bluuebunny/crossref_metadata_2025 huggingface dataset:
Recognition memory signals in the macaque hippocampus
Authors: Jutras Michael J. , Buffalo Elizabeth A.
Published: December 2009

The hippocampus plays a critical role in recognition memory in both monkeys and humans. However, neurophysiological studies have rarely reported recognition memory signals among hippocampal neurons. The majority of these previous studies used variants of the delayed match-to-sample task; however, studies of the effects of hippocampal damage in monkey and humans have shown that another task of recognition memory, the visual paired-comparison, or visual preferential looking task (VPLT), is more sensitive to hippocampal damage than the delayed matching tasks. Accordingly, to examine possible recognition memory signals in the hippocampus, we recorded the activity of 131 hippocampal neurons in two monkeys performing the VPLT. Eighty-eight neurons (67%) responded significantly to stimulus presentation relative to the baseline prestimulus period. A substantial proportion of these visually responsive neurons (36%) showed significant firing-rate modulations that reflected whether stimuli were novel or familiar. Additionally, these firing-rate modulations were correlated with recognition memory performance on the VPLT such that larger modulations by stimulus novelty were associated with better performance. Together, these results provide evidence for a neural signal in the hippocampus that may support recognition memory performance.
Mutant p53 drives metastasis and overcomes growth arrest/senescence in pancreatic cancer
Authors: Morton Jennifer P. , Timpson Paul , Karim Saadia A. , Ridgway Rachel A. , Athineos Dimitris , Doyle Brendan , Jamieson Nigel B. , Oien Karin A. , Lowy Andrew M. , Brunton Valerie G. , Frame Margaret C. , Evans T. R. Jeffry , Sansom Owen J.
Published: December 2009

TP53
mutation occurs in 50–75% of human pancreatic ductal adenocarcinomas (PDAC) following an initiating activating mutation in the
KRAS
gene. These p53 mutations frequently result in expression of a stable protein, p53
R175H
, rather than complete loss of protein expression. In this study we elucidate the functions of mutant p53 (

Trp53
R172H

), compared to knockout p53 (

Trp53
fl

), in a mouse model of PDAC. First we find that although Kras
G12D
is one of the major oncogenic drivers of PDAC, most Kras
G12D
-expressing pancreatic cells are selectively lost from the tissue, and those that remain form premalignant lesions. Loss, or mutation, of
Trp53
allows retention of the Kras
G12D
-expressing cells and drives rapid progression of these premalignant lesions to PDAC. This progression is consistent with failed growth arrest and/or senescence of premalignant lesions, since a mutant of p53,

p53
R172P

, which can still induce p21 and cell cycle arrest, is resistant to PDAC formation. Second, we find that despite similar kinetics of primary tumor formation, mutant p53
R172H
, as compared with genetic loss of p53, specifically promotes metastasis. Moreover, only mutant p53
R172H
-expressing tumor cells exhibit invasive activity in an in vitro assay. Importantly, in human PDAC, p53 accumulation significantly correlates with lymph node metastasis. In summary, by using ‘knock-in’ mutations of
Trp53
we have identified two critical acquired functions of a stably expressed mutant form of p53 that drive PDAC; first, an escape from Kras
G12D
-induced senescence/growth arrest and second, the promotion of metastasis.
General principles of attraction and competitive attraction as revealed by large-cage studies of moths responding to sex pheromone
Authors: Miller J. R. , McGhee P. S. , Siegert P. Y. , Adams C. G. , Huang J. , Grieshop M. J. , Gut L. J.
Published: December 2009

Knowledge of how insects are actually affected by sex pheromones deployed throughout a crop so as to disrupt mating has lacked a mechanistic framework sufficient for guiding optimization of this environmentally friendly pest-control tactic. Major hypotheses are competitive attraction, desensitization, and camouflage. Working with codling moths,
Cydia pomonella
, in field cages millions of times larger than laboratory test tubes and at substrate concentrations trillions of times less than those typical for enzymes, we nevertheless demonstrate that mating disruption sufficiently parallels enzyme (ligand) –substrate interactions so as to justify adoption of conceptual and analytical tools of biochemical kinetics. By doing so, we prove that commercial dispensers of codling moth pheromone first competitively attract and then deactivate males probably for the remainder of a night. No evidence was found for camouflage. We generated and now validate simple algebraic equations for attraction and competitive attraction that will guide optimization and broaden implementation of behavioral manipulations of pests. This analysis system also offers a unique approach to quantifying animal foraging behaviors and could find applications across the natural and social sciences.
Homozygous frameshift mutation in
TMCO1
causes a syndrome with craniofacial dysmorphism, skeletal anomalies, and mental retardation
Authors: Xin Baozhong , Puffenberger Erik G. , Turben Susan , Tan Haiyan , Zhou Aimin , Wang Heng
Published: December 2009

