Biodiversity conservation and conservation biotechnology tools

This special issue is dedicated to the in vitro tools and methods used to conserve the genetic diversity of rare and threatened plant species from around the world. Species that are on the brink of extinction because of the rapid loss of genetic diversity and habitat come mainly from resource-poor areas of the world and from global biodiversity hotspots and island countries. These species are unique because they are endemic, and only a few small populations or sometimes only a few individuals remain in the wild. Therefore, the challenges to support conservation by in vitro measures are many and varied. The editors of this invited issue solicited papers from experts from Asia, Africa, Europe, Australia, and North and South America. This compilation of articles describes the efforts in these diverse regions toward saving plants from extinction, and details the direct application of in vitro and cryopreservation methods. In addition, these contributions provide guidance on propagation of rare plants, including techniques for large-scale propagation, storage, and reintroduction. The in vitro techniques for conserving plant biodiversity include shoot apical or axillary-meristem-based micropropagation, somatic embryogenesis, cell culture technologies and embryo rescue techniques, as well as a range of in vitro cold storage and cryopreservation protocols, and they are discussed in depth in this issue.     

Plant Pathogens in Irrigation Water: Challenges and Opportunities

Plant pathogens in irrigation water were recognized early in the last century as a significant crop health issue. This issue has increased greatly in scope and degree of impact since that time and it will continue to be a problem as agriculture increasingly depends on the use of recycled water. Plant pathogens detected from water resources include 17 species of Phytophthora, 26 of Pythium, 27 genera of fungi, 8 species of bacteria, 10 viruses, and 13 species of plant parasitic nematodes. There is substantial evidence demonstrating that contaminated irrigation water is a primary, if not the sole, source of inoculum for Phytophthora diseases of numerous nursery, fruit, and vegetable crops. These findings pose great challenges and opportunities to the plant pathology community. A variety of water treatment methods are available but few have been assessed for agricultural purposes under commercial conditions. Investigations into their technical feasibility and economics are urgently needed. Aquatic ecology of plant pathogens is an emerging field of research that holds great promise for developing ecologically based water decontamination and other strategies of pathogen mitigation. Pathogen detection and monitoring as well as biological and economic thresholds are much-needed IPM tools and should be priorities of future research. Teaming with hydrologists, agricultural engineers, ecologists, geneticists, economists, statisticians, and farmers is essential to effectively attack such a complex issue of growing global importance. Research should proceed in conjunction with nutrient and pesticide management studies in a coordinated and comprehensive approach as they are interrelated components of water resource conservation and protection.     

Molecular immunology: At the border of centuries and at the interface of disciplines

This is a special issue of the journal Molekulyarnaya biologiya (Molecular Biology) focusing on topical problems in molecular immunology, virology, and the related fields of science, including molecular genetics, biochemistry, and cell biology. Several reviews are offered to the attention of our readers, as well as original experimental papers. This issue was prepared on a tight schedule and, certainly, cannot pretend to cover all the areas of the state-of-the-art science.     

Towards natural polyploid model organisms

Populations of natural allopolyploids with available and well‐developed genomic resources are currently hard to come by. These are needed because whole genome duplication and hybridization — both combined in allopolyploids — are significant processes in evolution, especially the evolution of plants. The new characterization of a naturally occurring allopolyploid in the genus Mimulus by Sweigart et al. in this issue of Molecular Ecology is therefore to be welcomed. Mimulus is rapidly emerging as a model system for evolutionary functional genomics. Sequences of the whole genome and 200 000 expressed sequence tags of diploid M. guttatus, a putative parent of the polyploid described in this issue, will soon be available. These will facilitate investigation of the fates of genes duplicated by whole genome duplication, and their effects on morphology, mating system and ecology in natural populations.     

Asian Federation of Biotechnology (AFOB)

Cover illustration: This issue is the first official special issue of Biotechnology Journal with the Asian Federation of Biotechnology (AFOB). In the cover, we use the grain as a symbol and analogy for biotechnology, as both the grain and biotechnology are common and uniting factors that link the member countries of the AFOB. Gran image credit: © Myimagine– Fotolia.com.     

