bluuebunny/crossref_metadata_2025 huggingface dataset:
Robust self-replication of combinatorial information via crystal growth and scission
Authors: Schulman Rebecca , Yurke Bernard , Winfree Erik
Published: April 2012

Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes. Crystal growth propagates a sequence of bits while mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and Darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chemical sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.
Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III
Authors: Bezerra Gustavo A. , Dobrovetsky Elena , Viertlmayr Roland , Dong Aiping , Binter Alexandra , Abramić Marija , Macheroux Peter , Dhe-Paganon Sirano , Gruber Karl
Published: April 2012

Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft (“entropy reservoir”) as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.
Structure of human Mad1 C-terminal domain reveals its involvement in kinetochore targeting
Authors: Kim Soonjoung , Sun Hongbin , Tomchick Diana R. , Yu Hongtao , Luo Xuelian
Published: April 2012

The spindle checkpoint prevents aneuploidy by delaying anaphase onset until all sister chromatids achieve proper microtubule attachment. The kinetochore-bound checkpoint protein complex Mad1-Mad2 promotes the conformational activation of Mad2 and serves as a catalytic engine of checkpoint signaling. How Mad1 is targeted to kinetochores is not understood. Here, we report the crystal structure of the conserved C-terminal domain (CTD) of human Mad1. Mad1 CTD forms a homodimer and, unexpectedly, has a fold similar to those of the kinetochore-binding domains of Spc25 and Csm1. Nonoverlapping Mad1 fragments retain detectable kinetochore targeting. Deletion of the CTD diminishes, does not abolish, Mad1 kinetochore localization. Mutagenesis studies further map the functional interface of Mad1 CTD in kinetochore targeting and implicate Bub1 as its receptor. Our results indicate that CTD is a part of an extensive kinetochore-binding interface of Mad1, and rationalize graded kinetochore targeting of Mad1 during checkpoint signaling.
Neural basis of egalitarian behavior
Authors: Dawes Christopher T. , Loewen Peter John , Schreiber Darren , Simmons Alan N. , Flagan Taru , McElreath Richard , Bokemper Scott E. , Fowler James H. , Paulus Martin P.
Published: April 2012

Individuals are willing to sacrifice their own resources to promote equality in groups. These costly choices promote equality and are associated with behavior that supports cooperation in humans, but little is known about the brain processes involved. We use functional MRI to study egalitarian preferences based on behavior observed in the “random income game.” In this game, subjects decide whether to pay a cost to alter group members’ randomly allocated incomes. We specifically examine whether egalitarian behavior is associated with neural activity in the ventromedial prefrontal cortex and the insular cortex, two regions that have been shown to be related to social preferences. Consistent with previous studies, we find significant activation in both regions; however, only the insular cortex activations are significantly associated with measures of revealed and expressed egalitarian preferences elicited outside the scanner. These results are consistent with the notion that brain mechanisms involved in experiencing the emotional states of others underlie egalitarian behavior in humans.
Single-wavelength two-photon excitation–stimulated emission depletion (SW2PE-STED) superresolution imaging
Authors: Bianchini Paolo , Harke Benjamin , Galiani Silvia , Vicidomini Giuseppe , Diaspro Alberto
Published: April 2012

We developed a new class of two-photon excitation–stimulated emission depletion (2PE-STED) optical microscope. In this work, we show the opportunity to perform superresolved fluorescence imaging, exciting and stimulating the emission of a fluorophore by means of a single wavelength. We show that a widely used red-emitting fluorophore, ATTO647N, can be two-photon excited at a wavelength allowing both 2PE and STED using the very same laser source. This fact opens the possibility to perform 2PE microscopy at four to five times STED-improved resolution, while exploiting the intrinsic advantages of nonlinear excitation.
Staphylococcal biofilm-forming protein has a contiguous rod-like structure
Authors: Gruszka Dominika T. , Wojdyla Justyna A. , Bingham Richard J. , Turkenburg Johan P. , Manfield Iain W. , Steward Annette , Leech Andrew P. , Geoghegan Joan A. , Foster Timothy J. , Clarke Jane , Potts Jennifer R.
Published: April 2012

Staphylococcus aureus
and
Staphylococcus epidermidis
form communities (called biofilms) on inserted medical devices, leading to infections that affect many millions of patients worldwide and cause substantial morbidity and mortality. As biofilms are resistant to antibiotics, device removal is often required to resolve the infection. Thus, there is a need for new therapeutic strategies and molecular data that might assist their development. Surface proteins
S. aureus
surface protein G (SasG) and accumulation-associated protein (
S. epidermidis
) promote biofilm formation through their “B” regions. B regions contain tandemly arrayed G5 domains interspersed with approximately 50 residue sequences (herein called E) and have been proposed to mediate intercellular accumulation through Zn
2+
-mediated homodimerization. Although E regions are predicted to be unstructured, SasG and accumulation-associated protein form extended fibrils on the bacterial surface. Here we report structures of E–G5 and G5–E–G5 from SasG and biophysical characteristics of single and multidomain fragments. E sequences fold cooperatively and form interlocking interfaces with G5 domains in a head-to-tail fashion, resulting in a contiguous, elongated, monomeric structure. E and G5 domains lack a compact hydrophobic core, and yet G5 domain and multidomain constructs have thermodynamic stabilities only slightly lower than globular proteins of similar size. Zn
2+
does not cause SasG domains to form dimers. The work reveals a paradigm for formation of fibrils on the 100-nm scale and suggests that biofilm accumulation occurs through a mechanism distinct from the “zinc zipper.” Finally, formation of two domains by each repeat (as in SasG) might reduce misfolding in proteins when the tandem arrangement of highly similar sequences is advantageous.
Universal conditions for exact path integration in neural systems
Authors: Issa John B. , Zhang Kechen
Published: April 2012

