Najm WI,Lie D,Shapiro J,Llenderrozos HJ
Department of Family Medicine, University of California-Irvine, Orange, CA 92868, USA. winajm@uci.edu
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Group medical visits as a teaching tool in a family medicine clerkship.
Fam Med. 2009 Oct;41(9):625-31
OBJECTIVE: We sought to determine medical students' learning outcomes following exposure to a 4-hour group medical visit (GMV) curriculum that focused on Spanish-speaking patients who had diabetes. The GMV was part of a 4-week block family medicine clerkship for third-year medical students. METHODS: We conducted a 1-year longitudinal, prospective study using a before and after survey and a qualitative analysis of end-of-clerkship reflective essays. Eleven survey questions captured change in knowledge about GMV resources, cultural knowledge, and attitudes toward the GMV model. RESULTS: Ninety students completed the surveys. Fifty students chose to write about the GMV experience in their reflective essays. On the survey, a significant change was found in students' knowledge about culture-specific diabetic resources, cultural knowledge, and self-reported knowledge and attitude about GMVs. Qualitative analysis of the narratives and essays supported and strengthened this finding of positive attitudes about the importance of cultural competency and physician role modeling in the context of the patient-doctor relationship. CONCLUSIONS: Exposure to a 4-hour GMV curriculum is associated with knowledge gain. It is also associated with a positive attitude change, congruent with learning about the relevance of patient-doctor relationship within a cross-cultural setting.
PMID: 19816825
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Aguilar RM,Steward O
Reeve-Irvine Research Center, University of California Irvine, Department of Anatomy and Neurobiology, 1105 Gillespie Neuroscience Research Facility, Irvine CA 92607-4292, USA.
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A bilateral cervical contusion injury model in mice: assessment of gripping strength as a measure of forelimb motor function.
Exp Neurol. 2009 Oct 5;:
Here, we describe a bilateral cervical contusion model for mice. Adult female mice received graded bilateral contusion injuries at cervical level 5 (C5) using a commercially available impactor (the IH device). Three separate experiments were carried out to define conditions that produce impairments in forelimb function without unacceptable impairment of general health. A grip strength meter (GSM) was used to assess gripping ability as a measure of forelimb motor function; lesion size was assessed histologically by staining cross sections for H and E and GFAP. In Experiment 1, mice received injuries of 30 kilodynes (kdyn); these produced minimal deficits on grip strength. In Experiment 2, mice received injuries of 75 kdyn and 100 kdyn. Injuries of 75 kdyn produced transient deficits in gripping that recovered between 3-15 dpi to about 90% of control; injuries of 100 kdyn produced deficits that recovered to about 50% of control. In Experiment 3, none of the mice that received injuries of 100 kdyn recovered gripping ability. Histological assessment revealed graded injuries that ranged from damage limited primarily to the dorsal column (DC) to damage to the DC, grey matter, ventral column and lateral column. Most lesions filled in with a fibrous tissue matrix, but fluid-filled cystic cavities were found in 13% of the 100 kdyn injury group and a combination of fibrous-filled/fluid-filled cystic cavities were found in 22% and 38% of the 75 kdyn and 100 kdyn injury groups, respectively. There was minimal urine retention following cervical contusion injuries indicating preservation of bladder function. Our results define conditions to produce graded bilateral cervical contusion injuries in mice and demonstrate the usefulness of the GSM for assessing forelimb motor function after cervical contusions.
PMID: 19815010
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Guo ZL,Tjen-A-Looi SC,Fu LW,Longhurst JC
Department of Medicine, School of Medicine, University of California, Susan-Samueli Center for Integrative Medicine, Irvine, Irvine, California 92697-4075, USA. zguo@uci.edu
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Nitric oxide in rostral ventrolateral medulla regulates cardiac-sympathetic reflexes: role of synthase isoforms.
