Biotic and abiotic constraints that facilitate host exclusivity of Gondwanamyces and Ophiostoma on Protea

Estimations of global fungal diversity are hampered by a limited understanding of the forces that dictate host exclusivity in saprobic microfungi. To consider this problem for Gondwanamyces and Ophiostoma found in the flower heads of Protea in South Africa, we determined the role of various factors thought to influence their host exclusivity. Results showed that various biotic and abiotic factors influence the growth and survival of these fungi in vitro. Monitoring temperature and relative humidity (RH) fluctuations within infructescences in vivo revealed considerable microclimatic differences between different Protea spp. Fungal growth and survival at different RH levels experienced in the field suggested that this factor does not play a major role in host exclusivity of these fungi. Maximum temperatures within infructescences and host preferences of the vectors of Gondwanamyces and Ophiostoma appear to play a substantial part in determining colonisation of Protea in general. However, these factors did not explain host exclusivity of specific fungal species towards particular Protea hosts. In contrast, differential growth of fungal species on media containing macerated tissue of Protea showed that Gondwanamyces and Ophiostoma grow best on tissue from their natural hosts. Thus, host chemistry plays a role in host exclusivity of these fungi, although some species grew vigorously on tissue of Protea spp. with which they are not naturally associated. A combination of host chemistry and temperature partially explains host exclusivity, but the relationship for these factors on the tested saprobic microfungi and their hosts is clearly complex and most likely includes combinations of various biotic and abiotic factors including those emerging from this study.     

Ophiostoma gemellus and Sporothrix variecibatus from mites infesting Protea infructescences in South Africa

Ophiostoma (Ophiostomatales) represents a large genus of fungi mainly known from associations with bark beetles (Curculionidae: Scolytinae) infesting conifers in the northern hemisphere. Few southern hemisphere native species are known, and the five species that consistently occur in the infructescences of Protea spp. in South Africa are ecologically unusual. Little is known about the vectors of Ophiostoma spp. from Protea infructescences, however recent studies have considered the possible role of insects and mites in the distribution of these exceptional fungi. In this study we describe a new species of Ophiostoma and a new Sporothrix spp. with affinities to Ophiostoma, both initially isolated from mites associated with Protea spp. They are described as Ophiostoma gemellus sp. nov. and Sporothrix variecibatus sp. nov. based on their morphology and comparisons of DNA sequence data of the 28S ribosomal, beta-tubulin and internal transcribed spacer (ITS1, 5.8S, ITS2) regions. DNA sequences of S. variecibatus were identical to those of a Sporothrix isolate obtained from Eucalyptus leaf litter in the same area in which S. variecibatus occurs in Protea infructescences. Results of this study add evidence to the view that mites are the vectors of Ophiostoma spp. that colonize Protea infructescences. They also show that DNA sequence comparisons are likely to reveal additional cryptic species of Ophiostoma in this unusual niche.     

Annual cycles are the most common reproductive strategy in African tropical tree communities

We present the first cross‐continental comparison of the flowering and fruiting phenology of tropical forests across Africa. Flowering events of 5446 trees from 196 species across 12 sites and fruiting events of 4595 trees from 191 species across 11 sites were monitored over periods of 6 to 29 years and analyzed to describe phenology at the continental level. To study phenology, we used Fourier analysis to identify the dominant cycles of flowering and fruiting for each individual tree and we identified the time of year African trees bloom and bear fruit and their relationship to local seasonality. Reproductive strategies were diverse, and no single regular cycle was found in >50% of individuals across all 12 sites. Additionally, we found annual flowering and fruiting cycles to be the most common. Sub‐annual cycles were the next most common for flowering, whereas supra‐annual patterns were the next most common for fruiting. We also identify variation in different subsets of species, with species exhibiting mainly annual cycles most common in West and West Central African tropical forests, while more species at sites in East Central and East African forests showed cycles ranging from sub‐annual to supra‐annual. Despite many trees showing strong seasonality, at most sites some flowering and fruiting occurred all year round. Environmental factors with annual cycles are likely to be important drivers of seasonal periodicity in trees across Africa, but proximate triggers are unlikely to be constant across the continent.     