In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure

Background  

Compactness of highly/broadly expressed genes in human has been explained as selection for efficiency, regional mutation biases or genomic design. However, highly expressed genes in flowering plants were shown to be less compact than lowly expressed ones. On the other hand, opposite facts have also been documented that pollen-expressed Arabidopsis genes tend to contain shorter introns and highly expressed moss genes are compact. This issue is important because it provides a chance to compare the selectionism and the neutralism views about genome evolution. Furthermore, this issue also helps to understand the fates of introns, from the angle of gene expression.     

Implications of Molecular and Morphological Data for Understanding Ateline Phylogeny

The ateline monkeys constitute as certain a monophyletic group as there is among primates. The group is intriguing because while their adaptations are well-documented and their monophyly as a group is unquestioned, their phylogenetic interrelationships are controversial. Molecular data indicate a phylogeny at odds with their morphology. Traditional morphological comparisons isolate Alouatta from the atelins, and link Ateles and Brachyteles as a sister group to the exclusion of Lagothrix. In contrast, several recent molecular studies point to a closer relationship between Brachyteles and Lagothrix than between Brachyteles and Ateles. At the heart of the problem lie the assumptions we make about the validity of data and the homology of observed traits. The fossil record further confounds the issue. We must account for the fossil record because it is positive evidence. But we cannot control how much of it there is or how much of it ever will be known. At this point in time, the ateline molecular and fossil record provoke us to examine critically our morphological approach to phylogenetic modeling.     

Phylogeny and biogeography in the evolution of migration: shorebirds of the Charadrius complex

Aim We explore whether molecular phylogeny and biogeography can complement evolutionary ecology in developing a method to address a long-standing issue in the evolution of migration: have migrations between breeding and non-breeding grounds, which may be on different continents, evolved through origins in the breeding grounds with successive shifts of the non-breeding distribution or vice versa? Methods To accommodate the biology of migration, we treated breeding and non-breeding distributions as characters to be mapped onto a phylogeny derived from mitochondrial DNA sequence data and so examined the ancestral home issue as a study in the direction of character evolution. Results Our main findings from applying this approach to a subset of the Charadrius complex of shorebirds (Aves: Charadriinae) are that a case can be made for shifts of breeding distributions having occurred in the ancestries of C. alexandrinus and C. veredus as those species evolved their present migration patterns. Our results also argue for a southern hemisphere origin (specifically South America) for the Charadrius complex as a whole. A South American origin implies other shifts in breeding distributions having occurred in the evolution of the species C. semipalmatus and C. vociferus. On applying the methods we developed for dealing with phylogenetic uncertainty, these results are reinforced and the merit of testing them further is suggested. Conclusions By way of a new approach to the evolution of migration, our study adds to a consensus emerging from the evolutionary ecology of migrant birds, arguing that shifts of breeding distributions are commonly, though not necessarily exclusively, involved in the evolution of migration.     

Cancer,stem cell misplacement and cancer stem cells

The cell of origin of cancer as well as cancer stem cells is still a mystery. In a recent issue of JCMM, Wang et al. challenged the conventional somatic genetic mutation model of multi‐stage carcinogenesis of breast cancer and proposed that ‘Invasive cancers are not necessary from preformed in situ tumours—an alternative way of carcinogenesis from misplaced stem cells’. If this stem cell misplacement theory could withstand future experimental evaluation, it may provide a paradigm shift in the prevention and management of cancer in the clinic.     

Emergent properties and the context objection to reduction

Reductionism is a central issue in the philosophy of biology. One common objection to reduction is that molecular explanation requires reference to higher-level properties, which I refer to as the context objection. I respond to this objection by arguing that a well-articulated notion of a mechanism and what I term mechanism extension enables one to accommodate the context-dependence of biological processes within a reductive explanation. The existence of emergent features in the context could be raised as an objection to the possibility of reduction via this strategy. I argue that this objection can be overcome by showing that there is no tenable argument for the existence of emergent properties that are not susceptible to a reductive explanation.     

