bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of InGaAs quantum dot molecules
Authors: Lee J. H. , Sablon K. , Wang Zh. M. , Salamo G. J.
Published: March 2008

The formation and evolution process of self-assembled InGaAs quantum dot molecules (QDMs) are studied in terms of configuration, volume, and types of QDMs. QDMs are formed around self-assembled GaAs nanoscale island induced by adapting a hybrid growth approach combining droplet homoepitaxy and Stranski–Krastanov mode. In distinction from our previous results [Lee et al., Appl. Phys. Lett. 89, 202101 (2006)], hexa-QDMs are fabricated without the formation of background QDs, which can be due to a combinational effects of enhanced intermixing of Ga and In atoms, enhanced surface diffusion (high mobility) of adatoms, and higher In desorption rate due to the higher thermal energy provided during the fabrication of QDMs. In addition, a detailed evolution mechanism from bi-QDMs (two QDs per each GaAs island) to hexa-QDMs (six QDs per island) is proposed based on atom diffusion, material transfer, and equilibrium dimension (saturation) of QDs. Under a fixed InAs coverage, depending on postannealing process after liquid Ga droplet formation, highly uniform as well as various types of QDMs can be fabricated and the resulting configurations show a very strong correlation with the size of initial GaAs islands. With relatively smaller GaAs islands, quad-QDMs (four QDs per island) with a squarelike configuration were formed and also, quad-QDMs with a rectangularlike positioning were fabricated with relatively larger size of islands, while hexa-QDMs were formed with middle sized ones. Relatively, broader size distribution of GaAs nanoisland can be a direct result of Ostwald ripening, which can be well controlled by adjusting postgrowth interruption of liquid Ga droplets.
Spectroscopic and structural studies of Sm2+ doped orthophosphate KSrPO4 crystal
Authors: Huang Yanlin , Kai Weifang , Cao Yonggang , Jang Kiwan , Lee Ho Sueb , Kim Ilgon , Cho Eunjin
Published: March 2008

Sm 2 + ions doped KSrPO4 were prepared by high-temperature solid-state reaction method. The samples were investigated by x-ray powder diffraction, photoluminescence excitation and emission spectra, and luminescence decay measurements. After excitation into the 4f55d1 levels, the emission of Sm2+ ions showed D05→FJ7 (J=0,1,2) emission together with the broad 5d→4f emission band. The luminescence of Sm2+ ions was sensitive to the temperature. With the decreasing of the temperature, the broad 5d→4f emission band of Sm2+ ions gradually quenched, while D05→FJ7 (J=0,1,2) emission lines could be clearly detectable. Based on the luminescence properties of Sm2+ ions and structure of KSrPO4 crystal, the crystallographic sites and the energy structure correlated with 4f→5d transitions of Sm2+ ions in KSrPO4 were discussed.
Functionally significant insulin-like growth factor I receptor mutations in centenarians
Authors: Suh Yousin , Atzmon Gil , Cho Mi-Ook , Hwang David , Liu Bingrong , Leahy Daniel J. , Barzilai Nir , Cohen Pinchas
Published: March 2008

Rather than being a passive, haphazard process of wear and tear, lifespan can be modulated actively by components of the insulin/insulin-like growth factor I (IGFI) pathway in laboratory animals. Complete or partial loss-of-function mutations in genes encoding components of the insulin/IGFI pathway result in extension of life span in yeasts, worms, flies, and mice. This remarkable conservation throughout evolution suggests that altered signaling in this pathway may also influence human lifespan. On the other hand, evolutionary tradeoffs predict that the laboratory findings may not be relevant to human populations, because of the high fitness cost during early life. Here, we studied the biochemical, phenotypic, and genetic variations in a cohort of Ashkenazi Jewish centenarians, their offspring, and offspring-matched controls and demonstrated a gender-specific increase in serum IGFI associated with a smaller stature in female offspring of centenarians. Sequence analysis of the
IGF1
and
IGF1
receptor (
IGF1R
) genes of female centenarians showed overrepresentation of heterozygous mutations in the
IGF1R
gene among centenarians relative to controls that are associated with high serum IGFI levels and reduced activity of the IGFIR as measured in transformed lymphocytes. Thus, genetic alterations in the human
IGF1R
that result in altered IGF signaling pathway confer an increase in susceptibility to human longevity, suggesting a role of this pathway in modulation of human lifespan.
RNAi-mediated suppression of
p
-coumaroyl-CoA 3′-hydroxylase in hybrid poplar impacts lignin deposition and soluble secondary metabolism
Authors: Coleman Heather D. , Park Ji-Young , Nair Ramesh , Chapple Clint , Mansfield Shawn D.
Published: March 2008

