Purple Matter, Membranes and ‘Molecular Pumps’ in Rhodopsin Research (1960s–1980s)

In the context of 1960s research on biological membranes, scientists stumbled upon a curiously coloured material substance, which became called the “purple membrane.” Interactions with the material as well as chemical analyses led to the conclusion that the microbial membrane contained a photoactive molecule similar to rhodopsin, the light receptor of animals’ retinae. Until 1975, the find led to the formation of novel objects in science, and subsequently to the development of a field in the molecular life sciences that comprised biophysics, bioenergetics as well as membrane and structural biology. Furthermore, the purple membrane and bacteriorhodopsin, as the photoactive membrane transport protein was baptized, inspired attempts at hybrid bio-optical engineering throughout the 1980s. A central motif of the research field was the identification of a functional biological structure, such as a membrane, with a reactive material substance that could be easily prepared and manipulated. Building on this premise, early purple membrane research will be taken as a case in point to understand the appearance and transformation of objects in science through work with material substances. Here, the role played by a perceptible material and its spontaneous change of colour, or reactivity, casts a different light on objects and experimental practices in the late twentieth century molecular life sciences. With respect to the impact of chemical working and thinking, the purple membrane and rhodopsins represent an influential domain straddling the life and chemical sciences as well as bio- and material technologies, which has received only little historical and philosophical attention. Re-drawing the boundary between the living and the non-enlivened, these researches explain and model organismic activity through the reactivity of macromolecular structures, and thus palpable material substances.     

Biomass production potential from Populus short rotation systems in Romania

The aim of this study was to assess the potential of biomass production by short rotation poplar in Romania without constraining agricultural food production. Located in the eastern part of Europe, Romania provides substantial land resources suitable for bioenergy production. The process‐oriented biogeochemical model Landscape DNDC was used in conjunction with the forest‐growth model PSIM to simulate the yield of poplar grown in short‐rotation coppice at different sites in Romania. The model was validated on five sites with different climatic conditions in Central Europe. Using regional site conditions, with climatic parameters and organic carbon content in soil being the most important, the biomass production potential of poplar plantations was simulated for agricultural areas across Romania. Results indicated a mean productivity of 12.2 ± 0.5 t ha^?1 year^?1 of poplar coppices on arable land in Romania. The highest yields were simulated for lowland areas in the south‐east and west and for the Mures valley, whereas the lowest yields – due to either temperature or water limitations – were found for the mountainous regions, the Danube valley, and the region west of Bucharest. The amount of abandoned arable land in the past 10 years indicates that around 10% of cropping land in production in 1999 (approximately 1 million ha) is available for bioenergy production systems today. Production of poplar grown in short‐rotation coppices on these areas would result in a yield of approximately 10 million tons of wood per year. The energy that can be generated by conversion of poplar short rotation coppice biomass may contribute up to approximately 8% of the national energy demand if these set‐aside areas are used for lignocellulosic bioenergy.     

Reproductive tactics influence cortisol levels in individual male gray-cheeked mangabeys (Lophocebus albigena)

Concentration of the hormone cortisol is often used as an indicator of stress, and chronically high cortisol levels are often associated with poor health. Among group living animals that compete for resources, agonistic social interactions can be expected to contribute to variation in cortisol levels within and among individuals over time. Reproductive tactics of males can change with individual quality, relatedness, and social structure, and affect cortisol levels. In gray-cheeked mangabey (Lophocebus albigena) groups, male rank is an important factor in social interactions, and males also move between groups while actively competing for females or sneaking copulations. During a 20-month study we observed the social behavior and collected 461 fecal samples from 24 adult male gray-cheeked mangabeys from five groups in Kibale National Park, Uganda. Aggressive interactions and the presence of females at the peak of sexual swelling were associated with elevated cortisol concentrations in all males. Independently, dominant (i.e., highest-ranking) males within groups had higher cortisol concentrations than subordinate males, and immigrant males had higher cortisol concentrations than dominant males.     

