bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptomic analyses support the similarity of gene expression between brain and testis in human as well as mouse
Authors: Guo J.H. , Huang Q. , Studholme D.J. , Wu C.Q. , Zhao Z
Published: August 2005

We previously revealed similarity in gene expression patterns between human brain and testis, based on digital differential display analyses of 760 human Unigenes. In the present work, we reanalyzed the gene expression data in many tissues of human and mouse for a large number of genes almost covering the respective whole genomes. The results indicated that both in human and in mouse, the gene expression profiles exhibited by brain, cerebellum and testis are most similar to each other compared with other tissues.
Analysis of the genomic region containing the tammar wallaby (Macropus eugenii) orthologues of MHC class III genes
Authors: Cross J.G.R. , Harrison G.A. , Coggill P. , Sims S. , Beck S. , Deakin J.E. , Marshall Graves J.A.
Published: August 2005

Major histocompatibility complex (MHC) molecules are central to development and regulation of the immune system in all jawed vertebrates. MHC class III cytokine genes from the tumor necrosis factor core family, including tumor necrosis factor (TNF) and lymphotoxin alpha and beta (LTA, LTB), are well studied in human and mouse. Orthologues have been identified in several other eutherian species and the cDNA sequences have been reported for a model marsupial, the tammar wallaby. Comparative genomics can help to determine gene function, to understand the evolution of a gene or gene family, and to identify potential regulatory regions. We therefore cloned the genomic region containing the tammar LTB, TNF, and LTA orthologues by “genome walking”, using primers designed from known tammar sequences and regions conserved in other species. We isolated two tammar BAC clones containing all three genes. These tammar genes show similar intergenic distances and the same transcriptional orientation as in human and mouse. Gene structures and sequences are also very conserved. By comparing the tammar, human and mouse genomic sequences we were able to identify candidate regulatory regions for these genes in mammals. Full length sequencing of BACs containing the three genes has been partially completed, and reveals the presence of a number of other tammar MHC III orthologues in this region.
Chromosomal localization of seven HSA3q13→q23 NotI linking clones on chicken microchromosomes: orthology of GGA14 and GGA15 to a gene-rich region of HSA3
Authors: Sazanov A.A. , Sazanova A.L. , Stekol’nikova V.A. , Kozyreva A.A. , Romanov M.N. , Malewski T. , Smirnov A.F.
Published: August 2005

Double-color fluorescence in situ hybridization was performed on chicken chromosomes using seven unique clones from the human chromosome 3-specific NotI linking libraries. Six of them (NL1-097, NL2-092, NL2-230, NLM-007, NLM-118, and NLM-196) were located on the same chicken microchromosome and NL1-290 on another. Two chicken microchromosome GGA15-specific BAC clones, JE024F14 containing the IGVPS gene and JE020G17 containing the ALDH1A1 gene, were cytogenetically mapped to the same microchromosome that carried the six NotI linking clones, allowing identification of this chromosome as GGA15. Two GGA14-specific clones, JE027C23 and JE014E08 containing the HBA gene cluster, were co-localized on the same microchromosome as NL1-290, suggesting that this chromosome was GGA14. The results indicated that the human chromosomal region HSA3q13→q23 is likely to be orthologous to GGA15 and GGA14. The breakpoint of evolutionary conservation of human and chicken chromosomes was detected on HSA3q13.3→q23 between NL1-290, on the one hand, and six other NotI clones, on the other hand. Considering the available chicken-human comparative mapping data, another breakpoint appears to exist between the above NotI loci and four other genes, TFRC, EIF4A2, SKIL and DHX36 located on HSA3q24→qter and GGA9. Based on human sequences within the NotI clones, localization of the six new chicken coding sequences orthologous to the human/rodent genes was suggested to be on GGA15 and one on GGA14. Microchromosomal location of seven NotI clones from the HSA3q21 T-band region can be considered as evidence in support of our hypothesis about the functional analogy of mammalian T-bands and avian microchromosomes.
Expanded comparative mapping between man and rabbit and detection of a new conserved segment between HSA22 and OCU4
Authors: Chantry-Darmon C. , Bertaud M. , Urien C. , Chadi-Taourit S. , Perrocheau M. , Rogel-Gaillard C. , Hayes H.
Published: August 2005

Rabbit, a domestic species exploited both in animal production and medical research has only recently begun to be included in gene mapping projects, in particular by the French National Institute of Agronomics. By 2002, less than 60 genes had been precisely localised on rabbit chromosomes, which led us to start a large-scale project on gene mapping in rabbit with the publication of 133 gene localisations in 2003 (Chantry-Darmon et al., 2003). Here, we report the localisation of 102 new genes resulting in good coverage of the rabbit genome and an eight-fold enrichment of the gene map. In addition, we have detected a new conserved segment between rabbit chromosome 4q15.3 and part of human chromosome 22 and thus improved the comparative map with the human genome.
The canine sarcoglycan delta gene: BAC clone contig assembly, chromosome assignment and interrogation as a candidate gene for dilated cardiomyopathy in Dobermann dogs
Authors: Stabej P. , Leegwater P.A.J. , Imholz S. , Versteeg S.A. , Zijlstra C. , Stokhof A.A. , Domanjko-Petriè A. , van Oost B.A.
Published: August 2005