Am J Physiol Heart Circ Physiol. 2009 Oct;297(4):H1478-86
Our previous studies have shown that nitric oxide (NO) synthase (NOS)-containing neurons in the rostral ventrolateral medulla (rVLM) are activated during cardiac sympathoexcitatory reflexes (Refs. 12 and 13). However, the precise function of NO in the rVLM in regulation of these reflexes has not been defined. Three isoforms of NOS, including neuronal NOS (nNOS), inducible NOS (iNOS), and endothelial NOS (eNOS), are located in the rVLM. We explored the role of NO, derived from different NOS isoforms in the rVLM, in processing cardiac-sympathetic reflexes using whole animal reflex and electrophysiological approaches. We found that, in anesthetized cats, increased mean arterial blood pressure and renal sympathetic nerve activity elicited by epicardial application of bradykinin (BK; 1-10 microg/ml, 50 microl) were significantly attenuated following unilateral rVLM microinjection of the nonselective NOS inhibitor, N(omega)-nitro-L-arginine methyl ester (50 nmol/50 nl), or a specific nNOS inhibitor, 7-nitroindazole (7-NI; 5-10 pmol/50 nl; both P < 0.05). In contrast, the responses of mean arterial blood pressure and renal sympathetic nerve activity to cardiac BK stimulation were unchanged by unilateral rVLM microinjection of N(omega)-nitro-D-arginine methyl ester (inactive isomer of N(omega)-nitro-L-arginine methyl ester, 50 nmol/50 nl), 3-6% methanol (7-NI vehicle), N(6)-(1-iminoethyl)-L-lysine (250 pmol/50 nl; iNOS inhibitor), or N(5)-(1-iminoethyl)-L-ornithine (250 nmol/50 nl; eNOS inhibitor). Furthermore, in separate cats, we noted that iontophoresis of 7-NI (0.1 mM) reduced the increased discharge of cardiovascular sympathoexcitatory rVLM neurons in response to cardiac stimulation with BK (P < 0.05). These neurons were characterized by their responses to inputs from baroreceptors, and their cardiac rhythmicity was determined through frequency and time domain analyses, correlating their discharge to arterial blood pressure and cardiac sympathetic efferent nerve activity. These data suggest that NO, specifically nNOS, mediates sympathetic cardiac-cardiovascular responses through its action in the rVLM.
PMID: 19684188
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Magliola R,Althabe M,Moreno G,Lenz AM,Pilan ML,Landry L,Balestrini M,Charroqui A,Vassallo JC,Salgado G,Martín A,Barretta J,Cornelis J,García Delucis P,Suárez J,Laura JP
UCI 35. Recuperación Cardiovascular, Hospital Nacional de Pediatría Prof. Dr. Juan P. Garrahan.
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[Cardiac surgical repair in newborns: five years' experience in neonatal open surgery]
Arch Argent Pediatr. 2009 Oct;107(5):417-22
INTRODUCTION: Four hundred newborns die every year in our country suffering from congenital heart disease. Definitive surgical repair, whenever possible, is nowadays the optimal therapeutic strategy. Our goal is to describe mortality and morbidity in neonatal surgery with cardiopulmonary bypass in a tertiary public hospital in Argentina. PATIENTS AND METHODS: Descriptive, retrospective study. Every patient, younger than 45 days, with cardiac surgery requiring cardiopulmonary bypass, at the Garrahan Hospital between 2004 and 2008 was included. Demographic, surgical and postoperative data were collected. Adjusted mortality risk analysis, and descriptive statistics from the most frequent diagnosis were performed. Results are expressed as median and rank or percentage. RESULTS: 200 newborns were operated, 62% males. Median age was 21 days (r 1- 45) and median weight 3.1 kg (r 1.6-6.2). Total anomalous pulmonary venous return, transposition of great arteries an hypoplastic left heart syndrome diagnoses accounted for 75% of the procedures. Median length of stay was 12 days (r 0-191), and 6 days of mechanical ventilation (r 0-180). Eighteen percent of the patients required peritoneal dialysis. Whole series mortality was 19% and fell to 14% in 2008. Unstable preoperative condition and postoperative complications increased mortality, OR= 2.23 (1.02-4.89) and OR= 10 (3.6-33.4), respectively. CONCLUSIONS: Our postoperative mortality is similar to those reported in foreign countries databases. Patients with unstable preoperative condition and post-operative complications had higher mortality.
PMID: 19809762
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Rappoport D,Furche F
Department of Chemistry, University of California, Irvine, CA 92697-2025, USA. d.rappoport@uci.edu.
