bluuebunny/crossref_metadata_2025 huggingface dataset:
Induced charge electro-osmotic concentration gradient generator
Authors: Jain Mranal , Yeung Anthony , Nandakumar K.
Published: March 2010

Biomolecule gradients play an important role in the understanding of various biological processes. Typically, biological cells are exposed to linear and nonlinear concentration gradients and their response is studied for understanding cell growth, cell migration, and cell differentiation mechanisms. Recent studies have demonstrated the use of microfluidic devices for precise and stable concentration gradient generation. However, most of the reported devices are geometrically complex and lack dynamic controllability. In this work, a novel microfluidic gradient generator is presented which utilizes the induced charge electro-osmosis (ICEO) by introducing conducting obstacle in the microchannel. With the ICEO flow component, significant transverse convection can be generated within the microchannel, which can, in turn, be used to create nonlinear as well as asymmetric gradients. The characteristics of the developed concentration gradient are dependent on the interplay between fixed charge electro-osmotic and ICEO flows. It is shown that the proposed device can switch between linear and nonlinear gradients by just altering the applied electric field. Finally, the formation of user-defined concentration profiles (linear, convex, and concave) is demonstrated by varying the conducting obstacle size.
Analyses of the intermediate energy levels in ZnTe:O alloys
Authors: Tablero C. , Martí A. , Luque A.
Published: March 2010

The isoelectronic doping of ZnTe with oxygen leads to deep levels on which carriers recombine radiatively via intermediate band states. The electronic density and the impurity-host character of these deep levels are analyzed using first principles, for the wurtzite and zinc-blende structures, different oxygen concentration, and different exchange-correlation approach.
Spotlight on ionic liquids
Authors: Castner Edward W. , Wishart James F.
Published: March 2010

Ionic liquids are an emerging class of materials with a diverse and extraordinary set of properties. Understanding the origins of these properties and how they can be controlled by design to serve valuable practical applications presents a wide array of challenges and opportunities to the chemical physics and physical chemistry community. We highlight here some of the significant progress already made and future research directions in this exciting area.
Camel usage and impacts at a permanent spring in central Australia: a case study
Authors: Brim-Box Jayne , Guest Tracey , Barker Peter , Jambrecina Mirjana , Moran Sean , Kulitja Rene
Published: March 2010

The impact of camel usage at a small rockhole (‘X’) on the Petermann Aboriginal Land Trust was evaluated from May 2007 through to July 2008. Camel usage and impacts were determined through multiple methods including ground cover, vegetation and macroinvertebrate surveys and through the use of surveillance cameras and depth loggers. Camels appear to use X most heavily in periods when rainfall is scant and more at night than during the day. However, in long periods with little or no rainfall, it appears that camels use X heavily during the day and night and there is little chance for X to re-fill. The low number of macroinvertebrates present during the study period suggests that the aquatic fauna is negatively impacted by the presence of camels, as was the vegetation surrounding X. Shrubs near X showed signs of heavy browsing and the ground cover became denuded of vegetation due to camel browsing and trampling during dry periods. This could lead to long-term alterations in drainage patterns and erosion of the site. Follow-up vegetation and ground cover surveys are needed to better assess these impacts. X was and is a traditional source of drinking water for people travelling through the country. Preliminary microbial analysis indicated that at certain periods X is not suitable for drinking, even if the water itself looks ‘clean’ or clear. The faecal contamination evident was most probably due to camel use of the waterhole. These results have been discussed with traditional owners, but further microbial analyses may be needed for longer-term assessments.
Who owns feral camels? Implications for managers of land and resources in central Australia
Authors: Garnett Stephen T. , Williams Greg , Ainsworth Gillian B. , O'Donnell Michael
Published: March 2010

This paper reviews the legislation relating to ownership of feral camels in Australia. We find that, as a general proposition, a feral camel is owned by neither the landowner nor the Government (the Crown), unless State or Territory legislation provides otherwise. This occurs in two limited situations and only for New South Wales and South Australia. Relevant State and Territory legislation can prescribe that feral camels cannot be taken or used without a relevant licence or permit, but only Western Australia and Queensland appear to do this. Lack of legislative certainty about ownership of camels has resulted in a clear market failure whereby there is also little or no private incentive to exercise control. This should be corrected by identifying explicitly that ownership is vested in the Crown. Legal analogues exist with respect to disease control and water management that could form the basis of an appropriate legislative framework.
Changes in Aboriginal perceptions of feral camels and of their impacts and management
Authors: Vaarzon-Morel P.
Published: March 2010