Dilated cardiomyopathy (DCM) is a common disease of the myocardium recognized in human, dog and experimental animals. Genetic factors are responsible for a large proportion of cases in humans, and 17 genes with DCM causing mutations have been identified. The genetic origin of DCM in the Dobermann dogs has been suggested, but no disease genes have been identified to date. In this paper, we describe the characterization and evaluation of the canine sarcoglycan delta (SGCD), a gene implicated in DCM in human and hamster. Bacterial artificial chromosomes (BACs) containing the canine SGCD gene were isolated with probes for exon 3 and exons 4–8 and were characterized by Southern blot analysis. BAC end sequences were obtained for four BACs. Three of the BACs overlapped and could be ordered relative to each other and the end sequences of all four BACs could be anchored on the preliminary assembly of the dog genome sequence (www. ensembl.org). One of the BACs of the partial contig was localized by fluorescent in situ hybridization to canine chromosome 4q22, in agreement with the dog genome sequence. Two highly informative polymorphic microsatellite markers in intron 7 of the SGCD gene were identified. In 25 DCM-affected and 13 non DCM-affected dogs seven different haplotypes could be distinguished. However, no association between any of the SGCD variants and the disease locus was apparent.
Cytogenetic comparison of saola (Pseudoryx nghetinhensis) and cattle (Bos taurus) using G- and Q-banding and FISH
Authors: Ahrens E. , Graphodatskaya D. , Nguyen B.X. , Stranzinger G.
Published: August 2005

In order to cytogenetically describe the new bovid species saola (Pseudoryx nghetinhensis), comparative G- and Q-banding of saola and cattle (Bos taurus) chromosomes as well as FISH-mapping of 32 type-I markers (29 Texas markers and three additional markers) on saola chromosomes were performed. Saola was shown to have a diploid number of 2n = 50 chromosomes possessing five biarmed autosomal pairs and an acrocentric X chromosome. Homology of saola and cattle chromosomes was indicated by banding patterns and by marker hybridization suggesting that all five biarmed pairs in saola originate from centric fusions involving ten cattle autosomes. However, small intrachromosomal rearrangements cannot be excluded. In this study the first preliminary homology map of these two species is presented.
Karyotypic evolution and organization of the highly repetitive DNA sequences in the Japanese shrew-moles, Dymecodon pilirostris and Urotrichus talpoides
Authors: Nakata A. , Yoshimura A. , Kuro-o M. , Obara Y.
Published: August 2005

The karyological relationship and organization of highly repetitive DNA sequences in Japanese shrew-moles were studied by zoo-blot hybridization and fluorescence in situ hybridization (FISH). When the genomic DNA of the eastern race of Urotrichus talpoides was digested with PstI, three fragments of highly repetitive DNA sequences, approximately 0.7, 0.9, and 1.4 kb in length, were observed as distinct bands. The results of FISH in the eastern race of U. talpoides using these three fragments separately as probes showed that the 0.7-kb PstI fragment was distributed in the centromeric regions of most chromosomes, and that the 0.9- and 1.4-kb fragments were predominantly located in the C-heterochromatin region of chromosome 13p. Although the western race of U. talpoides also had three PstI fragments, 0.9- and 1.4-kb PstI fragments were more ambiguous than those of the eastern race. The PstI- digested genomic DNA in Dymecodonpilirostris produced only a faint 0.9-kb band, and its signal patterns obtained by zoo-blot hybridization were clearly different from those of U. talpoides. The 0.7-kb fragment of U. talpoides hybridized strongly with the 0.9-kb fragment of D. pilirostris. In a FISH analysis, the 0.9-kb fragment of D. pilirostris hybridized with highly repetitive DNA in the centromeric regions of most chromosomes from both D. pilirostris and U. talpoides. Zoo-blot hybridization and FISH analyses suggest that the 0.9- and 1.4-kb PstI fragments were generated specifically in the genome of U. talpoides after the common ancestor differentiated into two extant shrew-mole species. A difference in the length of the centromeric elements between U. talpoides and D. pilirostris might be observed due to certain modifications of the repeating unit.
Heterochromatin differentiation shows the pathways of karyotypic evolution in Israeli mole rats (Spalax, Spalacidae, Rodentia)
Authors: Ivanitskaya E. , Belyayev A. , Nevo E.
Published: August 2005

C-banding, base-specific fluorochrome staining (CMA3/DA/DAPI), and comparative genomic hybridization (CGH) were used to analyze the constitutive heterochromatin in two Israeli Spalax species, S. galili (2n = 52) and S. judai (2n = 60). It was shown that C-positive centromeric heterochromatin and some telomeric sites comprise GC-rich DNA sequences in both species. Comparative genomic in situ hybridization revealed slight qualitative differences in highly repetitive sequences in the two Spalax species. Eight acrocentric pairs in S. judai that are involved in Robertsonian rearrangements, possessed composite heterochromatin with a preference of S. judai highly repetitive sequences in the proximal region. Heterochromatin of the sex chromosomes, two biarmed homologous pairs (4 and 5) in both species, and acrocentric chromosomes from the group with a variable centromere position in S. judai was entirely species-specific. The high level of homology in the composition of heterochromatin may relate to the recent divergence of Israeli Spalax. Interspecies heterochromatin differences are discussed in the context of possible mechanisms in the Spalax chromosome evolution.
Three cases with rare interstitial rearrangements of chromosome 1 characterized by multicolor banding
Authors: Polityko A. , Starke H. , Rumyantseva N. , Claussen U. , Liehr T. , Raskin S.
Published: August 2005

