The Emergence of Scaling in Sequence-based Physical Models of Protein Evolution

It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other systems has previously been explained using network growth models that, while motivated by biological processes, do not explicitly consider the underlying physics or biology. In the present work we explore a sequence-based model for the evolution protein structures and demonstrate that this model is able to recapitulate the scale-free nature observed in graphs of real protein structures. We find that this model also reproduces other statistical feature of the protein domain graph. This represents, to our knowledge, the first such microscopic, physics-based evolutionary model for a scale-free network of biological importance and as such has strong implications for our understanding of the evolution of protein structures and of other biological networks.Comment: 20 pages (including figures), 4 figures, to be submitted to PNA

Computational screening of structural and compositional factors for electrically conductive coordination polymers

The combination of organic and inorganic chemical building blocks to form metal–organic frameworks (MOFs) offers opportunities for producing functional materials suitable for energy generation, storage and conversion. However, such applications rely on robust electron transport and the design of conductive hybrid materials is still in its infancy. Here we apply density functional theory to assess the important structural and compositional factors for forming conducting MOFs. We focus on 1D metal–organic polymers as a model system and assess the choice of organic, inorganic and linking units. The results demonstrate that electronic communication is sensitive to the energy and symmetry of the frontier orbitals associated with the organic and inorganic building blocks and offers guidance on how to optimise electrical conduction in hybrid materials

Computational screening of structural and compositional factors for electrically conductive coordination polymers

The combination of organic and inorganic chemical building blocks to form metal-organic frameworks (MOFs) offers opportunities for producing functional materials suitable for energy generation, storage and conversion. However, such applications rely on robust electron transport and the design of conductive hybrid materials is still in its infancy. Here we apply density functional theory to assess the important structural and compositional factors for forming conducting MOFs. We focus on 1D metal-organic polymers as a model system and assess the choice of organic, inorganic and linking units. The results demonstrate that electronic communication is sensitive to the energy and symmetry of the frontier orbitals associated with the organic and inorganic building blocks and offers guidance on how to optimise electrical conduction in hybrid materials

First principles static and dynamic calculations for the transition metal hydride series MH4L3 (M= Fe, Ru and Os; L = NH3, PH3 and PF3)

International audienc

Neural processing of emotional facial stimuli in specific phobia: An fMRI study

Background Patients with specific phobia (SP) show altered brain activation when confronted with phobia-specific stimuli. It is unclear whether this pathogenic activation pattern generalizes to other emotional stimuli. This study addresses this question by employing a well-powered sample while implementing an established paradigm using nonspecific aversive facial stimuli. Methods N = 111 patients with SP, spider subtype, and N = 111 healthy controls (HCs) performed a supraliminal emotional face-matching paradigm contrasting aversive faces versus shapes in a 3-T magnetic resonance imaging scanner. We performed region of interest (ROI) analyses for the amygdala, the insula, and the anterior cingulate cortex using univariate as well as machine-learning-based multivariate statistics based on this data. Additionally, we investigated functional connectivity by means of psychophysiological interaction (PPI). Results Although the presentation of emotional faces showed significant activation in all three ROIs across both groups, no group differences emerged in all ROIs. Across both groups and in the HC > SP contrast, PPI analyses showed significant task-related connectivity of brain areas typically linked to higher-order emotion processing with the amygdala. The machine learning approach based on whole-brain activity patterns could significantly differentiate the groups with 73% balanced accuracy. Conclusions Patients suffering from SP are characterized by differences in the connectivity of the amygdala and areas typically linked to emotional processing in response to aversive facial stimuli (inferior parietal cortex, fusiform gyrus, middle cingulate, postcentral cortex, and insula). This might implicate a subtle difference in the processing of nonspecific emotional stimuli and warrants more research furthering our understanding of neurofunctional alteration in patients with SP.Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Peer Reviewe

Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder

Purpose We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). Methods Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. Results We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. Conclusion Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals

Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder

PURPOSE: We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). METHODS: Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. RESULTS: We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. CONCLUSION: Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata-Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals

Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation

<p>Abstract</p> <p>Background</p> <p>The ultimate goal of synthetic biology is the conception and construction of genetic circuits that are reliable with respect to their designed function (e.g. oscillators, switches). This task remains still to be attained due to the inherent synergy of the biological building blocks and to an insufficient feedback between experiments and mathematical models. Nevertheless, the progress in these directions has been substantial.</p> <p>Results</p> <p>It has been emphasized in the literature that the architecture of a genetic oscillator must include positive (activating) and negative (inhibiting) genetic interactions in order to yield robust oscillations. Our results point out that the oscillatory capacity is not only affected by the interaction polarity but by how it is implemented at promoter level. For a chosen oscillator architecture, we show by means of numerical simulations that the existence or lack of competition between activator and inhibitor at promoter level affects the probability of producing oscillations and also leaves characteristic fingerprints on the associated period/amplitude features.</p> <p>Conclusions</p> <p>In comparison with non-competitive binding at promoters, competition drastically reduces the region of the parameters space characterized by oscillatory solutions. Moreover, while competition leads to pulse-like oscillations with long-tail distribution in period and amplitude for various parameters or noisy conditions, the non-competitive scenario shows a characteristic frequency and confined amplitude values. Our study also situates the competition mechanism in the context of existing genetic oscillators, with emphasis on the Atkinson oscillator.</p

Evergreen broadleaf greenness and its relationship with leaf flushing, aging, and water fluxes

13 Pág. Departamento de Medio Ambiente y Agronomía​ (INIA)Remote sensing capabilities to monitor evergreen broadleaved vegetation are limited by the low temporal variability in the greenness signal. With canopy greenness computed from digital repeat photography (PhenoCam), we investigated how canopy greenness related to seasonal changes in leaf age and traits as well as variation of trees’ water fluxes (characterized by sap flow and canopy conductance). The results showed that sprouting leaves are mainly responsible for the rapid increase in canopy green chromatic coordinate (GCC) in spring. We found statistically significantly differences in leaf traits and spectral properties among leaves of different leaf ages. Specifically, mean GCC of young leaves was 0.385 ± 0.010 (mean ± SD), while for mature and old leaves was 0.369 ± 0.003, and 0.376 ± 0.004, respectively. Thus, the temporal dynamics of canopy GCC can be explained by changes in leaf spectral properties and leaf age. Sap flow and canopy conductance are both well explained by a combination of environmental drivers and greenness (96% and 87% of the variance explained, respectively). In particular, air temperature and vapor pressure deficit (VPD) explained most of sap flow and canopy conductance variance, respectively. Besides, GCC is an important explanatory variable for variation of canopy conductance may because GCC can represent the leaf ontogeny information. We conclude that PhenoCam GCC can be used to identify the leaf flushing for evergreen broadleaved trees, which carries important information about leaf ontogeny and traits. Thus, it can be helpful for better estimating canopy conductance which constraints water fluxes.The authors acknowledge the Alexander von Humboldt Foundation for supporting this research with the Max Planck Prize to Markus Reichstein. Yunpeng Luo and Mirco Migliavacca gratefully acknowledge the financial support from the China Scholarship Council. ADR acknowledges support for the PhenoCam network from the National Science Foundation ( DEB- 1702697 ). Javier Pacheco-Labrador and Mirco Migliavacca acknowledge the German Aerospace Center (DLR) project OBEF-Accross2 “The Potential of Earth Observations to Capture Patterns of Biodiversity” (Contract No. 50EE1912). The research also received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 721995 and Ministerio de Economíay Competitividad through FLUXPEC CGL2012-34383 and SynerTGE CGL2015-G9095-R (MINECO/FEDER, UE) projects.Peer reviewe

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique living laboratory for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity