The evolution of femoral osteology and soft tissues on the line to extant birds (Neornithes)

Femoral osteology and soft tissues evolved in a stepwise pattern in archosauromorph reptiles on the line to crown group birds. Crocodylia retains most ancestral archosaurian traits, whereas Dinosauromorpha (including birds) acquired many more derived traits. The complex sequence of changes included major shifts of several thigh muscle insertions. Medial rotation of the proximal femur (e.g. the femoral head) in archosaurs moved the greater trochanter laterally, bringing along the insertion of M. pubo-ischio-femoralis externus. Within Dinosauromorpha, the lesser trochanter moved proximally away from the trochanteric shelf. Presumably the lesser trochanter indicates the insertion of M. iliotrochantericus caudalis whereas the trochanteric shelf indicates the insertion of M. iliofemoralis externus. An accessory trochanter at the base of the lesser trochanter marks the insertion of M. pubo-ischio-femoralis internus 2 in tetanuran theropods. I propose hypotheses for the homologies of several intermuscular lines and other features on the femoral shaft. On the line to Neornithes, most changes of femoral morphology predated Aves and the origin of flight; few femoral features are unique to birds. Overall, the pattern of morphological evolution is consistent with stepwise functional evolution of the hindlimb within Dinosauromorpha on the line to Neornithes. The clade Ornithurae evolved the last few hindlimb apomorphies that characterize extant birds, in conjunction with more flexed hip and knee joints.     

Density of Parasites in Various Organs and the Relation to Numbers of Trypomastigotes in the Blood during Acute Infections of Trypanosoma cruzi in Mice*

Quantitative methods were used to (a) determine the density of Trypanosoma cruzi in organs of CF₁ mice following intraperitoneal inoculation of 50,000 trypomastigotes of a Brazil strain of T. cruzi and (b) study the relation of the numbers of these intracellular stages to the numbers of trypomastigotes in the blood. Tissue stages (predominantly amastigotes) in heart, skeletal muscle (triceps), diaphragm, cerebrum, cerebellum, and musculature of stomach, duodenum, esophagus, jejunum, cecum, and rectum increased in numbers during the 1st 3 weeks of infection, reached maximum density 21–28 days after inoculation and subsequently declined in numbers until mice were histologically negative for intracellular parasites by 30–40 days. The density of tissue stages in the urinary bladder, uterine body, and ileum was similar with the exception that maximum numbers of parasites were observed slightly earlier at 15 days. The greatest density of intracellular stages was seen in heart, urinary bladder, diaphragm, and triceps muscle where mean counts of 44.6–60.0 × 10⁶ parasites/cc of muscle were recorded while maximum density of parasites in the uterine body, cerebrum, stomach, cerebellum, duodenum, esophagus, jejunum, ileum, cecum, and rectum was 13.0 × 10⁶/cc of muscle or less. Amastigotes were not observed in sections of lymph node, thymus, salivary glands, liver, spleen, or kidney and only a single pseudocyst containing 5 amastigotes was seen in lung. With the exception of the brain and lung, intracellular parasites were located exclusively in the musculature. Trypomastigotes in the blood increased during the 1st 3 weeks of infection, reached maximum numbers 21–28 days after initiation of infection, and subsequently decreased until by 30–40 days parasites were observed only rarely in the blood of a few animals. Thus generally close correlation was noted between the numbers of intracellular stages of T. cruzi in the organs and trypomastigotes in the blood throughout acute Chagas’ disease in mice as evidenced by the concomitant increase in numbers of both stages, the coincidence of days of maximum parasite levels, and the simultaneous decline in numbers of both stages. The mean number of parasites/pseudocyst section varied in the organs studied. Of the 15 positive organs studied, the pseudocyst sections in skeletal muscle contained the highest mean number of parasites (64.3 parasites/pseudocyst section) and those pseudocyst sections seen in the musculature of the small intestine contained the lowest mean number (5.5–6.8 parasites/pseudocyst section respectively in ileum and jejunum). Serial sections of skeletal muscle, heart, urinary bladder, and stomach revealed the largest pseudocysts in skeletal muscle while those in the musculature of the urinary bladder were the smallest.     

