Comparing strategies to preserve evolutionary diversity

The likely future extinction of various species will result in a decline of two quantities: species richness and phylogenetic diversity (PD, or ‘evolutionary history’). Under a simple stochastic model of extinction, we can estimate the expected loss of these quantities under two conservation strategies: An ‘egalitarian’ approach, which reduces the extinction risk of all species, and a ‘targeted’ approach that concentrates conservation effort on the most endangered taxa. For two such strategies that are constrained to experience the same expected loss of species richness, we ask which strategy results in a greater expected loss of PD. Using mathematical analysis and simulation, we describe how the strategy (egalitarian versus targeted) that minimizes the expected loss of PD depends on the distribution of endangered status across the tips of the tree, and the interaction of this status with the branch lengths. For a particular data set consisting of a phylogenetic tree of 62 lemur species, with extinction risks estimated from the IUCN ‘Red List’, we show that both strategies are virtually equivalent, though randomizing these extinction risks across the tip taxa can cause either strategy to outperform the other. In the second part of the paper, we describe an algorithm to determine how extreme the loss of PD for a given decline in species richness can be. We illustrate the use of this algorithm on the lemur tree.     

Fixation technique to preserve the vacuolation ofPenicillium chrysogenum hyphae

Summary It has been shown that a paraformaldehyde/glutaraldehyde/phosphate buffer saline fixative can be used to preserve vacuolation ofPenicillium chrysogenum hyphae from submerged cultures for later image analysis characterisation. After fixing, the proportion of the hyphase as vacuoles and empty cells (in several samples from different fermentations with different initial percentage vacuolations) did not change significantly over about 70h, and there were only minor changes towards smaller vacuoles in the vacuolation size distributions over the same period. This fixation method will permit the storage of vacuolated hyphae, for later analysis either for physiological studies or for dynamic studies of the links between hyphal vacuolation and fragmentation.     

Bacteriocin: safest approach to preserve food products

Start of the 21st century with its universal call to feed the hungry is an appropriate time to refocus attention on food security and especially the impact of biopatenting on poor communities who are the primary victims of hunger in our world. Antibacterial metabolites of lactic acid bacteria and Bacillus spp have potential as natural preservatives to control the growth of spoilage and pathogenic bacteria in food. Among them, bacteriocin is used as a preservative in food due to its heat stability, wider pH tolerance and its proteolytic activity. Due to thermo stability and pH tolerance it can withstand heat and acidity/alkanity of food during storage condition. Bacteriocin are ribosomally synthesized peptides originally defined as proteinaceous compound affecting growth or viability of closely related organisms. Research is going on extensively to explore the nascent field of biopreservation. Scientists all over the world are showing their keen interest to isolate different types of bacteriocin producing strains and characterize bacteriocin produced by them for food preservation.     

Factors to preserve CpG-rich sequences in methylated CpG islands

Background

Mammalian CpG islands (CGIs) normally escape DNA methylation in all adult tissues and developmental stages. However, in our previous study we unexpectedly identified many methylated CGIs in human peripheral blood leukocytes. Methylated CpG dinucleotides convert to TpG dinucleotides through deaminization of their cytosine bases more frequently than hypomethylated CpG dinucleotides. Therefore, we wondered how methylated CGIs in germline or non-germline cells maintain their CpG-rich sequences. It is known that events such as germline hypomethylation, CpG selection, biased gene conversion (BGC), and frequent CpG fixation can contribute to the maintenance of CpG-rich sequences in methylated CGIs in germline or non-germline cells. However, it has not been investigated which of the processes maintain CpG-rich sequences of methylated CGIs in each genomic position.

Results

In this study, we comprehensively examined the contribution of the processes described above to the maintenance of CpG-rich sequences in methylated CGIs in germline and non-germline cells which were classified by genomic positions. Approximately 60–80% of CGIs with high methylation in H1 cell line (H1-HM) in all the genomic positions showed a low average CpG → TpG/CpA substitution rate. In contrast, fewer than half the numbers of CGIs with H1-HM in all the genomic positions showed a low average CpG → TpG/CpA substitution rate and low levels of methylation in sperm cells (SPM-LM). Furthermore, a small fraction of CGIs with a low average CpG → TpG/CpA substitution rate and high levels of methylation in sperm cells (SPM-HM) showed CpG selection.On the other hand, independent of the positions in genes, most CGIs with SPM-HM showed a slightly higher average TpG/CpA → CpG substitution rate compared with those with SPM-LM.

Conclusions

Relatively high numbers (approximately 60–80%) of CGIs with H1-HM in all the genomic positions preserve their CpG-rich sequences by a low CpG → TpG/CpA substitution rate caused mainly by their SPM-LM, and for those with SPM-HM partly by CpG selection and TpG/CpA → CpG fixation. BGC has little contribution to the maintenance of CpG-rich sequences of CGIs with SPM-HM which were classified by genomic positions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1286-x) contains supplementary material, which is available to authorized users.     