Animals are capable of navigation even in the absence of prominent landmark cues. This behavioral demonstration of path integration is supported by the discovery of place cells and other neurons that show path-invariant response properties even in the dark. That is, under suitable conditions, the activity of these neurons depends primarily on the spatial location of the animal regardless of which trajectory it followed to reach that position. Although many models of path integration have been proposed, no known single theoretical framework can formally accommodate their diverse computational mechanisms. Here we derive a set of necessary and sufficient conditions for a general class of systems that performs exact path integration. These conditions include multiplicative modulation by velocity inputs and a path-invariance condition that limits the structure of connections in the underlying neural network. In particular, for a linear system to satisfy the path-invariance condition, the effective synaptic weight matrices under different velocities must commute. Our theory subsumes several existing exact path integration models as special cases. We use entorhinal grid cells as an example to demonstrate that our framework can provide useful guidance for finding unexpected solutions to the path integration problem. This framework may help constrain future experimental and modeling studies pertaining to a broad class of neural integration systems.
Plant-activated bacterial receptor adenylate cyclases modulate epidermal infection in the
Sinorhizobium meliloti–Medicago
symbiosis
Authors: Tian Chang Fu , Garnerone Anne-Marie , Mathieu-Demazière Céline , Masson-Boivin Catherine , Batut Jacques
Published: April 2012

Legumes and soil bacteria called rhizobia have coevolved a facultative nitrogen-fixing symbiosis. Establishment of the symbiosis requires bacterial entry via root hair infection threads and, in parallel, organogenesis of nodules that subsequently are invaded by bacteria. Tight control of nodulation and infection is required to maintain the mutualistic character of the interaction. Available evidence supports a passive bacterial role in nodulation and infection after the microsymbiont has triggered the symbiotic plant developmental program. Here we identify in
Sinorhizobium meliloti
, the
Medicago
symbiont, a cAMP-signaling regulatory cascade consisting of three receptor-like adenylate cyclases, a Crp-like regulator, and a target gene of unknown function. The cascade is activated specifically by a plant signal during nodule organogenesis. Cascade inactivation results in a hyperinfection phenotype consisting of abortive epidermal infection events uncoupled from nodulation. These findings show that, in response to a plant signal, rhizobia play an active role in the control of infection. We suggest that rhizobia may modulate the plant’s susceptibility to infection. This regulatory loop likely aims at optimizing legume infection.
Kruppel-like factor 15 regulates skeletal muscle lipid flux and exercise adaptation
Authors: Haldar Saptarsi M. , Jeyaraj Darwin , Anand Priti , Zhu Han , Lu Yuan , Prosdocimo Domenick A. , Eapen Betty , Kawanami Daiji , Okutsu Mitsuharu , Brotto Leticia , Fujioka Hisashi , Kerner Janos , Rosca Mariana G. , McGuinness Owen P. , Snow Rod J. , Russell Aaron P. , Gerber Anthony N. , Bai Xiaodong , Yan Zhen , Nosek Thomas M. , Brotto Marco , Hoppel Charles L. , Jain Mukesh K.
Published: April 2012

The ability of skeletal muscle to enhance lipid utilization during exercise is a form of metabolic plasticity essential for survival. Conversely, metabolic inflexibility in muscle can cause organ dysfunction and disease. Although the transcription factor Kruppel-like factor 15 (KLF15) is an important regulator of glucose and amino acid metabolism, its endogenous role in lipid homeostasis and muscle physiology is unknown. Here we demonstrate that KLF15 is essential for skeletal muscle lipid utilization and physiologic performance. KLF15 directly regulates a broad transcriptional program spanning all major segments of the lipid-flux pathway in muscle. Consequently,
Klf15
-deficient mice have abnormal lipid and energy flux, excessive reliance on carbohydrate fuels, exaggerated muscle fatigue, and impaired endurance exercise capacity. Elucidation of this heretofore unrecognized role for KLF15 now implicates this factor as a central component of the transcriptional circuitry that coordinates physiologic flux of all three basic cellular nutrients: glucose, amino acids, and lipids.
Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation
Authors: Wang Po-hung , Blumberger Jochen
Published: April 2012

