bluuebunny/crossref_metadata_2025 huggingface dataset:
The effectiveness of deep placement of fertilisers is determined by crop species and edaphic conditions in Mediterranean-type environments: a review
Authors: Ma Qifu , Rengel Zed , Rose Terry
Published: February 2009

Much of our knowledge of plant growth in response to soil nutrient supply comes from studies under homogeneous soil conditions. However, the adoption of reduced or nil tillage and shallow banding of fertilisers at the time of seeding causes spatially variable distribution and availability of soil nutrients in agricultural lands. Soil available nutrients, particularly the poorly mobile ones such as phosphorus (P), potassium (K), zinc (Zn), manganese (Mn), and copper (Cu), stratify within the fertilised topsoil. In water-limited environments where the topsoil is prone to drying, soil nutrient stratification may influence nutrient availability and plant uptake because of impeded root growth or reduced diffusion of immobile nutrients to the root surface, or more likely a combination of both factors. Placing fertilisers deeper in the soil profile could increase nutrient acquisition and utilisation by plants as fertiliser nutrients are in the moist soil for a longer part of the growing season. However, the effectiveness of deep placement of fertilisers may also be determined by soil texture, tillage, fertilising history, nutrient mobility, and crop species. In Mediterranean-type climates of southern Australia, a yield response of winter crops to deep fertiliser mostly occurs on infertile sandy soils in low rainfall regions. This contrasts with the responses of winter and summer crops in northern Australia on soils with optimum-to-high nutrients but subjected to rapid and frequent drying of topsoil because of high temperatures and high evaporation demand during the growing season. The pattern of nutrient accumulation by crop species (indeterminate v. determinate) and the mobility of mineral nutrients in the phloem would also modify the effectiveness of deep-placed nutrients under drought. The complexity of plant responses to subsoil nutrition may suggest that before adopting deep fertiliser practice in a paddock it is essential to understand the effects of edaphic and climatic conditions, soil management, and plant–soil interactions in order to achieve maximum yield benefit.
Tillage system affects phosphorus form and depth distribution in three contrasting Victorian soils
Authors: Vu D. T. , Tang C. , Armstrong R. D.
Published: February 2009

Major changes in tillage practices have occurred over the past 2 decades across the diverse range of soil types and rainfall zones that characterise cropping systems in southern Australia. However, there has been little corresponding change in the management of nutrients, especially phosphorus (P). This study investigated the effects of tillage and crop rotations on the stratification and transformation of P in soil profiles from 3 tillage/rotation trials encompassing 3 agro-ecological zones of southern Australia. Soil samples were collected from field trials at Longerenong (Vertosol, average rainfall 420 mm), Walpeup (Calcarosol, rainfall 325 mm), and Rutherglen (Chromosol, rainfall 650 mm) in Victoria. Soil samples from various depths were sequentially analysed for organic and inorganic P fractions. Phosphorus accumulated in the surface soil (0–0.1 m) across all sites and tillage practices/rotations studied but the proportion of P in different chemical fractions varied markedly among soil types and tillage practice/rotation. In the sandy Calcarosol, a greater proportion of fertiliser P was transformed into labile (resin-P) forms, whereas it tended to accumulate in non-labile pools in the finer textured Vertosol and Chromosol. The effects of tillage and crop rotation were generally confined to the topsoil with P strongly stratified in the topsoil in direct-drill and zero-tillage treatments compared with conventional tillage. The implications for management of P fertilisers in Victorian cropping systems are discussed.
Regional-scale weather patterns and wildland fires in central Portugal
Authors: Hoinka Klaus P. , Carvalho Anabela , Miranda Ana Isabel
Published: February 2009

The characteristic evolution of the synoptic- and meso-scale wind, temperature and humidity pattern during wildland fire events in Portugal was determined by lagged covariances for the period 1980 to 2001. The daily burnt area was chosen as the parameter to be correlated with atmospheric fields provided by the European Centre for Medium-Range Weather Forecasts Reanalysis (ERA40) data. The related time series consisted of wildland fires with a daily burnt area of more than 500 ha in central Portugal. Five days in advance of a fire event, a strong positive anomaly existed in the surface pressure and in the 500-hPa geopotential field, both appearing to the west of the Iberian Peninsula and moving towards Brittany until lag zero. In advance of the fire event, the flow above Portugal came from the north, turning to easterlies at lag time zero and finally coming from the south-east during the post-event phase. Surface wind statistics taken at Castelo Branco supported these results. Smoke plumes from wildland fires detected by satellites indicated a similar flow structure, which was quite different to the averaged summertime flow above Portugal. Cross-covariance regression between the Iberian thermal low and burnt area showed that the peak amount of burnt area occurred up to 3 days after the appearance of a thermal low. This suggested that in the pre-phase of a wildland fire, heated air is transported from the peninsula’s centre towards Portugal.
What factors influence rapid post-fire site re-occupancy? A case study of the endangered Eastern Bristlebird in eastern Australia
Authors: Lindenmayer David B. , MacGregor Chris , Wood Jeff T. , Cunningham Ross B. , Crane Mason , Michael Damian , Montague-Drake Rebecca , Brown Darren , Fortescue Martin , Dexter Nick , Hudson Matt , Gill A. Malcolm
Published: February 2009