Development of novel LL-37 derived antimicrobial peptides with LPS and LTA neutralizing and antimicrobial activities for therapeutic application

New peptides for lipopolysaccharide (LPS) and lipoteichoic acid (LTA) neutralization in upper respiratory tract infections were developed and evaluated in terms of efficacy and safety for application in humans. Based on the sequence of the human antimicrobial peptide LL-37 we developed and investigated length variants, substitution analogues and modifications to stabilize the peptides to prevent enzymatic degradation and to improve efficacy. The most promising peptide appears P60.4, a 24 amino acid peptide with similar efficacy as LL-37 in terms of LPS and LTA neutralization and lower pro-inflammatory activity. In addition, the acetylated and amidated version of this peptide shows no toxicity and displays higher or equal antimicrobial activity compared to LL-37.     

JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins

MOTIVATION: After the publication of JVirGel 1.0 in 2003 we got many requests and suggestions from the proteomics community to further improve the performance of the software and to add additional useful new features. RESULTS: The integration of the PrediSi algorithm for the prediction of signal peptides for the Sec-dependent protein export into JVirGel 2.0 allows the exclusion of most exported preproteins from calculated proteomic maps and provides the basis for the calculation of Sec-based secretomes. A tool for the identification of transmembrane helices carrying proteins (JCaMelix) and the prediction of the corresponding membrane proteome was added. Finally, in order to directly compare experimental and calculated proteome data, a function to overlay and evaluate predicted and experimental two-dimensional gels was included. AVAILABILITY: JVirGel 2.0 is freely available as precompiled package for the installation on Windows or Linux operating systems. Furthermore, there is a completely platform-independent Java version available for download. Additionally, we provide a Java Server Pages based version of JVirGel 2.0 which can be operated in nearly all web browsers. All versions are accessible at http://www.jvirgel.de     

Prm1 Targeting to Contact Sites Enhances Fusion during Mating in Saccharomyces cerevisiae

