bluuebunny/crossref_metadata_2025 huggingface dataset:
Lintnerization of Two Amylose‐free Starches of A‐ and B‐Crystalline Types, Respectively
Authors: Bertoft Eric
Published: April 2004

Waxy maize starch (WMS) and potato amylopectin starch (PAPS), representing amylose‐free A‐ and B‐crystalline granules, respectively, were subjected to hydrolysis in diluted hydrochloric acid (lintnerization). The solubilization rate of the granules was dependent on the temperature, but there were only small differences between the samples. The compositions of the lintners obtained at 29°C were also similar, though the sensitivity to enzymatic debranching was different. The degree of debranching increased significantly if pullulanase and isoamylase were used successively. Because some branches remained resistant to enzymatic attack, the degree of scattered branching was difficult to estimate. The amount and composition of β‐limit dextrins suggested, however, that both starches contained scattered branches. Long chains and the shortest chains in the amylopectin molecules were sensitive to lintnerization and therefore probably located outside the crystallites. The composition of the PAPS lintners was dependent on the temperature of the lintnerization, whereas that of WMS lintners was not. The composition of a lintner from normal potato starch was compared with PAPS, and it is concluded that the presence of amylose has a higher effect than the type of crystallinity on the lintnerization results.
Midcareer and senior faculty learning communities: Learning throughout faculty careers
Authors: Blaisdell Muriel L. , Cox Milton D.
Published: April 2004

Faculty members' productivity may shift over time, not as a function of age but as a function of the amount of time a senior faculty member spends with colleagues (Bland and Bergquist, 1997). This chapter shows
how faculty learning communities can provide the opportunities and connections that senior and midcareer faculty need to continue productive academic lives.
On well‐posedness and conditioning in optimization
Authors: Zolezzi T.
Published: April 2004

We survey some results dealing with well‐posedness of scalar optimization problems, with applications to the optimal control of ordinary differential equations under plant perturbations. Then we deal with the definition of a condition number for optimization problems. Corresponding distance theorems are discussed, aiming to generalize the Eckart‐Young theorem to the infinite‐dimensional setting.
Taking the long view: a geological contribution to understanding the causes of global glaciation
Authors: Vaughan Alan
Published: April 2004

Modelling future climates is both a very difficult task and one of key importance to our future well-being. Why then would we want to make it more difficult by shortening our perspective to the most recent period, ignoring historical data that would provide the long perspective on key processes? Palaeoenvironmental research has resulted in important advances in our understanding of global changes in oceanic, atmospheric and biotic systems during glaciation and the onset of the current glacial epoch. However, few palaeoenvironmental studies extend farther back than half a million years, and, with the exception of the recently completed Cape Roberts drilling project, vanishingly few consider events prior to the Eocene (55–38 million years ago).
Magnetic properties of Upper Quaternary sediments from the Scotia Sea, Antarctica
Authors: Hamilton Norman , Pudsey Carol J.
Published: April 2004

Magnetic properties of bulk sediment samples taken from three cores from the Scotia Sea, Antarctica were determined using a fully-automated variable field translation balance. Fine-grained detrital magnetite is identified as the principal carrier of remanence in these Upper Quaternary sediments which were deposited under the influence of the Antarctic Circumpolar Current. Inferred magnetite grain-size is consistent with published bulk grain-size data for these cores. Pseudo-single domain grains characterize Holocene samples, and larger, multi-domain grains occur in glacial samples from two of the cores, whereas samples from the northernmost core site show dominantly multi-domain behaviour.
Transpressional deformation along the margin of Larsen Basin: new data from Pedersen Nunatak, Antarctic Peninsula
Authors: Valle R.A. Del , Miller H.
Published: April 2004

New structural data from the northern Antarctic Peninsula suggest that reverse faults and folds affecting the Pedersen Nunatak beds of the upper Mesozoic–Lower Cenozoic Larsen Basin succession were produced by transpressional forces acting parallel to the Weddell Sea coast of the Antarctic Peninsula during mid-Cretaceous compression of the Larsen Basin. At Pedersen Nunatak, Larsen Basin rocks are deformed into a series of synclines and anticlines that are cut by reverse faults.
Late Holocene stable isotope chronology and meltwater discharge event in Maxwell and Admiralty bays, King George Island, Antarctica
Authors: Khim Boo-Keun , Yoon Ho Il , Kim Yeadong , Shin Im Chul
Published: April 2004

Two short gravity cores were retrieved to obtain palaeoclimatic information from Maxwell and Admiralty bays, King George Island, South Shetland Islands. AMS 14C age dates, sediment properties (grain size, TOC and CaCO3) and stable oxygen and carbon isotope compositions of benthiδ foraminifera (Globocassidulina biora) show downcore variations that characterize depositional conditions during the late Holocene. In particular, δ18O values of benthic foraminifera are lowest at approximately 2500 yr bp in both cores. Allowδ18O time-equivalent excursion in both cores is interpreted to reflect a distinct subglacial meltwater discharge intensified by warm climatic conditions. An increased proportion of fine-grained detritus and higher TOC in the cores at this level suggests that enhanced meltwater supply may have resulted in increased primary productivity. This meltwater discharge event provides evidence of climatic instability during the late Holocene at King George Island.
Rediscovery of Nymphon gerlachei Giltay, 1935 (Arthropoda, Pycnogonida)
Authors: Bamber Roger N. , Mitchell Nicola J. , Ferrero Timothy J.
Published: April 2004

