bluuebunny/crossref_metadata_2025 huggingface dataset:
A Longitudinal Examination of Physiological Regulation in Cocaine‐Exposed Infants Across the First 7 Months of Life
Authors: Schuetze Pamela , Eiden Rina D. , Edwards Ellen P.
Published: January 2009

This study examined the association between prenatal exposure to cocaine and physiological regulation across the first 7 months of age. Measures of respiratory sinus arrhythmia (RSA) were obtained from 169 (82 cocaine‐exposed and 87 nonexposed) infants during baseline periods at 1 month and 7 months of age and during tasks designed to elicit positive and negative affect at 7 months of age. After controlling for maternal age, gestational age, and obstetrical risk, structural equation modeling indicated that the association between prenatal exposure to cocaine and baseline RSA at 7 months of age was direct even in the presence of an indirect effect through baseline RSA at 1 month of age. There were no indirect effects through maternal affect during mother‐infant interactions assessed at 1 month of age. Analyses also indicated a direct association between prenatal exposure to cocaine and RSA regulation to negative affect at 7 months of age.
Development of Vocal Protests From 3 to 18 Months
Authors: Chen Xin , Green James A. , Gustafson Gwen E.
Published: January 2009

Infants often protest the activities of their caregivers, and this particular social interaction may provide an important window on early communication and its development. This study used naturalistic methods to investigate the development of vocal protests. Fifteen mother‐infant dyads at each of 5 ages, from 3 to 18 months, were observed at home. Maternal behaviors of caregiving and prohibiting were tallied from videotapes, as were infants' protests of these behaviors. Maternal caregiving decreased with age, but maternal prohibitions increased. There were no changes over age in the probability of protesting maternal caregiving behavior; however, 12‐month‐olds were more likely to protest prohibitions than 6‐ or 8‐month‐olds. Older infants were also more likely to use intense protests, such as screams, than younger infants. These age‐related changes were mirrored by the differences in prohibitions and protests observed between 8‐month‐olds who could crawl and those who could not. Findings from this study were related to previous research on infant crying as an important part of the prelinguistic communication system.
Learning Words Over Time: The Role of Stimulus Repetition in Mutual Exclusivity
Authors: Mather Emily , Plunkett Kim
Published: January 2009

During the second year of life, infants develop a preference to attach novel labels to novel objects. This behavior is commonly known as “mutual exclusivity” (Markman, 1989). In an intermodal preferential looking experiment with 19.5‐ and 22.5‐month‐olds, stimulus repetition was critical for observing mutual exclusivity. On the first occasion that a novel label was presented with 1 familiar object and 1 novel object, looking behavior was unsystematic. However, on reexposure to the same stimuli, 22.5‐month‐olds looked preferentially at the novel object prior to the re‐presentation of the novel label. These findings suggest a powerful memory mechanism for novel labels and objects, enabling mutual exclusivity to emerge across repeated exposures to potential referents.
Age‐Specific Preferences for Infant‐Directed Affective Intent
Authors: Kitamura Christine , Lam Christa
Published: January 2009

This study examined the developmental course of infants' attentional preferences for 3 types of infant‐directed affective intent, which have been shown to be commonly used at particular ages in the first year of life. Specifically, Kitamura and Burnham (2003) found mothers' tone of voice in infant‐directed speech is most comforting between birth and 3 months, most approving at 6 months, and most directive at 9 months. Thus, the aim of this study was to assess whether there is a relation between the type of affective intent used by mothers at each age point, and infants' affective intent preferences. Each infant group, 3‐, 6‐, and 9‐month‐olds, was played the 3 types of affective intent alternating across a single test session. When analyzed across age, the interactions revealed the predicted developmental trajectory; that is, infant preferences transformed between 3 and 6 months from comforting to approving, and between 6 and 9 months, from approving to directive. However, when analyzed separately by age, it was shown that 3‐month‐olds preferred comforting to other types; 6‐month‐olds preferred approving to directive, but listened equally to approving and comforting; and 9‐month‐olds showed no preference for any type of affective intent. Because it was possible that 9‐month‐olds were more focused on phonetic and phonotactic information, a new group of 9‐month‐olds was tested with intonation‐only versions of the 3 affective intent types. Under these conditions, they were found to prefer directive to comforting, but not directive to approving types. The results of this study have implications for what infants pay attention to in their social and linguistic environment over the course of the first year.
Evidence of Early Strategies in Learning to Walk
Authors: Snapp‐Childs Winona , Corbetta Daniela
Published: January 2009

Learning to walk is a dynamic process requiring the fine coordination, assembly, and balancing of many body segments at once. For the young walker, coordinating all these behavioral levels may be quite daunting. In this study, we examine the whole‐body strategies to which infants resort to produce their first independent steps and progress over the first months of walking experience. Six infants were followed weekly from the onset of independent upright locomotion for 8 weeks, and then every other week until 4 months of walking experience. The walking kinematics from the infants' earliest steps were cluster‐analyzed and the infants were classified into 3 groups. Follow‐up comparisons with kinematics recordings were used to quantify the infants' strategies more precisely and track how these early forms of walking evolved over time. Results revealed that in the first weeks of independent walking, 3 infants used a stepping strategy, 1 used a twisting strategy, and 2 used a falling strategy to move their body forward and perform their first unsupported steps. As the infants gained walking experience, their walking patterns became more similar. These findings indicate that infants discover different solutions to use their body and control their balance when beginning to walk. With time, infants adopt a more efficient solution that incorporates and integrates elements of the different strategies.
To Share or Not to Share: When Do Toddlers Respond to Another's Needs?
Authors: Brownell Celia A. , Svetlova Margarita , Nichols Sara
Published: January 2009