We quantified the post-fire recovery of the endangered Eastern Bristlebird (Dasyornis brachypterus) at Booderee National Park, south-eastern Australia. Occurrence was recorded on 110 sites a year before, and for 3 years after a major unplanned fire in 2003. Although the Eastern Bristlebird is thought to be sensitive to wildfire, data indicated that the species either persisted continuously on burned sites or returned to previously occupied sites within 2 years. Post-fire site occupancy was associated with several factors: (1) pre-fire site occupancy; (2) vegetation type; (3) spatial heterogeneity in fire and the amount of unburned vegetation surrounding a site; and (4) site-level vegetation structure (e.g. diversity of understorey and midstorey plants). The most likely mechanism underpinning rapid re-occupancy was movement by resident birds to unburned parts elsewhere within their territories. The addition of intensive feral predator baiting within the present study suggests that predation may have a more important effect on populations after unplanned fires than formerly recognised. Our results have significant implications for fire management in areas where the Eastern Bristlebird occurs. Care should be taken with back-burning during unplanned fires and the spatial and temporal arrangement of prescribed fires to ensure unburned vegetation remains as refugia to facilitate bird persistence.
Modeling fire danger in data-poor regions: a case study from the Russian Far East
Authors: Loboda Tatiana V.
Published: February 2009

Wildland fire is a widespread phenomenon that affects how many ecosystems function and often threatens human life and property. Development of fire danger rating systems, aimed at identifying critical periods of high fire danger at early stages of its occurrence, is an important step for proactive fire and resource management. Development of such systems relies on long-term records of fire occurrence as well as numerous data sources for supporting information, but accurate and spatially explicit information is not available in many regions of the world affected by fire. Global satellite systems are becoming a major source of information for data-poor regions. The present paper describes a framework for modeling fire danger at a regional scale using publicly available data sources and global satellite imaging. It details a fuzzy logic-driven fire danger model developed for the Russian Far East using remotely sensed data. Fire activity recorded by the MODIS (Moderate Resolution Imaging Spectroradiometer) active fire product was analyzed for 2001–05 as a function of various parameters. Model performance was evaluated against 2006 data. Fire danger was evaluated within the model using the ordered weighted averaging approach with fuzzification. The model produces three scenarios. All output model scenarios provide a meaningful representation of fire danger levels in the region with the ‘trade-off’ scenario being the most applicable to mapping fire danger during low fire activity seasons.
Construction of empirical models for predicting Pinus sp. dead fine fuel moisture in NW Spain. I: Response to changes in temperature and relative humidity
Authors: Ruiz González Ana Daría , Vega Hidalgo Jose Antonio , Álvarez González Juan Gabriel
Published: February 2009

A statistical methodology is presented for developing moisture content models from repeated measurements made on non-destructive repeated measurements. Empirical vapour exchange models for dead fine fuels generated in Pinus radiata and P. pinaster stands are developed by using the methodology proposed. Experiments were carried out with five types of fuel particles (surface and aerial fine fuels) of the two species of pine, in Lugo (Galicia, north-west Spain). The samples of each fuel type were collected and placed inside an instrument shelter so that vapour exchange with the atmosphere was the only source of moisture in the fuels. Statistical criteria obtained from the residuals indicated that the fitted models were acceptable. The cross-validation results also confirmed the validity of the fitted models. The model underlined the decisive role played by the time lag in dead fine fuel moisture content variation.
Synthesis of sediment yields after wildland fire in different rainfall regimes in the western United States
Authors: Moody John A. , Martin Deborah A.
Published: February 2009

Measurements of post-fire sediment erosion, transport, and deposition collected within 2 years of a wildfire were compiled from the published literature (1927–2007) for sites across the western United States. Annual post-fire sediment yields were computed and grouped into four measurement methods (hillslope point and plot measurements, channel measurements of suspended-sediment and sediment erosion or deposition volumes). Post-fire sediment yields for each method were then grouped into eight different rainfall regimes. Mean sediment yield from channels (240 t ha–1) was significantly greater than from hillslopes (82 t ha–1). This indicated that on the time scale of wildfire (10–100 years) channels were the primary sources of available sediment. A lack of correlation of sediment yield with topographic slope and soil erodibility further suggested that sediment availability may be more important than slope or soil erodibility in predicting post-fire sediment yields. The maximum post-fire sediment yields were comparable to long-term sediment yields from major rivers of the world. Based on 80 years of data from the literature, wildfires have been an important geomorphic agent of landscape change when linked with sufficient rainfall. These effects are limited in spatial scale to the immediate burned area and to downstream channel corridors.
GABA expression in the mammalian taste bud functions as a route of inhibitory cell-to-cell communication
Authors: Cao Yu , Zhao Fang-li , Kolli Tamara , Hivley Randy , Herness Scott
Published: February 2009

Recent advances have underscored cell-to-cell communication as an important component of the operation of taste buds with individual taste receptor cells (TRCs) communicating with one another by means of a number of neurotransmitters and neuropeptides, although functional roles are not yet understood. Here, we characterize the presence, distribution pattern, phenotype, and functional consequences of a previously undescribed inhibitory route within the taste bud mediated by the classic neurotransmitter GABA and its receptors. By using immunocytochemistry, subsets of TRCs within rat taste buds were identified as expressing GABA, and its synthetic enzyme glutamate decarboxylase (GAD). GAD expression was verified with Western blotting. Immunofluorescent studies revealed complex coexpression patterns of GAD with the TRC protein markers gustducin, neural cell adhesion molecule, protein gene product 9.5, and synaptosomal-associated protein of 25 kDa that collectively outline hardwired signaling pathways of GABAergic TRCs. RT-PCR and immunocytochemistry demonstrated that both GABA
A
and GABA
B
receptors are expressed in the taste bud. The later was observed in a subset TRCs paracrine to GAD-expressing TRCs. Physiological effects of GABA were examined by patch clamp recordings. GABA and the GABA
A
agonists muscimol and isoguvacine enhanced isolated chloride currents in a dose-dependent manner. Also, GABA and the GABA
B
agonist baclofen both elicited increases of the inwardly rectifying potassium currents that could be blocked by the GABA
B
receptor antagonist CGP 35348 and the G protein blocker GDP-βS. Collectively, these data suggest that GABAergic TRCs are able to shape the final chemosensory output of the bud by means of processes of cell-to-cell modulation.
Activated TNF-α/NF-κB signaling via down-regulation of Fas-associated factor 1 in asbestos-induced mesotheliomas from
Arf
knockout mice
Authors: Altomare Deborah A. , Menges Craig W. , Pei Jianming , Zhang Lili , Skele-Stump Kristine L. , Carbone Michele , Kane Agnes B. , Testa Joseph R.
Published: February 2009

