Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria?

The cyclic nucleotide cyclic di-guanosine-monophosphate (c-diGMP) was recognized in the 1980s as a signaling compound that is involved in controlling the condensation of glucose moieties into cellulose polymers. More recent data from several different bacterial species now suggest that c-diGMP might have a general role as secondary messenger in modulating bacterial growth on surfaces by regulating cellular adhesion components and preparing cells for cell-cell and cell-surface interactions.     

The changing epitome of species identification – DNA barcoding

The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The ‘DNA barcodes’ show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.     

Conservation of remnant populations of Colchicum autumnale – The relative importance of local habitat quality and habitat fragmentation

Semi-natural habitat is extremely vulnerable to habitat fragmentation and degradation since its socio-economic value has decreased substantially during the last century in most parts of Europe. We evaluated the relative effects of habitat fragmentation and local environmental conditions on population structure and reproductive performance of the long-lived corm geophyte Colchicum autumnale in 17 highly fragmented populations. Habitat isolation did not affect patch occupancy, population structure or plant performance. In contrast, population size and local environment strongly affected population structure and reproductive performance. Densities of all life stages increased with increasing population size. Large populations also showed a higher reproductive performance and a larger proportion of new recruits. Relationships with local growth conditions pointed towards the importance of an open grassland sward for flower and fruit set and the presence of microsites for successful sexual recruitment. These results suggest that the distribution of C. autumnale consists of an assemblage of basically unconnected populations that are remnants of formerly larger populations. This is in accordance with the species' ability to grow clonally, allowing long-term persistence under deteriorating conditions that occurred during a long period of habitat fragmentation. In conclusion, our results indicate that local habitat and population size are more important than habitat fragmentation (i.e. calcareous grassland isolation and surface area) and argue in favour of a management that is primarily focused on local habitat restoration. This is preferentially accomplished by reintroducing grazing practices, complemented by regular setback of spontaneous succession towards forest.     

The importance of lake morphometry and catchment characteristics in limnology – ranking based on statistical analyses

This work introduces an interpretational key to quantify and understand how much of variations among lakes in fundamental ecosystem characteristics that may be related to lake morphometry, catchment area features, measurement uncertainties and other factors (mostly climate). The size and form of lakes regulate many general transport processes, such as sedimentation, internal loading and outflow, which in turn regulate many abiotic state variables, such as concentrations of phosphorus, colour, water chemical variables and water clarity, which regulate primary production, which regulate secondary production. This paper discusses relationships between key abiotic state variables, lake morphometry and catchment area characteristics using empirical/statistical analyses based on data from 95 lakes. It has been shown that of the studied variables Secchi depth depends most on morphometry (34%); 31% of the variations among the lakes in Secchi depth may be related to catchment area characteristics, 1% to uncertainties in empirical data and 34% to other (climatological) factors. The corresponding figures for alkalinity, which depends least on lake morphometry are, 0% related to morphometry, 34% to catchment conditions, 1% to empirical uncertainty and 58% to other causes. For all other studied variables, i.e., conductivity, hardness (CaMg), calcium, iron, colour, pH and phosphorus the corresponding figures vary between these values. The interpretational key helps to explain the mechanistic reasons for these statistical/empirical results.     

The importance of workplace accommodation for cancer survivors – The role of flexible work schedules and psychological help in returning to work

We investigate whether accommodating job attributes influence the probability of returning to work three years after a cancer diagnosis. Using a combination of Danish administrative data and a survey carried out among Danish breast, colon, and melanoma skin cancer survivors, we find that the probability of returning to work is significantly and positively correlated with a flexible work schedule during and after cancer treatment. The result is robust when controlling for pre-cancer work experience, job seniority, pre-cancer job dissatisfaction, and post-cancer ability to work. Furthermore, we show that the influence of a flexible schedule varies with respect to cancer survivors’ ability to work, level of education, and type of cancer.     

The ‘chicken or the egg’: which comes first,forest tree decline or loss of mycorrhizae?

Forest trees are experiencing massive declines globally caused by a multitude of stressors, both abiotic (pollution, fragmentation and climate change) and biotic (fungi, bacteria, viruses and insects). Mycorrhizal fungi aid plants in the requisition of nutrients through their mutualistic relationship with plant roots and are integral to tree health. Stresses affecting tree health will also influence mycorrhizal fungi directly or indirectly, and thus alter the pathways responsible for nutrient absorption. Such an intimate association is a true chicken or egg quandary; do external stressors cause a loss of mycorrhizae which leads to tree decline, does tree decline result in a loss of mycorrhizae, or is it a combination of both? A review of literature has identified six stressors known to contribute to tree decline and to impact directly on mycorrhizae; global climate change, pesticides, heavy metals, excess fertilizer, pathogens and habitat fragmentation. A few review papers have highlighted the link; however, what is missing is irrefutable empirical research. This review documents the known direct impacts of the six stressors on mycorrhizal communities and places this in the context of decline syndromes in long-lived forest trees. We also discuss methodologies available to identify fungi and future research needed to unravel the complex relationships between forest tree declines and their associated mycorrhizal fungi.     

