bluuebunny/crossref_metadata_2025 huggingface dataset:
The flat model structure on complexes of sheaves
Authors: Gillespie James
Published: March 2006

Let

C
h

(

O

)

\mathbf {Ch}(\mathcal {O})

be the category of chain complexes of

O

\mathcal {O}

-modules on a topological space

T
T

(where

O

\mathcal {O}

is a sheaf of rings on

T
T

). We put a Quillen model structure on this category in which the cofibrant objects are built out of flat modules. More precisely, these are the dg-flat complexes. Dually, the fibrant objects will be called dg-cotorsion complexes. We show that this model structure is monoidal, solving the previous problem of not having any monoidal model structure on

C
h

(

O

)

\mathbf {Ch}(\mathcal {O})

. As a corollary, we have a general framework for doing homological algebra in the category

S
h

(

O

)

\mathbf {Sh}(\mathcal {O})

of

O

\mathcal {O}

-modules. I.e., we have a natural way to define the functors

Ext
\operatorname {Ext}

and

Tor
\operatorname {Tor}

in

S
h

(

O

)

\mathbf {Sh}(\mathcal {O})

.
Picard-Hayman behavior of derivatives of meromorphic functions with multiple zeros
Authors: Nevo Shahar , Pang Xuecheng , Zalcman Lawrence
Published: March 2006

The derivative of a transcendental meromorphic function all of whose zeros are multiple assumes every nonzero complex value infinitely often.
SScore: an R package for detecting differential gene expression without gene expression summaries
Authors: Kennedy Richard E. , Kerns Robnet T. , Kong Xiangrong , Archer Kellie J. , Miles Michael F.
Published: March 2006

Summary:  SScore is an R package that facilitates the comparison of gene expression between Affymetrix GeneChips using the S-score algorithm. The S-score algorithm uses probe level data directly to assess differences in gene expression, without requiring a preliminary separate step of probe set expression summary estimation. Therefore, the algorithm avoids introduction of error associated with the expression summary estimation process and has been demonstrated to improve the accuracy of identifying differentially expressed genes. The S-score produces accurate results even when few or no replicates are available.

Availability: The R package SScore is available from Bioconductor at

Contact:  rkennedy@vcu.edu
SBMLToolbox: an SBML toolbox for MATLAB users
Authors: Keating Sarah M. , Bornstein Benjamin J. , Finney Andrew , Hucka Michael
Published: March 2006

Summary: We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML.

Availability: SBMLToolbox is freely available from

Contact:  s.m.keating@herts.ac.uk
PseudoPipe: an automated pseudogene identification pipeline
Authors: Zhang Zhaolei , Carriero Nicholas , Zheng Deyou , Karro John , Harrison Paul M. , Gerstein Mark
Published: March 2006

Motivation: Mammalian genomes contain many ‘genomic fossils’ i.e. pseudogenes. These are disabled copies of functional genes that have been retained in the genome by gene duplication or retrotransposition events. Pseudogenes are important resources in understanding the evolutionary history of genes and genomes.

Results: We have developed a homology-based computational pipeline (‘PseudoPipe’) that can search a mammalian genome and identify pseudogene sequences in a comprehensive and consistent manner. The key steps in the pipeline involve using BLAST to rapidly cross-reference potential “parent” proteins against the intergenic regions of the genome and then processing the resulting “raw hits” -- i.e. eliminating redundant ones, clustering together neighbors, and associating and aligning clusters with a unique parent. Finally, pseudogenes are classified based on a combination of criteria including homology, intron-exon structure, and existence of stop codons and frameshifts.

Availability: The PseudoPipe program is implemented in Python and can be downloaded at

Contact:  Mark.Gerstein@yale.edu or zhaolei.zhang@utoronto.ca
Guttural pouches, brain temperature and exercise in horses
Authors: Mitchell Graham , Fuller Andrea , Maloney Shane K , Rump Nicola , Mitchell Duncan
Published: March 2006

Selective brain cooling (SBC) is defined as the lowering of brain temperature below arterial blood temperature. Artiodactyls employ a carotid rete, an anatomical heat exchanger, to cool arterial blood shortly before it enters the brain. The survival advantage of this anatomy traditionally is believed to be a protection of brain tissue from heat injury, especially during exercise. Perissodactyls such as horses do not possess a carotid rete, and it has been proposed that their guttural pouches serve the heat-exchange function of the carotid rete by cooling the blood that traverses them, thus protecting the brain from heat injury. We have tested this proposal by measuring brain and carotid artery temperature simultaneously in free-living horses. We found that despite evidence of cranial cooling, brain temperature increased by about 2.5 °C during exercise, and consistently exceeded carotid temperature by 0.2–0.5 °C. We conclude that cerebral blood flow removes heat from the brain by convection, but since SBC does not occur in horses, the guttural pouches are not surrogate carotid retes.
Transient magnetic energy growth in spherical stationary flows
Authors: Livermore Philip W , Jackson Andrew
Published: March 2006

