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1.  Crystallization of sheep (Ovis aries) and goat (Capra hircus) haemoglobins under unbuffered low-salt conditions 
The haemoglobins from low oxygen affinity species, sheep and goat are crystallized under unbuffered low-salt conditions to explore the possibility of obtaining new crystal forms.
Haemoglobin is a tetrameric protein that plays a vital role in the transport of oxygen from the lungs to the tissues and of carbon dioxide back to the lungs. Even though a large amount of work has already been performed in this area, the study of the haemoglobin structures of avian and mammalian species is rather incomplete. Efforts are being made to understand the salient features of the species mentioned above. Here, whole blood plasma was collected from sheep and goat and purified by anion-exchange chromatography; the haemoglobins were crystallized by the hanging-drop vapour-diffusion method under unbuffered low-salt conditions using PEG 3350 as a precipitant. Data collection was carried out using a MAR345 image-plate detector system. Sheep haemoglobin crystallizes in the orthorhombic space group P212121 with one whole biological molecule (α2β2) in the asymmetric unit, with unit-cell parameters a = 60.231, b = 70.695, c = 131.479 Å. In contrast, goat haemoglobin crystallizes in the triclinic system with two biological molecules (α2β2) in the unit cell. The unit-cell parameters are a = 53.103, b = 69.382, c = 96.098 Å, α = 110.867, β = 91.133, γ = 109.437°.
doi:10.1107/S1744309107044296
PMCID: PMC2339733  PMID: 17909297
haemoglobin
2.  Purification, crystallization and preliminary crystallographic study of haemoglobin from camel (Camelus dromedarius): a high oxygen-affinity lowland species 
Haemoglobin from Camelus dromedarius provides an interesting case study of adaptation to life in deserts at extremely high temperatures. An ambition to unravel the integrated structural and functional aspects of the casual survival of this animal at high temperatures led the authors to specifically work on this problem. This work reports the preliminary crystallographic study of camel haemoglobin.
Haemoglobin is a prototypical allosteric protein that is mainly involved in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs in an intrinsically coordinated manner to maintain the viability of cells. Haemoglobin from Camelus dromedarius provides an interesting case study of adaptation to life in deserts at extremely high temperatures. An ambition to unravel the integrated structural and functional aspects of the casual survival of this animal at high temperatures led us to specifically work on this problem. The present work reports the preliminary crystallographic study of camel haemo­globin. Camel blood was collected and the haemoglobin was purified by anion-exchange chromatography and crystallized using the hanging-drop vapour-diffusion method under buffered high salt concentration using PEG 3350 as a precipitant. Intensity data were collected using a MAR 345 dtb image-plate detector system. Camel haemo­globin crystallized in the monoclinic space group P21, with one whole biological molecule (α2β2) in the asymmetric unit and unit-cell parameters a = 52.759, b = 116.782, c = 52.807 Å, β = 120.07°.
doi:10.1107/S1744309109024154
PMCID: PMC2720330  PMID: 19652336
haemoglobin; Camelus dromedarius; oxygen affinity
3.  Purification, crystallization and preliminary X-ray analysis of haemoglobin from ostrich (Struthio camelus) 
Purification, crystallization and preliminary X-ray analysis of haemoglobin from ostrich (Struthio camelus) has been carried out under 293 K temperature conditions. The ostrich is a large flightless bird which contains inositol tetrakisphosphate in erythrocytes and its whole blood oxygen affinity is higher. Efforts have been made to explore the structure–function relationship of ostrich heamoglobin.
Haemoglobin is a tetrameric protein that carries oxygen from the lungs to tissues and carbon dioxide from tissues back to the lungs. The oxygen-binding properties of haemoglobin are regulated through the binding of allosteric effectors. The respiratory system of avian species is unique and complex in nature when compared with that of mammals. In avian species, inositol pentaphosphate (inositol-P5) is present in the erythrocytes of the adult and is thought to be the major factor responsible for the relatively high oxygen affinity of the whole blood. The ostrich (Struthio camelus) is a large flightless bird which contains inositol tetrakisphosphate (inositol-P4) in its erythrocytes and its whole blood oxygen affinity is higher. Efforts have been made to explore the structure–function relationship of ostrich haemoglobin. Ostrich haemoglobin was purified using ion-exchange chromatography. Haemoglobin crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant in 50 mM phosphate buffer pH 7.2. Data were collected using a MAR345 image-plate detector system. The crystals of ostrich haemo­globin diffracted to 2.2 Å resolution. They belonged to the ortho­rhombic space group P212121 with one whole biological molecule in the asymmetric unit; the unit-cell parameters were a = 80.93, b = 81.68, c = 102.05 Å.
doi:10.1107/S1744309109019009
PMCID: PMC2705633  PMID: 19574638
haemoglobin; Struthio camelus
4.  Purification, crystallization and preliminary X-ray diffraction studies on avian haemoglobin from pigeon (Columba livia) 
Crystallization of pigeon haemoglobin at low pH (5.5) and high ionic concentration (1 M) using the hanging-drop vapour-diffusion method is reported.
