An anatomy of interactions among species in a seasonal world

Mathematical models merging biological and predictable seasonal dynamics were used to simulate four types of organism interactions: competition, prey-predation, mutualism and facilitation. By analysing trajectories for biomass in phase portraits (i.e. species 1 biomass plotted against species 2 biomass) graphically and numerically, we found that each of the four interaction types showed characteristic patterns ("fingerprints") in phase space. All the four interaction types could be distinguished, even though their time trajectories were strongly modified by seasonal forces. For each of the interaction types, we were able to identify characteristics of the interaction that most strongly distinguished it from the others. We could also assess the relative effect of species characteristics and seasonality on each of the four interactions. The simulations indicate that prey-predation is strongly influenced by seasonal forces and by the characteristics of the predator and its prey. A system variability index got a high value (SVI)=0.167 relative to those of the other interaction types (competition 0.01, mutualism 0.007 and facilitation 0.005). The result was obtained by calculating, angles between successive vectors linking pairs of samples and the positive x-axis and arranging these as frequency histograms for each of the four quadrants of the phase portrait. In an effort to capture circular motions and other characteristics of the trajectories sampled, angle frequencies were analysed using multivariate statistics (PCA), yielding "characteristic directions" in phase space. We believe that the characteristic patterns identified also will be found in real time series.     

Temperature-Induced Changes of Variable Fluorescence-Yield in Intact Leaves

Variable fluorescence (F_v) of intact leaves was measured whenthe temperature was lowered at a rate of 1–2?C per mn,from 20?C to –20?C. The quantum flux density of the excitinglight was 1–2 µE m^–2 sec^–1 in orderto sensitize F only at 20?C. The fluorescence yield decreasedrapidly at the freezing point of the leaf and upon further coolingthe fluorescence yield increased again. F_m was obtained a fewdegrees below the freezing point. Repeated freeze-thaw cycles caused successively increased damageto the thylakoid membranes on either the oxidizing or the reducingside of photosystem II. An eventual loss of F_v over F_o was typicalfor damage on the water splitting side of photosystem II, whereasdamage after the primary electron acceptor Q of photosystemII was characterized by an invariable fluorescence yield atF_m over the temperature range examined. (Received January 18, 1982; Accepted June 12, 1982)     

Genes and pseudogenes for human U2 RNA: Implications for the mechanism of pseudogene formation

Three loci, designated U2/4, U2/6 and U2/7, which contain sequences related to human U2 RNA, have been studied. The U2/6 locus contains a tandem array of bona fide U2 genes. U2/4 and U2/7, in contrast, contain pseudogenes whose sequences deviate significantly from that of mammalian U2 RNA. The two pseudogenes appear to have been created by different mechanisms. The sequences that flank the pseudogene in the U2/4 locus lack homology to the corresponding sequences in functional human U2 genes, except for 10 base-pairs immediately following the 3′ end. The conserved 3′-flanking segment is homologous to those nucleotides that are present in a U2 RNA precursor. No direct repeats flank the pseudogene in the U2/4 locus. The observations thus suggest that a complementary DNA copy of the U2 RNA precursor was inserted into a blunt-ended chromosomal break to generate the U2/4 locus.The U2/7 locus, in contrast, revealed flanking sequence homology when compared to functional U2 genes, both on the 5′ and 3′ sides of the pseudogene. The homology was interrupted on both sides by repetitive sequences belonging to the Alu family. On the 5′ side the homology continues beyond the Alu repeats whereas on the 3′ side it ends precisely at the Alu repeat. This Alu repeat is inserted in a region where a homocopolymeric region of alternating C and T residues is located in functional U2 loci. The observed organization of the U2/7 locus suggests that a previously functional U2 locus was invaded by Alu repeats and subsequently accumulated base substitutions to become a pseudogene.     

Three-dimensional structure of the two peptides that constitute the two-peptide bacteriocin plantaricin EF

The three-dimensional structures of the two peptides plantaricin E (plnE; 33 residues) and plantaricin F (plnF; 34 residues) constituting the two-peptide bacteriocin plantaricin EF (plnEF) have been determined by nuclear magnetic resonance (NMR) spectroscopy in the presence of DPC micelles. PlnE has an N-terminal alpha-helix (residues 10-21), and a C-terminal alpha-helix-like structure (residues 25-31). PlnF has a long central alpha-helix (residues 7-32) with a kink of 38+/-7 degrees at Pro20. There is some flexibility in the helix in the kink region. Both helices in plnE are amphiphilic, while the helix in plnF is polar in its N-terminal half and amphiphilic in its C-terminal half. The alpha-helical content obtained by NMR spectroscopy is in agreement with CD studies. PlnE has two GxxxG motifs which are putative helix-helix interaction motifs, one at residues 5 to 9 and one at residues 20 to 24, while plnF has one such motif at residues 30 to 34. The peptides are flexible in these GxxxG regions. It is suggested that the two peptides lie parallel in a staggered fashion relative to each other and interact through helix-helix interactions involving the GxxxG motifs.     