The human
CDKN2A
locus encodes 2 distinct proteins, p16(INK4A) and p14(ARF) [mouse p19(Arf)], designated INK4A (inhibitor of cyclin dependent kinase 4) and ARF (alternative reading frame) here, that are translated from alternatively spliced mRNAs. Human
ARF
is implicated as a tumor suppressor gene, mainly in association with the simultaneous deletion of
INK4A
. However, questions remain as to whether loss of
ARF
alone is sufficient to drive tumorigenesis. Here, we report that mice deficient for
Arf
are susceptible to accelerated asbestos-induced malignant mesothelioma (MM). MMs arising in
Arf
(+/−) mice consistently exhibit biallelic inactivation of
Arf
, but, unexpectedly, do not acquire additional recurrent genetic alterations that we previously identified in asbestos-induced MMs arising in
Nf2
(+/−) mice. Array CGH analysis was used to detect a recurrent deletion at chromosome 4C6 in MMs from
Arf
(+/−) mice. A candidate gene in this region,
Faf1
(FAS-associated factor 1), was further explored, because it encodes a protein implicated in tumor cell survival and in the pathogenesis of some human tumor types. We confirmed hemizygous loss of
Faf1
and down-regulation of Faf1 protein in a series of MMs from
Arf
(+/−) mice, and we then showed that Faf1 regulates TNF-α-mediated NF-κB signaling, a pathway previously implicated in asbestos-induced oncogenesis of human mesothelial cells. Collectively, these data indicate that
Arf
inactivation has a significant role in driving MM pathogenesis, and implicate Faf1 as a key component in the TNF-α/NF-κB signaling node that has now been independently implicated in asbestos-induced oncogenesis.
Protein stability and resistance to oxidative stress are determinants of longevity in the longest-living rodent, the naked mole-rat
Authors: Pérez Viviana I. , Buffenstein Rochelle , Masamsetti Venkata , Leonard Shanique , Salmon Adam B. , Mele James , Andziak Blazej , Yang Ting , Edrey Yael , Friguet Bertrand , Ward Walter , Richardson Arlan , Chaudhuri Asish
Published: February 2009

The widely accepted oxidative stress theory of aging postulates that aging results from accumulation of oxidative damage. Surprisingly, data from the longest-living rodent known, naked mole-rats [MRs; mass 35 g; maximum lifespan (MLSP) > 28.3 years], when compared with mice (MLSP 3.5 years) exhibit higher levels of lipid peroxidation, protein carbonylation, and DNA oxidative damage even at a young age. We hypothesize that age-related changes in protein structural stability, oxidation, and degradation are abrogated over the lifespan of the MR. We performed a comprehensive study of oxidation states of protein cysteines [both reversible (sulfenic, disulfide) and indirectly irreversible (sulfinic/sulfonic acids)] in liver from young and old C57BL/6 mice (6 and 28 months) and MRs (2 and >24 years). Furthermore, we compared interspecific differences in urea-induced protein unfolding and ubiquitination and proteasomal activity. Compared with data from young mice, young MRs have 1.6 times as much free protein thiol groups and similar amounts of reversible oxidative damage to cysteine. In addition, they show less urea-induced protein unfolding, less protein ubiquitination, and higher proteasome activity. Mice show a significant age-related increase in cysteine oxidation and higher levels of ubiquitination. In contrast, none of these parameters were significantly altered over 2 decades in MRs. Clearly MRs have markedly attenuated age-related accrual of oxidation damage to thiol groups and age-associated up-regulation of homeostatic proteolytic activity. These pivotal mechanistic interspecies differences may contribute to the divergent aging profiles and strongly implicate maintenance of protein stability and integrity in successful aging.
Surface charge of polyoxometalates modulates polymerization of the scrapie prion protein
Authors: Wille Holger , Shanmugam Maheswaran , Murugesu Muralee , Ollesch Julian , Stubbs Gerald , Long Jeffrey R. , Safar Jiri G. , Prusiner Stanley B.
Published: February 2009

