bluuebunny/crossref_metadata_2025 huggingface dataset:
Filling the Eastern European gap in millennium-long temperature reconstructions
Authors: Büntgen Ulf , Kyncl Tomáš , Ginzler Christian , Jacks David S. , Esper Jan , Tegel Willy , Heussner Karl-Uwe , Kyncl Josef
Published: January 2013

Tree ring–based temperature reconstructions form the scientific backbone of the current global change debate. Although some European records extend into medieval times, high-resolution, long-term, regional-scale paleoclimatic evidence is missing for the eastern part of the continent. Here we compile 545 samples of living trees and historical timbers from the greater Tatra region to reconstruct interannual to centennial-long variations in Eastern European May–June temperature back to 1040 AD. Recent anthropogenic warming exceeds the range of past natural climate variability. Increased plague outbreaks and political conflicts, as well as decreased settlement activities, coincided with temperature depressions. The Black Death in the mid-14th century, the Thirty Years War in the early 17th century, and the French Invasion of Russia in the early 19th century all occurred during the coldest episodes of the last millennium. A comparison with summer temperature reconstructions from Scandinavia, the Alps, and the Pyrenees emphasizes the seasonal and spatial specificity of our results, questioning those large-scale reconstructions that simply average individual sites.
Cytokinins can act as suppressors of nitric oxide in
Arabidopsis
Authors: Liu Wei-Zhong , Kong Dong-Dong , Gu Xue-Xin , Gao Hong-Bo , Wang Jin-Zheng , Xia Min , Gao Qian , Tian Li-Li , Xu Zhang-Hong , Bao Fang , Hu Yong , Ye Neng-Sheng , Pei Zhen-Ming , He Yi-Kun
Published: January 2013

Maintaining nitric oxide (NO) homeostasis is essential for normal plant physiological processes. However, very little is known about the mechanisms of NO modulation in plants. Here, we report a unique mechanism for the catabolism of NO based on the reaction with the plant hormone cytokinin. We screened for NO-insensitive mutants in
Arabidopsis
and isolated two allelic lines,
cnu1-1
and
1–2
(
continuous NO-unstressed 1
), that were identified as the previously reported
altered meristem program 1
(
amp1
) and as having elevated levels of cytokinins. A double mutant of
cnu1-2
and
nitric oxide overexpression 1
(
nox1
) reduced the severity of the phenotypes ascribed to excess NO levels as did treating the
nox1
line with
trans
-zeatin, the predominant form of cytokinin in
Arabidopsis
. We further showed that peroxinitrite, an active NO derivative, can react with zeatin in vitro, which together with the results in vivo suggests that cytokinins suppress the action of NO most likely through direct interaction between them, leading to the reduction of endogenous NO levels. These results provide insights into NO signaling and regulation of its bioactivity in plants.
Splicing factor SF2/ASF rescues IL-2 production in T cells from systemic lupus erythematosus patients by activating IL-2 transcription
Authors: Moulton Vaishali R. , Grammatikos Alexandros P. , Fitzgerald Lisa M. , Tsokos George C.
Published: January 2013

T cells from patients with systemic lupus erythematosus (SLE) produce insufficient amounts of the vital cytokine IL-2. We previously showed that SLE T cells express decreased levels of the T-cell receptor–CD3ζ chain and forced expression of CD3ζ into SLE T cells restores IL-2 production. We recently showed that the serine arginine protein splicing factor 2/alternative splicing factor (SF2/ASF) enhances the expression of CD3ζ chain by limiting the production of an unstable splice variant. Here we demonstrate that SF2/ASF levels are decreased in patients with SLE and more so in those with active disease. More importantly, we reveal a function of SF2/ASF, independent of T-cell receptor/CD3 signaling, whereby it is recruited to the IL-2 promoter, increases transcriptional activity, and enhances IL-2 production in SLE T cells. Our results demonstrate that SF2/ASF regulates IL-2 production and that decreased SF2/ASF expression in SLE T cells contributes to deficient IL-2 production.
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
Authors: Lin Yen-Lin , Meng Yilin , Jiang Wei , Roux Benoît
Published: January 2013

Tyrosine kinases present attractive drug targets for specific types of cancers. Gleevec, a well-known therapeutic agent against chronic myelogenous leukemia, is an effective inhibitor of Abl tyrosine kinase. However, Gleevec fails to inhibit closely homologous tyrosine kinases, such as c-Src. Because many structural features of the binding site are conserved, the molecular determinants responsible for binding specificity are not immediately apparent. Some have attributed the difference in binding specificity of Gleevec to subtle variations in ligand–protein interactions (binding affinity control), whereas others have proposed that it is the conformation of the DFG motif, in which ligand binding is only accessible to Abl and not to c-Src (conformational selection control). To address this issue, the absolute binding free energy was computed using all-atom molecular dynamics simulations with explicit solvent. The results of the free energy simulations are in good agreement with experiments, thereby enabling a meaningful decomposition of the binding free energy to elucidate the factors controlling Gleevec’s binding specificity. The latter is shown to be controlled by a conformational selection mechanism and also by differences in key van der Waals interactions responsible for the stabilization of Gleevec in the binding pocket of Abl.
Reprogramming of adult rod photoreceptors prevents retinal degeneration
Authors: Montana Cynthia L. , Kolesnikov Alexander V. , Shen Susan Q. , Myers Connie A. , Kefalov Vladimir J. , Corbo Joseph C.
Published: January 2013

A prime goal of regenerative medicine is to direct cell fates in a therapeutically useful manner. Retinitis pigmentosa is one of the most common degenerative diseases of the eye and is associated with early rod photoreceptor death followed by secondary cone degeneration. We hypothesized that converting adult rods into cones, via knockdown of the rod photoreceptor determinant
Nrl
, could make the cells resistant to the effects of mutations in rod-specific genes, thereby preventing secondary cone loss. To test this idea, we engineered a tamoxifen-inducible allele of
Nrl
to acutely inactivate the gene in adult rods. This manipulation resulted in reprogramming of rods into cells with a variety of cone-like molecular, histologic, and functional properties. Moreover, reprogramming of adult rods achieved cellular and functional rescue of retinal degeneration in a mouse model of retinitis pigmentosa. These findings suggest that elimination of Nrl in adult rods may represent a unique therapy for retinal degeneration.
Local and long-range functional connectivity is reduced in concert in autism spectrum disorders
Authors: Khan Sheraz , Gramfort Alexandre , Shetty Nandita R. , Kitzbichler Manfred G. , Ganesan Santosh , Moran Joseph M. , Lee Su Mei , Gabrieli John D. E. , Tager-Flusberg Helen B. , Joseph Robert M. , Herbert Martha R. , Hämäläinen Matti S. , Kenet Tal
Published: January 2013

Long-range cortical functional connectivity is often reduced in autism spectrum disorders (ASD), but the nature of local cortical functional connectivity in ASD has remained elusive. We used magnetoencephalography to measure task-related local functional connectivity, as manifested by coupling between the phase of alpha oscillations and the amplitude of gamma oscillations, in the fusiform face area (FFA) of individuals diagnosed with ASD and typically developing individuals while they viewed neutral faces, emotional faces, and houses. We also measured task-related long-range functional connectivity between the FFA and the rest of the cortex during the same paradigm. In agreement with earlier studies, long-range functional connectivity between the FFA and three distant cortical regions was reduced in the ASD group. However, contrary to the prevailing hypothesis in the field, we found that local functional connectivity within the FFA was also reduced in individuals with ASD when viewing faces. Furthermore, the strength of long-range functional connectivity was directly correlated to the strength of local functional connectivity in both groups; thus, long-range and local connectivity were reduced proportionally in the ASD group. Finally, the magnitude of local functional connectivity correlated with ASD severity, and statistical classification using local and long-range functional connectivity data identified ASD diagnosis with 90% accuracy. These results suggest that failure to entrain neuronal assemblies fully both within and across cortical regions may be characteristic of ASD.
Cortical energy demands of signaling and nonsignaling components in brain are conserved across mammalian species and activity levels
Authors: Hyder Fahmeed , Rothman Douglas L. , Bennett Maxwell R.
Published: January 2013

The continuous need for ion gradient restoration across the cell membrane, a prerequisite for synaptic transmission and conduction, is believed to be a major factor for brain’s high oxidative demand. However, do energy requirements of signaling and nonsignaling components of cortical neurons and astrocytes vary with activity levels and across species? We derived oxidative ATP demand associated with signaling (P
s
) and nonsignaling (P
ns
) components in the cerebral cortex using species-specific physiologic and anatomic data. In rat, we calculated glucose oxidation rates from layer-specific neuronal activity measured across different states, spanning from isoelectricity to awake and sensory stimulation. We then compared these calculated glucose oxidation rates with measured glucose metabolic data for the same states as reported by 2-deoxy-glucose autoradiography. Fixed values for P
s
and P
ns
were able to predict the entire range of states in the rat. We then calculated glucose oxidation rates from human EEG data acquired under various conditions using fixed P
s
and P
ns
values derived for the rat. These calculated metabolic data in human cerebral cortex compared well with glucose metabolism measured by PET. Independent of species, linear relationship was established between neuronal activity and neuronal oxidative demand beyond isoelectricity. Cortical signaling requirements dominated energy demand in the awake state, whereas nonsignaling requirements were ∼20% of awake value. These predictions are supported by
13
C magnetic resonance spectroscopy results. We conclude that mitochondrial energy support for signaling and nonsignaling components in cerebral cortex are conserved across activity levels in mammalian species.
Borna disease virus-induced neuronal degeneration dependent on host genetic background and prevented by soluble factors
Authors: Wu Yuan-Ju , Schulz Herbert , Lin Chia-Ching , Saar Kathrin , Patone Giannino , Fischer Heike , Hübner Norbert , Heimrich Bernd , Schwemmle Martin
Published: January 2013

Infection of newborn rats with Borne disease virus (BDV) results in selective degeneration of granule cell neurons of the dentate gyrus (DG). To study cellular countermechanisms that might prevent this pathology, we screened for rat strains resistant to this BDV-induced neuronal degeneration. To this end, we infected hippocampal slice cultures of different rat strains with BDV and analyzed for the preservation of the DG. Whereas infected cultures of five rat strains, including Lewis (LEW) rats, exhibited a disrupted DG cytoarchitecture, slices of three other rat strains, including Sprague–Dawley (SD), were unaffected. However, efficiency of viral replication was comparable in susceptible and resistant cultures. Moreover, these rat strain–dependent differences in vulnerability were replicated in vivo in neonatally infected LEW and SD rats. Intriguingly, conditioned media from uninfected cultures of both LEW and SD rats could prevent BDV-induced DG damage in infected LEW hippocampal cultures, whereas infection with BDV suppressed the availability of these factors from LEW but not in SD hippocampal cultures. To gain further insights into the genetic basis for this rat strain–dependent susceptibility, we analyzed DG granule cell survival in BDV-infected cultures of hippocampal neurons derived from the F1 and F2 offspring of the crossing of SD and LEW rats. Genome-wide association analysis revealed one resistance locus on chromosome (chr) 6q16 in SD rats and, surprisingly, a locus on chr3q21-23 that was associated with susceptibility. Thus, BDV-induced neuronal degeneration is dependent on the host genetic background and is prevented by soluble protective factors in the disease-resistant SD rat strain.
CYP714B1
and
CYP714B2
encode gibberellin 13-oxidases that reduce gibberellin activity in rice
Authors: Magome Hiroshi , Nomura Takahito , Hanada Atsushi , Takeda-Kamiya Noriko , Ohnishi Toshiyuki , Shinma Yuko , Katsumata Takumi , Kawaide Hiroshi , Kamiya Yuji , Yamaguchi Shinjiro
Published: January 2013