The developmental origins of sharing remain little understood. Using procedures adapted from research on prosocial behavior in chimpanzees, we presented 18‐ and 25‐month‐old children with a sharing task in which they could choose to deliver food to themselves only, or to both themselves and another person, thereby making it possible for them to share without personal sacrifice. The potential recipient, a friendly adult, was either silent about her needs and wants or made them explicit. Both younger and older toddlers chose randomly when the recipient was silent. However, when the recipient vocalized her desires 25‐month‐olds shared, whereas younger children did not. Thus, we demonstrate that children voluntarily share valued resources with others by the end of the second year of life, but that this depends on explicit communicative cues about another's need or desire.
The Development of Rational Imitation in 9‐ and 12‐Month‐Old Infants
Authors: Zmyj Norbert , Daum Moritz M. , Aschersleben Gisa
Published: January 2009

Studies on rational imitation have provided evidence for the fact that infants as young as 12 months of age engage in rational imitation. However, the developmental onset of this ability is unclear. In this study, we investigated whether 9‐ and 12‐month‐olds detect voluntary and implicit as well as nonvoluntary and explicit constraints in the head touch task. Three groups of infants watched video sequences, which displayed a person illuminating a lamp using the head. The hands of the model were either free, occupied by voluntarily holding a blanket, or nonvoluntarily restrained by being tied to the table. An additional control group of infants watched the model turning on the lamp by using the hand. Given that the majority of infants imitated the head touch when the model's hands were free, there was evidence for rational imitation in comparison to the condition in which the model's hands were tied to the table, but not in comparison to the condition in which the hands were occupied by holding a blanket. Nine‐month‐olds showed no differences in their behavior according to the condition. These findings clarify the onset of rational imitation by showing that 12‐month‐olds (but not 9‐month‐olds) take into account a situational constraint only when the constraint is nonvoluntary and explicit.
Jodi Nunnari: Keeping an eye on mitochondrial inheritance
Authors: Sedwick Caitlin
Published: January 2009

Nunnari is using cutting-edge microscopy techniques to explore mutations affecting mitochondrial fusion and fission in living cells and whole organisms.
Kank attenuates actin remodeling by preventing interaction between IRSp53 and Rac1
Authors: Chandra Roy Badal , Kakinuma Naoto , Kiyama Ryoiti
Published: January 2009

In this study, insulin receptor substrate (IRS) p53 is identified as a binding partner for Kank, a kidney ankyrin repeat–containing protein that functions to suppress cell proliferation and regulate the actin cytoskeleton. Kank specifically inhibits the binding of IRSp53 with active Rac1 (Rac1G12V) but not Cdc42 (cdc42G12V) and thus inhibits the IRSp53-dependent development of lamellipodia without affecting the formation of filopodia. Knockdown (KD) of Kank by RNA interference results in increased lamellipodial development, whereas KD of both Kank and IRSp53 has little effect. Moreover, insulin-induced membrane ruffling is inhibited by overexpression of Kank. Kank also suppresses integrin-dependent cell spreading and IRSp53-induced neurite outgrowth. Our results demonstrate that Kank negatively regulates the formation of lamellipodia by inhibiting the interaction between Rac1 and IRSp53.
Integrin α3β1–dependent β-catenin phosphorylation links epithelial Smad signaling to cell contacts
Authors: Kim Young , Kugler Matthias C. , Wei Ying , Kim Kevin K. , Li Xiaopeng , Brumwell Alexis N. , Chapman Harold A.
Published: January 2009

Injury-initiated epithelial to mesenchymal transition (EMT) depends on contextual signals from the extracellular matrix, suggesting a role for integrin signaling. Primary epithelial cells deficient in their prominent laminin receptor, α3β1, were found to have a markedly blunted EMT response to TGF-β1. A mechanism for this defect was explored in α3-null cells reconstituted with wild-type (wt) α3 or point mutants unable to engage laminin 5 (G163A) or epithelial cadherin (E-cadherin; H245A). After TGF-β1 stimulation, wt epithelial cells but not cells expressing the H245A mutant internalize complexes of E-cadherin and TGF-β1 receptors, generate phospho-Smad2 (p-Smad2)–pY654–β-catenin complexes, and up-regulate mesenchymal target genes. Although Smad2 phosphorylation is normal, p-Smad2–pY654–β-catenin complexes do not form in the absence of α3 or when α3β1 is mainly engaged on laminin 5 or E-cadherin in adherens junctions, leading to attenuated EMT. These findings demonstrate that α3β1 coordinates cross talk between β-catenin and Smad signaling pathways as a function of extracellular contact cues and thereby regulates responses to TGF-β1 activation.
Redox amplification of apoptosis by caspase-dependent cleavage of glutaredoxin 1 and S-glutathionylation of Fas
Authors: Anathy Vikas , Aesif Scott W. , Guala Amy S. , Havermans Marije , Reynaert Niki L. , Ho Ye-Shih , Budd Ralph C. , Janssen-Heininger Yvonne M.W.
Published: January 2009