Areas of endemism for passerine birds in the Atlantic forest, South America

Aim To use the method of parsimony analysis of endemism to identify areas of endemism for passerine birds in the Atlantic Forest, South America, and to compare the locations of these areas with areas previously identified for birds as well as other taxa. Location The Atlantic Forest, eastern South America. Methods We analysed a matrix composed of the presence (1) or absence (0) of 140 endemic species in 24 quadrats of 1 × 1 degree distributed along the Atlantic Forest to find the most parsimonious area cladogram. Results Fourteen most parsimonious cladograms were found and then summarized in a single consensus tree. Four areas of endemism were identified: Pernambuco, Central Bahia, Coastal Bahia, and Serra do Mar. Main conclusions Avian areas of endemism in the Atlantic Forest have significant generality, as they are highly nonrandom and congruent with those of other groups of organisms. A first hypothesis about the historical relationships among the four areas of avian endemism in the Atlantic Forest is delineated. There is a basal dichotomy among areas of endemism in the Atlantic Forest, with Pernambuco forming a northern cluster and Coastal Bahia, Central Bahia and Serra do Mar comprising a southern cluster. Within the southern cluster, Central Bahia and Serra do Mar are more closely related to each other than to Coastal Bahia.     

Relationship between osteology and aquatic locomotion in birds: determining modes of locomotion in extinct Ornithurae

The evolutionary history of aquatic invasion in birds would be incomplete without incorporation of extinct species. We show that aquatic affinities in fossil birds can be inferred by multivariate analysis of skeletal features and locomotion of 245 species of extant birds. Regularized discriminant analyses revealed that measurements of appendicular skeletons successfully separated diving birds from surface swimmers and flyers, while also discriminating among different underwater modes of swimming. The high accuracy of this method allows detection of skeletal characteristics that are indicative of aquatic locomotion and inference of such locomotion in bird species with insufficient behavioural information. Statistical predictions based on the analyses confirm qualitative assessments for both foot‐propelled (Hesperornithiformes) and wing‐propelled (Copepteryx) underwater locomotion in fossil birds. This is the first quantitative inference of underwater modes of swimming in fossil birds, enabling future studies of locomotion in extinct birds and evolutionary transitions among locomotor modes in avian lineage.     

中国现代人起源与演化的考古学思考

越来越多古人类学和旧石器时代考古学的发现与研究成果极大地改变了我们对现代人类起源、演化和适应理论问题的看法。中国作为东亚一个幅员辽阔的地理区域,已经成为这项研究的热点地带。来自该地区新的人类化石和石器组合对基于非洲和欧亚大陆西部记录构建的“现代人出自非洲说”（Recent Out-of-Africa）提出了挑战。新的古人类学研究结果表明,早期现代人出现于约100 kaBP的中国南方,可能（至少部分）是由那里的土著居民演化而来。一些古老型智人表现出了与早期古人类镶嵌或过渡性的体质特征,并可能与尼安德特人和丹尼索瓦人杂交混合。同时一些遗址出土的打制石器表现出了早期现代人类技术和行为的复杂性。中国北方的小石片石器主工业和南方的砾石石器主工业贯穿于整个更新世,然而从约40 kaBP开始,石叶技术开始出现在中国北部,紧随其后的是这些地区骨制工具和个人装饰品的出现,这表明,更新世晚期西伯利亚和中亚地区与我国北部可能存在着紧密的文化关系,东北亚地区可能存在着由西北向东南的迁移路线。人类化石和考古学证据表明,中国现代人类起源和适应的过程与机制可能与欧亚大陆西部有所不同。本文对有关中国现代人类起源与演化的考古学研究所取得的新发现和进展进行了总体回顾,从考古学角度阐述了对相关重要学术问题的看法,并为未来的研究提出了方向性建议。     

Key novelties in the evolution of the aquatic colonial phylum Bryozoa: evidence from soft body morphology