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Structure of endohedral fullerene Eu@C(74).
Phys Chem Chem Phys. 2009 Aug 14;11(30):6353-8
Structure determination of endohedral fullerenes in the absence of X-ray data is difficult and often controversial. Here we show that the structure of endohedral fullerene Eu@C(74) may be determined by density functional theory aided interpretation of its electronic, infrared and Raman spectra. The use of recently developed analytical polarizability gradient methods to simulate resonance-enhanced Raman spectra is crucial for this approach and allows for a nearly complete assignment of the experimental spectra. Eu@C(74) is assigned a pear-shaped C(2v) symmetric structure and shows strong ionic interaction between the encapsulated metal and the fullerene pi system.
PMID: 19809666
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Braunstein ML
Department of Cognitive Sciences, University of California, Irvine 92697-5100, USA. myron.braunstein@uci.edu
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Motion parallax with and without active head movements.
Perception. 2009;38(6):912-3; discussion 917-9
PMID: 19806986
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Vaughan E,Tinker T
Department of Psychology and Social Behavior, University of California, 3340 Social Ecology 2, Irvine, CA 92697, USA. evaughan@uci.edu
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Effective health risk communication about pandemic influenza for vulnerable populations.
Am J Public Health. 2009 Oct;99 Suppl 2:S324-32
The consequences of pandemic influenza for vulnerable populations will depend partly on the effectiveness of health risk communications. Strategic planning should fully consider how life circumstances, cultural values, and perspectives on risk influence behavior during a pandemic. We summarize recent scientific evidence on communication challenges and examine how sociocultural, economic, psychological, and health factors can jeopardize or facilitate public health interventions that require a cooperative public. If ignored, current communication gaps for vulnerable populations could result in unequal protection across society during an influenza pandemic. We offer insights on communication preparedness gleaned from scientific studies and the deliberations of public health experts at a meeting convened by the Centers for Disease Control and Prevention, May 1 and 2, 2008.
PMID: 19797744
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Liss MA,Leifer S,Sakakine G,Esparza M,Clayman RV
Department of Urology, University of California, Irvine, California 92868, USA. mliss@uci.edu
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The Liss maneuver: a nonendoscopic technique for difficult Foley catheterization.
J Endourol. 2009 Aug;23(8):1227-30
PURPOSE: Difficult male catheterization often results in the need for bedside cystoscopy; herein, we describe a simple maneuver that may preclude the need for a more involved and expensive endoscopic procedure. MATERIALS AND METHODS: A 0.035-inch Amplatz Super Stiff guidewire was placed floppy end first, down an 18F Foley catheter lumen; the guidewire was then clamped proximally to the body of the catheter at its point of exit. To test the added stiffness that the wire imparted to the tip and body of the catheter, different size Bardex I.C. Foley catheters were tested with a 0.035-inch 145-cm Amplatz Super Stiff guidewire placed in an Chattillon Force Gauge (TCM 201 Asset #4665) to measure bending force and tip strength in pounds of pressure. RESULTS: The catheter body bending force (stiffness) was increased on average 359%, but the tip of the catheter, holding the floppy end of the guidewire, showed no significant increase in stiffness. A trend was seen showing larger percent differences in stiffness for smaller catheters (12F and 14F); indeed, the guidewire shaft stiffness approached the same stiffness as the shaft of a standard 20F catheter, but the stiffness of the catheter's tip remained unchanged. Clinically, the guidewire stiffening technique was used successfully in five of six patients; the failure was in a patient with a hitherto undiagnosed 8F urethral stricture. CONCLUSION: In cases of difficult bladder catheter placement, the Super Stiff guidewire technique can be used to increase the stiffness of the catheter to navigate the torturous urethra with any size catheter before pursuing other more invasive and time-consuming techniques. If this maneuver fails, the same guidewire can be used in conjunction with the flexible endoscope to then place a Councill catheter.
PMID: 19558222
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Philips GT,Carew TJ
Department of Neurobiology and Behavior and the Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, CA 92607-4450, USA.
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It's all about timing.
Cell. 2009 Oct 2;139(1):23-5
In the formation of long-term memories, a "spaced" distribution of study sessions is more beneficial than closely spaced "massed" study sessions. Pagani et al. (2009) examine the molecular basis of this spacing effect in Drosophila and find a role for the SHP2 homolog, corkscrew, an activator of Ras/MAPK signaling, in establishing optimal spacing intervals.