Haemoglobin is a physiologically significant metalloprotein that is involved in the exchange of gases for sustaining life. The respiratory system of birds is unique and complex compared with that of mammals. Many investigations of avian haemoglobins have revealed the presence of inositol pentaphosphate (IP5), a principal allosteric effector that is involved in regulation of their function. Structural investigations of avian haemoglobins are presently not adequate to explain their function. Efforts have been made in this direction in order to understand the oxygen-binding affinity involved in adapting to hypoxia in avian haemoglobins. Fresh whole blood was collected from pigeon (Columba livia) and purified using a DEAE cellulose anion-exchange chromatographic column. Crystallization of pigeon haemoglobin was accomplished using the hanging-drop vapour-diffusion method using PEG 3350 as a precipitant in 50 mM sodium acetate buffer pH 5.5 with 1 M NaCl. Data collection was carried out using a MAR345 image-plate detector system. The crystals diffracted to 2 Å resolution. Pigeon haemoglobin crystallizes in a triclinic space group, with two whole biological molecules in the asymmetric unit and with unit-cell parameters a = 55.005, b = 65.528, c = 104.370 Å, α = 78.742, β = 89.819, γ = 65.320°.
doi:10.1107/S1744309108038505
PMCID: PMC2635874  PMID: 19194000
allosteric effectors; oxygen affinity; triclinic; avian haemoglobins
5.  Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin 
Parakeet (Psittacula krameri) haemoglobin has been purified and crystallized under low salt buffered conditions. Preliminary analysis of the crystal that belonged to monoclinic system (C2) is reported.
Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemo­globins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 Å resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 Å, β = 109.35°. Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.
doi:10.1107/S1744309109034071
PMCID: PMC2765893  PMID: 19851014
avian haemoglobin; Psittacula krameri
6.  Pseudogenization of a Sweet-Receptor Gene Accounts for Cats' Indifference toward Sugar 
PLoS Genetics  2005;1(1):e3.
Although domestic cats (Felis silvestris catus) possess an otherwise functional sense of taste, they, unlike most mammals, do not prefer and may be unable to detect the sweetness of sugars. One possible explanation for this behavior is that cats lack the sensory system to taste sugars and therefore are indifferent to them. Drawing on work in mice, demonstrating that alleles of sweet-receptor genes predict low sugar intake, we examined the possibility that genes involved in the initial transduction of sweet perception might account for the indifference to sweet-tasting foods by cats. We characterized the sweet-receptor genes of domestic cats as well as those of other members of the Felidae family of obligate carnivores, tiger and cheetah. Because the mammalian sweet-taste receptor is formed by the dimerization of two proteins (T1R2 and T1R3; gene symbols Tas1r2 and Tas1r3), we identified and sequenced both genes in the cat by screening a feline genomic BAC library and by performing PCR with degenerate primers on cat genomic DNA. Gene expression was assessed by RT-PCR of taste tissue, in situ hybridization, and immunohistochemistry. The cat Tas1r3 gene shows high sequence similarity with functional Tas1r3 genes of other species. Message from Tas1r3 was detected by RT-PCR of taste tissue. In situ hybridization and immunohistochemical studies demonstrate that Tas1r3 is expressed, as expected, in taste buds. However, the cat Tas1r2 gene shows a 247-base pair microdeletion in exon 3 and stop codons in exons 4 and 6. There was no evidence of detectable mRNA from cat Tas1r2 by RT-PCR or in situ hybridization, and no evidence of protein expression by immunohistochemistry. Tas1r2 in tiger and cheetah and in six healthy adult domestic cats all show the similar deletion and stop codons. We conclude that cat Tas1r3 is an apparently functional and expressed receptor but that cat Tas1r2 is an unexpressed pseudogene. A functional sweet-taste receptor heteromer cannot form, and thus the cat lacks the receptor likely necessary for detection of sweet stimuli. This molecular change was very likely an important event in the evolution of the cat's carnivorous behavior.