Prions are composed solely of an alternatively folded isoform of the prion protein (PrP), designated PrP
Sc
. N-terminally truncated PrP
Sc
, denoted PrP 27–30, retains infectivity and polymerizes into rods with the ultrastructural and tinctorial properties of amyloid. We report here that some polyoxometalates (POMs) favor polymerization of PrP 27-30 into prion rods, whereas other POMs promote assembly of the protein into 2D crystals. Antibodies reacting with epitopes in denatured PrP 27-30 also bound to 2D crystals treated with 3 M urea. These same antibodies did not bind to either native PrP
Sc
or untreated 2D crystals. By using small, spherical POMs with Keggin-type structures, the central heteroatom was found to determine whether prion rods or 2D crystals were preferentially formed. An example of a Keggin-type POM with a phosphorous heteroatom is the phosphotungstate anion (PTA). Both PTA and a Keggin-type POM with a silicon heteratom have low-charge densities and favor formation of prion rods. In contrast, POMs with boron or hydrogen heteroatoms exhibiting higher negative charges encouraged 2D crystal formation. The 2D crystals of PrP 27-30 produced by selective precipitation with POMs were larger and more well ordered than those obtained by sucrose gradient centrifugation. Our findings argue that the negative charge of Keggin-type POMs determines the quaternary structure adopted by PrP 27-30. The mechanism by which POMs function in competing prion polymerization pathways—one favoring 2D crystals and the other, amyloid fibrils—remains to be established.
Inherited disorders affecting mitochondrial function are associated with glutathione deficiency and hypocitrullinemia
Authors: Atkuri Kondala R. , Cowan Tina M. , Kwan Tony , Ng Angelina , Herzenberg Leonard A. , Herzenberg Leonore A. , Enns Gregory M.
Published: February 2009

Disorders affecting mitochondria, including those that directly affect the respiratory chain function or result from abnormalities in branched amino acid metabolism (organic acidemias), have been shown to be associated with impaired redox balance. Almost all of the evidence underlying this conclusion has been obtained from studies on patient biopsies or animal models. Since the glutathione (iGSH) system provides the main protection against oxidative damage, we hypothesized that untreated oxidative stress in individuals with mitochondrial dysfunction would result in chronic iGSH deficiency. We confirm this hypothesis here in studies using high-dimensional flow cytometry (Hi-D FACS) and biochemical analysis of freshly obtained blood samples from patients with mitochondrial disorders or organic acidemias. T lymphocyte subsets, monocytes and neutrophils from organic acidemia and mitochondrial patients who were not on antioxidant supplements showed low iGSH levels, whereas similar subjects on antioxidant supplements showed normal iGSH. Measures of iROS levels in blood were insufficient to reveal the chronic oxidative stress in untreated patients. Patients with organic acidemias showed elevated plasma protein carbonyls, while plasma samples from all patients tested showed hypocitrullinemia. These findings indicate that measurements of iGSH in leukocytes may be a particularly useful biomarker to detect redox imbalance in mitochondrial disorders and organic acidemias, thus providing a relatively non-invasive means to monitor disease status and response to therapies. Furthermore, studies here suggest that antioxidant therapy may be useful for relieving the chronic oxidative stress that otherwise occurs in patients with mitochondrial dysfunction.
Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform
Authors: Taylor R. J. , Falconnet D. , Niemistö A. , Ramsey S. A. , Prinz S. , Shmulevich I. , Galitski T. , Hansen C. L.
Published: February 2009

Cells have evolved biomolecular networks that process and respond to changing chemical environments. Understanding how complex protein interactions give rise to emergent network properties requires time-resolved analysis of cellular response under a large number of genetic perturbations and chemical environments. To date, the lack of technologies for scalable cell analysis under well-controlled and time-varying conditions has made such global studies either impossible or impractical. To address this need, we have developed a high-throughput microfluidic imaging platform for single-cell studies of network response under hundreds of combined genetic perturbations and time-varying stimulant sequences. Our platform combines programmable on-chip mixing and perfusion with high-throughput image acquisition and processing to perform 256 simultaneous time-lapse live-cell imaging experiments. Nonadherent cells are captured in an array of 2,048 microfluidic cell traps to allow for the imaging of eight different genotypes over 12 h and in response to 32 unique sequences of stimulation, generating a total of 49,000 images per run. Using 12 devices, we carried out >3,000 live-cell imaging experiments to investigate the mating pheromone response in
Saccharomyces cerevisiae
under combined genetic perturbations and changing environmental conditions. Comprehensive analysis of 11 deletion mutants reveals both distinct thresholds for morphological switching and new dynamic phenotypes that are not observed in static conditions. For example,
kss1
Δ,
fus3
Δ,
msg5
Δ, and
ptp2
Δ mutants exhibit distinctive stimulus-frequency-dependent signaling phenotypes, implicating their role in filtering and network memory. The combination of parallel microfluidic control with high-throughput imaging provides a powerful tool for systems-level studies of single-cell decision making.
Tat acetylation modulates assembly of a viral-host RNA–protein transcription complex
Authors: D'Orso Iván , Frankel Alan D.
Published: February 2009

HIV-1 Tat enhances viral transcription elongation by forming a ribonucleoprotein complex with transactivating responsive (TAR) RNA and P-TEFb, an elongation factor composed of cyclin T1 (CycT1) and Cdk9 that phosphorylates the C-terminal domain of RNA polymerase II. Previous studies have shown that Lys-28 in the activation domain (AD) of Tat is essential for HIV-1 transcription and replication and is acetylated by p300/CBP-associated factor (PCAF), but the mechanistic basis of the Lys-28 requirement is unknown. Here, we show that Lys-28 acetylation modulates the affinity and stability of HIV-1 Tat–CycT1–TAR complexes by enhancing an interaction with the CycT1 Tat–TAR recognition motif. High-affinity assembly correlates strongly with stimulation of transcription elongation in vitro and Tat activation in vivo. In marked contrast, bovine lentiviral Tat proteins have evolved a high-affinity TAR interaction that does not require PCAF-mediated acetylation of the Tat AD or CycT1 for RNA binding, whereas HIV-2 Tat has evolved an intermediate mechanism that uses a duplicated TAR element and CycT1 to enhance RNA affinity and consequently transcription activation. The coevolution of Tat acetylation, CycT1 dependence, and TAR binding affinity is seen in viral replication assays using Tat proteins that rely on CycT1 for TAR binding but are acetylation deficient, where compensatory mutations rapidly accrue in TAR to generate high-affinity, CycT1-independent complexes reminiscent of the bovine viruses. Thus, lysine acetylation can be used to modulate and evolve the strength of a viral-host RNA–protein complex, thereby tuning the levels of transcription elongation.
When lower entropy implies stronger Devaney chaos
Authors: Harańczyk Grzegorz , Kwietniak Dominik
Published: February 2009

