Nutrient utilization by bovine articular chondrocytes: a combined experimental and theoretical approach

A combined experimental-numerical approach was adopted to characterize glucose and oxygen uptake and lactate production by bovine articular chondrocytes in a model system. For a wide range of cell concentrations, cells in agarose were supplemented with either low or high glucose medium. During an initial culture phase of 48 h, oxygen was monitored noninvasively using a biosensor system. Glucose and lactate were determined by medium sampling. In order to quantify glucose and oxygen uptake, a finite element approach was adopted to describe diffusion and uptake in the experimental model. Numerical predictions of lactate, based on simple relations for cell metabolism, were found to agree well for low glucose, but not for high glucose medium. Oxygen did not play a role in either case. Given the close association between chondrocyte energy metabolism and matrix synthesis, a quantifiable prediction of utilization can present a valuable contribution in the optimization of tissue engineering conditions.     

Evolution of reproductive-immune interactions

The comparative approach in biological sciences has providedvaluable insights into the role of different organ systems inadaptation and evolution, and seeks to establish unifying themes.This approach also plays a key role in identifying model speciesand systems for the study of specific questions and problems.Further, by applying the concept of homology, information aboutnonmammalian species may be used either to directly understandmammalian/human regulatory processes, or to formulate hypothesesfor direct testing. Individual physiological systems functionin a milieu provided by the integrated activities of all ofthe systems to adapt, adjust and sustain the organism in itsenvironment. The overlapping interfaces between the differentphysiological systems provide fertile ground for new insightsand to enhance our knowledge. These interdisciplinary areasare of great importance if we are to understand the full complexityof organismal function. Of particular interest are the interactionsbetween the reproductive system and the immune system. The reproductivesystem is unique in that its primary role is to assure the continuityof the species, while the immune system provides internal protectionand thus facilitates continued health and survival. The modusoperandi of these 2 morphologically diffuse systems involveswidely distributed chemical signals in response to environmentalinput, and both systems must interact for the normal functioningof each. While the major focus of reproductive–immuneresearch has historically been with mammals, and has providedsubstantial insight into the interactions between these physiologicalsystems, comparative studies offer unique perspectives. Further,dysregulation of normal physiological interactions between thereproductive and immune systems can lead to disorders and diseaseseffecting one system or the other. Thus, comparative studiesof these interactions may shed some light upon the evolutionarymechanisms involved in such cases.     

Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI

Many restriction enzymes require binding of two copies of a recognition sequence for DNA cleavage, thereby introducing a loop in the DNA. We investigated looping dynamics of Type IIE restriction enzymes NaeI and NarI by tracking the Brownian motion of single tethered DNA molecules. DNA containing two endonuclease recognition sites spaced a few 100 bp apart connect small polystyrene beads to a glass surface. The position of a bead is tracked through video microscopy. Protein-mediated looping and unlooping is then observed as a sudden specific change in Brownian motion of the bead. With this method we are able to directly follow DNA looping kinetics of single protein–DNA complexes to obtain loop stability and loop formation times. We show that, in the absence of divalent cations, NaeI induces DNA loops of specific size. In contrast, under these conditions NarI mainly creates non-specific loops, resulting in effective DNA compaction for higher enzyme concentrations. Addition of Ca²⁺ increases the NaeI-DNA loop lifetime by two orders of magnitude and stimulates specific binding by NarI. Finally, for both enzymes we observe exponentially distributed loop formation times, indicating that looping is dominated by (re)binding the second recognition site.     

Cultivation of Denitrifying Bacteria: Optimization of Isolation Conditions and Diversity Study

An evolutionary algorithm was applied to study the complex interactions between medium parameters and their effects on the isolation of denitrifying bacteria, both in number and in diversity. Growth media with a pH of 7 and a nitrogen concentration of 3 mM, supplemented with 1 ml of vitamin solution but not with sodium chloride or riboflavin, were the most successful for the isolation of denitrifiers from activated sludge. The use of ethanol or succinate as a carbon source and a molar C/N ratio of 2.5, 20, or 25 were also favorable. After testing of 60 different medium parameter combinations and comparison with each other as well as with the standard medium Trypticase soy agar supplemented with nitrate, three growth media were highly suitable for the cultivation of denitrifying bacteria. All evaluated isolation conditions were used to study the cultivable denitrifier diversity of activated sludge from a municipal wastewater treatment plant. One hundred ninety-nine denitrifiers were isolated, the majority of which belonged to the Betaproteobacteria (50.4%) and the Alphaproteobacteria (36.8%). Representatives of Gammaproteobacteria (5.6%), Epsilonproteobacteria (2%), and Firmicutes (4%) and one isolate of the Bacteroidetes were also found. This study revealed a much more diverse denitrifying community than that previously described in cultivation-dependent research on activated sludge.     