Bioactive gibberellins (GAs) control many aspects of growth and development in plants. GA
1
has been the most frequently found bioactive GA in various tissues of flowering plants, but the enzymes responsible for GA
1
biosynthesis have not been fully elucidated due to the enzymes catalyzing the 13-hydroxylation step not being identified. Because of the lack of mutants defective in this enzyme, biological significance of GA 13-hydroxylation has been unknown. Here, we report that two cytochrome P450 genes,
CYP714B1
and
CYP714B2
, encode GA 13-oxidase in rice. Transgenic
Arabidopsis
plants that overexpress
CYP714B1
or
CYP714B2
show semidwarfism. There was a trend that the levels of 13-OH GAs including GA
1
were increased in these transgenic plants. Functional analysis using yeast or insect cells shows that recombinant CYP714B1 and CYP714B2 proteins can convert GA
12
into GA
53
(13-OH GA
12
) in vitro. Moreover, the levels of 13-OH GAs including GA
1
were decreased, whereas those of 13-H GAs including GA
4
(which is more active than GA
1
) were increased, in the rice
cyp714b1 cyp714b2
double mutant. These results indicate that CYP714B1 and CYP714B2 play a predominant role in GA 13-hydroxylation in rice. The double mutant plants appear phenotypically normal until heading, but show elongated uppermost internode at the heading stage. Moreover,
CYP714B1
and
CYP714B2
expression was up-regulated by exogenous application of bioactive GAs. Our results suggest that GA 13-oxidases play a role in fine-tuning plant growth by decreasing GA bioactivity in rice and that they also participate in GA homeostasis.
Birth, decay, and reconstruction of an ancient
TRIMCyp
gene fusion in primate genomes
Authors: Malfavon-Borja Ray , Wu Lily I. , Emerman Michael , Malik Harmit Singh
Published: January 2013

TRIM5
is a host antiviral gene with an evolutionary history of genetic conflict with retroviruses. The
TRIMCyp
gene encodes a protein fusion of
TRIM5
effector domains with the capsid-binding ability of a retrotransposed
CyclophilinA
(
CypA
), resulting in novel antiviral specificity against lentiviruses. Previous studies have identified two independent primate
TRIMCyp
fusions that evolved within the past 6 My. Here, we describe an ancient primate
TRIMCyp
gene (that we call
TRIMCypA3
), which evolved in the common ancestor of simian primates 43 Mya. Gene reconstruction shows that
CypA3
encoded an intact, likely active,
TRIMCyp
antiviral gene, which was subject to selective constraints for at least 10 My, followed by pseudogenization or loss in all extant primates. Despite its decayed status, we found
TRIMCypA3
gene fusion transcripts in several primates. We found that the reconstructed “newly born”
TrimCypA3
encoded robust and broad retroviral restriction activity but that this broad activity was lost via eight amino acid changes over the course of the next 10 My. We propose that
TRIMCypA3
arose in response to a viral pathogen encountered by ancestral primates but was subsequently pseudogenized or lost due to a lack of selective pressure. Much like imprints of ancient viruses, fossils of decayed genes, such as
TRIMCypA3
, provide unique and specific insight into paleoviral infections that plagued primates deep in their evolutionary history.
Control of transposon activity by a histone H3K4 demethylase in rice
Authors: Cui Xiekui , Jin Ping , Cui Xia , Gu Lianfeng , Lu Zhike , Xue Yongming , Wei Liya , Qi Jianfei , Song Xianwei , Luo Ming , An Gynheung , Cao Xiaofeng
Published: January 2013

Transposable elements (TEs) are ubiquitously present in plant genomes and often account for significant fractions of the nuclear DNA. For example, roughly 40% of the rice genome consists of TEs, many of which are retrotransposons, including 14% LTR- and ∼1% non-LTR retrotransposons. Despite their wide distribution and abundance, very few TEs have been found to be transpositional, indicating that TE activities may be tightly controlled by the host genome to minimize the potentially mutagenic effects associated with active transposition. Consistent with this notion, a growing body of evidence suggests that epigenetic silencing pathways such as DNA methylation, RNA interference, and H3K9me2 function collectively to repress TE activity at the transcriptional and posttranscriptional levels. It is not yet clear, however, whether the removal of histone modifications associated with active transcription is also involved in TE silencing. Here, we show that the rice protein JMJ703 is an active H3K4-specific demethylase required for TEs silencing. Impaired JMJ703 activity led to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons. Interestingly, loss of JMJ703 did not affect TEs (such as
Tos17
) previously found to be silenced by other epigenetic pathways. These results indicate that the removal of active histone modifications is involved in TE silencing and that different subsets of TEs may be regulated by distinct epigenetic pathways.
Brg1 governs distinct pathways to direct multiple aspects of mammalian neural crest cell development
Authors: Li Wei , Xiong Yiqin , Shang Ching , Twu Karen Y. , Hang Calvin T. , Yang Jin , Han Pei , Lin Chieh-Yu , Lin Chien-Jung , Tsai Feng-Chiao , Stankunas Kryn , Meyer Tobias , Bernstein Daniel , Pan Minggui , Chang Ching-Pin
Published: January 2013