How best to preserve and reveal the structural intricacies of cartilaginous tissue

No single processing technique is capable of optimally preserving each and all of the structural entities of cartilaginous tissue. Hence, the choice of methodology must necessarily be governed by the nature of the component that is targeted for analysis, for example, fibrillar collagens or proteoglycans within the extracellular matrix, or the chondrocytes themselves.This article affords an insight into the pitfalls that are to be encountered when implementing the available techniques and how best to circumvent them.Adult articular cartilage is taken as a representative pars pro toto of the different bodily types. In mammals, this layer of tissue is a component of the synovial joints, wherein it fulfills crucial and diverse biomechanical functions. The biomechanical functions of articular cartilage have their structural and molecular correlates. During the natural course of postnatal development and after the onset of pathological disease processes, such as osteoarthritis, the tissue undergoes structural changes which are intimately reflected in biomechanical modulations. The fine structural intricacies that subserve the changes in tissue function can be accurately assessed only if they are faithfully preserved at the molecular level. For this reason, a careful consideration of the tissue-processing technique is indispensable. Since, as aforementioned, no single methodological tool is capable of optimally preserving all constituents, the approach must be pre-selected with a targeted structure in view. Guidance in this choice is offered.     

Integrin signaling regulates spindle orientation in Drosophila to preserve the follicular-epithelium monolayer

Epithelia act as important physiological barriers and as structural components of tissues and organs. In the Drosophila ovary, follicle cells envelop the germline cysts to form a monolayer epithelium. During division, the orientation of the mitotic spindle in follicle cells is such that both daughter cells remain within the same plane, and the simple structure of the follicular epithelium is thus preserved. Here we show that integrins, heterodimeric transmembrane receptors that connect the extracellular matrix to the cell's cytoskeleton [1, 2], are required for maintaining the ovarian monolayer epithelium in Drosophila. Mosaic egg chambers containing integrin mutant follicle cells develop stratified epithelia at both poles. This stratification is due neither to abnormal cell proliferation nor to defects in the apical-basal polarity of the mutant cells. Instead, integrin function is required for the correct orientation of the mitotic apparatus both in mutant cells and in their immediately adjacent wild-type neighbors. We further demonstrate that integrin-mediated signaling, rather than adhesion, is sufficient for maintaining the integrity of the follicular epithelium. The above data show that integrins are necessary for preserving the simple organization of a specialized epithelium and link integrin-mediated signaling to the correct orientation of the mitotic spindle in this epithelial cell type.     

JNK1 is required to preserve cardiac function in the early response to pressure overload

Cardiac stress consistently activates c-Jun NH(2)-terminal kinase (JNK) pathways, however the role of different members of the JNK family is unclear. In this study, we applied pressure overload (TAC) in mice with selective deletion of the three JNK genes (Jnk1(-/-), Jnk2(-/-), and Jnk3(-/-)). Following TAC, all three JNK knockout mouse lines developed cardiac hypertrophy similar to wild-type mice (WT), but only JNK1(-/-) mice displayed a significant reduction in fractional shortening after 3 and 7 days of pressure overload, associated with a significant increase in terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling staining and marked inflammatory infiltrate. After the acute deterioration stage, JNK1(-/-) mice underwent a slow recovery followed by a steady progression of cardiac dysfunction, becoming indistinguishable from WT after 12 weeks of TAC. These data suggest that JNK1 plays a protective role in response to pressure overload, preventing the early deterioration in cardiac function following an acute increase in afterload.     

Free flaps to preserve below-knee amputation stumps: long-term evaluation

Five patients with insufficient soft-tissue coverage on below-knee amputation stumps have been treated with free-tissue transfer surgery to preserve a functional below-knee prosthetic level. The flaps employed include one latissimus dorsi myocutaneous flap, two latissimus dorsi muscle-skin graft flaps, one groin flap, and one foot-fillet flap. All five flaps survived; one patient required early venous anastomosis reexploration and revision. The patients have been followed for a mean duration of 5.5 years (range 3 to 8 years). The mean duration to first ambulation with a prosthesis was 3.6 months (range 2 to 7 months). Four of the five patients developed ulcerations on or adjacent to their flaps which required surgical revision. The patients required a mean of 1.28 prosthesis changes annually since surgery. The functional motion (mean active knee motion is 100 degrees) and ligamentous stability of the knee joints were well preserved in all patients. Five patients wear patella tendon-bearing prostheses, with one requiring an additional thigh corset. In two of the patients, nerve anastomoses to their flaps were performed. Both patients developed true cutaneous sensibility, but nevertheless experienced flap ulceration. All the patients are fully ambulatory on their free flaps. Free-tissue transfer can assist in preserving traumatic below-knee amputations so that patients can benefit from the functional advantage of a below-knee prosthetic device.     

Are predicted structures good enough to preserve functional sites?

BACKGROUND: A principal goal of structure prediction is the elucidation of function. We have studied the ability of computed models to preserve the microenvironments of functional sites. In particular, 653 model structures of a calcium-binding protein (generated using an ab initio folding protocol) were analyzed, and the degree to which calcium-binding sites were recognizable was assessed. RESULTS: While some model structures preserve the calcium-binding microenvironments, many others, including some with low root mean square deviations (rmsds) from the crystal structure of the native protein, do not. There is a very weak correlation between the overall rmsd of a structure and the preservation of calcium-binding sites. Only when the quality of the model structure is high (rmsd less than 2 A for atoms in the 7 A local neighborhood around calcium) does the modeling of the binding sites become reliable. CONCLUSIONS: Protein structure prediction methods need to be assessed in terms of their preservation of functional sites. High-resolution structures are necessary for identifying binding sites such as calcium-binding sites.