Vicissitudes of benefit sharing of crop genetic resources: downstream and upstream

In this article, we will first give a historic overview of the concept of benefit sharing and its appearance in official agreements, particularly with respect to crop genetic resources. It will become clear that, at present, benefit sharing is primarily considered as an instrument of compensation or exchange, and thus refers to commutative justice. However, we believe that such a narrow interpretation of benefit sharing disregards, and even undermines, much of its (historical) content and potency, especially where crop genetic resources are concerned. We argue that benefit sharing should not be based merely on commutative justice but rather on a broader model that is also grounded in the concept of distributive justice. This has repercussions for the application of benefit sharing, which we try to clarify by distinguishing between downstream and upstream benefit sharing. Upstream benefit sharing is not so much inspired by compensation for actions done, or the distribution downstream of benefits developed, but by the idea of shared decision-making on the research and development of resources fundamental to human welfare. Going upstream in the research process of crop genetic resources, and determining research agendas and improving crops according to the needs of the poor, benefit sharing may well be a tool to contribute to world food security and global justice. We concretize our ideas on upstream benefit sharing by introducing a set of criteria that determine the success of consultations on agricultural research agenda setting.     

Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection

Genome-scale engineering of living organisms requires precise and economical methods to efficiently modify many loci within chromosomes. One such example is the directed integration of chemically synthesized single-stranded deoxyribonucleic acid (oligonucleotides) into the chromosome of Escherichia coli during replication. Herein, we present a general co-selection strategy in multiplex genome engineering that yields highly modified cells. We demonstrate that disparate sites throughout the genome can be easily modified simultaneously by leveraging selectable markers within 500 kb of the target sites. We apply this technique to the modification of 80 sites in the E. coli genome.     

Global crop improvement networks to bridge technology gaps

To ensure future food security, there is an urgent need for improved co-ordination of agricultural research. While advances in biotechnology hold considerable promise, significant technology gaps exist that may reduce their impact. Examples include an incomplete knowledge of target breeding environments, a limited understanding and/or application of optimal crop management practices, and underfunded extension services. A better co-ordinated and more globalized approach to agricultural research through the implementation of Global Crop Improvement Networks (GCIN) is proposed. Such networks could underpin agricultural research and development by providing the following types of services: (i) increased resolution and precision of environmental information, including meteorological data, soil characteristics, hydrological data, and the identification of environmental 'hotspots' for a range of biotic, abiotic, and socio-economic constraints; (ii) augmented research capacity, including network-based variety and crop management trials, faster and more comprehensive diagnosis of emerging constraints, timely sharing of new technologies, opportunities to focus research efforts better by linking groups with similar productivity constraints and complementary skills, and greater control of experimental variables in field-based phenotyping; and (iii) increased communication and impacts via more effective dissemination of new ideas and products, the integration of information globally to elicit well-timed local responses to productivity threats, an increased profile, and the publicity of threats to food security. Such outputs would help target the translation of research from the laboratory into the field while bringing the constraints of rural communities closer to the scientific community. The GCIN could provide a lens which academia, science councils, and development agencies could use to focus in on themes of common interest, and working platforms to integrate novel research approaches on crop adaptation and rural development.     

Safeguarding bacterial resources promotes biotechnological innovation

Environmental research delivers valuable bacterial resources for biotechnology. We believe that systematic long-term preservation of bacteria will promote future biotechnological innovations, by safeguarding the accessibility of bacteria already recognized to have interesting features and providing a “pool” of bacterial resources for novel applied research. To this end, we want to advocate the incorporation of preservation tests in environmental or applied microbiological research. This paper introduces non-specialists to different preservation methods for bacteria. Several parameters that influence long-term storage of bacterial resources are explained and practical tips and guidelines are formulated. Also, the vital role of public culture collections is highlighted and the state-of-the-art of preservation of non-pure cultures is described.     

Habitat quality influences population distribution, individual space use and functional responses in habitat selection by a large herbivore

Identifying factors shaping variation in resource selection is central for our understanding of the behaviour and distribution of animals. We examined summer habitat selection and space use by 108 Global Positioning System (GPS)-collared moose in Norway in relation to sex, reproductive status, habitat quality, and availability. Moose selected habitat types based on a combination of forage quality and availability of suitable habitat types. Selection of protective cover was strongest for reproducing females, likely reflecting the need to protect young. Males showed strong selection for habitat types with high quality forage, possibly due to higher energy requirements. Selection for preferred habitat types providing food and cover was a positive function of their availability within home ranges (i.e. not proportional use) indicating functional response in habitat selection. This relationship was not found for unproductive habitat types. Moreover, home ranges with high cover of unproductive habitat types were larger, and smaller home ranges contained higher proportions of the most preferred habitat type. The distribution of moose within the study area was partly related to the distribution of different habitat types. Our study shows how distribution and availability of habitat types providing cover and high-quality food shape ungulate habitat selection and space use.