Reactive oxygen species (ROS) increase ligation of Fas (CD95), a receptor important for regulation of programmed cell death. Glutathionylation of reactive cysteines represents an oxidative modification that can be reversed by glutaredoxins (Grxs). The goal of this study was to determine whether Fas is redox regulated under physiological conditions. In this study, we demonstrate that stimulation with Fas ligand (FasL) induces S-glutathionylation of Fas at cysteine 294 independently of nicotinamide adenine dinucleotide phosphate reduced oxidase–induced ROS. Instead, Fas is S-glutathionylated after caspase-dependent degradation of Grx1, increasing subsequent caspase activation and apoptosis. Conversely, overexpression of Grx1 attenuates S-glutathionylation of Fas and partially protects against FasL-induced apoptosis. Redox-mediated Fas modification promotes its aggregation and recruitment into lipid rafts and enhances binding of FasL. As a result, death-inducing signaling complex formation is also increased, and subsequent activation of caspase-8 and -3 is augmented. These results define a novel redox-based mechanism to propagate Fas-dependent apoptosis.
The SCFSlimb ubiquitin ligase regulates Plk4/Sak levels to block centriole reduplication
Authors: Rogers Gregory C. , Rusan Nasser M. , Roberts David M. , Peifer Mark , Rogers Stephen L.
Published: January 2009

Restricting centriole duplication to once per cell cycle is critical for chromosome segregation and genomic stability, but the mechanisms underlying this block to reduplication are unclear. Genetic analyses have suggested an involvement for Skp/Cullin/F box (SCF)-class ubiquitin ligases in this process. In this study, we describe a mechanism to prevent centriole reduplication in Drosophila melanogaster whereby the SCF E3 ubiquitin ligase in complex with the F-box protein Slimb mediates proteolytic degradation of the centrosomal regulatory kinase Plk4. We identified SCFSlimb as a regulator of centriole duplication via an RNA interference (RNAi) screen of Cullin-based ubiquitin ligases. We found that Plk4 binds to Slimb and is an SCFSlimb target. Both Slimb and Plk4 localize to centrioles, with Plk4 levels highest at mitosis and absent during S phase. Using a Plk4 Slimb-binding mutant and Slimb RNAi, we show that Slimb regulates Plk4 localization to centrioles during interphase, thus regulating centriole number and ensuring the block to centriole reduplication.
TREM-2 (triggering receptor expressed on myeloid cells 2) is a phagocytic receptor for bacteria
Authors: N'Diaye Elsa-Noah , Branda Catherine S. , Branda Steven S. , Nevarez Lisette , Colonna Marco , Lowell Clifford , Hamerman Jessica A. , Seaman William E.
Published: January 2009

Phagocytosis, which is essential for the immune response to pathogens, is initiated by specific interactions between pathogens and cell surface receptors expressed by phagocytes. This study identifies triggering receptor expressed on myeloid cells 2 (TREM-2) and its signaling counterpart DAP12 as a molecular complex that promotes phagocytosis of bacteria. Expression of TREM-2–DAP12 enables nonphagocytic Chinese hamster ovary cells to internalize bacteria. This function depends on actin cytoskeleton dynamics and the activity of the small guanosine triphosphatases Rac and Cdc42. Internalization also requires src kinase activity and tyrosine phosphorylation. In bone marrow–derived macrophages, phagocytosis is decreased in the absence of DAP12 and can be restored by expression of TREM-2–DAP12. Depletion of TREM-2 inhibits both binding and uptake of bacteria. Finally, TREM-2–dependent phagocytosis is impaired in Syk-deficient macrophages. This study highlights a novel role for TREM-2–DAP12 in the immune response to bacterial pathogens.
Dynamic Coupling of Voltage Sensor and Gate Involved in Closed-State Inactivation of Kv4.2 Channels
Authors: Barghaan Jan , Bähring Robert
Published: January 2009

Voltage-gated potassium channels related to the Shal gene of Drosophila (Kv4 channels) mediate a subthreshold-activating current (ISA) that controls dendritic excitation and the backpropagation of action potentials in neurons. Kv4 channels also exhibit a prominent low voltage–induced closed-state inactivation, but the underlying molecular mechanism is poorly understood. Here, we examined a structural model in which dynamic coupling between the voltage sensors and the cytoplasmic gate underlies inactivation in Kv4.2 channels. We performed an alanine-scanning mutagenesis in the S4-S5 linker, the initial part of S5, and the distal part of S6 and functionally characterized the mutants under two-electrode voltage clamp in Xenopus oocytes. In a large fraction of the mutants (>80%) normal channel function was preserved, but the mutations influenced the likelihood of the channel to enter the closed-inactivated state. Depending on the site of mutation, low-voltage inactivation kinetics were slowed or accelerated, and the voltage dependence of steady-state inactivation was shifted positive or negative. Still, in some mutants these inactivation parameters remained unaffected. Double mutant cycle analysis based on kinetic and steady-state parameters of low-voltage inactivation revealed that residues known to be critical for voltage-dependent gate opening, including Glu 323 and Val 404, are also critical for Kv4.2 closed-state inactivation. Selective redox modulation of corresponding double-cysteine mutants supported the idea that these residues are involved in a dynamic coupling, which mediates both transient activation and closed-state inactivation in Kv4.2 channels.
Pentobarbital Produces Activation and Block of α1β2γ2S GABAA Receptors in Rapidly Perfused Whole Cells and Membrane Patches: Divergent Results Can Be Explained by Pharmacokinetics
Authors: Gingrich Kevin J. , Burkat Paul M. , Roberts William A.
Published: January 2009