Development of the cerebral vessels, pharyngeal arch arteries (PAAs). and cardiac outflow tract (OFT) requires multipotent neural crest cells (NCCs) that migrate from the neural tube to target tissue destinations. Little is known about how mammalian NCC development is orchestrated by gene programming at the chromatin level, however. Here we show that Brahma-related gene 1 (Brg1), an ATPase subunit of the Brg1/Brahma-associated factor (BAF) chromatin-remodeling complex, is required in NCCs to direct cardiovascular development. Mouse embryos lackingBrg1in NCCs display immature cerebral vessels, aberrant PAA patterning, and shortened OFT. Brg1 suppresses an apoptosis factor,Apoptosis signal-regulating kinase 1 (Ask1), and a cell cycle inhibitor,p21cip1, to inhibit apoptosis and promote proliferation of NCCs, thereby maintaining a multipotent cell reservoir at the neural crest. Brg1 also supportsMyosin heavy chain 11 (Myh11)expression to allow NCCs to develop into mature vascular smooth muscle cells of cerebral vessels. Within NCCs, Brg1 partners with chromatin remodeler Chromodomain-helicase-DNA-binding protein 7 (Chd7) on thePlexinA2promoter to activatePlexinA2,which encodes a receptor for semaphorin to guide NCCs into the OFT. Our findings reveal an important role for Brg1 and its downstream pathways in the survival, differentiation, and migration of the multipotent NCCs critical for mammalian cardiovascular development.
Structural basis for cytosolic double-stranded RNA surveillance by human oligoadenylate synthetase 1
Authors: Donovan Jesse , Dufner Matthew , Korennykh Alexei
Published: January 2013

The human sensor of double-stranded RNA (dsRNA) oligoadenylate synthetase 1 (hOAS1) polymerizes ATP into 2′,5′-linked iso-RNA (2-5A) involved in innate immunity, cell cycle, and differentiation. We report the crystal structure of hOAS1 in complex with dsRNA and 2′-deoxy ATP at 2.7 Å resolution, which reveals the mechanism of cytoplasmic dsRNA recognition and activation of oligoadenylate synthetases. Human OAS1 recognizes dsRNA using a previously uncharacterized protein/RNA interface that forms via a conformational change induced by binding of dsRNA. The protein/RNA interface involves two minor grooves and has no sequence-specific contacts, with the exception of a single hydrogen bond between the -NH
2
group of nucleobase G17 and the carbonyl oxygen of serine 56. Using a biochemical readout, we show that hOAS1 undergoes more than 20,000-fold activation upon dsRNA binding and that canonical or GU-wobble substitutions produce dsRNA mutants that retain either full or partial activity, in agreement with the crystal structure. Ultimately, the binding of dsRNA promotes an elaborate conformational rearrangement in the N-terminal lobe of hOAS1, which brings residues D75, D77, and D148 into proximity and creates coordination geometry for binding of two catalytic Mg
2+
ions and ATP. The assembly of this critical active-site structure provides the gate that couples binding of dsRNA to the production and downstream functions of 2-5A.
Propulsion of microorganisms by a helical flagellum
Authors: Rodenborn Bruce , Chen Chih-Hung , Swinney Harry L. , Liu Bin , Zhang H. P.
Published: January 2013

The swimming of a bacterium or a biomimetic nanobot driven by a rotating helical flagellum is often interpreted using the resistive force theory developed by Gray and Hancock and by Lighthill, but this theory has not been tested for a range of physically relevant parameters. We test resistive force theory in experiments on macroscopic swimmers in a fluid that is highly viscous so the Reynolds number is small compared to unity, just as for swimming microorganisms. The measurements are made for the range of helical wavelengths
λ
, radii
R
, and lengths
L
relevant to bacterial flagella. The experiments determine thrust, torque, and drag, thus providing a complete description of swimming driven by a rotating helix at low Reynolds number. Complementary numerical simulations are conducted using the resistive force theories, the slender body theories of Lighthill and Johnson, and the regularized Stokeslet method. The experimental results differ qualitatively and quantitatively from the predictions of resistive force theory. The difference is especially large for

and/or

, parameter ranges common for bacteria. In contrast, the predictions of Stokeslet and slender body analyses agree with the laboratory measurements within the experimental uncertainty (a few percent) for all
λ
,
R
, and
L
. We present code implementing the slender body, regularized Stokeslet, and resistive force theories; thus readers can readily compute force, torque, and drag for any bacterium or nanobot driven by a rotating helical flagellum.
Calling patterns in human communication dynamics
Authors: Jiang Zhi-Qiang , Xie Wen-Jie , Li Ming-Xia , Podobnik Boris , Zhou Wei-Xing , Stanley H. Eugene
Published: January 2013