p
-Coumaroyl-CoA 3′-hydroxylase (C3′H) is a cytochrome P450-dependent monooxygenase that catalyzes the 3′-hydroxylation of
p
-coumaroyl shikimate and
p
-coumaroyl quinate. We used RNA interference to generate transgenic hybrid poplar suppressed in C3′H expression and analyzed them with respect to transcript abundance, cell wall structure and chemical composition, and soluble metabolite levels. RT-PCR expression profiles confirmed the down-regulation of C3′H in a number of lines, which generally correlated very well with reduced total cell wall lignin content. The most strongly repressed line was chosen for further analysis and compared with the wild-type trees. In-depth characterization revealed that along with the significant decrease in total lignin content, a significant shift in lignin monomer composition was observed, favoring the generation of
p
-hydroxyphenyl units at the expense of guaiacyl units while the proportion of syringyl moieties remained constant. Suppression of C3′H also resulted in the accumulation of substantial pools of 1-
O-p
-coumaroyl-β-
d
-glucoside and other phenylpropanoid glycosides, and
p
-coumaroyl shikimate, providing further insight into the role of C3′H in the lignin biosynthetic pathway. The data presented indicate that when down-regulated, C3′H becomes a rate-limiting step in lignin biosynthesis and further support the involvement of hydroxycinnamic acid shikimate esters in the lignin biosynthetic pathway.
In vivo
hyperspectral confocal fluorescence imaging to determine pigment localization and distribution in cyanobacterial cells
Authors: Vermaas Wim F. J. , Timlin Jerilyn A. , Jones Howland D. T. , Sinclair Michael B. , Nieman Linda T. , Hamad Sawsan W. , Melgaard David K. , Haaland David M.
Published: March 2008

Hyperspectral confocal fluorescence imaging provides the opportunity to obtain individual fluorescence emission spectra in small (≈0.03-μm
3
) volumes. Using multivariate curve resolution, individual fluorescence components can be resolved, and their intensities can be calculated. Here we localize,
in vivo
, photosynthesis-related pigments (chlorophylls, phycobilins, and carotenoids) in wild-type and mutant cells of the cyanobacterium
Synechocystis
sp. PCC 6803. Cells were excited at 488 nm, exciting primarily phycobilins and carotenoids. Fluorescence from phycocyanin, allophycocyanin, allophycocyanin-B/terminal emitter, and chlorophyll
a
was resolved. Moreover, resonance-enhanced Raman signals and very weak fluorescence from carotenoids were observed. Phycobilin emission was most intense along the periphery of the cell whereas chlorophyll fluorescence was distributed more evenly throughout the cell, suggesting that fluorescing phycobilisomes are more prevalent along the outer thylakoids. Carotenoids were prevalent in the cell wall and also were present in thylakoids. Two chlorophyll fluorescence components were resolved: the short-wavelength component originates primarily from photosystem II and is most intense near the periphery of the cell; and the long-wavelength component that is attributed to photosystem I because it disappears in mutants lacking this photosystem is of higher relative intensity toward the inner rings of the thylakoids. Together, the results suggest compositional heterogeneity between thylakoid rings, with the inner thylakoids enriched in photosystem I. In cells depleted in chlorophyll, the amount of both chlorophyll emission components was decreased, confirming the accuracy of the spectral assignments. These results show that hyperspectral fluorescence imaging can provide unique information regarding pigment organization and localization in the cell.
Microfluidic high-throughput encapsulation and hydrodynamic self-sorting of single cells
Authors: Chabert Max , Viovy Jean-Louis
Published: March 2008

We present a purely hydrodynamic method for the high-throughput encapsulation of single cells into picoliter droplets, and spontaneous self-sorting of these droplets. Encapsulation uses a cell-triggered Rayleigh–Plateau instability in a flow-focusing geometry, and self-sorting puts to work two extra hydrodynamic mechanisms: lateral drift of deformable objects in a shear flow, and sterically driven dispersion in a compressional flow. Encapsulation and sorting are achieved on-flight in continuous flow at a rate up to 160 cells per second. The whole process is robust and cost-effective, involving no optical or electrical discrimination, active sorting, flow switching, or moving parts. Successful encapsulation and sorting of 70–80% of the injected cell population into drops containing one and only one cell, with <1% contamination by empty droplets, is demonstrated. The system is also applied to the direct encapsulation and sorting of cancerous lymphocytes from a whole blood mixture, yielding individually encapsulated cancer cells with a >10,000-fold enrichment as compared with the initial mix. The method can be implemented in simple “soft lithography” chips, allowing for easy downstream coupling with microfluidic cell biology or molecular biology protocols.
The thermodynamic H
+
/ATP ratios of the H
+
-ATPsynthases from chloroplasts and
Escherichia coli
Authors: Steigmiller Stefan , Turina Paola , Gräber Peter
Published: March 2008

The H
+
/ATP ratio is an important parameter for the energy balance of all cells and for the coupling mechanism between proton transport and ATP synthesis. A straightforward interpretation of rotational catalysis predicts that the H
+
/ATP coincides with the ratio of the c-subunits to β-subunits, implying that, for the chloroplast and
Escherichia coli
ATPsynthases, numbers of 4.7 and 3.3 are expected. Here, the energetics described by the chemiosmotic theory was used to determine the H
+
/ATP ratio for the two enzymes. The isolated complexes were reconstituted into liposomes, and parallel measurements were performed under identical conditions. The internal phase of the liposomes was equilibrated with the acidic medium during reconstitution, allowing to measure the internal pH with a glass electrode. An acid–base transition was carried out and the initial rates of ATP synthesis or ATP hydrolysis were measured with luciferin/luciferase as a function of ΔpH at constant
Q
= [ATP]/([ADP][P
i
]). From the shift of the equilibrium ΔpH as a function of
Q
the standard Gibbs free energy for phosphorylation, Δ
G
p
0
′; and the H
+
/ATP ratio were determined. It resulted Δ
G
p
0
′ = 38 ± 3 kJ·mol
−1
and H
+
/ATP = 4.0 ± 0.2 for the chloroplast and H
+
/ATP = 4.0 ± 0.3 for the
E. coli
enzyme, indicating that the thermodynamic H
+
/ATP ratio is the same for both enzymes and that it is different from the subunit stoichiometric ratio.
Rapid evolution of seed dispersal in an urban environment in the weedCrepis sancta
Authors: Cheptou P.-O. , Carrue O. , Rouifed S. , Cantarel A.
Published: March 2008