It is proved that the infimum of the topological entropy of continuous topologically exact interval (circle) maps is strictly smaller than the infimum of the topological entropy of continuous interval (circle) maps, which are topologically mixing, but not exact. Interpreting this result in terms of popular notions of chaos, one may say that on the interval (circle) lower entropy implies stronger Devaney chaos. Moreover, the infimum of the entropy of mixing circle maps is computed. These theorems may be considered as a completion of some results of Alsedà, Kolyada, Llibre, and Snoha (1999).
The Auslander-Reiten conjecture for Gorenstein rings
Authors: Araya Tokuji
Published: February 2009

The Nakayama conjecture is one of the most important conjectures in ring theory. The Auslander-Reiten conjecture is closely related to it. The purpose of this paper is to show that if the Auslander-Reiten conjecture holds in codimension one for a commutative Gorenstein ring

R
R

, then it holds for

R
R

.
Asymptotic depth of twisted higher direct image sheaves
Authors: Bär Renate , Brodmann Markus
Published: February 2009

Let

π
:
X
→

X

0

\pi :X \rightarrow X_{0}

be a projective morphism of schemes, such that

X

0

X_{0}

is Noetherian and essentially of finite type over a field

K
K

. Let

i
∈

N

0

i \in \mathbb {N}_{0}

, let

F

{\mathcal {F}}

be a coherent sheaf of

O

X

{\mathcal {O}}_{X}

-modules and let

L

{\mathcal {L}}

be an ample invertible sheaf over

X
X

. Let

Z

0

⊆

X

0

Z_{0} \subseteq X_{0}

be a closed set. We show that the depth of the higher direct image sheaf
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="script upper R Superscript i Baseline pi Subscript asterisk Baseline left-parenthesis script upper L Superscript n Baseline circled-times Subscript script upper O Sub Subscript upper X Subscript Baseline script upper F right-parenthesis">

R

i

π

∗

(

L

n

⊗

O

X

F

)

{\mathcal {R}}^{i}\pi _{*}({\mathcal {L}}^{n} \otimes _{{\mathcal {O}}_{X}} {\mathcal {F}})

along

Z

0

Z_{0}

ultimately becomes constant as

n
n

tends to

−
∞

-\infty

, provided

X

0

X_{0}

has dimension

≤
2

\leq 2

. There are various examples which show that the mentioned asymptotic stability may fail if

dim
⁡
(

X

0

)
≥
3

\dim (X_{0}) \geq 3

. To prove our stability result, we show that for a finitely generated graded module

M
M

over a homogeneous Noetherian ring

R
=

⨁

n
≥
0

R

n

R=\bigoplus _{n \geq 0}R_{n}

for which

R

0

R_{0}

is essentially of finite type over a field and an ideal

a

0

⊆

R

0

\mathfrak {a}_{0} \subseteq R_{0}

, the

a

0

\mathfrak {a}_{0}

-depth of the

n
n

-th graded component

H

R

+

i

(
M

)

n

H^{i}_{R_{+}}(M)_{n}

of the

i
i

-th local cohomology module of

M
M

with respect to

R

+

:=

⨁

k
>
0

R

k

R_{+}:=\bigoplus _{k>0}R_{k}

ultimately becomes constant in codimension

≤
2

\leq 2

as

n
n

tends to

−
∞

-\infty

.
Reduction theorems for Noether’s problem
Authors: Kang Ming-chang , Plans Bernat
Published: February 2009

Let

K
K

be any field, and

G
G

be a finite group. Let

G
G

act on the rational function field

K
(
x
(
g
)
:
g
∈
G
)

K(x(g):g\in G)

by

K
K

-automorphisms and

h
⋅
x
(
g
)
=
x
(
h
g
)

h\cdot x(g)=x(hg)

. Denote by

K
(
G
)
=
K
(
x
(
g
)
:
g
∈
G

)
G

K(G)=K(x(g):g\in G)^G

the fixed field. Noether’s problem asks whether

K
(
G
)

K(G)

is rational (= purely transcendental) over

K
K

. We will give several reduction theorems for solving Noether’s problem. For example, let

G
~

=
G
×
H

\widetilde {G}=G\times H

be a direct product of finite groups. Theorem. Assume that

K
(
H
)

K(H)

is rational over

K
K

. Then

K
(

G
~

)

K(\widetilde {G})

is rational over

K
(
G
)

K(G)

. In particular, if

K
(
G
)

K(G)

is rational (resp. retract rational) over

K
K

, so is

K
(

G
~

)

K(\widetilde {G})

over

K
K

.
A Littlewood-Richardson rule for Grassmannian permutations
Authors: Purbhoo Kevin , Sottile Frank
Published: February 2009

We give a combinatorial rule for computing intersection numbers on a flag manifold which come from products of Schubert classes pulled back from Grassmannian projections. This rule generalizes the known rule for Grassmannians.
The ghost dimension of a ring
Authors: Hovey Mark , Lockridge Keir
Published: February 2009

We introduce the concept of the ghost dimension gh.dim. 