The non-normality associated with the induction equation may lead to subcritical growth of magnetic field structures even if all linear eigenmodes decay. We compute the magnitude of these transient effects for a collection of predominantly axisymmetric stationary spherical flows and find without exception the dominance of axisymmetric field growth above all other symmetries. The transient growth is robust under small flow perturbations and can be understood by simple physical mechanisms: either field line shearing or stretching. Magnetic energy amplification of

is possible at magnetic Reynolds numbers of

, and such effects could therefore lead the system from a principally non-magnetic state into one where the magnetic field plays a significant role in the dynamics.
Planar velocity dynamos in a sphere
Authors: Bachtiar A.A , Ivers D.J , James R.W
Published: March 2006

The Earth's main magnetic field is generally believed to be due to a self-exciting dynamo process in the Earth's fluid outer core. A variety of antidynamo theorems exist that set conditions under which a magnetic field cannot be indefinitely maintained by dynamo action against ohmic decay. One such theorem, the
Planar Velocity Antidynamo Theorem
, precludes field maintenance when the flow is everywhere parallel to some plane, e.g. the equatorial plane. This paper shows that the proof of the Planar Velocity Theorem fails when the flow is confined to a sphere, due to diffusive coupling at the boundary. Then, the theorem reverts to a conjecture. There is a need to either prove the conjecture, or find a functioning planar velocity dynamo. To the latter end, this paper formulates the toroidal–poloidal spectral form of the magnetic induction equation for planar flows, as a basis for a numerical investigation. We have thereby determined magnetic field growth rates associated with various planar flows in spheres. For most flows, the induced magnetic field decays with time, supporting a planar velocity antidynamo conjecture for a spherical conducting fluid. However, one flow is exceptional, indicating that magnetic field growth can occur. We also re-examine some classical kinematic dynamo models, converting the flows where possible to planar flows. For the flow of Pekeris
et al
. (Pekeris, C. L., Accad, Y. & Shkoller, B. 1973 Kinematic dynamos and the Earth's magnetic field.
Phil. Trans. R. Soc. A
275
, 425–461), this conversion dramatically reduces the critical magnetic Reynolds number.
Does colonization asymmetry matter in metapopulations?
Authors: Vuilleumier Séverine , Possingham Hugh P
Published: March 2006

Despite the considerable evidence showing that dispersal between habitat patches is often asymmetric, most of the metapopulation models assume symmetric dispersal. In this paper, we develop a Monte Carlo simulation model to quantify the effect of asymmetric dispersal on metapopulation persistence. Our results suggest that metapopulation extinctions are more likely when dispersal is asymmetric. Metapopulation viability in systems with symmetric dispersal mirrors results from a mean field approximation, where the system persists if the expected per patch colonization probability exceeds the expected per patch local extinction rate. For asymmetric cases, the mean field approximation underestimates the number of patches necessary for maintaining population persistence. If we use a model assuming symmetric dispersal when dispersal is actually asymmetric, the estimation of metapopulation persistence is wrong in more than 50% of the cases. Metapopulation viability depends on patch connectivity in symmetric systems, whereas in the asymmetric case the number of patches is more important. These results have important implications for managing spatially structured populations, when asymmetric dispersal may occur. Future metapopulation models should account for asymmetric dispersal, while empirical work is needed to quantify the patterns and the consequences of asymmetric dispersal in natural metapopulations.
Complex population dynamics and complex causation: devils, details and demography
Authors: Benton Tim G , Plaistow Stewart J , Coulson Tim N
Published: March 2006

Population dynamics result from the interplay of density-independent and density-dependent processes. Understanding this interplay is important, especially for being able to predict near-term population trajectories for management. In recent years, the study of model systems—experimental, observational and theoretical—has shed considerable light on the way that the both density-dependent and -independent aspects of the environment affect population dynamics via impacting on the organism's life history and therefore demography. These model-based approaches suggest that (i) individuals in different states differ in their demographic performance, (ii) these differences generate structure that can fluctuate independently of current total population size and so can influence the dynamics in important ways, (iii) individuals are strongly affected by both current and past environments, even when the past environments may be in previous generations and (iv) dynamics are typically complex and transient due to environmental noise perturbing complex population structures. For understanding population dynamics of any given system, we suggest that ‘the devil is in the detail’. Experimental dissection of empirical systems is providing important insights into the details of the drivers of demographic responses and therefore dynamics and should also stimulate theory that incorporates relevant biological mechanism.
Leg regeneration stunts wing growth and hinders flight performance in a stick insect (
Sipyloidea sipylus
)
Authors: Maginnis Tara L
Published: March 2006

Major morphological structures are sometimes produced not once, but twice. For example, stick insects routinely shed legs to escape a predator or tangled moult, and these legs are subsequently re-grown. Here, I show that in
Sipyloidea sipylus
, re-growth of a leg during development causes adults to have disproportionately smaller wings and increases wing loading. These morphological consequences of leg regeneration led to significant reductions in several biologically relevant measures of individual flight performance. This previously unrecognized tradeoff between legs and wings reveals the integrated nature of phasmid phenotypes, and I propose how this tradeoff may have shaped phasmid evolution.
Mathematical models in physiology
Authors: Gavaghan David , Garny Alan , Maini Philip K , Kohl Peter
Published: March 2006

Computational modelling of biological processes and systems has witnessed a remarkable development in recent years. The search-term (
modelling OR modeling
) yields over 58 000 entries in PubMed, with more than 34 000 since the year 2000: thus, almost two-thirds of papers appeared in the last 5–6 years, compared to only about one-third in the preceding 5–6 decades.