PMID: 19804749
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Frank SA
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA. safrank@uci.edu
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The common patterns of nature.
J Evol Biol. 2009 Aug;22(8):1563-85
We typically observe large-scale outcomes that arise from the interactions of many hidden, small-scale processes. Examples include age of disease onset, rates of amino acid substitutions and composition of ecological communities. The macroscopic patterns in each problem often vary around a characteristic shape that can be generated by neutral processes. A neutral generative model assumes that each microscopic process follows unbiased or random stochastic fluctuations: random connections of network nodes; amino acid substitutions with no effect on fitness; species that arise or disappear from communities randomly. These neutral generative models often match common patterns of nature. In this paper, I present the theoretical background by which we can understand why these neutral generative models are so successful. I show where the classic patterns come from, such as the Poisson pattern, the normal or Gaussian pattern and many others. Each classic pattern was often discovered by a simple neutral generative model. The neutral patterns share a special characteristic: they describe the patterns of nature that follow from simple constraints on information. For example, any aggregation of processes that preserves information only about the mean and variance attracts to the Gaussian pattern; any aggregation that preserves information only about the mean attracts to the exponential pattern; any aggregation that preserves information only about the geometric mean attracts to the power law pattern. I present a simple and consistent informational framework of the common patterns of nature based on the method of maximum entropy. This framework shows that each neutral generative model is a special case that helps to discover a particular set of informational constraints; those informational constraints define a much wider domain of non-neutral generative processes that attract to the same neutral pattern.
PMID: 19538344
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Mulder GB,Pritchett K
University Laboratory Animal Resources, University of California-Irvine, 147 BSA, Irvine, California 92612-1310, USA.
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The Morris water maze.
Contemp Top Lab Anim Sci. 2003 Mar;42(2):49-50
PMID: 19757627
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Farid M,Steinert RF
Gavin Herbert Eye Institute, University of California, Irvine, California 92697-4375, USA. mfarid@uci.edu
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Patient selection for monovision laser refractive surgery.
Curr Opin Ophthalmol. 2009 Jul;20(4):251-4
PURPOSE OF REVIEW: To investigate the preoperative characteristics and updated patient selection criteria for presbyopic patients undergoing laser refractive surgery for monovision. RECENT FINDINGS: The role of age, sex, ocular dominance, amount of monovision, and hyperopic versus myopic treatments is reviewed and reported. The presbyopic female patient is less likely to reject monovision. Patients with a strong sighting preference do less well due to reduced interocular blur suppression. Although myopes represent the majority of monovision patients, laser-corrected monovision in hyperopes is a viable and satisfactory option. SUMMARY: Refractive surgery monovision correction represents an increasingly popular method for the presbyopic patient. Patient selection based on multiple preoperative characteristics is vitally important to the overall success and patient satisfaction.
PMID: 19491684
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German DP
Department of Zoology, University of Florida, Gainesville, FL, USA. dgerman@uci.edu
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Do herbivorous minnows have "plug-flow reactor" guts? Evidence from digestive enzyme activities, gastrointestinal fermentation, and luminal nutrient concentrations.
J Comp Physiol B. 2009 Aug;179(6):759-71
Few investigations have empirically analyzed fish gut function in the context of chemical reactor models. In this study, digestive enzyme activities, levels of gastrointestinal fermentation products [short chain fatty acids (SCFA)], luminal nutrient concentrations, and the mass of gut contents were measured along the digestive tract in herbivorous and carnivorous minnows to ascertain whether their guts function as "plug-flow reactors" (PFRs). Four of the species, Campostoma anomalum, C. ornatum, C. oligolepis, and C. pauciradii, are members of a monophyletic herbivorous clade, whereas the fifth species, Nocomis micropogon, is a carnivore from an adjacent carnivorous clade. In the context of a PFR model, the activities of amylase, trypsin and lipase, and the concentrations of glucose, protein, and lipid were predicted to decrease moving from the proximal to the distal intestine. I found support for this as these enzyme activities and nutrient concentrations generally decreased moving distally along the intestine of the four Campostoma species. Furthermore, gut content mass and the low SCFA concentrations did not change (increase or decrease) along the gut of any species. Combined with a previous investigation suggesting that species of Campostoma have rapid gut throughput rates, the data presented here generally support Campostoma as having guts that function as PFRs. The carnivorous N. micropogon showed some differences in the measured parameters, which were interpreted in the contexts of intake and retention time to suggest that PFR function breaks down in this carnivorous species.
