Cell organization of barb ridges in regenerating feathers of the quail: implications of the elongation of barb ridges for the evolution and diversification of feathers

This ultrastructural study on the regenerating feathers of quail describes the cellular organization of the barb ridges responsible for the ramification of adult feathers. Bilateral symmetry of the barb ridges determines the organization of feather cells into feather branching. The length of the barb ridges, derived from the number of cells associated to form the barbule plates, determines the length of the barbule branching. Long chains of barb cells form long barbs that branch from the rachis with an increase of feather size. Supportive cells function as spacers between the barbule cells. New cells derive from stem cells localized in the collar region of the feather follicle, as indicated from the re‐organization of collar cells into barb ridges (a morphogenetic process inherited from that of embryonic feathers), production of an embryonic type of keratin (feather keratin), permanence of periderm granules (typical embryonic organelles) in barb vane ridge cells. Variations in the process of barb ridge morphogenesis allow the fusion of ridges into a rachis. The differentiation of hooklets contributes to the origin of planar feathers. Separation between rachis and merging barb ridges is by supportive cells, derived from the marginal plates of the barb ridges. Speculations on the evolution and diversification of feathers are presented.     

Mercury accumulation in the muscles and feathers of pheasants, Phasianus colchicus (L. 1758)

Mercury concentrations were determined in muscles and feathers of 58 cock pheasants. Birds were collected from seven different polluted sites in southern Poland in 1987. The mercury concentrations in the muscle ranged from 0.010 to 0.026 mug g dry mass. The significantly highest values were found in muscle samples from Przylasek and Przemysl. The levels found in the flight feathers were higher than in breast feathers. Average concentrations in flight feathers ranged from 0.050 mug g (Przemysl) to 0.240 mug g dry mass (Przylasek). © Rapid Science 1998     

Size scaling and stiffness of avian primary feathers: implications for the flight of Mesozoic birds

The primary feathers of birds are subject to cyclical forces in flight causing their shafts (rachises) to bend. The amount the feathers deflect during flight is dependent upon the flexural stiffness of the rachises. By quantifying scaling relationships between body mass and feather linear dimensions in a large data set of living birds, we show that both feather length and feather diameter scale much closer to predictions for geometric similarity than they do to elastic similarity. Scaling allometry also indicates that the primary feathers of larger birds are relatively shorter and their rachises relatively narrower, compared to those of smaller birds. Two-point bending tests indicated that larger birds have more flexible feathers than smaller species. Discriminant functional analyses (DFA) showed that body mass, primary feather length and rachis diameter can be used to differentiate between different magnitudes of feather bending stiffness, with primary feather length explaining 63% of variance in rachis stiffness. Adding fossil measurement data to our DFA showed that Archaeopteryx and Confuciusornis do not overlap with extant birds. This strongly suggests that the bending stiffness of their primary feathers was different to extant birds and provides further evidence for distinctive flight styles and likely limited flight ability in Archaeopteryx and Confuciusornis.     

Biological monitoring of exposure to ambient lead and cadmium using avian feathers: A study from Northern India

Biological monitoring of exposure to ambient environmental lead and cadmium was performed using feathers of 26 species of birds native to Western Uttar Pradesh in Northern India. The rationale of this study was to address three questions. First, is there any avian species that can be treated as a suitable bioindicator of lead or cadmium present in the environment? Second, do the birds selectively accumulate lead and cadmium in their feathers and exhibit interspecies variation? Third, is there any threat to endangered species of this region from metal pollution? Average concentration of lead in the feathers of selected birds ranged from 3.40 µg/g in parrot to 301.6 µg/g in golden pheasant, whereas cadmium concentration was higher ranging from 40.20 µg/g in red crow to 450 µg/g in blue macaw. A comparison of results made through ANOVA revealed a significant difference in the concentration of lead (df = 25; F = 3965.54) and cadmium (df = 25; F = 8537.27) in their feathers. We hypothesize that feathers of synanthropic birds may be treated as suitable noninvasive tool to monitor the ambient environmental contamination by lead and cadmium. Their accumulation in endangered birds may lead to population decline causing serious ecological disturbances in the region.     

DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.     