Synopsis
Although sweet sugars are ubiquitous in human foods, they are seldom added to cat food, and owners usually do not feed sweets to their cats. This is because, in contrast to most other mammals, both domestic cats and their wild cousins, the big cats, do not show a preference for and, most likely, cannot detect sweet-tasting compounds. Other than this sweet blindness, the cat's sense of taste is normal. The molecular mechanism for this unique behavior towards sweets was not known, until now. Sweet compounds, including sugars and artificial sweeteners, are recognized by a special taste bud receptor composed of the products of two genes. The authors found that in cats, one of these genes is not functional and is not expressed. (It is called a pseudogene.) Because the sweet receptor cannot be formed, the cat cannot taste sweet stimuli. During the evolution of the cats' strictly carnivorous behavior, selection to maintain a functional receptor was apparently relaxed. This research provides a molecular explanation for the common observation that the cat lives in a different sensory world than the cat owner.
doi:10.1371/journal.pgen.0010003
PMCID: PMC1183522  PMID: 16103917
7.  Annotated features of domestic cat – Felis catus genome 
GigaScience  2014;3:13.
Background
Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors.
Findings
Here we report a preliminary annotation of the whole genome sequence of Cinnamon, a domestic cat living in Columbia (MO, USA), bisulfite sequencing of Boris, a male cat from St. Petersburg (Russia), and light 30× sequencing of Sylvester, a European wildcat progenitor of cat domestication. The annotation includes 21,865 protein-coding genes identified by a comparative approach, 217 loci of endogenous retrovirus-like elements, repetitive elements which comprise about 55.7% of the whole genome, 99,494 new SNVs, 8,355 new indels, 743,326 evolutionary constrained elements, and 3,182 microRNA homologues. The methylation sites study shows that 10.5% of cat genome cytosines are methylated. An assisted assembly of a European wildcat, Felis silvestris silvestris, was performed; variants between F. silvestris and F. catus genomes were derived and compared to F. catus.
Conclusions
The presented genome annotation extends beyond earlier ones by closing gaps of sequence that were unavoidable with previous low-coverage shotgun genome sequencing. The assembly and its annotation offer an important resource for connecting the rich veterinary and natural history of cats to genome discovery.
doi:10.1186/2047-217X-3-13
PMCID: PMC4138527  PMID: 25143822
Felis catus; Domestic cat; Felis silvestris silvestris; European wildcat; Genome sequence; Annotation; Assembly
8.  Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin 
The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique.
Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3121, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.
doi:10.1107/S2053230X14019943
PMCID: PMC4231857  PMID: 25372822
avian haemoglobin; great cormorant; Phalacrocorax carbo; molecular replacement
9.  Environmental determinants of spatial and temporal variations in the transmission of Toxoplasma gondii in its definitive hosts☆ 
Graphical abstract
Highlights
•Toxoplasma gondii seroprevalences in 112 European wildcats, 20 domestic cats and 47 hybrids are reported.•The seroprevalence (overall 65.2%) did not differ with the type of cat.•High farm densities and mild winters are associated with the highest seroprevalence.
Toxoplasmosis is a major zoonosis, and its prevention requires multiple approaches due to the complex life-cycle of its causative agent, Toxoplasma gondii. Environmental contamination by oocysts is a key factor in the transmission of T. gondii to both humans and meat-producing animals; however, its spatial and temporal variations are poorly understood. We analysed the distribution of T. gondii seropositivity in a sample of 210 cats, including the European wildcat (Felis silvestris silvestris), the domestic cat (Felis silvestris catus) and their hybrids that were collected in Central and Eastern France between 1996 and 2006. We searched for spatial variability among communes and temporal variations among years to relate this variability to landscape and meteorological conditions, which can affect the population dynamics of rodent hosts and the survival of oocysts. The overall seroprevalence was 65.2% (95% CI: 58.6–71.4). As expected, adults were more often infected than young individuals, while the occurrence of infection was not related to cat genotypes. Seroprevalence correlated significantly with farm density and the North-Atlantic Oscillation index, which describes temporal variations of meteorological conditions at the continental scale. The highest seroprevalence values were obtained in areas with high farm densities and during years with cool and moist winters. These results suggest that both farming areas and years with cool and wet winters are associated with increased T. gondii seroprevalence in cats. As cat infection determines the environmental contamination by oocysts, climate and landscape characteristics should be taken into account to improve the risk analysis and prevention of T. gondii.
doi:10.1016/j.ijppaw.2013.09.006
PMCID: PMC3862504  PMID: 24533347
Toxoplasmosis; Meteorological variations; Farm density; North-Atlantic Oscillation index; Felis silvestris; Felis catus
10.  Crystallization, preliminary X-ray diffraction studies and Raman microscopy of the major haemoglobin from the sub-Antarctic fish Eleginops maclovinus in the carbomonoxy form 
The major haemoglobin of the sub-Antarctic fish E. maclovinus is the first sub-Antarctic fish haemoglobin to be crystallized and its structural characterization will shed light on the molecular mechanisms of cold adaptation and the role of the Root effect in fish.