PMID: 19363616
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Das K,Rizzuto DS,Nenadic Z
Department of Psychology, University of California, Santa Barbara, CA 93106, USA. kdas@uci.edu
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Mental state estimation for brain--computer interfaces.
IEEE Trans Biomed Eng. 2009 Aug;56(8):2114-22
Mental state estimation is potentially useful for the development of asynchronous brain--computer interfaces. In this study, four mental states have been identified and decoded from the electrocorticograms (ECoGs) of six epileptic patients, engaged in a memory reach task. A novel signal analysis technique has been applied to high-dimensional, statistically sparse ECoGs recorded by a large number of electrodes. The strength of the proposed technique lies in its ability to jointly extract spatial and temporal patterns, responsible for encoding mental state differences. As such, the technique offers a systematic way of analyzing the spatiotemporal aspects of brain information processing and may be applicable to a wide range of spatiotemporal neurophysiological signals.
PMID: 19457738
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Kaiser ML,Rubinstein M,Vokes DE,Ridgway JM,Guo S,Gu M,Crumley RL,Armstrong WB,Chen Z,Wong BJ
Department of Surgery, University of California Irvine, Orange, CA 92612, USA.
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Laryngeal epithelial thickness: a comparison between optical coherence tomography and histology.
Clin Otolaryngol. 2009 Oct;34(5):460-6
OBJECTIVES: Optical coherence tomography, an imaging modality using near-infrared light, produces cross-sectional tissue images with a lateral pixel resolution of 10 microm. However, normative data is first needed on epithelial thickness for lesion characterisation, and, to date, little exists. The purpose of our study is to measure normal laryngeal epithelial thickness by in vivo optical coherence tomography, and compare these values to those obtained from fixed ex-vivo laryngectomy specimens. DESIGN AND SETTING: Prospective at a single medical center in California, United States. PARTICIPANTS: A total of 116 patients undergoing operative endoscopy. MAIN OUTCOME MEASURES: Optical coherence tomography images of clinically normal laryngeal subsites were selected. Calibrated measurements of epithelial thickness at various laryngeal subsites were recorded. Measurements of epithelial thickness from corresponding areas were obtained using optical micrometry on histologically normal regions of 15 total laryngectomy specimens. Descriptive statistics were performed. RESULTS: Mean epithelial optical coherence tomography thicknesses were: true vocal cords (81 microm), false vocal cords (78 microm), subglottis (61 microm), aryepiglottic folds (111 microm), laryngeal epiglottis (116 microm) and lingual epiglottis (170 microm). Epithelial thicknesses in fixed tissues were: true vocal cords (103 microm), false vocal cords (79 microm), aryepiglottic folds (205 microm) subglottis (61 microm), laryngeal epiglottis (38 microm) and lingual epiglottis (130 microm). CONCLUSIONS: Optical coherence tomography does not have the artifacts associated with conventional histologic techniques. The inevitable development of office-based optical coherence tomography devices will increase the precision of laryngeal measurements and contribute to the clinical application of this technology in diagnosing laryngeal disease.
PMID: 19793279
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Liu ZF,Burke K
Department of Chemistry, University of California, Irvine, California 92697-2025, USA. zhenfei.liu@uci.edu
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Adiabatic connection for strictly correlated electrons.
J Chem Phys. 2009 Sep 28;131(12):124124
Modern density functional theory (DFT) calculations employ the Kohn-Sham system of noninteracting electrons as a reference, with all complications buried in the exchange-correlation energy (E(XC)). The adiabatic connection formula gives an exact expression for E(XC). We consider DFT calculations that instead employ a reference of strictly correlated electrons. We define a "decorrelation energy" that relates this reference to the real system, and derive the corresponding adiabatic connection formula. We illustrate this theory in three situations, namely, the uniform electron gas, Hooke's atom, and the stretched hydrogen molecule. The adiabatic connection for strictly correlated electrons provides an alternative perspective for understanding DFT and constructing approximate functionals.
