Drivers of vegetative dormancy across herbaceous perennial plant species

Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life‐history costs of sprouting, and of dormancy. Short‐lived and mycoheterotrophic species have higher proportions of dormant plants than long‐lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.     

Neuroprotective effects of Mycoplasma hyorhinis against amyloid-β-peptide toxicity in SH-SY5Y human neuroblastoma cells are mediated by calpastatin upregulation in the mycoplasma-infected cells

Mycoplasmas are frequent contaminants of cell cultures. Contamination leads to altered synthetic and metabolic pathways. We have found that contamination of neuroblastoma SH-SY5Y cells by a strain of Mycoplasma hyorhinis derived from SH-SY5Y cell culture (NDMh) leads to increased levels of calpastatin (the endogenous inhibitor of the Ca(2+)-dependent protease, calpain) in NDMh-infected cells. We have now examined effects of amyloid-β-peptide (Aβ) (central to the pathogenesis of Alzheimer's disease) on uncontaminated (clean) and NDMh-infected SH-SY5Y cells. Aβ was toxic to clean cells, resulting in necrotic cell damage. Aβ treatment led to activation of calpain and enhanced proteolysis, cell swelling, cell membrane permeability to propidium iodide (PI) (without nuclear apoptotic changes), and diminished mitochondrial enzyme activity (XTT reduction). Aβ-toxicity was attenuated in the high calpastatin-containing NDMh-infected cells, as shown by inhibition of calpain activation and activity, no membrane permeability, normal cell morphology, and maintenance of mitochondrial enzyme activity (similar to attenuation of Aβ-toxicity in non-infected cells overexpressing calpastatin following calpastatin-plasmid introduction into the cells). By contrast, staurosporine affected both clean and infected cells, causing apoptotic damage (cell shrinkage, nuclear apoptotic alterations, caspase-3 activation and caspase-promoted proteolysis, without PI permeability, and without effect on XTT reduction). The results indicate that mycoplasma protects the cells against certain types of insults involving calpain. The ratio of calpastatin to calpain is an important factor in the control of calpain activity. Exogenous pharmacological means, including calpastatin-based inhibitors, have been considered for therapy of various diseases in which calpain is implicated. Mycoplasmas provide the first naturally occurring biological system that upregulates the endogenous calpain inhibitor, and thus may be of interest in devising treatments for some disorders, such as neurodegenerative diseases.     

The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes

It is known that there are several codes residing simultaneously on the DNA double helix. The two best-characterized codes are the genetic code—the code for protein production, and the code for DNA packaging into nucleosomes. Since these codes have to coexist simultaneously on the same DNA region, both must be degenerate to allow this coexistence. A-tracts are homopolymeric stretches of several adjacent deoxyadenosines on one strand of the double helix, having unusual structural properties, which were shown to exclude nucleosomes and as such are instrumental in setting the translational positioning of DNA within nucleosomes. We observe, cross-kingdoms, a strong codon bias toward the avoidance of long A-tracts in exon regions, which enables the formation of high density of nucleosomes in these regions. Moreover, long A-tract avoidance is restricted exclusively to nucleosome-occupied exon regions. We show that this bias in codon usage is sufficient for enabling DNA organization within nucleosomes without constraints on the actual code for proteins. Thus, there is inter-dependency of the two major codes within DNA to allow their coexistence. Furthermore, we show that modulation of A-tract occurrences in exon versus non-exon regions may result in a unique alternation of the diameter of the ‘30-nm’ fiber model.     

Theme section on mesophotic coral ecosystems: advances in knowledge and future perspectives

The Second International Mesophotic Coral Ecosystems (MCEs) workshop was held in Eilat, Israel, October 26–31, 2014. Here we provide an account of: (1) advances in our knowledge of MCE ecology, including the central question of the potential vertical connectivity between MCEs and shallow-water reefs (SWRs), and that of the validity of the deep-reef refugia hypothesis (DRRH); (2) the contribution of the 2014 MCE workshop to the central question presented in (1), as well as its contribution to novel MCE studies on corals, sponges, fish, and crabs; and (3) gaps, priorities, and recommendations for future research stemming from the workshop. Despite their close proximity to well-studied SWRs, and the growing evidence of their importance, our scientific knowledge of MCEs is still in its infancy. During the last five years, we have witnessed an ever-increasing scientific interest in MCEs, expressed in the exponential increase in the number of publications studying this unique environment. The emerging consensus is that lower MCE benthic assemblages represent unique communities, either of separate species or genetically distinct individuals within species, and any significant support for the DRRH will be limited to upper MCEs. Determining the health and stability of MCEs, their biodiversity, and the degree of genetic connectivity among SWRs and MCEs, will ultimately indicate the ability of MCEs to contribute to the resilience of SWRs and help to guide future management and conservation strategies. MCEs deserve therefore management consideration in their own right. With the technological advancements taking place in recent years that facilitate access to MCEs, the prospects for exciting and innovative discoveries resulting from MCE research, spanning a wide variety of fields, are immense.     