Immunotherapy for Alzheimer disease

Immunotherapy approaches for Alzheimer disease currently are among the leading therapeutic directions for the disease. Active and passive immunotherapy against the β-amyloid peptides that aggregate and accumulate in the brain of those afflicted by the disease have been shown by numerous groups to reduce plaque pathology and improve behavior in transgenic mouse models of the disease. Several ongoing immunotherapy clinical trials for Alzheimer disease are in progress. The background and ongoing challenges for these immunological approaches for the treatment of Alzheimer disease are discussed.Key words: Alzheimer disease, amyloid, tau, immunotherapy, vaccineThe publication in Nature on a vaccine approach for Alzheimer disease (AD) by Schenk and colleagues in 1999 initiated a push for treatment for this major disease of aging. AD neuropathology is characterized by the progressive loss of synapses and neurons, and the aberrant accumulation in the brain of β-amyloid peptides in plaques and the microtubule associated protein tau in neurofibrillary tangles. Mutations in familial forms of AD have been associated with elevated β-amyloid levels, whereas mutations in tau have been linked to familial forms of frontotemporal dementia. Remarkably, injection of β-amyloid peptides with Freund''s adjuvant into transgenic mice harboring a human AD mutation that develop AD-like neuropathology and progressive cognitive decline led to reduced β-amyloid plaque pathology.¹ This study was subsequently confirmed and extended by multiple groups to show also behavioral improvement in AD transgenic mice with active β-amyloid immunization.^2,3 Passive immunotherapy with antibodies directed at β-amyloid were similarly effective in reducing plaques and improving behavior in AD transgenic mice.⁴ A temporary setback occurred when the first clinical trial with β-amyloid vaccination was halted after 6% of patients developed an inflammatory reaction in the brain (chemical meningoencephalitis). A subsequent study supported clinical benefits among patients in this active vaccination trial.⁵ A more recent postmortem study on a subset of patients who had participated in the aborted trial supported active removal of β-amyloid plaques by inflammatory cells, but also indicated that 7 of the 8 patients who were studied at autopsy continued to have progressive cognitive decline despite the removal of amyloid plaques.⁶The critical mechanisms whereby active or passive vaccination against β-amyloid can affect the disease process remain uncertain. Recruitment and activation of microglia, the macrophage of the central nervous system, by β-amyloid antibodies is thought to lead to β-amyloid plaque removal. At the same time, fibrillar β-amyloid containing plaques, formerly viewed as the major toxic entities in AD, are increasingly viewed as potentially only pathological remnants of the disease. Smaller assemblies, particularly of two to twelve β-amyloid peptides (oligomers), are considered pathogenic, although the site of pathogenesis remains controversial. Secreted, extracellular β-amyloid oligomers have been shown to damage synapses.⁷ Some groups stress the aberrant accumulation of β-amyloid within neurons and synapses leading to subsequent extracellular localization following destruction of neurites and synapses.⁸ Evidence has been presented that antibodies targeting β-amyloid peptides up to 42–43 amino acids can block the toxic effects of extracellular β-amyloid oligomers on synapses.⁷ Interestingly, β-amyloid immunotherapy was also shown to clear intraneuronal β-amyloid in an AD transgenic mouse; the intraneuronal variety is a pool of β-amyloid that correlates with the onset of cognitive decline prior to plaques and tangles in these mice.⁹ Intriguingly, antibodies directed at the β-amyloid domain exposed to the extracellular space within the amyloid precursor protein (APP) were shown to be internalized by neurons, where they reduced the intraneuronal pool of β-amyloid and protected against synaptic damage in neurons cultured from AD transgenic mice.^10,11 It is possible that inefficient clearance of the intracellular pool of β-amyloid played a role in the continued cognitive decline in the seven of eight patients in the aborted active vaccination clinical trial studied at autopsy who showed clearance of β-amyloid plaques.Work on β-amyloid immunotherapy in AD contributed to a reevaluation of the role of the immune system in the brain. Previously, it was considered that the brain was immune privileged, and that antibodies entered the brain only with the breakdown of the blood brain barrier. Rare neuroimmunological disorders had suggested more complex interactions. Pathological antibodies directed at neuronal proteins could be found localizing to specific types of neurons in paraneoplastic diseases linked to diverse systemic cancers^12,13 or collagen-vascular diseases such as lupus.¹⁴ Such pathological antibodies can be directed at synaptic or even intracellular proteins in selective neurons in the brain, leading to localized neurological symptoms. For paraneoplastic diseases it is hypothesized that antibodies directed at the cancer cells cross-react with neuronal antigens. Since titers of antibodies can be higher in brain than in the blood, intrathecal synthesis of antibodies from sequestration of B cells has been proposed to occur in the brain.