Recently collected material from west of the Antarctic Peninsula has proven to be consistent with Nymphon gerlachei Giltay, 1935, previously known only from the holotype. The information now available on its intraspecific morphological variability has allowed the distinctions between this species and N. charcoti to be established.
High levels of genetic variability and population differentiation in Gressittacantha terranova (Collembola, Hexapoda) from Victoria Land, Antarctica
Authors: Fanciulli Pietro Paolo , Summa Domenico , Dallai Romano , Frati Francesco
Published: April 2004

Allozyme electrophoresis was used to assess genetic variability and differentiation in 22 populations of Gressittacantha terranova Wise (Hexapoda, Collembola) from a coastal area of Victoria Land between the Mariner Glacier and the Nansen Ice Sheet. Allelic frequencies were determined at five enzyme loci: Phi, Pgm, Hk, Mpi and Mdh. Levels of variability, estimated as rates of heterozygosity, were higher than those calculated for the same loci in taxonomically related and non-related species of non-Antarctic Collembola. Thus, in spite of the ecological simplicity of Antarctic terrestrial ecosystems, G. terranova is characterized by high levels of genetic variability, and the 22 populations could be divided into three geogaphic groups, separated by the Aviator and Campbell glaciers. Genetic differentaton reflects the geographic arrangement of the populations, suggesting that the glaciers are effective barriers to gene flow, and that the patchy distribution of collembolan species in Antarctica has the potential to induce, in the long term, microspeciation processes. Interestingly, detectable genetic differentiation was observed between six populations collected at Edmonson Point, even though these are very close to each other, indicating the impact of geographic isolation even within short distances. The only exception to the congruence between genetic and geographic structuring was provided by the population of Apostrophe Island, for which a recent introduction with individuals coming from southern populations is suggested.
Cold tolerance of the Antarctic springtail Gomphiocephalus hodgsoni (Collembola, Hypogastruridae)
Authors: Sinclair Brent J. , Sjursen Heidi
Published: April 2004

Cold tolerance of the springtail Gomphiocephalus hodgsoni Carpenter (Collembola: Hypogastruridae) was studied at Cape Bird, Ross Island, Antarctica (77°13′S, 166°26′E). Microclimate temperatures indicate a highly seasonal thermal environment, with winter minima <–39°C. Snow cover significantly buffers both minimum temperatures and cooling rates. Gomphiocephalus hodgsoni survives low temperatures by avoiding freezing. Mean low group supercooling points (SCPs) ranged from –35.4°C in October to –28.3°C in January. The lowest SCP measured was –38.0°C. The high SCP group was very small, making up only 18% of the population in January. In October, G. hodgsoni had a very high glycerol content (>80 μg mg−1 dry weight), although this declined rapidly to low levels (c. 7–10 μg mg−1 dry weight) in January. Quantities of glucose and trehalose were low during October, but steadily increased throughout the summer. Haemolymph osmolality was exceptionally high (up to 1755 mOsm kg−1) at the end of November, but this rapidly declined to c. 500 mOsm kg−1 by late December. The presence of thermal hystersis proteins was indicated by both osmometry on haemolymph samples and recrystallization inhibition studies of springtail homogenates. There was a strong relationship between glycerol content and SCP, but the relationship between haemolymph osmolality, SCP and carbohydrates is uncertain.
Radiocarbon dates from abandoned penguin colonies in the Antarctic Peninsula region
Authors: Emslie Steven D.
Published: April 2004

Sixty-three radiocarbon dates on organic remains from 21 abandoned colonies of chinstrap (Pygoscelis antarctica) and Adélie (P. adeliae) penguins on 12 islands in the Antarctic Peninsula region are evaluated for determining the occupation history of penguins in this region. This record also provides a means for assessing sea-level change, glacial advances and retreats, and population responses by penguins to these events. All conventional dates were corrected for the marine-carbon reservoir effect by applying a ΔR = 700±50 BP and marine calibration curves. The 63 calibrated dates give 2σ ranges (95% confidence intervals) from modern to 5990 yr BP. These dates indicate progressively older occupations from north to south along the Antarctic Peninsula. No sites older than approximately 540 BP occur in the northern peninsula, either because they have not yet been found or older sites have been destroyed by solifluction and glacial scouring. Three dates from one locality near Rothera Point, Adelaide Island, also were calibrated with a ΔR = 750 ± 50 and 800 ± 50 BP. No difference was found between calibrated dates using these two other ΔR values, indicating that local corrections for variation in upwelling intensity may not be necessary.
Geology of new localities on Tabarin Peninsula, northern Antarctic Peninsula
Authors: Valle Rodolfo A. Del , Morelli Jorge R. , Rinaldi Carlos A.
Published: April 2004

New outcrops of Hope Bay Formation and Larsen Basin rocks have been exposed by recent ice-retreat on Tabarin Peninsula, northern Antarctic Peninsula. Quartzose, very low-grade metasedimentary rocks, cropping out at Balegno Nunatak (63°28′53″S, 57°00′31″W) are assigned to the Permian–Triassic Hope Bay Formation, and dioritic rocks are assigned to the Antarctic Peninsula batholith. Sedimentary rocks exposed at Rubulis Nunatak (63°30′52″S, 57°07′29′W) closely resemble Lower Cretaceous sedimentary rocks cropping out at nearby Troilo Nunatak, western Tabarin Peninsula. These rocks are correlated with the lower Gustav Group (?Barremian–Coniacian) of the Larsen Basin. This new record confirs that the Larsen Basin extends over southern Tabarin Peninsula, where basin sediments are thought to be faulted against sediments of the Antarctic Peninsula magmatic arc.
Observations of cloud and precipitation particles on the Avery Plateau, Antarctic Peninsula
Authors: Lachlan-Cope Tom , Ladkin Russell , Turner John , Davison Paul
Published: April 2004