We identified an autosomal recessive condition in 11 individuals in the Old Order Amish of northeastern Ohio. The syndrome was characterized by distinctive craniofacial dysmorphism, skeletal anomalies, and mental retardation. The typical craniofacial dysmorphism included brachycephaly, highly arched bushy eyebrows, synophrys, long eyelashes, low-set ears, microdontism of primary teeth, and generalized gingival hyperplasia, whereas Sprengel deformity of scapula, fusion of spine, rib abnormities, pectus excavatum, and pes planus represented skeletal anomalies. The genome-wide homozygosity mapping using six affected individuals localized the disease gene to a 3.3-Mb region on chromosome 1q23.3-q24.1. Candidate gene sequencing identified a homozygous frameshift mutation, c.139_140delAG, in the transmembrane and coiled-coil domains 1 (
TMCO1)
gene, as the pathogenic change in all affected members of the extended pedigree. This mutation is predicted to result in a severely truncated protein (p.Ser47Ter) of only one-fourth the original length. The
TMCO1
gene product is a member of DUF841 superfamily of several eukaryotic proteins with unknown function. The gene has highly conserved amino acid sequence and is universally expressed in all human tissues examined. The high degree of conservation and the ubiquitous expression pattern in human adult and fetal tissues suggest a critical role for
TMCO1
. This report shows a
TMCO1
sequence variant being associated with a genetic disorder in human. We propose “TMCO1 defect syndrome” as the name of this condition.
A receptor-like cytoplasmic kinase, BIK1, associates with a flagellin receptor complex to initiate plant innate immunity
Authors: Lu Dongping , Wu Shujing , Gao Xiquan , Zhang Yulan , Shan Libo , He Ping
Published: December 2009

Plants and animals rely on innate immunity to prevent infections by detection of microbe-associated molecular patterns (MAMPs) through pattern-recognition receptors (PRRs). The plant PRR FLS2, a leucine-rich repeat-receptor kinase, recognizes bacterial flagellin and initiates immune signaling by association with another leucine-rich repeat-receptor-like kinase, BAK1. It remains unknown how the FLS2/BAK1 receptor complex activates intracellular signaling cascades. Here we identified the receptor-like cytoplasmic kinase BIK1 that is rapidly phosphorylated upon flagellin perception, depending on both FLS2 and BAK1. BIK1 associates with FLS2 and BAK1 in vivo and in vitro. BIK1 is phosphorylated by BAK1, and BIK1 also directly phosphorylates BAK1 and FLS2 in vitro. The flagellin phosphorylation site Thr
237
of BIK1 is required for its phosphorylation on BAK1 and FLS2, suggesting that BIK1 is likely first phosphorylated upon flagellin perception and subsequently transphosphorylates FLS2/BAK1 to propagate flagellin signaling. Importantly,
bik1
mutants are compromised in diverse flagellin-mediated responses and immunity to the nonpathogenic bacterial infection. Thus, BIK1 is an essential component in MAMP signal transduction, which links the MAMP receptor complex to downstream intracellular signaling.
Navigating molecular worms inside chemical labyrinths
Authors: Haranczyk M. , Sethian J. A.
Published: December 2009

Predicting whether a molecule can traverse chemical labyrinths of channels, tunnels, and buried cavities usually requires performing computationally intensive molecular dynamics simulations. Often one wants to screen molecules to identify ones that can pass through a given chemical labyrinth or screen chemical labyrinths to identify those that allow a given molecule to pass. Because it is impractical to test each molecule/labyrinth pair using computationally expensive methods, faster, approximate methods are used to prune possibilities, “triaging” the ability of a proposed molecule to pass through the given chemical labyrinth. Most pruning methods estimate chemical accessibility solely on geometry, treating atoms or groups of atoms as hard spheres with appropriate radii. Here, we explore geometric configurations for a moving “molecular worm,” which replaces spherical probes and is assembled from solid blocks connected by flexible links. The key is to extend the fast marching method, which is an ordered upwind one-pass Dijkstra-like method to compute optimal paths by efficiently solving an associated Eikonal equation for the cost function. First, we build a suitable cost function associated with each possible configuration, and second, we construct an algorithm that works in ensuing high-dimensional configuration space: at least seven dimensions are required to account for translational, rotational, and internal degrees of freedom. We demonstrate the algorithm to study shortest paths, compute accessible volume, and derive information on topology of the accessible part of a chemical labyrinth. As a model example, we consider an alkane molecule in a porous material, which is relevant to designing catalysts for oil processing.
Probiotics promote gut health through stimulation of epithelial innate immunity
Authors: Pagnini Cristiano , Saeed Rubina , Bamias Giorgos , Arseneau Kristen O. , Pizarro Theresa T. , Cominelli Fabio
Published: December 2009

Probiotic formulations are widely available and have a variety of proposed beneficial effects, including promotion of gut health. The mechanisms of action of probiotic bacteria in the intestine are still unclear but are generally attributed to an antiinflammatory effect. Here, we demonstrate that the multiple probiotic formulation VSL#3 prevents the onset of intestinal inflammation by local stimulation of epithelial innate immune responses (i.e., increased production of epithelial-derived TNF-α and restoration of epithelial barrier function in vivo). We also demonstrate that probiotic bacteria stimulate epithelial production of TNF-α and activate NF-κB in vitro. Our results support the hypothesis that probiotics promote gut health through stimulation, rather than suppression, of the innate immune system. Furthermore, our findings provide the perspective that defects in innate immunity may play a critical role in the pathogenesis and progression of intestinal disorders, such as inflammatory bowel disease.
Ebolavirus
VP35 uses a bimodal strategy to bind dsRNA for innate immune suppression
Authors: Kimberlin Christopher R. , Bornholdt Zachary A. , Li Sheng , Woods Virgil L. , MacRae Ian J. , Saphire Erica Ollmann
Published: December 2009