Millimolar concentrations of the barbiturate pentobarbital (PB) activate γ-aminobutyric acid (GABA) type A receptors (GABARs) and cause blockade reported by a paradoxical current increase or “tail” upon washout. To explore the mechanism of blockade, we investigated PB-triggered currents of recombinant α1β2γ2S GABARs in whole cells and outside-out membrane patches using rapid perfusion. Whole cell currents showed characteristic bell-shaped concentration dependence where high concentrations triggered tail currents with peak amplitudes similar to those during PB application. Tail current time courses could not be described by multi-exponential functions at high concentrations (≥3,000 μM). Deactivation time course decayed over seconds and was slowed by increasing PB concentration and application time. In contrast, macropatch tail currents manifested eightfold greater relative amplitude, were described by multi-exponential functions, and had millisecond rise times; deactivation occurred over fractions of seconds and was insensitive to PB concentration and application time. A parsimonious gating model was constructed that accounts for macropatch results (“patch” model). Lipophilic drug molecules migrate slowly through cells due to avid partitioning into lipophilic subcellular compartments. Inclusion of such a pharmacokinetic compartment into the patch model introduced a slow kinetic component in the extracellular exchange time course, thereby providing recapitulation of divergent whole cell results. GABA co-application potentiated PB blockade. Overall, the results indicate that block is produced by PB concentrations sixfold lower than for activation involving at least three inhibitory PB binding sites, suggest a role of blocked channels in GABA-triggered activity at therapeutic PB concentrations, and raise an important technical question regarding the effective rate of exchange during rapid perfusion of whole cells with PB.
RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens
Authors: Rieber Nora , Knapp Bettina , Eils Roland , Kaderali Lars
Published: January 2009

Summary: We present RNAither, a package for the free statistical environment R which performs an analysis of high-throughput RNA interference (RNAi) knock-down experiments, generating lists of relevant genes and pathways out of raw experimental data. The library provides a quality assessment of the signal intensities, as well as a broad range of options for data normalization, different statistical tests for the identification of significant siRNAs, and a significance analysis of the biological processes involving corresponding genes. The results of the analysis are presented as a set of HTML pages. Additionally, all values and plots are available as either text files or pdf and png files.

Availability:  http://bioconductor.org/

Contact:  RNAither@gmx.de
Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection
Authors: Wu Michael C. , Zhang Lingsong , Wang Zhaoxi , Christiani David C. , Lin Xihong
Published: January 2009

Motivation: Pathway and gene set-based approaches for the analysis of gene expression profiling experiments have become increasingly popular for addressing problems associated with individual gene analysis. Since most genes are not differently expressed, existing gene set tests, which consider all the genes within a gene set, are subject to considerable noise and power loss, a concern exacerbated in studies in which the degree of differential expression is moderate for truly differentially expressed genes. For a significantly differentially expressed pathway, it is also of substantial interest to select important genes that drive the differential expression of the pathway.

Methods: We develop a unified framework to jointly test the significance of a pathway and to select a subset of genes that drive the significant pathway effect. To achieve dimension reduction and gene selection, we decompose each gene pathway into a single score by using a regularized form of linear discriminant analysis, called sparse linear discriminant analysis (sLDA). Testing for the significance of the pathway effect proceeds via permutation of the sLDA score. The sLDA-based test is compared with competing approaches with simulations and two applications: a study on the effect of metal fume exposure on immune response and a study of gene expression profiles among Type II Diabetes patients.

Results: Our results show that sLDA-based testing provides a powerful approach to test for the significance of a differentially expressed pathway and gene selection.

Availability: An implementation of the proposed sLDA-based pathway test in the R statistical computing environment is available at http://www.hsph.harvard.edu/∼mwu/software/

Contact:  xlin@hsph.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Direct interaction between sensor kinase proteins mediates acute and chronic disease phenotypes in a bacterial pathogen
Authors: Goodman Andrew L. , Merighi Massimo , Hyodo Mamoru , Ventre Isabelle , Filloux Alain , Lory Stephen
Published: January 2009

The genome of the opportunistic pathogen Pseudomonas aeruginosa encodes over 60 two-component sensor kinases and uses several (including RetS and GacS) to reciprocally regulate the production of virulence factors involved in the development of acute or chronic infections. We demonstrate that RetS modulates the phosphorylation state of GacS by a direct and specific interaction between these two membrane-bound sensors. The RetS–GacS interaction can be observed in vitro, in heterologous systems in vivo, and in P. aeruginosa. This function does not require the predicted RetS phosphorelay residues and provides a mechanism for integrating multiple signals without cross-phosphorylation from sensors to noncognate response regulators. These results suggest that multiple two-component systems found in a single bacterium can form multisensor signaling networks while maintaining specific phosphorelay pathways that remain insulated from detrimental cross-talk.
Allosteric control of Escherichia coli rRNA promoter complexes by DksA
Authors: Rutherford Steven T. , Villers Courtney L. , Lee Jeong-Hyun , Ross Wilma , Gourse Richard L.
Published: January 2009