The development is fuelled both by the continuously improving tools and techniques available for bio-mathematical modelling and by the increasing demand in quantitative assessment of element inter-relations in complex biological systems. This has given rise to a worldwide public domain effort to build a computational framework that provides a comprehensive theoretical representation of integrated biological function—the Physiome.

The current and next issues of this journal are devoted to a small sub-set of this initiative and address biocomputation and modelling in physiology, illustrating the breadth and depth of experimental data-based model development in biological research from sub-cellular events to whole organ simulations.
Modulatory effect of calmodulin-dependent kinase II (CaMKII) on sarcoplasmic reticulum Ca
2+
handling and interval–force relations: a modelling study
Authors: Iribe Gentaro , Kohl Peter , Noble Denis
Published: March 2006

We hypothesize that slow inactivation of Ca
2+
/calmodulin-dependent kinase II (CaMKII) and its modulatory effect on sarcoplasmic reticulum (SR) Ca
2+
handling are important for various interval–force (I–F) relations, in particular for the beat interval dependency in transient alternans during the decay of post-extrasystolic potentiation. We have developed a mathematical model of a single cardiomyocyte to integrate various I–F relations, including alternans, by incorporating a conceptual CaMKII kinetics model into the SR Ca
2+
handling model. Our model integrates I–F relations, such as the beat interval-dependent twitch force duration, restitution and potentiation, positive staircase phenomenon and alternans. We found that CaMKII affects more or less all I–F relations, and it is a key factor for integration of the various I–F relations in our model. Alternans arises, in the model, out of a steep relation between SR Ca
2+
load and release, owing to SR load-dependent changes in the releasability of Ca
2+
via the ryanodine receptor. Beat interval-dependent CaMKII activity, owing to its kinetic properties and amplifying effect on SR Ca
2+
load dependency of Ca
2+
release, replicated the beat interval dependency of alternans, as observed experimentally. Additionally, our model enabled reproduction of the effects of various interventions on alternans, such as the slowing or accelerating of Ca
2+
release and/or uptake. We conclude that a slow time-dependent factor, represented in the model by CaMKII, is important for the integration of I–F relations, including alternans, and that our model offers a useful tool for further analysis of the roles of integrative Ca
2+
handling in myocardial I–F relations.
The functional role of cardiac T-tubules explored in a model of rat ventricular myocytes
Authors: Pásek Michal , Šimurda Jiři , Christé Georges
Published: March 2006

The morphology of the cardiac transverse-axial tubular system (TATS) has been known for decades, but its function has received little attention. To explore the possible role of this system in the physiological modulation of electrical and contractile activity, we have developed a mathematical model of rat ventricular cardiomyocytes in which the TATS is described as a single compartment. The geometrical characteristics of the TATS, the biophysical characteristics of ion transporters and their distribution between surface and tubular membranes were based on available experimental data. Biophysically realistic values of mean access resistance to the tubular lumen and time constants for ion exchange with the bulk extracellular solution were included. The fraction of membrane in the TATS was set to 56%. The action potentials initiated in current-clamp mode are accompanied by transient K
+
accumulation and transient Ca
2+
depletion in the TATS lumen. The amplitude of these changes relative to external ion concentrations was studied at steady-state stimulation frequencies of 1–5 Hz. Ca
2+
depletion increased from 7 to 13.1% with stimulation frequency, while K
+
accumulation decreased from 4.1 to 2.7%. These ionic changes (particularly Ca
2+
depletion) implicated significant decrease of intracellular Ca
2+
load at frequencies natural for rat heart.
Endogenous driving and synchronization in cardiac and uterine virtual tissues: bifurcations and local coupling
Authors: Benson Alan P , Clayton Richard H , Holden Arun V , Kharche Sanjay , Tong Wing C
Published: March 2006

Cardiac and uterine muscle cells and tissue can be either autorhythmic or excitable. These behaviours exchange stability at bifurcations produced by changes in parameters, which if spatially localized can produce an ectopic pacemaking focus. The effects of these parameters on cell dynamics have been identified and quantified using continuation algorithms and by numerical solutions of virtual cells. The ability of a compact pacemaker to drive the surrounding excitable tissues depends on both the size of the pacemaker and the strength of electrotonic coupling between cells within, between, and outside the pacemaking region.

We investigate an ectopic pacemaker surrounded by normal excitable tissue. Cell–cell coupling is simulated by the diffusion coefficient for voltage. For uniformly coupled tissues, the behaviour of the hybrid tissue can take one of the three forms: (i) the surrounding tissue electrotonically suppresses the pacemaker; (ii) depressed rate oscillatory activity in the pacemaker but no propagation; and (iii) pacemaker driving propagations into the excitable region.

