Human cytomegalovirus infection increases mitochondrial biogenesis

Fibroblasts infected by Human Cytomegalovirus (CMV) undergo a robust increase in mitochondrial biogenesis with a corresponding increase in mitochondrial activity that is partly dependent on the viral anti-apoptotic pUL37x1 protein (vMIA). The increased respiration activity is blocked by the mitochondrial translation inhibitor chloramphenicol, which additionally suppresses viral production. Intriguingly, chloramphenicol and pUL37x1 depletion have different effects on respiration capacity but similar effects on CMV production, suggesting that pUL37x1 promotes viral replication by efficient utilization of new mitochondria. These results argue for a role of pUL37x1 beyond controlling apoptosis.     

Host Restrictions of Avian Influenza Viruses: In Silico Analysis of H13 and H16 Specific Signatures in the Internal Proteins

Gulls are the primary hosts of H13 and H16 avian influenza viruses (AIVs). The molecular basis for this host restriction is only partially understood. In this study, amino acid sequences from Eurasian gull H13 and H16 AIVs and Eurasian AIVs (non H13 and H16) were compared to determine if specific signatures are present only in the internal proteins of H13 and H16 AIVs, using a bioinformatics approach. Amino acids identified in an initial analysis performed on 15 selected sequences were checked against a comprehensive set of AIV sequences retrieved from Genbank to verify them as H13 and H16 specific signatures. Analysis of protein similarities and prediction of subcellular localization signals were performed to search for possible functions associated with the confirmed signatures. H13 and H16 AIV specific signatures were found in all the internal proteins examined, but most were found in the non-structural protein 1 (NS1) and in the nucleoprotein. A putative functional signature was predicted to be present in the nuclear export protein. Moreover, it was predicted that the NS1 of H13 and H16 AIVs lack one of the nuclear localization signals present in NS1 of other AIV subtypes. These findings suggest that the signatures found in the internal proteins of H13 and H16 viruses are possibly related to host restriction.     

Aerobic Interval Training Partly Reverse Contractile Dysfunction and Impaired Ca2+ Handling in Atrial Myocytes from Rats with Post Infarction Heart Failure

Background

There is limited knowledge about atrial myocyte Ca²⁺ handling in the failing hearts. The aim of this study was to examine atrial myocyte contractile function and Ca²⁺ handling in rats with post-infarction heart failure (HF) and to examine whether aerobic interval training could reverse a potential dysfunction.

Methods and results

Post-infarction HF was induced in Sprague Dawley rats by ligation of the left descending coronary artery. Atrial myocyte shortening was depressed (p<0.01) and time to relaxation was prolonged (p<0.01) in sedentary HF-rats compared to healthy controls. This was associated with decreased Ca²⁺ amplitude, decreased SR Ca²⁺ content, and slower Ca²⁺ transient decay. Atrial myocytes from HF-rats had reduced sarcoplasmic reticulum Ca²⁺ ATPase activity, increased Na⁺/Ca²⁺-exchanger activity and increased diastolic Ca²⁺ leak through ryanodine receptors. High intensity aerobic interval training in HF-rats restored atrial myocyte contractile function and reversed changes in atrial Ca²⁺ handling in HF.

Conclusion

Post infarction HF in rats causes profound impairment in atrial myocyte contractile function and Ca²⁺ handling. The observed dysfunction in atrial myocytes was partly reversed after aerobic interval training.     

Single cell time-resolved quorum responses reveal dependence on cell density and configuration

Bacterial communication via quorum sensing has been extensively investigated in recent years. Bacteria communicate in a complex manner through the production, release, and reception of diffusible low molecular weight chemical signaling molecules. Much work has focused on understanding the basic mechanisms of quorum sensing. As more and more bacteria grow resistant to conventional antibiotics, the development of drugs that do not kill bacteria but instead interrupt their communication is of increasing interest. This study presents a method for analyzing bacterial communication by investigating single cell responses. Most conventional analysis methods for bacterial communication are based on the averaged response from many bacteria, masking how individual cells respond to their immediate environment. We applied a fiber-optic microarray to record cellular communication from single cells. Single cell quorum sensing systems have previously been employed, but the highly ordered array reported here is an improvement because it allows us to simultaneously investigate cellular communication in many different environments with known cellular densities and configurations. We employed this method to detect how genes under quorum regulation are induced or repressed over time on the single cell level and to determine whether cellular density and configuration are indicative of the single cell temporal patterns of gene expression.     

Taking practical learning in STEM education home: Examples from do‐it‐yourself experiments in plant biology

Practical teaching can give authentic learning experiences and teach valuable skills for undergraduate students in the STEM disciplines. One of the main ways of giving students such experiences, laboratory teaching, is met with many challenges such as budget cuts, increased use of virtual learning, and currently the university lockdowns due to the COVID‐19 pandemic. We highlight how at‐home do‐it‐yourself (DIY) experiments can be a good way to include physical interaction with your study organism, system, or technique to give the students a practical, authentic learning experience. We hope that by outlining the benefits of a practical, at‐home, DIY experiment we can inspire more people to design these teaching activities in the current remote teaching situation and beyond. By contributing two examples in the field of plant biology we enrich the database on experiments to draw inspiration from for these teaching methods.     