The nature of the cell cycle in neurons: Focus on a “non-canonical” pathway of DNA replication causally related to death

The mechanism whereby a reactivation of cell cycle in neurons causes cell death is beginning to be identified. In cellular models of Alzheimer's disease, activation of a non-canonical pathway of DNA replication contributes to neuronal death. This pathway involves the repair enzyme DNA polymerase-β, which is highly expressed in neurons of the Alzheimer's brain at early stages of the disease. Loading of DNA polymerase-β into the replication forks generates a death signal, which involves the tumor suppressor p53. The increasing knowledge of the main actors of the unscheduled DNA replication in neurons will pave the way for novel therapeutic interventions in Alzheimer's disease and other neurodegenerative disorders.     

The use of assembly polymerase chain reaction for cloning of a malarial epitope into Mycobacterium smegmatis – importance of overcoming codon bias

The cloning of an A:T-rich DNA fragment, the C-terminus of Plasmodium falciparum merozoite surface protein-1, into the G:C-rich Mycobacterium smegmatis resulted in delayed growth (6 days), a 10-fold decrease in the expected transformation efficiency and low level expression of the recombinant protein by the host cells. The technique of assembly PCR was used to assemble a series of oligonucleotides to generate a synthetic homologue of the plasmodium DNA fragment using mycobacterium codon bias. Cloning of the synthetic fragment into M. smegmatis resulted in normal growth (4 days), the expected level of transformation efficiency (10⁴ c.f.u. g^–1 DNA) and a substantial increase in the expression of the recombinant protein.     

DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures

DNA polymerase ζ (Pol ζ) and Rev1 are key players in translesion DNA synthesis. The error-prone Pol ζ can also participate in replication of undamaged DNA when the normal replisome is impaired. Here we define the nature of the replication disturbances that trigger the recruitment of error-prone polymerases in the absence of DNA damage and describe the specific roles of Rev1 and Pol ζ in handling these disturbances. We show that Pol ζ/Rev1-dependent mutations occur at sites of replication stalling at short repeated sequences capable of forming hairpin structures. The Rev1 deoxycytidyl transferase can take over the stalled replicative polymerase and incorporate an additional ‘C’ at the hairpin base. Full hairpin bypass often involves template-switching DNA synthesis, subsequent realignment generating multiply mismatched primer termini and extension of these termini by Pol ζ. The postreplicative pathway dependent on polyubiquitylation of proliferating cell nuclear antigen provides a backup mechanism for accurate bypass of these sequences that is primarily used when the Pol ζ/Rev1-dependent pathway is inactive. The results emphasize the pivotal role of noncanonical DNA structures in mutagenesis and reveal the long-sought-after mechanism of complex mutations that represent a unique signature of Pol ζ.     

The carbohydrate structures ofβ-galactosidase from human liver

Acid -galactosidase (EC3.2.1.23) was obtained from human liver in a pure monomeric state (M_r63 000). The carbohydrate content of the enzyme was established to be, 9% by weight; mannose,N-acetylglucosamine, galactose andN-acetylneuraminic acid were found to be the constituent monosaccharides. The carbohydrate structures of the enzyme were studied at the glycopeptide level by employing 500 MHz¹H-NMR spectroscopy, carbohydrate composition analysis and methylation analysis involving GLCMS. Based upon the intensities of relevant signals in the¹H-NMR spectrum, approximately 60% of the chains were found to be of theN-acetyllactosamine type, having the structure The rest appeared to be of the oligomannoside type (Man₅-₆GlcNAc₂Asn). The carbohydrate composition and methylation analysis results sustained these findings, although the calculation of the distribution based upon these techniques indicated a somewhat lower percentage ofN-acetyllactosamine type chains. There are approximately three oligosaccharide chains per molecule. These findings offer an explanation for the abnormal distribution of -galactosidase in tissues and cultured fibroblasts of patients with I-cell disease.     

Going with the wind – Adaptive dynamics of plant secondary meristems

The developmental plasticity of organisms is a natural consequence of adaptation. Classical approaches targeting developmental processes usually focus on genetics as the essential factor underlying phenotypic differences. However, such differences are often based on the inherent plasticity of developmental programs. Due to their dependence on environmental stimuli, plants represent ideal experimental systems in which to dissect the contribution of genetic and environmental variation to phenotypic plasticity. An evident example is the vast repertoire of growth forms observed in plant shoot systems. A fundamental factor underlying the broadness of this repertoire is the activity of secondary meristems, namely the axillary meristems that give rise to side shoots, and the cambium essential for stem thickening. Differential activities of both meristem types are crucial to the tremendous variation seen in higher plant architecture. In this review, we discuss the role of secondary meristems in the adaptation of plant growth forms, and the ways in which they integrate environmental input. In particular, we explore potential approaches for dissecting the degree to which this flexibility and its consequences for plant architecture is genetically predetermined and how much it represents an adaptive value.     

The in situ formation of DNA · DNA duplexes of Drosophila virilis satellite DNA

The DNA of Drosophila virilis brains and imaginal discs was labeled in vitro to a specific activity of 6 X 10(-5) dpm/mug, using an organ culture medium. The DNA was fractionated on neutral and alkaline CsC1 gradients and the heavy strands of satellite I annealed in situ to denatured polytene chromosomes from squash preparations of larval salivary glands. Nuclease S1 from Aspergillus oryzae was used to digest the unpaired ssDNA, resulting in a distinct labeling of the alpha-heterochromatin in the chromocenter and a small amount of diffused labeling in the proximal beta-heterochromatic part of the X-Chromsome.