Molecular techniques are currently the leading tools for reconstructing phylogenetic relationships, but our understanding of ancestral, plesiomorphic and apomorphic characters requires the study of the morphology of extant forms for testing these phylogenies and for reconstructing character evolution. This review highlights the potential of soft body morphology for inferring the evolution and phylogeny of the lophotrochozoan phylum Bryozoa. This colonial taxon comprises aquatic coelomate filter‐feeders that dominate many benthic communities, both marine and freshwater. Despite having a similar bauplan, bryozoans are morphologically highly diverse and are represented by three major taxa: Phylactolaemata, Stenolaemata and Gymnolaemata. Recent molecular studies resulted in a comprehensive phylogenetic tree with the Phylactolaemata sister to the remaining two taxa, and Stenolaemata (Cyclostomata) sister to Gymnolaemata. We plotted data of soft tissue morphology onto this phylogeny in order to gain further insights into the origin of morphological novelties and character evolution in the phylum. All three larger clades have morphological apomorphies assignable to the latest molecular phylogeny. Stenolaemata (Cyclostomata) and Gymnolaemata were united as monophyletic Myolaemata because of the apomorphic myoepithelial and triradiate pharynx. One of the main evolutionary changes in bryozoans is a change from a body wall with two well‐developed muscular layers and numerous retractor muscles in Phylactolaemata to a body wall with few specialized muscles and few retractors in the remaining bryozoans. Such a shift probably pre‐dated a body wall calcification that evolved independently at least twice in Bryozoa and resulted in the evolution of various hydrostatic mechanisms for polypide protrusion. In Cyclostomata, body wall calcification was accompanied by a unique detachment of the peritoneum from the epidermis to form the hydrostatic membraneous sac. The digestive tract of the Myolaemata differs from the phylactolaemate condition by a distinct ciliated pylorus not present in phylactolaemates. All bryozoans have a mesodermal funiculus, which is duplicated in Gymnolaemata. A colonial system of integration (CSI) of additional, sometimes branching, funicular cords connecting neighbouring zooids via pores with pore‐cell complexes evolved at least twice in Gymnolaemata. The nervous system in all bryozoans is subepithelial and concentrated at the lophophoral base and the tentacles. Tentacular nerves emerge intertentacularly in Phylactolaemata whereas they partially emanate directly from the cerebral ganglion or the circum‐oral nerve ring in myolaemates. Overall, morphological evidence shows that ancestral forms were small, colonial coelomates with a muscular body wall and a U‐shaped gut with ciliary tentacle crown, and were capable of asexual budding. Coloniality resulted in many novelties including the origin of zooidal polymorphism, an apomorphic landmark trait of the Myolaemata.     

Luminescence-Based Systems for Detection of Bacteria in the Environment

Abstract

The development of techniques for detection and tracking of microorganisms in natural environments has been accelerated by the requirement for assessment of the risks associated with environmental release of genetically engineered microbial inocula. Molecular marker systems are particularly appropriate for such studies and luminescence-based markers have the broadest range of applications, involving the introduction of prokaryotic (lux) or eukaryotic (luc) genes for the enzyme luciferase.

Lux or luc genes can be detected on the basis of unique DNA sequences by gene probing and PCR amplification, but the major advantage of luminescence-based systems is the ability to detect light emitted by marked organisms or by luciferase activity in cell-free extracts. Luminescent colonies can be detected by eye, providing distinction from colonies of indigenous organisms, and the sensitivity of plate counting can be increased greatly by CCD imaging. Single cells or microcolonies of luminescent organisms can also be detected in environmental samples by CCD image-enhanced microscopy, facilitating study of their spatial distribution. The metabolic activity of luminescence-marked populations can be quantified by luminometry and does not require extraction of cells or laboratory growth. Metabolic activity, and potential activity, of marked organisms therefore can be measured during colonization of soil particles and plant material in real time without disturbing the colonization process.

In comparison with traditional activity techniques, luminometry provides significant increases in sensitivity, accuracy, and, most importantly, selectivity, as activity can be measured in the presence of indigenous microbial communities. The sensitivity, speed, and convenience of luminescence measurements make this a powerful technique that is being applied to the study of an increasingly wide range of ecological problems. These include microbial survival and recovery, microbial predation, plant pathogenicity, phylloplane and rhizosphere colonization and reporting of gene expression in environmental samples.     

锡林河流域两类植物群落土壤呼吸特征的比较

采用碱液吸收法对锡林河流域一个半干旱典型草原群落的土壤呼吸进行了5个月的野外测定,并对其与气候因子和生物量之间的关系进行了分析。另选择了锡林河岸边的一个沼泽化草甸群落作为对比来研究土壤湿度和植被类型对土壤呼吸的影响。主要结果包括:1)两个群落土壤呼吸的季节动态基本一致,均出现了两个峰值,其中草原群落和草甸群落土壤呼吸速率的变化范围分别为312.8～1 738.9 mg C·m-2·d-1 和354.6～2 235.6 mg C·m-2·d-1。草甸群落的土壤呼吸速率明显高于草原群落,它们的日平均土壤呼吸速率分别为1 349.6 mg C·m-2·d-1和785.9mg C·m-2·d-1; 2)在草原群落中,土壤呼吸速率与土壤湿度的相关性比其与温度的关系更加显著,而在草甸群落正好相反,反映出这两种气候因子在不同生境中起着不同的作用。根据土壤呼吸与气温之间的回归关系外推出2001年生长季草原群落和草甸群落的土壤呼吸量分别为142.4 g C/m2 和 236.1 g C/m2;3)在草甸群落中,地上总生物量与土壤呼吸速率之间没有显著的相关关系,而地上部活体生物量与土壤呼吸速率之间则存有很显著的幂函数关系。在草原群落中,土壤呼吸速率与地上活体生物量或地上总生物量的相关性均很弱。     