However, real tissues are heterogeneous with spatial changes in cell–cell coupling. In the gravid uterus during early pregnancy, cells are weakly coupled, with the cell–cell coupling increasing during late pregnancy, allowing synchronous contractions during labour. These effects are investigated for a caricature uterine tissue by allowing both excitability and diffusion coefficient to vary stochastically with space, and for cardiac tissues by spatial gradients in the diffusion coefficient.
Historical approaches to post-combat disorders
Authors: Jones Edgar
Published: March 2006

Almost every major war in the last century involving western nations has seen combatants diagnosed with a form of post-combat disorder. Some took a psychological form (exhaustion, combat fatigue, combat stress reaction and post-traumatic stress disorder), while others were characterized by medically unexplained symptoms (soldier's heart, effort syndrome, shell shock, non-ulcer dyspepsia, effects of Agent Orange and Gulf War Syndrome). Although many of these disorders have common symptoms, the explanations attached to them showed considerable diversity often reflected in the labels themselves. These causal hypotheses ranged from the effects of climate, compressive forces released by shell explosions, side effects of vaccinations, changes in diet, toxic effects of organophosphates, oil-well fires or depleted-uranium munitions. Military history suggests that these disorders, which coexisted in the civilian population, reflected popular health fears and emerged in the gaps left by the advance of medical science. While the current Iraq conflict has yet to produce a syndrome typified by medically unexplained symptoms, it is unlikely that we have seen the last of post-combat disorders as past experience suggests that they have the capacity to catch both military planners and doctors by surprise.
Healthcare utilization and mortality among veterans of the Gulf War
Authors: Gray Gregory C , Kang Han K
Published: March 2006

The authors conducted an extensive search for published works concerning healthcare utilization and mortality among Gulf War veterans of the Coalition forces who served during the1990–1991 Gulf War. Reports concerning the health experience of US, UK, Canadian, Saudi and Australian veterans were reviewed. This report summarizes 15 years of observations and research in four categories: Gulf War veteran healthcare registry studies, hospitalization studies, outpatient studies and mortality studies. A total of 149 728 (19.8%) of 756 373 US, UK, Canadian and Australian Gulf War veterans received health registry evaluations revealing a vast number of symptoms and clinical conditions but no suggestion that a new unique illness was associated with service during the Gulf War. Additionally, no Gulf War exposure was uniquely implicated as a cause for post-war morbidity. Numerous large, controlled studies of US Gulf War veterans' hospitalizations, often involving more than a million veterans, have been conducted. They revealed an increased post-war risk for mental health diagnoses, multi-symptom conditions and musculoskeletal disorders. Again, these data failed to demonstrate that Gulf War veterans suffered from a unique Gulf War-related illness. The sparsely available ambulatory care reports documented that respiratory and gastrointestinal complaints were quite common during deployment. Using perhaps the most reliable data, controlled mortality studies have revealed that Gulf War veterans were at increased risk of injuries, especially those due to vehicular accidents. In general, healthcare utilization data are now exhausted. These findings have now been incorporated into preventive measures in support of current military forces. With a few diagnostic exceptions such as amyotrophic lateral sclerosis, mental disorders and cancer, it now seems time to cease examining Gulf War veteran morbidity and to direct future research efforts to preventing illness among current and future military personnel.
Reproductive health of Gulf War veterans
Authors: Doyle Patricia , Maconochie Noreen , Ryan Margaret
Published: March 2006

In this review we summarize the scientific literature on reproductive health following deployment to the first Gulf war by armed service personnel. All the studies examined had methodological limitations, making interpretation difficult. Nonetheless we conclude that for male veterans there is no strong or consistent evidence to date for an effect of service in the first Gulf war on the risk of major, clearly defined, birth defects or stillbirth in offspring conceived after deployment. Effects on specific rare defects cannot be excluded at this stage since none of the studies had the statistical power to examine them. For miscarriage and infertility, there is some evidence of small increased risks associated with service, but the role of bias is likely to be strong. For female veterans, there is insufficient information to make robust conclusions, although the weight of evidence to date does not indicate any major problem associated specifically with deployment to the Gulf. None of the studies have been able to examine risk according particular exposures, and so possible associations with specific exposures for smaller groups of exposed veterans cannot be excluded.

We suggest that the way forward to address the question of veterans' reproductive health with confidence in the future is prospective surveillance following deployment. Anything less will result in further problems of interpretation and continued anxiety for parents, as well as prospective parents, in the armed forces.
The impact of the 1991 Gulf War on the mind and brain: findings from neuropsychological and neuroimaging research
Authors: Vasterling Jennifer J , Bremner J. Douglas
Published: March 2006

Many veterans of the 1991 Gulf War (GW) have complained of somatic and cognitive symptoms that may be neurological in nature. However, whether or not changes in brain function are associated with GW service continues to be debated. Studies of GW veterans using objective, performance-based neuropsychological measures have yielded inconsistent findings, with those indicating deficits among GW veterans typically revealing only relatively mild levels of neuropsychological impairment. Further, performances on objective neuropsychological tasks show little correspondence to subjective perceptions of cognitive functioning. Although preliminary magnetic resonance spectroscopy (MRS) studies demonstrate reduced
N
-acetylaspartate-to-creatine (NAA/Cr) ratio in select brain regions among GW veterans who report health concerns, this work requires further replication with larger, more representative samples. There is no evidence from neuroimaging studies of a non-specific effect of GW service or of changes in brain structure or function related to health status when conventional radiological methods are used. Owing to the paucity of objective exposure, baseline health data, and the now significant time elapsed since the GW, aetiological issues may never be fully resolved. Therefore, research addressing clinical management of GW veterans with neuropsychological dysfunction and neuroimaging abnormalities may prove more fruitful than exclusive focus on aetiology.
Neurological disorders in Gulf War veterans
Authors: Rose Michael R , Brix Kelley Ann
Published: March 2006

