bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain
Authors: Wells Mark , Tidow Henning , Rutherford Trevor J. , Markwick Phineus , Jensen Malene Ringkjobing , Mylonas Efstratios , Svergun Dmitri I. , Blackledge Martin , Fersht Alan R.
Published: April 2008

Proteins with intrinsically disordered domains are implicated in a vast range of biological processes, especially in cell signaling and regulation. Having solved the quaternary structure of the folded domains in the tumor suppressor p53 by a multidisciplinary approach, we have now determined the average ensemble structure of the intrinsically disordered N-terminal transactivation domain (TAD) by using residual dipolar couplings (RDCs) from NMR spectroscopy and small-angle x-ray scattering (SAXS). Remarkably, not only were we able to measure RDCs of the isolated TAD, but we were also able to do so for the TAD in both the full-length tetrameric p53 protein and in its complex with a specific DNA response element. We determined the orientation of the TAD ensemble relative to the core domain, found that the TAD was stiffer in the proline-rich region (residues 64–92), which has a tendency to adopt a polyproline II (PPII) structure, and projected the TAD away from the core. We located the TAD in SAXS experiments on a complex between tetrameric p53 and four Taz2 domains that bind tightly to the TAD (residues 1–57) and acted as “reporters.” The p53-Taz2 complex was an extended cross-shaped structure. The quality of the SAXS data enabled us to model the disordered termini and the folded domains in the complex with DNA. The core domains enveloped the response element in the center of the molecule, with the Taz2-bound TADs projecting outward from the core.
Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell
Authors: Hongoh Yuichi , Sharma Vineet K. , Prakash Tulika , Noda Satoko , Taylor Todd D. , Kudo Toshiaki , Sakaki Yoshiyuki , Toyoda Atsushi , Hattori Masahira , Ohkuma Moriya
Published: April 2008

Termites harbor a symbiotic gut microbial community that is responsible for their ability to thrive on recalcitrant plant matter. The community comprises diverse microorganisms, most of which are as yet uncultivable; the detailed symbiotic mechanism remains unclear. Here, we present the first complete genome sequence of a termite gut symbiont—an uncultured bacterium named Rs-D17 belonging to the candidate phylum Termite Group 1 (TG1). TG1 is a dominant group in termite guts, found as intracellular symbionts of various cellulolytic protists, without any physiological information. To acquire the complete genome sequence, we collected Rs-D17 cells from only a single host protist cell to minimize their genomic variation and performed isothermal whole-genome amplification. This strategy enabled us to reconstruct a circular chromosome (1,125,857 bp) encoding 761 putative protein-coding genes. The genome additionally contains 121 pseudogenes assigned to categories, such as cell wall biosynthesis, regulators, transporters, and defense mechanisms. Despite its apparent reductive evolution, the ability to synthesize 15 amino acids and various cofactors is retained, some of these genes having been duplicated. Considering that diverse termite-gut protists harbor TG1 bacteria, we suggest that this bacterial group plays a key role in the gut symbiotic system by stably supplying essential nitrogenous compounds deficient in lignocelluloses to their host protists and the termites. Our results provide a breakthrough to clarify the functions of and the interactions among the individual members of this multilayered symbiotic complex.
RNA landscape of evolution for optimal exon and intron discrimination
Authors: Zhang Chaolin , Li Wen-Hsiung , Krainer Adrian R. , Zhang Michael Q.
Published: April 2008

Accurate pre-mRNA splicing requires primary splicing signals, including the splice sites, a polypyrimidine tract, and a branch site, other splicing-regulatory elements (SREs). The SREs include exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs), and intronic splicing silencers (ISSs), which are typically located near the splice sites. However, it is unclear to what extent splicing-driven selective pressure constrains exonic and intronic sequences, especially those distant from the splice sites. Here, we studied the distribution of SREs in human genes in terms of DNA strand-asymmetry patterns. Under a neutral evolution model, each mononucleotide or oligonucleotide should have a symmetric (Chargaff's second parity rule), or weakly asymmetric yet uniform, distribution throughout a pre-mRNA transcript. However, we found that large sets of unbiased, experimentally determined SREs show a distinct strand-asymmetry pattern that is inconsistent with the neutral evolution model, and reflects their functional roles in splicing. ESEs are selected in exons and depleted in introns and vice versa for ESSs. Surprisingly, this trend extends into deep intronic sequences, accounting for one third of the genome. Selection is detectable even at the mononucleotide level, so that the asymmetric base compositions of exons and introns are predictive of ESEs and ESSs. We developed a method that effectively predicts SREs based on strand asymmetry, expanding the current catalog of SREs. Our results suggest that human genes have been optimized for exon and intron discrimination through an RNA landscape shaped during evolution.
Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases
Authors: Zhang Xiaodong , Bruice Thomas C.
Published: April 2008