Dispersal is a ubiquitous trait in living organisms. Evolutionary theory postulates that the loss or death of propagules during dispersal episodes (cost of dispersal) should select against dispersal. The cost of dispersal is expected to be a strong selective force in fragmented habitats. We analyzed patchy populations of the weedCrepis sanctaoccupying small patches on sidewalks, around trees planted within the city of Montpellier (South of France), to investigate the recent evolutionary consequences of the cost of dispersal.C. sanctaproduces both dispersing and nondispersing seeds. First, we showed that, in urban patches, dispersing seeds have a 55% lower chance of settling in their patch compared with nondispersing seeds and, thus, fall on a concrete matrix unsuitable for germination. Second, we showed that the proportion of nondispersing seeds in urban patches measured in a common environment is significantly higher than in surrounding, unfragmented populations. Third, by using a quantitative genetic model, we estimated that the pattern is consistent with short-term evolution that occurs over ≈5–12 generations of selection, which is generated by a high cost of dispersal in urban populations. This study shows that a high cost of dispersal after recent fragmentation causes rapid evolution toward lower dispersal.
Cost-effective production of a vaginal protein microbicide to prevent HIV transmission
Authors: Ramessar Koreen , Rademacher Thomas , Sack Markus , Stadlmann Johannes , Platis Dimitris , Stiegler Gabriela , Labrou Nikos , Altmann Fritz , Ma Julian , Stöger Eva , Capell Teresa , Christou Paul
Published: March 2008

A series of small-molecule microbicides has been developed for vaginal delivery to prevent heterosexual HIV transmission, but results from human clinical trials have been disappointing. Protein-based microbicides, such as HIV-specific monoclonal antibodies, have been considered as an alternative approach. Despite their promising safety profile and efficacy, the major drawback of such molecules is the economy of large-scale production in mammalian cells, the current system of choice. Here, we show that an alternative biomanufacturing platform is now available for one of the most promising anti-HIV antibodies (2G12). Our data show that the HIV-neutralization capability of the antibody is equal to or superior to that of the same antibody produced in CHO cells. We conclude that this protein production system may provide a means to achieve microbicide ingredient manufacture at costs that would allow product introduction and manufacture in the developing world.
Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition
Authors: Shangary Sanjeev , Qin Dongguang , McEachern Donna , Liu Meilan , Miller Rebecca S. , Qiu Su , Nikolovska-Coleska Zaneta , Ding Ke , Wang Guoping , Chen Jianyong , Bernard Denzil , Zhang Jian , Lu Yipin , Gu Qingyang , Shah Rajal B. , Pienta Kenneth J. , Ling Xiaolan , Kang Sanmao , Guo Ming , Sun Yi , Yang Dajun , Wang Shaomeng
Published: March 2008

We have designed MI-219 as a potent, highly selective and orally active small-molecule inhibitor of the MDM2–p53 interaction. MI-219 binds to human MDM2 with a
K
i
value of 5 nM and is 10,000-fold selective for MDM2 over MDMX. It disrupts the MDM2–p53 interaction and activates the p53 pathway in cells with wild-type p53, which leads to induction of cell cycle arrest in all cells and selective apoptosis in tumor cells. MI-219 stimulates rapid but transient p53 activation in established tumor xenograft tissues, resulting in inhibition of cell proliferation, induction of apoptosis, and complete tumor growth inhibition. MI-219 activates p53 in normal tissues with minimal p53 accumulation and is not toxic to animals. MI-219 warrants clinical investigation as a new agent for cancer treatment.
Disclosure of the mycobacterial outer membrane: Cryo-electron tomography and vitreous sections reveal the lipid bilayer structure
Authors: Hoffmann Christian , Leis Andrew , Niederweis Michael , Plitzko Jürgen M. , Engelhardt Harald
Published: March 2008

The cell walls of mycobacteria form an exceptional permeability barrier, and they are essential for virulence. They contain extractable lipids and long-chain mycolic acids that are covalently linked to peptidoglycan via an arabinogalactan network. The lipids were thought to form an asymmetrical bilayer of considerable thickness, but this could never be proven directly by microscopy or other means. Cryo-electron tomography of unperturbed or detergent-treated cells of
Mycobacterium smegmatis
embedded in vitreous ice now reveals the native organization of the cell envelope and its delineation into several distinct layers. The 3D data and the investigation of ultrathin frozen-hydrated cryosections of
M. smegmatis
,
Myobacterium bovis
bacillus Calmette–Guérin, and
Corynebacterium glutamicum
identified the outermost layer as a morphologically symmetrical lipid bilayer. The structure of the mycobacterial outer membrane necessitates considerable revision of the current view of its architecture. Conceivable models are proposed and discussed. These results are crucial for the investigation and understanding of transport processes across the mycobacterial cell wall, and they are of particular medical relevance in the case of pathogenic mycobacteria.
The oldest North American primate and mammalian biogeography during the Paleocene–Eocene Thermal Maximum
Authors: Beard K. Christopher
Published: March 2008