This paper reports on a survey of Aboriginal perceptions of feral camels undertaken with Aboriginal people from 27 Aboriginal communities within the current feral camel range in central Australia. Research methods were qualitative, involving face-to-face semi-structured interviews. Views were sought on feral camel presence and impacts and people’s attitudes towards feral camel management. In just over two-thirds of the communities surveyed, interviewees reported seeing camels. Many interviewees in high camel density areas claimed that camels damage natural and cultural resources (such as water places and bush tucker) and affect their customary use of country. Roughly a third of interviewees also claimed that feral camels deprive native species of water. Damage to infrastructure and homelands was also reported, and concern was expressed over the danger that camels posed both on and off the roads. At the same time, camels are said to have positive benefits and most interviewees view them as a potential resource. Yet despite a widely held view among interviewees that camels need to be controlled, the majority were only prepared to consider limited management options. What is significant, however, is that Aboriginal views on feral camels today are not homogenous: there is a diversity of perspectives emerging in response to transformations being brought about by feral camels on Aboriginal land. The findings are discussed in the context of earlier studies on Aboriginal perceptions of feral animals in central Australia, which concluded that feral animals were thought not to be a significant land management problem but to ‘belong to country’. The implications of changing Aboriginal perceptions of feral camels are discussed for the development of a collaborative feral camel management strategy.
A GIS-based decision-making structure for managing the impacts of feral camels in Australia
Authors: Lamb David S. , Saalfeld William K. , McGregor Murray J. , Edwards Glenn P. , Zeng Benxaing , Vaarzon-Morel Petronella
Published: March 2010

Feral camels have severe negative impacts on key environmental economic and social/cultural assets across a wide area in Australia and their population is increasing. In this paper we utilised Multicriteria Evaluation (MCE) within a Geographic Information System (GIS) to create a decision tool for their management. Six management methods which are currently used for managing feral camels and their impacts: aerial culling, ground culling, exclusion fencing, and commercial extraction for live export, pet meat, or human consumption, were considered in the development of the tool. The decision tool used GIS-based MCE to determine the suitability of each of the management methods across the range of feral camels in Australia.
A range of method-dependent criteria and factors served as inputs to the GIS-based MCE, which produced a suitability map or surface for each of the management methods. The broad-scale nature, Australia wide, of the work resulted in the suitability maps generated being of limited value in identifying fine-scale priority locations for management. The suitability maps did serve to identify broad-scale, cross-jurisdictional management zones where one or more of the management methods may be applicable. Geographic Information System-based MCE was concluded to have the potential to identify the appropriate areas for the application of specific feral camel management methods. Four management zones were then defined within the area of Australia in which feral camels are present.
Broad specificity AhpC-like peroxiredoxin and its thioredoxin reductant in the sparse antioxidant defense system of
Treponema pallidum
Authors: Parsonage Derek , Desrosiers Daniel C. , Hazlett Karsten R. O. , Sun Yongcheng , Nelson Kimberly J. , Cox David L. , Radolf Justin D. , Poole Leslie B.
Published: March 2010

Little is known about the mechanisms by which
Treponema pallidum
(
Tp
), the causative agent of syphilis, copes with oxidative stress as it establishes persistent infection within its obligate human host. The
Tp
genomic sequence indicates that the bacterium’s antioxidant defenses do not include glutathione and are limited to just a few proteins, with only one, TP0509, offering direct defense against peroxides. Although this
Tp
peroxiredoxin (Prx) closely resembles AhpC-like Prxs,
Tp
lacks AhpF, the typical reductant for such enzymes. Functionally,
Tp
AhpC resembles largely eukaryotic, nonAhpC typical 2-Cys Prx proteins in using thioredoxin (Trx, TP0919) as an efficient electron donor and exhibiting broad specificity toward hydroperoxide substrates. Unlike many of the eukaryotic Prxs, however,
Tp
AhpC is relatively resistant to inactivation during turnover with hydroperoxide substrates. As is often observed in typical 2-Cys Prxs,
Tp
AhpC undergoes redox-sensitive oligomer formation. Quantitative immunoblotting revealed that
Tp
Trx and
Tp
AhpC are present at very high levels (over 100 and 300 μM, respectively) in treponemes infecting rabbit testes; their redox potentials, at -242 ± 1 and -192 ± 2 mV, respectively, are consistent with the role of
Tp
Trx as the cellular reductant of
Tp
AhpC. Transcriptional analysis of select antioxidant genes confirmed the presence of high mRNA levels for
ahpC
and
trx
which diminish greatly when spirochetes replicate under in vitro growth conditions. Thus,
T. pallidum
has evolved an extraordinarily robust, broad-spectrum AhpC as its sole mechanism for peroxide defense to combat this significant threat to treponemal growth and survival during infection.
Coherent and incoherent inference in phylogeography and human evolution
Authors: Templeton Alan R.
Published: March 2010

A hypothesis is nested within a more general hypothesis when it is a special case of the more general hypothesis. Composite hypotheses consist of more than one component, and in many cases different composite hypotheses can share some but not all of these components and hence are overlapping. In statistics, coherent measures of fit of nested and overlapping composite hypotheses are technically those measures that are consistent with the constraints of formal logic. For example, the probability of the nested special case must be less than or equal to the probability of the general model within which the special case is nested. Any statistic that assigns greater probability to the special case is said to be incoherent. An example of incoherence is shown in human evolution, for which the approximate Bayesian computation (ABC) method assigned a probability to a model of human evolution that was a thousand-fold larger than a more general model within which the first model was fully nested. Possible causes of this incoherence are identified, and corrections and restrictions are suggested to make ABC and similar methods coherent. Another coalescent-based method, nested clade phylogeographic analysis, is coherent and also allows the testing of individual components of composite hypotheses, another attribute lacking in ABC and other coalescent-simulation approaches. Incoherence is a highly undesirable property because it means that the inference is mathematically incorrect and formally illogical, and the published incoherent inferences on human evolution that favor the out-of-Africa replacement hypothesis have no statistical or logical validity.
Patterns of aging in the long-lived wandering albatross
Authors: Lecomte Vincent Julien , Sorci Gabriele , Cornet Stéphane , Jaeger Audrey , Faivre Bruno , Arnoux Emilie , Gaillard Maria , Trouvé Colette , Besson Dominique , Chastel Olivier , Weimerskirch Henri
Published: March 2010

