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1.  Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo 
Applied and Environmental Microbiology  2013;79(23):7290-7297.
Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.
doi:10.1128/AEM.02541-13
PMCID: PMC3837752  PMID: 24056463
2.  Rapid mRNA-Display Selection of an IL-6 Inhibitor Using Continuous-Flow Magnetic Separation** 
Since the invention of hybridoma technology, methods for generating affinity reagents that bind specific target molecules have revolutionized biology and medicine.[1] In the postgenomic era, there is a pressing need to accelerate the pace of ligand discovery to elucidate the functions of a rapidly growing number of newly characterized molecules and their modified states.[2] Nonimmunoglobulin-based proteins such as DARPins, affibodies, and monobodies represent attractive alternatives to traditional antibodies as these are small, soluble, disulfide-free, single-domain scaffolds that can be selected from combinatorial libraries and expressed in bacteria.[3] For example, monobodies—highly stable scaffolds based on the immunoglobulin VH-like 10th fibronectin type III (10Fn3) domain of human fibronectin[4]—have yielded antibody mimetics that bind to numerous targets for applications including intracellular inhibition,[5,6] therapeutics,[7] and biosensors.[6,8] These 10Fn3-based ligands can be derived from highly diverse libraries using techniques such as phage, ribosome, mRNA, bacterial, and yeast displays.[9]
doi:10.1002/anie.201101149
PMCID: PMC3747967  PMID: 21761516
antibodies; directed evolution; mRNA; ligand design; selection methods
3.  Correction: Elevational Patterns in Archaeal Diversity on Mt. Fuji 
PLoS ONE  2013;8(6):10.1371/annotation/405cf97b-8e07-492d-aa4f-3ff0c2545292.
doi:10.1371/annotation/405cf97b-8e07-492d-aa4f-3ff0c2545292
PMCID: PMC3731439
4.  Large-scale analysis of high-speed atomic force microscopy data sets using adaptive image processing 
Summary
Modern high-speed atomic force microscopes generate significant quantities of data in a short amount of time. Each image in the sequence has to be processed quickly and accurately in order to obtain a true representation of the sample and its changes over time. This paper presents an automated, adaptive algorithm for the required processing of AFM images. The algorithm adaptively corrects for both common one-dimensional distortions as well as the most common two-dimensional distortions. This method uses an iterative thresholded processing algorithm for rapid and accurate separation of background and surface topography. This separation prevents artificial bias from topographic features and ensures the best possible coherence between the different images in a sequence. This method is equally applicable to all channels of AFM data, and can process images in seconds.
doi:10.3762/bjnano.3.84
PMCID: PMC3512124  PMID: 23213638
adaptive algorithm; artifact correction; atomic force microscopy; high-speed atomic force microscope; image processing
5.  Elevational Patterns in Archaeal Diversity on Mt. Fuji 
PLoS ONE  2012;7(9):e44494.
Little is known of how archaeal diversity and community ecology behaves along elevational gradients. We chose to study Mount Fuji of Japan as a geologically and topographically uniform mountain system, with a wide range of elevational zones. PCR-amplified soil DNA for the archaeal 16 S rRNA gene was pyrosequenced and taxonomically classified against EzTaxon-e archaeal database. At a bootstrap cut-off of 80%, most of the archaeal sequences were classified into phylum Thaumarchaeota (96%) and Euryarchaeota (3.9%), with no sequences classified into other phyla. Archaeal OTU richness and diversity on Fuji showed a pronounced ‘peak’ in the mid-elevations, around 1500 masl, within the boreal forest zone, compared to the temperate forest zone below and the alpine fell-field and desert zones above. Diversity decreased towards higher elevations followed by a subtle increase at the summit, mainly due to an increase in the relative abundance of the group I.1b of Thaumarchaeota. Archaeal diversity showed a strong positive correlation with soil NH4+, K and NO3−. Archaeal diversity does not parallel plant diversity, although it does roughly parallel bacterial diversity. Ecological hypotheses to explain the mid diversity bulge on Fuji include intermediate disturbance effects, and the result of mid elevations combining a mosaic of upper and lower slope environments. Our findings show clearly that archaeal soil communities are highly responsive to soil environmental gradients, in terms of both their diversity and community composition. Distinct communities of archaea specific to each elevational zone suggest that many archaea may be quite finely niche-adapted within the range of soil environments. A further interesting finding is the presence of a mesophilic component of archaea at high altitudes on a mountain that is not volcanically active. This emphasizes the importance of microclimate – in this case solar heating of the black volcanic ash surface – for the ecology of soil archaea.