PMID: 19791869
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Villarreal LP
Center for Virus Research, University of California, Irvine, CA 92697, USA. lpvillar@uci.edu
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Persistence pays: how viruses promote host group survival.
Curr Opin Microbiol. 2009 Aug;12(4):467-72
Recently, we have realized that viruses numerically dominate all life. Although viruses are known to affect host survival in populations, this has not been previously evaluated in the context of host group selection. Group selection per se is not a currently accepted idea and its apparent occurrence is explained by statistical gene frequency models of kin selection. Viruses were not considered in such models. Prevalent views associate viruses and disease. Yet many viruses establish species-specific persistent, inapparent infections that are stable on an evolutionary time scale. Such persistent infections can have large effects on relative reproductive fitness of competing host populations. In this essay, I present arguments on how persistent infections can promote population survival. Mouse hepatitis virus is used as well studied examplar to re-evaluate the theoretical basis of the mouse haystack model of M Smith. This virus-centric re-examination concludes that viruses can indeed affect and promote relative group selection.
PMID: 19608458
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Perret D,Luo ZD
Department of Anesthesiology & Perioperative Care, School of Medicine, University of California Irvine, Irvine, California 92697; Department of Physical Medicine & Rehabilitation, School of Medicine, University of California Irvine, Irvine, California 92697.
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Targeting voltage-gated calcium channels for neuropathic pain management.
Neurotherapeutics. 2009 Oct;6(4):679-92
Voltage-gated calcium channels (VGCC) play obligatory roles in diverse physiological functions. Pathological conditions leading to changes in their biophysical properties and expression levels may cause malfunctions of VGCC-mediated activities, resulting in disease states. It is believed that changes in VGCC properties under pain-inducing conditions may play a causal role in the development of chronic pain, including nerve injury-induced pain or neuropathic pain. For the past several decades, preclinical and clinical research in developing VGCC blockers or modulators for chronic pain management has been fruitful, leading to some U.S. Food and Drug Administration-approved drugs currently available for chronic pain management. However, their efficacy in pain relief is limited in some patients, and their long-term use is limited by their side-effect profiles. Certainly, there is room for improvement in developing more subtype-specific VGCC blockers or modulators for chronic pain conditions. In this review, we summarized the most recent preclinical and clinical studies related to chronic pain medications acting on the VGCC. We also included clinical trials aiming to expand the application of approved VGCC drugs to different pain states derived from various pathological conditions, as well as drug combination therapies trying to improve the efficacies and side-effect profiles of current pain medications.
PMID: 19789072
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Sendroiu IE,Warner ME,Corn RM
Department of Chemistry, University of California-Irvine, Irvine, California 92697.
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Fabrication of silica-coated gold nanorods functionalized with DNA for enhanced surface plasmon resonance imaging biosensing applications.
Langmuir. 2009 Oct 6;25(19):11282-4
A novel method for preparing gold nanorods that are first coated with a thin silica film and then functionalized with single-stranded DNA (ssDNA) is presented. Coating the nanorods with 3-5 nm of silica improves their solubility and stability. Amine-modified ssDNA is attached to the silica-coated gold nanorods via a reductive amination reaction with an aldehyde trimethoxysilane monolayer. The nanorods exhibit an intense absorption band at 780 nm, and are used to enhance the sensitivity of surface plasmon resonance imaging (SPRI) measurements on DNA microarrays.
PMID: 19788208
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Zhang C,Truong KK,Zhou QY
Department of Pharmacology, University of California Irvine, Irvine, California, United States of America.
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Efferent projections of prokineticin 2 expressing neurons in the mouse suprachiasmatic nucleus.