Ebolavirus
causes a severe hemorrhagic fever and is divided into five distinct species, of which
Reston ebolavirus
is uniquely nonpathogenic to humans. Disease caused by
ebolavirus
is marked by early immunosuppression of innate immune signaling events, involving silencing and sequestration of double-stranded RNA (dsRNA) by the viral protein VP35. Here we present unbound and dsRNA-bound crystal structures of the dsRNA-binding domain of
Reston ebolavirus
VP35. The structures show that VP35 forms an unusual, asymmetric dimer on dsRNA binding, with each of the monomers binding dsRNA in a different way: one binds the backbone whereas the other caps the terminus. Additional SAXS, DXMS, and dsRNA-binding experiments presented here support a model of cooperative dsRNA recognition in which binding of the first monomer assists binding of the next monomer of the oligomeric VP35 protein. This work illustrates how
ebolavirus
VP35 could mask key recognition sites of molecules such as RIG-I, MDA-5, and Dicer to silence viral dsRNA in infection.
Temporal latitudinal-gradient dynamics and tropical instability of deep-sea species diversity
Authors: Yasuhara Moriaki , Hunt Gene , Cronin Thomas M. , Okahashi Hisayo
Published: December 2009

A benthic microfaunal record from the equatorial Atlantic Ocean over the past four glacial-interglacial cycles was investigated to understand temporal dynamics of deep-sea latitudinal species diversity gradients (LSDGs). The results demonstrate unexpected instability and high amplitude fluctuations of species diversity in the tropical deep ocean that are correlated with orbital-scale oscillations in global climate: Species diversity is low during glacial and high during interglacial periods. This implies that climate severely influences deep-sea diversity, even at tropical latitudes, and that deep-sea LSDGs, while generally present for the last 36 million years, were weakened or absent during glacial periods. Temporally dynamic LSDGs and unstable tropical diversity require reconsideration of current ecological hypotheses about the generation and maintenance of biodiversity as they apply to the deep sea, and underscore the potential vulnerability and conservation importance of tropical deep-sea ecosystems.
A tetrahedral entropy for water
Authors: Kumar Pradeep , Buldyrev Sergey V. , Stanley H. Eugene
Published: December 2009

We introduce the space-dependent correlation function
C

Q

(
r
) and time-dependent autocorrelation function
C

Q

(
t
) of the local tetrahedral order parameter
Q
≡
Q
(
r
,
t
). By using computer simulations of 512 waterlike particles interacting through the transferable interaction potential with five points (TIP5 potential), we investigate
C

Q

(
r
) in a broad region of the phase diagram. We find that at low temperatures
C

Q

(
t
) exhibits a two-step time-dependent decay similar to the self-intermediate scattering function and that the corresponding correlation time τ

Q

displays a dynamic cross-over from non-Arrhenius behavior for
T
>
T

W

to Arrhenius behavior for
T
<
T

W

, where
T

W

denotes the Widom temperature where the correlation length has a maximum as
T
is decreased along a constant-pressure path. We define a tetrahedral entropy
S

Q

associated with the local tetrahedral order of water molecules and find that it produces a major contribution to the specific heat maximum at the Widom line. Finally, we show that τ

Q

can be extracted from
S

Q

by using an analog of the Adam–Gibbs relation.
Recombination-induced tag exchange to track old and new proteins
Authors: Verzijlbergen Kitty F. , Menendez-Benito Victoria , van Welsem Tibor , van Deventer Sjoerd J. , Lindstrom Derek L. , Ovaa Huib , Neefjes Jacques , Gottschling Daniel E. , van Leeuwen Fred
Published: December 2009

The dynamic behavior of proteins is critical for cellular homeostasis. However, analyzing dynamics of proteins and protein complexes in vivo has been difficult. Here we describe recombination-induced tag exchange (RITE), a genetic method that induces a permanent epitope-tag switch in the coding sequence after a hormone-induced activation of Cre recombinase. The time-controlled tag switch provides a unique ability to detect and separate old and new proteins in time and space, which opens up opportunities to investigate the dynamic behavior of proteins. We validated the technology by determining exchange of endogenous histones in chromatin by biochemical methods and by visualizing and quantifying replacement of old by new proteasomes in single cells by microscopy. RITE is widely applicable and allows probing spatiotemporal changes in protein properties by multiple methods.
T-cell antagonism by short half-life pMHC ligands can be mediated by an efficient trapping of T-cell polarization toward the APC
Authors: Carreño Leandro J. , Riquelme Erick M. , González Pablo A. , Espagnolle Nicolas , Riedel Claudia A. , Valitutti Salvatore , Kalergis Alexis M.
Published: December 2009

