What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.     

What's in a crowd? Analysis of face-to-face behavioral networks

The availability of new data sources on human mobility is opening new avenues for investigating the interplay of social networks, human mobility and dynamical processes such as epidemic spreading. Here we analyze data on the time-resolved face-to-face proximity of individuals in large-scale real-world scenarios. We compare two settings with very different properties, a scientific conference and a long-running museum exhibition. We track the behavioral networks of face-to-face proximity, and characterize them from both a static and a dynamic point of view, exposing differences and similarities. We use our data to investigate the dynamics of a susceptible-infected model for epidemic spreading that unfolds on the dynamical networks of human proximity. The spreading patterns are markedly different for the conference and the museum case, and they are strongly impacted by the causal structure of the network data. A deeper study of the spreading paths shows that the mere knowledge of static aggregated networks would lead to erroneous conclusions about the transmission paths on the dynamical networks.     

Does autophagy mediate age-dependent effect of dietary restriction responses in the filamentous fungus Podospora anserina?

Autophagy is a well-conserved catabolic process, involving the degradation of a cell''s own components through the lysosomal/vacuolar machinery. Autophagy is typically induced by nutrient starvation and has a role in nutrient recycling, cellular differentiation, degradation and programmed cell death. Another common response in eukaryotes is the extension of lifespan through dietary restriction (DR). We studied a link between DR and autophagy in the filamentous fungus Podospora anserina, a multicellular model organism for ageing studies and mitochondrial deterioration. While both carbon and nitrogen restriction extends lifespan in P. anserina, the size of the effect varied with the amount and type of restricted nutrient. Natural genetic variation for the DR response exists. Whereas a switch to carbon restriction up to halfway through the lifetime resulted in extreme lifespan extension for wild-type P. anserina, all autophagy-deficient strains had a shorter time window in which ageing could be delayed by DR. Under nitrogen limitation, only PaAtg1 and PaAtg8 mediate the effect of lifespan extension; the other autophagy-deficient mutants PaPspA and PaUth1 had a similar response as wild-type. Our results thus show that the ageing process impinges on the DR response and that this at least in part involves the genetic regulation of autophagy.     

What's in a name? Aschersonia insperata: a new pleoanamorphic fungus with characteristics of Aschersonia and Hirsutella

A new anamorphic species from a Philippine tropical forest occurs as reddish-orange to orange, tuberculate stromata on unidentified homopteran larvae, and produces both Aschersonia and Hirsutella-like synanamorphs. A molecular phylogenetic analysis was conducted to determine the most appropriate generic placement for this fungus. Based on its phylogenetic relationships, a comparison of the complexity and persistence of each anamorph, and the speculated relevance of each synanamorph to survival, we describe the new fungus as Aschersonia insperata sp. nov.     

Misunderstanding in the classification of diabetes mellitus. What's in a name?

To assess whether physicians, residents, medical students, hospital diagnosis coders, and patients properly use the designations insulin-dependent diabetes mellitus (IDDM) and non-insulin-dependent diabetes mellitus (NIDDM) that were established by criteria of the National Diabetes Data Group, we reviewed clinic and hospital records and administered questionnaires. Although essentially all cases of true IDDM were identified as such and most cases of NIDDM not requiring insulin therapy were correctly identified by all groups, patients with NIDDM on insulin therapy were misidentified as having IDDM by 38% of residents in internal medicine clinics and 68% of primary care and surgical subspecialty residents. On a survey, of 22 patients with NIDDM on insulin therapy, 17 (77%) considered themselves to have IDDM. Thus, patients who have NIDDM by the established criteria who are on insulin therapy are commonly mislabeled as having IDDM. We present an approach for dealing with this problem by adapting nomenclature focusing on insulin deficiency and resistance. It would probably also be helpful to separately identify the subset of patients with "insulin-deficient diabetes" who are ketosis-prone. It is important to use immunologic profiling (islet cell antibody testing) and insulin sensitivity or deficiency testing (C-peptide levels).     

What's in a name?

Have you ever wondered why professionals have so many complicated names for things? Two reasons come to mind: efficient communication, but also 'show'. Connecting with a wider audience means learning to tread the fine line between perfect accuracy and being understood.     

What's in a name?

The names of organisms have major impacts on the geopolitical world. The current state of flux in the taxonomy of the genera Cryptosporidium and Giardia illustrates the effects that names can have on environmental and governmental policy. Taxonomy remains a vital science that is very much alive in the application of modern methods for describing morphologically cryptic species.     

What's in a centromere?

The complete sequence of rice centromere 8 reveals a small amount of centromere-specific satellite sequence in blocks interrupted by retrotransposons and other repetitive DNA, in an arrangement that is strikingly similar in overall size and content to other centromeres of multicellular eukaryotes.