bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards the Identification of Type II Secretion Signals in a Nonacylated Variant of Pullulanase from
Klebsiella oxytoca
Authors: Francetić Olivera , Pugsley Anthony P. 
Published: September 2005

ABSTRACT

Pullulanase (PulA) from the gram-negative bacterium
Klebsiella oxytoca
is a 116-kDa surface-anchored lipoprotein of the isoamylase family that allows growth on branched maltodextrin polymers. PulA is specifically secreted via a type II secretion system. PelBsp-PulA, a nonacylated variant of PulA made by replacing the lipoprotein signal peptide (sp) with the signal peptide of pectate lyase PelB from
Erwinia chrysanthemi
, was efficiently secreted into the medium. Two 80-amino-acid regions of PulA, designated A and B, were previously shown to promote secretion of β-lactamase (BlaM) and endoglucanase CelZ fused to the C terminus. We show that A and B fused to the PelB signal peptide can also promote secretion of BlaM and CelZ but not that of nuclease NucB or several other reporter proteins. However, the deletion of most of region A or all of region B, either individually or together, had only a minor effect on PelBsp-PulA secretion. Four independent linker insertions between amino acids 234 and 324 in PelBsp-PulA abolished secretion. This part of PulA, region C, could contain part of the PulA secretion signal or be important for its correct presentation. Deletion of region C abolished PelBsp-PulA secretion without dramatically affecting its stability. PelBsp-PulA-NucB chimeras were secreted only if the PulA-NucB fusion point was located downstream from region C. The data show that at least three regions of PulA contain information that influences its secretion, depending on their context, and that some reporter proteins might contribute to the secretion of chimeras of which they are a part.
Transcriptional Program of Early Sporulation and Stationary-Phase Events in
Clostridium acetobutylicum
Authors: Alsaker Keith V. , Papoutsakis Eleftherios T. 
Published: September 2005

ABSTRACT

DNA microarray analysis of
Clostridium acetobutylicum
was used to examine the genomic-scale gene expression changes during the shift from exponential-phase growth and acidogenesis to stationary phase and solventogenesis. Self-organizing maps were used to identify novel expression patterns of functional gene classes, including aromatic and branched-chain amino acid synthesis, ribosomal proteins, cobalt and iron transporters, cobalamin biosynthesis, and lipid biosynthesis. The majority of pSOL1 megaplasmid genes (in addition to the solventogenic genes
aad
-
ctfA
-
ctfB
and
adc
) had increased expression at the onset of solventogenesis, suggesting that other megaplasmid genes may play a role in stationary-phase phenomena. Analysis of sporulation genes and comparison with published
Bacillus subtilis
results indicated conserved expression patterns of early sporulation genes, including
spo0A
, the
sigF
operon, and putative canonical genes of the σ
H
and σ
F
regulons. However,
sigE
expression could not be detected within 7.5 h of initial
spo0A
expression, consistent with the observed extended time between the appearance of clostridial forms and endospore formation. The results were compared with microarray comparisons of the wild-type strain and the nonsolventogenic, asporogenous M5 strain, which lacks the pSOL1 megaplasmid. While some results were similar, the expression of primary metabolism genes and heat shock proteins was higher in M5, suggesting a difference in metabolic regulation or a butyrate stress response in M5. The results of this microarray platform and analysis were further validated by comparing gene expression patterns to previously published Northern analyses, reporter assays, and two-dimensional protein electrophoresis data of metabolic genes (including all major solventogenesis genes), sporulation genes, heat shock proteins, and other solventogenesis-induced gene expression.
Site-Directed Mutagenesis and Structural Studies Suggest that the Germination Protease, GPR, in Spores ofBacillusSpecies Is an Atypical Aspartic Acid Protease
Authors: Carroll Thomas M. , Setlow Peter 
Published: September 2005