Modern technologies not only provide a variety of communication modes (e.g., texting, cell phone conversation, and online instant messaging), but also detailed electronic traces of these communications between individuals. These electronic traces indicate that the interactions occur in temporal bursts. Here, we study intercall duration of communications of the 100,000 most active cell phone users of a Chinese mobile phone operator. We confirm that the intercall durations follow a power-law distribution with an exponential cutoff at the population level but find differences when focusing on individual users. We apply statistical tests at the individual level and find that the intercall durations follow a power-law distribution for only 3,460 individuals (3.46%). The intercall durations for the majority (73.34%) follow a Weibull distribution. We quantify individual users using three measures: out-degree, percentage of outgoing calls, and communication diversity. We find that the cell phone users with a power-law duration distribution fall into three anomalous clusters: robot-based callers, telecom fraud, and telephone sales. This information is of interest to both academics and practitioners, mobile telecom operators in particular. In contrast, the individual users with a Weibull duration distribution form the fourth cluster of ordinary cell phone users. We also discover more information about the calling patterns of these four clusters (e.g., the probability that a user will call the
c

r

-th most contact and the probability distribution of burst sizes). Our findings may enable a more detailed analysis of the huge body of data contained in the logs of massive users.
Inhibition of triple-negative breast cancer models by combinations of antibodies to EGFR
Authors: Ferraro Daniela A. , Gaborit Nadège , Maron Ruth , Cohen-Dvashi Hadas , Porat Ziv , Pareja Fresia , Lavi Sara , Lindzen Moshit , Ben-Chetrit Nir , Sela Michael , Yarden Yosef
Published: January 2013

Breast tumors lacking expression of human epidermal growth factor receptor 2 (HER2) and the estrogen and the progesterone receptors (triple negative; TNBC) are more aggressive than other disease subtypes, and no molecular targeted agents are currently available for their treatment. Because TNBC commonly displays EGF receptor (EGFR) expression, and combinations of monoclonal antibodies to EGFR effectively inhibit other tumor models, we addressed the relevance of this strategy to treatment of TNBC. Unlike a combination of the clinically approved monoclonal antibodies, cetuximab and panitumumab, which displaced each other and displayed no cooperative effects, several other combinations resulted in enhanced inhibition of TNBC’s cell growth both in vitro and in animals. The ability of certain antibody mixtures to remove EGFR from the cell surface and to promote its intracellular degradation correlated with the inhibitory potential. However, unlike EGF-induced sorting of EGFR to lysosomal degradation, the antibody-induced pathway displayed independence from the intrinsic kinase activity and dimer formation ability of EGFR, and it largely avoided the recycling route. In conclusion, although TNBC clinical trials testing EGFR inhibitors reported lack of benefit, our results offer an alternative strategy that combines noncompetitive antibodies to achieve robust degradation of EGFR and tumor inhibition.
Caulobacter
chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement
Authors: Hong Sun-Hae , Toro Esteban , Mortensen Kim I. , de la Rosa Mario A. Díaz , Doniach Sebastian , Shapiro Lucy , Spakowitz Andrew J. , McAdams Harley H.
Published: January 2013

We measured the distance between fluorescent-labeled DNA loci of various interloci contour lengths in
Caulobacter crescentus
swarmer cells to determine the in vivo configuration of the chromosome. For DNA segments less than about 300 kb, the mean interloci distances, 〈
r
〉, scale as
n
0.22
, where
n
is the contour length, and cell-to-cell distribution of the interloci distance
r
is a universal function of
r/n
0.22
with broad cell-to-cell variability. For DNA segments greater than about 300 kb, the mean interloci distances scale as
n
, in agreement with previous observations. The 0.22 value of the scaling exponent for short DNA segments is consistent with theoretical predictions for a branched DNA polymer structure. Predictions from Brownian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confinement are also consistent with a branched DNA structure, and simulated interloci distance distributions predict that confinement leads to “freezing” of the supercoiled configuration. Lateral positions of labeled loci at comparable positions along the length of the cell are strongly correlated when the longitudinal locus positions differ by <0.16 μm. We conclude that the chromosome structure is supercoiled locally and elongated at large length scales and that substantial cell-to-cell variability in the interloci distances indicates that in vivo crowding prevents the chromosome from reaching an equilibrium arrangement. We suggest that the force causing rapid transport of loci remote from the
parS
centromere to the distal cell pole may arise from the release at the polar region of potential energy within the supercoiled DNA.
Properties of hydrophobic free energy found by gas–liquid transfer
Authors: Baldwin Robert L.
Published: January 2013

The hydrophobic free energy in current use is based on transfer of alkane solutes from liquid alkanes to water, and it has been argued recently that these values are incorrect and should be based instead on gas–liquid transfer data. Hydrophobic free energy is measured here by gas–liquid transfer of hydrocarbon gases from vapor to water. The new definition reduces more than twofold the values of the apparent hydrophobic free energy. Nevertheless, the newly defined hydrophobic free energy is still the dominant factor that drives protein folding as judged by ΔCp, the change in heat capacity, found from the free energy change for heat-induced protein unfolding. The ΔCp for protein unfolding agrees with ΔCp values for solvating hydrocarbon gases and disagrees with ΔCp for breaking peptide hydrogen bonds, which has the opposite sign. The ΔCp values for the enthalpy of liquid–liquid and gas–liquid transfer are similar. The plot of free energy against the apparent solvent-exposed surface area is given for linear alkanes, but only for a single conformation, the extended conformation, of these flexible-chain molecules. The ability of the gas–liquid hydrophobic factor to predict protein stability is tested and reasonable agreement is found, using published data for the dependences on temperature of the unfolding enthalpy of ribonuclease T1 and the solvation enthalpies of the nonpolar and polar groups.
Minimization of thermodynamic costs in cancer cell invasion
Authors: Liu Liyu , Duclos Guillaume , Sun Bo , Lee Jeongseog , Wu Amy , Kam Yoonseok , Sontag Eduardo D. , Stone Howard A. , Sturm James C. , Gatenby Robert A. , Austin Robert H.
Published: January 2013

