The first specimen of Archaeopteryx from the Upper Jurassic Mörnsheim Formation of Germany

From an initial isolated position as the oldest evolutionary prototype of a bird, Archaeopteryx has, as a result of recent fossil discoveries, become embedded in a rich phylogenetic context of both more and less crownward stem-group birds. This has prompted debate over whether Archaeopteryx is simply a convergently bird-like non-avialan theropod. Here we show, using the first synchrotron microtomographic examination of the genus, that the eighth or Daiting specimen of Archaeopteryx possesses a character suite that robustly constrains it as a basal avialan (primitive bird). The specimen, which comes from the Mörnsheim Formation and is thus younger than the other specimens from the underlying Solnhofen Formation, is distinctive enough to merit designation as a new species, Archaeopteryx albersdoerferi sp. nov., but is recovered in close phylogenetic proximity to Archaeopteryx lithographica. Skeletal innovations of the Daiting specimen, such as fusion and pneumatization of the cranial bones, well vascularized pectoral girdle and wing elements, and a reinforced configuration of carpals and metacarpals, suggest that it may have had more characters seen in flying birds than the older Archaeopteryx lithographica. These innovations appear to be convergent on those of more crownward avialans, suggesting that Bavarian archaeopterygids independently acquired increasingly bird-like traits over time. Such mosaic evolution and iterative exploration of adaptive space may be typical for major functional transitions like the origin of flight.     

Early Pleistocene Equus (Equidae,Perissodactyla) from Andersson Loc. 32 in Qixian,Shanxi, China

The Equus specimens of Andersson Loc. 32 in Qixian, Shanxi previously identified as Equus cf. sanmeniensis are rediscovered in this research. The skull has moderate size, deep nasal notch, clear preorbital fossa, undulated lateral outline, upper cheek tooth with simple fossette and incisor with incomplete cup, should be identified as Equus teilhardi. The mandible has cheek tooth with V-shaped linguaflexid, incisor with incomplete cup, moderate size, strong pli caballinid and deep ectoflexid on molar, should be identified as Equus qingyangensis. This skull is first record of a complete cranial material of E. teilhardi, reveals many important cranial features of E. teilhardi, supports anatomical comparison and phylogenetic discussion with other stenonid horses. The morphological differences between E. teilhardi and E. qingyangensis show their different niches, further explain the reason of their coexistence. Incomplete cup on incisor is an unstable feature. It has been found in several species of stenonid horses, likely a remaining feature derived from the most primitive Equus, Equus simplicidens. The small-sized stenonid horses with short limbs and incisors with incomplete cups likely have relation with E. teilhardi, such as Equus yunnanensis and Equus stehlini. E. qingyangensis has most primitive features in Eurasian stenonid horses.     

Development of α4 integrin DNA aptamer as a potential therapeutic tool for multiple sclerosis

One of the most important molecules for multiple sclerosis pathogenesis is α4 integrin, which is responsible for autoreactive leukocytes migration into the brain. The monoclonal antibody, natalizumab, was introduced to market for blocking the extravasation of autoreactive leukocytes via inhibition of α4 integrin. However, the disadvantages of antibodies provided a suitable background for other agents to be replaced with antibodies. Considering the profound advantages of aptamers over antibodies, aptamer isolation against α4 integrin was intended in the current study. The α4 integrin-specific aptamers were selected using cell-systematic evolution of ligands by exponential enrichment (SELEX) method with human embryonic kidney (HEK)-293T overexpressing α4 integrin and HEK-293T as target and control cells, respectively. Evaluation of selected aptamer was performed through flow cytometric analysis. The selected clones were then sequenced and analyzed for any possible secondary structure and affinity. The results of this study led to isolation of 13 different single-stranded DNA clones in 11 rounds of selection which were categorized to three clusters based on common structural motifs and the equilibrium dissociation constant (K _d) of the most stable structure was calculated. The evaluation of SELEX progress showed growth in aptamer affinity with increasing of the number of cycles. Taken together, the findings of this study demonstrated the isolation of α4-specific single-stranded DNA aptamers with suitable affinity for ligand, which can further be replaced with natalizumab.     

Rapid detection of Phytophthora nicotianae by simple DNA extraction and real‐time loop‐mediated isothermal amplification assay

Phytophthora nicotianae is a phytopathogenic oomycete with a wide host range and worldwide distribution. Rapid detection and diagnosis at the early stages of disease development are important for the effective control of P. nicotianae. In this study, we designed a simple and rapid loop‐mediated isothermal amplification (LAMP)‐based detection method for P. nicotianae. We tested three DNA extraction methods and selected the Kaneka Easy DNA Extraction Kit version 2, which is rapid and robust for LAMP‐based detection. The designed primers were tested using mycelial DNA from 35 species (81 isolates) of Phytophthora, 12 species (12 isolates) of Pythium, one isolate of Phytopythium and one isolate each from seven other soil‐borne pathogens. All of the 42 P. nicotianae isolates were detected by these primers, and no other isolates gave positive results. Three isolates were tested for the sensitivity of the reaction, and the lowest amounts of template DNA that could be detected were 10 fg for two isolates and 1 fg for the third. The target was detected within 25 min in all tested samples, including DNA extracted from both inoculated and naturally infected plants. In contrast, PCR assays with P. nicotianae‐specific primers failed or showed weakened detection in several samples. Thus, we found that the rapid DNA extraction and LAMP assay methods developed in this study can be used to detect P. nicotianae with high sensitivity, specificity and stability.     