The Escherichia coli DksA protein inserts into the RNA polymerase (RNAP) secondary channel, modifying the transcription initiation complex so that promoters with specific kinetic characteristics are regulated by changes in the concentrations of ppGpp and NTPs. We used footprinting assays to determine the specific kinetic intermediate, RPI, on which DksA acts. Genetic approaches identified substitutions in the RNAP switch regions, bridge helix, and trigger loop that mimicked, reduced, or enhanced DksA function on rRNA promoters. Our results indicate that DksA binding in the secondary channel of RPI disrupts interactions with promoter DNA at least 25 Å away, between positions −6 and +6 (the transcription start site is +1). We propose a working model in which the trigger loop and bridge helix transmit effects of DksA to the switch region(s), allosterically affecting switch residues that control clamp opening/closing and/or that interact directly with promoter DNA. DksA thus inhibits the transition to RPI. Our results illustrate in mechanistic terms how transcription factors can regulate initiation promoter-specifically without interacting directly with DNA.
Differential DNA damage signaling accounts for distinct neural apoptotic responses in ATLD and NBS
Authors: Shull Erin R.P. , Lee Youngsoo , Nakane Hironobu , Stracker Travis H. , Zhao Jingfeng , Russell Helen R. , Petrini John H.J. , McKinnon Peter J.
Published: January 2009

The MRN complex (Mre11/RAD50/NBS1) and ATM (ataxia telangiectasia, mutated) are critical for the cellular response to DNA damage. ATM disruption causes ataxia telangiectasia (A-T), while MRN dysfunction can lead to A-T-like disease (ATLD) or Nijmegen breakage syndrome (NBS). Neuropathology is a hallmark of these diseases, whereby neurodegeneration occurs in A-T and ATLD while microcephaly characterizes NBS. To understand the contrasting neuropathology resulting from Mre11 or Nbs1 hypomorphic mutations, we analyzed neural tissue from Mre11ATLD1/ATLD1 and Nbs1ΔB/ΔB mice after genotoxic stress. We found a pronounced resistance to DNA damage-induced apoptosis after ionizing radiation or DNA ligase IV (Lig4) loss in the Mre11ATLD1/ATLD1 nervous system that was associated with defective Atm activation and phosphorylation of its substrates Chk2 and p53. Conversely, DNA damage-induced Atm phosphorylation was defective in Nbs1ΔB/ΔB neural tissue, although apoptosis occurred normally. We also conditionally disrupted Lig4 throughout the nervous system using Nestin-cre (Lig4Nes-Cre), and while viable, these mice showed pronounced microcephaly and a prominent age-related accumulation of DNA damage throughout the brain. Either Atm−/− or Mre11ATLD1/ATLD1 genetic backgrounds, but not Nbs1ΔB/ΔB, rescued Lig4Nes-Cre microcephaly. Thus, DNA damage signaling in the nervous system is different between ATLD and NBS and likely explains their respective neuropathology.
Dscam and DSCAM: complex genes in simple animals, complex animals yet simple genes
Authors: Schmucker Dietmar , Chen Brian
Published: January 2009

Cadherins and the immunoglobulin (Ig) proteins give rise to a multitude of surface receptors, which function as diverse cell adhesion molecules (CAMs) or signal-transducing receptors. These functions are often interdependent, and rely on a high degree of specificity in homophilic binding as well as heterophilic interactions. The Drosophila receptor Dscam is an exceptional example of homophilic binding specificity involved in a number of important biological processes, such as neural wiring and innate immunity. Combinatorial use of alternatively spliced Ig-domains enables the generation of an estimated 18,000 isoform-specific homophilic receptor pairs. Although isoform diversity of Dscam is unique to arthropods, recent genetic analysis of vertebrate DSCAM (Down Syndrome Cell Adhesion Molecule) genes has revealed an intriguing conservation of molecular functions underlying neural wiring. This review covers the multiple functions of Dscam across different species highlighting its remarkable versatility as well as its conserved basic functions in neural development. We discuss how an unprecedented expansion of complex alternative splicing has been uniquely employed by arthropods to generate diverse surface receptors, important for cell–cell communication, molecular self-recognition in neurons, and innate immune defenses. We end with a speculative hypothesis reconciling the striking differences in Dscam and DSCAM gene structures with their conserved functions in molecular recognition underlying neural circuit formation.
A splicer that represses (translation)
Authors: Wharton Robin P.
Published: January 2009

Regulated translation and subcellular localization of maternal mRNAs underlies establishment of the antero–posterior axis in the Drosophila oocyte. In this issue of Genes & Development, Besse et al. (pp. 195–207) show that a molecule better known as a regulator of alternative splicing in the nucleus, polypyrimidine tract-binding protein (PTB), is required for repression of oskar mRNA in the cytoplasm. Their work suggests that PTB need not engage oskar mRNA in the nucleus for efficient repression, providing an important counterexample to the increasingly popular idea that cytoplasmic regulation initiates in the nucleus.
Evaluation of automated silver‐enhanced in situ hybridization (SISH) for detection of HER2 gene amplification in breast carcinoma excision and core biopsy specimens
Authors: Shousha S , Peston D , Amo‐Takyi B , Morgan M , Jasani B
Published: January 2009

Aims:  To validate the use of the silver‐enhanced in situ hybridization (SISH) technique in assessing HER2 status of breast carcinoma in excision biopsy specimens, and to assess its reliability in determining HER2 status in core biopsy specimens.