Surface-based observations were taken of cloud and precipitation particles on the Avery Plateau (66°50.34′S 65°29.58′W), Antarctic Peninsula from 25 November to 13 December 1995. This paper considers cloud parameters on three days during this period when the cloud base reached ground level and snow was falling. It was found that on all three days more ice crystals were present in the cloud than would be expected from simple theoretical considerations. The rate of snowfall decreased as the number of ice crystals increased, the large number of ice crystals present effectively suppressing the formation of large precipitation-sized crystals. The source of the ice nuclei that allowed the formation of the large number of crystals is not known for certain but is thought to be the snow surface, possibly in the form of very fine ice crystals blown from the surface during blowing/drifting snow episodes.
Migrations and foraging of juvenile southern elephant seals from Macquarie Island within CCAMLR managed areas
Authors: van den Hoff John , Burton Harry R. , Hindell Mark A. , Sumner Michael D. , McMahon Clive R.
Published: April 2004

Twenty-three juvenile (8–14 months of age) southern elephant seals (Mirounga leonina L.) from Macquarie Island were tracked during 1993 and 1995. Migratory tracks and ocean areas with concentrated activity, presumed to be foraging grounds, were established from location data gathered by attached geolocation-time depth recorders. The seals ranged widely (811–3258 km) and foraging activity centred on oceanographic frontal systems, especially the Antarctic Polar Front and bathymetric features such as the Campbell Plateau region. The seals spent 58.6% of their sea time within managed fishery areas while the remainder was spent on the high seas, an area of unregulated fishing. The Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) areas 58.4.1, 88.2 and especially 88.1 were important and distant foraging areas for these juvenile elephant seals. From fisheries records, diet and the foraging ecology studies of the seals there appears to be little, if any, overlap or conflict between the seals and commercial fishing operations within the regulated commercial areas. However, attention is drawn to the possibility of future interactions if Southern Ocean fisheries expand or new ones commence.
An Efficient Synthesis of 5,5′-(Tetradecane-1,14-diyl)bis(2-methylbenzene-1,3-diol) and Related Substances
Authors: Tran Van H. , Roufogalis Basil D. , Duke Colin C.
Published: April 2004

An efficient and versatile method was developed to synthesize
5,5′-(tetradecane-1,14-diyl)bis(2-methylbenzene-1,3-diol) (striatol), a
minor component of the plant Grevillea striata
(Proteaceae family). Other substances prepared in high yield by the method
include 5,5′-(dodecane-1,12-diyl)bis(2-methylbenzene-1,3-diol),
5,5′-(decane-1,10-diyl)bis(2-methylbenzene-1,3-diol),
5,5′-(octane-1,8-diyl)bis(2-methylbenzene-1,3-diol) and
2-methyl-5-nonylresorcinol
Synthesis of the Tetrahydrooxazolo[2,3-b][3]benzazepin-3(2H)-one System and X-Ray Crystal Structure of an 11a-Ethoxy Derivative
Authors: Bremner John B. , Rezaie Robert , Skelton Brian W. , White Allan H.
Published: April 2004

Photolysis of the N-chloroacetyl imide derivative
3-chloroacetyl-7,8-dimethoxy-4,5-dihydro-1H-3-benzazepin-2(3H)-one
(2) in aqueous acetonitrile gave
11a-hydroxy-8,9-dimethoxy-5,6,11,11a-tetrahydro-oxazolo[2,3-b][3]benzazepin-3(2H)-one
(4) in 81% yield. This representative of a new heterocyclic system
could be converted into the 11a-ethoxy derivative (5) by recrystallization
from ethanol. The structure of (5) was confirmed by a room-temperature
single-crystal X-ray study. Crystals are monoclinic,
Cc, a
17·623(9), b 7·550(4),
c 12·872(3) Å, β 112·55(4)°,
Z = 4; conventional R on
F was 0·034 for 1072 ‘observed’ (I
> 3σ(I)) reflections.
Metabolic syndrome without obesity: Hepatic overexpression of 11β-hydroxysteroid dehydrogenase type 1 in transgenic mice
Authors: Paterson Janice M. , Morton Nicholas M. , Fievet Catherine , Kenyon Christopher J. , Holmes Megan C. , Staels Bart , Seckl Jonathan R. , Mullins John J.
Published: April 2004

In obese humans and rodents there is increased expression of the key glucocorticoid (GC) regenerating enzyme, 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1), in adipose tissue. This increased expression appears to be of pathogenic importance because transgenic mice overexpressing 11β-HSD1 selectively in adipose tissue exhibit a full metabolic syndrome with visceral obesity, dyslipidemia, insulin-resistant diabetes, and hypertension. In this model, while systemic plasma GC levels are unaltered, GC delivery to the liver via the portal vein is increased. 11β-HSD1 is most highly expressed in liver where inhibition or deficiency of its activity improves glucose and lipid homeostasis. To determine the potential contribution of elevated intrahepatic GCs alone toward development of insulin-resistant syndromes we generated transgenic mice expressing increased 11β-HSD1 activity selectively in the liver under transcriptional control of hepatic regulatory sequences derived from the human apoE gene (apoE-HSD1). Transgenic lines with 2- and 5-fold-elevated 11β-HSD1 activity exhibited mild insulin resistance without altered fat depot mass. ApoE-HSD1 transgenic mice exhibited fatty liver and dyslipidemia with increased hepatic lipid synthesis/flux associated with elevated hepatic LXRα and PPARα mRNA levels as well as impaired hepatic lipid clearance. Further, apoE-HSD1 transgenic mice have a marked, transgene-dose-associated hypertension paralleled by incrementally increased liver angiotensinogen expression. These data suggest that elevated hepatic expression of 11β-HSD1 may relate to the pathogenesis of specific fatty liver, insulin-resistant, and hypertensive syndromes without obesity in humans as may occur in, for example, myotonic dystrophy, and possibly, the metabolically obese, normal-weight individual.
Structural and functional analysis of
Aplysia
attractins, a family of water-borne protein pheromones with interspecific attractiveness
Authors: Painter Sherry D. , Cummins Scott F. , Nichols Amy E. , Akalal David-B. G. , Schein Catherine H. , Braun Werner , Smith John S. , Susswein Abraham J. , Levy Miriam , de Boer Pamela A. C. M. , ter Maat Andries , Miller Mark W. , Scanlan Cory , Milberg Richard M. , Sweedler Jonathan V. , Nagle Gregg T.
Published: April 2004