Molecular dynamics and hybrid quantum mechanics/molecular mechanics have been used to investigate the mechanisms of
+
AdoMet methylation of protein-Lys-NH
2
catalyzed by the lysine methyltransferase enzymes: histone lysine monomethyltransferase SET7/9, Rubisco large-subunit dimethyltransferase, viral histone lysine trimethyltransferase, and the Tyr245Phe mutation of SET7/9. At neutrality in aqueous solution, primary amines are protonated. The enzyme reacts with Lys-NH
3
+
and
+
AdoMet species to provide an Enz·Lys-NH
3
+
·
+
AdoMet complex. The close positioning of two positive charges lowers the

pK
a

of the Lys-NH
3
+
entity, a water channel appears, and the proton escapes to the aqueous solvent; then the reaction Enz·Lys-NH
2
·
+
AdoMet → Enz·Lys-N(Me)H
2
+
·AdoHcy occurs. Repeat of the sequence provides dimethylated lysine, and another repeat yields a trimethylated lysine. The sequence is halted at monomethylation when the conformation of the Enz·Lys-N(Me)H
2
+
·
+
AdoMet has the methyl positioned to block formation of a water channel. The sequence of reactions stops at dimethylation if the conformation of Enz·Lys-N(Me)
2
H
+
·
+
AdoMet has a methyl in position, which forbids the formation of the water channel.
Decreased corticolimbic allopregnanolone expression during social isolation enhances contextual fear: A model relevant for posttraumatic stress disorder
Authors: Pibiri Fabio , Nelson Marianela , Guidotti Alessandro , Costa Erminio , Pinna Graziano
Published: April 2008

Mice subjected to social isolation (3–4 weeks) exhibit enhanced contextual fear responses and impaired fear extinction. These responses are time-related to a decrease of 5α-reductase type I (5α-RI) mRNA expression and allopregnanolone (Allo) levels in selected neurons of the medial prefrontal cortex, hippocampus, and basolateral amygdala. Of note, the cued fear response was not different between group housed and socially isolated mice. In socially isolated mice,
S
-norfluoxetine, a selective brain steroidogenic stimulant (SBSS), in doses (0.45–1.8 μmol/kg) that increase brain Allo levels but fail to inhibit serotonin reuptake, greatly attenuates enhanced contextual fear response. SKF 105,111 (a potent 5α-RI inhibitor) decreases corticolimbic Allo levels and enhances the contextual fear response in group housed mice, which suggests that social isolation alters emotional responses by reducing the positive allosteric modulation of Allo at GABA
A
receptors in corticolimbic circuits. Thus, these procedures model emotional hyperreactivity, including enhanced contextual fear and impaired contextual fear extinction, which also is observed in posttraumatic stress disorder (PTSD) patients. A recent clinical study reported that cerebrospinal fluid Allo levels also are down-regulated in PTSD patients and correlate negatively with PTSD symptoms and negative mood. Thus, protracted social isolation of mice combined with tests of fear conditioning may be a suitable model to study emotional behavioral components associated with neurochemical alterations relating to PTSD. Importantly, drugs like SBSSs, which rapidly increase corticolimbic Allo levels, normalize the exaggerated contextual fear responses resulting from social isolation, suggesting that selective activation of neurosteroidogenesis may be useful in PTSD therapy.
Quality control of overexpressed membrane proteins
Authors: Geertsma Eric R. , Groeneveld Maarten , Slotboom Dirk-Jan , Poolman Bert
Published: April 2008

Overexpression of membrane proteins in
Escherichia coli
frequently leads to the formation of aggregates or inclusion bodies, which is undesirable for most studies. Ideally, one would like to optimize the expression conditions by monitoring simultaneously and rapidly both the amounts of properly folded and aggregated membrane protein, a requirement not met by any of the currently available methods. Here, we describe a simple gel-based approach with green fluorescent protein as folding indicator to detect well folded and aggregated proteins simultaneously. The method allows for rapid screening and, importantly, pinpointing the most likely bottlenecks in protein production.
Impact of a Brief Training on Medical Resident Screening for Alcohol Misuse and Illicit Drug Use
Authors: Gunderson Erik W. , Levin Frances R. , Owen Patricia
Published: April 2008

Educational initiatives are needed to improve primary care substance use screening. This study assesses the impact on 24 medical residents of a 2.5‐day curriculum combining experiential and manual‐based training on screening for alcohol misuse and illicit drug use. A retrospective chart review of new primary care outpatients demonstrated that nearly all were asked about current alcohol use before and after curriculum participation. Adherence to national screening guidelines on quantification of alcohol consumption modestly improved (p < .05), as did inquiry about current illicit drug use (p < .05). Continued efforts are needed to enhance educational initiatives for primary care physicians.
Use of Dronabinol for Cannabis Dependence: Two Case Reports and Review
Authors: Levin Frances R. , Kleber Herbert D.
Published: April 2008

Marijuana is the most commonly used illicit drug in the United States and throughout the world. Despite this, the number of laboratory studies that have assessed pharmacologic agents to target cannabis withdrawal symptoms or reduce the reinforcing effects of marijuana has been modest. Unlike alcohol, cocaine, opiates, or nicotine, there has been a minimal number of clinical pharmacologic treatment trials that have targeted marijuana use. Based on recent laboratory studies, dronabinol (delta‐9‐tetrahydrocannabinol) has been shown to reduce cannabis withdrawal symptoms and the subjective effects of marijuana. Given that agonist agents have been found to be effective for opiate and nicotine dependence, the clinical utility of dronabinol for cannabis dependence is a reasonable approach. Two case reports using dronabinol are presented. The potential benefit, as well as questions that arise from the use of this medication in cannabis‐abusing populations, is presented. Also, future areas of research that might be explored are discussed.
Contextual Influences on Polydrug Use among Young, Low‐Income Women: Effects of Neighborhood and Personal Networks
Authors: Wu Z. Helen , Eschbach Karl , Grady James J.
Published: April 2008

