Does the presence of grassy strips and landscape grain affect the spatial distribution of aphids and their carabid predators?

• 1 We investigated, over the course of 2 years, the spatial distribution and abundance of two species of aphid, Metopolophium dirhodum and Sitobion avenae, and predatory species of carabid. This was undertaken in 24 wheat fields in ‘coarse‐grain’ and ‘fine‐grain’ landscapes in western France. A greater percentage of the latter landscape was covered by hedgerows and grassland and the total area covered by fields and the average size of the fields were smaller.
• 2 The effects on aphid abundance of the distance from field margins, the presence of grassy strips and carabid abundance were determined in both landscapes.
• 3 Both aphid species were more abundant in the ‘fine‐grain’ landscape, which may have been a result of the higher density of semi‐natural elements. In both types of landscape, the total numbers of aphids were negatively correlated with the distance from the field margin. This may have been because aphids were dispersing from overwintering sites in field margins. The abundance of M. dirhodum was strongly negatively correlated with the presence of grassy strips in the ‘coarse‐grain’ landscape, although there were no such significant correlations for either of the aphid species in the ‘fine‐grain’ landscape.
• 4 Aphid and carabid abundances were negatively correlated in the ‘fine‐grain’ and positively in ‘coarse‐grain’ landscape.
• 5 The results obtained in the present study emphasize the importance of semi‐natural areas in agricultural landscapes in shaping the spatial distribution of aphids and carabid beetles, their natural enemies, at different spatial scales.

     

Lorentz force in water: evidence that hydronium cyclotron resonance enhances polymorphism

Abstract

There is an ongoing question regarding the structure forming capabilities of water at ambient temperatures. To probe for different structures, we studied effects in pure water following magnetic field exposures corresponding to the ion cyclotron resonance of H₃O⁺. Included were measurements of conductivity and pH. We find that under ion cyclotron resonance (ICR) stimulation, water undergoes a transition to a form that is hydroxonium-like, with the subsequent emission of a transient 48.5?Hz magnetic signal, in the absence of any other measurable field. Our results indicate that hydronium resonance stimulation alters the structure of water, enhancing the concentration of EZ-water. These results are not only consistent with Del Giudice's model of electromagnetically coherent domains, but they can also be interpreted to show that these domains exist in quantized spin states.     

Scale matters

During meiosis in many organisms, homologous chromosomes engage in numerous recombination events initiated by DNA double-strand breaks (DSBs) formed by the Spo11 protein. DSBs are distributed nonrandomly, which governs how recombination influences inheritance and genome evolution. The chromosomal features that shape DSB distribution are not well understood. In the budding yeast Saccharomyces cerevisiae, trimethylation of lysine 4 of histone H3 (H3K4me3) has been suggested to play a causal role in targeting Spo11 activity to small regions of preferred DSB formation called hotspots. The link between H3K4me3 and DSBs is supported in part by a genome-wide spatial correlation between the two. However, this correlation has only been evaluated using relatively low-resolution maps of DSBs, H3K4me3 or both. These maps illuminate chromosomal features that influence DSB distributions on a large scale (several kb and greater) but do not adequately resolve features, such as chromatin structure, that act on finer scales (kb and shorter). Using recent nucleotide-resolution maps of DSBs and meiotic chromatin structure, we find that the previously described spatial correlation between H3K4me3 and DSB hotspots is principally attributable to coincident localization of both to gene promoters. Once proximity to the nucleosome-depleted regions in promoters is accounted for, H3K4me3 status has only modest predictive power for determining DSB frequency or location. This analysis provides a cautionary tale about the importance of scale in genome-wide analyses of DSB and recombination patterns.     

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy.NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. Due to difficulty in crystallization to provide single crystals suitable for X-ray crystallography, the NMR technique is extremely valuable, especially as it provides information on the solution state rather than the solid state. Herein we describe all steps that are required for full three-dimensional structure determinations by NMR. The protocol includes sample preparation in an NMR tube, 1D and 2D data collection and processing, peak assignment and integration, molecular mechanics calculations, and structure analysis. Importantly, the analysis was first conducted without any preset metal-ligand bonds, to assure a reliable structure determination in an unbiased manner.     

Monoclonal antibodies in neuro-oncology

Monoclonal antibodies (mAbs) are used with increasing success against many tumors but, for brain tumors, the blood-brain barrier (BBB) is a special concern. The BBB prevents antibody entry to the normal brain; however, its role in brain tumor therapy is more complex. The BBB is closest to normal at micro-tumor sites; its properties and importance change as the tumor grows. In this review, evolving insight into the role of the BBB is balanced against other factors that affect efficacy or interpretation when mAbs are used against brain tumor targets. As specific examples, glioblastoma multiforme (GBM), primary central nervous system lymphoma (PCNSL) and blood-borne metastases from breast cancer are discussed in the context of treatment, respectively, with the mAbs bevacizumab, rituximab, and trastuzumab, each of which is already widely used against tumor outside the brain. It is suggested that success against brain tumors will require getting past the BBB in two senses: physically, to better attack brain tumor targets and conceptually, to give equal attention to problems that are shared with other tumor sites.     