PLoS One. 2009;4(9):e7151
The suprachiasmatic nucleus (SCN) in the hypothalamus is the predominant circadian clock in mammals. To function as a pacemaker, the intrinsic timing signal from the SCN must be transmitted to different brain regions. Prokineticin 2 (PK2) is one of the candidate output molecules from the SCN. In this study, we investigated the efferent projections of PK2-expressing neurons in the SCN through a transgenic reporter approach. Using a bacterial artificial chromosome (BAC) transgenic mouse line, in which the enhanced green fluorescence protein (EGFP) reporter gene expression was driven by the PK2 promoter, we were able to obtain an efferent projections map from the EGFP-expressing neurons in the SCN. Our data revealed that EGFP-expressing neurons in the SCN, hence representing some of the PK2-expressing neurons, projected to many known SCN target areas, including the ventral lateral septum, medial preoptic area, subparaventricular zone, paraventricular nucleus, dorsomedial hypothalamic nucleus, lateral hypothalamic area and paraventricular thalamic nucleus. The efferent projections of PK2-expressing neurons supported the role of PK2 as an output molecule of the SCN.
PMID: 19784373
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Corbin-Lickfett KA,Chen IH,Cocco MJ,Sandri-Goldin RM
Department of Microbiology and Molecular Genetics and Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA.
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The HSV-1 ICP27 RGG box specifically binds flexible, GC-rich sequences but not G-quartet structures.
Nucleic Acids Res. 2009 Sep 26;:
Herpes simplex virus 1 (HSV-1) protein ICP27, an important regulator for viral gene expression, directly recognizes and exports viral RNA through an N-terminal RGG box RNA binding motif, which is necessary and sufficient for RNA binding. An ICP27 N-terminal peptide, including the RGG box RNA binding motif, was expressed and its binding specificity was analyzed using EMSA and SELEX. DNA oligonucleotides corresponding to HSV-1 glycoprotein C (gC) mRNA, identified in a yeast three-hybrid analysis, were screened for binding to the ICP27 N-terminal peptide in EMSA experiments. The ICP27 N-terminus was able to bind most gC substrates. Notably, the ICP27 RGG box was unable to bind G-quartet structures recognized by the RGG domains of other proteins. SELEX analysis identified GC-rich RNA sequences as a common feature of recognition. NMR analysis of SELEX and gC sequences revealed that sequences able to bind to ICP27 did not form secondary structures and conversely, sequences that were not able to bind to ICP27 gave spectra consistent with base-pairing. Therefore, the ICP27 RGG box is unique in its recognition of nucleic acid sequences compared to other RGG box proteins; it prefers flexible, GC-rich substrates that do not form stable secondary structures.
PMID: 19783816
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Girard YA,Travinsky B,Schotthoefer A,Fedorova N,Eisen RJ,Eisen L,Barbour AG,Lane RS
Department of Environmental Science, Policy and Management, University of California Berkeley, 137 Mulford Hall, Berkeley, CA 94720-3114; Departments of Microbiology & Molecular Genetics and Medicine, University of California Irvine, 3012 Hewitt Hall, Irvine, CA 92697; Division of Vector-Borne Infectious Diseases, National Center for Zoonotic, Vector-Borne and Enteric Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80522; Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523.
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Population structure of the Lyme borreliosis spirochete Borrelia burgdorferi in the western black-legged tick (Ixodes pacificus) in northern California.
Appl Environ Microbiol. 2009 Sep 25;:
Factors potentially contributing to the lower incidence of Lyme borreliosis (LB) in the far-western, as compared to the northeastern, US include tick host-seeking behavior resulting in fewer human tick encounters, lower densities of Borrelia burgdorferi-infected vector ticks in peridomestic environments, and genetic variation among B. burgdorferi spirochetes to which humans are exposed. We determined the population structure of B. burgdorferi in over 200 infected nymphs of the primary bridging vector to humans, Ixodes pacificus, collected in Mendocino County, CA. This was accomplished by sequence typing the spirochete lipoprotein ospC and the 16S-23S rRNA intergenic spacer (IGS). Thirteen ospC alleles belonging to 12 genotypes were found in California and the two most abundant, ospC H3 and E3, have not been detected in ticks in the Northeast. The most prevalent ospC/IGS biallelic profile in the population, found in about 22% of ticks, was a new B. burgdorferi strain defined by ospC genotype H3. Eight of the most common ospC genotypes in the northeastern US, including I and K which are associated with disseminated human infections, were absent in Mendocino County nymphs. OspC H3 was associated with hardwood-dominated habitats where reservoir western gray squirrels are commonly infected with LB spirochetes. The differences in B. burgdorferi population structure in California ticks compared to the Northeast emphasize the need for a greater understanding of the genetic diversity of spirochetes infecting California LB patients.