20th International Symposium on Shiftwork and Working Time: Biological Mechanisms,Recovery, and Risk Management in the 24-h Society

This dedicated issue of Chronobiology International is devoted to the selected proceedings of the 20th International Symposium on Shift Work and Working Time held in Stockholm, Sweden, 28 June to 1 July 2011. It constitutes the fifth such issue of the journal since 2004 dedicated to the selected proceedings to the meetings of the Working Time Society. The key theme of the 20th Symposium was “Biological Mechanisms, Recovery, and Risk Management in the 24-h Society.” The collection of papers of this dedicated issue represents the best of contemporary research on the effects of night and rotating shift schedules on worker health and safety. The contents cover such topics as sleep restriction, injuries, health, and performance of night work and rotating shiftwork, plus light treatment as a countermeasure against the circadian disruption of shiftwork. The majority of the papers are observational field studies, including some of large sample size, and three studies are well-designed laboratory experiments. (Author correspondence: goran.kecklund@stress.su.se)     

Azole resistance in aspergillosis: The next threat?

During the past years, aspergilli less susceptible to antifungals have begun to emerge, and antifungal drug resistance may partially account for treatment failures. Resistance of Aspergillus fumigatus clinical isolates to itraconazole, voriconazole, and posaconazole has been reported with increasing frequency, although it is considered an uncommon phenomenon. Molecular biologists have begun to shed light on the mechanisms of A. fumigatus resistance to azoles. Several mechanisms of resistance have been described, such as point mutations of cyp51A and reduced concentrations of intracellular drug. The latter mechanism might be the result of either overexpression of efflux pumps or reduced drug penetration. The issue of cross-resistance between the newer triazoles is of concern and depends on cyp51 mutations. Fungal drug resistance is an issue because of the limited number of antifungal compounds. Patients receiving long-term azole treatment are at highest risk for developing multidrug-resistant A. fumigatus infections.     

Studies on the morphology,cytology, and distribution ofLeucojum subgenusRuminia

The following is a summary of part of a lecture held on february 13th 1974 at the Pädagogische Hochschule Berlin. A more detailed publication is under preparation.The following note has been based on studies parallel to those ofDamboldt & Phitos (cf. p. 119 of this issue). Results are complementary or corroborate each other. Our understanding of the interesting relationships between MediterraneanLeucojum taxa is thus improved. This justifies the parallel publication of the two articles in one issue of this journal (Editor).     

Polyploidy, hybridization and reticulate evolution: lessons from the Brassicaceae

The family Brassicaceae is well known for its large variation in chromosome numbers, common occurrence of polyploids and many reports of interspecific gene flow. The present review summarizes studies from the past decades on polyploidization and hybridization events, recognizing them as important evolutionary forces in the family. Attention is drawn to the issue of the reconstruction of reticulated pattern of evolution resulting from allopolyploid and homoploid hybrid speciation. The research of various authors on several Brassicaceae genera is presented and discussed in the context of our current understanding of polyploid and hybrid evolution. Model species, Arabidopsis thaliana and Brassica taxa, are referred to only marginally, major focus is on a comprehensive survey of studies on about a dozen best explored non-model genera (e.g. Cardamine, Draba, Rorippa, Thlaspi). The increasing amount of genetic and genomic resources available for Brassicaceae model species provides excellent opportunities for comparative genetic and genomic studies. Future research directions and challenges are thus outlined, in order to obtain more detailed insights into the evolution of polyploid and hybrid genomes.     

Update on: Shigella new serogroups/serotypes and their antimicrobial resistance

Shigellosis represents a major burden of disease in developing countries. A low infectious dose allows the disease to be spread effectively. Although shigellosis is mostly a self‐limiting disease, antibiotics are recommended to reduce deaths, disease symptoms and organism‐shedding time. However, in India, antimicrobial resistance among the genus Shigella is more common than among any other enteric bacteria. Notably, new serotypes or subserotypes in Shigella are reported from various parts of the world. Identification of new subserotypes of Shigella spp. is becoming a major issue as these strains are nontypeable by conventional serotyping. The commercially available antisera may not cover all possible epitopes of the O lipopolysaccharide antigen of Shigella serotypes. Therefore, molecular methods which most closely approach the resolution of full serotyping are necessary to identify such strains. In addition, the knowledge of a prevalent serotype in various geographic regions may assist in formulating strategies such as the development of a vaccine to prevent infection especially when the immunity to disease is serotype specific, and to understand the disease burden caused by new Shigella serotypes.     