Patterns of nest relief during incubation,and incubation period variability in the yellow-eyed penguin (Megadyptes antipodes)

Abstract

Daily nest checks were used to determine the yellow-eyed penguin’s pattern of nest relief during incubation, and to examine the inter-pair variability in incubation period. Nests at two breeding areas on the Otago Peninsula were visited between September and December in 1985 and 1986. At each visit, status of the nest and the identity and behaviour of the sitting bird was recorded. Incubation is shared between the sexes, with males tending to sit longer than females. Incubation spells ranged from 1–7 days with a mode of 1–2 days. Records of lone incubation following mate death show the yelloweyed penguin to be capable of 15 day unrelieved spells at the nest The incubation period of the yellow-eyed penguin ranges from 39–51 days and is the most variable of all penguins. This variability is because of the failure of some individuals to adequately cover the clutch until up to 5 days after the laying of the second egg.     

Home-range use, activity, and density of caracal in relation to prey density

Two male and three female caracal Felis caracal were radio-tracked over a 1-year period in arid shrub on the west coast of South Africa, by day and night over at least 130 days for each caracal, and uninterrupted for up to 120 h at a time. These results, on short-term use of space, were related to concurrent availability of prey. The use by caracal of specific plant communities showed a significant positive correlation to prey biomass of rodents. Males had much larger home-ranges (26.9±0.75 km²) than females (7.39±1.68 km²). Male home-ranges overlapped completely with those of females, whereas female ranges overlapped between 0 and 19%. Caracal were active by night and day; onset of activity was affected more by ambient temperature (T_A) than photoperiod. Caracal were active significantly longer on nights colder than 20°C. Females ceased activity at T_A > 20°C, males at T_A > 22°C. Males foraged faster than females (667 vs. 312 m h⁻¹) and moved more than twice the distance of females during an active period. Calculated density of caracal was between 0.23 and 0.47 km⁻².     

Molecular modeling,dynamics studies and density functional theory approaches to identify potential inhibitors of SIRT4 protein from Homo sapiens : a novel target for the treatment of type 2 diabetes

Type 2 diabetes is one of the biggest health challenges in the world and WHO projects it to be the 7th leading cause of death in 2030. It is a chronic condition affecting the way our body metabolizes sugar. Insulin resistance is high risk factor marked by expression of Lipoprotein Lipases and Peroxisome Proliferator-Activated Receptor that predisposes to type 2 diabetes. AMP-dependent protein kinase in AMPK signaling pathway is a central sensor of energy status. Deregulation of AMPK signaling leads to inflammation, oxidative stress, and deactivation of autophagy which are implicated in pathogenesis of insulin resistance. SIRT4 protein deactivates AMPK as well as directly inhibits insulin secretion. SIRT4 overexpression leads to dyslipidimeia, decreased fatty acid oxidation, and lipogenesis which are the characteristic features of insulin resistance promoting type 2 diabetes. This makes SIRT4 a novel therapeutic target to control type 2 diabetes. Virtual screening and molecular docking studies were performed to obtain potential ligands. To further optimize the geometry of protein–ligand complexes Quantum Polarized Ligand Docking was performed. Binding Free Energy was calculated for the top three ligand molecules. In view of exploring the stereoelectronic features of the ligand, density functional theory approach was implemented at B3LYP/6-31G* level. 30 ns MD simulation studies of the protein–ligand complexes were done. The present research work proposes ZINC12421989 as potential inhibitor of SIRT4 with docking score (?7.54 kcal/mol), docking energy (?51.34 kcal/mol), binding free energy (?70.21 kcal/mol), and comparatively low energy gap (?0.1786 eV) for HOMO and LUMO indicating reactivity of the lead molecule.     

Computational insights into the binding pattern of mitochondrial calcium uniporter inhibitor through homology modeling,molecular dynamics simulation,binding free energy prediction and density functional theory calculation

Abstract

The mitochondrial calcium uniporter (MCU) is the critical protein of the inner mitochondrial membrane that is the primary mediator for calcium uptake into the mitochondrial matrix. Herein we built the optimal homology model of human MCU which was refined through all-atom molecular dynamics simulation. Then, the binding mode of known inhibitor was predicted through molecular docking method, along with molecular dynamics simulation and binding free energy calculation to verify the docking result and stability of the protein-inhibitor complex. Finally, density functional theory (DFT) calculation enhanced our understanding of the molecular interaction of MCU inhibitor. Our research would provide a deeper insight into the interactions between human MCU and its inhibitor, which boosts to develop novel therapy against MCU related disease.