R
R

of a ring

R
R

. This is the longest nontrivial chain of maps in the derived category emanating from a perfect complex such that each map is zero on homology. We show that w.dim. 

R
≤

R\leq

gh.dim. 

R
R

with equality if

R
R

is coherent or w.dim. 

R
=
1

R=1

.
𝐾-trivial degrees and the jump-traceability hierarchy
Authors: Barmpalias George , Downey Rod , Greenberg Noam
Published: February 2009

For every order

h
h

such that

∑
n

1

/

h
(
n
)

\sum _n 1/h(n)

is finite, every

K
K

-trivial degree is

h
h

-jump-traceable. This motivated Cholak, Downey and Greenberg to ask whether this traceability property is actually equivalent to

K
K

-triviality, thereby giving the hoped for combinatorial characterisation of lowness for Martin-Löf randomness. We show however that the

K
K

-trivial degrees are properly contained in those that are

h
h

-jump-traceable for every convergent order

h
h

.
On the existence of infinite energy solutions for nonlinear Schrödinger equations
Authors: Braz e Silva Pablo , Ferreira Lucas , Villamizar-Roa Elder
Published: February 2009

We derive new results about existence and uniqueness of local and global solutions for the nonlinear Schrödinger equation, including self-similar solutions. Our analysis is performed in the framework of weak-

L

p

L^{p}

spaces.
Area growth rate of the level surface of the potential function on the 3-dimensional steady gradient Ricci soliton
Authors: Guo Hongxin
Published: February 2009

In this short note we show that on a 3-dimensional steady gradient Ricci soliton with positive curvature and which is

κ
\kappa

-noncollapsed on all scales, the scalar curvature and the mean curvature of the level surface of the potential function both decay linearly. Consequently we prove that the area of the level surface grows linearly.
Cyclic behavior of the Cesàro operator on 𝐿₂(0,∞)
Authors: González M. , León-Saavedra F.
Published: February 2009

In this paper we study the cyclic properties of the infinite continuous Cesàro operator defined on

L
2

(
0
,
∞
)

L^2(0,\infty )

by
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis upper C Subscript normal infinity Baseline f right-parenthesis left-parenthesis x right-parenthesis equals StartFraction 1 Over x EndFraction integral Subscript 0 Superscript x Baseline f left-parenthesis s right-parenthesis d s">

(

C
∞

f
)
(
x
)
=

1
x

∫
0
x

f
(
s
)
d
s

(C_\infty f)(x)=\frac {1}{x}\int _0^x f(s) ds

. Despite this operator being cyclic, we show that it is not supercyclic; even more, it is not weakly supercyclic. These results complement some recent ones on the cyclic behavior of Cesàro operators.
Semisimplicity criteria for irreducible Hopf algebras in positive characteristic
Authors: Masuoka Akira
Published: February 2009

We prove that a finite-dimensional irreducible Hopf algebra

H
H

in positive characteristic is semisimple if and only if it is commutative and semisimple if and only if the restricted Lie algebra

P
(
H
)

P(H)

of the primitives is a torus. This generalizes Hochschild’s theorem on restricted Lie algebras, and also generalizes Demazure and Gabriel’s and Sweedler’s results on group schemes in the special but essential situation with a finiteness assumption added.
M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
Authors: Yanover Chen , Singh Mona , Zaslavsky Elena
Published: February 2009

Motivation: Identifying regulatory elements in genomic sequences is a key component in understanding the control of gene expression. Computationally, this problem is often addressed by motif discovery, where the goal is to find a set of mutually similar subsequences within a collection of input sequences. Though motif discovery is widely studied and many approaches to it have been suggested, it remains a challenging and as yet unresolved problem.

Results: We introduce SAMF (Solution-Aggregating Motif Finder), a novel approach for motif discovery. SAMF is based on a Markov Random Field formulation, and its key idea is to uncover and aggregate multiple statistically significant solutions to the given motif finding problem. In contrast to many earlier methods, SAMF does not require prior estimates on the number of motif instances present in the data, is not limited by motif length, and allows motifs to overlap. Though SAMF is broadly applicable, these features make it particularly well suited for addressing the challenges of prokaryotic regulatory element detection. We test SAMF's ability to find transcription factor binding sites in an Escherichia coli dataset and show that it outperforms previous methods. Additionally, we uncover a number of previously unidentified binding sites in this data, and provide evidence that they correspond to actual regulatory elements.

Contact:  cyanover@fhcrc.org, msingh@cs.princeton.edu,elenaz@cs.princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A new ensemble-based algorithm for identifying breath gas marker candidates in liver disease using ion molecule reaction mass spectrometry
Authors: Netzer M. , Millonig G. , Osl M. , Pfeifer B. , Praun S. , Villinger J. , Vogel W. , Baumgartner C.
Published: February 2009

Motivation: Alcoholic fatty liver disease (AFLD) and non-AFLD (NAFLD) can progress to severe liver diseases such as steatohepatitis, cirrhosis and cancer. Thus, the detection of early liver disease is essential; however, minimal invasive diagnostic methods in clinical hepatology still lack specificity.