T-cell activation results from productive T-cell receptor (TCR) engagement by a cognate peptide–MHC (pMHC) complex on the antigen presenting cell (APC) surface, a process leading to the polarization of the T-cell secretory machinery toward the APC interface. We have previously shown that the half-life of the TCR/pMHC interaction and the density of pMHC on the APC are two parameters determining T-cell activation. However, whether the half-life of the TCR/pMHC interaction can modulate the efficiency of T-cell secretory machinery polarization toward an APC still remains unclear. Here, by using altered peptide ligands conferring different half-lives to the TCR/pMHC interaction, we have tested how this parameter can control T-cell polarization. We observed that only TCR/pMHC interactions with intermediate half-lives can promote the assembly of synapses that lead to T-cell activation. Strikingly, intermediate half-life interactions can be competed out by short half-life interactions, which can efficiently promote T-cell polarization and antagonize T-cell activation that was induced by activating intermediate half-life interactions. However, short TCR/pMHC interactions fail at promoting phosphorylation of signaling molecules at the T-cell–APC contact interface, which are needed for T-cell activation. Our data suggest that although intermediate half-life pMHC ligands promote assembly of activating synapses, this process can be inhibited by short half-life antagonistic pMHC ligands, which promote the assembly of non activating synapses.
Functionality of the voltage-gated proton channel truncated in S4
Authors: Sakata Souhei , Kurokawa Tatsuki , Nørholm Morten H. H. , Takagi Masahiro , Okochi Yoshifumi , von Heijne Gunnar , Okamura Yasushi
Published: December 2009

The voltage sensor domain (VSD) is the key module for voltage sensing in voltage-gated ion channels and voltage-sensing phosphatases. Structurally, both the VSD and the recently discovered voltage-gated proton channels (Hv channels) voltage sensor only protein (VSOP) and Hv1 contain four transmembrane segments. The fourth transmembrane segment (S4) of Hv channels contains three periodically aligned arginines (R1, R2, R3). It remains unknown where protons permeate or how voltage sensing is coupled to ion permeation in Hv channels. Here we report that Hv channels truncated just downstream of R2 in the S4 segment retain most channel properties. Two assays, site-directed cysteine-scanning using accessibility of maleimide-reagent as detected by Western blotting and insertion into dog pancreas microsomes, both showed that S4 inserts into the membrane, even if it is truncated between the R2 and R3 positions. These findings provide important clues to the molecular mechanism underlying voltage sensing and proton permeation in Hv channels.
Bandit solutions provide unified ethical models for randomized clinical trials and comparative effectiveness research
Authors: Press William H.
Published: December 2009

As electronic medical records enable increasingly ambitious studies of treatment outcomes, ethical issues previously important only to limited clinical trials become relevant to unlimited whole populations. For randomized clinical trials, adaptive assignment strategies are known to expose substantially fewer patients to avoidable treatment failures than strategies with fixed assignments (e.g., equal sample sizes). An idealized adaptive case—the two-armed Bernoulli bandit problem—can be exactly optimized for a variety of ethically motivated cost functions that embody principles of duty-to-patient, but the solutions have been thought computationally infeasible when the numbers of patients in the study (the “horizon”) is large. We report numerical experiments that yield a heuristic approximation that applies even to very large horizons, and we propose a near-optimal strategy that remains valid even when the horizon is unknown or unbounded, thus applicable to comparative effectiveness studies on large populations or to standard-of-care recommendations. For the case in which the economic cost of treatment is a parameter, we give a heuristic, near-optimal strategy for determining the superior treatment (whether more or less costly) while minimizing resources wasted on any inferior, more expensive, treatment. Key features of our heuristics can be generalized to more complicated protocols.
Defined factors induce reprogramming of gastrointestinal cancer cells
Authors: Miyoshi Norikatsu , Ishii Hideshi , Nagai Ken-ichi , Hoshino Hiromitsu , Mimori Koshi , Tanaka Fumiaki , Nagano Hiroaki , Sekimoto Mitsugu , Doki Yuichiro , Mori Masaki
Published: December 2009

Although cancer is a disease with genetic and epigenetic origins, the possible effects of reprogramming by defined factors remain to be fully understood. We studied the effects of the induction or inhibition of cancer-related genes and immature status-related genes whose alterations have been reported in gastrointestinal cancer cells. Retroviral-mediated introduction of induced pluripotent stem (iPS) cell genes was necessary for inducing the expression of immature status-related proteins, including Nanog, Ssea4, Tra-1-60, and Tra-1-80 in esophageal, stomach, colorectal, liver, pancreatic, and cholangiocellular cancer cells. Induced cells, but not parental cells, possessed the potential to express morphological patterns of ectoderm, mesoderm, and endoderm, which was supported by epigenetic studies, indicating methylation of DNA strands and the histone H3 protein at lysine 4 in promoter regions of pluripotency-associated genes such as
NANOG
. In in vitro analysis induced cells showed slow proliferation and were sensitized to differentiation-inducing treatment, and in vivo tumorigenesis was reduced in NOD/SCID mice. This study demonstrated that pluripotency was manifested in induced cells, and that the induced pluripotent cancer (iPC) cells were distinct from natural cancer cells with regard to their sensitivity to differentiation-inducing treatment. Retroviral-mediated introduction of iPC cells confers higher sensitivity to chemotherapeutic agents and differentiation-inducing treatment.
Prepubertal human spermatogonia and mouse gonocytes share conserved gene expression of germline stem cell regulatory molecules
Authors: Wu Xin , Schmidt Jonathan A. , Avarbock Mary R. , Tobias John W. , Carlson Claire A. , Kolon Thomas F. , Ginsberg Jill P. , Brinster Ralph L.
Published: December 2009