Mate attraction in
Aplysia
involves a long-distance water-borne signal (the protein pheromone attractin), which is released during egg laying.
Aplysia californica
attractin attracts species that produce closely related attractins, such as
Aplysia brasiliana
, whose geographic distribution does not overlap that of
A. californica
. This finding suggests that other mollusks release attractin-related pheromones to form and maintain breeding aggregations. We describe four additional members of the attractin family:
A. brasiliana
,
Aplysia fasciata
,
Aplysia depilans
(which aggregates with
A. fasciata
aggregations), and
Aplysia vaccaria
(which aggregates with
A. californica
aggregations). On the basis of their sequence similarity with
A. californica
attractin, the attractin proteins fall into two groups:
A. californica
,
A. brasiliana
, and
A. fasciata
(91–95% identity), and
A. depilans
and
A. vaccaria
(41–43% identity). The sequence similarity within the attractin family, the conserved six cysteines, and the compact fold of the NMR solution structure of
A. californica
attractin suggest a common fold for this pheromone family containing two antiparallel helices. The second helix contains the IEECKTS sequence conserved in
Aplysia
attractins. Mutating surface-exposed charged residues within this heptapeptide sequence abolishes attractin activity, suggesting that the second helix is an essential part of the receptor-binding interface.
Dual architectural roles of HU: Formation of flexible hinges and rigid filaments
Authors: van Noort John , Verbrugge Sander , Goosen Nora , Dekker Cees , Dame Remus Thei
Published: April 2004

The nucleoid-associated protein HU is one of the most abundant proteins in
Escherichia coli
and has been suggested to play an important role in bacterial nucleoid organization and regulation. Although the regulatory aspects of HU have been firmly established, much less is understood about the role of HU in shaping the bacterial nucleoid. In both functions (local) modulation of DNA architecture seems an essential feature, but information on the mechanical properties of this type of sequence-independent nucleoprotein complex is scarce. In this study we used magnetic tweezers and atomic force microscopy to quantify HU-induced DNA bending and condensation. Both techniques revealed that HU can have two opposing mechanical effects depending on the protein concentration. At concentrations <100 nM, individual HU dimers induce very flexible bends in DNA that are responsible for DNA compaction up to 50%. At higher HU concentrations, a rigid nucleoprotein filament is formed in which HU appears to arrange helically around the DNA without inducing significant condensation.
Specialization of primary auditory cortex processing by sound exposure in the “critical period”
Authors: Nakahara Haruka , Zhang Li I. , Merzenich Michael M.
Published: April 2004

Environmental acoustic exposure to a complex tone sequence within the critical period in infant rats resulted in the emergence of large-scale, selective changes that radically altered primary auditory cortex (A1) organization. In the sound exposure-revised A1, responses were segregated into two explicit zones representing spectrally and temporally separated lower and higher frequency tone sequence progressions. Cortical neurons between these two A1 zones were poorly driven by sound stimuli. Stimulus sequence-specific (“combination-selective”) responses emerged in the A1 of exposed rats. These selective representational changes induced in the critical period persisted into adulthood. These results show that the temporal order and pace of early, repetitive postnatal auditory inputs strongly affect the emergent and enduring functional organization of A1.
Deficiency of carbohydrate response element-binding protein (ChREBP) reduces lipogenesis as well as glycolysis
Authors: Iizuka Katsumi , Bruick Richard K. , Liang Guosheng , Horton Jay D. , Uyeda Kosaku
Published: April 2004

The liver provides for long-term energy needs of the body by converting excess carbohydrate into fat for storage. Insulin is one factor that promotes hepatic lipogenesis, but there is increasing evidence that glucose also contributes to the coordinated regulation of carbohydrate and fat metabolism in liver by mechanisms that are independent of insulin. In this study, we show that the transcription factor, carbohydrate response element-binding protein (ChREBP), is required both for basal and carbohydrate-induced expression of several liver enzymes essential for coordinated control of glucose metabolism, fatty acid, and the synthesis of fatty acids and triglycerides
in vivo
.
Invasion of a rocky intertidal shore by the tunicatePyura praeputialisin the Bay of Antofagasta, Chile
Authors: Castilla Juan Carlos , Guiñez Ricardo , Caro Andrés U. , Ortiz Verónica
Published: April 2004