doi:10.1371/journal.pone.0044494
PMCID: PMC3435261  PMID: 22970233
6.  Pharmacodynamic Analysis of a Serine Protease Inhibitor, MK-4519, against Hepatitis C Virus Using a Novel In Vitro Pharmacodynamic System 
The development of new antiviral compounds active against hepatitis C virus (HCV) has surged in recent years. In order for these new compounds to be efficacious in humans, optimal dosage regimens for each compound must be elucidated. We have developed a novel in vitro pharmacokinetic/pharmacodynamic system, the BelloCell system, to identify optimal dosage regimens for anti-HCV compounds. In these experiments, genotype 1b HCV replicon-bearing cells (2209-23 cells) were inoculated onto carrier flakes in BelloCell bottles and treated with MK-4519, a serine protease inhibitor. Our dose-ranging studies illustrated that MK-4519 inhibited replicon replication in a dose-dependent manner, yielding a 50% effective concentration (EC50) of 1.8 nM. Dose-fractionation studies showed that shorter dosing intervals resulted in greater replicon suppression, indicating that the time that the concentration is greater than the EC50 is the pharmacodynamic parameter for MK-4519 linked with inhibition of replicon replication. Mutations associated with resistance to serine protease inhibitors were detected in replicons harvested from all treatment arms. These data suggest that MK-4519 is highly active against genotype 1b HCV, but monotherapy is not sufficient to prevent the amplification of resistant replicons. In summary, our findings show that the BelloCell system is a useful and clinically relevant tool for predicting optimal dosage regimens for anti-HCV compounds.
doi:10.1128/AAC.05383-11
PMCID: PMC3294889  PMID: 22155837
7.  Focused electron beam induced deposition: A perspective 
Summary
Background: Focused electron beam induced deposition (FEBID) is a direct-writing technique with nanometer resolution, which has received strongly increasing attention within the last decade. In FEBID a precursor previously adsorbed on a substrate surface is dissociated in the focus of an electron beam. After 20 years of continuous development FEBID has reached a stage at which this technique is now particularly attractive for several areas in both, basic and applied research. The present topical review addresses selected examples that highlight this development in the areas of charge-transport regimes in nanogranular metals close to an insulator-to-metal transition, the use of these materials for strain- and magnetic-field sensing, and the prospect of extending FEBID to multicomponent systems, such as binary alloys and intermetallic compounds with cooperative ground states.
Results: After a brief introduction to the technique, recent work concerning FEBID of Pt–Si alloys and (hard-magnetic) Co–Pt intermetallic compounds on the nanometer scale is reviewed. The growth process in the presence of two precursors, whose flux is independently controlled, is analyzed within a continuum model of FEBID that employs rate equations. Predictions are made for the tunability of the composition of the Co–Pt system by simply changing the dwell time of the electron beam during the writing process. The charge-transport regimes of nanogranular metals are reviewed next with a focus on recent theoretical advancements in the field. As a case study the transport properties of Pt–C nanogranular FEBID structures are discussed. It is shown that by means of a post-growth electron-irradiation treatment the electronic intergrain-coupling strength can be continuously tuned over a wide range. This provides unique access to the transport properties of this material close to the insulator-to-metal transition. In the last part of the review, recent developments in mechanical strain-sensing and the detection of small, inhomogeneous magnetic fields by employing nanogranular FEBID structures are highlighted.
Conclusion: FEBID has now reached a state of maturity that allows a shift of the focus towards the development of new application fields, be it in basic research or applied. This is shown for selected examples in the present review. At the same time, when seen from a broader perspective, FEBID still has to live up to the original idea of providing a tool for electron-controlled chemistry on the nanometer scale. This has to be understood in the sense that, by providing a suitable environment during the FEBID process, the outcome of the electron-induced reactions can be steered in a controlled way towards yielding the desired composition of the products. The development of a FEBID-specialized surface chemistry is mostly still in its infancy. Next to application development, it is this aspect that will likely be a guiding light for the future development of the field of focused electron beam induced deposition.