Metastasis, the truly lethal aspect of cancer, occurs when metastatic cancer cells in a tumor break through the basement membrane and penetrate the extracellular matrix. We show that MDA-MB-231 metastatic breast cancer cells cooperatively invade a 3D collagen matrix while following a glucose gradient. The invasion front of the cells is a dynamic one, with different cells assuming the lead on a time scale of 70 h. The front cell leadership is dynamic presumably because of metabolic costs associated with a long-range strain field that precedes the invading cell front, which we have imaged using confocal imaging and marker beads imbedded in the collagen matrix. We suggest this could be a quantitative assay for an invasive phenotype tracking a glucose gradient and show that the invading cells act in a cooperative manner by exchanging leaders in the invading front.
STOP gene
Phactr4
is a tumor suppressor
Authors: Solimini Nicole L. , Liang Anthony C. , Xu Chunxiao , Pavlova Natalya N. , Xu Qikai , Davoli Teresa , Li Mamie Z. , Wong Kwok-Kin , Elledge Stephen J.
Published: January 2013

Significance

Cell proliferation control is central to tumor suppression. We previously identified hundreds of suppressors of tumorigenesis and/or proliferation (STOP) genes that restrain normal cell proliferation. Here we show that one such STOP gene, phosphatase and actin regulator 4 (
PHACTR4
), acts to prevent tumorigenesis. Phactr4 suppresses proliferation and transformation in vitro and tumorigenesis in vivo.
PHACTR4
is significantly mutated or downregulated in several cancers, and reintroduction of Phactr4 limits proliferation and tumor growth in cells from these cancers. Thus, our studies provide strong evidence that
PHACTR4
is a tumor suppressor.
∆FosB differentially modulates nucleus accumbens direct and indirect pathway function
Authors: Grueter Brad A. , Robison Alfred J. , Neve Rachael L. , Nestler Eric J. , Malenka Robert C.
Published: January 2013

Synaptic modifications in nucleus accumbens (NAc) medium spiny neurons (MSNs) play a key role in adaptive and pathological reward-dependent learning, including maladaptive responses involved in drug addiction. NAc MSNs participate in two parallel circuits, direct and indirect pathways that subserve distinct behavioral functions. Modification of NAc MSN synapses may occur in part via changes in the transcriptional potential of certain genes in a cell type–specific manner. The transcription factor ∆FosB is one of the key proteins implicated in the gene expression changes in NAc caused by drugs of abuse, yet its effects on synaptic function in NAc MSNs are unknown. Here, we demonstrate that overexpression of ∆FosB decreased excitatory synaptic strength and likely increased silent synapses onto D1 dopamine receptor–expressing direct pathway MSNs in both the NAc shell and core. In contrast, ∆FosB likely decreased silent synapses onto NAc shell, but not core, D2 dopamine receptor–expressing indirect pathway MSNs. Analysis of NAc MSN dendritic spine morphology revealed that ∆FosB increased the density of immature spines in D1 direct but not D2 indirect pathway MSNs. To determine the behavioral consequences of cell type-specific actions of ∆FosB, we selectively overexpressed ∆FosB in D1 direct or D2 indirect MSNs in NAc in vivo and found that direct (but not indirect) pathway MSN expression enhances behavioral responses to cocaine. These results reveal that ∆FosB in NAc differentially modulates synaptic properties and reward-related behaviors in a cell type- and subregion-specific fashion.
Snapshots of a protein folding intermediate
Authors: Yamada Seiji , Bouley Ford Nicole D. , Keller Gretchen E. , Ford William C. , Gray Harry B. , Winkler Jay R.
Published: January 2013

We have investigated the folding dynamics of
Thermus thermophilus
cytochrome
c
552
by time-resolved fluorescence energy transfer between the heme and each of seven site-specific fluorescent probes. We have found both an equilibrium unfolding intermediate and a distinct refolding intermediate from kinetics studies. Depending on the protein region monitored, we observed either two-state or three-state denaturation transitions. The unfolding intermediate associated with three-state folding exhibited native contacts in β-sheet and C-terminal helix regions. We probed the formation of a refolding intermediate by time-resolved fluorescence energy transfer between residue 110 and the heme using a continuous flow mixer. The intermediate ensemble, a heterogeneous mixture of compact and extended polypeptides, forms in a millisecond, substantially slower than the ∼100-μs formation of a burst-phase intermediate in cytochrome
c
. The surprising finding is that, unlike for cytochrome
c
, there is an observable folding intermediate, but no microsecond burst phase in the folding kinetics of the structurally related thermostable protein.
Aire’s plant homeodomain(PHD)-2 is critical for induction of immunological tolerance
Authors: Yang Siyoung , Bansal Kushagra , Lopes Jared , Benoist Christophe , Mathis Diane
Published: January 2013