[NiFe]-hydrogenases are fascinating biological catalysts with potential application in biofuel cells. However, a severe problem in practical application is the strong sensitivity of hydrogenase to gaseous inhibitor molecules such as CO and O
2
. Recently, a number of successful protein engineering studies have been reported that aimed at lowering the access of diatomic inhibitors to the active site pocket, but the molecular mechanism conferring increased resistance remained unclear. Here we use a multiscale simulation approach combining molecular dynamics with a master equation formalism to explain the steady drop in CO diffusion rate observed for the mutants V74M L122A, V74M L122M, and V74M of
Desulfovibrio fructosovorans
[NiFe]-hydrogenase. We find that diffusion in these variants is controlled by two gates, one between residues 74 and 476 and the other between residues 74 and 122. The existence of two control points in different locations explains why the reduction in the experimental diffusion rate does not simply correlate with the width of the main gas channel. We also find that in the more effective mutation (V74M) CO molecules are still able to reach the active site through transitions that are gated by the microsecond dihedral motions of the side chain of R476 and the thermal fluctuations of the width of the gas channel defined by M74 and L122. Reflecting on the molecular information gained from simulation, we discuss future mutation experiments that could further lower the diffusion rates of small ligands inhibiting [NiFe]-hydrogenase.
ESR spectroscopy identifies inhibitory Cu
2+
sites in a DNA-modifying enzyme to reveal determinants of catalytic specificity
Authors: Yang Zhongyu , Kurpiewski Michael R. , Ji Ming , Townsend Jacque E. , Mehta Preeti , Jen-Jacobson Linda , Saxena Sunil
Published: April 2012

The relationship between DNA sequence recognition and catalytic specificity in a DNA-modifying enzyme was explored using paramagnetic Cu
2+
ions as probes for ESR spectroscopic and biochemical studies. Electron spin echo envelope modulation spectroscopy establishes that Cu
2+
coordinates to histidine residues in the EcoRI endonuclease homodimer bound to its specific DNA recognition site. The coordinated His residues were identified by a unique use of Cu
2+
-ion based long-range distance constraints. Double electron-electron resonance data yield Cu
2+
-Cu
2+
and Cu
2+
-nitroxide distances that are uniquely consistent with one Cu
2+
bound to His114 in each subunit. Isothermal titration calorimetry confirms that two Cu
2+
ions bind per complex. Unexpectedly, Mg
2+
-catalyzed DNA cleavage by EcoRI is profoundly inhibited by Cu
2+
binding at these hitherto unknown sites, 13 Å away from the Mg
2+
positions in the catalytic centers. Molecular dynamics simulations suggest a model for inhibition of catalysis, whereby the Cu
2+
ions alter critical protein-DNA interactions and water molecule positions in the catalytic sites. In the absence of Cu
2+
, the Mg
2+
-dependence of EcoRI catalysis shows positive cooperativity, which would enhance EcoRI inactivation of foreign DNA by irreparable double-strand cuts, in preference to readily repaired single-strand nicks. Nonlinear Poisson-Boltzmann calculations suggest that this cooperativity arises because the binding of Mg
2+
in one catalytic site makes the surface electrostatic potential in the distal catalytic site more negative, thus enhancing binding of the second Mg
2+
. Taken together, our results shed light on the structural and electrostatic factors that affect site-specific catalysis by this class of endonucleases.
Fire-free land use in pre-1492 Amazonian savannas
Authors: Iriarte José , Power Mitchell J. , Rostain Stéphen , Mayle Francis E. , Jones Huw , Watling Jennifer , Whitney Bronwen S. , McKey Doyle B.
Published: April 2012

The nature and scale of pre-Columbian land use and the consequences of the 1492 “Columbian Encounter” (CE) on Amazonia are among the more debated topics in New World archaeology and paleoecology. However, pre-Columbian human impact in Amazonian savannas remains poorly understood. Most paleoecological studies have been conducted in neotropical forest contexts. Of studies done in Amazonian savannas, none has the temporal resolution needed to detect changes induced by either climate or humans before and after A.D. 1492, and only a few closely integrate paleoecological and archaeological data. We report a high-resolution 2,150-y paleoecological record from a French Guianan coastal savanna that forces reconsideration of how pre-Columbian savanna peoples practiced raised-field agriculture and how the CE impacted these societies and environments. Our combined pollen, phytolith, and charcoal analyses reveal unexpectedly low levels of biomass burning associated with pre-A.D. 1492 savanna raised-field agriculture and a sharp increase in fires following the arrival of Europeans. We show that pre-Columbian raised-field farmers limited burning to improve agricultural production, contrasting with extensive use of fire in pre-Columbian tropical forest and Central American savanna environments, as well as in present-day savannas. The charcoal record indicates that extensive fires in the seasonally flooded savannas of French Guiana are a post-Columbian phenomenon, postdating the collapse of indigenous populations. The discovery that pre-Columbian farmers practiced fire-free savanna management calls into question the widely held assumption that pre-Columbian Amazonian farmers pervasively used fire to manage and alter ecosystems and offers fresh perspectives on an emerging alternative approach to savanna land use and conservation that can help reduce carbon emissions.
Social environment is associated with gene regulatory variation in the rhesus macaque immune system
Authors: Tung Jenny , Barreiro Luis B. , Johnson Zachary P. , Hansen Kasper D. , Michopoulos Vasiliki , Toufexis Donna , Michelini Katelyn , Wilson Mark E. , Gilad Yoav
Published: April 2012