Methods and results:  Routinely processed paraffin sections of 65 excised breast carcinomas and 56 available preoperative core biopsy specimens from the same patients were selected from the archives for testing with the SISH technique using the automated Ventana Benchmark XT machine. For each case, two sections were used, one for the assessment of HER2 gene amplification and the other for assessment of chromosome 17. Of the 65 excision specimens tested, sections of 53 cases were also available for fluorescence in situ hybridization (FISH) examination. HER2 gene amplification was detected by SISH in 14 (21%) out of 65 excision specimens and in eight (14%) out of 56 core biopsy specimens. The results of SISH and FISH were identical in 50 (94%) out of the 53 excision cases examined by the two techniques. Two cases were SISH−, FISH+, and one case was the other way round. SISH results of core biopsy specimens and corresponding excision biopsy specimens were identical in 50 (89%) out of 56 cases. Four cases (7%) were SISH− in cores but positive in excision specimens, whereas two cases were the other way round.

Conclusions:  The results validate the use of the SISH technique for assessing HER2 status of excised breast carcinoma tissue sections. The results are comparable to those obtained with FISH, but SISH has the advantage of having a permanent end result that can be visualized by an ordinary light microscope. There is a reasonable 89% concordance between SISH results obtained in core and excision biopsy specimens. However, it may be prudent to postpone doing SISH, if possible, until sections of the resected specimen are available, as these seem to be more reliable.
Membranous and cytoplasmic staining of Ki67 is associated with HER2 and ER status in invasive breast carcinoma
Authors: Faratian Dana , Munro Alison , Twelves Christopher , Bartlett John MS
Published: January 2009

Aims:  Membranous and cytoplasmic Ki67 immunoreactivity has recently been observed in a number of histopathological entities, but frequency of occurrence and relationship to prognosis in more common cancers have not been described. The aim was to describe the pattern and frequency of membranous/cytoplasmic Ki67 in a cohort of invasive breast carcinomas, and their associations with grade, HER2 amplification and oestrogen receptor (ER) expression.

Methods and results:  Three hundred and twenty‐two cases of invasive ductal carcinoma were assessed for histological grade, Ki67 (MIB‐1 clone) proliferation index and pattern of immunoreactivity, ER expression by immunohistochemistry, and HER2 amplification status by fluorescence in situ hybridization. Overall, 26/322 (8%) breast carcinomas showed membranous/cytoplasmic Ki67, and expression was significantly associated with grade 3, HER2‐amplified and ER− tumours. Membranous/cytoplasmic Ki67 was not, however, an independent prognostic factor on multivariate analysis.

Conclusions:  Membranous/cytoplasmic Ki67 identifies a group of breast carcinomas that may be important to consider separately in prognostic and predictive studies. The mechanism of subcellular Ki67 relocalization remains elusive and further studies are required to establish both the cause and effect of this unusual pattern of Ki67 immunoreactivity.
Dirofilarial human cases in the Old World, attributed to Dirofilaria immitis : a critical analysis
Authors: Pampiglione Silvio , Rivasi Francesco , Gustinelli Andrea
Published: January 2009

Aims:  To review 28 cases of human dirofilariasis reported in the last 30 years in the Old World and attributed, by their respective authors, to Dirofilaria immitis or a species of Dirofilaria other than D. repens.

Methods and results:  Each case was analysed by examining the published accounts or by discussions with the authors, who were interviewed whenever possible.

Conclusions:  On the basis of these analyses we conclude that there is as yet no proof demonstrating with certainty that Old World D. immitis plays a pathogenic role in humans. It remains to be explained why D. immitis causes pulmonary infections in humans in the Americas while, in the Old World, this location appears, instead, to be always associated with D.repens, even though the former species is at times more frequent than the latter both in dogs and in the vectors. To explain this apparently different pathogenic power, two hypotheses are proposed: (i) there are perhaps twin populations with different genotypes on the two sides of the Atlantic, with different infective capacity for man and dog; (ii) the infective capacity to humans of the parasite could be modified, only in the Old World, by some unidentified factor, possibly inherent to the vector, that affects the complex mechanism of the vector–parasite relationship, affecting the survival of the larvae.
DMBT1 expression distinguishes anorectal from cutaneous melanoma
Authors: Helmke Burkhard Maria , Renner Marcus , Poustka Annemarie , Schirmacher Peter , Mollenhauer Jan , Kern Michael André
Published: January 2009

Aims:  Anorectal melanoma (AM) forms a rare but highly malignant subset of mucosal melanoma with an extremely poor prognosis. Although AMs display histological and immunohistochemical features very similar to cutaneous melanoma (CM), no association exists either with exposure to ultraviolet light or with melanocytic naevi. While AMs are clearly distinguished from CM by displaying few BRAF mutations, they are commonly indistinguishable from CM at the level of gene expression. The aim was to carry out expression analyses of classical immunohistochemical markers and of the protein deleted in malignant brain tumours 1 (DMBT1) in cases of primary anorectal malignant melanoma and CM.