How does an animal age in natural conditions? Given the multifaceted nature of senescence, identifying the effects of age on physiology and behavior remains challenging. We investigated the effects of age on a broad array of phenotypic traits in a wild, long-lived animal, the wandering albatross. We studied foraging behavior using satellite tracking and activity loggers in males and females (age 6–48+ years), and monitored reproductive performance and nine markers of baseline physiology known to reflect senescence in vertebrates (humoral immunity, oxidative stress, antioxidant defenses, and hormone levels). Age strongly affected foraging behavior and reproductive performance, but not baseline physiology. Consistent with results of mammal and human studies, age affected males and females differently. Overall, our findings demonstrate that age, sex, and foraging ability interact in shaping aging patterns in natural conditions. Specifically, we found an unexpected pattern of spatial segregation by age; old males foraged in remote Antarctica waters, whereas young and middle-aged males never foraged south of the Polar Front. Old males traveled a greater distance but were less active at the sea surface, and returned from sea with elevated levels of stress hormone (corticosterone), mirroring a low foraging efficiency. In contrast to findings in captive animals and short-lived birds, and consistent with disposable soma theory, we found no detectable age-related deterioration of baseline physiology in albatrosses. We propose that foraging efficiency (i.e., the ability of individuals to extract energy from their environment) might play a central role in shaping aging patterns in natural conditions.
Intra- and intercellular fluctuations in Min-protein dynamics decrease with cell length
Authors: Fischer-Friedrich Elisabeth , Meacci Giovanni , Lutkenhaus Joe , Chaté Hugues , Kruse Karsten
Published: March 2010

Self-organization of proteins in space and time is of crucial importance for the functioning of cellular processes. Often, this organization takes place in the presence of strong random fluctuations due to the small number of molecules involved. We report on stochastic switching of the Min-protein distributions between the two cell halves in short
Escherichia coli
cells. A computational model provides strong evidence that the macroscopic switching is rooted in microscopic noise on the molecular scale. In longer bacteria, the switching turns into regular oscillations that are required for positioning of the division plane. As the pattern becomes more regular, cell-to-cell variability also lessens, indicating cell length-dependent regulation of Min-protein activity.
Multiple aquatic invasions by an endemic, terrestrial Hawaiian moth radiation
Authors: Rubinoff Daniel , Schmitz Patrick
Published: March 2010

Insects are the most diverse form of life on the planet, dominating both terrestrial and freshwater ecosystems, yet no species has a life stage able to breath, feed, and develop either continually submerged or without access to water. Such truly amphibious insects are unrecorded. In mountain streams across the Hawaiian Islands, some caterpillars in the endemic moth genus
Hyposmocoma
are truly amphibious. These larvae can breathe and feed indefinitely both above and below the water's surface and can mature completely submerged or dry. Remarkably, a molecular phylogeny based on 2,243 bp from both nuclear (elongation factor 1α and carbomoylphosphate synthase) and mitochondrial (cytochrome oxidase I) genes representing 216 individuals and 89 species of
Hyposmocoma
reveals that this amphibious lifestyle is an example of parallel evolution and has arisen from strictly terrestrial clades at least three separate times in the genus starting more than 6 million years ago, before the current high islands existed. No other terrestrial genus of animals has sponsored so many independent aquatic invasions, and no other insects are able to remain active indefinitely above and below water. Why and how
Hyposmocoma
, an overwhelmingly terrestrial group, repeatedly evolved unprecedented aquatic species is unclear, although there are many other evolutionary anomalies across the Hawaiian archipelago. The uniqueness of the community assemblages of Hawaii's isolated biota is likely critical in generating such evolutionary novelty because this amphibious ecology is unknown anywhere else.
Two competing orientation patterns explain experimentally observed anomalies in growing actin networks
Authors: Weichsel Julian , Schwarz Ulrich S.
Published: March 2010

The lamellipodium of migrating animal cells protrudes by directed polymerization of a branched actin network. The underlying mechanisms of filament growth, branching, and capping can be studied in in vitro assays. However, conflicting results have been reported for the force–velocity relation of such actin networks, namely both convex and concave shapes as well as history dependencies. Here we model branching as a reaction that is independent of the number of existing filaments, in contrast to capping, which is assumed to be proportional to the number of existing filaments. Using both stochastic network simulations and deterministic rate equations, we show that such a description naturally leads to the stability of two qualitatively different stationary states of the system, namely a ± 35° and a +70/0/-70° orientation pattern. Changes in network growth velocity induce a transition between these two patterns. For sufficiently different protrusion efficiency of the two network architectures, this leads to hysteresis in the growth velocity of actin networks under force. Dependent on the history of the system, convex and concave regimes are obtained for the force–velocity relation. Thus a simple generic model can explain the experimentally observed anomalies, with far reaching consequences for cell migration.
Genetic variation of melatonin productivity in laboratory mice under domestication
Authors: Kasahara Takaoki , Abe Kuniya , Mekada Kazuyuki , Yoshiki Atsushi , Kato Tadafumi
Published: March 2010

