DR3/LARD spliced mRNA variants’ frequency in colorectal cancer

Many variants of the DR3/LARD death receptor mRNA are derived during alternative splicing. Different DR3/LARD mRNAs encode the membrane and soluble forms of the receptor, which perform different functions. The frequency of the spliced mRNA variants of DR3/LARD was assessed by RT-PCR in patients with colorectal cancer and in cancer cell lines. Four forms of the DR3/LARD death receptor mRNA were detected with different frequencies in the studied samples. Two of them encoded the membrane molecules (LARD 1a mRNA and DR3β mRNA) and two other forms expressed the soluble forms of the receptor (LARD 3 mRNA and soluble DR3β mRNA). In the blood of healthy volunteers, 11 variants (spectra) of DR3/LARD mRNA forms were identified, and the full spectrum that included all four variants of DR3/LARD mRNA dominated. In blood and tumor center samples from patients with colon cancer, six spectra of DR3/LARD mRNA were found. The diversity of the DR3/LARD mRNA spectra was decreased in colon cancer patients due to the reduced frequency of soluble DR3β mRNA. In samples of tumor centers, the spectrum with the absence of only mRNA of the soluble DR3β form dominated. In the blood of patients, two spectra prevailed, i.e., the full spectrum and LARD 1a mRNA and LARD 3 mRNA. Only these two spectra of DR3/LARD mRNA were also found in cancer cell lines. Distinctions in the frequency of DR3/LARD mRNA spectra in healthy volunteers and patients with colorectal cancer can define the different susceptibility of immunocompetent and tumor cells to apoptosis signals.     

DNA structural features on borders of ERBB2 amplicons in breast cancer

In 25–30% of cases of breast cancer tumors, the amplification of the chromosome fragment around ERBB2 underlies the increased expression of genes adjacent to ERBB2. The increased expression of genes within ERBB2-containing amplicons may impact not only the growth and development of the tumor, but also the sensitivity of the tumor to different types of anti-cancer therapies. The initial cause of the amplification and the exact borders of ERBB2-amplified chromosome fragment are still not completely characterized. No specific DNA sequences were found on the junction regions during intrachromosomal DNA amplification. We hypothesized that amplification borders can be specified by the structural peculiarities of DNA, rather than the particular DNA sequence. This study focused on the mapping of ERBB2 amplification borders in breast cancer and the search for unusual structural features of DNA at the borders of the identified amplicons. The copy number of ten genes adjacent to ERBB2 was evaluated by real time PCR in 162 breast cancer samples. Several ERBB2-containing amplicons of various lengths were revealed. In the majority of the analyzed samples, the borders of these amplicons were located within ZNFN1A3 and RARA genes. A bioinformatics analysis of the nucleotide sequence peculiarities around ERBB2 gene revealed the presence of AT-rich DNA regions with a high degree of flexibility. These regions were able to form stable secondary structures. Positions of these sites strongly coincide with the positions of the ERBB2-containing amplicon borders found in real time PCR experiments. Based on the obtained results, one can suppose that the structural features of DNA are involved in the formation of ERBB2-containing amplicon borders in breast cancer cells and the data are of importance for understanding the mechanisms of oncogene amplification.     

Ecosystem engineering,environmental decay and environmental states of landscapes

Although environmental modification by ecosystem engineers influences species distributions and abundances and ecological process rates, general determinants of the environmental states of engineered landscapes are not well understood. Here we develop a general, spatially implicit model of engineered landscapes that includes parameters driving engineer populations (demographics, environmental modification) and environmental decay. We show that average environmental states and heterogeneities of landscapes are the result of a balance between parameters determining engineering rates and decay rates that can be expressed as a net engineering ratio (NER). This ratio highlights the need to include environmental decay in ecosystem engineering studies. Moreover, it defines a significant engineer as one that can alter the environment despite decay and generates expectations for different kinds of effects on the engineer, other species and ecological processes depending on ratio values. Finally, it suggests that, in general, decay places limits as to what can be inferred about engineer population dynamics from environmental dynamics and vice versa.     

Comparative phylogeography of Australo‐Papuan mangrove‐restricted and mangrove‐associated avifaunas

The world's richest mangrove‐restricted avifauna is in Australia and New Guinea. The history of differentiation of the species involved and their patterns of intraspecific genetic variation remain poorly known. Here, we use sequence data derived from two mitochondrial protein‐coding genes to study the evolutionary history of eight co‐distributed mangrove‐restricted and mangrove‐associated birds from the Australian part of this region. Utilizing a comparative phylogeographical framework, we observed that the study species present concordantly located phylogeographical breaks across their shared geographical distribution, a plausible signature of common mechanisms of vicariance underlying this pattern. Barriers such as the Canning Gap, Bonaparte Gap, and the Carpentarian Gaps all had important but varying degrees of impact on the studied species. The Burdekin Gap along Australia's eastern seaboard probably had only a minor influence as a barrier to gene flow in mangrove birds. Statistical phylogeographical simulations were able to discriminate among alternative scenarios involving six different geographical and temporal population separations. Species exhibiting recent colonizations into mangroves include Rhipidura phasiana, Myiagra ruficollis, and Myzomela erythrocephala. By contrast, Peneoenanthe pulverulenta, Pachycephala melanura, Pachycephala lanioides, Zosterops luteus, and Colluricincla megarhyncha all had deeper histories, reflected as more marked phylogeographical divisions separating populations on the eastern seaboard/Cape York Peninsula from more western regions such as the Arnhem Land, the Pilbara, and the Kimberley. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 574–598.     