The blood of the sub-Antarctic fish Eleginops maclovinus (Em) contains three haemoglobins. The major haemoglobin (Hb1Em) displays the Root effect, a drastic decrease in the oxygen affinity and a loss of cooperativity at acidic pH. The carbomonoxy form of HbEm1 has been crystallized in two different crystal forms, orthorhombic (Ortho) and hexagonal (Hexa), and high-resolution diffraction data have been collected for both forms (1.45 and 1.49 Å resolution, respectively). The high-frequency resonance Raman spectra collected from the two crystal forms using excitation at 514 nm were almost indistinguishable. Hb1Em is the first sub-Antarctic fish Hb to be crystallized and its structural characterization will shed light on the molecular mechanisms of cold adaptation and the role of the Root effect in fish haemoglobins.
doi:10.1107/S1744309110038698
PMCID: PMC3001669  PMID: 21045316
cold adaptation; Eleginops maclovinus; haemichrome; haemoglobin; oxygen affinity; Raman microspectroscopy
11.  Purification, crystallization and preliminary X-ray analysis of Enterococcus casseliflavus aminoglycoside-2′′-phosphotransferase-IVa 
Aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] is an enzyme that is responsible for high-level gentamicin resistance in E. casseliflavus isolates. Three different crystals of wild-type substrate-free APH(2′′)-IVa have been prepared and preliminary X-ray diffraction experiments have been undertaken on all three crystal forms.
The deactivation of aminoglycoside antibiotics by chemical modification is one of the major sources of bacterial resistance to this family of therapeutic compounds, which includes the clinically relevant drugs streptomycin, kanamycin and gentamicin. The aminoglycoside phosphotransferases (APHs) form one such family of enzymes responsible for this resistance. The gene encoding one of these enzymes, aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] from Enterococcus casseliflavus, has been cloned and the protein (comprising 306 amino-acid residues) has been expressed in Escherichia coli and purified. The enzyme was crystallized in three substrate-free forms. Two of the crystal forms belonged to the orthorhombic space group P212121 with similar unit-cell parameters, although one of the crystal forms had a unit-cell volume that was approximately 13% smaller than the other and a very low solvent content of around 38%. The third crystal form belonged to the monoclinic space group P21 and preliminary X-ray diffraction analysis was consistent with the presence of two molecules in the asymmetric unit. The orthorhombic crystal forms of apo APH(2′′)-IVa both diffracted to 2.2 Å resolution and the monoclinic crystal form diffracted to 2.4 Å resolution; synchrotron diffraction data were collected from these crystals at SSRL (Stanford, California, USA). Structure determination by molecular replacement using the structure of the related enzyme APH(2′′)-IIa is proceeding.
doi:10.1107/S1744309109050039
PMCID: PMC2805544  PMID: 20057078
aminoglycoside-2′′-phosphotransferase-IVa; Enterococcus casseliflavus; antibiotic resistance
12.  Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein tyrosine phosphatase γ in three different crystal forms 
The design, expression and purification of receptor protein tyrosine phosphatase γ and two mutants and their crystallization in three different crystal forms are described.
Protein tyrosine phosphatase γ is a membrane-bound receptor and is designated RPTPγ. RPTPγ and two mutants, RPTPγ(V948I, S970T) and RPTPγ(C858S, S970T), were recombinantly expressed and purified for X-ray crystallographic studies. The purified enzymes were crystallized using the hanging-drop vapor-diffusion method. Crystallographic data were obtained from several different crystal forms in the absence and the presence of inhibitor. In this paper, a description is given of how three different crystal forms were obtained that were used with various ligands. An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form was only obtained in the presence of a particularly elaborated inhibitor.
doi:10.1107/S1744309111017209
PMCID: PMC3144792  PMID: 21795790
protein tyrosine phosphatases; hydrolases; inhibitor complexes
13.  Structural studies of haemoglobin from pisces species shortfin mako shark (Isurus oxyrinchus) at 1.9 Å resolution 
Journal of Synchrotron Radiation  2013;20(Pt 6):843-847.
Shortfin mako shark haemoglobin adopts an unliganded deoxy T state conformation, which is shown from the quaternary structural features, interface interactions and heme binding sites of different subunits of haemoglobin with high-resolution X-ray data.
Haemoglobin (Hb) is a tetrameric iron-containing protein that carries oxygen from the lungs to tissues and carbon dioxide from tissues back to the lungs. Pisces are the advanced aquatic vertebrates capable of surviving at wide depth ranges. The shortfin mako shark (SMS) is the pelagic, largest, fastest and most sophisticated species of the shark kingdom with well developed eyes. Mostly the pisces species are cold blooded in nature. Distinctly, the SMSs are warm-blooded animals with an advanced circulatory system. SMSs are capable of maintaining elevated muscle temperatures up to 33 K above the ambient water temperatures at a depth of 150–500 m. SMSs have a diverged air-breathing mechanism compared with other vertebrates. The haemoglobin molecule consists of four polypeptide chains, namely two α chains, each with 140 amino acids and two β chains each having 136 amino acids. The SMS Hb was found to crystallize in monoclinic space group P21 using the hanging-drop vapour-diffusion method at room temperature. The crystal packing parameters for the SMS Hb structure contain one whole biological molecule in the asymmetric unit with a solvent content of 47%. The SMS Hb quaternary structural features interface–interface interactions and heme binding sites are discussed with different state Hbs and the results reveal that SMS Hb adopts an unliganded deoxy T state conformation.