Aire impacts immunological tolerance by regulating the expression of a large set of genes in thymic medullary epithelial cells, thereby controlling the repertoire of self-antigens encountered by differentiating thymocytes. Both humans and mice lacking Aire develop multiorgan autoimmunity. Currently, there are few molecular details on how Aire performs this crucial function. The more amino-terminal of its two plant homeodomains (PHDs), PHD1, helps Aire target poorly transcribed loci by “reading” the methylation status of a particular lysine residue of histone-3, a process that does not depend on the more carboxyl-terminal PHD-2. This study addresses the role of PHD2 in Aire function by comparing the behavior of wild-type and PHD2-deleted Aire in both transfected cells and transgenic mice. PHD2 was required for Aire to interact with sets of protein partners involved in chromatin structure/binding or transcription but not with those implicated in pre-mRNA processing; it also was not required for Aire’s nuclear translocation or regional distribution. PHD2 strongly influenced the ability of Aire to regulate the medullary epithelial cell transcriptome and so was crucial for effective central tolerance induction. Thus, Aire’s two PHDs seem to play distinct roles in the scenario by which it assures immunological tolerance.
Comprehensive developmental profiles of gene activity in regions and subregions of the
Arabidopsis
seed
Authors: Belmonte Mark F. , Kirkbride Ryan C. , Stone Sandra L. , Pelletier Julie M. , Bui Anhthu Q. , Yeung Edward C. , Hashimoto Meryl , Fei Jiong , Harada Corey M. , Munoz Matthew D. , Le Brandon H. , Drews Gary N. , Brady Siobhan M. , Goldberg Robert B. , Harada John J.
Published: January 2013

Significance

Seeds are complex structures that are comprised of the embryo, endosperm, and seed coat. Despite their importance for food, fiber, and fuel, the cellular processes that characterize different regions of the seed are not known. We profiled gene activity genome-wide in every organ, tissue, and cell type of
Arabidopsis
seeds from fertilization through maturity. The resulting mRNA datasets provide unique insights into the cellular processes that occur in understudied seed regions, revealing unexpected overlaps in the functional identities of seed regions and enabling predictions of gene regulatory networks. This dataset is an essential resource for studies of seed biology.
Centrarchid Assemblages in Floodplain Lakes of the Mississippi Alluvial Valley
Authors: Alfermann T. J. , Miranda L. E.
Published: January 2013

The family Centrarchidae is a principal and visible component of the ichthyofauna in most warmwater ecosystems in North America, and many of its species provide key recreational fisheries. We examined the significance of various local environmental factors to 13 centrarchid species in 53 floodplain lakes (remnant channels) of the Mississippi alluvial valley to identify major environmental gradients influential in structuring centrarchid assemblages. With few exceptions, changes in forest representation in the land cover, both in the lakeshore and the catchment, had the strongest associations with centrarchid assemblages. Other influential factors included depth, water clarity, and primary productivity. Connectivity to adjacent streams was weakly correlated with centrarchid assemblage structure and correlated only with a small number of species. Lake area did not appear to affect centrarchid assemblages. Recognition that land cover has the strongest correlation with centrarchid assemblage composition suggests a landscape basis for developing management plans. However, conservation and restoration of native centrarchid assemblages in these unique ecosystems will require both watershed management to curtail inputs and in‐lake management to reverse years of neglect.
Length Frequency Age Estimations of American Eel Recruiting to the Upper St. Lawrence River and Lake Ontario
Authors: Zhu Xinhua , Zhao Yingming , Mathers Alastair , Corkum Lynda D.
Published: January 2013

We applied length frequency analysis (LFA) with multiple model inference to estimate the age structure of American EelAnguilla rostratarecruiting to the upper St. Lawrence River and Lake Ontario system between 1975 and 2008. The LFA results were used to derive a composite relative abundance index for 48 cohorts from 1967 to 2004. The size of eel recruits was influenced by both year and season and consistently increased from July to October. Age composition and mean length at age varied greatly from year to year. On average, eels spent about 6 years in the lower St. Lawrence River before they recruited to Lake Ontario. A nonsymmetric distribution function, such as lognormal or Gamma function, was selected to describe length‐at‐age observations of American Eels. Recruiting cohorts appeared to be relatively strong from the late 1960s to the late 1970s but subsequently declined exponentially. Some recovery signs were found for the last 8 years, but cohorts have been weak since 1988. A validation study showed that the LFA with multiple model inference approach can successfully estimate the age structure from length frequency observations. Our results provide scientific support for underlying eel habitat restoration and protection efforts in Lake Ontario and the upper St Lawrence River.
Entrepreneurship as a leap of faith
Authors: Judge William Q. , Douglas Thomas J.
Published: January 2013

Entrepreneurial start-ups require a “leap of faith”. Since a person’s faith represents a belief in something for which there is limited information and considerable uncertainty, this suggests that the entrepreneur’s faith orientation may influence the start-up
process for some entrepreneurs. Due to the paucity of research in this area and the need to better understand the start-up process, this study utilized an inductive, longitudinal research design. Specifically, we studied the new venture creation process for four entrepreneurs operating throughout
the USA over a five-year period from 2005 to 2009. As a result of this study, new theoretical insights are generated on entrepreneurial motivations, creativity, expectations, and emotions for those entrepreneurs who seek to integrate their faith journey with a new entrepreneurial start-up.
Spiritual identity, stakeholder attributes, and family business workplace spirituality stakeholder salience
Authors: Mitchell Ronald K. , Robinson Robert E. , Marin Alejandra , Lee Jae Hwan , Randolph Angela F.
Published: January 2013