Melatonin is a pineal hormone produced at night; however, many strains of laboratory mice are deficient in melatonin. Strangely enough, the gene encoding HIOMT enzyme (also known as ASMT) that catalyzes the last step of melatonin synthesis is still unidentified in the house mouse (
Mus musculus
) despite the completion of the genome sequence. Here we report the identification of the mouse
Hiomt
gene, which was mapped to the pseudoautosomal region (PAR) of sex chromosomes. The gene was highly polymorphic, and nonsynonymous SNPs were found in melatonin-deficient strains. In C57BL/6 strain, there are two mutations, both of which markedly reduce protein expression. Mutability of the
Hiomt
likely due to a high recombination rate in the PAR could be the genomic basis for the high prevalence of melatonin deficiency. To understand the physiologic basis, we examined a wild-derived strain, MSM/Ms, which produced melatonin more under a short-day condition than a long-day condition, accompanied by increased
Hiomt
expression. We generated F2 intercrosses between MSM/Ms and C57BL/6 strains and N2 backcrosses to investigate the role of melatonin productivity on the physiology of mice. Although there was no apparent effect of melatonin productivity on the circadian behaviors, testis development was significantly promoted in melatonin-deficient mice. Exogenous melatonin also had the antigonadal action in mice of a melatonin-deficient strain. These findings suggest a favorable impact of melatonin deficiency due to
Hiomt
mutations on domestic mice in breeding colonies.
MIPs are ancestral ligands for the sex peptide receptor
Authors: Kim Young-Joon , Bartalska Katarina , Audsley Neil , Yamanaka Naoki , Yapici Nilay , Lee Ju-Youn , Kim Yong-Chul , Markovic Milica , Isaac Elwyn , Tanaka Yoshiaki , Dickson Barry J.
Published: March 2010

Upon mating, females of many animal species undergo dramatic changes in their behavior. In
Drosophila melanogaster
, postmating behaviors are triggered by sex peptide (SP), which is produced in the male seminal fluid and transferred to female during copulation. SP modulates female behaviors via sex peptide receptor (SPR) located in a small subset of internal sensory neurons that innervate the female uterus and project to the CNS. Although required for postmating responses only in these female sensory neurons, SPR is expressed broadly in the CNS of both sexes. Moreover, SPR is also encoded in the genomes of insects that lack obvious SP orthologs. These observations suggest that SPR may have additional ligands and functions. Here, we identify myoinhibitory peptides (MIPs) as a second family of SPR ligands that is conserved across a wide range of invertebrate species. MIPs are potent agonists for
Drosophila
,
Aedes
, and
Aplysia
SPRs in vitro, yet are unable to trigger postmating responses in vivo. In contrast to SP, MIPs are not produced in male reproductive organs, and are not required for postmating behaviors in
Drosophila
females. We conclude that MIPs are evolutionarily conserved ligands for SPR, which are likely to mediate functions other than the regulation of female reproductive behaviors.
Specific estrogen sulfotransferase (SULT1E1) substrates and molecular imaging probe candidates
Authors: Cole Graham B. , Keum Gyochang , Liu Jie , Small Gary W. , Satyamurthy Nagichettiar , Kepe Vladimir , Barrio Jorge R.
Published: March 2010

This work focuses on the development of specific substrates for estrogen sulfotransferase (SULT1E1) to produce molecular imaging probes for this enzyme. SULT1E1 is a key enzyme in estrogen homeostasis, playing a central role in the prevention and development of human disease. In vitro sulfation assays showed alkyl and aryl substitutions to a fused heterocyclic system modeled after β-naphthol (βN), based on compounds that interact with the estrogen receptor, rendered several molecules with enhanced specificity for SULT1E1 over SULT1A1*1, SULT1A1*2, SULT1A3, and SULT2A1. Several 6-hydroxy-2-arylbenzothiazoles tested demonstrated excellent affinity—
V
max
/
K

m

ratios—and specificity for SULT1E1.
K

m

values ranged from 0.12–2.36 μM. A strong correlation was observed between polarity of the 4′-sustituent on the 2-aryl moiety (Hammett
σ

p

) and the log(
V
max
/
K

m

) (
r
 = 0.964). Substrate sensitivity is influenced by the acidity of the 6-phenolic group demonstrated by correlating its
1
H NMR chemical shift (
δ
OH
) with the log(
V
max
/
K

m

) (
r
 = 0.963). Acidity is mediated by the electron withdrawing capacity of the 4′-substituent outlined by the correlation of the C-2
13
C NMR chemical shift (
δ
C2
) with the log(
V
max
/
K