In this report, we describe three unrelated patients with similar symptoms such as mental retardation, growth delay and multiple phenotypic abnormalities. GTG-banding analysis revealed karyotypes with add(1p) in two cases and an add(1q) in the third. Fluorescence in situ hybridization (FISH) analysis using high resolution multicolor banding (MCB) characterized the aberrations of the abnormal chromosomes 1 as a (sub)terminal duplication and inverted duplications, respectively. Although three different chromosomal regions i.e. 1p36.1, 1p36.2→1p31.3 and 1q41→1q44 were involved, all three patients had similar patterns of dysmorphic findings. These cases demonstrate the power of MCB in the characterization of small interstitial chromosomal aberrations and resulted in the characterization of three previously unreported congenital chromosome 1 rearrangements.
Molecular cytogenetic characterization of ring chromosome 4 in a female having a chromosomally normal child
Authors: Lee M.-H. , Park S.-Y. , Kim Y.-M. , Kim J.-M. , Yoo K.-J. , Lee H.-H. , Ryu H.-M.
Published: August 2005

We present the clinical and molecular findings of mosaic ring chromosome 4. The patient was referred to us for infertility and short stature. Results of three repeated cytogenetic analyses from lymphocytes showed a similar mosaic karyotype with multiple cell-lines [46,XX,r(4)/45,XX,–4/46,XX,dic r(4)/47,XX,r(4),+r(4)/46,XX]. FISH showed deletion of the 4p subtelomeric region and the 4q telomeric region from the ring chromosome 4. The breakpoints were mapped using molecular analysis. Parental karyotypes were normal. During the course of this study, the patient became pregnant without assisted reproductive technology. The result of amniocentesis performed at 16 weeks gestation showed a normal karyotype. Delivery was uncomplicated. This is the first report, to our knowledge, of the presence of ring chromosome 4 having various mosaic conditions in a female having a chromosomally normal fetus.
Pure trisomy 19p syndrome in an infant with an extra ring chromosome
Authors: Novelli A. , Ceccarini C. , Bernardini L. , Zuccarello D. , Digilio M.C. , Mingarelli R. , Dallapiccola B.
Published: August 2005

We report a 12-month-old infant evaluated for severe hypotonia, psychomotor retardation, and facial dysmorphisms, including round face, high prominent forehead, downward slanted palpebral fissures, hypertelorism, short nose, chubby cheeks, long philtrum, anteverted lower lip, low-set asymmetric and dysmorphic ears. Karyotype analysis disclosed an extra mosaic ring chromosome, which included the whole 19p arm. Four additional patients with supernumerary ring 19 chromosomes have been reported, but none of them had pure trisomy 19p.
Expression of Interleukin-16 in Allergic Rhinitis
Authors: Karaki Masayuki , Dobashi Hiroaki , Kobayashi Ryuichi , Tokuda Michiaki , Ishida Toshihiko , Mori Nozomu
Published: August 2005

Background: Interleukin-16 (IL-16) has been characterized as a chemoattractant for a variety of CD4+ T cells. Several inflammatory diseases, including allergic disorders, have been reported to correlate with IL-16. We first examined the IL-16 expression of serum and mucosal tissue in patients with allergic rhinitis. Methods: Forty-eight patients with a clinical history of house dust mite (HDM) or pollen-sensitive allergic rhinitis were included in this study. Serum IL-16 was analyzed by enzyme-linked immunosorbent assay (ELISA). IL-16 expression of nasal mucosa was detected by immunohistochemistry. Results: IL-16 levels were elevated in the serum of patients with allergic rhinitis compared with normal controls. In particular, serum IL-16 levels in HDM-sensitive patients were higher than those in pollen-sensitive patients. IL-16 was significantly correlated with eosinophils in the peripheral blood of allergic rhinitis patients. Histologically, IL-16 was expressed in infiltrated lymphocytes and nasal gland cells. Conclusions: Our data indicate that one of the sources of elevated serum IL-16 in allergic patients may be gland cells and lymphocytes in allergic nasal mucosa. This IL-16 cytokine may be strongly associated with the developmental mechanism of allergic rhinitis.
Historical Descriptions of Multiple Sclerosis
Authors: Pearce J.M.S.
Published: August 2005

Modern understanding of multiple sclerosis is firmly founded on the labours of many neuroscientists of the last two centuries. The cost of the disease to its victims is nowhere better displayed than in their personal accounts of their illnesses. Two figures stand out: the high-born aristocrat, Augustus D’Este and his diaries of the early 19th century and the courageous if histrionic Bruce Frederick Cummings in the early 20th century. This paper cannot do justice to their major contributions, but seeks to summarise them to give the flavour of their symptoms, disabilities and the way they were regarded by doctors and the people at large. The early medical studies of Carswell, Cruveilhier, Charcot and many others are briefly reviewed as relevant settings to these personal histories.
Iron Stores Modulate Hepatic Hepcidin Expression by an HFE-Independent Pathway
Authors: Gehrke Sven G. , Herrmann Thomas , Kulaksiz Hasan , Merle Uta , Bents Karin , Kaiser Iris , Riedel Hans-Dieter , Stremmel Wolfgang
Published: August 2005