This study assessed contextual risks for polydrug use in a triethnic sample (non‐Hispanic white, African American, Hispanic) of young women with a low income. For the current analysis, a total of 712 young women aged 18 to 31 years who sought care in state‐funded family planning clinics in southeast Texas from December 2001 to May 2003 participated in the survey. The main outcome of the study was the number of illicit drugs (including marijuana, MDMA [ecstasy], crack cocaine, and other hard drugs) used in the last 12 months. Of the 712 subjects, 198 (28%) reported using illicit drugs in the past 12 months. Neighborhood socioeconomic status was significantly associated with drug use in a bivariate model. The proportion of women living in the most advantaged neighborhoods who reported drug use was more than twice that of women living in the most disadvantaged neighborhoods. However, the significance of neighborhood socioeconomic status was eliminated after controlling for ethnicity or for personal network characteristics in a multivariate ordinal logistic regression model. In contrast, in multivariate models, personal network indicators, such as a larger number of monthly contacts with friends (odds ratio [OR] = 1.32, 95% confidence interval [CI] = 1.11, 1.56) and a larger number of friends who used illicit drugs (OR = 1.47, 95% CI = 1.33, 1.62) were associated with increased drug use. In addition, not being currently married (vs. being married) (OR = 2.73, 95% CI = 1.44, 5.16) was associated with a larger number of drugs used in the last 12 months. In conclusion, we found that neighborhood socioeconomic status was not directly associated with more drug use when controlling for ethnicity or for personal network characteristics. Personal networks may mediate the relationships between neighborhood and drug use. Strategies to reduce polydrug use should target personal networks where friends use illicit drugs.
Electron cyclotron current drive calculated for ITER conditions using different models
Authors: Marushchenko N.B. , Maassberg H. , Turkin Yu.
Published: April 2008

The current drive efficiency for the ITER reference scenario 2 has been calculated by the newly developed ray-tracing code TRAVIS for both the upper and the equatorial launchers. For comparison, two adjoint approach models are applied, the high-speed-limit model and a model with the parallel momentum conservation taken into account. It is shown that in the angle range expected as optimal launch angles the momentum conservation correction produces a non-negligible contribution in ECCD, leading to the necessity to revise the previous predictions carefully. Additionally, the scenario with reduced magnetic field is checked. It is shown that the ECCD efficiency (as well as the deposition profile) for the equatorial launcher may be significantly changed due to unwanted absorption at the higher (parasitic) harmonics.
Link Floer homology and the Thurston norm
Authors: Ozsváth Peter , Szabó Zoltán
Published: April 2008

We show that link Floer homology detects the Thurston norm of a link complement. As an application, we show that the Thurston polytope of an alternating link is dual to the Newton polytope of its multi-variable Alexander polynomial. To illustrate these techniques, we also compute the Thurston polytopes of several specific link complements.
On the radius of injectivity of null hypersurfaces
Authors: Klainerman Sergiu , Rodnianski Igor
Published: April 2008

We investigate the regularity of past (future) boundaries of points in regular, Einstein vacuum spacetimes. We provide conditions, expressed in terms of a space-like foliation and which imply, in particular, uniform

L
2

L^2

bounds for the curvature tensor, sufficient to ensure the local nondegeneracy of these boundaries. More precisely we provide a uniform lower bound on the radius of injectivity of the null boundaries

N

±

(
p
)

\mathcal {N}^{\pm }(p)

of the causal past (future) sets

J

±

(
p
)

\mathcal {J}^{\pm }(p)

. Such lower bounds are essential in understanding the causal structure and the related propagation properties of solutions to the Einstein equations. They are particularly important in construction of an effective Kirchoff-Sobolev type parametrix for solutions of wave equations on

M

\mathbf {M}

. Such parametrices are used by the authors in a forthcoming paper to prove a large data break-down criterion for solutions of the Einstein vacuum equations.
Orbit equivalence for Cantor minimal ℤ²-systems
Authors: Giordano Thierry , Matui Hiroki , Putnam Ian , Skau Christian
Published: April 2008

We show that every minimal, free action of the group

Z

2

\mathbb {Z}^{2}

on the Cantor set is orbit equivalent to an AF-relation. As a consequence, this extends the classification of minimal systems on the Cantor set up to orbit equivalence to include AF-relations,

Z

\mathbb {Z}

-actions and

Z

2

\mathbb {Z}^{2}

-actions.
Global existence for energy critical waves in 3-d domains
Authors: Burq Nicolas , Lebeau Gilles , Planchon Fabrice
Published: April 2008

We prove that the defocusing quintic wave equation, with Dirichlet boundary conditions, is globally well posed on

H
0
1

(
Ω
)
×

L
2

(
Ω
)

H^1_0(\Omega ) \times L^2( \Omega )

for any smooth (compact) domain

Ω
⊂

R

3

\Omega \subset \mathbb {R}^3

. The main ingredient in the proof is an

L
5

L^5

spectral projector estimate, obtained recently by Smith and Sogge, combined with a precise study of the boundary value problem.
On the Cachazo-Douglas-Seiberg-Witten conjecture for simple Lie algebras
Authors: Kumar Shrawan
Published: April 2008