Results: Ion molecule reaction mass spectrometry (IMR-MS) was applied to a total of 126 human breath gas samples comprising 91 cases (AFLD, NAFLD and cirrhosis) and 35 healthy controls. A new feature selection modality termed Stacked Feature Ranking (SFR) was developed to identify potential liver disease marker candidates in breath gas samples, relying on the combination of different entropy- and correlation-based feature ranking methods including statistical hypothesis testing using a two-level architecture with a suggestion and a decision layer. We benchmarked SFR against four single feature selection methods, a wrapper and a recently described ensemble method, indicating a significantly higher discriminatory ability of up to 10–15% for the SFR selected gas compounds expressed by the area under the ROC curve (AUC) of 0.85–0.95. Using this approach, we were able to identify unexpected breath gas marker candidates in liver disease of high predictive value. A literature study further supports top-ranked markers to be associated with liver disease. We propose SFR as a powerful tool for biomarker search in breath gas and other biological samples using mass spectrometry.

Availability: The algorithm SFR and IMR-MS datasets are available under http://biomed.umit.at/page.cfm?pageid=526

Contact:  michalel.netzer@umit.at; christian.baumgartner@umit.at
Benthic impacts of recreational divers in a Mediterranean Marine Protected Area
Authors: Luna Beatriz , Pérez Carlos Valle , Sánchez-Lizaso Jose Luis
Published: February 2009

Luna, B., Valle Pérez, C., and Sánchez-Lizaso, J. L. 2009. Benthic impacts of recreational divers in a Mediterranean Marine Protected Area. – ICES Journal of Marine Science, 66: 517–523. The features of many Marine Protected Areas (MPAs) have increased scuba diving tourism in these areas. Impacts caused by recreational scuba activity vary widely among different divers with differing underwater behaviour. We studied diver underwater behaviour, the effects on the natural environment, and the characteristics that may influence diver behaviour. In all, 181 recreational divers were followed, and contacts and the effects produced were recorded. Information on diver profile and dive features was recorded. Field sampling revealed that 175 of the divers observed (96.7%) made at least one contact with the seabed, with a mean contact of 41.20 ± 3.55 (mean ± s.e.) per diver per 10 min. Flapping was the most frequent type of contact, and the main damage by this action was to raise sediment. Contact with the seabed was greater for males than for females, inexperienced divers than for experienced divers, camera or lantern (dive light) users than for non-users, and divers unaccompanied by a dive leader or who had not been briefed about avoiding seabed contact before undertaking a dive than for accompanied or briefed divers. A greater understanding of the causes of harmful behaviour may be useful for stricter management, reducing diving damage and assuring the sustainability of this activity in MPAs.
Priming of short-term potentiation and synaptic tagging/capture mechanisms by ryanodine receptor activation in rat hippocampal CA1
Authors: Sajikumar Sreedharan , Li Qin , Abraham Wickliffe C. , Xiao Zhi Cheng
Published: February 2009

Activity-dependent changes in synaptic strength such as long-term potentiation (LTP) and long-term depression (LTD) are considered to be cellular mechanisms underlying learning and memory. Strengthening of a synapse for a few seconds or minutes is termed short-term potentiation (STP) and is normally unable to take part in the processes of synaptic tagging/capture due to its inability to set the “synaptic tags.” Here, we report that priming of synapses with ryanodine receptor agonists such as ryanodine (10 μM) or caffeine (10 mM) facilitates subsequent synaptic tagging/capture, enabling an STP protocol to establish a late-LTP in response to strong tetanization of a heterosynaptic input. We identified calcium/calmodulin-dependent protein kinase II (CaMKII) as mediating the primed synaptic tag setting, which persisted for 1 h. We also identified protein kinase Mζ (PKMζ), presumably captured from the strongly tetanized heterosynaptic input, as a plasticity-related protein maintaining the LTP at the tagged synapses. In addition, synaptic tags in primed STP were erased or interfered with by delivering low-frequency depotentiating stimulation 5 or 10 min after its induction, thus preventing capture of newly synthesized proteins. These data reveal a novel form of metaplasticity, whereby ryanodine receptor activation lowers the threshold for subsequent synaptic tagging/capture, thus priming weakly activated synapses for heterosynaptic interactions that promote long-term functional plasticity.
TheArabidopsisProteasome RPT5 Subunits Are Essential for Gametophyte Development and Show Accession-Dependent Redundancy
Authors: Gallois Jean-Luc , Guyon-Debast Anouchka , Lécureuil Alain , Vezon Daniel , Carpentier Virginie , Bonhomme Sandrine , Guerche Philippe
Published: February 2009

We investigated the role of the ubiquitin proteasome system (UPS), which allows proteins to be selectively degraded, during gametophyte development in Arabidopsis thaliana. Three mutant alleles altering the UPS were isolated in the Wassilewskija (Ws) accession: they affect the Regulatory Particle 5a (RPT5a) gene, which (along with RPT5b) encodes one of the six AAA-ATPases of the proteasome regulatory particle. In the heterozygous state, all three mutant alleles displayed 50% pollen lethality, suggesting that RPT5a is essential for male gametophyte development. However, a fourth mutant in the Columbia (Col) accession did not display such a phenotype because the RPT5b Col allele complements the rpt5a defect in the male gametophyte, whereas the RPT5b Ws allele does not. Double rpt5a rpt5b mutants showed a complete male and female gametophyte lethal phenotype in a Col background, indicating that RPT5 subunits are essential for both gametophytic phases. Mitotic divisions were affected in double mutant gametophytes correlating with an absence of the proteasome-dependent cyclinA3 degradation. Finally, we show that RPT5b expression is highly increased when proteasome functioning is defective, allowing complementation of the rpt5a mutation. In conclusion, RPT5 subunits are not only essential for both male and female gametophyte development but also display accession-dependent redundancy and are crucial in cell cycle progression.
Arabidopsis Photorespiratory Serine Hydroxymethyltransferase Activity Requires the Mitochondrial Accumulation of Ferredoxin-Dependent Glutamate Synthase
Authors: Jamai Aziz , Salomé Patrice A. , Schilling Stephen H. , Weber Andreas P.M. , McClung C. Robertson
Published: February 2009