Variation in the social environment is a fundamental component of many vertebrate societies. In humans and other primates, adverse social environments often translate into lasting physiological costs. The biological mechanisms associated with these effects are therefore of great interest, both for understanding the evolutionary impacts of social behavior and in the context of human health. However, large gaps remain in our understanding of the mechanisms that mediate these effects at the molecular level. Here we addressed these questions by leveraging the power of an experimental system that consisted of 10 social groups of female macaques, in which each individual's social status (i.e., dominance rank) could be experimentally controlled. Using this paradigm, we show that dominance rank results in a widespread, yet plastic, imprint on gene regulation, such that peripheral blood mononuclear cell gene expression data alone predict social status with 80% accuracy. We investigated the mechanistic basis of these effects using cell type-specific gene expression profiling and glucocorticoid resistance assays, which together contributed to rank effects on gene expression levels for 694 (70%) of the 987 rank-related genes. We also explored the possible contribution of DNA methylation levels to these effects, and identified global associations between dominance rank and methylation profiles that suggest epigenetic flexibility in response to status-related behavioral cues. Together, these results illuminate the importance of the molecular response to social conditions, particularly in the immune system, and demonstrate a key role for gene regulation in linking the social environment to individual physiology.
Coupling actin flow, adhesion, and morphology in a computational cell motility model
Authors: Shao Danying , Levine Herbert , Rappel Wouter-Jan
Published: April 2012

Cell migration is a pervasive process in many biology systems and involves protrusive forces generated by actin polymerization, myosin dependent contractile forces, and force transmission between the cell and the substrate through adhesion sites. Here we develop a computational model for cell motion that uses the phase-field method to solve for the moving boundary with physical membrane properties. It includes a reaction-diffusion model for the actin-myosin machinery and discrete adhesion sites which can be in a “gripping” or “slipping” mode and integrates the adhesion dynamics with the dynamics of the actin filaments, modeled as a viscous network. To test this model, we apply it to fish keratocytes, fast moving cells that maintain their morphology, and show that we are able to reproduce recent experimental results on actin flow and stress patterns. Furthermore, we explore the phase diagram of cell motility by varying myosin II activity and adhesion strength. Our model suggests that the pattern of the actin flow inside the cell, the cell velocity, and the cell morphology are determined by the integration of actin polymerization, myosin contraction, adhesion forces, and membrane forces.
Thermodynamic glass transition in a spin glass without time-reversal symmetry
Authors: Baños Raquel Alvarez , Cruz Andres , Fernandez Luis Antonio , Gil-Narvion Jose Miguel , Gordillo-Guerrero Antonio , Guidetti Marco , Iñiguez David , Maiorano Andrea , Marinari Enzo , Martin-Mayor Victor , Monforte-Garcia Jorge , Muñoz Sudupe Antonio , Navarro Denis , Parisi Giorgio , Perez-Gaviro Sergio , Ruiz-Lorenzo Juan Jesus , Schifano Sebastiano Fabio , Seoane Beatriz , Tarancon Alfonso , Tellez Pedro , Tripiccione Raffaele , Yllanes David
Published: April 2012

Spin glasses are a longstanding model for the sluggish dynamics that appear at the glass transition. However, spin glasses differ from structural glasses in a crucial feature: they enjoy a time reversal symmetry. This symmetry can be broken by applying an external magnetic field, but embarrassingly little is known about the critical behavior of a spin glass in a field. In this context, the space dimension is crucial. Simulations are easier to interpret in a large number of dimensions, but one must work below the upper critical dimension (i.e., ind < 6) in order for results to have relevance for experiments. Here we show conclusive evidence for the presence of a phase transition in a four-dimensional spin glass in a field. Two ingredients were crucial for this achievement: massive numerical simulations were carried out on the Janus special-purpose computer, and a new and powerful finite-size scaling method.
Heritable polymorphism predisposes to high
BAALC
expression in acute myeloid leukemia
Authors: Eisfeld Ann-Kathrin , Marcucci Guido , Liyanarachchi Sandya , Döhner Konstanze , Schwind Sebastian , Maharry Kati , Leffel Benjamin , Döhner Hartmut , Radmacher Michael D. , Bloomfield Clara D. , Tanner Stephan M. , de la Chapelle Albert
Published: April 2012