The carnivorous plant described as Sarracenia alata contains two cryptic species

Modern methods for species delimitation provide biologists with the power to detect cryptic diversity in nearly any system. To illustrate the application of such methods, we collected data (21 sequence loci) from a carnivorous plant in southeastern North America and applied several recently developed methods (Gaussian clustering, Structurama, BPP, spedeSTEM). The pale pitcher plant Sarracenia alata inhabits the southeastern USA along the northern coast of the Gulf of Mexico. Sarracenia alata populations are separated by the Mississippi River and Atchafalaya Basin, a known biogeographical barrier in this region, but the cohesiveness of S. alata as currently classified has not been tested rigorously. Multiple analytical approaches (including allelic clustering and species trees methods) suggest that S. alata comprises two cryptic lineages that correspond to the eastern and western portions of the plant's distribution. That such clear genetic evidence for cryptic diversity exists within S. alata and is in conflict with other sources of data (e.g. morphology, environmental differentiation) illustrates a conundrum faced by those who investigate species boundaries: genetic data are often the first type of data to accumulate evidence of differentiation, but most existing taxonomic treatments are based on nongenetic data. Our results suggest that S. alata as currently described contains two cryptic species, and we recommend the elevation of the western populations to species status. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 737–746.     

Geometric morphometrics as a tool for interpreting evolutionary transitions in the black fly wing (Diptera: Simuliidae)

A geometric morphometric analysis was conducted on wing‐vein landmarks on exemplar species of the family Simuliidae of the following genera: Parasimulium, Gymnopais, Twinnia, Helodon, Prosimulium, Greniera, Stegopterna, Tlalocomyia, Cnephia, Ectemnia, Metacnephia, Austrosimulium, and Simulium. Generalized least squares superimposition was performed on landmarks, followed by a principal component analysis on resulting Procrustes distances. Patterns of shape change along the principal component axes were visualized using the thin‐plate spline. The analysis revealed wing shape diversity through (1) the insertion points of the subcosta and R₁, resulting in the terminus of the costa exhibiting a trend towards a more apical position on the wing, and (2) the insertion point of the humeral cross vein, resulting in the anterior branch of the media exhibiting a trend toward a more basal position on the wing. Canonical variates analysis of Procrustes distances successfully assigned all exemplar species into their a priori taxonomic groupings. The diversity in wing shape reveals a trend towards decreased length of basal radial cell and increased costalization of anterior wing veins in the evolutionary transition from plesiomorphic prosimuliines to more derived simuliines. The functional significance of these evolutionary transitions is discussed. © 2013 The Linnean Society of London     

OBSERVATIONS ON THE SLATY EGRET EGRETTA VINACEIGULA IN NORTHERN NAMIBIA

Hines, C.J.H. 1992. Observations on the Slaty Egret Egretta vinaceigula in northern Namibia. Ostrich 63: 118–122.

The Slaty Egret is an endemic African resident with a limited distribution in Botswana, Zambia and Namibia. Distribution records for Namibia are reviewed and information on movements and habitat preferences is given. Diet and feeding habits are described. Two colonies of Slaty Egrets containing eggs and chicks were found on temporary wetlands in eastern Bushmanland. Nests and eggs are described and egg measurements and weights given. The plumage of immature birds is described as well as the variation in adult plumages. The conservation status of the species is reviewed, and the possible importance of temporary wetlands to the Slaty Egret is discussed.     

Another charadriiform-like bird from the lower Eocene of Denmark

We describe an exceptionally well-preserved partial skeleton of a new bird from the early Eocene Fur Formation of Denmark. Like other fossils from these marine deposits, the partial skeleton is three-dimensionally preserved and articulated. This new Danish specimen consists of a skull, vertebral column, ribs, pelvis, and hindlimbs. Concerning characters of the pelvis, tibiotarsus and tarsometatarsus, the new fossil bears morphological affinities to charadriiform birds (shorebirds and relatives). A phylogenetic analysis of higher neomithine (modern birds) taxa also supports a close relationship between the new specimen and modern Charadriiformes. The morphologies of the skull and vertebrae, however, distinguish the new fossil from all recent charadriiform families.     

6. ANOTHER NOTE ON SAROTHRURA ELEGANS

Summary

Dowsett-Lemaire, F. 1983. Studies of a breeding population of Waller's Redwinged Starlings in montane forests of south-central Africa. Ostrich. 54:105-112.

The breeding biology and behaviour of Waller's Redwinged Starling Onychognuthus walleri was studied for two seasons in forest patches on the Nyika Plateau, 2 200 m ad. (Mala?i-Zambia). In general behaviour (e.g. strong pair bond, fidelity to the nest site), O. walleri resembles other species of the genus. Twenty-six egg-laying records are from late August to mid-November (i.e. end of dry season to early rains). Suitable nest sites (natural holes in trees) seem to be in short supply, and the non-breeding population is far in excess of the breeding one. Incubation periods lasted 13 days (2) to 16 days (1). One nestling period was 29 days. Insects are more important than fruits in the diet of nestlings. Annual breeding productivity is low (0,5-0,6 young/breeding pair) because of heavy nest predation, and at tunes insect-food shortages leading to starvation of young. There were few re-laying attempts, and only one abnormal attempt at a second brood.

Two other congeneric species, the Slenderbilled Redwinged Starling O. tenuirostris and the African Redwinged Starling O. morio also breed on the Nyika. Notes on their feeding habits, numbers and nest sites are given. One nest site of O. tenuirostris on a wet rock face by waterfalls was taken over by O. morio in the following season.