Background/Aims: In HFE-related hereditary hemochromatosis an inappropriately low hepatic expression of the iron-regulatory peptide hepcidin (encoded by HAMP) has been suggested to cause iron overload. The aim of the present study was to evaluate whether the hepatic expression of HAMP in relation to iron stores requires HFE or might involve other important iron-related genes including HJV (encoding hemojuvelin) and TFR2 (encoding transferrin receptor-2). Methods: Using quantitative RT-PCR, the iron-dependent hepatic expression patterns of HAMP, HJV, and TFR2 were evaluated in human and murine HFE-related hemochromatosis. Results: The overall level of hepatic HAMP expression in human and murine HFE-related hemochromatosis is impaired but can still be modulated by iron stores. Moreover, we demonstrate an HFE-independent correlation between the expression of HAMP and TFR2 in mouse and human livers. On the other hand, a strong correlation between the hepatic expression of HAMP and HJV was only found in hemochromatosis patients and Hfe-deficient mice. Conclusion: The central pathogenetic step in HFE-related hemochromatosis is an impaired basal expression of HAMP rather than a lack of HAMP upregulation in response to iron stores. An HFE-independent pathway that seems to involve TFR2 and HJV can regulate HAMP expression under conditions of iron overload.
Tacrolimus and Cyclosporinein vitro and in vivo Induce Osteopontin mRNA and Protein Expression in Renal Tissues
Authors: Khanna Ashwani
Published: August 2005

The mechanism of immunosuppression-linked nephrotoxicity in organ transplantation remains to be solved. Expression of osteopontin (OPN), a multifunctional secreted glycoprotein, has been associated with various forms of renal injuries. In this study, using in vitro and in vivo models, we examined the effects of cyclosporine (CsA) and tacrolimus (TAC) on OPN mRNA and protein expression. We also examined if CsA- and TAC-induced OPN expression is dependent on transforming growth factor (TGF)-β expression. For in vivo experiments mice and rats were injected with CsA (25 mg/kg) and TAC (0.2 mg/kg). For in vitro experiments, human proximal tubular epithelial (PTE) cells were treated with CsA and TAC for 4 h. To study the in vivo effect of TGF-β on OPN mRNA, mice were injected with recombinant TGF-β protein (3 mg/kg). The expression of OPN was also studied in CsA-treated PTE cells with and without anti-TGF-β antibody. At the end of in vitro and in vivo treatments, RNA was isolated from kidney tissue and renal cells reverse transcribed to cDNA and amplified for OPN mRNA. Using immunochemistry and Western blot analysis OPN protein expression was also studied in vivo and in vitro, respectively. Both in vitro and in vivo treatment with CsA and TAC resulted in significantly increased OPN mRNA and protein expression. TGF-β treatment in vivo also resulted in a significantly increased OPN mRNA expression and anti-TGF-β antibody but not the control antibody in vivo in CsA-treated mice, and in vitro in CsA-treated PTE cells inhibited OPN mRNA expression. OPN may contribute to the CsA- and TAC-induced nephrotoxicity in organ transplant recipients and the increased OPN expression might be mediated by TGF-β.
Tyrosine phosphorylation and the small GTPase rac cross-talk in regulation of endothelial barrier function
Authors: Seebach Jochen , Mädler Hans-Jürgen , Wojciak-Stothard Beata , Schnittler Hans-Joachim
Published: August 2005

Endothelial barrier function depends on the integrity of intercellular adherens junctions controlled by the association of VEcadherin/ catenin complex with cortical actin filaments. Both tyrosine phosphorylation/dephosphorylation of junctional proteins and actin reorganization mediated by rho-GTPases regulate barrier function but the relationship between these regulatory mechanisms is unclear. Here we studied the effects of factors increasing protein tyrosine phosphorylation, pervanadate (PV) and VEGF, on distribution of VE-cadherin, F-actin polymerization and transendothelial electrical resistance (TER) in human umbilical vein endothelial cells (HUVECs). Changes in protein tyrosine phosphorylation of cytoplasmic and junctional proteins, as well as the activity of rho-GTPase rac1, were also measured. We report for the first time that PV and VEGF induced a rapid transient increase in endothelial barrier function accompanied by rac1 activation, a differentiated tyrosine phosphorylation of theVE-cadherin/catenin complex, recruitment of actin filament to cell junctions and ruffle formation. A sustained decrease in endothelial barrier function was observed at later times of PV and VEGF treatment. Expression of dominant negative rac1, N17rac1 abolished the barrier-enhancing effects of PV andVEGF, while the sustained decrease in barrier function was unaffected. These observations bring into focus early shortterm effects of protein tyrosine phosphorylation in cells, often overshadowed by more pronounced and long-lasting later effects and may play an important role in the regulation of endothelial barrier function.
Clopidogrel inhibits platelet-leukocyte adhesion and plateletdependent leukocyte activation
Authors: Manarini Stefano , Dell’Elba Giuseppe , Martelli Nicola , Napoleone Emanuela , Santo Angelomaria Di , Savi Pierre , Lorenzet Roberto , Evangelista Virgilio
Published: August 2005