We prove a part of the Cachazo-Douglas-Seiberg-Witten conjecture uniformly for any simple Lie algebra

g

\mathfrak {g}

. The main ingredients in the proof are: Garland’s result on the Lie algebra cohomology of

u

^

:=

g

⊗
t

C

[
t
]

\hat {\mathfrak {u}} := \mathfrak {g}\otimes t\mathbb {C}[t]

; Kostant’s result on the ‘diagonal’ cohomolgy of

u

^

\hat {\mathfrak {u}}

and its connection with abelian ideals in a Borel subalgebra of

g

\mathfrak {g}

; and a certain deformation of the singular cohomology of the infinite Grassmannian introduced by Belkale-Kumar.
William Parry. 3 July 1934 — 20 August 2006
Authors: Rees S. M.
Published: April 2008

Bill Parry was born in Coventry in 1934 and died in Coventry in 2006. In between these dates was a life that developed in an unpredictable fashion. Out of inauspicious beginnings, by dint of exceptional personal qualities as well as intellect, Bill forged links with the new and foreign field of ergodic theory, became a leading exponent, and was the prime mover in establishing the field in the UK.
Error estimates on bond-length and angle corrections from TLS analysis
Authors: Haestier James , Sadki Mustapha , Thompson Amber L. , Watkin David
Published: April 2008

Librational motion within a crystal structure distorts the measured bond distances and angles from their physical values. TLS analysis of a rigid molecule or a rigid part of a molecule allows the calculation of bond-length and angle corrections. Until now, no estimate of the error on these corrections has been available. A method is presented for propagating the errors on the anisotropic displacement parameters (ADPs) to the bond-length and angle corrections which are a function of the libration tensor. The numerical significance of approximations made during the calculation is discussed.
MATCHING FUNCTION FOR THE JAPANESE LABOUR MARKET: RANDOM OR STOCK–FLOW?
Authors: Sasaki Masaru
Published: April 2008

This paper estimates outflow equations for the unemployed and job vacancies under random and stock–flow matching using Japanese data. We find that for the outflow of the unemployed, the stock–flow matching model fits better than the random matching model at the quarterly frequency, but not at the monthly frequency. In contrast, the outflow of vacancies is affected by the stock of the unemployed as well as its inflow at both monthly and quarterly frequencies. In addition, we calculate the exit rates of the unemployed and job vacancies to show the relationship between the exit rates and the durations of unemployment and job vacancies.
Nesting habitat of Arapaima gigas (Schinz) in Amazonian floodplains
Authors: Castello L.
Published: April 2008

Most nests of Arapaima gigas in floodplains of the Amazon were built at the margins of the forests surrounding temporary or permanent lakes and their connecting channels. They were found under forested levees in locations that were shallow and sandy. From 2000 to 2005, the adult population increased six‐fold but nest density increased only two‐fold.
Expanding the foraging history of juvenile Pacific salmon: combining stomach‐content and macroparasite‐ community analyses for studying marine diets
Authors: Baldwin R. E. , Miller T. W. , Brodeur R. D. , Jacobson K. C.
Published: April 2008

Stomach contents and macroparasites were examined from the same fishes collected off Oregon and California in June and August of 2000 and 2002 to provide a more comprehensive description of the diet of juvenile Chinook salmon Oncorhynchus tshawytscha and coho salmon Oncorhynchus kisutch during their first few months at sea. Temporal and spatial similarities of the two data sets were assessed using multivariate analyses. Both stomach contents and macroparasite communities indicated that fishes, euphausiids and hyperiid amphipods were consumed by both salmonid species, although their relative contribution to each species diet was highly variable. In June, the greater abundances of parasite species in Chinook salmon compared to coho salmon suggested that Chinook salmon consumed more infected intermediate hosts (crustaceans or larval fishes) shortly after ocean entry (April and May). Although the macroparasite analysis lacked the specificity of stomach analysis in identifying prey, macroparasites can provide a longer term history of feeding and diet information for fishes with empty stomachs.
Reproductive biology of the smooth‐hound shark Mustelus mustelus (L.) in the Gulf of Gabès (south‐central Mediterranean Sea)
Authors: Saïdi B. , Bradaï M. N. , Bouaïn A.
Published: April 2008

The reproductive biology of the smooth‐hound shark Mustelus mustelus was studied in the Gulf of Gabès (southern Tunisia). Females were found to mature between 1075 and 1230 mm total length (LT) whereas males matured between 880 and 1120 mm LT. The LT at which 50% of the population reached maturity was 971 and 1172 mm for males and females, respectively. Male gonads were symmetrical in terms of mass and both functional, whereas in females only the right ovary was functional. The seasonal changes in the oocytes and testes development, embryo length and the occurrence of near‐term and post‐partum females showed that this species displayed a clearly defined annual reproductive cycle with parturition occurring during late April and early May, after a gestation period of 10–11 months. Mating took place during May and early June and fertilization occurred from early June to early July. The embryo sex ratio was not significantly different from unity. Litter size varied from four to 18 embryos and was positively correlated with maternal LT. The young were born with a LT of 340–420 mm.
Differential digestion and evacuation rates of prey in a warm‐temperate grouper, gagMycteroperca microlepis(Goode & Bean)
Authors: Berens E. J. , Murie D. J.
Published: April 2008