Cognitive function in adolescence and the risk for premature diabetes and cardiovascular mortality in adulthood

Background

Epidemiological studies have demonstrated a relationship between cognitive function in youth and the future risk of death. Less is known regarding the relationship with diabetes related death. This study assessed the relationship between cognitive function in late adolescence and the risk for diabetes, cardiovascular- (CVD) and all-cause mortality in adulthood.

Methods

This retrospective study linked data from 2,277,188 16–19 year olds who had general intelligence tests (GIT) conducted during pre-military recruitment assessment with cause of death as coded by the Israel Central Bureau of Statistics. The associations between cognitive function and cause-specific mortality were assessed using Cox models.

Results

There were 31,268 deaths that were recorded during 41,916,603 person-years of follow-up, with a median follow-up of 19.2 (IQR 10.7, 29.5) years. 3068, 1443, 514 and 457 deaths were attributed to CVD, CHD, stroke, and diabetes, respectively. Individuals in the lowest GIT vs. highest GIT quintiles in unadjusted models had the highest risk for all-cause mortality (HR 1.84, 95% CI 1.78, 1.91), total CVD (HR 3.32, 95% CI 2.93, 3.75), CHD (HR 3.49 95% CI 2.92, 4.18), stroke (HR 3.96 95% CI 2.85, 5.5) and diabetes-related (HR 6.96 95% CI 4.68, 10.36) mortality. These HRs were attenuated following adjustment for age, sex, birth year, body-mass index, residential socioeconomic status, education and country of origin for all-cause (HR 1.23, 95% CI 1.17, 1.28), CVD (HR 1.76, 95% CI 1.52, 2.04), CHD (HR 1.7 95% CI 1.37, 2.11), stroke (HR 2.03, 95% CI 1.39, 2.98) and diabetes-related (HR 3.14 95% CI 2.00, 4.94) mortality. Results persisted in a sensitivity analyses limited to participants with unimpaired health at baseline and that accounted competing risk.

Conclusions

This analysis of over 2 million demonstrates a strong relationship between cognitive function at youth and the risk for diabetes, all-cause and CVD-related mortality independent of adolescent obesity.

     

Mycorrhizal fungal spore community structure in a manipulated prairie

Most plant communities support a diverse assemblage of arbuscular mycorrhizal fungi (AMF). AMF communities have the potential to affect plant community structure and vice versa. We examined AMF sporulation in a 4.5‐ha reconstructed prairie in Eau Claire County, Wisconsin. In fall 2003, the site was planted with varied numbers and combinations of native prairie species from four functional guilds: C₃ grasses/sedges, C₄ grasses, legume, and nonleguminous forbs. We hypothesized that more diverse plant seeding mixtures would promote AMF diversity. To examine the interaction between plant and fungal communities, plots were divided and subplots treated with the fungicide chlorothalonil to suppress AMF, enriched with ammonium nitrate fertilizer, treated with both fungicide and nitrogen, or remained untreated (control). Soil samples were collected during the summers of 2004, 2006, and 2007 from each subplot. Spores of AMF were extracted, identified to species, and enumerated. Initial plant seeding diversity did not significantly influence spore abundance, fungal diversity, plant productivity, or plant richness 4 years after establishment. Fungal species richness was positively, but weakly, correlated with plant productivity (r² = 0.11) and plant richness (r² = 0.09). Fungal community composition changed significantly over time; nitrogen addition, fungicide application, and site characteristics also shaped community composition. After 4 years of treatment, nitrogen and fungicide reduced AMF richness, changed sporulation patterns among AMF taxa, and reduced diversity and productivity in plant communities. Divergence in AMF community is being mirrored by changes in the plant community independent of initial seeding treatments, though causation could not be determined.     

Student-centered introductory biology course: evidence for deep learning

Our interpretative study that was carried out in a science and engineering oriented university examined the ways students in an introductory biology course perceived their learning in the course that was substantially changed to allow student-centered learning. The instructional change was framed by the view of learning as a sociocultural activity as well as a cognitive process that can take place face-to-face or through online interaction. Most of the lectures were substituted with individual learning and project-based, small-group learning that lasted one month. Data were collected through interviews with students and instructors, and through observations. In the paper, we show evidence for deep learning that was associated by the students and the instructors with short-term, meaningful activities in a setting that included collaborative peer learning; and replacing most lectures by small group learning that ended in a mini-conference. Deep learning was evidenced by the ways students reflected on how they organised and applied knowledge using deep learning strategies.