ABSTRACTGermination protease (GPR) initiates the degradation of small, acid-soluble spore proteins (SASP) during germination of spores ofBacillusandClostridiumspecies. The GPR amino acid sequence is not homologous to members of the major protease families, and previous work has not identified residues involved in GPR catalysis. The current work has focused on identifying catalytically essential amino acids by mutagenesis ofBacillus megaterium gpr. A residue was selected for alteration if it (i) was conserved among spore-forming bacteria, (ii) was a potential nucleophile, and (iii) had not been ruled out as inessential for catalysis. GPR variants were overexpressed inEscherichia coli, and the active form (P41) was assayed for activity against SASP and the zymogen form (P46) was assayed for the ability to autoprocess to P41. Variants inactive against SASP and unable to autoprocess were analyzed by circular dichroism spectroscopy and multiangle laser light scattering to determine whether the variant's inactivity was due to loss of secondary or quaternary structure, respectively. Variation of D127 and D193, but no other residues, resulted in inactive P46and P41, while variants of each form were well structured and tetrameric, suggesting that D127 and D193 are essential for activity and autoprocessing. Mapping these two aspartate residues and a highly conserved lysine onto theB. megateriumP46crystal structure revealed a striking similarity to the catalytic residues and propeptide lysine of aspartic acid proteases. These data indicate that GPR is an atypical aspartic acid protease.
Site-Directed Mutagenesis and Expression of the Soluble Form of the Family IIIa Cellulose Binding Domain from the Cellulosomal Scaffolding Protein of
Clostridium cellulovorans
Authors: Murashima Koichiro , Kosugi Akihiko , Doi Roy H. 
Published: September 2005

ABSTRACT

The planar and anchoring residues of the family IIIa cellulose binding domain (CBD) from the cellulosomal scaffolding protein of
Clostridium cellulovorans
were investigated by site-directed mutagenesis and cellulose binding studies. By fusion with maltose binding protein, the family IIIa recombinant wild-type and mutant CBDs from
C. cellulovorans
were expressed as soluble forms. Cellulose binding tests of the mutant CBDs indicated that the planar strip residues played a major role in cellulose binding and that the anchoring residues played only a minor role.
Commutator-Based (A)[X]n(SU(2)×Sn) NMR Cluster Systems: Establishment of the Universality of [n](Sn) Salients and Constraints on ϕ±11(1.1) Polarisations to the [1n] Salient: Permutational Spin Symmetry (PSS) Within NMR Spin Dynamics - an Analytic View
Authors: Temme Francis P. 
Published: September 2005

Analytic SU(2) × Sn dual tensorial (DT) spin dynamics over uniform NMR spins is invoked in examining the modern quantum basis for the universal non-observability rule which governs dominant intracluster JXX' couplings of (A)[X]n NMR systems as a specific form of (abstract) permutational spin symmetry (PSS) with well defined properties on spin-alone space. This is shown to be linked to DT constraints that apply to the cross-product ϕ1±1(1.1) polarisation development i.e., as being confined to [1n](Sn) (Liouvillian) salient, with the existence of [n] (rotating frame) null subspaces. Both these arise within the spin dynamics of (A)[X]2 spin systems (or subsystems thereof) within (a hierarchy of) dominant JXX' governing the internal L(0); such spin systems provide analytic sequels to comparative spin dynamics studies of XX' PSS and AX broken-PSS systems in a Liouvillian coupled tensorial basis formalism, since both draw on (Sanctuary B. C.: Mol. Phys. 1985, 55, 1017), and on the realisation that proper PSS over a (uniform) spin-space L(0) = [H(0),.] zeroth-order Liouvillian and its internal (hierarchical subsets of) JXX' (Temme F. P.: J. Mol. Struct. (THEOCHEM) 2002, 547, 153) i.e., for abstract Sn ↓ G group embeddings. The present work also examines the general irrep-structure of DT spin symmetries for the extent of unit-character irreps and the role of Sn ⊃ Sn-1 ⊃ .. ⊃ [2](S2) group chains in defining the Sn multiple invariants under democratic recoupling of PSS of uniform spin systems. As group measures, these properties apply to both (A)[X]n and [AX]n PSS symmetries, with the invariant cardinality |SI|(n) being related to time-reversal invariance (TRI) and its inherent democratic recoupling (DR) over Weyl (I • I) pairs. For [X]2n uniform spin clusters, |SI|(2n) is best derived via n-fold polyhedral combinatorics of the underlying DR (Temme F. P.: Proc. R. Soc. London, Ser. A 2005, 461, 321) i.e., as an augmented post-Weyl view of the essential role of TRI in (group) invariant cardinality, with the Sn-invariants represented by certain Sn subduction properties.
Neck-Sealing in early Islam
Authors: Robinson Chase 
Published: September 2005