doi:10.1107/S0909049513021572
PMCID: PMC3795541  PMID: 24121325
haemoglobin; shark; monoclinic; oxygen transport; crystal structure; heme; tetramer
14.  Molecular cloning of ion channels in Felis catus that are related to periodic paralyses in man: a contribution to the understanding of the genetic susceptibility to feline neck ventroflexion and paralysis 
Biology Open  2014;3(9):785-793.
ABSTRACT
Neck ventroflexion in cats has different causes; however, the most common is the hypokalemia associated with flaccid paralysis secondary to chronic renal failure. In humans, the most common causes of acute flaccid paralysis are hypokalemia precipitated by thyrotoxicosis and familial forms linked to mutations in sodium, potassium, and calcium channel genes. Here, we describe the sequencing and analysis of skeletal muscle ion channels in Felis catus that could be related to periodic paralyses in humans, contributing to the understanding of the genetic susceptibility to feline neck ventroflexion and paralysis. We studied genomic DNA from eleven cats, including five animals that were hyperthyroid with hypokalemia, although only one presented with muscle weakness, and six healthy control domestic cats. We identified the ion channel ortholog genes KCNJ2, KCNJ12, KCNJ14, CACNA1S and SCN4A in the Felis catus genome, together with several polymorphic variants. Upon comparative alignment with other genomes, we found that Felis catus provides evidence for a high genomic conservation of ion channel sequences. Although we hypothesized that neck ventroflexion in cats could be associated with a thyrotoxic or familial periodic paralysis channel mutation, we did not identify any previously detected human channel mutation in the hyperthyroid cat presenting hypokalemia. However, based on the small number of affected cats in this study, we cannot yet rule out this molecular mechanism. Notwithstanding, hyperthyroidism should still be considered as a differential diagnosis in hypokalemic feline paralysis.
doi:10.1242/bio.20148003
PMCID: PMC4163655  PMID: 25063199
Potassium channel; Inward rectifier; Felis catus; Kir2.x; KCNJ2; KCNJ12; KCNJ18; CACNA1S; SCN4A; Cat
15.  Crystallization and preliminary X-ray analysis of allene oxide synthase, cytochrome P450 CYP74A2, from Parthenium argentatum  
Allene oxide synthase, an atypical cytochrome P450 from Parthenium argentatum, was crystallized and diffraction data were collected to 2.4 Å resolution.
Oxylipins are oxygenated derivatives of fatty acids and pivotal signaling molecules in plants and animals. Allene oxide synthase (AOS) is a key cytochrome P450 CYP74 enzyme involved in the biosynthesis of plant oxylipin jasmonates to convert 13(S)-hydroperoxide to allene oxide. Guayule (Parthenium argentatum) AOS, CYP74A2, was expressed in Escherichia coli. Protein was purified using affinity chromatography and size exclusion chromatography, and then crystallized. Two different crystal forms were obtained from 0.2 M (NH4)H2PO4, 50% MPD, 0.1 M Tris, pH 8.5 at 277 K using the hanging-drop vapor-diffusion method. Preliminary X-ray analysis was carried out, and the crystals were found to belong to the tetragonal space group I422 with cell parameters a = b = 126.5, c = 163.9 Å, and the monoclinic space group C2 with cell parameters a = 336.5, b = 184.2, c = 159.0 Å, β = 118.6°. Diffraction data were collected to 2.4 Å resolution from a tetragonal form of crystal using a home X-ray source.
doi:10.1107/S1744309108017545
PMCID: PMC2443977  PMID: 18607105
allene oxide synthase; cytochrome P450 CYP74A2; oxylipin; jasmonate; guayule (Parthenium argentatum); crystallization
16.  Vocal correlates of sender-identity and arousal in the isolation calls of domestic kitten (Felis silvestris catus) 
Frontiers in Zoology  2012;9:36.
Introduction
Human speech does not only communicate linguistic information but also paralinguistic features, e.g. information about the identity and the arousal state of the sender. Comparable morphological and physiological constraints on vocal production in mammals suggest the existence of commonalities encoding sender-identity and the arousal state of a sender across mammals. To explore this hypothesis and to investigate whether specific acoustic parameters encode for sender-identity while others encode for arousal, we studied infants of the domestic cat (Felis silvestris catus). Kittens are an excellent model for analysing vocal correlates of sender-identity and arousal. They strongly depend on the care of their mother. Thus, the acoustical conveyance of sender-identity and arousal may be important for their survival.