Next‐generation field courses: Integrating Open Science and online learning

As Open Science practices become more commonplace, there is a need for the next generation of scientists to be well versed in these aspects of scientific research. Yet, many training opportunities for early career researchers (ECRs) could better emphasize or integrate Open Science elements. Field courses provide opportunities for ECRs to apply theoretical knowledge, practice new methodological approaches, and gain an appreciation for the challenges of real‐life research, and could provide an excellent platform for integrating training in Open Science practices. Our recent experience, as primarily ECRs engaged in a field course interrupted by COVID‐19, led us to reflect on the potential to enhance learning outcomes in field courses by integrating Open Science practices and online learning components. Specifically, we highlight the opportunity for field courses to align teaching activities with the recent developments and trends in how we conduct research, including training in: publishing registered reports, collecting data using standardized methods, adopting high‐quality data documentation, managing data through reproducible workflows, and sharing and publishing data through appropriate channels. We also discuss how field courses can use online tools to optimize time in the field, develop open access resources, and cultivate collaborations. By integrating these elements, we suggest that the next generation of field courses will offer excellent arenas for participants to adopt Open Science practices.     

Mound building termites contribute to savanna vegetation heterogeneity

With biomass densities comparable to large ungulates and megaherbivores, termites play a key functional role in many tropical savanna ecosystems. This study focuses on vegetated termite mounds (termitaria) constructed by the Termitidae species Macrotermes herus. We studied how resource rich termitaria affect graminoid herbs (Poaceae and Cyperaceae), forbs and woody species composition and diversity. The density of termitaria explained 89% of the variation in dense thickets in the area. Fire tolerant Acacia species dominated the open savanna while fire sensitive species like Grewia spp. and the succulent Euphorbia candelabrum were restricted to termite mounds. Termitaria plots had four times the mean number of woody species and supported three times as many forb species as the adjacent savanna. For woody species, both the Shannon–Wiener index and the Shannon evenness index were higher on temitaria than on the savanna. There were no differences for graminoid herbs, except for the Shannon evenness index which was higher on termitaria. Our results indicate that graminoid herb richness peaks at lower productivity levels than trees and forbs in savanna ecosystems, as also recently found in temperate areas.     

The influence of missing value imputation on detection of differentially expressed genes from microarray data

MOTIVATION: Missing values are problematic for the analysis of microarray data. Imputation methods have been compared in terms of the similarity between imputed and true values in simulation experiments and not of their influence on the final analysis. The focus has been on missing at random, while entries are missing also not at random. RESULTS: We investigate the influence of imputation on the detection of differentially expressed genes from cDNA microarray data. We apply ANOVA for microarrays and SAM and look to the differentially expressed genes that are lost because of imputation. We show that this new measure provides useful information that the traditional root mean squared error cannot capture. We also show that the type of missingness matters: imputing 5% missing not at random has the same effect as imputing 10-30% missing at random. We propose a new method for imputation (LinImp), fitting a simple linear model for each channel separately, and compare it with the widely used KNNimpute method. For 10% missing at random, KNNimpute leads to twice as many lost differentially expressed genes as LinImp. AVAILABILITY: The R package for LinImp is available at http://folk.uio.no/idasch/imp.     

Bioreactor design for propagation of somatic embryos

Six identical bioreactors were constructed and built at the Agricultural University of Norway to provide optimal conditions for plant cell regeneration from cells into somatic embryos (clonal or somatic seeds). This was made possible through cooperation in COST87 by a European network in a working group on regeneration from plant cell cultures. The bioreactor design provides gentle stirring through a slow-speed stirrer that regularly changes direction of rotation to prevent quiet zones in the suspension in which cells can settle and grow. In addition, the oxygen is provided, bubble-free, through thin silicone tubing loops that are hanging loose, moving with the liquid to prevent cell growth on these tubes. We used off-the-shelf components whenever possible, to reduce the costs to a minimum, which was another aim of the construction. The result was a suite of relatively inexpensive computer-controlled bioreactors that could control temperature, oxygen, pH, stirrer speed and stirrer direction. In addition, we have provided different light spectral qualities by simple means of filtering the light. Using the present software, the parameters can be set up to alter every hour during the 24-h day/night cycle. All our cultures have improved growth in the bioreactors compared to identical cultures in Erlenmeyer flasks. The cultures used are: embryogenic cultures of carrot (Daucus carota), Norway spruce (Picea abies), birch (Betula pendula), cyclamen (Cyclamen persicum) and shoot cultures of Christmas begonia (Begonia x cheimantha). The paper also discusses recommendations for improvements of the current system for future revisions.