doi:10.3762/bjnano.3.70
PMCID: PMC3458607  PMID: 23019557
atomic force microscopy; binary systems; electron beam induced deposition; granular metals; micro Hall magnetometry; radiation-induced nanostructures; strain sensing
8.  Effect of Half-Life on the Pharmacodynamic Index of Zanamivir against Influenza Virus Delineated by a Mathematical Model▿  
Intravenous zanamivir is recommended for the treatment of hospitalized patients with complicated oseltamivir-resistant influenza virus infections. In a companion paper, we show that the time above the 50% effective concentration (time>EC50) is the pharmacodynamic (PD) index predicting the inhibition of viral replication by intravenous zanamivir. However, for other neuraminidase inhibitors, the ratio of the area under the concentration-time curve to the EC50 (AUC/EC50) is the most predictive index. Our objectives are (i) to explain the dynamically linked variable of intravenous zanamivir by using different half-lives and (ii) to develop a new, mechanism-based population pharmacokinetic (PK)/PD model for the time course of viral load. We conducted dose fractionation studies in the hollow-fiber infection model (HFIM) system with zanamivir against an oseltamivir-resistant influenza virus. A clinical 2.5-h half-life and an artificially prolonged 8-h half-life were simulated for zanamivir. The values for the AUC from 0 to 24 h (AUC0-24) of zanamivir were equivalent for the two half-lives. Viral loads and zanamivir pharmacokinetics were comodeled using data from the present study and a previous dose range experiment via population PK/PD modeling in S-ADAPT. Dosing every 8 h (Q8h) suppressed the viral load better than dosing Q12h or Q24h at the 2.5-h half-life, whereas all regimens suppressed viral growth similarly at the 8-h half-life. The model provided unbiased and precise individual (Bayesian) (r2, >0.96) and population (pre-Bayesian) (r2, >0.87) fits for log10 viral load. Zanamivir inhibited viral release (50% inhibitory concentration [IC50], 0.0168 mg/liter; maximum extent of inhibition, 0.990). We identified AUC/EC50 as the pharmacodynamic index for zanamivir at the 8-h half-life, whereas time>EC50 best predicted viral suppression at the 2.5-h half-life, since the trough concentrations approached the IC50 for the 2.5-h but not for the 8-h half-life. The model explained data at both half-lives and holds promise for optimizing clinical zanamivir dosage regimens.
doi:10.1128/AAC.01629-10
PMCID: PMC3067163  PMID: 21263045
9.  Zanamivir, at 600 Milligrams Twice Daily, Inhibits Oseltamivir-Resistant 2009 Pandemic H1N1 Influenza Virus in an In Vitro Hollow-Fiber Infection Model System▿  
In 2009, a novel H1N1 influenza A virus emerged and spread worldwide, initiating a pandemic. Various isolates obtained from disparate parts of the world were shown to be uniformly resistant to the adamantanes but sensitive to the neuraminidase inhibitors oseltamivir and zanamivir. Over time, resistance to oseltamivir became more prevalent among pandemic H1N1 virus isolates, while most remained susceptible to zanamivir. The government has proposed the use of intravenous (i.v.) zanamivir to treat serious influenza virus infections among hospitalized patients. To use zanamivir effectively for patients with severe influenza, it is necessary to know the optimal dose and schedule of administration of zanamivir that will inhibit the replication of oseltamivir-sensitive and -resistant influenza viruses. Therefore, we performed studies using the in vitro hollow-fiber infection model system to predict optimal dosing regimens for zanamivir against an oseltamivir-sensitive and an oseltamivir-resistant virus. Our results demonstrated that zanamivir, at a dose of 600 mg given twice a day (Q12h), inhibited the replication of oseltamivir-sensitive and oseltamivir-resistant influenza viruses throughout the course of the experiment. Thus, our findings suggest that intravenous zanamivir, at a dose of 600 mg Q12h, could be used to treat hospitalized patients suffering from serious infections with oseltamivir-sensitive or -resistant influenza viruses.
doi:10.1128/AAC.01628-10
PMCID: PMC3067184  PMID: 21263046
10.  Novel innate cancer killing activity in humans 
Background
In this study, we pilot tested an in vitro assay of cancer killing activity (CKA) in circulating leukocytes of 22 cancer cases and 25 healthy controls.
Methods
Using a human cervical cancer cell line, HeLa, as target cells, we compared the CKA in circulating leukocytes, as effector cells, of cancer cases and controls. The CKA was normalized as percentages of total target cells during selected periods of incubation time and at selected effector/target cell ratios in comparison to no-effector-cell controls.