Clopidogrel is considered to be an important therapeutic advance in anti-platelet therapy. We investigated whether inhibition by clopidogrel results in a reduced capacity of platelets to adhere and stimulate pro-atherothrombotic and inflammatory functions in polymorphonuclear leukocytes (PMN) and in monocytes (MN). An eventual effect on these processes could further substantiate anti-atherothrombotic properties of this drug. The effects of clopidogrel or of its active metabolite were investigated on ADP or thrombin receptor-induced platelet activation and on platelet-leukocyte interactions ex vivo in the mouse or in vitro in isolated human cells or whole blood, respectively. Clopidogrel inhibited platelet aggregation, expression of P-selectin, platelet-PMN adhesion and platelet-dependent ROS production in mouse PMN. Similarly pretreatment of human platelets with the active metabolite of clopidogrel in vitro resulted in a profound inhibition of platelet P-selectin expression, platelet-PMN adhesion and production of ROS by PMN. Pretreatment with the active metabolite of clopidogrel significantly impaired the ability of platelets to up-regulate the expression of TF procoagulant activity in MN, in a washed cell system. Moreover, the active metabolite of clopidogrel inhibited rapidTF exposure on platelet as well as on leukocyte surfaces in whole blood. By reducing platelet-dependent up-regulation of inflammatory and pro-atherothrombotic functions in leukocytes, clopidogrel may reduce inflammation that underlies the chronic process of atherosclerosis and its acute complications.
Rates of proximal deep vein thrombosis as assessed by compression ultrasonography in patients receiving prolonged thromboprophylaxis with low molecular weight heparin after major orthopedic surgery
Authors: Hesselschwerdt Hans-Jürgen , Dieter Paar W. , von Hanstein Karl-Ludwig , Schellong Sebastian
Published: August 2005

Patients undergoing major orthopedic surgery are at an increased risk of thromboembolism even after the acute postoperative phase. Therefore, prolonged thromboprophylaxis is currently recommended and widely used. The length of hospital stay after major orthopedic surgery is steadily decreasing and most patients are transferred to specialized rehabilitation centers in the early postoperative phase. Consequently, thromboprophylaxis is usually given during the rehabilitation period. Previously there have been no systematic studies of how many patients with asymptomatic thrombosis are transferred to a rehabilitation center or how many patients develop deep vein thrombosis (DVT) during rehabilitation. In the present study, 238 patients who had undergone major orthopedic surgery were examined by compression ultrasonography on day 1 or 2 and on day 20 of their rehabilitation phase in order to detect asymptomatic proximal DVT. Sonograms were read centrally with blinding to the clinical course of the patients. All patients received standard thromboprophylaxis during the acute postoperative phase. Prolonged thromboprophylaxis with enoxaparin was given during the rehabilitation phase. The mean duration of thromboprophylaxis was 36.8 days. At admission to the rehabilitation center, proximal DVT was identified in 16 patients (6.7%). New proximal DVT at discharge from the rehabilitation center was identified in 3.2% of patients following prolonged thromboprophylaxis with enoxaparin. In conclusion, a considerable percentage of patients with asymptomatic proximal DVT are transferred to rehabilitation centers following major orthopedic surgery. Using prolonged thromboprophylaxis, new proximal DVTs will still develop during rehabilitation, but at a low rate.
Generation of genetically-altered mice producing very low levels of coagulation factor VII
Authors: Xu Haifeng , Liang Zhong , Martin J. Andrew , Suckow Mark , Castellino Francis J. , Rosen Elliot D.
Published: August 2005

It has been shown earlier that mice with a total targeted deletion of the factorVII gene (FVII-/-) die perinatally, thereby precluding study of adult animals with this total deficiency. Consequently, mice producing very low levels of FVII were developed by targeted replacement of the wild-type (WT) murine FVII gene with its corresponding cDNA, under control of the tetracycline transactivator (tTA) promoter. When backcrossed into the C57Bl/6 strain, unchallenged mice containing two replaced FVIItTA alleles (FVIItTA/tTA) produce approximately 0.7% of WT FVII levels, but yet live to adulthood despite displaying severely downregulated overall thrombin production and spontaneously developing cardiac fibrosis at a young adult age. This genetically- altered mouse line provides an excellent animal model to study consequences of a severe FVII deficiency in unchallenged mice and in mice subjected to a variety of experimental challenges.
The Impact of Ice Crystal Shapes, Size Distributions, and Spatial Structures of Cirrus Clouds on Solar Radiative Fluxes
Authors: Schlimme I. , Macke A. , Reichardt J.
Published: August 2005

The solar radiative properties of cirrus clouds depend on ice particle shape, size, and orientation, as well as on the spatial cloud structure. Radiation schemes in atmospheric circulation models rely on estimates of cloud optical thickness only. In the present work, a Monte Carlo radiative transfer code is applied to various cirrus cloud scenarios to obtain the radiative response of uncertainties in the above-mentioned microphysical and spatial cloud properties (except orientation). First, plane-parallel homogeneous (0D) clouds with different crystal shapes (hexagonal columns, irregular polycrystals) and 114 different size distributions have been considered. The resulting variabilities in the solar radiative fluxes are in the order of a few percent for the reflected and about 1% for the diffusely transmitted fluxes. Largest variabilities in the order of 10% to 30% are found for the solar broadband absorptance. However, these variabilities are smaller than the flux differences caused by the choice of ice particle geometries.