In this paper, we argue that the spiritual identity of members of a family business can positively or negatively impact the salience of stakeholders to the complex coalition of decision-makers that comprises managers in that business. Utilizing stakeholder salience theory and role theory,
we examine the complex theoretical relationships among spiritual identity, stakeholder attributes, and family business stakeholder salience. This examination reveals the multidimensionality of workplace spirituality and the need for finer-grained distinctions in stakeholder attributes, to
better represent the complexities inherent in a family business context. This article develops four propositions, through which we offer the following contributions to the literature on family business workplace spirituality: (1) new analysis frameworks for future use, (2) prototypical descriptions
of stakeholder types and representative vignettes for making finer-grained distinctions, (3) multidimensional implications for exploring the somewhat unexpected or under-considered topics in the workplace spirituality literature, and (4) proposals for family-business-specific effects for workplace
spirituality on outcomes that arise from inherent family ties in businesses.
The intellectual frameworks and theoretical limits of Arab feminist thought
Authors: Al-Ghanim Kaltham
Published: January 2013

This is a critical assessment of the intellectual and theoretical underpinnings of Feminism in the Arab world across the different phases in its evolution. The paper notes what has been achieved in respect of some specific issues but takes the view that overall the movement has failed to transform the views, consciousness and situation of most Arab women. Attempts to incorporate and/or redefine women’s aspirations and roles in Islamic terms are seen as having taken over from earlier feminist voices. Where these voices do remain they are confined to a narrow intellectual elite and have failed to galvanize or inform women across the socio-economic spectrum. The article concludes that the contemporary feminist movement is repeating the same errors as in the past by adopting intellectual perspectives that do not suit the intellectual, ideological and value foundations of Arab culture. There is a need, therefore, to revise the intellectual foundations of the movement and make a rapprochement between this current and the reality of Arab societies.
Perlecan regulates bidirectional Wnt signaling at the Drosophila neuromuscular junction
Authors: Kamimura Keisuke , Ueno Kohei , Nakagawa Jun , Hamada Rie , Saitoe Minoru , Maeda Nobuaki
Published: January 2013

Heparan sulfate proteoglycans (HSPGs) play pivotal roles in the regulation of Wnt signaling activity in several tissues. At the Drosophila melanogaster neuromuscular junction (NMJ), Wnt/Wingless (Wg) regulates the formation of both pre- and postsynaptic structures; however, the mechanism balancing such bidirectional signaling remains elusive. In this paper, we demonstrate that mutations in the gene of a secreted HSPG, perlecan/trol, resulted in diverse postsynaptic defects and overproduction of synaptic boutons at NMJ. The postsynaptic defects, such as reduction in subsynaptic reticulum (SSR), were rescued by the postsynaptic activation of the Frizzled nuclear import Wg pathway. In contrast, overproduction of synaptic boutons was suppressed by the presynaptic down-regulation of the canonical Wg pathway. We also show that Trol was localized in the SSR and promoted postsynaptic accumulation of extracellular Wg proteins. These results suggest that Trol bidirectionally regulates both pre- and postsynaptic activities of Wg by precisely distributing Wg at the NMJ.
FBH1 promotes DNA double-strand breakage and apoptosis in response to DNA replication stress
Authors: Jeong Yeon-Tae , Rossi Mario , Cermak Lukas , Saraf Anita , Florens Laurence , Washburn Michael P. , Sung Patrick , Schildkraut Carl L. , Pagano Michele
Published: January 2013

Proper resolution of stalled replication forks is essential for genome stability. Purification of FBH1, a UvrD DNA helicase, identified a physical interaction with replication protein A (RPA), the major cellular single-stranded DNA (ssDNA)–binding protein complex. Compared with control cells, FBH1-depleted cells responded to replication stress with considerably fewer double-strand breaks (DSBs), a dramatic reduction in the activation of ATM and DNA-PK and phosphorylation of RPA2 and p53, and a significantly increased rate of survival. A minor decrease in ssDNA levels was also observed. All these phenotypes were rescued by wild-type FBH1, but not a FBH1 mutant lacking helicase activity. FBH1 depletion had no effect on other forms of genotoxic stress in which DSBs form by means that do not require ssDNA intermediates. In response to catastrophic genotoxic stress, apoptosis prevents the persistence and propagation of DNA lesions. Our findings show that FBH1 helicase activity is required for the efficient induction of DSBs and apoptosis specifically in response to DNA replication stress.
PINK1 drives Parkin self-association and HECT-like E3 activity upstream of mitochondrial binding
Authors: Lazarou Michael , Narendra Derek P. , Jin Seok Min , Tekle Ephrem , Banerjee Soojay , Youle Richard J.
Published: January 2013

Genetic studies indicate that the mitochondrial kinase PINK1 and the RING-between-RING E3 ubiquitin ligase Parkin function in the same pathway. In concurrence, mechanistic studies show that PINK1 can recruit Parkin from the cytosol to the mitochondria, increase the ubiquitination activity of Parkin, and induce Parkin-mediated mitophagy. Here, we used a cell-free assay to recapitulate PINK1-dependent activation of Parkin ubiquitination of a validated mitochondrial substrate, mitofusin 1. We show that PINK1 activated the formation of a Parkin–ubiquitin thioester intermediate, a hallmark of HECT E3 ligases, both in vitro and in vivo. Parkin HECT-like ubiquitin ligase activity was essential for PINK1-mediated Parkin translocation to mitochondria and mitophagy. Using an inactive Parkin mutant, we found that PINK1 stimulated Parkin self-association and complex formation upstream of mitochondrial translocation. Self-association occurred independent of ubiquitination activity through the RING-between-RING domain, providing mechanistic insight into how PINK1 activates Parkin.