We present a review of neurological function in Gulf War veterans (GWV). Twenty-two studies were reviewed, including large hospitalization and registry studies, large population-based epidemiological studies, investigations of a single military unit, small uncontrolled studies of ill veterans and small controlled studies of veterans. In nearly all studies, neurological function was normal in most GWVs, except for a small proportion who were diagnosed with compression neuropathies (carpal tunnel syndrome or ulnar neuropathy). In the great majority of controlled studies, there were no differences in the rates of neurological abnormalities in GWVs and controls. In a national US study, the incidence of amyotrophic lateral sclerosis (ALS) seems to be significantly increased in GWVs, compared to the rate in controls. However, it is possible that military service, in general, might be associated with an increased risk of ALS, rather than Gulf War service in particular. Taken together, the conclusion is that if a neurological examination in a GWV is within normal limits, then extensive neurological testing is unlikely to diagnose occult neurological disorders.
The challenges of exposure assessment in health studies of Gulf War veterans
Authors: Glass Deborah C , Sim Malcolm R
Published: March 2006

A variety of exposures have been investigated in Gulf War veterans' health studies. These have most commonly been by self-report in a postal questionnaire but modelling and bio-monitoring have also been employed. Exposure assessment is difficult to do well in studies of any workplace environment. It is made more difficult in Gulf War studies where there are a number and variety of possible exposures, no agreed metrics for individual exposures and few contemporary records associating the exposure with an individual. In some studies, the exposure assessment was carried out some years after the war and in the context of media interest. Several studies have examined different ways to test the accuracy of exposure reporting in Gulf War cohorts. There is some evidence from Gulf War studies that self-reported exposures were subject to recall bias but it is difficult to assess the extent. Occupational exposure-assessment methodology can provide insights into the exposure-assessment process and how to do it well. This is discussed in the context of the Gulf War studies. Alternative exposure-assessment methodologies are presented, although these may not be suitable for widespread use in veteran studies. Due to the poor quality of and accessibility of objective military exposure records, self-assessed exposure questionnaires are likely to remain the main instrument for assessing the exposure for a large number of veterans. If this is to be the case, then validation methods with more objective methods need to be included in future study designs.
Immunological dysfunction, vaccination and Gulf War illness
Authors: Peakman Mark , Skowera Ania , Hotopf Matthew
Published: March 2006

One candidate cause of Gulf War illness is vaccination against infectious diseases including medical counter-measures against biological weapons. One influential theory has suggested that such mass-vaccination caused a shift in immune response to a Type 2 cytokine pattern (Th2), which it was suggested was accompanied by a chronic fatigue syndrome-like illness. This article critically appraises this theory. We start by examining epidemiological evidence, which indicates that single vaccines are unlikely to be a substantial cause of Gulf War illness, but that there was a modest relationship with multiple vaccines, which was strongest in those vaccinated while deployed to the Gulf. These relationships may be affected by recall bias. We conclude by examining the results of immunological studies carried out in veterans or in a relevant settingin vitro. The balance of evidence from immunological studies on veterans returning from the War, including those developing multi-symptom illness, is that the immune response has not become polarized towards Th2. In summary, the epidemiological evidence for a multiple vaccine effect on Gulf War-related illness remains a potentially important aetiological lead, but mechanistic studies available at this stage do not identify any immunological basis for it.
Regulation of Flowering in the Long-Day Grass Lolium temulentum by Gibberellins and the FLOWERING LOCUS T Gene
Authors: King Rod W. , Moritz Thomas , Evans Lloyd T. , Martin Jerome , Andersen Claus H. , Blundell Cheryl , Kardailsky Igor , Chandler Peter M.
Published: April 2006

Seasonal control of flowering often involves leaf sensing of daylength coupled to time measurement and generation and transport of florigenic signals to the shoot apex. We show that transmitted signals in the grass Lolium temulentum may include gibberellins (GAs) and the FLOWERING LOCUS T (FT) gene. Within 2 h of starting a florally inductive long day (LD), expression of a 20-oxidase GA biosynthetic gene increases in the leaf; its product, GA20, then increases 5.7-fold versus short day; its substrate, GA19, decreases equivalently; and a bioactive product, GA5, increases 4-fold. A link between flowering, LD, GAs, and GA biosynthesis is shown in three ways: (1) applied GA19 became florigenic on exposure to LD; (2) expression of LtGA20ox1, an important GA biosynthetic gene, increased in a florally effective LD involving incandescent lamps, but not with noninductive fluorescent lamps; and (3) paclobutrazol, an inhibitor of an early step of GA biosynthesis, blocked flowering, but only if applied before the LD. Expression studies of a 2-oxidase catabolic gene showed no changes favoring a GA increase. Thus, the early LD increase in leaf GA5 biosynthesis, coupled with subsequent doubling in GA5 content at the shoot apex, provides a substantial trail of evidence for GA5 as a LD florigen. LD signaling may also involve transport of FT mRNA or protein because expression of LtFT and LtCONSTANS increased rapidly, substantially (>80-fold for FT), and independently of GA. However, because a LD from fluorescent lamps induced LtFT expression but not flowering, the nature of the light response of FT requires clarification.
Functional Characterization of Ice Plant SKD1, an AAA-Type ATPase Associated with the Endoplasmic Reticulum-Golgi Network, and Its Role in Adaptation to Salt Stress
Authors: Jou Yingtzy , Chiang Chih-Pin , Jauh Guang-Yuh , Yen Hungchen Emilie
Published: April 2006