Results
Our results showed that CKA similar to that of our previous study of SR/CR mice was present in human circulating leukocytes but at profoundly different levels in individuals. Overall, males have a significantly higher CKA than females. The CKA levels in cancer cases were lower than that in healthy controls (mean ± SD: 36.97 ± 21.39 vs. 46.28 ± 27.22). Below-median CKA was significantly associated with case status (odds ratio = 4.36; 95% Confidence Interval = 1.06, 17.88) after adjustment of gender and race.
Conclusions
In freshly isolated human leukocytes, we were able to detect an apparent CKA in a similar manner to that of cancer-resistant SR/CR mice. The finding of CKA at lower levels in cancer patients suggests the possibility that it may be of a consequence of genetic, physiological, or pathological conditions, pending future studies with larger sample size.
doi:10.1186/1475-2867-11-26
PMCID: PMC3170245  PMID: 21813015
11.  Vascular Wall ACE is not required for Atherogenesis in ApoE-/- mice 
Atherosclerosis  2009;209(2):352-358.
Background
It has been proposed that elements of the renin angiotensin system expressed in the arterial wall are critical for the development of atherosclerosis. Angiotensin converting enzyme (ACE) is highly expressed by the endothelium and is responsible for a critical enzymatic step in the generation of angiotensin II. However, the functional contribution of ACE expression in the vascular wall in atherogenesis is unknown. Therefore, we made use of unique genetic models in which mice without expression of ACE in the vascular wall were crossed with apoE-/- mice in order to determine the contribution of tissue ACE expression to atherosclerotic lesion formation.
Methods and Results
Mice expressing either a soluble form of ACE (ACE 2/2) or mice with somatic ACE expression restricted to the liver and kidney (ACE 3/3) on an ApoE-/- background were placed on a standard chow or Western diet for 6 months. Atherosclerotic lesion area in the ACE 2/2 mice was significantly lower than that seen in the ACE 3/3 mice. However, these animals also had significantly lower blood pressure and reduced plasma ACE activity which precluded establishing a specific causal relationship between absent tissue ACE activity and decreased atherosclerotic lesion extent. Therefore, we studied the ACE 3/3 mice which are normotensive and lack vascular ACE expression. In the ACE 3/3 animals, atherosclerotic lesion area was no different from wild type controls despite reduced plasma ACE activity.
Conclusions
We concluded that under these experimental conditions, expression of ACE in the arterial wall is not required for atherosclerotic lesion formation.
doi:10.1016/j.atherosclerosis.2009.09.069
PMCID: PMC2846193  PMID: 19880118
angiotensin; atherosclerosis; endothelium
12.  Acoustophoretic synchronization of mammalian cells in microchannels 
Analytical chemistry  2010;82(7):3094-3098.
We report the first use of ultrasonic standing waves to achieve cell cycle phase synchronization in mammalian cells in a high-throughput and reagent-free manner. The acoustophoretic cell synchronization (ACS) device utilizes volume-dependent acoustic radiation force within a microchannel to selectively purify target cells of desired phase from an asynchronous mixture based on cell cycle-dependent fluctuations in size. We show that ultrasonic separation allows for gentle, scalable and label-free synchronization with high G1 phase synchrony (~84%) and throughput (3×106 cells/hour/microchannel).
doi:10.1021/ac100357u
PMCID: PMC2848285  PMID: 20199060
13.  Perspectives on utilizing unique features of microfluidics technology for particle and cell sorting 
JALA (Charlottesville, Va.)  2009;14(6):331-340.
Sample preparation is often the most tedious and demanding step in an assay, but it also plays an essential role in determining the quality of results. As biological questions and analytical methods become increasingly sophisticated, there is a rapidly growing need for systems that can reliably and reproducibly separate cells and particles with high purity, throughput and recovery. Microfluidics technology represents a compelling approach in this regard, allowing precise control of separation forces for high performance separation in inexpensive, or even disposable, devices. In addition, microfluidics technology enables the fabrication of arrayed and integrated systems that operate either in parallel or in tandem, in a capacity that would be difficult to achieve in macro-scale systems. In this report, we use recent examples from our work to illustrate the potential of microfluidic cell- and particle-sorting devices. We demonstrate the potential of chip-based high-gradient magnetophoresis that enable high-purity separation through reversible trapping of target particles paired with high-stringency washing with minimal loss. We also describe our work in the development of devices that perform simultaneous multi-target sorting, either through precise control of magnetic and fluidic forces or through the integration of multiple actuation forces into a single monolithic device. We believe that such devices may serve as a powerful “front-end” module of highly integrated analytical platforms capable of providing actionable diagnostic information directly from crude, unprocessed samples - the success of such systems may hold the key to advancing point-of-care diagnostics and personalized medicine.