Modelling time‐varying low‐temperature‐induced mortality rates for pupae of Tuta absoluta (Gelechiidae,Lepidoptera)

In a series of laboratory experiments, acclimated pupae of Tuta absoluta were exposed to various constant low temperatures in order to estimate their maximum survival times (Kaplan–Meier, Lt_99.99). A Weibull function was fitted to the data points, describing maximum survival time as a function of temperature. In another experiment at ?6°C, the progress of mortality increasing with exposure time was identified. These values were fitted by a sigmoidal function converging asymptotically to 100% mortality for very long exposure times. Analysing mortality data from the maximum survival experiment by a generalized linear model showed a significant common slope parameter (p < .001) that reveals parallelism of the survival curves at each temperature if a log time axis is used. These curves appear stretched (time scaled) if plotted with a nonlogarithmic time axis. By combining these mathematical relations, it was possible to calculate a species‐specific ‘mortality surface’ which exhibits mortalities, depending on temperature and duration of exposure. In order to accumulate hourly mortalities for courses of varying temperatures, an algorithm was developed which yields mortality values from that surface taking into account the attained mortality level. In validation experiments, recorded mortalities were compared against modelled mortalities. Prediction of mortality was partially supported by the model, but pupae experiencing intensely fluctuating temperatures showed decreased mortality, probably caused by rapid cold hardening during exposure. Despite this observation, mortality data converged to distinct levels very close to 100% depending on the intensity of temperature fluctuations that were characteristic for different types of experiments. The highest mortality limit occurred at intensely fluctuating temperatures in laboratory experiments. This constituted a benchmark that was not reached under various field conditions. Thus, it was possible to identify temperature limits for the extinction of field populations of Tuta absoluta pupae.     

Genetic analysis of mutations that alter cell fates in maize leaves: Dominant Liguleless mutations

The three major components of the maize leaf are the blade, the sheath, and at their junction, the ligular region. Each exhibits specific cell types and organization. Four dominant Liguleless (Lg) mutations (Lg3-O, Lg4-O, Lg*347, and Lg*9167) in at least three different genes cause a similar morphological phenotype in leaves, although each mutation affects a distinct domain of the blade. Mutant leaves display regions of altered cell fate in the blade, occompanied by elimination of ligule and auricle at their wild-type positions and development of ligule and auricle in the blade at the borders of the altered regions. The affected blade cells are transformed into sheath-like cells, as determined by morphological and genetic tests. Lg4-O expressivity is highly dependent on genetic background. For example, two different backgrounds may specify converse patterns of phenotypic expression. Lg4-O expressivity is also affected by the heterochronic mutation Teopod2 (Tp2). Gene dosage experiments indicate that Lg4-O is a neomorph. Interactions between recessive lg mutations (which eliminate ligular structures) and the dominant Lg mutations suggest that the lg⁺ genes act after the Lg mutations. Lg3-O and Lg4-O act semidominantly, and interact with each other and with other mutations in the Knotted1 (Kn1)-like family (a family in which dominant mutant alleles cause blade to sheath transformation phenotypes). These interactions suggest that the above Kn1-like mutations may function similarly in the leaf. We discuss the similarities between the Lg mutations and the other mutations of the Kn1-like family, which led us to postulate that lg3 and lg4 are members of a growing family of kn1-like (knox) homeobox genes that are identified by dominant mutant alleles causing leaf transformation phenotypes. We also propose that certain key characteristics of this family of dominant neomorphic mutations are important for generating meaningful morphological changes during evolution. © 1996 Wiley-Liss, Inc.     

Current biogeographical roles of the Kunlun Mountains

Large‐scale patterns of biodiversity and formation have garnered increasing attention in biogeography and macroecology. The Qinghai‐Tibet Plateau (QTP) is an ideal area for exploring these issues. However, the QTP consists of multiple geographic subunits, which are understudied. The Kunlun Mountains is a geographical subunit situated in the northern edge of the QTP, in northwest China. The diversity pattern, community phylogenetic structures, and biogeographical roles of the current flora of the Kunlun Mountains were analyzed by collecting and integrating plant distribution, regional geological evolution, and phylogeography. A total of 1911 species, 397 genera, and 75 families present on the Kunlun Mountains, of which 29.8% of the seed plants were endemic to China. The mean divergence time (MDT) of the Kunlun Mountains flora was in the early Miocene (19.40 Ma). Analysis of plant diversity and MDT indicated that the eastern regions of the Kunlun Mountains were the center of species richness, endemic taxa, and ancient taxa. Geographical origins analysis showed that the Kunlun Mountains flora was diverse and that numerous clades were from East Asia and Tethyan. Analysis of geographical origins and geological history together highlighted that the extant biodiversity on the Kunlun Mountains appeared through species recolonization after climatic fluctuations and glaciations during the Quaternary. The nearest taxon index speculated that habitat filtering was the most important driving force for biodiversity patterns. These results suggest that the biogeographical roles of the Kunlun Mountains are corridor and sink, and the corresponding key processes are species extinction and immigration. The Kunlun Mountains also form a barrier, representing a boundary among multiple floras, and convert the Qinghai‐Tibet Plateau into a relatively closed geographical unit.     

Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome

All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized to have formed de novo, from noncoding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from noncoding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodeled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodeling event. These genes with out-of-frame components represent ∼2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.