m

) (
r
 = 0.987). 2-[4-(Methylamino)phenyl]-6-hydroxybenzothiazole (
2b
) was radiolabeled with carbon-11 (
11
C-(
2b
)) and used in vivo for microPET scanning and tissue metabolite identification. High PET signal was paralleled with the presence of radiolabeled
11
C-(
2b
)-6-O-sulfate and the SULT1E1 protein detected by western blot. Because this and other members of this family presenting specificity for SULT1E1 can be labeled with carbon-11 or fluorine-18, in vivo assays of SULT1E1 functional activity are now feasible in humans.
Lethal protein produced in response to competition between sibling bacterial colonies
Authors: Be’er Avraham , Ariel Gil , Kalisman Oren , Helman Yael , Sirota-Madi Alexandra , Zhang H.P. , Florin E.-L. , Payne Shelley M. , Ben-Jacob Eshel , Swinney Harry L.
Published: March 2010

Sibling
Paenibacillus dendritiformis
bacterial colonies grown on low-nutrient agar medium mutually inhibit growth through secretion of a lethal factor. Analysis of secretions reveals the presence of subtilisin (a protease) and a 12 kDa protein, termed sibling lethal factor (Slf). Purified subtilisin promotes the growth and expansion of
P. dendritiformis
colonies, whereas Slf is lethal and lyses
P. dendritiformis
cells in culture. Slf is encoded by a gene belonging to a large family of bacterial genes of unknown function, and the gene is predicted to encode a protein of approximately 20 kDa, termed
dendritiformis
sibling bacteriocin. The 20 kDa recombinant protein was produced and found to be inactive, but exposure to subtilisin resulted in cleavage to the active, 12 kDa form. The experimental results, combined with mathematical modeling, show that subtilisin serves to regulate growth of the colony. Below a threshold concentration, subtilisin promotes colony growth and expansion. However, once it exceeds a threshold, as occurs at the interface between competing colonies, Slf is then secreted into the medium to rapidly reduce cell density by lysis of the bacterial cells. The presence of genes encoding homologs of
dendritiformis
sibling bacteriocin in other bacterial species suggests that this mechanism for self-regulation of colony growth might not be limited to
P. dendritiformis
.
p
-adic coupling of mock modular forms and shadows
Authors: Guerzhoy Pavel , Kent Zachary A. , Ono Ken
Published: March 2010

A “mock modular form” is the holomorphic part of a harmonic Maass form
f
. The nonholomorphic part of
f
is a period integral of its “shadow,” a cusp form
g
. A direct method for relating the coefficients of shadows and mock modular forms is not known. We solve these problems when the shadow is an integer weight newform. Our solution is
p
-adic, and it relies on our definition of an algebraic “regularized mock modular form.” As an application, we consider the modular solution to the cubic “arithmetic-geometric mean.”
Cultural differences are not always reducible to individual differences
Authors: Na Jinkyung , Grossmann Igor , Varnum Michael E. W. , Kitayama Shinobu , Gonzalez Richard , Nisbett Richard E.
Published: March 2010

We show that differences in social orientation and in cognition that exist between cultures and social classes do not necessarily have counterparts in individual differences within those groups. Evidence comes from a large-scale study conducted with 10 measures of
independent
vs.
interdependent
social orientation and 10 measures of
analytic
vs.
holistic
cognitive style. The social measures successfully distinguish between interdependence (viewing oneself as embedded in relations with others) and independence (viewing oneself as disconnected from others) at the group level. However, the correlations among the measures were negligible. Similar results were obtained for the cognitive measures, for which there are no coherent individual differences despite the validity of the construct at the group level. We conclude that behavioral constructs that distinguish among groups need not be valid as measures of individual differences.
Coordination of Rab8 and Rab11 in primary ciliogenesis
Authors: Knödler Andreas , Feng Shanshan , Zhang Jian , Zhang Xiaoyu , Das Amlan , Peränen Johan , Guo Wei
Published: March 2010

Primary cilia are microtubule-based membrane projections located at the surface of many cells. Defects in primary cilia formation have been implicated in a number of genetic disorders, such as Bardet-Biedl Syndrome and Polycystic Kidney Disease. Recent studies have demonstrated that polarized vesicular transport involving Rab8 and its guanine nucleotide-exchange factor Rabin8 is essential for primary ciliogenesis. Here we report that Rabin8 is a direct downstream effector of Rab11, which functions in membrane trafficking from the trans-Golgi network and recycling endosomes. Rab11, in its GTP-bound form, interacts with Rabin8 and kinetically stimulates the guanine nucleotide-exchange activity of Rabin8 toward Rab8. Rab11 is enriched at the base of the primary cilia and inhibition of Rab11 function by a dominant-negative mutant or RNA interference blocks primary ciliogenesis. Our results suggest that Rab GTPases coordinate with each other in the regulation of vesicular trafficking during primary ciliogenesis.
Influence of annealing conditions on the mechanical and microstructural behavior of electroplated Cu-TSV
Authors: Okoro Chukwudi , Vanstreels Kris , Labie Riet , Lühn Ole , Vandevelde Bart , Verlinden Bert , Vandepitte Dirk
Published: March 2010