Prey‐specific gastric evacuation rates and digestion state indices were modelled for gagMycteroperca microlepis, a large warm‐temperate grouper, consuming meals of either baitfish (scaled sardineHarengula jaguana) or crab (purple swimmer crabPortunus gibbesii). Power exponential models best fit the wet and dry mass gastric evacuation data and the average digestion indices over post‐prandial time (PPT), regardless of prey type or gag size (AdjustedR2≥ 0·79). Gag mass (M) or total length (LT) incorporated into an expanded power exponential model, along with exponential scalars, resulted in highly predictive (R2≥ 0·87) gastric evacuation and average digestion state models. The expanded power exponential models fit to the baitfish and crab wet mass gastric evacuation data differed significantly (Kimura’s likelihood ratio test (LRT), bothP< 0·001). Gag consuming crab showed a digestive lag period of at least 4 h (wet mass) and took a longer time to complete digestion relative to gag consuming baitfish. Gag, as well as many other warm‐temperate and tropical groupers, consume a mixture of fish and crab prey and they will therefore require the development of a consumption model that incorporates mixed‐prey gastric evacuation models.
First record of the paedomorphic fish Schindleria (Gobioidei, Schindleriidae) from the Red Sea
Authors: Abu El‐Regal M. , Kon T.
Published: April 2008

A male specimen of the paedomorphic fish Schindleria sp. was collected by plankton net, in February 2005, from a reef lagoon from Hurghada on the Egyptian coast of the northern Red Sea. This is the first record of the Schindleriidae in the Red Sea.
Distribution of immunoreactive thyroxine in the endostyle and thyroid tissue of the sea lamprey Petromyzon marinus L., 1758
Authors: Raine J. C. , Leatherland J. F.
Published: April 2008

Anti‐thyroxine (T4) immunostaining in the endostyle and thyroid tissue during metamorphosis of sea lamprey Petromyzon marinus suggested that T4 synthesis occurs on the luminal surface of the apical membrane of selected cells of the endostyle, and that a ‘classical’ endocrine thyroid function was only evident in post‐transformed animals.
Measurement of jaw viscoelasticity in newborn and adult lesser spotted dogfish Scyliorhinus canicula (L., 1758)
Authors: Fahle S. R. , Thomason J. C.
Published: April 2008

Jaw viscoelasticity of newborn and adult lesser spotted dogfish Scyliorhinus canicula was measured using dynamic mechanical analysis. Jaws of newborn animals were significantly more viscoelastic than those of adults. As a result, newborn lesser spotted dogfish might be unable to consume hard prey items, unlike adults.
Applicability of ASTER imagery in mapping land use /cover as a basis for biodiversity studies in drylands of northern Ethiopia
Authors: Aynekulu Ermias , Kassawmar Tibebu , Tamene Luelseged
Published: April 2008

We evaluated the applicability of the Visible and Near Infrared bands (15 m spatial resolution) of the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) imagery in mapping land use/cover in the drylands of northern Ethiopia. Ground Control Points were collected from the field using Geographic Positioning System in which half of them were used for classification and the remaining for accuracy assessment. The image was classified into four dominant land use/cover types that represent the major habitats of the study site. Image classification was done using pixel‐based supervised classification with the Maximum Likelihood Classification algorithm. The accuracy of classification was evaluated using error matrix and Kappa statistics. Finally, we found an overall classification accuracy of 80% and this implies that ASTER imagery can be used as a good source of data in mapping biodiversity at habitat scale in data scarce drylands of northern Ethiopia.
Tree species composition and local use in agricultural landscapes of west Usambaras Tanzania
Authors: Munishi P. K. T. , Philipina F. , Temu R. P. C. , Pima N. E.
Published: April 2008

Species richness and diversity in agricultural landscapes are important characteristics of agro‐ecosystems that determine their potential for biodiversity conservation. This study assessed species composition, richness, diversity and local use of on‐farm trees in predominantly agricultural landscape in the Usambaras, north‐eastern Tanzania. Assessments were carried out in 90 randomly selected individual farmlands. We identified 47 tree species belonging to 23 families and used by local people for various purposes. The most dominant species were Albizia gummifera (Gmel) C. A. Sm. (mkenge), Parinari excelsa Sabine ssp holstii (Engl.) R. Grah. (muula), Newtonia buchananii (Bak.) Gilb. and Bout (mkufi), Syzygium guineense (Willd) D.C. (mshihwi), Ficus capensis L. (mvumo) and Casearia engleri (Gilg) (mkokoko). These species are indigenous and were retained from existing ones during farm clearing. The species diversity (by the Simpson’s and Shannon–Wiener diversity indices of 0.07 and 2.8 respectively) is comparable with that of adjacent natural forests. There are apparently high on‐farm tree species richness and diversity, the conservation of which can contribute to ex‐situ biodiversity conservation. On‐farm tree management should be encouraged, especially where there is population pressure on the existing natural forests. Research to enhance sustainability of the farming system is important for biodiversity management on farmlands.
Factors influencing the occurrence of entomopathogenic nematodes in the Central Rift Valley Region of Kenya
Authors: Mwaniki S. W. , Nderitu J. H. , Olubayo F. , Kimenju J. W. , Nguyen Khuong
Published: April 2008