The influence of cloud inhomogeneities on the radiative fluxes has been examined with the help of time series of Raman lidar extinction coefficient profiles as input for the radiative transfer calculations. Significant differences between results for inhomogeneous and plane-parallel clouds were found. These differences are in the same order of magnitude as those arising from using extremely different crystal shapes for the radiative transfer calculations. From this sensitivity study, the ranking of cirrus cloud properties according to their importance in solar broadband radiative transfer is optical thickness, ice crystal shape, ice particle size, and spatial structure.
The Accuracy of Determining Three-Dimensional Radiative Transfer Effects in Cumulus Clouds Using Ground-Based Profiling Instruments
Authors: Pincus Robert , Hannay Cécile , Evans K. Franklin
Published: August 2005

Three-dimensional radiative transfer calculations are accurate, though computationally expensive, if the spatial distribution of cloud properties is known. The difference between these calculations and those using the much less expensive independent column approximation is called the 3D radiative transfer effect. Assessing the magnitude of this effect in the real atmosphere requires that many realistic cloud fields be obtained, and profiling instruments such as ground-based radars may provide the best long-term observations of cloud structure. Cloud morphology can be inferred from a time series of vertical profiles obtained from profilers by converting time to horizontal distance with an advection velocity, although this restricts variability to two dimensions. This paper assesses the accuracy of estimates of the 3D effect in shallow cumulus clouds when cloud structure is inferred in this way. Large-eddy simulations provide full three-dimensional, time-evolving cloud fields, which are sampled every 10 s to provide a “radar’s eye view” of the same cloud fields. The 3D effect for shortwave surface fluxes is computed for both sets of fields using a broadband Monte Carlo radiative transfer model, and intermediate calculations are made to identify reasons why estimates of the 3D effect differ in these fields. The magnitude of the 3D effect is systematically underestimated in the two-dimensional cloud fields because there are fewer cloud edges that cause the effect, while the random error in hourly estimates is driven by the limited sample observed by the profiling instrument.
The Relative Importance of Scavenging, Oxidation, and Ice-Phase Processes in the Production and Wet Deposition of Sulfate
Authors: Spiridonov Vlado , Curic Mladjen
Published: August 2005

The relative importance of various processes to sulfate production and wet deposition is examined by using a cloud-resolving model coupled with a sulfate chemistry submodel. Results using different versions of the model are then compared and principal differences with respect to their dynamics, microphysics, and chemistry are carefully discussed. The results imply that the dominant microphysical and chemical conversions of sulfate in the 3D run are nucleation, scavenging, and oxidation. Due to the lower cloud water and rainwater pH, oxidation does not contribute as significantly to the sulfate mass in the 2D run as the 3D.

Sensitivity tests have revealed that in-cloud scavenging in the 2D run for continental nonpolluted and continental polluted clouds accounted for 29.4% and 31.5% of the total sulfur deposited, respectively. The 3D run shows a lower percentage contribution to sulfur deposition for about 28.2% and 29.6%. In addition, subcloud scavenging for the 2D run contributed about 32.7% and 38.2%. In-cloud oxidation in the 2D run accounted for about 24.5% to 30.4% of the total sulfur mass deposited. Subcloud oxidation contributed from 21.0% to 20.6% of the total sulfur mass removed by wet deposition. In-cloud oxidation for the 3D run shows slightly lower percentage values when compared to those from the 2D run. The relative contribution of subcloud oxidation for continental nonpolluted and polluted clouds exceeds those values in the 2D run by approximately 7% and 10%, respectively. Ignoring the ice phase and considering those types of convective clouds in the 2D run may lead to a higher value of the total sulfur mass removed by the wet deposition of about 33.9% to 39.2% for the continental nonpolluted and 36.2% to 45.6% for the continental polluted distributions relative to the base runs.
Parameterizing the Difference in Cloud Fraction Defined by Area and by Volume as Observed with Radar and Lidar
Authors: Brooks Malcolm E. , Hogan Robin J. , Illingworth Anthony J.
Published: August 2005

Most current general circulation models (GCMs) calculate radiative fluxes through partially cloudy grid boxes by weighting clear and cloudy fluxes by the fractional area of cloud cover (Ca), but most GCM cloud schemes calculate cloud fraction as the volume of the grid box that is filled with cloud (Cυ). In this paper, 1 yr of cloud radar and lidar observations from Chilbolton in southern England, are used to examine this discrepancy. With a vertical resolution of 300 m it is found that, on average, Ca is 20% greater than Cυ, and with a vertical resolution of 1 km, Ca is greater than Cυ by a factor of 2. The difference is around a factor of 2 larger for liquid water clouds than for ice clouds, and also increases with wind shear. Using Ca rather than Cυ, calculated on an operational model grid, increases the mean total cloud cover from 53% to 63%, and so is of similar importance to the cloud overlap assumption.

A simple parameterization, Ca = [1 + e(−f )(C−1υ − 1)]−1, is proposed to correct for this underestimate based on the observation that the observed relationship between the mean Ca and Cυ is symmetric about the line Ca = 1 − Cυ. The parameter f is a simple function of the horizontal (H) and vertical (V) grid-box dimensions, where for ice clouds f = 0.0880 V 0.7696 H−0.2254 and for liquid clouds f = 0.1635 V 0.6694 H−0.1882.

Implementing this simple parameterization, which excludes the effect of wind shear, on an independent 6-month dataset of cloud radar and lidar observations, accounts for the mean underestimate of Ca for all horizontal and vertical resolutions considered to within 3% of the observed Ca, and reduces the rms error for each individual box from typically 100% to approximately 30%. Small biases remain for both weakly and strongly sheared cases, but this is significantly reduced by incorporating a simple shear dependence in the calculation of the parameter f, which also slightly improves the overall performance of the parameterization for all of the resolutions considered.
Prediction Rules for Regime Changes and Length in a New Regime for the Lorenz Model
Authors: Yadav Rama Shankar , Dwivedi Suneet , Mittal Ashok Kumar
Published: August 2005

Despite the widespread use of the Lorenz model as a conceptual model for predictability studies in meteorology, only Evans et al. seem to have studied the prediction of occurrence of regime changes and their duration. In this paper, simpler rules are presented for forecasting regime changes and their lengths, with near-perfect forecasting accuracy. It is found that when |x(t)| is greater than a critical value xc, the current regime will end after it completes the current orbit. Moreover, the length n of the new regime increases monotonically with the maximum value xm of |x(t)| in the previous regime. A best-fit cubic expression provides a very good estimate of n for the next regime, given xm for the previous regime.