In this paper, the effect of annealing condition on the microstructural and mechanical behavior of copper through-silicon via (Cu-TSV) is studied. The hardness of Cu-TSV scaled with the Hall–Petch relation, with the average hardness values of 1.9 GPa, 2.2 GPa and 2.3–2.8 GPa, respectively for the annealed, room temperature (RT) aged and the as-deposited samples. The increase in hardness toward the top of the as-deposited sample is related to the decrease in grain size. The annealed and the as-deposited samples showed a constant elastic modulus (E-modulus) value across the length of Cu-TSV of 140 GPa and 125 GPa respectively, while the RT aged sample showed a degradation in E-modulus from the bottom of the TSV (140 GPa) to the top (110 GPa). These differences in E-modulus values and trends under the different test conditions were found to be unrelated with the crystallographic texture of the samples, but could be related to the presence of residual stresses. No correlation is found between the hardness and E-modulus data. This is attributed to the coupling and competitive effects of grain size and residual stresses, with the grain size effect having a dominant influence on hardness, while the presence of residual stresses dominated the E-modulus result.
Vibrio communis sp. nov., isolated from the marine animals Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis and Litopenaeus vannamei
Authors: Chimetto Luciane A. , Cleenwerck Ilse , Alves Nelson , Silva Bruno Sergio , Brocchi Marcelo , Willems Anne , De Vos Paul , Thompson Fabiano L.
Published: March 2010

EightVibrioisolates originating from the marine coralsMussismilia hispidaandPhyllogorgia dilatataand the zoanthidsPalythoa caribaeorumandPalythoa variabilisin Brazil and the Pacific white shrimp (Litopenaeus vannamei) in Ecuador were studied by means of a polyphasic approach. The novel isolates formed a tight monophyletic group in the genusVibrioand were closely related to species of theVibrio harveyigroup, to which they showed more than 99 % 16S rRNA gene sequence similarity. Analysis based on concatenated sequences of the following seven genes, 16S rRNA,gyrB,recA,rpoA,topA,pyrHandmreB(5633 bp in length), showed clear separation between the isolates and species of theV. harveyigroup. Amplified fragment length polymorphism (AFLP) analysis, performed previously, revealed that a representative isolate of this group, LMG 20370, was clearly separate from knownVibriospecies (it belonged to the so-called AFLP cluster A31). DNA–DNA hybridization (DDH) experiments with representative isolates and type strains of theV. harveyispecies group revealed high DDH between the novel isolates (more than 74 %) and less than 70 % DDH towards type strains of relatedVibriospecies, proving the novel species status of the isolates. Phenotypically, the novel species belongs to the arginine dihydrolase (A)-negative, lysine decarboxylase (L)-positive and ornithine decarboxylase (O)-positive (A−/L+/O+) cluster reported previously. Most species of theV. harveyigroup (i.e.Vibrio rotiferianus,V. harveyi,V. parahaemolyticusandV. alginolyticus) also belong to this A−/L+/O+ cluster. However, several phenotypic features can be used for the identification of the novel species. In contrast to its closest phylogenetic neighbours, the novel species exhibits esterase (C4) andN-acetyl-β-glucosaminidase activities, but it does not produce acetoin, does not use citrate,α-ketoglutaric acid or propionic acid and does not ferment melibiose. The novel species can also be differentiated on the basis of the presence of the fatty acids C17 : 0,C17 : 1ω8c, iso-C17 : 0and iso-C13 : 0and the absence of the fatty acid C18 : 0. The nameVibrio communissp. nov. is proposed for this taxon. Strain R-40496T(=LMG 25430T=CAIM 1816T) is the type strain.
Reclassification of ‘Dactylosporangium variesporum’ as Saccharothrix variisporea corrig. (ex Tomita et al. 1977) sp. nov., nom. rev.
Authors: Kim Byung-Yong , Brown Roselyn , Labeda David P. , Goodfellow Michael
Published: March 2010

In the course of a polyphasic study it was observed that ‘Dactylosporangium variesporum’ NRRL B-16296 is misclassified in the genus Dactylosporangium as it exhibits properties consistent with its assignment to the genus Saccharothrix. Phylogenetic analyses based on 16S rRNA gene sequences show that the strain falls within the evolutionary radiation of the genus Saccharothrix, a result which is supported by corresponding chemotaxonomic and morphological markers. The strain is phylogenetically most closely, albeit loosely, related to Saccharothrix espanaensis, but can be readily distinguished from this and other species of the genus Saccharothrix with validly described names by using a range of phenotypic properties. The combined genotypic and phenotypic data demonstrate conclusively that this strain should be classified as a new species in the genus Saccharothrix for which the name Saccharothrix variisporea sp. nov. is proposed. The type strain is NRRL B-16296T (=ATCC 31203T =DSM 43911T =JCM 3273T =NBRC 14104T).
Dyella thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soil of sunflower (Helianthus annuus L.)
Authors: Anandham Rangasamy , Kwon Soon-Wo , Indira Gandhi Pandiyan , Kim Soo-Jin , Weon Hang-Yeon , Kim Yi-Seul , Sa Tong-Min , Kim Yong-Ki , Jee Hyeong-Jin
Published: March 2010