Results
We recorded calls of 18 kittens in an experimentally-induced separation paradigm, where kittens were spatially separated from their mother and siblings. In the Low arousal condition, infants were just separated without any manipulation. In the High arousal condition infants were handled by the experimenter. Multi-parametric sound analyses revealed that kitten isolation calls are individually distinct and differ between the Low and High arousal conditions. Our results suggested that source- and filter-related parameters are important for encoding sender-identity, whereas time-, source- and tonality-related parameters are important for encoding arousal.
Conclusion
Comparable findings in other mammalian lineages provide evidence for commonalities in non-verbal cues encoding sender-identity and arousal across mammals comparable to paralinguistic cues in humans. This favours the establishment of general concepts for voice recognition and emotions in humans and animals.
doi:10.1186/1742-9994-9-36
PMCID: PMC3551667  PMID: 23259698
Affect-intensity; Individual signature; Infant; Mammal; Cat; Vocalisation
17.  Crystallization and initial X-ray diffraction studies of the flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from the soil bacterium Paracoccus denitrificans  
The flavin-dependent enzyme FerB from P. denitrificans has been purified and both native and SeMet-substituted FerB have been crystallized. The two variants crystallized in two different crystallographic forms belonging to the monoclinic space group P21 and the orthorhombic space group P21212, respectively. X-ray diffraction data were collected to 1.75 Å resolution for both forms.
The flavin-dependent enzyme FerB from Paracoccus denitrificans reduces a broad range of compounds, including ferric complexes, chromate and most notably quinones, at the expense of the reduced nicotinamide adenine dinucleotide cofactors NADH or NADPH. Recombinant unmodified and SeMet-substituted FerB were crystallized under similar conditions by the hanging-drop vapour-diffusion method with microseeding using PEG 4000 as the precipitant. FerB crystallized in several different crystal forms, some of which diffracted to approximately 1.8 Å resolution. The crystals of native FerB belonged to space group P21, with unit-cell parameters a = 61.6, b = 110.1, c = 65.2 Å, β = 118.2° and four protein molecules in the asymmetric unit, whilst the SeMet-substituted form crystallized in space group P21212, with unit-cell parameters a = 61.2, b = 89.2, c = 71.5 Å and two protein molecules in the asymmetric unit. Structure determination by the three-wavelength MAD/MRSAD method is now in progress.
doi:10.1107/S1744309110005099
PMCID: PMC2852337  PMID: 20383015
flavoenzymes; quinone reductases; Paracoccus denitrificans
18.  An Autosomal Genetic Linkage Map of the Domestic Cat, Felis silvestris catus 
Genomics  2008;93(4):305-313.
We report on the completion of an autosomal genetic linkage (GL) map of the domestic cat (Felis silvestris catus). Unlike two previous linkage maps of the cat constructed with a hybrid pedigree between the domestic cat and the Asian leopard cat, this map was generated entirely with domestic cats, using a large multi-generational pedigree (n=256) maintained by the Nestlé Purina PetCare Company. Four hundred eighty-three simple tandem repeat (STR) loci have been assigned to linkage groups on the cat’s 18 autosomes. A single linkage group spans each autosome. The length of the cat map, estimated at 4370 cM, is long relative to most reported mammalian maps. A high degree of concordance in marker order was observed between the third-generation map and the 1.5 Mb-resolution radiation hybrid (RH) map of the cat. Using the cat 1.9X whole-genome sequence, we identified map coordinates for 85#x00025; of the loci in the cat assembly, with high concordance observed in marker order between the linkage map and the cat sequence assembly. The present version represents a marked improvement over previous cat linkage maps as it (i) nearly doubles the number of markers that were present in the second-generation linkage map in the cat, (ii) provides a linkage map generated in a domestic cat pedigree which will more accurately reflect recombination distances than previous maps generated in a hybrid pedigree, and (iii) provides single linkage groups spanning each autosome. Marker order was largely consistent between this and the previous maps, though the use of a hybrid pedigree in the earlier versions appears to have contributed to some suppression of recombination. The improved linkage map will provide an added resource for the mapping of phenotypic variation in the domestic cat and the use of this species as a model system for biological research.
doi:10.1016/j.ygeno.2008.11.004
PMCID: PMC2656606  PMID: 19059333
Domestic cat; Genetic linkage map; STRs; microsatellites
19.  Cats of the Pharaohs: Genetic Comparison of Egyptian Cat Mummies to their Feline Contemporaries 
Journal of archaeological science  2012;39(10):3217-3223.
