Corticioid basidiomycetes associated with bark beetles,including seven new Entomocorticium species from North America and Cylindrobasidium ipidophilum,comb. nov

Antonie van Leeuwenhoek - Seven new Entomocorticium species (Peniophoraceae) are described based on morphology and phylogenetic analyses. Along with the type species (E. dendroctoni),...     

Regenerative potential of human muscle stem cells in chronic inflammation

Introduction

Chronic inflammation is a profound systemic modification of the cellular microenvironment which could affect survival, repair and maintenance of muscle stem cells. The aim of this study was to define the role of chronic inflammation on the regenerative potential of satellite cells in human muscle.

Methods

As a model for chronic inflammation, 11 patients suffering from rheumatoid arthritis (RA) were included together with 16 patients with osteoarthritis (OA) as controls. The mean age of both groups was 64 years, with more females in the RA group compared to the OA group. During elective knee replacement surgery, a muscle biopsy was taken from the distal musculus vastus medialis. Cell populations from four RA and eight OA patients were used for extensive phenotyping because these cell populations showed no spontaneous differentiation and myogenic purity greater than 75% after explantation.

Results

After mononuclear cell explantation, myogenic purity, viability, proliferation index, number of colonies, myogenic colonies, growth speed, maximum number of population doublings and fusion index were not different between RA and OA patients. Furthermore, the expression of proteins involved in replicative and stress-induced premature senescence and apoptosis, including p16, p21, p53, hTERT and cleaved caspase-3, was not different between RA and OA patients. Mean telomere length was shorter in the RA group compared to the OA group.

Conclusions

In the present study we found evidence that chronic inflammation in RA does not affect the in vitro regenerative potential of human satellite cells. Identification of mechanisms influencing muscle regeneration by modulation of its microenvironment may, therefore, be more appropriate.     

Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia

Host-pathogen interactions are complex processes, and revealing these interactions is challenging. Beauveria bassiana is a destructive pathogen to the economically beneficial silkworm, Bombyx mori, but is also a good pathogenic material for investigating insect responses to fungal infection. For better understanding of the molecular regulation of immune response and the interactive mechanism between the silkworm and B. bassiana, suppression subtractive hybridization was employed to identify differentially expressed genes in the pathogen-stimulated silkworm larvae. Complementary DNA libraries were constructed, in which 240 clones were sequenced. A total of 77 genes were found to be involved in the infection process, among which 55 were known genes and 22 were novel. Expression profiling of 6 genes by quantitative PCR showed that they were induced by fungal challenge. This study establishes the first step to understanding the molecular mechanisms by which silkworm responds to fungal infection.     

Seed morphology,presence of areoles and water entry at imbibition of <i>Vicia dasycarpa</i> Ten. cv. Tolse F.C.A

The morphological characteristics of the seeds of Vicia dasycarpa Ten. cv. Tolse FCA were studied in relation to the area of imbibition water entry and were considered the presence of areoles. Seeds were analyzed using a stereo, optical and scanning electron microscope (SEM). The determination of the initial water entry area was carried out by immersing the seeds in a solution of tetrazolium (1%). This study showed that this species has seeds with a halo framing the hilum, an inconspicuous dry aril and a deltoid micropyle. The seedcoat pattern is papillose. The tracheid bar is surrounded by a ring of parenchymatous cells, and the tracheids show slight warty and non-vestured pits. It was confirmed the presence of an endospermic radicle pocket that surrounds and protect the radical tip. Two pairs of cotyledonar areoles were identified. It was established that the entry of water during imbibition starts in the area of the lens -having cracks- and moves in the sagittal plane. Both citological characteristic of tracheid bar and areoles presence show an apomorfous state between the Papiplionoids.     

SVA elements: a hominid-specific retroposon family

SVA is a composite repetitive element named after its main components, SINE, VNTR and Alu. We have identified 2762 SVA elements from the human genome draft sequence. Genomic distribution analysis indicates that the SVA elements are enriched in G+C-rich regions but have no preferences for inter- or intragenic regions. A phylogenetic analysis of the elements resulted in the recovery of six subfamilies that were named SVA_A to SVA_F. The composition, age and genomic distribution of the subfamilies have been examined. Subfamily age estimates based upon nucleotide divergence indicate that the expansion of four SVA subfamilies (SVA_A, SVA_B, SVA_C and SVA_D) began before the divergence of human, chimpanzee and gorilla, while subfamilies SVA_E and SVA_F are restricted to the human lineage. A survey of human genomic diversity associated with SVA_E and SVA_F subfamily members showed insertion polymorphism frequencies of 37.5% and 27.6%, respectively. In addition, we examined the amplification dynamics of SVA elements throughout the primate order and traced their origin back to the beginnings of hominid primate evolution, approximately 18 to 25 million years ago. This makes SVA elements the youngest family of retroposons in the primate order.     