¹⁵ The interaction between the immune system and the brain is therefore viewed as increasingly complex, with antibodies not only gaining access to the brain but also nerve cells, where they can even alter intracellular biology.¹⁰ These findings open up new possibilities for antibody-directed therapies for diseases of the nervous system.Currently, leading concerns for β-amyloid immunotherapy are the potential development of chemical meningoencephalitis and micro-hemorrhages in the brain. Involvement of T cells in damage to the brain vasculature is considered to contribute to these potential side effects. In addition, the β-amyloid released upon antibody-induced removal of plaques may damage blood vessels as β-amyloid is cleared from the brain via the vasculature.¹⁶ Recently, a phase 2 Elan/Wyeth study using passive β-amyloid immunotherapy with a humanized monoclonal antibody described (at the 2008 International Conference on Alzheimer''s disease) significant benefits in patients not harboring the apolipoprotein E4 (apoE4) allele genetic risk factor for late onset AD. In contrast, no clear therapeutic benefit and more cases with brain inflammation occurred in those with the apoE4 allele linked with an increased risk for AD. Why apoE4 carriers did not benefit in this β-amyloid immunotherapy trial is unknown, but has prompted separation of patients into E4 negative and positive groups in subsequent clinical trials. The less robust than hoped for effects even in the apoE4 negative patients has further dampened expectations. The reason for why the human studies are not showing the protection seen in the transgenic mouse studies could relate to β-amyloid playing less of a role in the more typical late onset AD than it does in the rare autosomal dominant familial forms used to generate the AD transgenic mice. It is also not clear which β-amyloid epitope(s) should be targeted by antibodies to maximize potential benefits while minimizing side effects in AD patients. Optimizing antibody specificity for immunotherapy is further complicating by the varied conformations of different β-amyloid aggregation states. In addition, β-amyloid immunotherapy may be more challenging in patients with AD because it is not effective in reducing tau tangle pathology.⁶ Most immunotherapy studies were done on transgenic AD mouse models that deposit β-amyloid plaques, but not tau tangles. In the more recently generated triple transgenic AD mouse that develops both plaques and tangles, β-amyloid antibodies reversed β-amyloid pathology and early pre-tangle tau pathology, but not hyperphosphorylated tau aggregates.⁸ Recent evidence supports that β-amyloid neurotoxicity acts synergistic with tau,¹⁷ and that both pathologies begin at synapses.¹⁸ Interestingly, tau immunotherapy was reported to protect against tau pathology in transgenic mice harboring mutant tau.¹⁹ Thus, dual immunotherapy targeting of both β-amyloid and tau can be considered. Finally, immunotherapy at earlier stages of the disease process may be more effective.In summary, the β-amyloid vaccine heralded a new era of therapeutic research for AD and despite some setbacks is actively being pursued in several ongoing clinical trials. It continues to be among the leading hopes in the AD research community. Another major effort to specifically block the generation of β-amyloid is also progressing, although not without setbacks along the way. For example, the protease involved in the final cleavage to liberate β-amyloid was found to be involved in multiple other important activities, such as cleavage of Notch. Antibody approaches are also being applied in efforts to block secretase cleavage to generate β-amyloid.²⁰ Finally, there remains some worry that β-amyloid peptides have an as yet unknown normal biological function, although cumulative immunotherapy and other therapeutic studies in animal models have provided sufficient support for the continued pursuit of β-amyloid lowering as a treatment for AD.     

Prefermentation improves xylose utilization in simultaneous saccharification and co-fermentation of pretreated spruce

Background  

Simultaneous saccharification and fermentation (SSF) is a promising process option for ethanol production from lignocellulosic materials. However, both the overall ethanol yield and the final ethanol concentration in the fermentation broth must be high. Hence, almost complete conversion of both hexoses and pentoses must be achieved in SSF at a high solid content. A principal difficulty is to obtain an efficient pentose uptake in the presence of high glucose and inhibitor concentrations. Initial glucose present in pretreated spruce decreases the xylose utilization by yeast, due to competitive inhibition of sugar transport. In the current work, prefermentation was studied as a possible means to overcome the problem of competitive inhibition. The free hexoses, initially present in the slurry, were in these experiments fermented before adding the enzymes, thereby lowering the glucose concentration.