Invasion by marine nonindigenous species (NIS) is a spread phenomenon. The tunicatePyura praeputialisshows pronounced disjoint geographical distribution: along thousands of kilometers in wave-swept headlands on the southeastern coast of Australia, from where it appears to have originated, and exclusively along 60–70 km inside the Bay of Antofagasta, Chile. mtDNA sequences suggested that the species invaded this rocky shore recently. We used field manipulations and juvenileP. praeputialistransplant techniques to test hypotheses regarding the capacity of the tunicate to survive and grow at different sites and tidal heights inside and outside Antofagasta, and its competitive performance for primary space (inside the Bay) against the native musselPerumytilus purpuratus. We conclude that survival and growth ofP. praeputialisshowed no significant differences among sites inside and outside the Bay, and suggest that the restrictive distribution of the species in Chile is caused by a specific oceanographic retention mechanism and/or its brief larval dispersal. We demonstrated that, inside the Bay,P. praeputialisoutcompetesPerumytilusfrom the Mid–Low intertidal, constrainingPerumytilusto the Upper Mid-Intertidal, modifying the local pattern of intertidal zonation. We show that predation onP. praeputialisjuveniles by starfish and snails constitutes a regulatory mechanism for the setting of its low intertidal limit. Major ecological impacts caused by NIS invasions to rocky shores by aggressive primary space users may result in negative aspects, but also may contribute to biodiversity enhancement. We call attention to the need for increment manipulations and testing of ecological hypotheses regarding marine NIS.
A mutant spacer sequence between -35 and -10 elements makes the

P
lac

promoter hyperactive and cAMP receptor protein-independent
Authors: Liu Mofang , Tolstorukov Michael , Zhurkin Victor , Garges Susan , Adhya Sankar
Published: April 2004

To determine whether the spacer region between the -35 and -10 elements plays any sequence-specific role, we randomized the GC-rich sequence (
-20
CCGGCTCG
-13
) within the spacer region of the cAMP-dependent
lac
promoter and selected an activator-independent mutant, which showed extraordinarily high intrinsic activity. The hyperactive promoter is obtained by incorporation of a specific 10-bp-long AT-rich DNA sequence within the spacer, referred to as the -15 sequence, which must be juxtaposed to the upstream end of the -10 sequence for the hyperactivity. The transcription enhancement functions only in the presence of a -35 element. The spacer sequence enhanced both RNA polymerase binding and open complex formation. Isolated in the
lac
promoter, it also enhanced transcription when placed at two other unrelated promoters. Sequence analysis shows a low GC content and an abundance of stereochemically flexible TG:CA and TA:TA dimeric steps in the -18/-9 region and a strong correlation between the presence of flexible dimeric steps in this region and the intrinsic strength of the promoter.
Secreted transforming growth factor β2 activates NF-κB, blocks apoptosis, and is essential for the survival of some tumor cells
Authors: Lu Tao , Burdelya Lyudmila G. , Swiatkowski Shannon M. , Boiko Alexander D. , Howe Philip H. , Stark George R. , Gudkov Andrei V.
Published: April 2004

The basis of constitutive activation of NF-κB, essential for survival and resistance to apoptosis in many tumors, is not well understood. We find that transforming growth factor β2 (TGFβ2), predominantly in its latent form, is secreted by several different types of tumor cell lines that exhibit constitutively active NF-κB and that TGFβ2 potently stimulates the activation of NF-κB in reporter cells. Suppression of TGFβ2 expression by small interfering RNA kills prostate cancer PC3 cells, indicating that the TGFβ2–NF-κB pathway is important for their viability. These findings identify TGFβ2 as a potential target for therapeutic strategies to inhibit the growth of tumor cells that depend on constitutively active NF-κB, or to sensitize them to treatment with cytotoxic drugs.
Selective vulnerability of dentate granule cells prior to amyloid deposition in PDAPP mice: Digital morphometric analyses
Authors: Wu Chi-Cheng , Chawla Faisal , Games Dora , Rydel Russell E. , Freedman Stephen , Schenk Dale , Young Warren G. , Morrison John H. , Bloom Floyd E.
Published: April 2004

Increasing evidence from mouse models of Alzheimer's disease shows that overexpression of a mutant form of the amyloid precursor protein (APP) and its product, β-amyloid peptide, initiate pathological changes before amyloid deposition. To evaluate the cytological basis for one of these early changes, namely reduced volume of the dentate gyrus (DG), we have used high-throughput diOlistic cell loading and 3D neuronal reconstruction to investigate potential dendritic pathology of granule cells (GCs) in 90-day-old PDAPP mice. Labeled GCs from fixed hippocampal slices were selected randomly and imaged digitally by using confocal laser-scanning microscopy. The dendritic complexity of GCs was quantified according to subordinate morphological parameters, including soma position within the granule cell layer (superficial versus deep) and topographic location within the DG (dorsal versus ventral blade) along the anterior-posterior hippocampal axis. Initial analysis, which included all sampled GC types, revealed a 12% reduction of total dendritic length in PDAPP mice compared with littermate controls. Further analysis, performed with refined subgroups, found that superficially located GCs in the dorsal blade were profoundly altered, exhibiting a 23% loss in total dendritic length, whereas neurons in the ventral blade were unaffected. Superficial GCs were particularly vulnerable (a 32% reduction) in the posterior region of the DG. Furthermore, the dendritic reductions of this select group were uniformly localized within middle-to-outer portions of the dentate molecular layer. We conclude that substantial dendritic pathology is evident in 90-day-old PDAPP mice for a spatially defined subset of GCs well before amyloid accumulation occurs.
Directed evolution of protein enzymes using nonhomologous random recombination
Authors: Bittker Joshua A. , Le Brian V. , Liu Jane M. , Liu David R.
Published: April 2004