A Gram-negative, aerobic, motile, rod-shaped, thiosulfate-oxidizing bacterium, designated ATSB10T, was isolated from rhizosphere soil of sunflower (Helianthus annuus L.). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ATSB10T was closely related to members of the genera Dyella (96.4–98.1 % 16S rRNA gene sequence similarity) and Luteibacter (96.4–97.0 %) and Fulvimonas soli LMG 19981T (96.7 %) and Frateuria aurantia IFO 3245T (97.8 %). The predominant fatty acids were iso-C16 : 0, iso-C17 : 1
ω9c and iso-C15 : 0. The major quinone was Q-8. The G+C content of the genomic DNA was 66.0 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, an unknown phospholipid, unknown aminophospholipids and an unknown aminolipid. On the basis of phenotypic properties, phylogenetic distinctiveness and DNA–DNA relatedness, strain ATSB10T represents a novel species in the genus Dyella, for which the name Dyella thiooxydans sp. nov. is proposed. The type strain is ATSB10T (=KACC 12756T =LMG 24673T).
Arcobacter trophiarum sp. nov., isolated from fattening pigs
Authors: De Smet Sarah , Vandamme Peter , De Zutter Lieven , On Stephen L. W. , Douidah Laid , Houf Kurt
Published: March 2010

In the course of a longitudinal study elucidating the dynamics of Arcobacter populations in pigs, 16 isolates of Gram-reaction-negative, rod-shaped, slightly curved, non-spore-forming bacteria were grouped by amplified fragment length polymorphism analysis into a distinct phenon within the genus Arcobacter. Fragments were generated for all isolates in a genus-specific PCR assay, but no amplicon was obtained in a species-specific multiplex-PCR test. Numerical analysis of the whole-cell protein profiles also showed that all isolates clustered in a single group that was distinct from related members of the genus Arcobacter. DNA–DNA hybridizations between two representative strains, designated 64T and 122, of the isolates obtained exhibited a mean DNA–DNA relatedness of 72 %. DNA–DNA hybridizations between strains 64T and 122 and reference strains of other animal-related bacteria of the genus Arcobacter revealed binding values of 47 % or less. The DNA G+C contents of the two representative strains were 28.5 and 28.4 mol%, respectively, and analysis of three marker genes identified Arcobacter cryaerophilus, A. thereius, A. cibarius and A. skirrowii as their closest phylogenetic neighbours. Strains 64T and 122 could be distinguished from other members of the genus Arcobacter by means of biochemical tests for catalase and urease activities, nitrate reduction, indoxyl acetate hydrolysis, lack of growth at 37 °C, growth in 2 % (w/v) NaCl, growth on 0.1 % sodium deoxycholate and non-supplemented Campylobacter charcoal-deoxycholate base medium and resistance to cephalothin (32 mg l−1) and cefoperazone (64 mg l−1). Additionally, a PCR assay was developed for the detection and identification of strains 64T and 122, which represent a novel species of the genus Arcobacter, for which the name Arcobacter trophiarum sp. nov. is proposed. The type strain is strain 64T (=LMG 25534T =CCUG 59229T).
Genome assembly quality: Assessment and improvement using the neutral indel model
Authors: Meader Stephen , Hillier LaDeana W. , Locke Devin , Ponting Chris P. , Lunter Gerton
Published: March 2010

We describe a statistical and comparative-genomic approach for quantifying error rates of genome sequence assemblies. The method exploits not substitutions but the pattern of insertions and deletions (indels) in genome-scale alignments for closely related species. Using two- or three-way alignments, the approach estimates the amount of aligned sequence containing clusters of nucleotides that were wrongly inserted or deleted during sequencing or assembly. Thus, the method is well-suited to assessing fine-scale sequence quality within single assemblies, between different assemblies of a single set of reads, and between genome assemblies for different species. When applying this approach to four primate genome assemblies, we found that average gap error rates per base varied considerably, by up to sixfold. As expected, bacterial artificial chromosome (BAC) sequences contained lower, but still substantial, predicted numbers of errors, arguing for caution in regarding BACs as the epitome of genome fidelity. We then mapped short reads, at approximately 10-fold statistical coverage, from a Bornean orangutan onto the Sumatran orangutan genome assembly originally constructed from capillary reads. This resulted in a reduced gap error rate and a separation of error-prone from high-fidelity sequence. Over 5000 predicted indel errors in protein-coding sequence were corrected in a hybrid assembly. Our approach contributes a new fine-scale quality metric for assemblies that should facilitate development of improved genome sequencing and assembly strategies.
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
Authors: Quinlan Aaron R. , Clark Royden A. , Sokolova Svetlana , Leibowitz Mitchell L. , Zhang Yujun , Hurles Matthew E. , Mell Joshua C. , Hall Ira M.
Published: March 2010

Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that ∼16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.
Significance of Light, Sugar, and Amino Acid Supply for Diurnal Gene Regulation in Developing Barley Caryopses
Authors: Mangelsen Elke , Wanke Dierk , Kilian Joachim , Sundberg Eva , Harter Klaus , Jansson Christer
Published: March 2010

