Evidence for a strong correlation between transcription factor protein disorder and organismic complexity

Studies of diverse phylogenetic lineages reveal that protein disorder increases in concert with organismic complexity but that differences nevertheless exist among lineages. To gain insight into this phenomenology, we analyzed all of the transcription factor (TF) families for which sequences are known for 17 species spanning bacteria, yeast, algae, land plants, and animals and for which the number of different cell types has been reported in the primary literature. Although the fraction of disordered residues in TF sequences is often moderately or poorly correlated with organismic complexity as gauged by cell-type number (r20.8). Furthermore, the correlation between the fraction of disordered residues and cell-type number becomes stronger when confined to the TF families participating in cell cycle, cell size, cell division, cell differentiation, or cell proliferation, and other important developmental processes. The data also indicate that evolutionarily simpler organisms allow for the detection of subtle differences in the conserved IDRs of TFs as well as changes in variable IDRs, which can influence the DNA recognition and multifunctionality of TFs through direct or indirect mechanisms. Although strong correlations cannot be taken as evidence for causeand-effect relationships, we interpret our data to indicate that increasing TF disorder likely was an important factor contributing to the evolution of organismic complexity and not merely a concurrent unrelated effect of increasing organismic complexity

Evolution of Protein Ductility in Duplicated Genes of Plants

Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of diverse phylogenetic lineages have revealed: (1) that protein ductility increases in concert with organismic complexity, and (2) that distributions of IDPs and IDRs along the chromosomes of plant species are non-random and correlate with variations in the rates of the genetic recombination and chromosomal rearrangement. Here, we show that approximately 50% of aligned residues in paralogs across a spectrum of algae, bryophytes, monocots, and eudicots are IDRs and that a high proportion (ca. 60%) are in disordered segments greater than 30 residues. When three types of IDRs are distinguished (i.e., identical, similar and variable IDRs) we find that species with large numbers of chromosome and endoduplicated genes exhibit paralogous sequences with a higher frequency of identical IDRs, whereas species with small chromosomes numbers exhibit paralogous sequences with a higher frequency of similar and variable IDRs. These results are interpreted to indicate that genome duplication events influence the distribution of IDRs along protein sequences and likely favor the presence of identical IDRs (compared to similar IDRs or variable IDRs). We discuss the evolutionary implications of gene duplication events in the context of ductile/disordered residues and segments, their conservation, and their effects on functionality

Leaf shape influences the scaling of leaf dry mass vs. area: a test case using bamboos

Key message A highly significant and positive scaling relationship between bamboo leaf dry mass and leaf surface area was observed; leaf shape (here, represented by the quotient of leaf width and length) had a significant influence on the scaling exponent of leaf dry mass vs. area. Context The scaling of leaf dry mass vs. leaf area is important for understanding how plants effectively intercept sunlight and invest carbon to do so. However, comparatively few, if any, studies have focused on whether leaf shape influences this scaling relationship. Aims In order to explore the effects of leaf shape on the scaling relationship between leaf dry mass and area, we examined 101 species, varieties, forms, and cultivars of bamboo growing in China and identified the relationship between the scaling exponent of leaf dry mass vs. area and leaf shape. This taxon was used because its leaf shape is conserved across species and, therefore, easily quantified. Methods Ten thousand and forty-five leaves from 101 bamboo species, varieties, forms, and cultivars growing in China were collected, and leaf dry mass, the quotient of leaf width and length, leaf area, and leaf dry mass per unit area were measured. The effect of leaf shape that can be easily quantified using the quotient of leaf width and length on the relevant and ecologically important scaling exponents was explored using this data base. Results Leaf dry mass and area differed significantly across bamboo genera, and even within the same genus. However, a statistically robust log-log linear and positive scaling relationship was observed for mass and area with a 1.115 scaling exponent (95% CI = 1.107, 1.122; r(2) = 0.907). Leaf shape had a significant influence on the numerical values of the scaling exponent of leaf dry mass vs. area. When the median of the quotient of leaf width and length was below 0.125, the numerical value of the scaling exponent increased with increasing quotient of leaf width and length. When the median of the quotient of leaf width and length was above 0.125, the scaling exponent numerically decreased toward 1.0. Conclusion We show, for the first time, that a significant relationship exists between leaf shape and the numerical values of scaling exponents governing the scaling of leaf dry mass with respect to leaf area. In addition, we show that with the quotient of leaf width and length increasing mean LMA increases, which implies a negative correlation between mean LMA and the estimated exponent of leaf dry mass vs. area for the grouped data based on the sorted quotients of leaf width and length

Multiple Front Propagation Into Unstable States

The dynamics of transient patterns formed by front propagation in extended nonequilibrium systems is considered. Under certain circumstances, the state left behind a front propagating into an unstable homogeneous state can be an unstable periodic pattern. It is found by a numerical solution of a model of the Fr\'eedericksz transition in nematic liquid crystals that the mechanism of decay of such periodic unstable states is the propagation of a second front which replaces the unstable pattern by a another unstable periodic state with larger wavelength. The speed of this second front and the periodicity of the new state are analytically calculated with a generalization of the marginal stability formalism suited to the study of front propagation into periodic unstable states. PACS: 47.20.Ky, 03.40.Kf, 47.54.+rComment: 12 page

Inheritance of deleterious mutations at both BRCA1 and BRCA2 in an international sample of 32,295 women

Background: Most BRCA1 or BRCA2 mutation carriers have inherited a single (heterozygous) mutation. Transheterozygotes (TH) who have inherited deleterious mutations in both BRCA1 and BRCA2 are rare, and the consequences of transheterozygosity are poorly understood. Methods: From 32,295 female BRCA1/2 mutation carriers, we identified 93 TH (0.3 %). "Cases" were defined as TH, and "controls" were single mutations at BRCA1 (SH1) or BRCA2 (SH2). Matched SH1 "controls" carried a BRCA1 mutation found in the TH "case". Matched SH2 "controls" carried a BRCA2 mutation found in the TH "case". After matching the TH carriers with SH1 or SH2, 91 TH were matched to 9316 SH1, and 89 TH were matched to 3370 SH2. Results: The majority of TH (45.2 %) involved the three common Jewish mutations. TH were more likely than SH1 and SH2 women to have been ever diagnosed with breast cancer (BC; p = 0.002). TH were more likely to be diagnosed with ovarian cancer (OC) than SH2 (p = 0.017), but not SH1. Age at BC diagnosis was the same in TH vs. SH1 (p = 0.231), but was on average 4.5 years younger in TH than in SH2 (p < 0.001). BC in TH was more likely to be estrogen receptor (ER) positive (p = 0.010) or progesterone receptor (PR) positive (p = 0.013) than in SH1, but less likely to be ER positive (p < 0.001) or PR positive (p = 0.012) than SH2. Among 15 tumors from TH patients, there was no clear pattern of loss of heterozygosity (LOH) for BRCA1 or BRCA2 in either BC or OC. Conclusions: Our observations suggest that clinical TH phenotypes resemble SH1. However, TH breast tumor marker characteristics are phenotypically intermediate to SH1 and SH2