In the human testis, beginning at ≈2 months of age, gonocytes are replaced by adult dark (Ad) and pale (Ap) spermatogonia that make up the spermatogonial stem cell (SSC) pool. In mice, the SSC pool arises from gonocytes ≈6 days after birth. During puberty in both species, complete spermatogenesis is established by cells that differentiate from SSCs. Essentially pure populations of prepubertal human spermatogonia and mouse gonocytes were selected from testis biopsies and validated by confirming the presence of specific marker proteins in cells. Stem cell potential of germ cells was demonstrated by transplantation to mouse testes, following which the cells migrated to the basement membrane of the seminiferous tubule and were maintained similar to SSCs. Differential gene expression profiles generated between germ cells and testis somatic cells demonstrated that expression of genes previously identified as SSC and spermatogonial-specific markers (e.g., zinc-finger and BTB-domain containing 16, ZBTB16) was greatly elevated in both human spermatogonia and mouse gonocytes compared to somatic cells. Several genes were expressed at significantly higher levels in germ cells of both species. Most importantly, genes known to be essential for mouse SSC self-renewal (e.g., Ret proto-oncogene,
Ret
; GDNF-family receptor α1,
Gfr
α
1
; and B-cell CLL/lymphoma 6, member B,
Bcl6b
) were more highly expressed in both prepubertal human spermatogonia and mouse gonocytes than in somatic cells. The results indicate remarkable conservation of gene expression, notably for self-renewal genes, in these prepubertal germline cells between two species that diverged phylogenetically ≈75 million years ago.
Accumulation of a differentiation regulator specifies transit amplifying division number in an adult stem cell lineage
Authors: Insco Megan L. , Leon Arlene , Tam Cheuk Ho , McKearin Dennis M. , Fuller Margaret T.
Published: December 2009

A key feature of many adult stem cell lineages is that stem cell daughters destined for differentiation undergo several transit amplifying (TA) divisions before initiating terminal differentiation, allowing few and infrequently dividing stem cells to produce many differentiated progeny. Although the number of progenitor divisions profoundly affects tissue (re)generation, and failure to control these divisions may contribute to cancer, the mechanisms that limit TA proliferation are not well understood. Here, we use a model stem cell lineage, the
Drosophila
male germ line, to investigate the mechanism that counts the number of TA divisions. The
Drosophila
Bag of Marbles (Bam) protein is required for male germ cells to cease spermatogonial TA divisions and initiate spermatocyte differentiation [McKearin DM, et al. (1990)
Genes Dev
4:2242–2251]. Contrary to models involving dilution of a differentiation repressor, our results suggest that the switch from proliferation to terminal differentiation is triggered by accumulation of Bam protein to a critical threshold in TA cells and that the number of TA divisions is set by the timing of Bam accumulation with respect to the rate of cell cycle progression.
Laser microdissection of
Arabidopsis
cells at the powdery mildew infection site reveals site-specific processes and regulators
Authors: Chandran Divya , Inada Noriko , Hather Greg , Kleindt Christiane K. , Wildermuth Mary C.
Published: December 2009

To elucidate host processes and components required for the sustained growth and reproduction of the obligate biotrophic fungus
Golovinomyces orontii
on
Arabidopsis thaliana
, laser microdissection was used to isolate cells at the site of infection at 5 days postinfection for downstream global
Arabidopsis
expression profiling. Site-specific profiling increased sensitivity dramatically, allowing us to identify specific host processes, process components, and their putative regulators hidden in previous whole-leaf global expression analyses. For example, 67 transcription factors exhibited altered expression at the powdery mildew (PM) infection site, with subsets of these playing known or inferred roles in photosynthesis, cold/dehydration responses, defense, auxin signaling, and the cell cycle. Using integrated informatics analyses, we constructed putative regulatory networks for a subset of these processes and provided strong support for host cell cycle modulation at the PM infection site. Further experimentation revealed induced host endoreduplication occurred exclusively at the infection site and led us to identify MYB3R4 as a transcriptional regulator of this process. Induced endoreduplication was abrogated in
myb3r4
mutants, and
G. orontii
growth and reproduction were reduced. This suggests that, by increasing gene copy number, localized endoreduplication serves as a mechanism to meet the enhanced metabolic demands imposed by the fungus, which acquires all its nutrients from the plant host.
miRNA-processing enzyme Dicer is necessary for cardiac outflow tract alignment and chamber septation
Authors: Saxena Ankur , Tabin Clifford J.
Published: December 2009

MicroRNAs (miRNAs) have previously been implicated in a number of developmental processes, including development of the ventricular myocardium of the heart. To determine what, if any, additional roles miRNAs play in cardiogenesis, we deleted the miRNA-processing enzyme Dicer specifically in the developing murine heart. Embryos lacking cardiac Dicer lived longer than reported in previous studies using different alleles to remove cardiac Dicer activity and displayed a highly penetrant phenotype of double outlet right ventricle with a concurrent ventricular septal defect. Before the defect’s onset, Pitx2c and Sema3c, both required for outflow tract morphogenesis, were up-regulated in Dicer-deficient hearts. Interestingly, mesenchymal apoptosis in the outflow tract normally required for outflow tract alignment was greatly decreased in the mutants, likely contributing directly to the observed phenotype. In sum, we demonstrate here a specific developmental process, that of outflow tract morphogenesis, being hindered by the deletion of miRNAs during cardiogenesis.
Autoreactivity in an HIV-1 broadly reactive neutralizing antibody variable region heavy chain induces immunologic tolerance
Authors: Verkoczy Laurent , Diaz Marilyn , Holl T. Matt , Ouyang Ying-Bin , Bouton-Verville Hilary , Alam S. Munir , Liao Hua-Xin , Kelsoe Garnett , Haynes Barton F.
Published: December 2009