Undoubted primates first appear almost synchronously in the fossil records of Asia, Europe, and North America. This temporal pattern has complicated efforts to reconstruct the early dispersal history of primates in relation to global climate change and eustatic fluctuations in sea level. Here, I describe fossils from the Tuscahoma Formation on the Gulf Coastal Plain of Mississippi documenting an anatomically primitive species ofTeilhardinathat is older than other North American and European primates. Consistent with its antiquity, a phylogenetic analysis of dental characters recognizesTeilhardina magnoliana, sp. nov., as the most basal member of this genus currently known from either North America or Europe. Its stratigraphic provenance demonstrates that primates originally colonized North America near the base of the Paleocene–Eocene Thermal Maximum (PETM), but before an important fall in eustatic sea level. Correlation based on carbon isotope stratigraphy and sequence stratigraphy indicates that the earliest North American primates inhabited coastal regions of the continent for thousands of years before they were able to colonize the Rocky Mountain Interior. The transient provincialism displayed by early North American primates corresponds to similar biogeographic patterns noted among fossil plants. Decreased precipitation in the Rocky Mountain Interior during the early part of the PETM may have been an important factor in maintaining biotic provincialism within North America at this time. These results underscore the need to obtain multiple, geographically dispersed records bearing on significant macroevolutionary events such as the PETM.
SymRK defines a common genetic basis for plant root endosymbioses with arbuscular mycorrhiza fungi, rhizobia, and
Frankia
bacteria
Authors: Gherbi Hassen , Markmann Katharina , Svistoonoff Sergio , Estevan Joan , Autran Daphné , Giczey Gabor , Auguy Florence , Péret Benjamin , Laplaze Laurent , Franche Claudine , Parniske Martin , Bogusz Didier
Published: March 2008

Root endosymbioses vitally contribute to plant nutrition and fitness worldwide. Nitrogen-fixing root nodulation, confined to four plant orders, encompasses two distinct types of associations, the interaction of legumes (Fabales) with rhizobia bacteria and actinorhizal symbioses, where the bacterial symbionts are actinomycetes of the genus
Frankia
. Although several genetic components of the host–symbiont interaction have been identified in legumes, the genetic basis of actinorhiza formation is unknown. Here, we show that the receptor-like kinase gene
SymRK
, which is required for nodulation in legumes, is also necessary for actinorhiza formation in the tree
Casuarina glauca.
This indicates that both types of nodulation symbiosis share genetic components. Like several other legume genes involved in the interaction with rhizobia,
SymRK
is also required for the interaction with arbuscular mycorrhiza (AM) fungi. We show that
SymRK
is involved in AM formation in
C. glauca
as well and can restore both nodulation and AM symbioses in a
Lotus japonicus symrk
mutant. Taken together, our results demonstrate that
SymRK
functions as a vital component of the genetic basis for both plant–fungal and plant–bacterial endosymbioses and is conserved between legumes and actinorhiza-forming Fagales.
Invasive plants transform the three-dimensional structure of rain forests
Authors: Asner Gregory P. , Hughes R. Flint , Vitousek Peter M. , Knapp David E. , Kennedy-Bowdoin Ty , Boardman Joseph , Martin Roberta E. , Eastwood Michael , Green Robert O.
Published: March 2008

Biological invasions contribute to global environmental change, but the dynamics and consequences of most invasions are difficult to assess at regional scales. We deployed an airborne remote sensing system that mapped the location and impacts of five highly invasive plant species across 221,875 ha of Hawaiian ecosystems, identifying four distinct ways that these species transform the three-dimensional (3D) structure of native rain forests. In lowland to montane forests, three invasive tree species replace native midcanopy and understory plants, whereas one understory invader excludes native species at the ground level. A fifth invasive nitrogen-fixing tree, in combination with a midcanopy alien tree, replaces native plants at all canopy levels in lowland forests. We conclude that this diverse array of alien plant species, each representing a different growth form or functional type, is changing the fundamental 3D structure of native Hawaiian rain forests. Our work also demonstrates how an airborne mapping strategy can identify and track the spread of certain invasive plant species, determine ecological consequences of their proliferation, and provide detailed geographic information to conservation and management efforts.
Cloning and identification of an oxytocin/vasopressin-like receptor and its ligand from insects
Authors: Stafflinger Elisabeth , Hansen Karina K. , Hauser Frank , Schneider Martina , Cazzamali Giuseppe , Williamson Michael , Grimmelikhuijzen Cornelis J. P.
Published: March 2008