A salt-induced gene mcSKD1 (suppressor of K+ transport growth defect) able to facilitate K+ uptake has previously been identified from the halophyte ice plant (Mesembryanthemum crystallinum). The sequence of mcSKD1 is homologous to vacuolar protein sorting 4, an ATPase associated with a variety of cellular activities-type ATPase that participates in the sorting of vacuolar proteins into multivesicular bodies in yeast (Saccharomyces cerevisiae). Recombinant mcSKD1 exhibited ATP hydrolytic activities in vitro with a half-maximal rate at an ATP concentration of 1.25 mm. Point mutations on active site residues abolished its ATPase activity. ADP is both a product and a strong inhibitor of the reaction. ADP-binding form of mcSDK1 greatly reduced its catalytic activity. The mcSKD1 protein accumulated ubiquitously in both vegetative and reproductive parts of plants. Highest accumulation was observed in cells actively engaging in the secretory processes, such as bladder cells of leaf epidermis. Membrane fractionation and double-labeling immunofluorescence showed the predominant localization of mcSKD1 in the endoplasmic reticulum-Golgi network. Immunoelectron microscopy identified the formation of mcSKD1 proteins into small aggregates in the cytosol and associated with membrane continuum within the endomembrane compartments. These results indicated that this ATPase participates in the endoplasmic reticulum-Golgi mediated protein sorting machinery for both housekeeping function and compartmentalization of excess Na+ under high salinity.
Sustained activation of c‐jun‐N‐terminal kinase plays a critical role in arsenic trioxide‐induced cell apoptosis in multiple myeloma cell lines
Authors: Kajiguchi Tomohiro , Yamamoto Kazuhito , Iida Shinsuke , Ueda Ryuzo , Emi Nobuhiko , Naoe Tomoki
Published: March 2006

Multiple myeloma (MM) is a presently incurable B‐cell malignancy, and newer biologically based therapies are needed. Arsenic trioxide (ATO) has been established as a therapeutic agent for relapsed acute promyelocytic leukemia patients, and has been used for MM patients in clinical trials. In this study, we investigated the role of c‐jun‐N‐terminal kinase (JNK) in ATO‐induced apoptosis in MM lines. The exogenous interleukin (IL)‐6 dependent MM line, ILKM‐3, and independent MM lines, U266 and XG‐7, were treated with a therapeutic concentration of ATO with or without JNK inhibitor 1 (a JNK‐specific inhibitor) and anisomycin (a JNK activator). Their cell growth, cell cycle, JNK activation and NF‐κB activation were investigated. ATO induced apoptosis in U266 and ILKM‐3 regardless of their exogenous IL‐6 dependency. This apoptosis, accompanied with decreased mitochondrial transmembrane potential, sustained activation of JNK but not cell cycle arrest. Pretreatment of JNK inhibitor prevented ATO‐induced apoptosis in ATO‐sensitive lines. Combined treatment with ATO and anisomycin induced sustained activation of JNK and apoptosis in the ATO‐insensitive MM line, XG‐7. Results of various time period treatments of ATO showed that sustained activation of JNK was needed in ATO‐induced apoptosis in MM. IkBα phosphorylation was not associated with ATO‐sensitivity of MM lines. These findings suggest that sustained activation of JNK plays a critical role in ATO‐induced apoptosis in MM cell lines. Cotreatment with ATO and the agent, which can induce sustained activation of JNK, might improve the outcome in MM therapy. (Cancer Sci 2006; 97)
Existence of a no effect level for MeIQx hepatocarcinogenicity on a background of thioacetamide‐induced liver damage in rats
Authors: Kang Jin Seok , Wanibuchi Hideki , Morimura Keiichirou , Totsuka Yukari , Yoshimura Isao , Fukushima Shoji
Published: March 2006

As exposure to heterocyclic amines might increase the risk of liver cancer, we investigated the carcinogenic potential of MeIQx under conditions of liver damage caused by TAA. Male, 6‐week‐old F344 rats (n = 280) were divided into 14 groups; groups 1–7 received TAA (0.03% in drinking water) and groups 8–14 received water for the first 12 weeks. Thereafter, the animals received MeIQx at doses from 0, 0.001, 0.01, 0.1, 1, 10 to 100 p.p.m. (groups 1–7 and 8–14, respectively) in pellet basal diet for 16 weeks. All survivors were killed at week 28 for assessment of numbers and areas of GST‐P positive foci, considered to be pre‐neoplastic lesions of the liver. Values were increased significantly in all the groups receiving TAA→MeIQx compared to MeIQx alone (P < 0.01). Numbers of GST‐P positive foci were significantly increased in groups 7 and 14 (treated with 100 p.p.m. MeIQx) as compared to 0 p.p.m.‐MeIQx (groups 1 and 8) (P < 0.01), along with areas in group 14 compared to group 8 (P < 0.01). However, with the maximum likelihood method, the data for numbers of GST‐P positive foci (groups 1–7 and groups 8–14) fitted the hockey stick regression model, representing no differences from groups 1–5 and from groups 8–13, despite a linear dose‐dependent increase of MeIQx‐DNA adducts from 0.1 to 100 p.p.m. We conclude that there is a no effect level for MeIQx hepatocarcinogenicity, even on a background of TAA‐induced liver damage. (Cancer Sci 2006; 97)
Plant harvest impacts and sustainability in Bwindi Impenetrable National Park, S.W. Uganda
Authors: Bitariho Robert , McNeilage Alastair , Babaasa Dennis , Barigyira Robert
Published: March 2006