Fossil ghost ranges are most common in some of the oldest and some of the youngest strata

Biologists routinely compare inferences about the order of evolutionary branching (phylogeny) with the order in which groups appear in the fossil record (stratigraphy). Where they conflict, ghost ranges are inferred: intervals of geological time where a fossil lineage should exist, but for which there is no direct evidence. The presence of very numerous and/or extensive ghost ranges is often believed to imply spurious phylogenies or a misleadingly patchy fossil record, or both. It has usually been assumed that the frequency of ghost ranges should increase with the age of rocks. Previous studies measuring ghost ranges for whole trees in just a small number of temporal bins have found no significant increase with antiquity. This study uses a much higher resolution approach to investigate the gappiness implied by 1,000 animal and plant cladograms over 77 series and stages of the Phanerozoic. It demonstrates that ghost ranges are indeed relatively common in some of the oldest strata. Surprisingly, however, ghost ranges are also relatively common in some of the youngest, fossil-rich rocks. This pattern results from the interplay between several complex factors and is not a simple function of the completeness of the fossil record. The Early Palaeozoic record is likely to be less organismically and stratigraphically complete, and its fossils -- many of which are invertebrates-may be more difficult to analyse cladistically. The Late Cenozoic is subject to the pull of the Recent, but this accounts only partially for the increased gappiness in the younger strata.     

Transposases are the most abundant,most ubiquitous genes in nature

Genes, like organisms, struggle for existence, and the most successful genes persist and widely disseminate in nature. The unbiased determination of the most successful genes requires access to sequence data from a wide range of phylogenetic taxa and ecosystems, which has finally become achievable thanks to the deluge of genomic and metagenomic sequences. Here, we analyzed 10 million protein-encoding genes and gene tags in sequenced bacterial, archaeal, eukaryotic and viral genomes and metagenomes, and our analysis demonstrates that genes encoding transposases are the most prevalent genes in nature. The finding that these genes, classically considered as selfish genes, outnumber essential or housekeeping genes suggests that they offer selective advantage to the genomes and ecosystems they inhabit, a hypothesis in agreement with an emerging body of literature. Their mobile nature not only promotes dissemination of transposable elements within and between genomes but also leads to mutations and rearrangements that can accelerate biological diversification and—consequently—evolution. By securing their own replication and dissemination, transposases guarantee to thrive so long as nucleic acid-based life forms exist.     

Panmixia defines the genetic diversity of a unique arthropod‐dispersed fungus specific to Protea flowers

Knoxdaviesia proteae, a fungus specific to the floral structures of the iconic Cape Floral Kingdom plant, Protea repens, is dispersed by mites phoretic on beetles that pollinate these flowers. Although the vectors of K. proteae have been identified, little is known regarding its patterns of distribution. Seed bearing infructescences of P. repens were sampled from current and previous flowering seasons, from which K. proteae individuals were isolated and cultured. The genotypes of K. proteae isolates were determined using 12 microsatellite markers specific to this species. Genetic diversity indices showed a high level of similarity between K. proteae isolates from the two different infructescence age classes. The heterozygosity of the population was high (0.74 ± 0.04), and exceptional genotypic diversity was encountered (Ĝ = 97.87%). Population differentiation was negligible, owing to the numerous migrants between the infructescence age classes (N_m = 47.83) and between P. repens trees (N_m = 2.96). Parsimony analysis revealed interconnected genotypes, indicative of recombination and homoplasies, and the index of linkage disequilibrium confirmed that outcrossing is prevalent in K. proteae ( = 0.0067; P = 0.132). The high diversity and panmixia in this population is likely a result of regular gene flow and an outcrossing reproductive strategy. The lack of genetic cohesion between individuals from a single P. repens tree suggests that K. proteae dispersal does not primarily occur over short distances via mites as hypothesized, but rather that long-distance dispersal by beetles plays an important part in the biology of these intriguing fungi.     