We previously reported that some of the rare broadly reactive, HIV-1 neutralizing antibodies are polyreactive, leading to the hypothesis that induction of these types of neutralizing antibody may be limited by immunologic tolerance. However, the notion that such antibodies are sufficiently autoreactive to trigger B cell tolerance is controversial. To test directly whether rare neutralizing HIV-1 antibodies can activate immunologic tolerance mechanisms, we generated a knock-in mouse in which the Ig heavy chain (HC) variable region rearrangement (VHDJH) from the polyreactive and broadly neutralizing human monoclonal antibody 2F5 was targeted into the mouseIghlocus. In vitro, this insertion resulted in chimeric human/mouse 2F5 antibodies that were functionally similar to the human 2F5 antibody, including comparable reactivity to human and murine self-antigens. In vivo, the 2F5 VHDJHinsertion supported development of large- and small pre-B cells that expressed the chimeric human/mouse Igμ chain but not the production of immature B cells expressing membrane IgM. The developmental arrest exhibited in 2F5 VHDJHknock-in mice is characteristic of other knock-in strains that express the Ig HC variable region of autoreactive antibodies and is consistent with the loss of immature B cells bearing 2F5 chimeric antibodies to central tolerance mechanisms. Moreover, homozygous 2F5 VHDJHknock-in mice support reduced numbers of residual splenic B cells with low surface IgM density, severely diminished serum IgM levels, but normal to elevated quantities of serum IgGs that did not react with autoantigens. These features are consistent with elimination of 2F5 HC autoreactivity by additional negative selection mechanism(s) in the periphery.
Sinorhizobium meliloti
phospholipase C required for lipid remodeling during phosphorus limitation
Authors: Zavaleta-Pastor Maritza , Sohlenkamp Christian , Gao Jun-Lian , Guan Ziqiang , Zaheer Rahat , Finan Turlough M. , Raetz Christian R. H. , López-Lara Isabel M. , Geiger Otto
Published: December 2009

Rhizobia are Gram-negative soil bacteria able to establish nitrogen-fixing root nodules with their respective legume host plants. Besides phosphatidylglycerol, cardiolipin, and phosphatidylethanolamine, rhizobial membranes contain phosphatidylcholine (PC) as a major membrane lipid. Under phosphate-limiting conditions of growth, some bacteria replace their membrane phospholipids with lipids lacking phosphorus. In
Sinorhizobium meliloti,
these phosphorus-free lipids are sulfoquinovosyl diacylglycerol, ornithine-containing lipid, and diacylglyceryl trimethylhomoserine (DGTS). Pulse–chase experiments suggest that the zwitterionic phospholipids phosphatidylethanolamine and PC act as biosynthetic precursors of DGTS under phosphorus-limiting conditions. A
S. meliloti
mutant, deficient in the predicted phosphatase SMc00171 was unable to degrade PC or to form DGTS in a similar way as the wild type. Cell-free extracts of
Escherichia coli
, in which SMc00171 had been expressed, convert PC to phosphocholine and diacylglycerol, showing that SMc00171 functions as a phospholipase C. Diacylglycerol , in turn, is the lipid anchor from which biosynthesis is initiated during the formation of the phosphorus-free membrane lipid DGTS. Inorganic phosphate can be liberated from phosphocholine. These data suggest that, in
S. meliloti
under phosphate-limiting conditions, membrane phospholipids provide a pool for metabolizable inorganic phosphate, which can be used for the synthesis of other essential phosphorus-containing biomolecules. This is an example of an intracellular phospholipase C in a bacterial system; however, the ability to degrade endogenous preexisting membrane phospholipids as a source of phosphorus may be a general property of Gram-negative soil bacteria.
Delayed wave of c-Fos expression in the dorsal hippocampus involved specifically in persistence of long-term memory storage
Authors: Katche Cynthia , Bekinschtein Pedro , Slipczuk Leandro , Goldin Andrea , Izquierdo Ivan A. , Cammarota Martin , Medina Jorge H.
Published: December 2009

Memory formation is a temporally graded process during which transcription and translation steps are required in the first hours after acquisition. Although persistence is a key characteristic of memory storage, its mechanisms are scarcely characterized. Here, we show that long-lasting but not short-lived inhibitory avoidance long-term memory is associated with a delayed expression of c-Fos in the hippocampus. Importantly, this late wave of c-Fos is necessary for maintenance of inhibitory avoidance long-term storage. Moreover, inhibition of transcription in the dorsal hippocampus 24 h after training hinders persistence but not formation of long-term storage. These findings indicate that a delayed phase of transcription is essential for maintenance of a hippocampus-dependent memory trace. Our results support the hypothesis that recurrent rounds of consolidation-like events take place late after learning in the dorsal hippocampus to maintain memories.
Involvement of the Toll-like receptor 4 pathway and use of TNF-α antagonists for treatment of the mucopolysaccharidoses
Authors: Simonaro Calogera M. , Ge Yi , Eliyahu Efrat , He Xingxuan , Jepsen Karl J. , Schuchman Edward H.
Published: December 2009