The dual affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase for O2 and CO2 results in the net loss of fixed carbon and energy in a process termed photorespiration. The photorespiratory cycle is complex and occurs in three organelles, chloroplasts, peroxisomes, and mitochondria, which necessitates multiple steps to transport metabolic intermediates. Genetic analysis has identified a number of mutants exhibiting photorespiratory chlorosis at ambient CO2, including several with defects in mitochondrial serine hydroxymethyltransferase (SHMT) activity. One class of mutants deficient in SHMT1 activity affects SHM1, which encodes the mitochondrial SHMT required for photorespiration. In this work, we describe a second class of SHMT1-deficient mutants defective in a distinct gene, GLU1, which encodes Ferredoxin-dependent Glutamate Synthase (Fd-GOGAT). Fd-GOGAT is a chloroplastic enzyme responsible for the reassimilation of photorespiratory ammonia as well as for primary nitrogen assimilation. We show that Fd-GOGAT is dual targeted to the mitochondria and the chloroplasts. In the mitochondria, Fd-GOGAT interacts physically with SHMT1, and this interaction is necessary for photorespiratory SHMT activity. The requirement of protein–protein interactions and complex formation for photorespiratory SHMT activity demonstrates more complicated regulation of this crucial high flux pathway than anticipated.
Crystal structure of trypanosoma cruzi tyrosine aminotransferase: Substrate specificity is influenced by cofactor binding mode
Authors: Blankenfeldt Wulf , Montemartini‐Kalisz Marisa , Kalisz Henryk M. , Hecht Hans‐Jürgen , Nowicki Cristina
Published: February 2009

The crystal structure of tyrosine aminotransferase (TAT) from the parasitic protozoan Trypanosoma cruzi, which belongs to the aminotransferase subfamily Iγ, has been determined at 2.5 Å resolution with the R‐value R = 15.1%. T. cruzi TAT shares less than 15% sequence identity with aminotransferases of subfamily Iα but shows only two larger topological differences to the aspartate aminotransferases (AspATs). First, TAT contains a loop protruding from the enzyme surface in the larger cofactor‐binding domain, where the AspATs have a kinked α‐helix. Second, in the smaller substrate‐binding domain, TAT has a four‐stranded antiparallel β‐sheet instead of the two‐stranded β‐sheet in the AspATs. The position of the aromatic ring of the pyridoxal‐5′‐phosphate cofactor is very similar to the AspATs but the phosphate group, in contrast, is closer to the substrate‐binding site with one of its oxygen atoms pointing toward the substrate. Differences in substrate specificities of T. cruzi TAT and subfamily Iα aminotransferases can be attributed by modeling of substrate complexes mainly to this different position of the cofactor‐phosphate group. Absence of the arginine, which in the AspATs fixes the substrate side‐chain carboxylate group by a salt bridge, contributes to the inability of T. cruzi TAT to transaminate acidic amino acids. The preference of TAT for tyrosine is probably related to the ability of Asn17 in TAT to form a hydrogen bond to the tyrosine side‐chain hydroxyl group.
Carbocations in the synthesis of prostaglandins by the cyclooxygenase of pgh synthase? a radical departure!
Authors: Dean Antony M. , Dean Francis M.
Published: February 2009

Evidence already available is used to demonstrate that although prostaglandin G/H synthase hydroxylates arachidonic acid through radical intermediates, it effects cyclizations through a carbocation center at C‐10. This is produced following migration of H to the initial radical at C‐13 and a 1 oxidation. Under orbital symmetry control, the cyclizations can give only the ring size andtransstereochemistry actually observed. After cyclization, the H‐shift reverses to take the sequence back into current radical theory for hydroxylation at C‐15. Thus 10, 10‐difluoroarachidonic acid cannot be cyclized, although it can be hydroxylated. Acetylation of Ser516 in the isoform synthase‐2 is considered to oppose carbocation formation and/or H‐migration and so prevent cyclizations while permitting hydroxylations; the associated inversion of chirality at C‐15 can then readily be accommodated without the change in conformation required by other schemes. Suicide inhibition occurs when carbocations form stable bonds upon (thermal) contact with adjacent heteroatoms, etc. Because the cyclooxygenase and peroxidase functions operate simultaneously through the same heme, phenol acts as reducing cosubstrate for the cyclooxygenase, thus enabling it to promote PGG2production and protect the enzyme from oxidative destruction.
Enhanced protein fold recognition using secondary structure information from nmr
Authors: Ayers Daniel J. , Gooley Paul R. , Widmer‐Cooper Asaph , Torda Andrew E.
Published: February 2009

NMR offers the possibility of accurate secondary structure for proteins that would be too large for structure determination. In the absence of an X‐ray crystal structure, this information should be useful as an adjunct to protein fold recognition methods based on low resolution force fields. The value of this information has been tested by adding varying amounts of artificial secondary structure data and threading a sequence through a library of candidate folds. Using a literature test set, the threading method alone has only a one‐third chance of producing a correct answer among the top ten guesses. With realistic secondary structure information, one can expect a 60–80% chance of finding a homologous structure. The method has then been applied to examples with published estimates of secondary structure. This implementation is completely independent of sequence homology, and sequences are optimally aligned to candidate structures with gaps and insertions allowed. Unlike work using predicted secondary structure, we test the effect of differing amounts of relatively reliable data.