Communicated by Ramaswamy H. Sarma     

Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase--a density functional study

The enzyme myeloperoxidase shows several unusual properties compared to other peroxidases, e.g. a red-shifted absorption spectrum and a peroxidase activity towards chloride. It has been suggested that this is caused by the unusual covalent links between the heme group and the surrounding protein, but whether it is caused by the two ester links to Glu-242 and Asp-94 or the sulfonium ion linkage to Met-243 is unclear. To investigate these suggestions, we have used density functional theory to study the structure, spectra, and reduction potential of 25 models of myeloperoxidase in the reduced (Fe^II) and oxidized (Fe^III) states, as well as in the compound I (formally Fe^VO) and II (Fe^IVO or Fe^IVOH) states, using appropriate models of the linkages to the Asp, Glu, and Met residues (including the back-bone connection between Glu-242 and Met-243) in varying combinations. The calculated spectral shifts indicate that both the ester and sulfonium linkages play a role in the spectral shift. On the other hand, the sulfonium linkage seems to be mainly responsible for the high positive reduction potential for the both ferric/ferrous and compound I/II couples of myeloperoxidase.     

Baculovirus production for gene therapy: the role of cell density,multiplicity of infection and medium exchange

One of the major concerns regarding the use of insect cells and baculovirus expression vectors for the production of recombinant proteins is the drop in production observed when infecting cultures at high cell densities; this work attempts to understand this so-called cell density effect in the scope of baculovirus production for gene therapy purposes. A Spodoptera frugiperda insect cell line (Sf-9) was cultured and infected in serum-free medium, and the patterns of production of a recombinant baculovirus expressing the green fluorescent protein (GFP) were analyzed at different cell concentrations at infection (CCIs) and multiplicities of infection (MOIs). The results confirm that a cell density effect on productivity occurs which is dependent on the MOI used, with a high MOI “delaying” the drop in production to higher cell densities. Medium replacement at the time of infection using a high MOI considerably improved baculovirus production, with the different production indicators, namely the titer, specific yield, amplification factor, and time of harvesting, increasing with cell concentration for the CCI range tested. Virus titers as high as 2.6 × 10¹⁰ IP.mL⁻¹ were obtained in cultures infected at 3.5 × 10⁶ cells.mL⁻¹, while the amplification factor was roughly 19 times higher than the highest value obtained without medium exchange.     

The density distribution of gene loci over the genetic map ofEscherichia coli: Its structural,functional and evolutionary implications

Summary A quantitative analysis was carried out on the dispersion of gene loci over theE. coli genetic map. Therefore, the map was divided into regions characterized by an homogeneous gene density. This created a distribution pattern of gene loci that contained a symmetry axis located near to the origin of DNA replication. The pattern could be subdivided into a set of 22 functional domains containing gene loci whose products revealed a biochemical or functional relatedness. A correlation was found between the boundary positions of these domains and the distribution of F plasmid- and DNA insertion sites over theE. coli chromosome. The structural, functional and evolutionary implications of these findings are discussed.     

The density of graptoloid skeletal tissue, and its implication for the volume and density of the soft tissue

It has been proposed by many authors that a mechanism is necessary to achieve neutral buoyancy in graptoloids. Calculations are given to show the range of densities needed for both soft and skeletal tissues to achieve this, and it is concluded that a large volume of soft tissue, containing low density fats, is the most likely mechanism. This is not readily compatible with the rhabdopleuran model of the graptolite mid.     

Genetic estimates of annual reproductive success in male brown bears: the effects of body size, age, internal relatedness and population density

1. We studied male yearly reproductive success (YRS) and its determinants (phenotypic characteristics, age, population density) in two Scandinavian brown bear populations, using molecular techniques to determine paternity. 2. We found a significant difference in male YRS between the study areas, with lower YRS in the south than in the north. 3. In general, older and larger males had higher YRS. Older males may be more experienced in competition for reproduction (male dominance). Large body size is of direct benefit in male-male competition and of advantage in endurance competition for the access to females. 4. Age was relatively more important for YRS in the north and body size was more important in the south, due perhaps to differences in male age structure due to illegal killing. A single old male dominated the reproduction in the north during the study, which resulted most probably in the relatively higher importance of age in the north. In the south, with a more even male age structure, no single male was able to dominate, probably resulting in a more intense competition among males, with body size as the deciding factor. 5. Male YRS was correlated positively with population density. This may be related to the structure of the expanding bear population, with female densities declining towards the population edge. 6. Internal relatedness, a measure of genetic heterozygosity, was correlated negatively with YRS, suggesting that outbred individuals have a higher YRS. Individual heterozygosity at key or many loci may reflect male physical qualities and condition-sensitive traits, which may benefit males directly in contest or in sperm competition.