Methods and results:  Expression analyses of classical immunohistochemical markers (S100, HMB45, Melan A and MiTF) and of the protein DMBT1 were carried out in 27 cases of primary anorectal malignant melanoma and 26 cases of CM. All AM cases analysed showed expression of at least three of the classical markers for melanoma. However, immunohistochemistry showed 19 out of 27 AM to be positive for DMBT1, which represented a statistically significant difference (P = 0.0009) compared with CM (six out of 26), which more commonly are negative for DMBT1 expression.

Conclusion:  These results identify DMBT1 as a molecular feature that may allow distinction between AM and CM and support the notion that AM represents an entity molecularly distinct from CM.
Expression of BAFF‐R and TACI in reactive lymphoid tissues and B‐cell lymphomas
Authors: Wada Kiriko , Maeda Kunihiko , Tajima Katsushi , Kato Takeo , Kobata Tetsuji , Yamakawa Mitsunori
Published: January 2009

Aims:  The receptor for B‐cell‐activating factor belonging to the tumour necrosis factor family (BAFF‐R) and transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI) have been established as binding molecules to BAFF. The aim of this study was to determine the pathological diagnostic roles and clinical significance of these BAFF‐binding receptors in B‐cell neoplasms.

Methods and results:  Expression of BAFF‐R and TACI was examined immunohistochemically in reactive lymphoid tissues and B‐cell lymphomas including diffuse large B‐cell lymphoma (DLBCL), follicular lymphoma (FL), mantle cell lymphoma (MCL), marginal zone B‐cell lymphoma (MZBCL) and plasma cell myeloma (PCM). In reactive tissues BAFF‐R was expressed exclusively in the cells of the mantle zone and within the germinal centres (GCs), whereas TACI appeared positive in the scattered cells in extrafollicular areas. There were variable patterns of expression of BAFF‐R and TACI amongst the different types of B‐cell lymphomas (MCL and FL: BAFF‐R+TACI−; PCM: BAFF‐R−TACI+; DLBCL and MZBCL: variable expression). Reverse transcriptase‐polymerase chain reaction studies supported these results. The overall survival of the BAFF‐R+ DLBCL group was significantly better than that of the BAFF‐R− group.

Conclusions:  These results indicate that the assessment of expression of BAFF‐binding receptors aids subclassification and prognostication of DLBCL.
Glacial refugia influence plant diversity patterns in the Mediterranean Basin
Authors: Médail Frédéric , Diadema Katia
Published: January 2009

Aim  The aims of this study were to assess the distribution of putative Mediterranean refugia of plants, to compare the locations of refugia and those of regional hotspots of plant biodiversity, and to provide a critical analysis of the Mediterranean refugium paradigm. Furthermore, we consider how biogeographical and genetic results can be combined to guide global conservation strategies.

Location  The Mediterranean region.

Methods  We started from a detailed analysis of the scientific literature (1993–2007) in order to identify refugia in the Mediterranean region, based on intra‐specific phylogeographical studies of plant species. We used population locations together with gene‐pool identity to establish the database, comparing patterns of phylogeographical concordance with the locations of Mediterranean refugia. We then tested the biogeographical congruence between two biodiversity components, namely phylogeographical refugia and regional hotspots.

Results  We identified 52 refugia in the Mediterranean bioclimatic region and confirmed the role played by the three major peninsulas, with a shared total of 25 refugia. We emphasize the importance of areas that have previously been attributed a lesser role (large Mediterranean islands, North Africa, Turkey, Catalonia). Of the 52 refugia identified, 33 are situated in the western Mediterranean Basin and 19 in the eastern part. The locations of the phylogeographically defined refugia are significantly associated with the 10 regional hotspots of plant biodiversity, with 26 of these refugia (i.e. 50%) occurring within the hotspots.

Main conclusions  The locations of refugia are determined by complex historical and environmental factors, the cumulative effects of which need to be considered because they have occurred since the Tertiary, rather than solely during the last glacial period. Refugia represent climatically stable areas and constitute a high conservation priority as key areas for the long‐term persistence of species and genetic diversity, especially given the threat posed by the extensive environmental change processes operating in the Mediterranean region. The refugia defined here represent ‘phylogeographical hotspots’; that is, significant reservoirs of unique genetic diversity favourable to the evolutionary processes of Mediterranean plant species.
Large‐scale spatial patterns in the distribution of Collembola (Hexapoda) species in Antarctic terrestrial ecosystems
Authors: Caruso Tancredi , Hogg Ian D. , Carapelli Antonio , Frati Francesco , Bargagli Roberto
Published: January 2009

Aim  We tested whether the distribution of three common springtail species (Gressittacantha terranova, Gomphiocephalus hodgsoni and Friesea grisea) in Victoria Land (Antarctica) could be modelled as a function of latitude, longitude, altitude and distance from the sea.

Location  Victoria Land, Ross Dependency, Antarctica.

Methods  Generalized linear models were constructed using species presence/absence data relative to geographical features (latitude, longitude, altitude, distance from sea) across the species’ entire ranges. Model results were then integrated with the known phylogeography of each species and hypotheses were generated on the role of climate as a major driver of Antarctic springtail distribution.

Results  Based on model selection using Akaike’s information criterion, the species’ distributions were: hump‐shaped relative to longitude and monotonic with altitude for Gressittacantha terranova; hump‐shaped relative to latitude and monotonic with altitude for Gomphiocephalus hodgsoni; and hump‐shaped relative to longitude and monotonic with latitude, altitude and distance from the sea for Friesea grisea.