The deceptive nature of UVA tanning versus the modest protective effects of UVB tanning on human skin

The relationship between human skin pigmentation and protection from ultraviolet (UV) radiation is an important element underlying differences in skin carcinogenesis rates. The association between UV damage and the risk of skin cancer is clear, yet a strategic balance in exposure to UV needs to be met. Dark skin is protected from UV-induced DNA damage significantly more than light skin owing to the constitutively higher pigmentation, but an as yet unresolved and important question is what photoprotective benefit, if any, is afforded by facultative pigmentation (i.e. a tan induced by UV exposure). To address that and to compare the effects of various wavelengths of UV, we repetitively exposed human skin to suberythemal doses of UVA and/or UVB over 2 weeks after which a challenge dose of UVA and UVB was given. Although visual skin pigmentation (tanning) elicited by different UV exposure protocols was similar, the melanin content and UV-protective effects against DNA damage in UVB-tanned skin (but not in UVA-tanned skin) were significantly higher. UVA-induced tans seem to result from the photooxidation of existing melanin and its precursors with some redistribution of pigment granules, while UVB stimulates melanocytes to up-regulate melanin synthesis and increases pigmentation coverage, effects that are synergistically stimulated in UVA and UVB-exposed skin. Thus, UVA tanning contributes essentially no photoprotection, although all types of UV-induced tanning result in DNA and cellular damage, which can eventually lead to photocarcinogenesis.     

Mobile element-based forensic genomics

Mobile elements are commonly referred to as selfish repetitive DNA sequences. However, mobile elements represent a unique and underutilized group of molecular markers. Several of their characteristics make them ideally suited for use as tools in forensic genomic applications. These include their nature as essentially homoplasy-free characters, they are identical by descent, the ancestral state of any insertion is known to be the absence of the element, and many mobile element insertions are lineage specific. In this review, we provide an overview of mobile element biology and describe the application of certain mobile elements, especially the SINEs and other retrotransposons, to forensic genomics. These tools include quantitative species-specific DNA detection, analysis of complex biomaterials, and the inference of geographic origin of human DNA samples.     

An alu-based phylogeny of lemurs (infraorder: lemuriformes)

LEMURS (INFRAORDER: Lemuriformes) are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ～55-60 million years ago (mya). Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs), to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus) was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction) verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the exclusion of Eulemur and Varecia, with Varecia the sister lineage to the other three genera.     

Airway house dust extract exposures modify allergen-induced airway hypersensitivity responses by TLR4-dependent and independent pathways

TLR ligands and other allergen-nonspecific immunostimulatory molecules are ubiquitous in ambient air and have profound modulatory activities in animal models of allergic asthma. However, several of these molecules have been shown to promote exaggerated Th2-biased airway hypersensitivity responses (AHRs), whereas others attenuate the asthmatic phenotype. Therefore, it has proven difficult to extrapolate experimental results with purified molecules toward a more general understanding of the allergen-nonspecific immunomodulatory influence of living environments on the natural history of allergic asthma. These investigations determined how regular and intermittent airway exposures to an unpurified, but sterile house dust extract standard (HDEst) affected the OVA-specific AHR and immune status of previously Th2-sensitized mice. Low-dose daily and high-dose intermittent HDEst exposures modulated ongoing AHRs considerably, reducing eosinophil recruitment and methacholine responsiveness, while increasing neutrophilic inflammation. However, only daily airway delivery of low-dose HDEst attenuated OVA-specific Th2 cytokine production and Th2-biased AHRs to allergen challenge 1 mo later. Finally, whereas LPS mimicked many of the immunomodulatory characteristics of HDEst in this murine asthma model, daily airway HDEst delivery was highly effective in attenuating the AHR of OVA/alum-sensitized TLR4-deficient mice. Taken together, these investigations provide direct evidence that living environments contain allergen-nonspecific immunostimulatory molecules that influence the airway hypersensitivity status of allergen-sensitized mice by TLR4-dependent and independent mechanisms.     

Four species of Zygophiala (Schizothyriaceae, Capnodiales) are associated with the sooty blotch and flyspeck complex on apple

Sooty blotch and flyspeck (SBFS) is a complex of fungi that cause late-season blemishes of apple and pear fruit that cosmetically damage the cuticle, which result in fruit that are unacceptable to consumers. Previous studies reported that a single, wide-host-range species, Schizothyrium pomi (presumed anamorph Zygophiala jamaicensis), caused flyspeck on apple. In the present study we compared morphology and DNA phylogeny (ITS, LSU) of 139 fungal strains isolated from flyspeck signs from 39 apple orchards in 14 midwestern and eastern states (USA). Parsimony analysis, supported by cultural characteristics and morphology in vitro, provided support to delimit the flyspeck isolates into four species of Zygophiala, two of which are known to be sexual. Three of these species are described as new. Based on DNA phylogeny, species of Schizothyrium were shown to cluster with members of the genus Mycosphaerella in the Capnodiales, having similar asci and ascospores but morphologically distinct ascomata. These data question the value of ascomatal morphology at the ordinal level, although it still appears to be relevant at the family level, delimiting the thyrothecial Schizothyriaceae from other families in the Capnodiales.