Sustainable utilization of forest resources has been widely adopted as a conservation strategy, but that sustainability has rarely been empirically tested. Plant resource extraction from Bwindi Impenetrable National Park (BINP) by local communities has been legalized and controlled in areas called multiple use zones (MUZs). Through a series of systematic transects and plots, we determined harvest impacts of two mostly harvested medicinal plants of Rytigynia kigeziensis VERDC.l and Ocotea usambarensis Engl in BINP. The plots were placed in MUZs and non‐MUZs. Data on biomass production and population dynamics were collected from the plots. We also analysed forest society records for the past 3 years to determine annual plant resource offtakes from BINP. Bark production of the two plants in MUZs and non‐MUZs are not significantly different, suggesting an insignificant change in bark production because of bark harvest. Annual bark harvests of the two plants are between 0.26–1.64% of available bark stock. These are too low to cause any noticeable negative impacts and are sustainable. Annual bark harvest of R. kigeziensis and O. usambarensis should be increased from the original 1% to about 3% of available bark stock to allow more involvement of the marginalized poor people like Batwa in BINP.
Diversity of vascular plants on Ssese islands in Lake Victoria, central Uganda
Authors: Ssegawa Paul , Nkuutu David N.
Published: March 2006

Diversity and distribution of trees [≥5 cm diameter at breast height (dbh)], shrubs and herbs was assessed in thirty 0.05‐ha (10 × 50 m) plots of a tropical high forest in the Ssese islands of Lake Victoria, central Uganda. The aim was to determine the floristic richness and composition of the forests. We recorded 179 species belonging to 70 families and 146 genera. Of these, nine families had five species or more. Rubiaceae was the richest with fourteen species followed by Euphorbiaceae (thirteen), Apocynaceae (ten) and Moraceae (nine). The majority of the families (35) were represented by one species each. Fifty‐eight herbaceous species, 39 lianas, ten shrubs and 72 species of trees were recorded. The commonest species recorded in the forest included: Uapaca guineensis Mull. Arg., Tabernaemontana pachysiphon Stapf., and Aframomum luteoalbum (K Schum.) K. Schum. Among the rare species encountered were Ficus densistipulata De Willd., Englerophytum oblanceolatum (S. Moore) Pennington, and Afromomum zambeziacum (Bak.) K. Schum. The present study has shown that the Ssese islands are floristically rich in species and compare well with other mainland forests. Species richness, rarity and uniqueness of habitats can be considered as approaches in the prioritization of conservation sites within the fragmented forests of Ssese islands.
Forb diversity and community similarity of kopjes in the Serengeti National Park, Tanzania
Authors: Poelchau Monica Frances , Mistry Shahroukh
Published: March 2006

The forb communities of kopjes (rock outcrops) in the Simba, Maasai and Loliondo areas of the Serengeti National Park were examined to determine differences in species composition from surrounding grassland communities, and among sites within kopje and grassland communities. Species diversity measures and multivariate ordination techniques were used to examine the community similarity and species turnover between sites. All measures of forb species diversity were higher on the kopje sites with the exception of one grassland site, and the community composition significantly differed between these two habitat types, with more species and families exclusive to the kopje habitat. Species turnover was very high in grassland habitats, with two of the three areas (Simba and Loliondo) exhibiting a complete change in species composition. Kopjes, on the other hand, had remarkably similar forb communities, suggesting that the populations of the species present on these rock outcrops form patch structures. The distinct flora and higher diversity of kopje forbs raise interesting questions regarding distribution, dispersal and patch dynamics.
Elevational variation in diversity and composition of land‐snail faunas in a Tanzanian forest
Authors: Tattersfield Peter , Seddon Mary B. , Ngereza Christine , Rowson Ben
Published: March 2006

We sampled terrestrial molluscs at fifteen elevations between 400 and 2000 m in Mwanihana Forest Reserve, Tanzania and recorded 84 taxa. Four diversity measures – species density (DP), species richness (D20) and observed (SO) and interpolated (SI) alpha diversity – were measured; beta diversity and abundance were also investigated. Mean elevational range was 470 m. DP, D20, alpha diversity and mollusc abundance increased with elevation, but alpha diversity peaked at 1695 m (SO) or 1500 m (SI) and declined at higher elevations. Maximum beta diversity was at 1000 m. Soil pH was negatively correlated with elevation and DP. Cluster analysis divided the sites into lowland (400–900 m) and highland (>1000 m) groups. Axis 1 of a canonical correspondence analysis was associated with altitude and suggested a faunal discontinuity at 1000 m. Variation within the highland (>1000 m) and lowland faunal sets was related to elevation and forest structure respectively. The findings indicate that mollusc diversity peaks at intermediate elevations. This may be related to the combined effects of low rainfall conditions at low elevations and increasing effects of soil leaching at high elevations, both of which may limit mollusc diversity and abundance. Diversity at intermediate altitudes may be further elevated because of faunal mixing of lowland and highland groups.
The role of salinity and sodicity in the dieback of Acacia xanthophloea in Ngorongoro Caldera, Tanzania
Authors: Mills A. J.
Published: March 2006