We recently reported the development of nonhomologous random recombination (NRR) as a method for nucleic acid diversification and applied NRR to the evolution of DNA aptamers. Here, we describe a modified method, protein NRR, that enables proteins to access diversity previously difficult or impossible to generate. We investigated the structural plasticity of protein folds and the ability of helical motifs to function in different contexts by applying protein NRR and
in vivo
selection to the evolution of chorismate mutase (CM) enzymes. Functional CM mutants evolved using protein NRR contained many insertions, deletions, and rearrangements. The distribution of these changes was not random but clustered in certain regions of the protein. Topologically rearranged but functional enzymes also emerged from these studies, indicating that multiple connectivities can accommodate a functional CM active site and demonstrating the ability to generate new domain connectivities through protein NRR. Protein NRR was also used to randomly recombine CM and fumarase, an unrelated but also α-helical protein. Whereas the resulting library contained fumarase fragments in many contexts before functional selection, library members surviving selection for CM activity invariably contained a CM core with fumarase sequences found only at the termini or in one loop. These results imply that internal helical fragments cannot be swapped between these proteins without the loss of nearly all CM activity. Our findings suggest that protein NRR will be useful in probing the functional requirements of enzymes and in the creation of new protein topologies.
Defective Suppressor Function of Human CD4+ CD25+ Regulatory T Cells in Autoimmune Polyglandular Syndrome Type II
Authors: Kriegel Martin A. , Lohmann Tobias , Gabler Christoph , Blank Norbert , Kalden Joachim R. , Lorenz Hanns-Martin
Published: April 2004

In autoimmune polyglandular syndromes (APS), several organ-specific autoimmune diseases are clustered. Although APS type I is caused by loss of central tolerance, the etiology of APS type II (APS-II) is currently unknown. However, in several murine models, depletion of CD4+ CD25+ regulatory T cells (Tregs) causes a syndrome resembling human APS-II with multiple endocrinopathies. Therefore, we hypothesized that loss of active suppression in the periphery could be a hallmark of this syndrome. Tregs from peripheral blood of APS-II, control patients with single autoimmune endocrinopathies, and normal healthy donors showed no differences in quantity (except for patients with isolated autoimmune diseases), in functionally important surface markers, or in apoptosis induced by growth factor withdrawal. Strikingly, APS-II Tregs were defective in their suppressive capacity. The defect was persistent and not due to responder cell resistance. These data provide novel insights into the pathogenesis of APS-II and possibly human autoimmunity in general.
Somatic Hypermutation Is Limited by CRM1-dependent Nuclear Export of Activation-induced Deaminase
Authors: McBride Kevin M. , Barreto Vasco , Ramiro Almudena R. , Stavropoulos Pete , Nussenzweig Michel C.
Published: April 2004

Somatic hypermutation (SHM) and class switch recombination (CSR) are initiated in activated B lymphocytes by activation-induced deaminase (AID). AID is thought to make lesions in DNA by deaminating cytidine residues in single-stranded DNA exposed by RNA polymerase during transcription. Although this must occur in the nucleus, AID is found primarily in the cytoplasm. Here we show that AID is actively excluded from the nucleus by an exportin CRM1-dependent pathway. The AID nuclear export signal (NES) is found at the carboxyl terminus of AID in a region that overlaps a sequence required for CSR but not SHM. We find that AID lacking a functional NES causes more hypermutation of a nonphysiologic target gene in transfected fibroblasts. However, the NES does not impact on the rate of mutation of immunoglobulin genes in B lymphocytes, suggesting that the AID NES does not limit AID activity in these cells.
Ent5p Is Required with Ent3p and Vps27p for Ubiquitin-dependent Protein Sorting into the Multivesicular Body
Authors: Eugster Anne , Pécheur Eve-Isabelle , Michel Fabrice , Winsor Barbara , Letourneur François , Friant Sylvie
Published: April 2004

At the late endosomes, cargoes destined for the interior of the vacuole are sorted into invaginating vesicles of the multivesicular body. Both PtdIns(3,5)P2 and ubiquitin are necessary for proper sorting of some of these cargoes. We show that Ent5p, a yeast protein of the epsin family homologous to Ent3p, localizes to endosomes and specifically binds to PtdIns(3,5)P2 via its ENTH domain. In cells lacking Ent3p and Ent5p, ubiquitin-dependent sorting of biosynthetic and endocytic cargo into the multivesicular body is disrupted, whereas other trafficking routes to the vacuole are not affected. Ent3p and Ent5p are associated with Vps27p, a FYVE domain containing protein that interacts with ubiquitinated cargoes and is required for protein sorting into the multivesicular body. Therefore, Ent3p and Ent5p are the first proteins shown to be connectors between PtdIns(3,5)P2- and the Vps27p-ubiquitin-driven sorting machinery at the multivesicular body.
Selective Stimulation of Caveolar Endocytosis by Glycosphingolipids and Cholesterol
Authors: Sharma Deepak K. , Brown Jennifer C. , Choudhury Amit , Peterson Timothy E. , Holicky Eileen , Marks David L. , Simari Robert , Parton Robert G. , Pagano Richard E.
Published: April 2004