Overexpression of the brain and acute leukemia, cytoplasmic (
BAALC
) gene is implicated in myeloid leukemogenesis and associated with poor outcome in both acute myeloid leukemia (AML) and acute lymphoblastic leukemia patients. Additionally, high
BAALC
expression occurs in glioblastoma, melanoma, and childhood gastrointestinal stroma tumors, suggesting an oncogenic role for
BAALC
. However, the mechanisms underlying the deregulated expression are unknown. We hypothesized that a common heritable genetic feature located
in cis
might account for overexpression of
BAALC
in an allele-specific manner. By sequencing the genomic region of
BAALC
we identified nine informative single nucleotide polymorphisms (SNPs) and tested them for a possible association with
BAALC
expression levels. We show that
BAALC
overexpression occurs in the presence of the T allele of SNP rs62527607[GT], which creates a binding site for the activating RUNX1 transcription factor in the
BAALC
promoter region. The mechanism is demonstrated experimentally in vitro using luciferase reporter assays and electrophoretic mobility shift assay (EMSA) analysis. The association of high
BAALC
expression with the T allele and its correlations with
RUNX1
expresser status are shown in vivo in a test set (
n
= 253) and validation set (
n
= 105) of samples from cytogenetically normal AML patients from different populations. Thus, we identify a heritable genomic feature predisposing to overexpression of an oncogene, thereby possibly leading to enhanced AML leukemogenesis. Our findings further suggest that genomic variants might become useful tools in the practice of personalized medicine.
The
E. coli
CsgB nucleator of curli assembles to β-sheet oligomers that alter the CsgA fibrillization mechanism
Authors: Shu Qin , Crick Scott L. , Pinkner Jerome S. , Ford Bradley , Hultgren Scott J. , Frieden Carl
Published: April 2012

Curli are extracellular proteinaceous functional amyloid aggregates produced by
Escherichia coli
,
Salmonella
spp., and other enteric bacteria. Curli mediate host cell adhesion and invasion and play a critical role in biofilm formation. Curli filaments consist of CsgA, the major subunit, and CsgB, the minor subunit. In vitro, purified CsgA and CsgB exhibit intrinsically disordered properties, and both are capable of forming amyloid fibers similar in morphology to those formed in vivo. However, in vivo, CsgA alone cannot form curli fibers, and CsgB is required for filament growth. Thus, we studied the aggregation of CsgA and CsgB both alone and together in vitro to investigate the different roles of CsgA and CsgB in curli formation. We found that though CsgA and CsgB individually are able to self-associate to form aggregates/fibrils, they do so using different mechanisms and with different kinetic behavior. CsgB rapidly forms structured oligomers, whereas CsgA aggregation is slower and appears to proceed through large amorphous aggregates before forming filaments. Substoichiometric concentrations of CsgB induce a change in the mechanism of CsgA aggregation from that of forming amorphous aggregates to that of structured intermediates similar to those of CsgB alone. Oligomeric CsgB accelerated the aggregation of CsgA, in contrast to monomeric CsgB, which had no effect. The structured β-strand oligomers formed by CsgB serve as nucleators for CsgA aggregation. These results provide insights into the formation of curli in vivo, especially the nucleator function of CsgB.
Heterosis of
Arabidopsis
hybrids between C24 and Col is associated with increased photosynthesis capacity
Authors: Fujimoto Ryo , Taylor Jennifer M. , Shirasawa Sachiko , Peacock W. James , Dennis Elizabeth S.
Published: April 2012

Arabidopsis thaliana
shows hybrid vigor (heterosis) in progeny of crosses between Columbia-0 and C24 accessions. Hybrid vigor was evident as early as mature seeds and in seedlings 3 d after sowing (DAS). At 3 DAS, genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes that have greater than midparent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll, and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3–7 DAS period. At 10 DAS, only 118 genes had expression levels different from the expected midparent value in the hybrid, and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increases in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation, we found that an inhibitor of photosynthesis eliminated heterosis and that higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low-level heterosis (Landsberg
erecta
x Columbia-0), chloroplast-targeted genes were not up-regulated and leaf areas were only marginally increased.
Using translational enhancers to increase transgene expression in
Drosophila
Authors: Pfeiffer Barret D. , Truman James W. , Rubin Gerald M.
Published: April 2012

The ability to specify the expression levels of exogenous genes inserted in the genomes of transgenic animals is critical for the success of a wide variety of experimental manipulations. Protein production can be regulated at the level of transcription, mRNA transport, mRNA half-life, or translation efficiency. In this report, we show that several well-characterized sequence elements derived from plant and insect viruses are able to function in
Drosophila
to increase the apparent translational efficiency of mRNAs by as much as 20-fold. These increases render expression levels sufficient for genetic constructs previously requiring multiple copies to be effective in single copy, including constructs expressing the temperature-sensitive inactivator of neuronal function

Shibire
ts1

, and for the use of cytoplasmic GFP to image the fine processes of neurons.
Implementing a Statewide Screening, Brief Intervention, and Referral to Treatment (SBIRT) Service in Rural Health Settings: New Mexico SBIRT
Authors: Gonzales Arturo , Westerberg Verner S. , Peterson Thomas R. , Moseley Ana , Gryczynski Jan , Mitchell Shannon Gwin , Buff Gary , Schwartz Robert P.
Published: April 2012