More than 20 years ago, an oxytocin/vasopressin-like peptide, CLITNCPRGamide, was isolated from the locust,
Locusta migratoria
[Proux JP,
et al.
(1987) Identification of an arginine vasopressin-like diuretic hormone from
Locusta migratoria. Biochem Biophys Res Commun
149:180–186]. However, no similar peptide could be identified in other insects, nor could its prohormone be cloned, or its physiological actions be established. Here, we report that the recently sequenced genome from the red flour beetle
Tribolium castaneum
contains a gene coding for an oxytocin/vasopressin-like peptide, identical to the locust peptide, which we named inotocin (for insect oxytocin/vasopressin-like peptide) and a gene coding for an inotocin G protein-coupled receptor (GPCR). We cloned the
Tribolium
inotocin preprohormone and the inotocin GPCR and expressed the GPCR in CHO cells. This GPCR is strongly activated by low concentrations of inotocin (EC
50
, 5 × 10
−9
M), demonstrating that it is the inotocin receptor. Quantitative RT-PCR (qPCR) showed that in adult
Tribolium
, the receptor is mainly expressed in the head and much less in the hindgut and Malpighian tubules, suggesting that the inotocin/receptor couple does not play a role in water homeostasis. Surprisingly, qPCR also showed that the receptor is 30× more expressed in the first larval stages than in adult animals. The inotocin/receptor couple can also be found in the recently sequenced genome from the parasitic wasp
Nasonia vitripennis
but not in any other holometabolous insect with a completely sequenced genome (
12
Drosophila
species, the malaria mosquito
Anopheles gambiae
, the yellow fever mosquito
Aedes aegypti
, the silk worm
Bombyx mori
, and the honey bee
Apis mellifera
), suggesting that this neuropeptide system is confined to basal holometabolous insects. Furthermore, we identified an oxytocin/vasopressin-like peptide and receptor in the recently sequenced genome from the water flea
Daphnia pulex
(Crustacea). To our knowledge, this is the first report on the molecular cloning of an oxytocin/vasopressin-like receptor and its ligand from arthropods.
Real-time electron transfer in respiratory complex I
Authors: Verkhovskaya Marina L. , Belevich Nikolai , Euro Liliya , Wikström Mårten , Verkhovsky Michael I.
Published: March 2008

Electron transfer in complex I from
Escherichia coli
was investigated by an ultrafast freeze-quench approach. The reaction of complex I with NADH was stopped in the time domain from 90 μs to 8 ms and analyzed by electron paramagnetic resonance (EPR) spectroscopy at low temperatures. The data show that after binding of the first molecule of NADH, two electrons move via the FMN cofactor to the iron–sulfur (Fe/S) centers N1a and N2 with an apparent time constant of ≈90 μs, implying that these two centers should have the highest redox potential in the enzyme. The rate of reduction of center N2 (the last center in the electron transfer sequence) is close to that predicted by electron transfer theory, which argues for the absence of coupled proton transfer or conformational changes during electron transfer from FMN to N2. After fast reduction of N1a and N2, we observe a slow, ≈1-ms component of reduction of other Fe/S clusters. Because all elementary electron transfer rates between clusters are several orders of magnitude higher than this observed rate, we conclude that the millisecond component is limited by a single process corresponding to dissociation of the oxidized NAD
+
molecule from its binding site, where it prevents entry of the next NADH molecule. Despite the presence of approximately one ubiquinone per enzyme molecule, no transient semiquinone formation was observed, which has mechanistic implications, suggesting a high thermodynamic barrier for ubiquinone reduction to the semiquinone radical. Possible consequences of these findings for the proton translocation mechanism are discussed.
Layered metal sulfides: Exceptionally selective agents for radioactive strontium removal
Authors: Manos Manolis J. , Ding Nan , Kanatzidis Mercouri G.
Published: March 2008

In this article, we report the family of robust layered sulfides K
2x
Mn

x

Sn
3-x
S
6
(
x
= 0.5–0.95) (KMS-1). These materials feature hexagonal [Mn

x

Sn

3-
x

S
6
]

2
x
−

slabs of the CdI
2
type and contain highly mobile K
+
ions in their interlayer space that are easily exchangeable with other cations and particularly strontium. KMS-1 display outstanding preference for strontium ions in highly alkaline solutions containing extremely large excess of sodium cations as well as in acidic environment where most alternative adsorbents with oxygen ligands are nearly inactive. The implication of these results is that simple layered sulfides should be considered for the efficient remediation of certain nuclear wastes.
Identification of phosphatidylinositol 4-kinase type II β as HLA class II-restricted target in graft versus leukemia reactivity
Authors: Griffioen Marieke , van der Meijden Edith D. , Slager Elisabeth H. , Honders M. Willy , Rutten Caroline E. , van Luxemburg-Heijs Simone A. P. , von dem Borne Peter A. , van Rood Johannes J. , Willemze Roel , Falkenburg J. H. Frederik
Published: March 2008

Patients with hematological malignancies can be successfully treated with HLA-matched T cell-depleted allogeneic stem cell transplantation (alloSCT) and subsequent donor lymphocyte infusions (DLIs). The efficacy of DLI is mediated by donor T cells recognizing minor histocompatibility antigens (mHags) on malignant recipient cells. Because HLA class II molecules are predominantly expressed on hematopoietic cells, mHag-specific CD4
+
T cells may selectively mediate graft versus leukemia (GvL) reactivity without graft versus host disease (GvHD). In this study, we used a recombinant bacteria cDNA library for the identification of the first autosomal HLA class II (HLA-DQB1*0603)-restricted mHag LB-PI4K2B-1S encoded by the broadly expressed phosphatidylinositol 4-kinase type II β gene. A polyclonal CD4
+
T cell response against LB-PI4K2B-1S was demonstrated in a patient with relapsed chronic myeloid leukemia (CML) who responded to DLI after HLA-matched alloSCT. LB-PI4K2B-1S-specific CD4
+
T cells recognized and lysed the CD34
+
CML cells of the patient and other leukemic cells as well as high HLA-DQ-expressing normal hematopoietic cells. HLA-DQ expression on normal cells of nonhematopoietic origin was moderately up-regulated by IFN-γ and not sufficient for T cell recognition. We hypothesize that LB-PI4K2B-1S-specific CD4
+
T cells contributed to the antitumor response by both directly eliminating malignant cells as effector cells and stimulating CD8
+
T cell immunity as helper cells.
DNA binding shifts the redox potential of the transcription factor SoxR
Authors: Gorodetsky Alon A. , Dietrich Lars E. P. , Lee Paul E. , Demple Bruce , Newman Dianne K. , Barton Jacqueline K.
Published: March 2008