PMID: 19783741
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Martiny AC,Kathuria S,Berube PM
Department of Earth System Science and Ecology, University of California, Irvine, CA 92697, USA. amartiny@uci.edu
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Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes.
Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10787-92
The marine cyanobacterium Prochlorococcus is the most abundant photosynthetic organism in oligotrophic regions of the oceans. The inability to assimilate nitrate is considered an important factor underlying the distribution of Prochlorococcus, and thought to explain, in part, low abundance of Prochlorococcus in coastal, temperate, and upwelling zones. Here, we describe the widespread occurrence of a genomic island containing nitrite and nitrate assimilation genes in uncultured Prochlorococcus cells from marine surface waters. These genes are characterized by low GC content, form a separate phylogenetic clade most closely related to marine Synechococcus, and are located in a different genomic region compared with an orthologous cluster found in marine Synechococcus strains. This sequence distinction suggests that these genes were not transferred recently from Synechococcus. We demonstrate that the nitrogen assimilation genes encode functional proteins and are expressed in the ocean. Also, we find that their relative occurrence is higher in the Caribbean Sea and Indian Ocean compared with the Sargasso Sea and Eastern Pacific Ocean, which may be related to the nitrogen availability in each region. Our data suggest that the ability to assimilate nitrite and nitrate is associated with microdiverse lineages within high- and low-light (LL) adapted Prochlorococcus ecotypes. It challenges 2 long-held assumptions that (i) Prochlorococcus cannot assimilate nitrate, and (ii) only LL adapted ecotypes can use nitrite. The potential for previously unrecognized productivity by Prochlorococcus in the presence of oxidized nitrogen species has implications for understanding the biogeography of Prochlorococcus and its role in the oceanic carbon and nitrogen cycles.
PMID: 19549842
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Yang ZH,van Faassen M,Burke K
Department of Chemistry, University of California, Irvine, California 92697, USA. zenghuiy@uci.edu
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Must Kohn-Sham oscillator strengths be accurate at threshold?
J Chem Phys. 2009 Sep 21;131(11):114308
The exact ground-state Kohn-Sham (KS) potential for the helium atom is known from accurate wave function calculations of the ground-state density. The threshold for photoabsorption from this potential matches the physical system exactly. By carefully studying its absorption spectrum, we show the answer to the title question is no. To address this problem in detail, we generate a highly accurate simple fit of a two-electron spectrum near the threshold, and apply the method to both the experimental spectrum and that of the exact ground-state Kohn-Sham potential.
PMID: 19778114
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Charvet CJ,Owerkowicz T,Striedter GF
Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California, Irvine, Calif. 92687-4550, USA. ccharvet@uci.edu
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Phylogeny of the telencephalic subventricular zone in sauropsids: evidence for the sequential evolution of pallial and subpallial subventricular zones.
Brain Behav Evol. 2009;73(4):285-94
The telencephalon of birds and placental mammals harbors a proliferative subventricular zone (SVZ) in the subpallium as well as the pallium. Turtles, which are phylogenetically intermediate between bird, and mammals, exhibit at best a rudimentary SVZ. This suggests that SVZs evolved independently in mammals and birds, but it is not clear whether subpallial and pallial SVZs evolved with the origin of birds or in some earlier, non-avian sauropsid ancestor. To answer this question, we examined the brains of embryonic alligators (Ferguson stages 15-22) because crocodilians are the closest extant sister group to birds. To visualize the SVZ we labeled mitotic cells with antibodies against phosphorylated histone-3 (pH3) and proliferating cells with antibodies against proliferating cell nuclear antigen (PCNA). We found that the telencephalon of alligators contains an SVZ only in the subpallium. Because turtles, lizards and amphibians seem to lack SVZs, our finding suggests that a subpallial SVZ evolved in the last common ancestor of birds and crocodilians. Given that placental mammals and birds, but not marsupial mammals or reptiles, possess an SVZ within their pallium, we conclude that a pallial SVZ probably evolved independently in birds and placental mammals.
PMID: 19641308
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