Enzyme replacement therapy is currently available for three of the mucopolysaccharidoses (MPSs) but has limited effects on the skeletal lesions. We investigated the involvement of the Toll-like receptor 4 (TLR4) signaling pathway in the pathogenesis of MPS bone and joint disease, and the use of the anti-TNF-α drug, Remicade (Centocor, Inc.), for treatment. TLR4 KO (TLR4(lps−/−)) mice were interbred with MPS VII mice to produce double-KO (DKO) animals. The DKO mice had longer and thinner faces and longer femora as revealed by micro-computed tomography analysis compared with MPS VII mice. Histological analyses also revealed more organized and thinner growth plates. The serum levels of TNF-α were normalized in the DKO animals, and the levels of phosphorylated STAT1 and STAT3 in articular chondrocytes were corrected. These findings led us to evaluate the effects of Remicade in MPS VI rats. When initiated at 1 month of age, i.v. treatment prevented the elevation of TNF-α, receptor activator of NF-κB, and other inflammatory molecules not only in the blood but in articular chondrocytes and fibroblast-like synoviocytes (FLSs). Treatment of 6-month-old animals also reduced the levels of these molecules to normal. The number of apoptotic articular chondrocytes in MPS VI rats was similarly reduced, with less infiltration of synovial tissue into the underlying bone. These studies revealed the important role of TLR4 signaling in MPS bone and joint disease and suggest that targeting TNF-α may have positive therapeutic effects.
Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution
Authors: Jun Se-Ran , Sims Gregory E. , Wu Guohong A. , Kim Sung-Hou
Published: December 2009

We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features arel-mers of amino acids, and each organism is represented by a profile of frequencies of all features. The selection of feature length is critical in the FFP method, and we have developed a procedure for identifying the optimal feature lengths for inferring the phylogeny of prokaryotes, strictly speaking, a proteome phylogeny. Our FFP trees are constructed with whole proteomes of 884 prokaryotes, 16 unicellular eukaryotes, and 2 random sequences. To highlight the branching order of major groups, we present a simplified proteome FFP tree of monophyletic class or phylum with branch support. In our whole-proteome FFP trees (i) Archaea, Bacteria, Eukaryota, and a random sequence outgroup are clearly separated; (ii) Archaea and Bacteria form a sister group when rooted with random sequences; (iii) Planctomycetes, which possesses an intracellular membrane compartment, is placed at the basal position of the Bacteria domain; (iv) almost all groups are monophyletic in prokaryotes at most taxonomic levels, but many differences in the branching order of major groups are observed between our proteome FFP tree and trees built with other methods; and (v) previously “unclassified” genomes may be assigned to the most likely taxa. We describe notable similarities and differences between our FFP trees and those based on other methods in grouping and phylogeny of prokaryotes.
Living Dialogues in One Neighborhood: Moving toward Understanding across Discourses and Practices of Literacy and Schooling
Authors: Rogers Theresa , Tyson Cynthia , Marshall Elizabeth
Published: December 2009

Drawing on a critical discourse perspective, we examine the “living dialogues,” or the complex interplay between discourses, in one neighborhood to recontextualize the often polarized debates about literacy instruction within education. Focusing on three children, their families, teachers, and classrooms, we argue that the creation of more inclusive school literacy practices requires a consideration of how discourses function within and across homes, communities, and schools. Thus we focus less on the merits or limits of one instructional method than on how living dialogues reflect particular and situated beliefs about language and literacy practices. Within this theoretical frame, classrooms arise as contextualized spaces where the living dialogues of unique discourse communities intersect, and where the relational discourses that shape and reflect classroom practices have the potential to open up or close down instructional spaces for children. A critical discourse perspective re-situates debates around literacy instruction and allows us to engage in complex ways with the dilemmas and possibilities of school-based literacy practices.

Perhaps the most insidious and least understood form of segregation is that of the word. For if the word has the potency to revive and make us free, it has also the power to bind, imprison, and destroy. - Ralph Ellison
Critical Issues: Circles of Kinship, Friendship, Position, and Power: Examining the Community in Community-Based Literacy Research
Authors: Moje Elizabeth B.
Published: December 2009

Literacy research conducted in communities of practice outside classrooms and schools has proliferated in the last decade with little attention given to what it means to talk about literacy in “the community.” This article explores issues surrounding community-based literacy research and suggests that, although well intentioned, literacy researchers risk overdetermining, essentializing, and romanticizing what it means to engage in community-based literacy if we do not define and question what is meant by community. The need to define and complicate community as a construct is important, because communities are becoming more complex, and sometimes less communal, with the diversity and rapid change of new times and fast capitalism (Hall, 1995; Lankshear, 1997; Luke & Luke, 1999, in press). This piece examines various definitions of community that have framed community-based literacy studies to date and argues for concerted efforts to define and complicate perspectives on community in future research.
Connecting, Resisting, and Searching for Safer Places: Students Respond to Mildred Taylor's the Friendship
Authors: Möller Karla J. , Allen JoBeth
Published: December 2009