Electrochemistry measurements on DNA-modified electrodes are used to probe the effects of binding to DNA on the redox potential of SoxR, a transcription factor that contains a [2Fe-2S] cluster and is activated through oxidation. A DNA-bound potential of +200 mV versus NHE (normal hydrogen electrode) is found for SoxR isolated from
Escherichia coli
and
Pseudomonas aeruginosa
. This potential value corresponds to a dramatic shift of +490 mV versus values found in the absence of DNA. Using Redmond red as a covalently bound redox reporter affixed above the SoxR binding site, we also see, associated with SoxR binding, an attenuation in the Redmond red signal compared with that for Redmond red attached below the SoxR binding site. This observation is consistent with a SoxR-binding-induced structural distortion in the DNA base stack that inhibits DNA-mediated charge transport to the Redmond red probe. The dramatic shift in potential for DNA-bound SoxR compared with the free form is thus reconciled based on a high-energy conformational change in the SoxR–DNA complex. The substantial positive shift in potential for DNA-bound SoxR furthermore indicates that, in the reducing intracellular environment, DNA-bound SoxR is primarily in the reduced form; the activation of DNA-bound SoxR would then be limited to strong oxidants, making SoxR an effective sensor for oxidative stress. These results more generally underscore the importance of using DNA electrochemistry to determine DNA-bound potentials for redox-sensitive transcription factors because such binding can dramatically affect this key protein property.
Broad bandwidth of perceptual learning in the visual system of adults with anisometropic amblyopia
Authors: Huang Chang-Bing , Zhou Yifeng , Lu Zhong-Lin
Published: March 2008

Recent studies have demonstrated that training adult amblyopes in simple visual tasks leads to significant improvements of their spatial vision. One critical question is: How much can training with one particular stimulus and task generalize to other stimuli and tasks? In this study, we estimated the bandwidth of perceptual learning in teenage and adult observers with anisometropic amblyopia and compared it to that of normal observers. We measured and compared contrast sensitivity functions—i.e., sensitivity to sine-wave gratings of various spatial frequencies—before and after training at a single spatial frequency in teenagers and adults with and without amblyopia. We found that the bandwidth of perceptual learning in the amblyopic visual system is much broader than that of the normal visual system. The broader bandwidth, suggesting more plasticity and wider generalization in the amblyopic visual system, provides a strong empirical and theoretical basis for perceptual learning as a potential treatment for amblyopia.
Towards feasible and sustainable environmental protection for all
Authors: Lettinga Gatze
Published: March 2008

Proper concepts and technologies for attaining a sustainable, robust and social-economically affordable protection of the life environment for all people are available. They consist of concepts of Decentralised Sanitation and Resource Recovery and Reuse that are comprised of the use of treatment methods based on the Natural Biological Mineralization Route. The major difficulty is to get these systems/concepts implemented; it is more sociology than technology. Generally the short-term economic interests of well-established structures comprise the major bottleneck for making progress on the route to sustainable and robust public sanitation. However, regarding the enormous social and economic benefits of the decentralized sanitation and resource recovery-concept, natural mineralization-based treatment systems irrevocably will be substitute, for the nowadays applied, highly centralised sanitation concepts with their complex and expensive treatment methods. This process already is on the way in the industrial sector of environmental technology in many countries, while in the public sanitation sector promising developments occur in India and Latin America. Consequently there are reasons to be optimistic for a drastic improvement of the life conditions of the poor.
Increasing dominance of Nile tilapia,Oreochromis niloticus(L) in Lake Victoria, Kenya: Consequences for the Nile perchLates niloticus(L) fishery
Authors: Njiru M. , Ojuok J. , Getabu A. , Jembe T. , Owili M. , Ngugi C.
Published: March 2008

Nile tilapia, Oreochromis niloticus and Nile perch, Lates niloticus were introduced into Lake Victoria in the 1950s and 1960s. The former was to boost the then declining tilapiine fishery, while the latter was to convert the abundant bony haplochromines to fish flesh. Fish samples were collected by bottom trawling from 1998 to 2000 and in 2004 to 2005 from the Kenya waters of Lake Victoria. The goal was to evaluate the current population characteristics and ecology of the species. Length frequency distribution and size at maturity of Nile tilapia depicted a stable population with high proportions (30%) of mature fish, unlike Nile perch where more than 98% of the individuals were immature. Nile tilapia previously distributed in < 10 m, were caught in areas up to 20 m depth. Catches of Nile tilapia have increased from < 1% in 1970-80s to > 25% in 2005; while Nile perch declined from 95% in 1990s to 58% in 2005.