Prm1 is a pheromone-regulated membrane glycoprotein involved in the plasma membrane fusion event of Saccharomyces cerevisiae mating. Although this function suggests that Prm1 should act at contact sites in pairs of mating yeast cells where plasma membrane fusion occurs, only a small percentage of the total Prm1 was actually detected on the plasma membrane. We therefore investigated the intracellular transport of Prm1 and how this transport contributes to cell fusion. Two Prm1 chimeras that were sorted away from the contact site had reduced fusion activity, indicating that Prm1 indeed functions at contact sites. However, most Prm1 is located in endosomes and other cytoplasmic organelles and is targeted to vacuoles for degradation. Mutations in a putative endocytosis signal in a cytoplasmic loop partially stabilized the Prm1 protein and caused it to accumulate on the plasma membrane, but this endocytosis mutant actually had reduced mating activity. When Prm1 was expressed from a galactose-regulated promoter and its synthesis was repressed at the start of mating, vanishingly small amounts of Prm1 protein remained at the time when the plasma membranes came into contact. Nevertheless, this stable pool of Prm1 was retained at polarized sites on the plasma membrane and was sufficient to promote plasma membrane fusion. Thus, the amount of Prm1 expressed in mating yeast is far in excess of the amount required to facilitate fusion.Membrane fusion has been studied extensively in the context of viral infection and intracellular membrane fusion. These fusion events are mediated by fusases—proteins that mediate membrane fusion. Some of the best-studied fusases are the SNAREs (soluble N-ethylmaleimide-sensitive factors) that mediate fusion of intracellular organelles and the hemagglutinin (HA) protein of influenza virus that mediates fusion of the viral envelope membrane with host endosomes (13). However, little is known about how the plasma membranes of two cells fuse during cell fusion.Cell fusion is essential for the development of multicellular organisms. Some cell fusion processes involve a single pair of cells, as in sperm-egg fusion. Many other developmental processes require multiple fusion events, as in fusion of myoblasts for muscle formation. However, all fusion events must overcome a common obstacle—maintaining the integrity and selective permeability of the two plasma membranes while fusing the hydrophobic cores of their phospholipid bilayers.We study cell fusion in mating pairs of the yeast Saccharomyces cerevisiae. This organism offers a genetically tractable model amenable to many biochemical and cell biological assays. The mating pathway in yeast is comprised of 5 steps: pheromone signaling, adhesion, degradation of the intervening cell walls, plasma membrane fusion, and karyogamy. S. cerevisiae has two haploid mating types: MATa and MATα. Haploid cells secrete pheromones that bind to G-protein-coupled receptors on the surface of cells of the opposite mating type. Pheromone binding activates a signaling cascade that causes cell cycle arrest, expression of pheromone-inducible genes, and polarized growth to form a mating projection (or shmoo tip). The binding of two cells of opposite mating type to form a mating pair is mediated by complementary agglutinins located on the shmoo tips. Then, the cell walls of the two cells are joined to form a unified wall protecting the mating pair, and the walls between the two cells are degraded. This allows the plasma membranes to come into contact and fuse. The initial fusion pore between cells expands to allow cytoplasmic mixing and, ultimately, karyogamy. After mating is complete, the mitotic cell cycle resumes, and a diploid daughter cell buds from the neck connecting the two parent cells (5, 30).This work focuses on Prm1, a glycoprotein that promotes the plasma membrane fusion step of mating. PRM1 was discovered in a bioinformatic screen designed to identify Prm (pheromone-regulated membrane) proteins (11). Prm1 has four transmembrane domains and functions as a disulfide-linked dimer (20). Prm1-deficient mating pairs experience one of three fates: arrest as late prezygotes (unfused mating pairs with no intervening cell walls), lysis once their plasma membranes come into contact, or fusion. Electron microscopy revealed that the two plasma membranes in a late prezygote were only ∼8 nm apart but did not fuse. Additional studies showed that ∼30% of prm1Δ mating pairs lyse after membrane contact (1, 14). However, 50% of prm1Δ mating pairs fuse on standard yeast extract-peptone-dextrose (YPD) medium, implying that Prm1 is important, but not required, for fusion. Mating becomes more dependent upon Prm1 activity if Ca²⁺ or ergosterol is limiting (1, 15).On the basis of its apparent role in membrane fusion, Prm1 should be targeted to the contact sites where membranes fuse. Surprisingly, only a small amount of Prm1 was found at contact sites, and even less was at shmoo tips or at bud tips in mitotic cells expressing Prm1 from a constitutive promoter. These observations prompted further investigation of Prm1''s intracellular transport. The results revealed that Prm1 does indeed function at contact sites. However, except for the small pool that promotes fusion, Prm1 proteins are transported to vacuoles and rapidly degraded.     

Diazotrophic Community Structure and Function in Two Successional Stages of Biological Soil Crusts from the Colorado Plateau and Chihuahuan Desert

The objective of this study was to characterize the community structure and activity of N₂-fixing microorganisms in mature and poorly developed biological soil crusts from both the Colorado Plateau and Chihuahuan Desert. Nitrogenase activity was approximately 10 and 2.5 times higher in mature crusts than in poorly developed crusts at the Colorado Plateau site and Chihuahuan Desert site, respectively. Analysis of nifH sequences by clone sequencing and the terminal restriction fragment length polymorphism technique indicated that the crust diazotrophic community was 80 to 90% heterocystous cyanobacteria most closely related to Nostoc spp. and that the composition of N₂-fixing species did not vary significantly between the poorly developed and mature crusts at either site. In contrast, the abundance of nifH sequences was approximately 7.5 times greater (per microgram of total DNA) in mature crusts than in poorly developed crusts at a given site as measured by quantitative PCR. 16S rRNA gene clone sequencing and microscopic analysis of the cyanobacterial community within both crust types demonstrated a transition from a Microcoleus vaginatus-dominated, poorly developed crust to mature crusts harboring a greater percentage of Nostoc and Scytonema spp. We hypothesize that ecological factors, such as soil instability and water stress, may constrain the growth of N₂-fixing microorganisms at our study sites and that the transition to a mature, nitrogen-producing crust initially requires bioengineering of the surface microenvironment by Microcoleus vaginatus.