Dieback of Acacia xanthophloea (Benth.) has opened up the once densely forested Lerai area in Ngorongoro Caldera, Tanzania. Soil samples were taken from profiles in the Ngorongoro Conservation Area and Lake Manyara National Park at sites of dieback and at sites with healthy A. xanthophloea trees. Dieback sites had significantly greater electrical conductivity (EC), water‐soluble Na+, K+, Cl−, SO and sodium adsorption ratios (SAR) than healthy sites. The following mean values were recorded: EC (179 versus 70 mS m−1; P < 0.001, Student's t‐test, n = 8 and 10, respectively; 40–60 cm); Na+ (99 versus 30 mmolc kg−1, P < 0.001, n = 7 and 8 respectively); K+ (11 versus 3 mmolc kg−1, P < 0.05); Cl− (36 versus 7 mmolc kg−1, P < 0.01); SO (31 versus 5 mmolc kg−1, P < 0.01); and SAR (28 versus 8 mmol l−1/2, P < 0.01). Water‐soluble Na+, Cl− and SO concentrations in the Lerai profiles have probably resulted in toxicity and osmotic stress which contributed to dieback. Accumulation of salts may have occurred because of reduced flow of freshwater through Lerai and/or flow of water from Lake Magadi into Lerai. Forest recovery may be possible if salinity is reduced. Management strategies for reducing salinity have been implemented and included re‐establishing streams that flow through Lerai. Exclusion of elephants (Loxodonta africana) from Lerai is another management strategy presently under consideration.
Spatial and temporal patterns in Arvicanthis niloticus (Desmarest, 1822) as revealed by radio‐tracking
Authors: Hoffmann Anke , Eckhoff Katja , Klingel Hans
Published: March 2006

Arvicanthis niloticus was radio‐tracked in the grasslands of the Queen Elizabeth National Park in Uganda. Home range sizes calculated by Ranges V® using the Minimum Convex Polygon Method (at 95%) were on average 5.5 times larger in the bushland–grassland mosaic than those in the Abutilon guineense–Ocimum suave bushland. An inverse relation between home range size and population density was found. In both habitats the species was highly active during daylight hours but differed in activity patterns.
Will tree euphorbias (Euphorbia tetragona and Euphorbia triangularis) survive under the impact of black rhinoceros (Bicornis diceros minor) browsing in the Great Fish River Reserve, South Africa?
Authors: Heilmann Linda C. , de Jong Karen , Lent Peter C. , de Boer Willem F.
Published: March 2006

The impact of black rhinoceros (Bicornis diceros minor) on the tree euphorbias Euphorbia tetragona and Euphorbia triangularis was studied in the Great Fish River Reserve, South Africa. Black rhinoceros pushed over about 5–7% of the trees in a 2‐month period. There was a preference of rhinos for smaller trees, however this preference did not guarantee euphorbia survival in the larger size classes. This means that tree euphorbias could very well disappear from all areas accessible to rhinos. Rhino feeding choices were correlated with higher plant moisture content, higher nitrogen content, and a higher digestibility.
A policy tool for establishing a balance between wildlife habitat preservation and the use of natural resources by rural people in South Africa
Authors: Bouare Oumar
Published: March 2006

In this paper, a model is set up to determine the size of the wildlife population compatible with the extraction of the maximum output by rural people from natural resources. It is found that when the size of human population increases, to obtain the maximum output of food, the size of wildlife population decreases if the human population is growing faster than or at the same rate as that of the wildlife population; whereas the size of the wildlife population increases if the human population is growing slower than that of the wildlife. Furthermore, in the event that the increase in the size of the wildlife population is unable to reach the level compatible with the extraction of the maximum output of food, the improvement of the wildlife habitat and supplementing rural people's income with the proceeds of tourism are proposed as policies to maintain a balance between the preservation of the wildlife habitat and the use of natural resources by rural people.
C‐terminal nucleophosmin mutations are uncommon in chronic myeloid disorders
Authors: Caudill Jonathan S. C. , Sternberg Alexander J. , Li Chin‐Yang , Tefferi Ayalew , Lasho Terra L. , Steensma David P.
Published: March 2006

C‐terminal somatic mutations in nucleophosmin (NPM), a nucleolar shuttling protein that binds p53 and p19Arf, were recently described in karyotypically normal acute myeloid leukaemia (AML). We analysed primary marrow samples from 150 patients with various chronic myeloid disorders for mutations in the NPM1 gene encoding NPM. NPM1 mutations (tetranucleotide duplication) were detected in three patients, all of whom had chronic myelomonocytic leukaemia (CMML) and a short (<1 year) survival, with rapid progression to overt AML. All other patients were NPM1‐wild type in the region analysed. In conclusion, C‐terminal NPM mutations are uncommon in chronic myeloid neoplasia, but if present may represent an evolving leukaemic clone.