A survey for entomopathogenic nematodes in the central Rift valley region of Kenya was conducted at altitudes between 1800 and 3000 m above sea level and from croplands and noncropland habitats. The sampling depth was 0–30 cm. GPS (global positioning system) was used to measure site positions. One hundred and twelve soil samples were collected and entomopathogenic nematodes trapped throughGalleria mellonella. Entomopathogenic nematode presence was demonstrated byG. mellonellamortality and viable ones bulked through the same host.Nematode recoveries from two consecutive extractions were 30% per extraction and 52% for cumulative extractions. Recoveries from agro ecological zones ranged between 18% and 71%. Recovery frequency was higher from disturbed cropland habitats than the stable noncrop habitats.Steinernemaspecies were more frequent thanHeterorhabditis (9 : 1). Nematode occurrence clustered at 2–3% carbon and pH 5.3–6.3 with no specific pattern demonstrated from soil types. Nematode species of the two genera from high altitudes lost their culturing ability within 1 month of isolation.There was a tendency for recovering both nematode genera at the shores of water bodies. This is the first report ofSteinernema yirgalemenseandS. weiseriin Kenya and ofS. kariiin the central Rift valley region. TheHeterorhabditisspecies has not been confirmed yet. This has widened the genetic base of entomopathogenic nematodes from Kenya. The entomopathogenic nematodes are available for developement as biological control agents of athropod pests.
Identifying suitable conservation targets: can GIS‐based modelling serve to link coarse‐scale complementarity to local selection of conservation sites?
Authors: Tushabe Herbert , Fjeldså Jon
Published: April 2008

Complementarity analysis based on overlaying large numbers of species distribution maps is increasingly being employed by conservationists to determine conservation priorities. This method is used because of its efficiency in representing selected species in a minimal number of areas, thus maximizing the number of conserved species in relation to area. As such analyses are mostly based on coarse spatial scales, it is essential to test the efficiency and accuracy of these methods, and to develop supplementary analyses that allow us to translate the result into identification of conservation sites of a manageable size. Here we test the effectiveness of a coarse‐scale (continent‐wide) analysis using a more detailed (nation‐wide) logical inductive model based on point records. We find that, although there are differences in the effectiveness at these scales, most of the areas identified by the fine‐scale data are nested within those identified by the coarse approach. We also find that areas identified as important for birds fit well within the current national focal areas for conservation in Uganda.
Determination of changes occurred in the microflora of cig kofte (raw meat balls) at different storage temperatures
Authors: Ardic Mustafa , Durmaz Hisamettin
Published: April 2008

The aim of this study was to investigate the effect of different storage temperatures on the microbiological characteristics and pH values of cig kofte during storage. Storage temperature affected significantly total aerobic mesophilic bacteria (TAMB), coliforms, yeasts and moulds, lactic acid bacteria (LAB) and Staphylococcus aureus counts of cig kofte which had lower counts in refrigerator storage than in room storage following sixth hour for TAMB (P < 0.001), coliform (P < 0.01, P < 0.001), S. aureus (P < 0.01, P < 0.001) and LAB (P < 0.001) and at the end of storage for yeasts and moulds (P < 0.001). Listeria and Salmonella spp. could not be detected at both refrigerator temperature and room temperature storage. In order to minimise the contamination level of cig kofte, use of best microbial quality minced meat and ingredients as well as good personnel hygiene is required and preserved. In addition, Cig kofte should be kept in refrigerator when leftovers remain for additional meals.
Antioxidant potential of rice bran extracts and its effects on stabilisation of cookies under ambient storage
Authors: Bhanger Muhammad Iqbal , Iqbal Shahid , Anwar Farooq , Imran Muhammad , Akhtar Mubeena , Zia‐ul‐Haq Muhammad
Published: April 2008

Methanolic extracts of rice bran (MRB) were found to be the richest in phenolics than all the other extraction media, i.e. water, 80% methanol, 70% ethanol, diethyl ether. Thermal stability of MRB was determined by evaluating antioxidant activity of heated extracts in linoleic acid system. Cookies were prepared in sunflower oil premixed with MRB at different concentrations, i.e. 500, 1000 and 2000 ppm, and with butylated hydroxytoluene and α‐tocopherol at 200 ppm. Oxidative stability of cookies was measured by storing under ambient conditions for an year with periodical analysis after every 2 months. Fatty acid composition was determined by gas–liquid chromatography. A regular decrease in unsaturated fatty acids (USFA) and increase in saturated fatty acids was observed with the increase in storage period; all the stabilised samples showed appreciably less decrease in USFA than that of control sample. Induction period ranged from 14.73 to 31.22 h while control exhibited 7.5 h. Peroxide value, iodine value and free fatty acids were chosen as the parameters for quality evaluation of cookies. Results suggest rice bran to be a potential source of antioxidants for stabilisation of cookies.
Influence of processing and storage on the antioxidant activity of apple derivatives
Authors: Sacchetti Giampiero , Cocci Emiliano , Pinnavaia GianGaetano , Mastrocola Dino , Rosa Marco Dalla
Published: April 2008