Similar forecasting rules are also obtained for regime changes in the forced Lorenz model. This model was introduced by Palmer and used as a conceptual model to explore the effects of sea surface temperature on seasonal mean rainfall. It was found that for the forced Lorenz model, the critical value xc changed linearly with the forcing parameter providing bias to one of the regimes. Similar regime prediction rules have been found in some other two-regime attractors. It seems these forecasting rules are a generic property of a large class of two-regime attractors. Although as a conceptual model, the Lorenz model cannot be taken very literally, these results suggest a relationship between magnitudes of maximum anomaly in one regime, for example, the active spell, and duration of the subsequent break spell.
Zonal Momentum Budget of the Madden–Julian Oscillation: The Source and Strength of Equivalent Linear Damping
Authors: Lin Jia-Lin , Zhang Minghua , Mapes Brian
Published: August 2005

Linear, dissipative models with resting base states are sometimes used in theoretical studies of the Madden–Julian oscillation (MJO). Linear mechanical damping in such models ranges from nonexistent to strong, since an observational basis for its source and strength has been lacking. This study examines the zonal momentum budget of a composite MJO over the equatorial western Pacific region, constructed using filtering and regression techniques from 15 yr (1979–93) of daily global reanalysis data. Two different reanalyses (NCEP–NCAR and ERA-15) give qualitatively similar results for all major terms, including the budget residual, whose structure is consistent with its interpretation as eddy momentum flux convergence (EMFC) in convection.

The results show that the MJO is a highly viscous oscillation, with a 3–5-day equivalent linear damping time scale, in the upper as well as lower troposphere. Upper-level damping is mainly in the form of large-scale advection terms, which are linear in MJO amplitude but involve horizontal and vertical background flow. Specifically, the leading terms are the advection of time-mean zonal shear by MJO vertical motion anomalies and advection of MJO wind anomalies by time-mean ascent. This upper-level damping in the western Pacific is mostly confined between 10°N and 10°S. In contrast, zonal wind damping in the lower troposphere involves EMFC (budget residual) and zonal mean linear meridional advection.

Stated another way, the strong upper-level damping necessitates upper-level geopotential height gradients to maintain the observed zonal wind anomalies over the time scales implied by the MJO’s low frequency. The existence of the background flow thus tends to shift MJO temperature perturbations westward so that the warm anomaly ahead (east) of the convective center is shifted back into the convection. This shifting effect is fully realized only for anomalies with a period much longer than the 3–5-day damping time.
Coupling Diffuse Sky Radiation and Surface Albedo
Authors: Pinty Bernard , Lattanzio Alessio , Martonchik John V. , Verstraete Michel M. , Gobron Nadine , Taberner Malcolm , Widlowski Jean-Luc , Dickinson Robert E. , Govaerts Yves
Published: August 2005

New satellite instruments have been delivering a wealth of information regarding land surface albedo. This basic quantity describes what fraction of solar radiation is reflected from the earth’s surface. However, its concept and measurements have some ambiguity resulting from its dependence on the incidence angles of both the direct and diffuse solar radiation. At any time of day, a surface receives direct radiation in the direction of the sun, and diffuse radiation from the various other directions in which it may have been scattered by air molecules, aerosols, and cloud droplets. This contribution proposes a complete description of the distribution of incident radiation with angles, and the implications in terms of surface albedo are given in a mathematical form, which is suitable for climate models that require evaluating surface albedo many times. The different definitions of observed albedos are explained in terms of the coupling between surface and atmospheric scattering properties. The analytical development in this paper relates the various quantities that are retrieved from orbiting platforms to what is needed by an atmospheric model. It provides a physically simple and practical approach to evaluation of land surface albedo values at any condition of sun illumination irrespective of the current range of surface anisotropic conditions and atmospheric aerosol load. The numerical differences between the various definitions of albedo for a set of typical atmospheric and surface scattering conditions are illustrated through numerical computation.
Baroclinic Multiple Zonal Jets on the Sphere
Authors: Lee Sukyoung
Published: August 2005

Multiple zonal jets are investigated with a two-level primitive equation model on the sphere in which both baroclinicity and planetary radius are varied. As in the case for a two-layer quasigeostrophic model on a β-plane channel, it is found both that the Rhines scale successfully predicts the meridional scale of the multiple zonal jets, and that these jets are maintained in part by an eddy momentum flux divergence associated with slow baroclinic waves at the interjet minimum.

A scaling analysis suggests that njets∝ (a/θm)1/2, with the constraints ζe ≡ 8 sin2f (θm/▵θ ) > 1 and njets ≥ 1, where njets is the number of the jets, a the planetary radius, θm one-half of the pole-to-equator potential temperature difference, ξe the supercriticality of the two-layer Phillips model, Δθ the potential temperature difference between the two levels, and ϕ the latitude. The number of jets simulated by the model agrees with this scaling, provided that Ljet ≤ a, where Ljet is the jet scale.