We analyze the discussion that developed when four fifth-grade girls, three African American and one Hispanic, and Karla Möller, a European American, transacted with Mildred Taylor's The Friendship (1987). Framing our analysis within the intersection of reader-response theory and sociocultural and critical theories of literacy learning, we show how participants' responses to Taylor's text and adult and peer guidance helped to create a response development zone that allowed for a dialectic of connecting with and resisting the evocation. The girls, all struggling readers, used reading, writing, and discussion to address comprehension difficulties and construct multiple levels of meaning. They became increasingly aware of historical racism and connected that knowledge to events from their own experience, including encounters with the Klan and memories of a relative's murder. We present the group's discussion as a metaphorical play and the girls as spectators who become actors as they engaged in this “theater of discourse” (Boal, 1985).
Weaving Chains of Affect and Cognition: A Young Child's Understanding of CD-ROM Talking Books
Authors: Labbo Linda D. , Kuhn Melanie R.
Published: December 2009

This qualitative case study employed Wittrock's Generative Learning Model to examine in-depth one kindergarten child's comprehension when reading considerate and inconsiderate CD-ROM talking books in a classroom computer center. A CD-ROM talking book consists of a story told through multimedia modes of information that has been digitized on a CD. Considerate CD-ROM talking books are those that include multimedia effects that are congruent with and integral to the story. Inconsiderate CD-ROM talking books are those that include multimedia effects that are incongruent with or incidental to the story. Findings indicate that considerate CD-ROM talking books supported the child's understanding and retelling of the story and involved meaning-making processes that wove together affective responses, cognitive processes, and metacognitive activity; however, inconsiderate CD-ROM talking books resulted in the child's inability to retell the story in a cohesive way and fostered passive viewing. Implications for research and practice are drawn.
In Rehearsal: Complicating Authority in Undergraduate Critical-Inquiry Classrooms
Authors: Fecho Bob , Commeyras Michelle , Eurydice  , Bauer Bouchereau , Font George
Published: December 2009

If we in teacher education want emerging teachers to inquire into the complexities of authority and to reimagine how it might operate in schools, then we need firsthand experience troubling it in our own classrooms. To this end, we - three reading education professors - problematized our classroom authority as we sought to enact critical inquiries with preservice teachers. In this qualitative study, our contention is that preservice teachers, in addition to eventually having to manage curriculum, must also face the reality of having to function as authority figures while still maintaining a classroom conducive to meaning making. However, in order to interrupt their traditional images of teacher as authority figure, they need to experience contrasting images. This article provides three lenses through which to explore how authority can be reimagined in critical-inquiry reading education courses.
“Only Connect!”: Cross-Cultural Connections in the Reading Lives of Preservice Teachers and Children
Authors: Wolf Shelby A. , Ballentine Darcy , Hill Lisa A.
Published: December 2009

In this research, we present case studies of three Anglo American preservice teachers - Clara, Luke, & Varla - as they worked with children of color and/or poverty - Sam, Reggie, and Lucinda - over the course of a semester. In a university class entitled the Literacy/Social Studies Block, we asked the preservice teachers to look within to explore their own literary backgrounds in a reading-autobiography assignment. And we encouraged them to look about as they read and discussed literature with diverse children in the Child as Teacher Project. Here we argue that the combination of autobiographical accounts with reflective field experiences helps preservice teachers reconsider their life stories in reading in order to build bridges of literacy to and with children.
Transitions into Teaching: Learning to Teach Writing in Teacher Education and Beyond
Authors: Grossman Pamela L. , Valencia Sheila W. , Evans Kate , Thompson Clarissa , Martin Susan , Place Nancy
Published: December 2009

This longitudinal study followed 10 beginning teachers from their last year of preservice education into their first 3 years of full-time teaching. Using sociocultural theory, we describe how these teachers appropriated a set of pedagogical tools for teaching writing. Data sources included approximately 5 interviews and at least 5 classroom observations a year, as well as observations and interviews with cooperating teachers, supervisors, and mentor teachers. The analysis suggests that teachers drew on pedagogical tools introduced during teacher education to develop their classroom practice. Conceptual tools that were buttressed with practical strategies proved to be most influential. The settings in which teachers taught also shaped teachers' developing understanding and practice. Finally, pedagogical tools developed during teacher education were even more evident during the teachers' 2nd year of teaching, as they tried to approximate their goal of good language arts instruction. The results of this study suggest the danger of making claims about what teachers do and do not learn during teacher education based only on data from their 1st year of teaching.
From High School to College: Student Perspectives on Literacy Practices
Authors: Harklau Linda
Published: December 2009

There are few naturalistic studies of how individuals experience and perceive the literate transition from high school to college. This yearlong study followed 4 female language-minority students through their last semester in high school and first semester in college. Taking a literacy-as-social-practice perspective, the study focused on these students' perceptions of reading and writing they encountered across the curriculum. The study found that what students found new or more challenging in college literacy practices was not necessarily predicted in a developmental perspective, but was better understood as contextualized in their high school literacy experiences. The article argues that high school literacy practices should not be seen merely as an underformed version of collegiate practices, but rather should be interpreted in light of the particular population and purposes secondary schools serve. The study shows that a social-practice perspective can serve as a useful supplement and counterpoint to cognitively oriented approaches to literate development in young adults. In particular, it is argued that they hold potential to render the emic perspectives of learners themselves more prominent in literacy research.