This is a report on the New Mexico Screening, Brief Intervention, and Referral to Treatment (SBIRT) project conducted over 5 years as part of a national initiative launched by the Substance Abuse and Mental Health Services Administration with the aim of increasing integration of substance use services and medical care. Throughout the state, 53,238 adults were screened for alcohol and/or drug use problems in ambulatory settings, with 12.2% screening positive. Baseline substance use behaviors among 6,360 participants eligible for brief intervention, brief treatment, or referral for treatment are examined and the process of implementation and challenges for sustainability are discussed.
Jung's metaphysics
Authors: Mills Jon
Published: April 2012

Despite it being the focal point of his theoretical system, I argue that Jung's notion of the archetypes is one of his least understood concepts because it was nebulous to Jung himself. Jung vacillated between viewing archetypes as analogous to primordial images and ideas inherited from our ancestral past, formal a priori categories of mind, cosmic projections, emotional and valuational agencies, and numinous mystical experience, but the question remains whether a ‘suprapersonal’ or ‘transubjective’ psyche exists. In what follows, I will be preoccupied with tracing the theoretical development of Jung's thesis on the collective unconscious, with a special emphasis on the archetypes, and hence pointing out the metaphysical implications of his thought. It is not possible to critique his entire body of work in the context of this abbreviated article; therefore, the reader should be aware that I am limiting myself to a narrow scope of interest in explicating and analyzing the philosophical viability of his major concepts. The greater question is whether the archetypes adequately answer to the question of origins, of an omnipresent and eternal dimension to the nature and structure of psychic reality.
DDB2 promotes chromatin decondensation at UV-induced DNA damage
Authors: Luijsterburg Martijn S. , Lindh Michael , Acs Klara , Vrouwe Mischa G. , Pines Alex , van Attikum Haico , Mullenders Leon H. , Dantuma Nico P.
Published: April 2012

Nucleotide excision repair (NER) is the principal pathway that removes helix-distorting deoxyribonucleic acid (DNA) damage from the mammalian genome. Recognition of DNA lesions by xeroderma pigmentosum group C (XPC) protein in chromatin is stimulated by the damaged DNA-binding protein 2 (DDB2), which is part of a CUL4A–RING ubiquitin ligase (CRL4) complex. In this paper, we report a new function of DDB2 in modulating chromatin structure at DNA lesions. We show that DDB2 elicits unfolding of large-scale chromatin structure independently of the CRL4 ubiquitin ligase complex. Our data reveal a marked adenosine triphosphate (ATP)–dependent reduction in the density of core histones in chromatin containing UV-induced DNA lesions, which strictly required functional DDB2 and involved the activity of poly(adenosine diphosphate [ADP]–ribose) polymerase 1. Finally, we show that lesion recognition by XPC, but not DDB2, was strongly reduced in ATP-depleted cells and was regulated by the steady-state levels of poly(ADP-ribose) chains.
Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks
Authors: Poulsen Maria , Lukas Claudia , Lukas Jiri , Bekker-Jensen Simon , Mailand Niels
Published: April 2012

Nonproteolytic ubiquitylation of chromatin surrounding deoxyribonucleic acid double-strand breaks (DSBs), mediated by the RNF8/RNF168 ubiquitin ligases, plays a key role in recruiting repair factors, including 53BP1 and BRCA1, to reestablish genome integrity. In this paper, we show that human RNF169, an uncharacterized E3 ubiquitin ligase paralogous to RNF168, accumulated in DSB repair foci through recognition of RNF168-catalyzed ubiquitylation products by its motif interacting with ubiquitin domain. Unexpectedly, RNF169 was dispensable for chromatin ubiquitylation and ubiquitin-dependent accumulation of repair factors at DSB sites. Instead, RNF169 functionally competed with 53BP1 and RAP80–BRCA1 for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of their recruitment to DSB sites. By delaying accumulation of 53BP1 and RAP80 at damaged chromatin, RNF169 stimulated homologous recombination and restrained nonhomologous end joining, affecting cell survival after DSB infliction. Our results show that RNF169 functions in a noncanonical fashion to harness RNF168-mediated protein recruitment to DSB-containing chromatin, thereby contributing to regulation of DSB repair pathway utilization.
BRCA1 regulates microRNA biogenesis via the DROSHA microprocessor complex
Authors: Kawai Shinji , Amano Atsuo
Published: April 2012

MicroRNAs (miRNAs) are noncoding RNAs that function as key posttranscriptional regulators of gene expression. miRNA maturation is controlled by the DROSHA microprocessor complex. However, the detailed mechanism of miRNA biogenesis remains unclear. We show that the tumor suppressor breast cancer 1 (BRCA1) accelerates the processing of miRNA primary transcripts. BRCA1 increased the expressions of both precursor and mature forms of let-7a-1, miR-16-1, miR-145, and miR-34a. In addition, this tumor suppressor was shown to be directly associated with DROSHA and DDX5 of the DROSHA microprocessor complex, and it interacted with Smad3, p53, and DHX9 RNA helicase. We also found that BRCA1 recognizes the RNA secondary structure and directly binds with primary transcripts of miRNAs via a DNA-binding domain. Together, these results suggest that BRCA1 regulates miRNA biogenesis via the DROSHA microprocessor complex and Smad3/p53/DHX9. Our findings also indicate novel functions of BRCA1 in miRNA biogenesis, which may be linked to its tumor suppressor mechanism and maintenance of genomic stability.
SNX17 protects integrins from degradation by sorting between lysosomal and recycling pathways
Authors: Steinberg Florian , Heesom Kate J. , Bass Mark D. , Cullen Peter J.
Published: April 2012