Internalization of some plasma membrane constituents, bacterial toxins, and viruses occurs via caveolae; however, the factors that regulate caveolar internalization are still unclear. Here, we demonstrate that a brief treatment of cultured cells with natural or synthetic glycosphingolipids (GSLs) or elevation of cholesterol (either by acute treatment with mβ-cyclodextrin/cholesterol or by alteration of growth conditions) dramatically stimulates caveolar endocytosis with little or no effect on other endocytic mechanisms. These treatments also stimulated the movement of GFP-labeled vesicles in cells transfected with caveolin-1-GFP and reduced the number of surface-connected caveolae seen by electron microscopy. In contrast, overexpression of caveolin-1 decreased caveolar uptake, but treatment with GSLs reversed this effect and stimulated caveolar endocytosis. Stimulation of caveolar endocytosis did not occur using ceramide or phosphatidylcholine and was not due to GSL degradation because similar results were obtained using a nonhydrolyzable GSL analog. Stimulated caveolar endocytosis required src kinase and PKC-α activity as shown by i) use of pharmacological inhibitors, ii) expression of kinase inactive src or dominant negative PKCα, and iii) stimulation of src kinase activity upon addition of GSLs or cholesterol. These results suggest that caveolar endocytosis is regulated by a balance of caveolin-1, cholesterol, and GSLs at the plasma membrane.
PaVESy: Pathway Visualization and Editing System
Authors: Lüdemann Alexander , Weicht Daniel , Selbig Joachim , Kopka Joachim
Published: April 2004

Summary: A data managing system for editing and visualization of biological pathways is presented. The main component of PaVESy (Pathway Visualization and Editing System) is a relational SQL database system. The database design allows storage of biological objects, such as metabolites, proteins, genes and respective relations, which are required to assemble metabolic and regulatory biological interactions. The database model accommodates highly flexible annotation of biological objects by user-defined attributes. In addition, specific roles of objects are derived from these attributes in the context of user-defined interactions, e.g. in the course of pathway generation or during editing of the database content. Furthermore, the user may organize and arrange the database content within a folder structure and is free to group and annotate database objects of interest within customizable subsets. Thus, we allow an individualized view on the database content and facilitate user customization. A JAVA-based class library was developed, which serves as the database programming interface to PaVESy. This API provides classes, which implement the concepts of object persistence in SQL databases, such as entries, interactions, annotations, folders and subsets. We created editing and visualization tools for navigation in and visualization of the database content. User approved pathway assemblies are stored and may be retrieved for continued modification, annotation and export. Data export is interfaced with a range of network visualization programs, such as Pajek or other software allowing import of SBML or GML data format.

Availability:  http://pavesy.mpimp-golm.mpg.de/
RISC is a 5′ phosphomonoester-producing RNA endonuclease
Authors: Martinez Javier , Tuschl Thomas
Published: April 2004

Gene silencing in the process of RNA interference is mediated by a ribonucleoprotein complex referred to as RNA-induced silencing complex (RISC). Here we describe the molecular mechanism of target RNA cleavage using affinity-purified minimal RISC from human cells. Cleavage proceeds via hydrolysis and the release of a 3′-hydroxyl and a 5′-phosphate terminus. Substitution of the 2′-hydroxyl group at the cleavage site by 2′-deoxy had no significant effect, suggesting that product release and/or a conformational transition rather than a chemical step is rate-limiting. Substitution by 2′-O-methyl at the cleavage site substantially reduced cleavage, which is presumably due to steric interference. Mutational analysis of the target RNA revealed that mismatches across from the 5′ or the 3′ end of the siRNA had little effect and that substrate RNAs as short as 15 nucleotides were cleaved by RISC.
Return migration of one‐sea‐winter Atlantic salmon in the River Tana
Authors: Karppinen P. , Erkinaro J. , Niemelä E. , Moen K. , Økland F.
Published: April 2004

Fifty‐three one‐sea‐winter Atlantic salmonSalmo salar(45–63 cmLT) were radio‐tagged in the Tana fjord, Barents Sea, in 1995. Thirty‐seven fish (70%) entered the freshwater zone of the River Tana in an average of 3 days after release in the fjord. The migration speeds in the lowest river section below the first riffle area were significantly higher than in the subsequent river section below the second riffle area. Similarly, the observed time spent in the first riffle area was significantly lower than in the next riffle area. The majority of Atlantic salmon entered the river during the hours of high tide and the subsequent ebb tide. In addition, most river entries were recorded around midnight. No effects of river flow on the river entry or migration speed were detected, but the migration speed of Atlantic salmon in both river sections examined was greater at lower temperatures. Twenty‐eight fish (72%) were recaptured in the river, 71% of them with weirs and gillnets, and 29% by rod and line. Over half of the Atlantic salmon (54%) were recaptured within 3 weeks following river entry, and within the first 100 km of the river (56%). The results are discussed in relation to earlier studies on multi‐sea‐winter Atlantic salmon in the River Tana.
Changes in movement, range and habitat preferences of adult grayling from late summer to early winter
Authors: Nykänen M. , Huusko A. , Lahti M.
Published: April 2004

Radio‐tagged adult graylingThymallus thymallus(n = 22), monitored from mid August to mid December 1999 in the River Kuusinkijoki, Finland, shifted by the end of September (water temperature 10·0–14·5° C) from riffle sites to deeper and slower pool sites 0·7–1·6 km up‐ or downstream. In early winter (c. 0° C water temperature), eight of 13 fish still under study made a further shift into new pool sites, possibly triggered by ice formation. The summer range of grayling in the riffles was smaller (mean ± s.d. length: 75 ± 146 m) than the autumn range (99 ± 46 m) in the pools, but gross daily movements were equally short in both the seasons (18 ± 34 m and 15 ± 7 m, respectively). In late summer, adult grayling preferred water depths 80–120 cm and mean velocities >40 cm s−1. In autumn, the preferred ranges were 100–240 cm and <30 cm s−1, respectively. Substratum was mainly boulders in the summer sites, and gravel or pebbles in the autumn sites.
Patterns of oocyte growth, vitellogenin and gonadal steroid concentrations in greenback flounder
Authors: Sun B. , Pankhurst N. W.
Published: April 2004