AbstractArabic and Syriac sources for early Islam, especially for seventh- and eighth-century Syria and Iraq, describe the use of neck sealings in the administration of the poll tax, which was levied upon non-Muslims. This article evaluates the relevant literary, historical and material evidence, including some surviving sealings, and proposes that at origin, neck-sealing related to other stigmatizing practices, and was principally symbolic and punitive. Des texts arabes et syriques, particulièrement originaires de la Syrie et de l'Iraq des septième et huitième siècles, décrivent l'usage des sceaux en pendentif pour l'application de la capitation qui était imposée aux non-musulmans. Cet article étudie les sources littéraires, historiques et archéologiques, y compris des sceaux qui nous restent, et suggère que à l'origine, les sceaux étaient liés à d'autres pratiques discriminatives/stigmatisantes, et étaient avant tout symboliques et punitives.
Climatological Features of Cutoff Low Systems in the Northern Hemisphere
Authors: Nieto Raquel , Gimeno Luis , de la Torre Laura , Ribera Pedro , Gallego David , García-Herrera Ricardo , García José Agustín , Nuñez Marcelino , Redaño Angel , Lorente Jerónimo 
Published: September 2005

Abstract
This study presents the first multidecadal climatology of cutoff low systems in the Northern Hemisphere. The climatology was constructed by using 41 yr (1958–98) of NCEP–NCAR reanalysis data and identifying cutoff lows by means of an objective method based on imposing the three main physical characteristics of the conceptual model of cutoff low (the 200-hPa geopotential minimum, cutoff circulation, and the specific structure of both equivalent thickness and thermal front parameter fields).
Several results were confirmed and climatologically validated: 1) the existence of three preferred areas of cutoff low occurrence (the first one extends through southern Europe and the eastern Atlantic coast, the second one is the eastern North Pacific, and the third one is the northern China–Siberian region extending to the northwestern Pacific coast; the European area is the most favored region); 2) the known seasonal cycle, with cutoff lows forming much more frequently in summer than in winter; 3) the short lifetime of cutoff lows, most cutoff lows lasted 2–3 days and very few lasted more than 5 days; and 4) the mobility of the system, with few cutoff lows being stationary. Furthermore, the long study period has made it possible (i) to find a bimodal distribution in the geographical density of cutoff lows for the European sector in all the seasons (with the exception of winter), a summer displacement to the ocean in the American region, and a summer extension to the continent in the Asian region, and (ii) to detect northward and westward motion especially in the transitions from the second to third day of occurrence and from the third to fourth day of occurrence.
The long-term cutoff low database built in this study is appropriate to study the interannual variability of cutoff low occurrence and the links between cutoff lows and jet stream systems, blocking, or major modes of climate variability as well as the global importance of cutoff low in the stratosphere–troposphere exchange mechanism, which will be the focus of a subsequent paper.
Role of Antecedent Land Surface Conditions on North American Monsoon Rainfall Variability*
Authors: Zhu Chunmei , Lettenmaier Dennis P. , Cavazos Tereza 
Published: September 2005