The FERM-like domain–containing sorting nexins of the SNX17/SNX27/SNX31 family have been proposed to mediate retrieval of transmembrane proteins from the lysosomal pathway. In this paper, we describe a stable isotope labeling with amino acids in culture–based quantitative proteomic approach that allows an unbiased, global identification of transmembrane cargoes that are rescued from lysosomal degradation by SNX17. This screen revealed that several integrins required SNX17 for their stability, as depletion of SNX17 led to a loss of β1 and β5 integrins and associated a subunits from HeLa cells as a result of increased lysosomal degradation. SNX17 bound to the membrane distal NPXY motif in β integrin cytoplasmic tails, thereby preventing lysosomal degradation of β integrins and their associated a subunits. Furthermore, SNX17-dependent retrieval of integrins did not depend on the retromer complex. Consistent with an effect on integrin recycling, depletion of SNX17 also caused alterations in cell migration. Our data provide mechanistic insight into the retrieval of internalized integrins from the lysosomal degradation pathway, a prerequisite for subsequent recycling of these matrix receptors.
Proinflammatory cytokine signaling required for the generation of natural killer cell memory
Authors: Sun Joseph C. , Madera Sharline , Bezman Natalie A. , Beilke Joshua N. , Kaplan Mark H. , Lanier Lewis L.
Published: April 2012

Although natural killer (NK) cells are classified as innate immune cells, recent studies demonstrate that NK cells can become long-lived memory cells and contribute to secondary immune responses. The precise signals that promote generation of long-lived memory NK cells are unknown. Using cytokine receptor-deficient mice, we show that interleukin-12 (IL-12) is indispensible for mouse cytomegalovirus (MCMV)-specific NK cell expansion and generation of memory NK cells. In contrast to wild-type NK cells that proliferated robustly and resided in lymphoid and nonlymphoid tissues for months after MCMV infection, IL-12 receptor–deficient NK cells failed to expand and were unable to mediate protection after MCMV challenge. We further demonstrate that a STAT4-dependent IFN-γ–independent mechanism contributes toward the generation of memory NK cells during MCMV infection. Understanding the full contribution of inflammatory cytokine signaling to the NK cell response against viral infection will be of interest for the development of vaccines and therapeutics.
Aboveground Root Collar Excavation of Peach Trees for Armillaria Root Rot Management
Authors: Schnabel G. , Agudelo P. , Henderson G. W. , Rollins P. A.
Published: April 2012

Root collar excavation (RCE) has been applied to established citrus trees and grapevines for Armillaria root rot (ARR) control but, despite its demonstrated effectiveness, this cultural management system is not routinely used for ARR protection in disease-infested replant sites. One major drawback is the difficulty of excavating the belowground root collar, the potential of excavated roots to be covered again with surrounding soil, and the associated labor cost. In this study, a new cultural method was investigated that resulted in trees with aboveground excavated root collars, potentially eliminating many of the drawbacks. Experimental peach trees were planted in two commercial orchards (designated Landrum and Monetta) in South Carolina; each tree replaced one that had declined from ARR disease the year before. Trees were planted approximately 40 cm higher than normal in open-bottom Smart Pots and root collars were excavated above ground level 8 months later. Five years after planting, 30 and 70% of all control trees (planted according to grower standard) had declined from ARR disease in Landrum and Monetta, respectively, whereas only 0 and 10%, respectively, of trees in the aboveground root collar excavation (AGRCE) treatment had declined. The difference in disease pressure between the two locations could not be attributed to differences in nematode pressure. Nonexcavated trees in Smart Pots revealed significantly less tree decline (P ≤ 0.05) compared with the control but tree decline in both locations was greater compared with the AG-RCE treatment (P ≤ 0.05). Trees in the AG-RCE treatment were as vigorous as the controls but produced more root suckers. In this ‘prototype’ study, we demonstrate the potential of aboveground root collar excavation for ARR management. Its potential for commercial use is discussed.
The Chloroplast Triggers Developmental Reprogramming When MUTS HOMOLOG1 Is Suppressed in Plants
Authors: Xu Ying-Zhi , Santamaria Roberto de la Rosa , Virdi Kamaldeep S. , Arrieta-Montiel Maria P. , Razvi Fareha , Li Shaoqing , Ren Guodong , Yu Bin , Alexander Danny , Guo Lining , Feng Xuehui , Dweikat Ismail M. , Clemente Tom E. , Mackenzie Sally A.
Published: April 2012