Main conclusions  No single distributional pattern was shared by the three species. While distributions were partially a response to climatic spatial clines, the patterns observed strongly suggest that past geological events have influenced the observed distributions. Accordingly, present‐day spatial patterns are likely to have arisen from the interaction of historical and environmental drivers. Future studies will need to integrate a range of spatial and temporal scales to further quantify their respective roles.
Putative glacial refugia of Cedrus atlantica deduced from Quaternary pollen records and modern genetic diversity
Authors: Cheddadi R. , Fady B. , François L. , Hajar L. , Suc J.‐P. , Huang K. , Demarteau M. , Vendramin G. G. , Ortu E.
Published: January 2009

Aim  To investigate the impact of past environmental changes on Cedrus atlantica and its current genetic diversity, and to predict its future distribution.

Location  Morocco, Algeria and Tunisia.

Methods  Eleven fossil pollen records from these three countries were used to locate putative glacial refugia and to reconstruct past climate changes. A mechanistic vegetation distribution model was used to simulate the distribution of C. atlantica in the year 2100. In addition, a genetic survey was carried out on modern Moroccan C. atlantica.

Results  Pollen records indicate that Cedrus was present during the last glacial period, probably in scattered refugia, in Tunisia, Algeria and Morocco. In the Tunisian and Algerian sites, cedar expanded during the late glacial and the early Holocene, then disappeared after c. 8000 yr bp. Reconstructed mean annual precipitation and January temperature show that the last glacial period in Morocco was cooler by 10–15°C and drier by c. 300–400 mm year−1 than the climate today. Modern chloroplast microsatellites of 15 C. atlantica populations in Morocco confirm the presence of multiple refugia and indicate that cedar recolonized the Moroccan mountains fairly recently. Model simulation indicates that by the year 2100 the potential distribution of C. atlantica will be much restricted with a potential survival area located in the High Atlas.

Main conclusions  Environmental changes in northern Africa since the last glacial period have had an impact on the geographical distribution of C. atlantica and on its modern genetic diversity. It is possible that by the end of this century C. atlantica may be unable to survive in its present‐day locations. To preserve the species, we suggest that seedlings from modern C. atlantica populations located in the High Atlas mountains, where a high genetic diversity is found, be transplanted into the western High Atlas.
Sailing through the Late Pleistocene: unusual historical demography of an East Asian endemic, the Chinese Hwamei (Leucodioptron canorum canorum), during the last glacial period
Authors: LI SHOU‐HSIEN , YEUNG CAROL K‐L. , FEINSTEIN JULIE , HAN LIANXIAN , LE MANH HUNG , WANG CHI‐XAN , DING PING
Published: January 2009

Pleistocene climate fluctuations shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Late Pleistocene for East Asia, a region of great topographical complexity and presumably milder historical climate, remains poorly understood. We analysed 3.86 kb of the mitochondrial genome of 186 Chinese Hwamei birds,Leucodioptron canorum canorum, and found that contrary to the conventional expectation of population decline during cold periods (stadials), the demographic history of this species shows continuous population growth since the penultimate glacial period (about 170 000 years ago). Refugia were identified in the south, coastal regions, and northern inland areas, implying that topographic complexity played a substantial role in providing suitable habitats for the Chinese Hwamei during cold periods. Intermittent gene flow between these refugia during the warmer periods (interstadials) might have resulted in a large effective population of this bird through the last glacial period.
New Zealand triplefin fishes (family Tripterygiidae): contrasting population structure and mtDNA diversity within a marine species flock
Authors: HICKEY ANTHONY J. R. , LAVERY SHANE D. , HANNAN DANIELLE A. , BAKER C. SCOTT , CLEMENTS KENDALL D.
Published: January 2009

Triplefin fishes (Family Tripterygiidae) dominate the New Zealand temperate coastal fish fauna in diversity (26 endemic species, 14 genera). Most species appear to have evolved as a local radiation and mostly occupy sympatric distributions throughout New Zealand. To investigate the forces driving current gene‐flow patterns and past evolutionary histories, we searched for common patterns of population genetic subdivision within eight species sampled throughout their distributions [mitchochondrial DNA (mtDNA) control region, n = 1086]. We hypothesised that common phylogeographical and population differentiation patterns would reveal past or ongoing physical processes, with differences reflecting stochastic or species‐specific processes. Striking differences between species were apparent, with strong phylogeographical structure detected in Grahamina capito and the estuarine species G. nigripenne. G. capito fell into three distinct geographically restricted lineages. G. nigripenne largely separated into northern and southern lineages (ΦST 0.834). Strong population structuring and isolation by distance was evident in Bellapiscis medius, B. lesleyae and Forsterygion lapillum (ΦST 0.686, 0.436 and 0.115, respectively). High gene flow was apparent in G. gymnota and Ruanoho whero, and F. varium. However, for the latter species, isolation was apparent with samples collected from the offshore Three Kings Islands. Overall, a strong relationship was found between habitat depth and population structure among species, and species inhabiting shallower water habitats showed lower genetic diversity with higher levels of population subdivision. High‐latitude populations generally showed low haplotype and nucleotide diversity. These data suggest that processes resulting from intraspecific differences in habitat preference, climatic histories and/or larval ecologies have subdivided populations of shallow water triplefin species.