New friends for Ago2 in neuronal plasticity

MicroRNAs have emerged as central regulators of cellular homeostasis and increasing evidence suggests that they play a key role in neuronal plasticity. Major efforts are made to define microRNA networks and their targets in the brain. The mechanisms by which microRNA activity is regulated are, however, relatively unexplored. In this issue of The EMBO Journal, Störchel et al ( 2015 ) screened for proteins that affect microRNA function in neurons. They identify Nova1 and Ncoa3 as novel regulators of miRNA activity and demonstrate that both proteins are essential for neuronal plasticity in a microRNA‐dependent manner.     

On Abortion: Exploring Psychological Meaning and Attitudes in a Sample of Mexican Gynecologists

Elective abortion has become an issue of ethical and political debate in many countries including Mexico. As gynecologists are directly involved in the practice of abortion, it is important to know the psychological meaning that the term ‘elective abortion’ has for them. This study explores the psychological meaning and attitudes toward elective abortion of one hundred and twenty‐three Mexican gynecologists. We used the semantic networks technique, which analyzed the words the participants associated with the term ‘elective abortion’. The defining words most frequently used by participants implied a negative sanction. There were important differences by gender and religiosity: male gynecologists, as well as those with strong religious beliefs (mainly Catholics), revealed a more negative psychological meaning and more negative attitudes than females or physicians with weak religious beliefs. A contribution of the present study is that it highlights the importance of psychology to enhancing understanding of the issue of elective abortion.     

A multi‐protein complex controls cAMP signalling and filamentation in the fungal pathogen Candida albicans

Candida albicans is an opportunistic fungal pathogen of humans. The ability of the fungus to grow as both yeast and filamentous forms is essential for its pathogenicity. Morphogenesis of C. albicans is largely regulated through the secondary messenger cAMP, produced by the soluble adenylyl cyclase, Cyr1p. Recent evidence suggests that Cyr1p can be directly stimulated by environmental cues to increase cytoplasmic cAMP levels and thus promote hyphal development. In this issue of Molecular Microbiology, Zou et al. demonstrate that, in response to some environmental cues, Cyr1p functions as part of a tripartite complex additionally involving Cap1p and G‐actin. All three proteins in the complex are required to raise cytosolic cAMP levels after stimulation with serum and bacterial peptidoglycan. The formation of such a complex highlights the importance of precise regulation of Cyr1p activity in response to host environmental cues.     

Genomics of clinal variation in Drosophila: disentangling the interactions of selection and demography

Clines in phenotypes and genotype frequencies across environmental gradients are commonly taken as evidence for spatially varying selection. Classical examples include the latitudinal clines in various species of Drosophila, which often occur in parallel fashion on multiple continents. Today, genomewide analysis of such clinal systems provides a fantastic opportunity for unravelling the genetics of adaptation, yet major challenges remain. A well‐known but often neglected problem is that demographic processes can also generate clinality, independent of or coincident with selection. A closely related issue is how to identify true genic targets of clinal selection. In this issue of Molecular Ecology, three studies illustrate these challenges and how they might be met. Bergland et al. report evidence suggesting that the well‐known parallel latitudinal clines in North American and Australian D. melanogaster are confounded by admixture from Africa and Europe, highlighting the importance of distinguishing demographic from adaptive clines. In a companion study, Machado et al. provide the first genomic comparison of latitudinal differentiation in D. melanogaster and its sister species D. simulans. While D. simulans is less clinal than D. melanogaster, a significant fraction of clinal genes is shared between both species, suggesting the existence of convergent adaptation to clinaly varying selection pressures. Finally, by drawing on several independent sources of evidence, Bo?i?evi? et al. identify a functional network of eight clinal genes that are likely involved in cold adaptation. Together, these studies remind us that clinality does not necessarily imply selection and that separating adaptive signal from demographic noise requires great effort and care.     

A new flavor of entry exclusion in ICE elements provides a selective advantage for the element and its host

Entry exclusion has been described in many bacterial conjugation systems, but their molecular mechanisms are not well understood. In the current issue, Avello et al. describe a new exclusion system in the conjugative element ICEBs1. They identify the yddJ gene as the functional exclusion gene and its target as the protein product of the conG gene. They provide evidence for a possible mechanism and for the contribution of the system to reduce fitness costs of ICE expression.