Abstract
Possible links between North American Monsoon System (NAMS) seasonal [June–July–August–September (JJAS)] precipitation and premonsoon seasonal land surface conditions including precipitation (P), surface air temperature (Ts), soil moisture (Sm), and snow water equivalent (SWE) anomalies are explored during the 1950–2000 period. A statistically significant inverse relationship is found between monsoon precipitation in an area defined as the Monsoon West (Arizona and western New Mexico) and antecedent winter precipitation in the southwestern (SW) United States and the mountainous region in Utah and Colorado (the predictor area). This linkage is strong during 1965–90 and weak otherwise, as has been suggested by previous studies. A land surface feedback hypothesis is proposed to explain this relationship: more winter P leads to more winter and early spring SWE in the predictor area, hence more spring and early summer Sm, and lower spring and early summer Ts, which induces a weaker onset (and less precipitation) of the NAMS and vice versa. All three links in this hypothesis were tested and the existence of a land memory associated with winter precipitation and snow, which can persist until June, was confirmed. However, the results show that this land memory contributes little to the magnitude of NAM precipitation. Winter snow is negatively correlated to late spring Ts in the SW mountainous region, but not in extreme years. In fact, the premonsoon (June) Ts over the U.S. southwest is inversely related to monsoon precipitation, which is the reverse of what is expected based on the hypothesis. The lack of a significant Sm–Ts–P relationship in most of the SW suggests, based on the constructed Sm dataset, that local premonsoon soil wetness conditions play a minor role in the strength of the monsoon. A strong positive relationship between June Ts anomalies and the large-scale midtropospheric circulation before the onset of the monsoon was found, suggesting that the controlling factor for the premonsoon Ts anomalies may not be local (i.e., not from the land surface). The results suggest that further research is needed to elucidate the nature of land–sea–atmosphere interactions as related to the onset of the monsoon.
Investigation of Hydrological Variability in West Africa Using Land Surface Models
Authors: Li K. Y. , Coe M. T. , Ramankutty N. 
Published: September 2005

AbstractThe availability of freshwater is a particularly important issue in Africa where large portions of the continent are arid or semiarid and climate is highly variable. Sustainable water resource management requires the assessment of hydrological variability in response to nature climate fluctuation. In this study, a land surface model, the Integrated Biosphere Simulator (IBIS), and a hydrological routing model, the Hydrological Routing Algorithm (HYDRA), are used to investigate the hydrological variability in two large basins, the Lake Chad basin (LCB) and the Niger River basin (NRB), located in West Africa, over the period from 1950 to 1995. The IBIS land surface hydrological module was calibrated and validated for arid and semiarid Africa, and major enhancements were made to the module, including the development of a dynamic root water–extraction formulation, the incorporation of a Green–Ampt infiltration parameterization, and modification to the prescribed root distribution, the runoff module, and weather generator. The results show that the hydrology in this area is highly variable over time and space. The coefficient of variance (CV) of annual rainfall ranges from 10%–15% in the southern portions of the basins to 30%–40% in the northern portions. The annual evapotranspiration (ET) varies with a slightly lower CV compared to the rainfall, but the runoff is extremely sensitive to the rainfall fluctuation, particularly in the central portions of the basins (8°–13°N in LCB and 12°–16°N in NRB) where the CVs in runoff are as high as 100%–200%. The annual river discharge varies largely in concert with the rainfall fluctuation, with the CV being 37% in LCB and 23%–63% in NRB. In terms of the whole basin, the relative hydrologic variability (rainfall, evapotranspiration, runoff, and river discharge) is significantly higher in the dry period than in the wet period, and the interannual variability in runoff is more than twice as high as compared to rainfall or ET.
The Sensitivity of the Tropical-Mean Radiation Budget
Authors: Clement Amy C. , Soden Brian 
Published: September 2005