Functional synergism between the most common polymorphism in human alanine:glyoxylate aminotransferase and four of the most common disease-causing mutations

The autosomal recessive disorder primary hyperoxaluria type 1 (PH1) is caused by a deficiency of the liver-specific pyridoxal-phosphate-dependent enzyme alanine:glyoxylate aminotransferase (AGT). Numerous mutations and polymorphisms in the gene encoding AGT have been identified, but in only a few cases has the causal relationship between genotype and phenotype actually been demonstrated. In this study, we have determined the effects of the most common naturally occurring amino acid substitutions (both normal polymorphisms and disease-causing mutations) on the properties, especially specific catalytic activity, of purified recombinant AGT. The results presented in this paper show the following: 1) normal human His-tagged AGT can be expressed at high levels in Escherichia coli and purified in a correctly folded, dimerized and catalytically active state; 2) presence of the common P11L polymorphism decreases the specific activity of purified recombinant AGT by a factor of three; 3) AGTs containing four of the most common PH1-specific mutations (G41R, F152I, G170R, and I244T) are all soluble and catalytically active in the absence of the P11L polymorphism, but in its presence all lead to protein destabilization and aggregation into inclusion bodies; 4) naturally occurring and artificial amino acid substitutions that lead to peroxisome-to-mitochondrion AGT mistargeting in mammalian cells also lead to destabilization and aggregation in E. coli; and 5) the PH1-specific G82E mutation abolishes AGT catalytic activity by interfering with cofactor binding, as does the artificial K209R mutation at the putative site of cofactor Shiff base formation. These results are discussed in the light of the high allelic frequency ( approximately 20%) of the P11L polymorphism and its importance in determining the phenotypic manifestations of mutations in PH1.     

Y-STR genetic structure of the most common surnames in Korea

The genetic pattern of the Y-chromosomal short tandem repeat (Y-STR) haplotypes of 542 unrelated males having the five most common surnames was analyzed to evaluate their usefulness for Korean forensic science and to provide the basic information for Korean genetic genealogy. We identified 439 Y-STR haplotypes, with 385 (87.7%) being found once. Each of the most common Korean surnames examined here showed high haplotype diversity (>0.9949), indicating that Y-STR haplotypes are very heterogeneous within each surname. Population genetic analysis showed that there are little genetic difference among five surnames due to the genetic heterogeneity within each surname and the various kinds of non surname-specific haplotypes (33.6%: 182/542) distributed among five surnames. Surname prediction may not be adequate for narrowing down the suspect list in Korean forensic science, and additional Y-STR haplotype data of thebon-gwans are needed.     

Migratory moths as dispersal vectors of an introduced plant-pathogenic fungus in Japan

The plant-pathogenic fungus Claviceps paspali infects florets of the dallisgrass Paspalum dilatatum and induces the plant to produce honeydew (containing massive amounts of conidia), which in turn attracts insects for dispersal of the fungal spores. In Japan, the association between C. paspali and its host plant is common, although both P. dilatatum and C. paspali are introduced species. To determine the dispersal agents of the introduced C. paspali, we examined which insects sapped the P. dilatatum honeydew produced by C. paspali. The study was conducted from September to October 2003 in central Japan. Adults of 48 moth species and two lacewing species visited infected spikelets of P. dilatatum and sapped the honeydew at night. The dominant moths, which carried C. paspali conidia on their proboscises, migrate long distances every year. Therefore, migratory moths may transmit C. paspali spores from diseased to healthy host plants and may have spread C. paspali to other areas in Japan where C. paspali did not previously exist.     

