings of PBL. Results reveal that students generally rate their PBL experiences positively however, project-PBL is rated more positively than case-PBL on all parameters studied. These results invite further consideration of the differences in working with cases and projects. Two central differences are discussed; the nature of the problem as the trigger of learning and students' possibilities for directing their own learning processes. The study demonstrates that introducing project-PBL may contribute significantly in problem-based medical education. However, the need for extensive research into advantages and limitations of the combined use of case- and project-PBL is also emphasised

Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif

Extent: 13p.Background: Powdery mildew and rust fungi are widespread, serious pathogens that depend on developing haustoria in the living plant cells. Haustoria are separated from the host cytoplasm by a plant cell-derived extrahaustorial membrane. They secrete effector proteins, some of which are subsequently transferred across this membrane to the plant cell to suppress defense. Results: In a cDNA library from barley epidermis containing powdery mildew haustoria, two-thirds of the sequenced ESTs were fungal and represented ~3,000 genes. Many of the most highly expressed genes encoded small proteins with N-terminal signal peptides. While these proteins are novel and poorly related, they do share a three-amino acid motif, which we named "Y/F/WxC", in the N-terminal of the mature proteins. The first amino acid of this motif is aromatic: tyrosine, phenylalanine or tryptophan, and the last is always cysteine. In total, we identified 107 such proteins, for which the ESTs represent 19% of the fungal clones in our library, suggesting fundamental roles in haustoria function. While overall sequence similarity between the powdery mildew Y/F/WxC-proteins is low, they do have a highly similar exon-intron structure, suggesting they have a common origin. Interestingly, searches of public fungal genome and EST databases revealed that haustoria-producing rust fungi also encode large numbers of novel, short proteins with signal peptides and the Y/F/WxC-motif. No significant numbers of such proteins were identified from genome and EST sequences from either fungi which do not produce haustoria or from haustoria-producing Oomycetes. Conclusion: In total, we identified 107, 178 and 57 such Y/F/WxC-proteins from the barley powdery mildew, the wheat stem rust and the wheat leaf rust fungi, respectively. All together, our findings suggest the Y/F/WxC-proteins to be a new class of effectors from haustoria-producing pathogenic fungi.Dale Godfrey, Henrik Böhlenius, Carsten Pedersen, Ziguo Zhang, Jeppe Emmersen and Hans Thordal-Christense

PBL and critical thinking disposition in Chinese medical students – A randomized cross-sectional study

 The purpose of this study was to explore the relationship of problem-based learning (PBL) and the development of critical thinking disposition (CT) and academic achievement in Chinese medical students using a cross-sectional randomized design. Medical students from China Medical University (CMU) were randomized to PBL or non-PBL teaching at the commencement of the study. After five years of study, CT was scored by a Chinese version of the California Critical Thinking Disposition Inventory (CCTDI-CV). The score achieved on a Computer Case Simulation (CCS) test evaluated academic performance. Total CT score was higher in PBL students (n=170) than non-PBL students (n=83) (304.7±36.8 vs. 279.2±39.4, p < 0.01). Subscale CT-scores were significant in favor of PBL in six of the seven subscales (truth seeking, open-mindedness, analyticity, systematicity, inquisitiveness, maturity). There was no significant difference in terms of gender on the total CT score, though minor differences were seen in subscales favoring female PBL students. PBL students had higher CCS scores than non-PBL students, but not significantly (112.8±20.6 vs. 107.3±16.5; p=0.11). There was no significant correlation between CCS scores and CCTDI-CV results. Male students scored slightly higher on the CCS test compared to female students (male 113.4±18.9 vs. female 109.7±19.7), but the difference was not significant. This study concludes that in Chinese medical students, PBL teaching was related to a higher disposition of critical thinking, but not to improved academic skills

A Comparative Analysis of the Wound Healing-Related Heterogeneity of Adipose-Derived Stem Cells Donors

Adipose-derived Stem cells (ASCs) are on the verge of being available for large clinical trials in wound healing. However, for developing advanced therapy medicinal products (ATMPs), potency assays mimicking the mode of action are required to control the product consistency of the cells. Thus, greater effort should go into the design of product assays. Therefore, we analyzed three ASC-based ATMPs from three different donors with respect to their surface markers, tri-lineage differentiation, proliferation, colony-forming unit capacity, and effect on fibroblast proliferation and migration, endothelial proliferation, migration, and angiogenesis. Furthermore, the transcriptome of all three cell products was analyzed through RNA-sequencing. Even though all products met the criteria by the International Society for Cell and Gene Therapy and the International Federation for Adipose Therapeutics and Science, we found one product to be consistently superior to others when exploring their potency in the wound healing specific assays. Our results indicate that certain regulatory genes associated with extracellular matrix and angiogenesis could be used as markers of a superior ASC donor from which to use ASCs to treat chronic wounds. Having a panel of assays capable of predicting the potency of the product would ensure the patient receives the most potent product for a specific indication, which is paramount for successful patient treatment and acceptance from the healthcare system

Mass spectrometry analysis of adipose-derived stem cells reveals a significant effect of hypoxia on pathways regulating extracellular matrix

Over-represented biological processes by gene ontology analysis of proteins identified in the secretome fraction. (DOCX 63 kb

Support for mobilising medical students to join the COVID-19 pandemic emergency healthcare workforce:a cross-sectional questionnaire survey

Objective To identify what motivates medical students to join a pandemic emergency healthcare workforce.Design Cross-sectional study.Setting Aalborg University, Denmark.Participants All medical students.Main outcome measures Motivational points as perceived by the students to be important. Demographic characteristics and 11 motivational domains scored on a Visual Analog Scale from 0 (low) to 100 (high) responding to the question: ‘To what degree are the following statements important for you to join a national emergency preparedness workforce?’ The questionnaire was developed by an expert panel in a process of four iterations.Results A total of 486 students of 688 (70.6%) completed the survey within 7 days in March 2020. 80% had decided to join the pandemic emergency healthcare workforce. Ranked median scores for motivational statements in each domain were: care, 100; learn, 90; pride, 83; team, 77; needed, 75; safety, 75; supervision, 75; job, 73; duty, 66; salary, 62; historic, 50. Supervision (p<0.001), salary (p<0.001) and duty (p=0.001) were given increasing priority with advancing study years. Interestingly, students added that support by the university and clarification of study plans were priorities.Conclusions Results guide decision-makers and colleagues on how to motivate or reinforce medical students in joining the pandemic emergency healthcare workforce. Importantly, students emphasised protection for themselves