In model runs with a large planet where multiple zonal jets exist, the time–mean eddy heat flux is found to be consistent with the diffusive picture of Held and Larichev. In contrast, for the model runs with the planetary size equal to that of Earth, baroclinic adjustment is found to be more relevant. These results are consistent with the finding that in the large-planet (Earth-like) model runs, the jet/eddy scale is smaller than (comparable to) the corresponding planetary radius.
The Effects of Stratification on Flow Separation
Authors: Ambaum Maarten H. P. , Marshall David P.
Published: August 2005

Separation of stratified flow over a two-dimensional hill is inhibited or facilitated by acceleration or deceleration of the flow just outside the attached boundary layer. In this note, an expression is derived for this acceleration or deceleration in terms of streamline curvature and stratification. The expression is valid for linear as well as nonlinear deformation of the flow. For hills of vanishing aspect ratio a linear theory can be derived and a full regime diagram for separation can be constructed. For hills of finite aspect ratio scaling relationships can be derived that indicate the presence of a critical aspect ratio, proportional to the stratification, above which separation will occur as well as a second critical aspect ratio above which separation will always occur irrespective of stratification.
Tropical Zonal Momentum Balance in the NCEP Reanalyses
Authors: Dima Ioana M. , Wallace John M. , Kraucunas Ian
Published: August 2005

The seasonal cycle of the zonal-mean zonal momentum balance in the Tropics is investigated using NCEP reanalysis data. It is found that the climatological stationary waves in the tropical upper troposphere, which are dominated by the equatorial Rossby wave response to tropical heating, produce an equatorward eddy flux of westerly momentum in the equatorial belt. The resulting westerly acceleration in the tropical upper troposphere is balanced by the advection of easterly momentum associated with the cross-equatorial mean meridional circulation. The eddy momentum fluxes and the cross-equatorial flow both tend to be strongest during the monsoon seasons, when the maximum diabatic heating is off the equator, and weakest during April–May, the season of strongest equatorial symmetry of the heating. The upper-level Rossby wave pattern exhibits a surprising degree of equatorial symmetry and follows a similar seasonal progression. Solutions of the nonlinear shallow water wave equation also show a predominantly equatorially symmetric response to a heat source centered off the equator.
Small-Scale Drop Size Variability: Impact on Estimation of Cloud Optical Properties
Authors: Knyazikhin Y. , Myneni R. B. , Marshak A. , Wiscombe W. J. , Larsen M. L. , Martonchik J. V.
Published: August 2005

Most cloud radiation models and conventional data processing techniques assume that the mean number of drops of a given radius is proportional to volume. The analysis of microphysical data on liquid water drop sizes shows that, for sufficiently small volumes, this proportionality breaks down; the number of cloud drops of a given radius is instead proportional to the volume raised to a drop size–dependent nonunit power. The coefficient of proportionality, a generalized drop concentration, is a function of the drop size. For abundant small drops the power is unity as assumed in the conventional approach. However, for rarer large drops, it falls increasingly below unity. This empirical fact leads to drop clustering, with the larger drops exhibiting a greater degree of clustering. The generalized drop concentration shows the mean number of drops per cluster, while the power characterizes the occurrence frequency of clusters. With a fixed total number of drops in a cloud, a decrease in frequency of clusters is accompanied by a corresponding increase in the generalized concentration. This initiates a competing process missed in the conventional models: an increase in the number of drops per cluster enhances the impact of rarer large drops on cloud radiation while a decrease in the frequency suppresses it. Because of the nonlinear relationship between the number of clustered drops and the volume, these two opposite tendencies do not necessarily compensate each other. The data analysis suggests that clustered drops likely have a stronger radiative impact compared to their unclustered counterpart; ignoring it results in underestimation of the contribution from large drops to cloud horizontal optical path.
Bimodality of the Planetary-Scale Atmospheric Wave Amplitude Index
Authors: Christiansen Bo
Published: August 2005

The evidence for multiple flow regimes in the planetary-scale atmospheric wave amplitude index (WAI) is studied using the 56 winters from the NCEP reanalysis data. The regimes are identified by bimodality in the probability density estimates. Both the probability density of the WAI alone and the probability density in the two-dimensional space spanned by the WAI and its temporal rate of change are examined. The latter procedure allows us to exploit the quasi stationarity of the regimes and increase the statistical significance. The statistical significance of bimodality in the probability densities is tested by a Monte Carlo approach using surrogate time series that preserve the full autocorrelation spectrum of the original WAI. By using a longer dataset and including the rate of change, some of the questions raised in previous studies about the robustness and statistical significance of the bimodality of the WAI are resolved.

Statistically significant bimodality is found in the WAI based on the 500-hPa height. The probability density of the WAI shows considerable low-frequency variability on decadal scales. However, the bimodality is reproduced in all decadal subperiods although without statistical significance. The last decade has been dominated by a strong (disturbed) regime while a weak (zonal) regime dominates the previous decades. This recent change toward the disturbed regime is statistically significant. Imprints of the regimes are found at other tropospheric levels including the sea level. In particular, the regimes are found with statistical significance in the WAI based on the sea level pressure for the subperiod 1979–2003. Systematically varying the upper and lower boundaries of the latitudinal interval over which the geopotential height is averaged shows that the bimodality of the WAI is rather sensitive to these parameters, but also that statistically significant bimodality is found for a range of intervals with the lower boundary at 45°–50°N.