The ancient Egyptians mummified an abundance of cats during the Late Period (664 - 332 BC). The overlapping morphology and sizes of developing wildcats and domestic cats confounds the identity of mummified cat species. Genetic analyses should support mummy identification and was conducted on two long bones and a mandible of three cats that were mummified by the ancient Egyptians. The mummy DNA was extracted in a dedicated ancient DNA laboratory at the University of California – Davis, then directly sequencing between 246 and 402 bp of the mtDNA control region from each bone. When compared to a dataset of wildcats (Felis silvestris silvestris, F. s. tristrami, and F. chaus) as well as a previously published worldwide dataset of modern domestic cat samples, including Egypt, the DNA evidence suggests the three mummies represent common contemporary domestic cat mitotypes prevalent in modern Egypt and the Middle East. Divergence estimates date the origin of the mummies’ mitotypes to between two and 7.5 thousand years prior to their mummification, likely prior to or during Egyptian Predyanstic and Early Dynastic Periods. These data are the first genetic evidence supporting that the ancient Egyptians used domesticated cats, F. s. catus, for votive mummies, and likely implies cats were domesticated prior to extensive mummification of cats.
doi:10.1016/j.jas.2012.05.005
PMCID: PMC3426309  PMID: 22923880
ancient DNA; Felis silvestris catus; mitochondrial; control region; domestication
20.  The Genetic Integrity of the Ex Situ Population of the European Wildcat (Felis silvestris silvestris) Is Seriously Threatened by Introgression from Domestic Cats (Felis silvestris catus) 
PLoS ONE  2014;9(8):e106083.
Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction.
doi:10.1371/journal.pone.0106083
PMCID: PMC4146591  PMID: 25162450
21.  Cloning, expression, purification, crystallization and preliminary X-ray analysis of the human RuvBL1–RuvBL2 complex 
A truncated variant of the human RuvBL1–RuvBL2 complex was cloned, expressed, purified and crystallised. Synchrotron diffraction data to 4 Å resolution were used to carry out a preliminary crystallographic analysis of the complex.
The complex of RuvBL1 and its homologue RuvBL2, two evolutionarily highly conserved eukaryotic proteins belonging to the AAA+ (ATPase associated with diverse cellular activities) family of ATPases, was co-expressed in Escherichia coli. For crystallization purposes, the flexible domains II of RuvBL1 and RuvBL2 were truncated. The truncated RuvBL1–RuvBL2 complex was crystallized using the hanging-drop vapour-diffusion method at 293 K. The crystals were hexagonal-shaped plates and belonged to either the orthorhombic space group C2221, with unit-cell parameters a = 111.4, b = 188.0, c = 243.4 Å and six monomers in the asymmetric unit, or the monoclinic space group P21, with unit-cell parameters a = 109.2, b = 243.4, c = 109.3 Å, β = 118.7° and 12 monomers in the asymmetric unit. The crystal structure could be solved by molecular replacement in both possible space groups and the solutions obtained showed that the complex forms a dodecamer.
doi:10.1107/S174430910802558X
PMCID: PMC2531268  PMID: 18765919
RuvBL1; RuvBL2; ATPases
22.  Angiostrongylus chabaudi Biocca, 1957: a new parasite for domestic cats? 
Parasites & Vectors  2014;7(1):588.
Background
Natural infection with a species of Angiostrongylus has been reported only once in wildcats from central Italy by Biocca in 1957. The causative species of this infection was identified as Angiostrongylus chabaudi. Following this report, this parasite had never been found in either wild or domestic cats.
Findings
The lungs and the pulmonary arteries of an adult female cat (Felis silvestris catus), road-killed in Sardinia, Italy, were macroscopically examined and dissected under a light microscope for the presence of parasites. A slender nematode was detected and its morphometrical features were consistent with those of A. chabaudi. Morphological data were supplemented by sequencing of the partial cytochrome oxidase c subunit 1 (cox1) gene, as well as the internal transcribed spacer 2 (ITS2) of the rDNA. Nucleotide sequences displayed 99% homology with the ITS2 sequence [GenBank KM216825.1] of a specimen of Angiostrongylus sp. recovered recently from the pulmonary artery of a wildcat in Germany and 91% with cox1 sequence [GenBank GU138118.1] of Angiostrongylus vasorum.
Conclusion
The results of the present study indicate, for the first time, that A. chabaudi may also infect domestic cats, and thus should be considered in the diagnosis of metastrongyloid species infecting their cardio-pulmonary system.
doi:10.1186/s13071-014-0588-1
PMCID: PMC4308007  PMID: 25515026
Angiostrongylus chabaudi; Metastrongyloidea; Angiostrongylidae; Cat; Cardio-pulmonary nematodes
23.  Crystallization and preliminary X-ray diffraction analysis of the peptidylprolyl isomerase Par27 of Bordetella pertussis  
Par27 from B. pertussis, the prototype of a new group of parvulins has been crystallized in two different crystal forms.