Multicellular eukaryotes demonstrate nongenetic, heritable phenotypic versatility in their adaptation to environmental changes. This inclusive inheritance is composed of interacting epigenetic, maternal, and environmental factors. Yet-unidentified maternal effects can have a pronounced influence on plant phenotypic adaptation to changing environmental conditions. To explore the control of phenotypy in higher plants, we examined the effect of a single plant nuclear gene on the expression and transmission of phenotypic variability in Arabidopsis (Arabidopsis thaliana). MutS HOMOLOG1 (MSH1) is a plant-specific nuclear gene product that functions in both mitochondria and plastids to maintain genome stability. RNA interference suppression of the gene elicits strikingly similar programmed changes in plant growth pattern in six different plant species, changes subsequently heritable independent of the RNA interference transgene. The altered phenotypes reflect multiple pathways that are known to participate in adaptation, including altered phytohormone effects for dwarfed growth and reduced internode elongation, enhanced branching, reduced stomatal density, altered leaf morphology, delayed flowering, and extended juvenility, with conversion to perennial growth pattern in short days. Some of these effects are partially reversed with the application of gibberellic acid. Genetic hemicomplementation experiments show that this phenotypic plasticity derives from changes in chloroplast state. Our results suggest that suppression of MSH1, which occurs under several forms of abiotic stress, triggers a plastidial response process that involves nongenetic inheritance.
Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis
Authors: Rego Natalia , Bianchi Sergio , Moreno Pilar , Persson Helena , Kvist Anders , Pena Alvaro , Oppezzo Pablo , Naya Hugo , Rovira Carlos , Dighiero Guillermo , Pritsch Otto
Published: April 2012

As an approach to determining the aetiology of chronic lymphocytic leukaemia (CLL), we searched for a virus expressed in human CLL B‐cells by combining high‐throughput sequencing and digital subtraction. Pooled B‐cell mRNA transcriptomes from five CLL patients and five healthy donors were sequenced with 454 Life Sciences technology. Human reads were excluded by BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST‐like alignment tool) searches. Remaining reads were screened with BLAST against viral databases. Purified B‐cells from two CLL patients, with and without stimulation by phorbol‐esters, were sequenced using Illumina technology to achieve depth of sequencing. Burrows‐Wheeler Aligner mapping and BLAST searches were used for the Illumina data. Pyrosequencing resulted in about 400 000 reads per sample. No viral candidate could be found. Illumina single‐end sequencing for 115 cycles yielded an average of 26 ± 2·5 million filtered reads per sample, of which 2·2 ± 0·6 million remained unmapped to human references. BLAST searches of these reads against viral and human databases assigned nine reads to an Epstein‐Barr virus origin, in one sample following phorbol‐ester stimulation. Other reads showing a putative viral origin were dismissed after further analysis. Despite an in‐depth analysis of the CLL transcriptome reaching more than 100 million sequences, we have not found evidence for a putative viral candidate in CLL.
Responses of soil microbial respiration to thermal stress in alpine steppe on the Tibetan plateau
Authors: Chang X. , Wang S. , Luo C. , Zhang Z. , Duan J. , Zhu X. , Lin Q. , Xu B.
Published: April 2012

Extensive research has focused on the temperature sensitivity of microbial respiration in tundra and alpine meadows. However, the response of microbial respiration to thermal stress in alpine steppe soils, which have less organic matter and greater aeration, has received less attention. We investigated spatial and temporal variations in microbial respiration using an incubation experiment under different temperature (0, 15 and 30°C) and different percentages of water‐holding capacity (WHC) (50 and 100%) conditions in the alpine steppe, and using a subsequent cooling experiment determined the ‘thermal stress' of soil microorganisms in response to increased temperature in the alpine steppe ecosystem. Microbial respiration rates decreased with increasing temperature at both 50 and 100% WHC for three sampling locations. Thermal stress of soil microorganisms under increased temperatures was found in the alpine steppe because subsequent cooling led to an increase in microbial respiration rates. Soil moisture did not affect microbial respiration, but the temperature sensitivity (Q10) of microbial respiration varied with the interactive effect between soil moisture and sampling location. Our findings suggest that the response of microbial respiration to high temperature may not be always positive as bacteria may experience thermal stress in the alpine steppe. Therefore, it is necessary to include thermal stress responses in alpine steppe models, as they may represent an important negative feedback effect on microbial respiration.
Contrasting population demographics and reproductive investment of white crappie in three eutrophic reservoirs
Authors: Michaletz P. H.
Published: April 2012

Abstract  White crappie, Pomoxis annularis Rafinesque, provides important sport fisheries across North America but sometimes exhibits slow growth and fails to reach sizes acceptable to anglers. Three dissimilar white crappie populations were studied to assess whether differences in growth were associated with size and age at maturity and subsequent larval production. Similar to other species, female white crappie matured at younger ages and smaller sizes and contained larger ovaries in the population with the slowest growth; this population also had the lowest annual mortality. Larval production (number m−3) in this population was intermediate to that of the other populations. Attempts to improve growth of white crappie in the slow‐growing population will probably be hindered by these individuals’ greater reproductive investment, which reduces the amount of energy available for somatic growth.