Radioisotope-dilution technique for determining endogenous manganese in feces of the growing rat

A conventional balance study with growing rats was conducted to evaluate experimental conditions for determining endogenous fecal manganese (Mn) excretion and, hence, true Mn absorption by the isotope-dilution technique. Thirty-four rats, with a mean initial live weight of 60 g, allotted to three groups of 8 animals and one group of 10 animals, were injected intramuscularly with a⁵⁴Mn tracer dose and sacrificed after 4, 8, 12, and 16 d, respectively. In liver and serum, the specific radioactivity of Mn was the lowest among the tissues analyzed and its exponential rate of decrease over the period of d 4–16 was the highest. During the 8-d period, from d 9–16, apparent Mn absorption averaged 14.1% of intake (128.5 μg Mn/d). Assuming that the specific activity of Mn in liver of d 11 or, alternatively, in serum of d 16, was on the average representative of that of endogenous Mn in feces of d 9–16, it was computed that Mn of endogenous origin accounted for 9.0 and 9.3% of the total fecal excretion of the metal, and that true absorption amounted to 21.9 and 22.1% of Mn intake, respectively.     

Comparative Analysis of Rapidly Transported Axonal Proteins in Sensory Neurons of the Frog and Rat

³⁵S-labeled proteins carried by fast axonal transport in sciatic sensory axons of bullfrog and rat were separated electrophoretically on discontinuous polyacrylamide gradient slab gels. In contrast to the previously reported similarity in the electrophoretic profiles of rapidly transported proteins from functionally different neurons, we have found that there is very little correspondence in the profiles of these proteins in functionally similar neurons from two widely studied species. We also found very little correspondence between the two species in the profiles of locally synthesized sciatic nerve protein. The results demonstrate the difficulty inherent in comparing the electrophoretic profiles obtained using these two model systems for the study of rapidly transported axonal proteins. In particular, relationships between the major rapidly transported proteins in the two species could_not be analyzed with this technique.     

Chloroquine Intoxication Induces Ganglioside Storage in Nervous Tissue: A Chemical and Histopathological Study of Brain, Spinal Cord, Dorsal Root Ganglia, and Retina in the Miniature Pig

Abstract :
The effect of chronic chloroquine intoxication on lipid composition, particularly the gangliosides, was studied in the nervous system of miniature pigs, type Göttingen. The tissues examined were cerebrum, spinal cord, dorsal root ganglia and retina. Chloroquine was given in the diet in doses of 2.0-3.5 g/kg food. The intoxication of the pigs was started at the age of 100–240 days and continued for 177-219 days. The control pigs received the same diet without chloroquine. The ganglioside concentration was increased in all the tissues examined. Dorsal root ganglia and retina were the tissues affected most and showed a twofold increase. This corresponded to the light and electron microscopically demonstrated extensive storage process in the perikarya of dorsal root ganglion cells and inner ganglion cells of the retina. Under light microscopy the storage material was granular, intensely PAS-positive and dissolved by paraffin embedding. The electron microscopical equivalent consisted of conglomerates of membranous lysosomal residual bodies. In cerebrum the ganglioside concentration was increased by 12%. Storage in the brain varied widely between different systems and types of cells. The allocortex was much more affected than the isocortex. Certain inhibitory ganglion cell types, such as the basket cells, exhibited the most massive storage of all. The spinal medulla was morphologically less involved but showed approximately the same ganglioside increase, though not statistically significant. With the exception of cerebrum the increase in the tissues examined involved all the individual gangliosides, most severely ganglioside GM2 and three fucogangliosides. In cerebrum only the ganglioside GM2 was increased more than the other gangliosides. Chloroquine intoxication did not affect the concentration of phospholipids or cholesterol in the cerebrum, spinal cord or dorsal root ganglia, but in retina the acidic phospholipids were significantly increased.     

Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHN alpha, in a globular protein. Use of 3JHN alpha for identification of helical secondary structure

The vicinal amide proton-C alpha proton spin-spin coupling constants, JHN alpha, in the globular protein basic pancreatic trypsin inhibitor (BPTI) have been measured using phase-sensitive correlated spectroscopy at high digital resolution. In conjunction with the crystal structure of BPTI, these data were used to calibrate the correlation between 3JHN alpha and the dihedral angle phi. The resulting "BPTI curve" is 3JHN alpha = 6.4 cos2 theta - 1.4 cos theta + 1.9 (theta = [phi - 60 degrees]). It is further shown that measurement of the spin-spin couplings 3JHN alpha presents an independent, reliable method for identification of the location of helical structure in the amino acid sequence of proteins.     

IL-4 modulates the histamine content of mast cells in a mast cell/fibroblast co-culture through a Stat6 signaling pathway in fibroblasts

IL-4 plays a crucial role in the pathogenesis of allergic diseases, such as the induction of IgE synthesis and the development of mast cells. To further understand the effect of IL-4 on mast cells in skin, we utilized a mast cell/fibroblast co-culture system as an in vitro model of dermal mast cells. IL-4 induced mast cell growth in the culture with fibroblasts. Immunoblot analysis revealed that IL-4 activated Stat6 in both mast cells and fibroblasts. The over-expression of dominant-negative Stat6 in fibroblasts in the presence of IL-4 decreased the histamine content per mast cell, but not the number of mast cells. In contrast, the over-expression of constitutively-active Stat6 in fibroblasts increased the histamine content per mast cell, indicating that the activation of Stat6 in fibroblasts supports the maturation of mast cells co-cultured with fibroblasts.     

The effect of ‘probe binding’ on the quantitative determination of the proton-motive force in bacteria

The electrical potential across the cytoplasmic membrane of bacteria can be calculated from the distribution of the lipophilic cation tetraphenylphosphonium between the bulk phases of the medium and the cytoplasm. In order to determine the bulk phase concentrations, information about the binding of the probe to the cellular components is required. In de-energized cells of Rhodopseudomonas sphaeroides the binding appears to be proportional to the free probe concentration. The bulk phase concentrations can only be determined when knowledge is available about the distribution of the binding of the probe over the different cellular components. In this report, models for binding are presented which are based on the assumption that the binding is an energy-independent process. These models allow a proper calculation of the electrical potential when the binding of the probe to the different cellular components is known.     

Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure

The development of electrostatic interactions during the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) is investigated by pH-dependent rate equilibrium free energy relationships. We show that Asp8, among six acidic residues, is involved in non-native, electrostatic interactions with K12 in the transition state for folding as well as in the denatured state. The perturbed native state pK(a) of D8 (pK(a) = 3.0) appears to be maintained through non-native interactions in both the transition state and the denatured state. Mutational effects on the stability of the transition state for protein (un)folding are often analyzed in respect to change in ground states. Thus, the interpretation of transition state analysis critically depends on an understanding of mutational effects on both the native and denatured state. Increasing evidence for structurally biased denatured states under physiological conditions raises concerns about possible denatured state effects on folding studies. We show that the structural interpretation of transition state analysis can be altered dramatically by denatured state effects.     

Specificity of the initial collapse in the folding of the cold shock protein

The two-state folding reaction of the cold shock protein from Bacillus caldolyticus (Bc-Csp) is preceded by a rapid chain collapse. A fast shortening of intra-protein distances was revealed by F?rster resonance energy transfer (FRET) measurements with protein variants that carried individual pairs of donor and acceptor chromophores at various positions along the polypeptide chain. Here we investigated the specificity of this rapid compaction. Energy transfer experiments that probed the stretching of strand beta2 and the close approach between the strands beta1 and beta2 revealed that the beta1-beta2 hairpin is barely formed in the collapsed form, although it is native-like in the folding transition state of Bc-Csp. The time course of the collapse could not be resolved by pressure or temperature jump experiments, indicating that the collapsed and extended forms are not separated by an energy barrier. The co-solute (NH4)2SO4 stabilizes both native Bc-Csp and the collapsed form, which suggests that the large hydrated SO4(2-) ions are excluded from the surface of the collapsed form in a similar fashion as they are excluded from folded Bc-Csp. Ethylene glycol increases the stability of proteins because it is excluded preferentially from the backbone, which is accessible in the unfolded state. The collapsed form of Bc-Csp resembles the unfolded form in its interaction with ethylene glycol, suggesting that in the collapsed form the backbone is still accessible to water and small molecules. Our results thus rule out that the collapsed form is a folding intermediate with native-like chain topology. It is better described as a mixture of compact conformations that belong to the unfolded state ensemble. However, some of its structural elements are reminiscent of the native protein.