The increase in Nile tilapia catches and its spread into deeper waters is attributed to declining stocks of the predatory Nile perch, availability of suitable food and the species occupying vacant niches left by declining stocks of indigenous species, especially the haplochromines. Increase of anoxic conditions in the lake is also precluding Nile perch thereby affording tilapia refuge. The previously herbivorous tilapia has diversified its diet to include insects and fish. All these factors could be contributing to an increase in Nile tilapia biomass in the lake. If management measures to reduce Nile perch exploitation and its rapid decline are not instituted, the next important demersal commercial fishery in Lake Victoria will probably be Nile tilapia. The establishment of Nile tilapia will be replacing a multimillion-dollar export industry of Nile perch, which will have several economic consequences. However, biodiversity in the lake is expected to increase and thus so will the availability of protein to local communities.
General nutrient distribution in the water column of Northern Lake Tanganyika
Authors: Nahimana David , Brion Natacha , Baeyens Willy , Ntakimazi Gaspard
Published: March 2008

A one-year's sampling programme of ammonium, nitrate and nitrite, and silica was performed at a station located in the pelagic area of northern Lake Tanganyika, about 4 km offshore in the vicinity of Bujumbura city. Sampling was generally conducted twice a month and water samples were collected at 10 m intervals between 0 and 100 m depth and analyzed spectrophotometrically for dissolved inorganic nutrients. Physico-chemical parameters were determined during field work with specific probes, and further work was done in the laboratory for dissolved oxygen, which was measured using the Winkler method. Meteorological data allowed for the distinction of four contrasting seasonal situations: 1) September to December 2004 with low rainfall and decreasing wind speed, 2) December 2004 to April 2005 with low wind speed and high rainfall, 3) April to June 2005 with sporadic rainfall and slightly increasing wind speed, and 4) June to August 2005, a typical dry season with no rainfall and high wind speed. Low to high temperature stratification periods were recorded and seemed to be linked to the hydrodynamics of the lake. Below the mixed layer the water is generally anoxic, but in July a deepening of the oxygenated mixed layer down to the bottom was recorded. Within the photic zone, phytoplankton activity implied most of the year undetectable levels of nitrate and nitrite. However, strongly fluctuating and surprisingly high levels of ammonium and the lowest concentrations for silicates were observed. While ammonium accumulates in the dark anoxic waters, nitrate and nitrite peak levels are mostly observed between 30 and 70 m depth due to nitrification processes. Below the photic depth and down to the bottom, silicates increased due to biogenic silica dissolution. Our data mostly corroborate earlier works and confirm the strong coupling of meteorological data and water column properties in northern Lake Tanganyika.
Heterogeneity in physical, chemical and plankton-community structures in Lake Tanganyika.
Authors: Langenberg V. T. , Tumba J.-m. , Tshibangu K. , Lukwesa C. , Chitamwebwa D. , Bwebwa D. , Makasa L. , Roijackers R.
Published: March 2008

From 28 August to 6 September 1995, we monitored the lake-wide physical, chemical and biological properties of the pelagic waters in Lake Tanganyika. The aim of this study was to examine the spatial environmental variability and its relation to fluctuations in plankton abundance and community assembly.

Trade winds had triggered an overall downward tilt of the isotherms; accumulation of warm surface waters and intensified stratification towards the north along with upwelling increased mixing, combined with decreased stratification towards the south. Dissolved oxygen, turbidity, conductivity, phosphorus and chlorophyll-a were higher; whereas temperature and pH were lower in southern than in northern waters. We observed a transition zone (6 to 7°S) where vertical water column structures changed from northern to southern conditions. This did not include the river Rusizi affected regions north of 4°S.

High spatial heterogeneity in nutrient supply and degree of mixing had a strong impact on the plankton community. While the northern environments appeared to be based on reduced internal nutrient loading, lower phytoplankton biomass and smaller sized zooplankton with an important role of Cyclopoids, the mixed environments in the south seemed to be based on increased phosphorus availability and larger sized zooplankton dominated by Calanoid grazers.

We emphasise that wind-driven formation of a gradual change in physical and chemical properties of the productive zones along the north-south axis of Lake Tanganyika is of importance in regionally determining nutrient flows. This consequently affects plankton community structures and composition, and therefore food web structure and functioning.
Relationship between phytoplankton paleoproduction and diversity in contrasting trophic states
Authors: Das Biplob , Nordin Rick , Mazumder Asit
Published: March 2008

With the increasing rate of species extinctions following anthropogenic perturbation, there is a growing interest in biodiversity research. Although productivity and species richness relationships have been tested and applied in contemporary aquatic ecological studies, none have been applied to paleoecology with contrasting trophic states. The present study explores the applicability of a contemporary production and species richness relationship in high-resolution paleoecological records with low, intermediate and mid to high productive aquatic systems. Results from our study reveal that diatom species richness was positively correlated in low to intermediate productive lakes. In contrast, the relationship was hump shaped (unimodal) in a mid to high productive system concurrent with the species diversity analyses. Contrasting relationships between diatom species richness and stable isotope records (δ13C and δ15N) suggested that the nutrient biogeochemical cycle might play an important role in controlling species richness. From fossil pigment records we show that the variations in algal functional group signatures were highest in intermediate state. Collectively, these results suggest that the hump shaped (unimodal) relationship between diatom species richness and production might be limited to high productive systems with maximum richness and diversity in intermediate states, which is also supported in contemporary studies. Moreover, fossil pigment records as proxies for algal functional groups reveal that in a mid to high productive system with intense watershed scale disturbances, community composition of algal functional groups declined favoring certain diatoms. Our results demonstrate the applicability of production and diversity relationship theory in paleo-perspective and that recent watershed scale land use changes might affect the species diversity in aquatic systems.
Application of a Vegetation-Based Index of Biotic Integrity for Lake Erie coastal marshes in Ohio
Authors: Mack John J. , Avdis Nikki Husat , Braig Eugene C. , Johnson David L.
Published: March 2008