The caryopses of barley (Hordeum vulgare), as of all cereals, are complex sink organs optimized for starch accumulation and embryo development. While their early to late development has been studied in great detail, processes underlying the caryopses’ diurnal adaptation to changes in light, temperature, and the fluctuations in phloem-supplied carbon and nitrogen have remained unknown. In an attempt to identify diurnally affected processes in developing caryopses at the early maturation phase, we monitored global changes of both gene expression and metabolite levels. We applied the 22 K Barley1 GeneChip microarray and identified 2,091 differentially expressed (DE) genes that were assigned to six major diurnal expression clusters. Principal component analysis and other global analyses demonstrated that the variability within the data set relates to genes involved in circadian regulation, storage compound accumulation, embryo development, response to abiotic stress, and photosynthesis. The correlation of amino acid and sugar profiles with expression trajectories led to the identification of several hundred potentially metabolite-regulated DE genes. A comparative analysis of our data set and publicly available microarray data disclosed suborgan-specific expression of almost all diurnal DE genes, with more than 350 genes specifically expressed in the pericarp, endosperm, or embryo tissues. Our data reveal a tight linkage between day/night cycles, changes in light, and the supply of carbon and nitrogen. We present a model that suggests several phases of diurnal gene expression in developing barley caryopses, summarized as starvation and priming, energy collection and carbon fixation, light protection and chaperone activity, storage and growth, and embryo development.
A Conserved Mechanism of Bract Suppression in the Grass Family
Authors: Whipple Clinton J. , Hall Darren H. , DeBlasio Stacy , Taguchi-Shiobara Fumio , Schmidt Robert J. , Jackson David P.
Published: March 2010

Suppression of inflorescence leaf, or bract, growth has evolved multiple times in diverse angiosperm lineages, including the Poaceae and Brassicaceae. Studies of Arabidopsis thaliana mutants have revealed several genes involved in bract suppression, but it is not known if these genes play a similar role in other plants with suppressed bracts. We identified maize (Zea mays) tassel sheath (tsh) mutants, characterized by the loss of bract suppression, that comprise five loci (tsh1-tsh5). We used map-based cloning to identify Tsh1 and found that it encodes a GATA zinc-finger protein, a close homolog of HANABA TARANU (HAN) of Arabidopsis. The bract suppression function of Tsh1 is conserved throughout the grass family, as we demonstrate that the rice (Oryza sativa) NECK LEAF1 (NL1) and barley (Hordeum vulgare) THIRD OUTER GLUME (TRD) genes are orthologous with Tsh1. Interestingly, NL1/Tsh1/TRD expression and function are not conserved with HAN. The existence of paralogous NL1/Tsh1/TRD-like genes in the grasses indicates that the NL1/Tsh1/TRD lineage was created by recent duplications that may have facilitated its neofunctionalization. A comparison with the Arabidopsis genes regulating bract suppression further supports the hypothesis that the convergent evolution of bract suppression in the Poaceae involved recruitment of a distinct genetic pathway.
Optimization of data collection taking radiation damage into account
Authors: Bourenkov Gleb P. , Popov Alexander N.
Published: March 2010

To take into account the effects of radiation damage, new algorithms for the optimization of data-collection strategies have been implemented in the software package BEST. The intensity variation related to radiation damage is approximated by log-linear functions of resolution and cumulative X-ray dose. Based on an accurate prediction of the basic characteristics of data yet to be collected, BEST establishes objective relationships between the accessible data completeness, resolution and signal-to-noise statistics that can be achieved in an experiment and designs an optimal plan for data collection.
Introduction to phasing
Authors: Taylor Garry L.
Published: March 2010

When collecting X-ray diffraction data from a crystal, we measure the intensities of the diffracted waves scattered from a series of planes that we can imagine slicing through the crystal in all directions. From these intensities we derive the amplitudes of the scattered waves, but in the experiment we lose the phase information; that is, how we offset these waves when we add them together to reconstruct an image of our molecule. This is generally known as the `phase problem'. We can only derive the phases from some knowledge of the molecular structure. In small-molecule crystallography, some basic assumptions about atomicity give rise to relationships between the amplitudes from which phase information can be extracted. In protein crystallography, theseab initiomethods can only be used in the rare cases in which there are data to at least 1.2 Å resolution. For the majority of cases in protein crystallography phases are derived either by using the atomic coordinates of a structurally similar protein (molecular replacement) or by finding the positions of heavy atoms that are intrinsic to the protein or that have been added (methods such as MIR, MIRAS, SIR, SIRAS, MAD, SAD or combinations of these). The pioneering work of Perutz, Kendrew, Blow, Crick and others developed the methods of isomorphous replacement: adding electron-dense atoms to the protein without disturbing the protein structure. Nowadays, methods from small-molecule crystallography can be used to find the heavy-atom substructure and the phases for the whole protein can be bootstrapped from this prior knowledge. More recently, improved X-ray sources, detectors and software have led to the routine use of anomalous scattering to obtain phase information from either incorporated selenium or intrinsic sulfurs. In the best cases, only a single set of X-ray data (SAD) is required to provide the positions of the anomalous scatters, which together with density-modification procedures can reveal the structure of the complete protein.