AbstractA key disagreement exists between global climate model (GCM) simulations and satellite observations of the decadal variability in the tropical-mean radiation budget. Measurements from the Earth Radiation Budget Experiment (ERBE) over the period 1984–2001 indicate a trend of increasing longwave emission and decreasing shortwave reflection that no GCM can currently reproduce. Motivated by these results, a series of model sensitivity experiments is performed to investigate hypotheses that have been advanced to explain this discrepancy. Specifically, the extent to which a strengthening of the Hadley circulation or a change in convective precipitation efficiency can alter the tropical-mean radiation budget is assessed. Results from both model sensitivity experiments and an empirical analysis of ERBE observations suggest that the tropical-mean radiation budget is remarkably insensitive to changes in the tropical circulation. The empirical estimate suggests that it would require at least a doubling in strength of the Hadley circulation in order to generate the observed decadal radiative flux changes. In contrast, rather small changes in a model’s convective precipitation efficiency can generate changes comparable to those observed, provided that the precipitation efficiency lies near the upper end of its possible range. If, however, the precipitation efficiency of tropical convective systems is more moderate, the model experiments suggest that the climate would be rather insensitive to changes in its value. Further observations are necessary to constrain the potential effects of microphysics on the top-of-atmosphere radiation budget.
Statistical Modeling in Nonlinear Systems
Authors: Campbell Edward P. 
Published: September 2005

Abstract
The use of linear statistical methods in building climate prediction models is examined, particularly the use of anomalies. The author’s perspective is that the climate system is a nonlinear interacting system, so the impact of modeling using anomalies rather than observed data directly is considered. With reference to the Lorenz system and a simple model for regime dependence, it is shown that anomalies impair our ability to reconstruct nonlinear dynamics. Some alternative approaches in the literature that offer an attractive way forward are explored, focusing on Bayesian hierarchical methods to construct so-called physical–statistical models. The author’s view is that anomalies should be reserved in most cases as a tool for enhancing graphical representations of climate data. The exceptions are when the implicit assumptions underlying the use of anomalies are met or when an anomaly representation is physically motivated.
A Closer Comparison of Early and Late-Winter Atmospheric Trends in the Northern Hemisphere
Authors: Hu Yongyun , Tung Ka Kit , Liu Jiping 
Published: September 2005

Abstract
Decadal trends are compared in various fields between Northern Hemisphere early winter, November–December (ND), and late-winter, February–March (FM), months using reanalysis data. It is found that in the extratropics and polar region the decadal trends display nearly opposite tendencies between ND and FM during the period from 1979 to 2003. Dynamical trends in late winter (FM) reveal that the polar vortex has become stronger and much colder and wave fluxes from the troposphere to the stratosphere are weaker, consistent with the positive trend of the Arctic Oscillation (AO) as found in earlier studies, while trends in ND appear to resemble a trend toward the low-index polarity of the AO. In the Tropics, the Hadley circulation shows significant intensification in both ND and FM, with stronger intensification in FM. Unlike the Hadley cell, the Ferrel cell shows opposite trends between ND and FM, with weakening in ND and strengthening in FM. Comparison of the observational results with general circulation model simulations is also discussed.
Relationships between South Atlantic SST Variability and Atmospheric Circulation over the South African Region during Austral Winter
Authors: Reason C. J. C. , Jagadheesha D. 
Published: September 2005

Abstract
The Southwestern Cape (SWC) region of South Africa is characterized by winter rainfall brought mainly via cold fronts and by substantial interannual variability. Previous work has found evidence that the interannual variability in SWC winter rainfall may be related to sea surface temperature (SST) in the South Atlantic Ocean and to large-scale ocean–atmosphere interaction in this region. During wet winters, SST tends to be anomalously warm (cool) in the southwest Atlantic and southeast Atlantic (central South Atlantic). Atmospheric general circulation model experiments with various idealized SST anomalies in the South Atlantic are used to explore mechanisms potentially associated with the rainfall variability. The model results suggest that the atmosphere is sensitive to subtropical–midlatitude SST anomalies in the South Atlantic during winter. Locally, there are changes to the jet position and strength, low-level relative vorticity, and convergence of moisture and latent heat flux that lead to changes in rainfall over the SWC. The model response to the SST forcing also shows large-scale anomalies in the midlatitude Southern Hemisphere circulation, namely, an Antarctic Oscillation–type mode and wavenumber-3 changes, similar to those observed during anomalous winters in the region.