New species of Gondwanamyces from dying Euphorbia trees in South Africa

Gondwanamyces and its Custingophora anamorphs were first described from Protea infructescences in South Africa. Subsequently these unusual fungi were also found on Cecropia in Central America. During an investigation into the decline and death of native Euphorbia trees in South Africa, several fungal isolates resembling the anamorph state of Gondwanamyces were obtained from diseased tissues. In this study these isolates are identified based on morphology and comparisons of DNA sequences. Two previously unknown Gondwanamyces species were identified, both were associated with damage caused by beetles (Cossonus sp.). Inoculation studies showed that the new species of Gondwanamyces are pathogenic on Euphorbia ingens and may contribute to the decline of these trees.     

Dynamic choices are most accurate in small groups

According to the classic results of Galton and Condorcet, as well as in modern decision-making models, accuracy in groups increases with group size. However, these studies do not consider the naturally occurring situation in which individuals dynamically re-evaluate their decision with a possible change of opinion. The dynamics of re-evaluation in groups are very different to individual re-evaluation because individuals influence the group and the group influences the individual. We find that individual accuracy in a group is higher when individuals re-evaluate because all members have more access to social information, while in single decisions, those deciding first have less. This improvement is smaller in large groups as in this case errors can cascade across the members of the group before re-evaluation can correct them. The net result is a maximal accuracy at a small group size. We also analyzed the case in which individuals are influenced only by a small number of the other individuals. In this case, cascading errors affect the interacting subgroups but are very unlikely to reach the whole group. This results in a local optimum at a small group size but also an optimum at a very large size. We thus suggest that re-evaluation dynamics can make small and very large groups optimal. Also, features that may be seen as limitations, like an influence from only a small number of individuals, may turn to be beneficial when considering local animal interactions, here filtering out cascading of errors in the group when reconsideration dynamics takes place.     

The mechanisms of action of phototherapy in the treatment of the most common dermatoses

Phototherapy denotes the use of ultraviolet (UV) light in the management of several dermatoses. Most phototherapy regimens utilize ultraviolet radiation of different wavelenghts. Currently, irradiations with broadband UVB (290-320 nm), narrowband UVB (311-313 nm), 308 nm excimer laser, UVA 1 (340-400 nm), UVA with psoralen (PUVA), and extracorporeal photochemotherapy (photopheresis) are being used. The interplay of the various photobiologic pathways is far from being completely understood. Disordes that may benefit from such approach are numerous, with psoriasis, atopic dermatitis, cutaneous T-cell lymphomas, morphea, and vitiligo as main indications. The immunomodulatory effects of UVB radiation primarily affect the epidermis and superficial dermis, while UVA radiation affects mid and deep dermal components, especially blood vessels. UVB radiation is absorbed by endogenous chromophores, such as nuclear DNA, which initiates a cascade of events. Absorption of UV light by nucleotides causes the formation of DNA photoproducts and suppresses DNA synthesis. In addition UV light stimulates synthesis of prostaglandins and cytokines that play important roles in immune suppression. It may reduce the number of Langerhans cells, cutaneous T lymphocytes and mast cells in the dermis. UV radiation can also affect extranuclear molecular targets located in the cytoplasm and cell membrane. Immune suppression, alteration in cytokine expression, and cell cycle arrest may all contribute to the suppression of disease activity. PUVA is a form of chemophototherapy which uses UVA light to activate chemicals known as psoralens, hence psoralen ultraviolet A. The conjunction of psoralens with epidermal DNA inhibits DNA replication and causes cell cycle arrest. Psoralen photosensitization also causes an alteration in the expression of cytokines and cytokine receptors. Psoralens interact with RNA, proteins and other cellular components and indirectly modify proteins and lipids via singlet oxygen-mediated reactions or by generating of free radicals. Infiltrating lymphocytes are strongly suppressed by PUVA, with variable effects on different T-cell subsets. Psoralens and UV radiation also stimulate melanogenesis. Extracorporeal photopheresis is technique used in treatment of erythrodermic cutaneous lymphomas. It is very potent in induction of lymphocyte apoptosis. Despite the introduction of numerous effective systemic medications and biologic agents in dermatology, phototherapy remains a reliable, and often preferred option for several dermatoses.