The pattern of oocyte development in association with changes of plasma concentrations of vitellogenin (Vtg), 17β‐oestradiol (E2) and testosterone (T) was investigated in maturing female greenback flounder Rhombosolea tapirina over the first part of a reproductive season (February to June). Examination of oocyte size‐frequency distributions showed that the oocyte developmental pattern in R. tapirina is multiple group synchrony, and that reproductively mature fish were present at all sampling times. There were no significant temporal variations in the gonado‐somatic index (IG), hepato‐somatic index (IH), or plasma concentrations of Vtg, E2 and T during the sampling period, which indicates that reproductive development is not synchronized within the population. Significant increases in IG, IH and plasma concentrations of Vtg, E2 and T, however, were observed in vitellogenic fish, and in fish undergoing final maturation. A positive relationship was also found between the growth of oocytes and plasma concentrations of Vtg, E2 and T, although the patterns of increase were different for each variable. Plasma concentrations of Vtg and E2 rose steadily across oocyte sizes from 100 to 450 μm, but the rate of increase of plasma E2 was slower than that of Vtg, and both reached a saturated concentration at oocyte sizes of c. 450 μm. In contrast, plasma concentrations of T showed no marked increase until oocytes grew beyond 400 μm.
Artificial hybrid between Anguilla anguilla and A. japonica
Authors: Okamura A. , Zhang H. , Utoh T. , Akazawa A. , Yamada Y. , Horie N. , Mikawa N. , Tanaka S. , Oka H. P.
Published: April 2004

Interspecific hybrids were obtained by artificial insemination between male European eels Anguilla anguilla and female Japanese eels Anguilla japonica. The hybrid larvae developed normally and survived up to 30 days post‐hatching similarly to normal A. japonica larvae.
Partial purification of proteases that are generated by processing of the Northern shrimp Pandalus borealis and which can tenderize beef
Authors: Aoki Hitoshi , Ahsan Md. Nazmul , Matsuo Kenji , Hagiwara Toshihiko , Watabe Shugo
Published: April 2004

The crude extracts obtained from the heads of Northern shrimps, Pandalus borealis, (adapted to cold), showed considerable collagenolytic activities. When tested for beef tenderization, resulted in an overdegradation of meat proteins, which was detected organoleptically. Subsequently, four fractions with proteolytic activity were partially purified from the crude extracts by hydroxyapatite followed by MonoQ or Superdex 200 column chromatography. Warner‐Bratzler shear force values of steaks treated with three protease fractions (Q, S2, S3) at 10 °C were significantly lower (P < 0.01) than that of the control and the enzyme preparations were completely inactivated after mild heat treatment. These results suggest that the potential for Northern shrimp enzymes to be used in industrial processes, particularly in the food industry, is quite large, where working at lower temperatures to prevent undesirable chemical reactions is necessary.
The emulsifying properties of a polysaccharide isolated from the fruit of Cordia abyssinica
Authors: Benhura Mudadi Albert Nhamoiesu , Chidewe Cathrine Katayi
Published: April 2004

Polysaccharide was isolated from Cordia abyssinica and its effect, at differing concentrations, on its emulsifying ability was determined. Emulsions of vegetable oil containing up to 1% of the polysaccharide in phosphate pH 7.4 buffer, were prepared by using a hand piston homogenizer. Emulsification was assessed by diluting samples of the emulsions in sodium dodecyl sulphate and measuring absorbance at 500 nm. Addition of increasing concentrations of the polysaccharide up to 1% enhanced emulsification and emulsion stability. Above 1% concentration the polysaccharide solutions were too viscous for making emulsions conveniently. At a constant concentration of the polysaccharide, addition of up to a 1% concentration of salt enhanced emulsion formation. Further addition of salt above 1% resulted in no further changes in emulsifying ability, but the stability of the emulsions formed decreased on increasing the concentration of salt above 1%. The effect of pH on emulsifying ability was investigated by preparing emulsions using buffers of different pH, from pH 3 to pH 13. The polysaccharide had poor emulsifying ability below pH 7. Emulsifying ability increased with pH between pH 7 and 11. At pH above 11 there was a decrease in emulsifying ability.
Metabolism of oligosaccharides and aldehydes and production of organic acids in soymilk by probiotic bifidobacteria
Authors: Tsangalis Dimitri , Shah Nagendra P.
Published: April 2004

Four strains of Bifidobacterium were assessed for α‐galactosidase activity in MRS broth using p‐nitrophenyl‐α‐d‐galactopyranoside as substrate. Bifidobacteria were then used to ferment soymilk prepared from soy protein isolate (SPI), with and without d‐glucose and l‐cysteine supplementation. Measurements of pH and the quantification of oligosaccharides, organic acids and aldehydes in soymilk were done after 0, 12, 24, 36 and 48 h of incubation. The presence of d‐raffinose stimulated the α‐galactosidase activity of B. longum BB536 (BB536) and B. pseudolongum 20099 (BP20099). In soymilk, oligosaccharides and aldehydes were effectively metabolized by Bifidobacterium; d‐glucose and l‐cysteine supplementation enhanced the hydrolysis of raffinose and stachyose. BB536 and BP20099 degraded a significantly greater level of oligosaccharides and aldehydes than B. animalis Bb‐12 and B. longum 1941 (P < 0.05). Raffinose and stachyose were completely metabolized by BB536 after 48 h. In soymilk without any supplementation, hexanal and pentanal were not detected after 12 h of fermentation with BB536 and BP20099. BB536 was the highest producer of organic acids, with an average acetic acid/l(+)‐lactic acid ratio of 0.7.