Density functional theory for strongly interacting electrons

We present an alternative to the Kohn-Sham formulation of density functional theory for the ground-state properties of strongly interacting electronic systems. The idea is to start from the limit of zero kinetic energy and systematically expand the universal energy functional of the density in powers of a "coupling constant" that controls the magnitude of the kinetic energy. The problem of minimizing the energy is reduced to the solution of a strictly correlated electron problem in the presence of an effective potential, which plays in our theory the same role that the Kohn-Sham potential plays in the traditional formulation. We discuss several schemes for approximating the energy functional, and report preliminary results for low-density quantum dots.Comment: Revised version, to appear in Phys. Rev. Let

Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi : is the picture complete?

Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.</p

Evolutionary flexibility of protein complexes

<p>Abstract</p> <p>Background</p> <p>Proteins play a key role in cellular life. They do not act alone but are organised in complexes. Throughout the life of a cell, complexes are dynamic in their composition due to attachments and shared components. Experimental and computational evidence indicate that consecutive addition and secondary losses of components played a major role in the evolution of some complexes, mostly without affecting the core function. Here, we analysed in a large scale approach whether this flexibility in evolution is only limited to a distinct number of complexes or represents a more general trend.</p> <p>Results</p> <p>Focussing on human protein complexes, we based our analysis on a manually curated dataset from HPRD. In total, 1,060 complexes with 6,136 proteins from 2,187 unique genes were considered. We computed interologs in 25 different species and predicted the composition of complexes. Over the analysed species, the composition of most complexes was highly flexible and only 25% of all genes were never lost. Even if one component was lost at a particular point in time, the fraction of observed second, independent losses of additional components was high (75% of all complexes affected). Still, loss of whole complexes happened rarely. This biological signal deviated significantly from random models. We exemplified this trend on the anaphase promoting complex (APC) where a core is highly conserved throughout all metazoans, but flexibility in certain components is observable.</p> <p>Conclusion</p> <p>Consecutive additions and losses of distinct units is a fundamental process in the evolution of protein complexes. These evolutionary events affecting genes coding for units in human protein complexes showed a significantly different phylogenetic pattern compared to randomly selected genes. Determination of taxon specific attachments or losses might be linked to specific cellular or morphological features. Thus, protein complexes contain not only structural and functional, but also evolutionary cores.</p

Modelling understorey dynamics in temperate forests under global change : challenges and perspectives

The understorey harbours a substantial part of vascular plant diversity in temperate forests and plays an important functional role, affecting ecosystem processes such as nutrient cycling and overstorey regeneration. Global change, however, is putting these understorey communities on trajectories of change, potentially altering and reducing their functioning in the future. Developing mitigation strategies to safeguard the diversity and functioning of temperate forests in the future is challenging and requires improved predictive capacity. Process-based models that predict understorey community composition over time, based on first principles of ecology, have the potential to guide mitigation endeavours but such approaches are rare. Here, we review fourteen understorey modelling approaches that have been proposed during the last three decades. We evaluate their inclusion of mechanisms that are required to predict the impact of global change on understorey communities. We conclude that none of the currently existing models fully accounts for all processes that we deem important based on empirical and experimental evidence. Based on this review, we contend new models are needed to project the complex impacts of global change on forest understoreys. Plant functional traits should be central to such future model developments, as they drive community assembly processes and provide valuable information on the functioning of the understorey. Given the important role of the overstorey, a coupling of understorey models to overstorey models will be essential to predict the impact of global change on understorey composition and structure, and how it will affect the functioning of temperate forests in the future

Монастырь Сурб-Хач – очаг национальной армянской культуры

Сегодня современное общество и наука все чаще обращает свои взоры на великую культуру ушедших эпох. Армянский монастырь Сурб-Хач - один из немногих памятников древней архитектуры Крыма, дошедших до наших дней. Поднять из забытья этот уникальный комплекс - одна из задач, которую ставит перед собой авторСьогодні сучасне суспільство і наука все частіше обертає свої погляди на велику культуру епох, що пішли. Вірменський монастир Сурб-Хач - один з небагатьох пам'ятників стародавньої архітектури Криму, що дійшли до наших днів. Підняти із забуття цей унікальний комплекс - одна із задач, яку ставить перед собою авто

Pengaruh Kerjasama Pasiad Indonesia dengan Indonesia Dibidang Pendidikan Menengah

This study describes the effect of PASIAD Indonesia cooperation with Indonesia in the field of secondary education. PASIAD Indonesia is a non-governmental organization (NGO) engaged in educational, social, economic and cultural PASIAD Indonesia began working in secondary education in Indonesia since 1995. Until now PASIAD Indonesia has collaborated with 7 private foundations and 3 local governments to hold 10 high school.Perspective that used in this research is Pluralisme perspective. The theory used in this research is International Coorporation dan Transnational Advocacy Network ( TAN). This research used a qualitative method that is an explanatory. by using the techniques of data collection through literature and documentation, ie by collecting data from books, journals, magazines, newspapers, and other sources (document analysis).As a result, the effect of Indonesian PASIAD cooperation with Indonesia in the field of secondary education a positive impact on improving the quality of secondary education in Indonesia. Where PASIAD Indonesia Conducting scientific competition in national and international scale that encourage student creativity thinking and promote the spirit of competition to the students. besides school work partners PASIAD also always present medals to Indonesian state education can improve the image of Indonesia in the international arenaKey words : PASIAD Indonesia, non govermental organization, Transnationa Advocacy Network, secondary education

Особенности процесса обезвоживания угольной пульпы на вибрирующей волнообразной поверхности

На основі лабораторних технологічних досліджень процесу зневоднення вугільної пльпи на вібруючій хвилеподібній поверхні з двома рівнями знакозмінної кривини на основі сит динамічно активних стрічкових СДАС-дефлектор представлені осбливості переміщення надрешетного матеріалу в умовах дії високочастотних коливань і змінних значень режимних і конструктивних параметрів. Наведені графіки залежностей вологості надрешетного продукту від різних умов технологічного процесу. Виконаний аналіз цих залежностей.On the base of laboratory reseachs of the process dewatering of the coal pulp on the vibrating undulating surface with two levels sign-variable curve on the base of sieves of dynamical active belting SDAB-deflector was adduced peculiarity of the displacement oversieve material in the condirions acting high-frequency vibrations and variable meanings of the regime and constructive parameters. The plots of dependences of the moisture oversieve product from the different conditions of the technological process is adduce. The analysis of this dependences was implemented

Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome

Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio- generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of nextgeneration sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBiogenerated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome sanalyses to facilitate functional studies into an organism’s biology

Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1

Polycomb group proteins, as part of the Polycomb repressive complexes, are essential in gene repression through chromatin compaction by canonical PRC1, mono-ubiquitylation of histone H2A by non-canonical PRC1 and tri-methylation of histone H3K27 by PRC2. Despite prevalent models emphasizing tight functional coupling between PRC1 and PRC2, it remains unclear whether this paradigm indeed reflects the evolution and functioning of these complexes. Here, we conduct a comprehensive analysis of the presence or absence of cPRC1, nPRC1 and PRC2 across the entire eukaryotic tree of life, and find that both complexes were present in the Last Eukaryotic Common Ancestor (LECA). Strikingly, ~42% of organisms contain only PRC1 or PRC2, showing that their evolution since LECA is largely uncoupled. The identification of ncPRC1-defining subunits in unicellular relatives of animals and fungi suggests ncPRC1 originated before cPRC1, and we propose a scenario for the evolution of cPRC1 from ncPRC1. Together, our results suggest that crosstalk between these complexes is a secondary development in evolution.</p

Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1

Polycomb group proteins, as part of the Polycomb repressive complexes, are essential in gene repression through chromatin compaction by canonical PRC1, mono-ubiquitylation of histone H2A by non-canonical PRC1 and tri-methylation of histone H3K27 by PRC2. Despite prevalent models emphasizing tight functional coupling between PRC1 and PRC2, it remains unclear whether this paradigm indeed reflects the evolution and functioning of these complexes. Here, we conduct a comprehensive analysis of the presence or absence of cPRC1, nPRC1 and PRC2 across the entire eukaryotic tree of life, and find that both complexes were present in the Last Eukaryotic Common Ancestor (LECA). Strikingly, ~42% of organisms contain only PRC1 or PRC2, showing that their evolution since LECA is largely uncoupled. The identification of ncPRC1-defining subunits in unicellular relatives of animals and fungi suggests ncPRC1 originated before cPRC1, and we propose a scenario for the evolution of cPRC1 from ncPRC1. Together, our results suggest that crosstalk between these complexes is a secondary development in evolution