Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study

Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants.Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included), submitted to Chemical Physic

Optimasi Metode Cryotherapy Untuk Mengeliminasi Virus Pada Tunas Kentang in Vitro

Penggunaan benih kentang generasi awal dan bebas virus merupakan kunci keberhasilan produksi kentang berkualitas. Cryotherapy (perendaman dalam nitrogen cair) merupakan teknik terbaru untuk mengeliminasi virus pada benih kentang. Salah satu kendala dalam penerapan teknologi cryotherapy ialah tingkat daya hidup eksplan yang masih rendah. Penelitian ini bertujuan untuk mengetahui efektifitas teknik enkapsulasi-dehidrasi untuk mendapatkan tunas yang sehat setelah perendaman dalam nitrogen cair. Ujung tunas in vitro ukuran 2–3 mm dari empat genotipe kentang di prakultur selama 3 hari secara bertahap pada media MS dengan penambahan gula 0,25 M, 0,5 M, dan 0, 75 M. Kemudian tunas dienkapsulasi, didehidrasi selama 5 jam, lalu direndam dalam nitrogen cair selama 60 menit lalu dihangatkan kembali dalam waterbath selama 3 menit. Tunas dalam kapsul kemudian dikulturkan pada media MS +30 g/l sukrosa + 8 g/l agar + 0,4 mg/l BAP + 1 mg/l GA3 untuk pemulihan, lalu dipelihara di ruang kultur dengan suhu 24oC. Daya hidup ujung tunas diamati pada minggu ke-8 dengan menggunakan kriteria skoring sebagai berikut: (1) pemutihan jaringan dan tidak ada respons pertumbuhan, (2) kalus mencokelat, (3) kalus hijau, (4) tumbuh tunas, dan (5) planlet sehat. Hasil penelitian menunjukkan daya hidup ujung tunas bervariasi antargenotipe. Skor daya hidup berkisar 1–2 (frekuensi 2–10) pada perlakuan nitrogen cair, yang menunjukkan tidak ada respons pertumbuhan tunas, beberapa memperlihatkan pertumbuhan kalus. Tunas pada perlakuan kontrol (tanpa perendaman dalam nitrogen cair) menunjukkan skor daya hidup 5 (frekuensi 1–7), di mana ujung tunas mampu beregenerasi menjadi planlet

A dynamical trichotomy for structured populations experiencing positive density-dependence in stochastic environments

Positive density-dependence occurs when individuals experience increased survivorship, growth, or reproduction with increased population densities. Mechanisms leading to these positive relationships include mate limitation, saturating predation risk, and cooperative breeding and foraging. Individuals within these populations may differ in age, size, or geographic location and thereby structure these populations. Here, I study structured population models accounting for positive density-dependence and environmental stochasticity i.e. random fluctuations in the demographic rates of the population. Under an accessibility assumption (roughly, stochastic fluctuations can lead to populations getting small and large), these models are shown to exhibit a dynamical trichotomy: (i) for all initial conditions, the population goes asymptotically extinct with probability one, (ii) for all positive initial conditions, the population persists and asymptotically exhibits unbounded growth, and (iii) for all positive initial conditions, there is a positive probability of asymptotic extinction and a complementary positive probability of unbounded growth. The main results are illustrated with applications to spatially structured populations with an Allee effect and age-structured populations experiencing mate limitation

Teknik Pemuliaan Kentang dan Produksi Bibit Kentang Bebas Virus di Texas, USA

Kentang merupakan sumber karbohidrat penting di negara maju seperti Amerika Serikat, Eropa dan Australia. Produktivitas kentang di Amerika Serikat mencapai 40 ton/ha. Berbagai varietas kentang juga tersedia dengan kegunaan yang berbeda seperti untuk keripik, kentang goreng (french fries), kentang rebus dan kentang panggang. Tulisan ini bertujuan untuk memaparkan teknik pemuliaan kentang untuk mendapatkan berbagai varietas serta metode perbanyakan benih kentang bebas virus melalui teknik kultur jaringan di Texas. Kunci utama keberhasilan pemuliaan kentang di Texas adalah ketersediaan sumber daya genetik kentang yang luas, serta evaluasi di lapang (field day) untuk genotipe-genotipe potential hasil pemuliaan yang melibatkan para peneliti, petani, pelaku pasar dan media. Teknik kultur jaringan digunakan untuk perbanyakan benih terpilih, serta meminimalisasi penyebaran penyakit yang berasal dari umbi seperti virus kentang PVX, PVY dan PLRV. Penggunaan teknik kultur jaringan juga mampu menekan biaya produksi benih karena mengurangi penggunaan ruang untuk stok benih dan perbanyakan di rumah kaca. Tahapan pemuliaan, produksi benih di lapang, evaluasi varietas, introduksi benih in vitro, perbanyakan in vitro, teknik eliminasi virus dan produksi benih di rumah kaca dideskripsikan pada tulisan ini

Stable Heterogeneity for the Production of Diffusible Factors in Cell Populations

The production of diffusible molecules that promote survival and growth is common in bacterial and eukaryotic cell populations, and can be considered a form of cooperation between cells. While evolutionary game theory shows that producers and non-producers can coexist in well-mixed populations, there is no consensus on the possibility of a stable polymorphism in spatially structured populations where the effect of the diffusible molecule extends beyond one-step neighbours. I study the dynamics of biological public goods using an evolutionary game on a lattice, taking into account two assumptions that have not been considered simultaneously in existing models: that the benefit of the diffusible molecule is a non-linear function of its concentration, and that the molecule diffuses according to a decreasing gradient. Stable coexistence of producers and non-producers is observed when the benefit of the molecule is a sigmoid function of its concentration, while strictly diminishing returns lead to coexistence only for very specific parameters and linear benefits never lead to coexistence. The shape of the diffusion gradient is largely irrelevant and can be approximated by a step function. Since the effect of a biological molecule is generally a sigmoid function of its concentration (as described by the Hill equation), linear benefits or strictly diminishing returns are not an appropriate approximations for the study of biological public goods. A stable polymorphism of producers and non-producers is in line with the predictions of evolutionary game theory and likely to be common in cell populations

The origin of life: chemical evolution of a metabolic system in a mineral honeycomb?

For the RNA-world hypothesis to be ecologically feasible, selection mechanisms acting on replicator communities need to be invoked and the corresponding scenarios of molecular evolution specified. Complementing our previous models of chemical evolution on mineral surfaces, in which selection was the consequence of the limited mobility of macromolecules attached to the surface, here we offer an alternative realization of prebiotic group-level selection: the physical encapsulation of local replicator communities into the pores of the mineral substrate. Based on cellular automaton simulations we argue that the effect of group selection in a mineral honeycomb could have been efficient enough to keep prebiotic ribozymes of different specificities and replication rates coexistent, and their metabolic cooperation protected from extensive molecular parasitism. We suggest that mutants of the mild parasites persistent in the metabolic system can acquire useful functions such as replicase activity or the production of membrane components, thus opening the way for the evolution of the first autonomous protocells on Earth

Selection for Replicases in Protocells

PMCID: PMC3649988This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Fast flowing populations are not well mixed

In evolutionary dynamics, well-mixed populations are almost always associated with all-to-all interactions; mathematical models are based on complete graphs. In most cases, these models do not predict fixation probabilities in groups of individuals mixed by flows. We propose an analytical description in the fast-flow limit. This approach is valid for processes with global and local selection, and accurately predicts the suppression of selection as competition becomes more local. It provides a modelling tool for biological or social systems with individuals in motion.Comment: 19 pages, 8 figure