Proteins with both peptidylprolyl isomerase (PPIase) and chaperone activities play a crucial role in protein folding in the periplasm of Gram-negative bacteria. Few such proteins have been structurally characterized and to date only the crystal structure of SurA from Escherichia coli has been reported. Par27, the prototype of a new group of parvulins, has recently been identified. Par27 exhibits both chaperone and PPIase activities in vitro and is the first identified parvulin protein that forms dimers in solution. Par27 has been expressed in E. coli. The protein was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. Form A, which belongs to space group P2 (unit-cell parameters a = 42.2, b = 142.8, c = 56.0 Å, β = 95.1°), diffracts to 2.8 Å resolution, while form B, which belongs to space group C222 (unit-cell parameters a = 54.6, b = 214.1, c = 57.8 Å), diffracts to 2.2 Å resolution. Preliminary diffraction data analysis agreed with the presence of one monomer in the asymmetric unit of the orthorhombic crystal form and two in the monoclinic form.
doi:10.1107/S1744309108024731
PMCID: PMC2531267  PMID: 18765910
peptidylprolyl isomerases; Par27; parvulins; Bordetella pertussis
24.  Expression, crystallization and preliminary X-ray analysis of a ferric binding protein from Thermus thermophilus HB8 
The cloning, expression, purification, crystallization and preliminary X-ray analysis of a ferric binding protein encoded by T. thermophilus HB8 in apo and iron-bound holo states are presented. Four different crystal forms were obtained.
A ferric binding protein from Thermus thermophilus HB8 (TtFbpA) was expressed, purified and crystallized using the hanging-drop vapour-diffusion method. Four different crystal forms were obtained and characterized by X-ray diffraction. Two crystal forms with TtFbpA in the apo state belonged to the orthorhombic space group P212121 (unit-cell parameters a = 42.1, b = 139.3, c = 326.5 Å and a = 42.1, b = 139.3, c = 218.9 Å). The third form with TtFbpA also in the apo state belonged to the monoclinic space group P21 (unit-cell parameters a = 66.5, b = 61.7, c = 73.9 Å, β = 111.7°). The fourth form, with TtFbpA in the iron-bound holo state as confirmed by an atomic absorption spectrophotometry assay, belonged to the trigonal space group P3121 or P3221 (unit-cell parameters a = 63.6, b = 63.6, c = 266.7 Å, α = β = 90.0, γ = 120.0°).
doi:10.1107/S1744309111012929
PMCID: PMC3107153  PMID: 21636922
ferric binding protein; Thermus thermophilus HB8; apo state; iron-bound holo state
25.  Superoxide reductase from Nanoarchaeum equitans: expression, purification, crystallization and preliminary X-ray crystallographic analysis 
Diffraction-quality crystals of N. equitans neelaredoxin have been produced. The expression, purification and crystallization of the protein and preliminary X-ray crystallographic analysis of the crystals are reported.
Superoxide reductases (SORs) are the most recent oxygen-detoxification system to be identified in anaerobic and microaerobic bacteria and archaea. SORs are metalloproteins that are characterized by their possession of a catalytic nonhaem iron centre in the ferrous form coordinated by four histidine ligands and one cysteine ligand. Ignicoccus hospitalis, a hyperthermophilic crenarchaeon, is the only organism known to date to serve as a host for Nanoarchaeum equitans, a nanosized hyperthermophilic archaeon isolated from a submarine hot vent which completely depends on the presence of and contact with I. hospitalis cells for growth to occur. Similarly to I. hospitalis, N. equitans has a neelaredoxin (a 1Fe-type SOR) that keeps toxic oxygen species under control, catalysing the one-electron reduction of superoxide to hydrogen peroxide. Blue crystals of recombinant N. equitans SOR in the oxidized form (12.7 kDa, 109 residues) were obtained using polyethylene glycol (PEG 2000 MME) as precipitant. These crystals diffracted to 1.9 Å resolution at 100 K and belonged to the orthorhombic space group P212121, with unit-cell parameters a = 51.88, b = 82.01, c = 91.30 Å. Cell-content analysis suggested the presence of four monomers in the asymmetric unit. The Matthews coefficient (V M) was determined to be 1.9 Å3 Da−1, corresponding to an estimated solvent content of 36%. Self-rotation function and native Patterson calculations suggested a tetramer with 222 point-group symmetry, similar to other 1Fe-SORs. The three-dimensional structure will be determined by the molecular-replacement method.
doi:10.1107/S1744309111009432
PMCID: PMC3087648  PMID: 21543869
superoxide reductases; Nanoarchaeum equitans; oxidative stress; neelaredoxins

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