Substantial effort in recent years has been invested in developing monitoring protocols and indicators for assessing the health of coastal wetlands of the Great Lakes. Most efforts have collected data exclusively in Great Lakes coastal wetlands and have not evaluated coastal wetland indicator development in the context of other wetland types in the state, province, or region. “Inland” freshwater wetlands are also subject to multiple hydrologic cycles of differing time scales and in some landscape contexts may be as hydrologically variable as Great Lakes coastal wetlands. The Ohio Environmental Protection Agency developed a Vegetation Index of Biotic Integrity (VIBI) for wetlands based on vascular plants as the indicator taxa group. The extension of the VIBI to Lake Erie coastal marshes was evaluated. Least-impacted Lake Erie marshes did not have significantly lower (or higher) scores (p < 0.001) although the upper 75th percentile of coastal wetland scores was not as high as the upper 75th percentile of inland wetland VIBI scores. Significant correlations (p < 0.01) were observed with two different human disturbance gradients in a combined data set of inland and coastal wetlands. Simultaneous metric evaluation using Principal Components Analysis showed some separation in metric performance between inland and coastal wetlands but also clear overlap, especially between reference-quality inland and coastal systems. Ordination of species presence and abundance data revealed similar patterns with some separation between inland and coastal wetlands but considerable overlap in species composition. Lake Erie coastal marshes represent another type of emergent marsh system. With minor modifications, the VIBI, developed with inland wetland data sets, worked well for assessing Lake Erie coastal wetlands in Ohio. The analysis of data from Ohio coastal wetlands with a larger inland reference data set shows the advantages of treating Great Lakes coastal wetlands as a type of freshwater wetland and working toward indicator development in the context of an overall state or provincial wetland classification and assessment program.
Lake Tanganyika ecosystem management strategies
Authors: Nkotagu Hudson H.
Published: March 2008

Lake Tanganyika is a large East African rift valley system holding about 1/6 of the world's liquid freshwater with about 2000 species of organisms (fauna and flora), of which about 700 are endemic. The lake faces a number of threats including excess sedimentation, overfishing, pollution, habitat destruction, along with climate change. Efforts to better understand these involved an assessment of the magnitude of the threats, through the Lake Tanganyika Biodiversity project (LTBP) in which a number of outputs such as Draft conventions, special study reports and the Strategic Action Programme were achieved. The preparation of detailed projects to address the threats through the Lake Tanganyika Management Planning Projects (LTMPP) was another strategy, as well as projects prepared for management of catchment and pollution control, along with fishing management. It can be concluded that Lake Tanganyika faces essentially man-induced threats compounded by climate change, probably resulting in declining productivity of the lake and declining water levels. It is concluded that in order to maintain sustainability of the lake, both regional and global joint efforts are required.
Simulation of the hydrodynamic regime of Jebel Ali Harbor, Dubai, United Arab Emirates
Authors: Maraqa Munjed A. , Ali Ayub , Imran Hassan D. , Hamza Waleed , Awadi Saed Al
Published: March 2008

Jebel Ali Harbor in Dubai is one of the largest man-made ports in the world. Due to its bottle-like nature, it is anticipated that little mixing or wave action occurs within the harbor; however, no study has been conducted to investigate the harbor's hydrodynamic regime. In this paper, the circulation pattern in Jebel Ali Harbor is presented. The vertical profile of temperature and salinity shows that the harbor water is fairly well-mixed, justifying the use of a depth-averaged, 2-D model. Modeling the hydrodynamic pattern of Jebel Ali Harbor was carried out using MIKE21 model. Although tide is the main driving force of circulation in the harbor, wind and Coriolis forces were taken into account in the simulation. Simulation results showed that both dead and eddy zones exis. As the harbor receives treated wastewater from several industries located in the area, flushing out of a conservative tracer by the advection-dispersion process was also simulated using MIKE21. Results revealed that the flushing time of a conservative tracer from the harbor varies significantly with the discharge location. Simulated results showed that understanding the hydrodynamic regime of Jebel Ali Harbor is useful for selecting the location and time for discharging tracers into the harbor.
A Stochastic Description of the Learning Behaviour of an Individual Subject
Authors: Audley R. J.
Published: March 2008

A stochastic process for the description of learning behaviour in a two-choice situation, a special case of a family of processes given in an earlier paper, is introduced. It can be used to describe individual learning data, including both the choice sequence and the latency of the choices within the description. This has the advantage that parameter estimates may be based separately on the latencies and on the choice sequence, and the agreement between these estimates can be taken as an indication of the validity of the stochastic description.

The process is fitted to fifty learning trials of an albino rat. Only two parameters are employed in the description of the sequence of choices made by the subject, and a further one to include the response latencies. No generality is claimed for the success of the particular process employed in this one example, which is given only as an illustration of the possible value of the method.
The Effect of Interpolated Experience on Visual Recognition
Authors: Hunter Ian M. L. , Duthie John H.
Published: March 2008

Two hundred twelve-year-old children were shown a circle-with-gap figure and, five minutes later, required to recognize this figure from among a graded series of similar figures. The interpolation of circles with different sizes of gap resulted in retroactive interference, the recognition error being either positive or negative according to the nature of the interpolated figures. The results also draw attention to the dependence of certain recognition errors on the age of the subject and indicate a developmental trend in the perceiving and recognizing of simple figures.