The antioxidant activity of seven apple varieties was determined on fresh fruits and processed products (dried fruits and purees) and during storage. The antioxidant activity of apples correlated with the total phenol concentration but not with ascorbic acid concentration. Apple derivatives showed a lower antioxidant activity than the counterparts of the fresh fruits and the occurrence of browning phenomena during processing resulted in lower antioxidant activity. Dried fruits showed higher antioxidant activity per gram of dried matter than fruit purees probably because of the lower total thermal effect of processing. The antioxidant activity of all products increased within the first month of storage, and then declined. The extent of early increase was related to the polyphenol content of the fruit. Packaging conditions further influenced the antioxidant activity increase during storage possibly by affecting the oxygen availability.
Nutritional quality of storage proteins during germination of Indian bean (Dolichos lablab. var. lignosus) seeds
Authors: Ramakrishna Vadde , Jhansi Rani Pochana , Ramakrishna Rao Pillatla
Published: April 2008

The dry Indian bean seed composed of starch is the major component (33%) and protein accounted for 25% of dry weight. The ability of germination to increase the nutritional quality of storage proteins was studied by germinating the Indian bean seeds for 0, 8, 16, 24 and 32 h and evaluated the nutritional quality through an in vitro protein digestibility (IVPD), protein efficiency ratio (PER), apparent and true digestibility. The IVPD of raw Indian bean seeds by pepsin alone was 60.12% and the digestibility by pepsin and trypsin together improved to 64.24%. The in vitro digestibility by both processes increased appreciably with germination and marked increase was noticed in the early stage of germination. The PER values followed the same pattern as the value of weight gain of rats fed with diets containing raw and germinated Indian bean. The lowest PER values were observed with raw bean diet. However, the value increased in rats fed with diets of Indian bean germinated for different intervals of time, reaching comparable PER values with the group maintained on casein diet. The true and apparent nitrogen digestibility of raw bean low being only 82 and 72%, respectively observed with casein diet. Diets with germinated bean protein showed a marked increase in both parameters, although the values were still less than that displayed by the casein fed rats. Germination is a simple biochemical enrichment tool and significantly improves palatability, digestibility and the nutritive utilisation of proteins in Indian bean seeds.
Regulation of mycothiol metabolism by σR and the thiol redox sensor anti‐sigma factor RsrA
Authors: Newton Gerald L. , Fahey Robert C.
Published: April 2008

Mycothiol (MSH) is the major thiol in Actinobacteria and plays a role analogous to that of glutathione. The biosynthetic pathway has been established in mycobacteria and is initiated by the glycosyltransferase MshA. A key mycothiol‐dependent detoxification pathway utilizes the amidase (Mca) to cleave mycothiol S‐conjugates to produce GlcN‐Ins and a mercapturic acid excreted from the cell. How expression of mycothiol genes is regulated in mycobacteria has been unclear so the report in this issue by Park and Roe showing that in Streptomyces coelicolor the redox controlled anti‐sigma factor RsrA that binds the regulator σR controls key elements of mycothiol metabolism is a major advance. Conditions that deplete thiols are shown to induce directly expression of sigR, rsrA, mshA and mca, as well as the thioredoxin reductase–thioredoxin system, generating an autoregulatory cycle that persists until the thiol‐depleting condition is alleviated. Evidence for indirect induction of mshB–D to support mycothiol biosynthesis is also presented. It was shown in vitro that mycothiol, like reduced thioredoxin and dithiothreitol, can reduce oxidized RsrA to activate its binding to σR. These studies establish for the first time how mycothiol metabolism is regulated to cope with stress from thiol reactive toxins.
Sweet to the extreme: protein glycosylation in Archaea
Authors: Yurist‐Doutsch Sophie , Chaban Bonnie , VanDyke David J. , Jarrell Ken F. , Eichler Jerry
Published: April 2008

Post‐translational modifications account for much of the biological diversity generated at the proteome level. Of these, glycosylation is the most prevalent. Long thought to be unique to Eukarya, it is now clear that both Bacteria and Archaea are also capable of N‐glycosylation, namely the covalent linkage of oligosaccharides to select target asparagine residues. However, while the eukaryal and bacterial N‐glycosylation pathways are relatively well defined, little is known of the parallel process in Archaea. Of late, however, major advances have been made in describing the process of archaeal N‐glycosylation. Such efforts have shown, as is often the case in archaeal biology, that protein N‐glycosylation in Archaea combines particular aspects of the eukaryal and bacterial pathways along with traits unique to this life form. For instance, while the oligosaccharides of archaeal glycoproteins include nucleotide‐activated sugars formed by bacterial pathways, the lipid carrier on which such oligosaccharides are assembled is the same as used in eukaryal N‐glycosylation. By contrast, transfer of assembled oligosaccharides to their protein targets shows Archaea‐specific properties. Finally, addressing N‐glycosylation from an archaeal perspective is providing new general insight into this event, as exemplified by the solution of the first crystal structure of an oligosaccharide transferase from an archaeal source.
Stochastic assembly of chemoreceptor clusters in Escherichia coli
Authors: Thiem Sebastian , Sourjik Victor
Published: April 2008