Prediction of methionine oxidation risk in monoclonal antibodies using a machine learning method

ABSTRACT

Monoclonal antibodies (mAbs) have become a major class of protein therapeutics that target a spectrum of diseases ranging from cancers to infectious diseases. Similar to any protein molecule, mAbs are susceptible to chemical modifications during the manufacturing process, long-term storage, and in vivo circulation that can impair their potency. One such modification is the oxidation of methionine residues. Chemical modifications that occur in the complementarity-determining regions (CDRs) of mAbs can lead to the abrogation of antigen binding and reduce the drug’s potency and efficacy. Thus, it is highly desirable to identify and eliminate any chemically unstable residues in the CDRs during the therapeutic antibody discovery process. To provide increased throughput over experimental methods, we extracted features from the mAbs’ sequences, structures, and dynamics, used random forests to identify important features and develop a quantitative and highly predictive in silico methionine oxidation model.     

Methodologies to decipher the cell secretome

The cell secretome is a collection of proteins consisting of transmembrane proteins (TM) and proteins secreted by cells into the extracellular space. A significant portion (~ 13–20%) of the human proteome consists of secretory proteins. The secretory proteins play important roles in cell migration, cell signaling and communication. There is a plethora of methodologies available like Serial Analysis of Gene Expression (SAGE), DNA microarrays, antibody arrays and bead-based arrays, mass spectrometry, RNA sequencing and yeast, bacterial and mammalian secretion traps to identify the cell secretomes. There are many advantages and disadvantages in using any of the above methods. This review aims to discuss the methodologies available along with their potential advantages and disadvantages to identify secretory proteins. This review is a part of a Special issue on The Secretome. This article is part of a Special Issue entitled: An Updated Secretome.     

ASPECTS OF COMPARATIVE PLANKTON ECOLOGY IN CASCADING MGENI RIVER RESERVOIRS (MIDMAR,ALBERT FALLS,AND NAGLE): AN OVERVIEW

Summary

An overview of a three year study of abundance, community structure and succession of zooplankton and phytoplankton in relation to physical limnological conditions in Lakes Midmar and Albert Falls is presented, along with findings on zooplankton from a nine month study of Lake Nagle. Physical stability increased between Midmar (mean summer N² = 6.55 × 10⁴ s²) and Albert Falls (N² = 8.70 × 10⁴ s²), in line with elevations in water temperature. Phytoplankton richness and diversity was similar in these reservoirs, although zooplankton species richness increased downstream. Abundance levels of both phyto- and zoo-plankton were broadly comparable in these two reservoirs. In Midmar and Albert Falls, overall mean (± SD) chlorophyll levels were 3.60 ± 1.54 and 3.41 ± 1.41 μg 1¹, with corresponding overall average zooplankton standing stocks of 0.85 and 0.76 g m² dry mass, dropping to 0.54 g m² in Nagle (for which spring to midsummer data are missing).

Ruderal and colonist phytoplankters were persistently dominant both in Midmar and Albert Falls, in keeping with the continuous (if incomplete) mixing patterns evident in these reservoirs. Few stress tolerant algae occurred. The summer ruderal assemblage was unexpectedly dominated by diatoms in the physically more stable conditions of Albert Falls, but not Midmar. Mean zooplankton grazer-induced instantaneous mortality rates for planktonic algae for the whole study were estimated (by regression predictions) as 0.17 d¹ in both lakes. Phytoplankton was not studied in Nagle.

Changes in zooplankton community structure between Midmar and Nagle largely involved progressive increases in the contribution of smaller-bodied cladocerans (comprising both sequentially smaller species of Daphnia (D. pulex, D. longispina, D. laevis), and additional genera such as Diaphanosoma, Ceriodapnia, Moina and Bosmina). As with a parallel progressive switch between Metadiaptomus meridianus and Tropodiaptomus spectabilis over this series of reservoirs, (and the temporal separation of “co-existing” populations in Albert Falls), which has been shown experimentally to be strongly temperature-linked, changes in absolute temperature are implicated as a primary causal factor in the shifts in cladoceran species composition. Temporal occurrences of these species also indicate the primacy of temperature.     

Reproductive strategy of Labeo senegalensis Valenciennes 1842 (Teleostei: Cyprinidae) in the Ouémé basin,Benin

Aspects of the reproductive biology and population structure of Labeo senegalensis were investigated in the Ouémé River between April 2005 and March 2006. Reproductive strategy was investigated using gonadosomatic index, ovarian structure and fecundity. Average size-at-first-maturity (L ₅₀) was estimated at 29 cm TL for females and 25.7 cm TL for males. The average sex ratio (1:0.96) was not significantly different from unity. Oocyte diameter frequency distribution suggests synchronous development with a single total spawning. Absolute fecundity ranged between 12 948 and 74 832 eggs. Labeo senegalensisis a highly fecund fish that presents a seasonal cycle of reproduction from May to October during the rainy season.     

Genetically distinct Dutch-domesticated Clarias gariepinus used in aquaculture in southern Africa

Clarias gariepinus, a catfish species widely distributed in Africa including South Africa, is naturally absent from the Western Cape and the coastal Eastern Cape provinces. Because of its potential as an aquaculture species it has been widely used in aquaculture ventures in South Africa, specifically a stock known as Dutch catfish, a domesticated strain developed in the Netherlands. Mitochondrial DNA markers indicate that this stock is genetically distinct from the natural populations of C. gariepinus in South Africa. It could potentially pose a threat to South Africa's natural biodiversity if these fish were to escape from aquaculture farms, or was deliberately introduced into inland waters.