Chemoreceptors and cytoplasmic chemotaxis proteins in Escherichia coli form clusters that play a key role in signal processing. These clusters localize at cell poles and at specific positions along the cell body which correspond to future division sites, but the details of cluster formation and the mechanism of cluster distribution remain unclear. Here, we used fluorescence microscopy to investigate how the numbers and sizes of receptor clusters depend on the expression level of chemotaxis proteins and on the cell length. We show that the average cluster number saturates at high levels of protein expression at approximately 3.7 clusters per cell, well below the number of available positioning sites. Correspondingly, distances between clusters in filamentous cells saturate at an average of 1 μm but, even at saturating expression levels, individual cluster numbers and distances show a broad distribution around the mean. Our data imply a stochastic mode of cluster assembly, where a defined average interval between clusters along the cell body arises from competition between nucleation of new clusters and growth of existing clusters. Upon subsequent anchorage to defined lateral sites, clusters grow with rates that inversely depend on their size, and become polar upon several rounds of cell division.
The β‐1,3‐glucanosyltransferase gas4p is essential for ascospore wall maturation and spore viability in Schizosaccharomyces pombe
Authors: De Medina‐Redondo María , Arnáiz‐Pita Yolanda , Fontaine Thierry , Del Rey Francisco , Latgé Jean Paul , De Aldana Carlos R. Vázquez
Published: April 2008

Meiosis is the developmental programme by which sexually reproducing diploid organisms generate haploid gametes. In yeast, meiosis is followed by spore morphogenesis. The formation of the Schizosaccharomyces pombe ascospore wall requires the co‐ordinated activity of enzymes involved in the biosynthesis and modification of its components, such as glucans. During sporogenesis, the β‐1,3‐glucan synthase bgs2p synthesizes linear β‐1,3‐glucans, which remain unorganized and alkali‐soluble until covalent linkages are set up between β‐1,3‐glucans and other cell wall components. Several proteins belonging to the glycoside hydrolase family 72 (GH72) with β‐1,3‐glucanosyltransferase activity have been described in other organisms, such as the Saccharomyces cerevisiae Gas1p or the Aspergillus fumigatus Gel1p. Here we describe the characterization of gas4+, a new gene that encodes a protein of the GH72 family. Deletion of this gene does not lead to any apparent defect during vegetative growth, but homozygous gas4Δ diploids show a sporulation defect. Although meiosis occurs normally, ascospores are unable to mature or to germinate. The expression of gas4+ is strongly induced during sporulation and a yellow fluorescent protein (YFP)–gas4p fusion protein localizes to the ascospore periphery during sporulation. We conclude that gas4p is required for ascospore maturation in S. pombe.
kinC/D‐mediated heterogeneous expression of spo0A during logarithmical growth in Bacillus subtilis is responsible for partial suppression of φ29 development
Authors: Castilla‐Llorente Virginia , Salas Margarita , Meijer Wilfried J. J.
Published: April 2008

The host of the lytic bacteriophage φ29 is the spore‐forming bacterium Bacillus subtilis. When infection occurs during early stages of sporulation, however, φ29 development is suppressed and the infecting phage genome becomes trapped into the developing spore. Recently, we have shown that Spo0A, the key transcriptional regulator for entry into sporulation, is directly responsible for suppression of the lytic φ29 cycle in cells having initiated sporulation. Surprisingly, we found that φ29 development is suppressed in a subpopulation of logarithmically growing culture and that spo0A is heterogeneously expressed during this growth stage. Furthermore, we showed that kinC and, to a minor extent, kinD, are responsible for heterogeneous expression levels of spo0A during logarithmical growth that are below the threshold to activate sporulation, but sufficient for suppression of the lytic cycle of φ29. Whereas spo0A was known to be heterogeneously expressed during the early stages of sporulation, our findings show that this also occurs during logarithmical growth. These insights are likely to have important consequences, not only for the life cycle of φ29, but also for B. subtilis developmental processes.
The receiver domain of FrzE, a CheA–CheY fusion protein, regulates the CheA histidine kinase activity and downstream signalling to the A‐ and S‐motility systems of Myxococcus xanthus
Authors: Inclán Yuki F. , Laurent Sophie , Zusman David R.
Published: April 2008

The Frz chemosensory system is a two‐component signal transduction pathway that controls cell reversals and directional movements for the two motility systems in Myxococcus xanthus. To trigger cell reversals, FrzE, a hybrid CheA–CheY fusion protein, autophosphorylates the kinase domain at His‐49, and phosphoryl groups are transferred to aspartate residues (Asp‐52 and Asp‐220) in the two receiver domains of FrzZ, a dual CheY‐like protein that serves as the pathway output. The role of the receiver domain of FrzE was unknown. In this paper, we characterize the FrzE protein in vitro and show that the receiver domain of FrzE negatively regulates the autophosphorylation activity of the kinase domain of FrzE. Unexpectedly, it does not appear to play a direct role in phospho‐relay as in most other histidine kinase receiver domain hybrid systems. The regulatory role of the FrzE receiver domain suggests that it may interact with or be phosphorylated by an unknown protein. We also show the dynamics of motility system‐specific marker proteins in FrzE mutants as cells move forward and reverse. Our studies indicate that the two motility systems are functionally co‐ordinated and that any system‐specific branching of the pathway most likely occurs downstream of FrzE.