doi:10.1016/j.jala.2009.06.003
PMCID: PMC2782830  PMID: 20161387
Sample preparation; Cell sorting; Magnetophoresis; Microfluidics
14.  Disruption of PTH Receptor 1 in T Cells Protects against PTH-Induced Bone Loss 
PLoS ONE  2010;5(8):e12290.
Background
Hyperparathyroidism in humans and continuous parathyroid hormone (cPTH) treatment in mice cause bone loss by regulating the production of RANKL and OPG by stromal cells (SCs) and osteoblasts (OBs). Recently, it has been reported that T cells are required for cPTH to induce bone loss as the binding of the T cell costimulatory molecule CD40L to SC receptor CD40 augments SC sensitivity to cPTH. However it is unknown whether direct PTH stimulation of T cells is required for cPTH to induce bone loss, and whether T cells contribute to the bone catabolic activity of PTH with mechanisms other than induction of CD40 signaling in SCs.
Methodology/Principal Findings
Here we show that silencing of PTH receptor 1 (PPR) in T cells blocks the bone loss and the osteoclastic expansion induced by cPTH, thus demonstrating that PPR signaling in T cells is central for PTH-induced reduction of bone mass. Mechanistic studies revealed that PTH activation of the T cell PPR stimulates T cell production of the osteoclastogenic cytokine tumor necrosis factor α (TNF). Attesting to the relevance of this effect, disruption of T cell TNF production prevents PTH-induced bone loss. We also show that a novel mechanism by which TNF mediates PTH induced osteoclast formation is upregulation of CD40 expression in SCs, which increases their RANKL/OPG production ratio.
Conclusions/Significance
These findings demonstrate that PPR signaling in T cells plays an essential role in PTH induced bone loss by promoting T cell production of TNF. A previously unknown effect of TNF is to increase SC expression of CD40, which in turn increases SC osteoclastogenic activity by upregulating their RANKL/OPG production ratio. PPR-dependent stimulation of TNF production by T cells and the resulting TNF regulation of CD40 signaling in SCs are potential new therapeutic targets for the bone loss of hyperparathyroidism.
doi:10.1371/journal.pone.0012290
PMCID: PMC2924900  PMID: 20808842
15.  The spectrum of resistance in SR/CR mice: the critical role of chemoattraction in the cancer/leukocyte interaction 
BMC Cancer  2010;10:179.
Background
Spontaneous regression/complete resistance (SR/CR) mice are a unique colony of mice that possess an inheritable, natural cancer resistance mediated primarily by innate cellular immunity. This resistance is effective against sarcoma 180 (S180) at exceptionally high doses and these mice remain healthy.
Methods
In this study, we challenged SR/CR mice with additional lethal transplantable mouse cancer cell lines to determine their resistance spectrum. The ability of these transplantable cancer cell lines to induce leukocyte infiltration was quantified and the percentage of different populations of responding immune cells was determined using flow cytometry.
Results
In comparison to wild type (WT) mice, SR/CR mice showed significantly higher resistance to all cancer cell lines tested. However, SR/CR mice were more sensitive to MethA sarcoma (MethA), B16 melanoma (B16), LL/2 lung carcinoma (LL/2) and J774 lymphoma (J774) than to sarcoma 180 (S180) and EL-4 lymphoma (EL-4). Further mechanistic studies revealed that this lower resistance to MethA and LL/2 was due to the inability of these cancer cells to attract SR/CR leukocytes, leading to tumor cell escape from resistance mechanism. This escape mechanism was overcome by co-injection with S180, which could attract SR/CR leukocytes allowing the mice to resist higher doses of MethA and LL/2. S180-induced cell-free ascites fluid (CFAF) co-injection recapitulated the results obtained with live S180 cells, suggesting that this chemoattraction by cancer cells is mediated by diffusible molecules. We also tested for the first time whether SR/CR mice were able to resist additional cancer cell lines prior to S180 exposure. We found that SR/CR mice had an innate resistance against EL-4 and J774.
Conclusions
Our results suggest that the cancer resistance in SR/CR mice is based on at least two separate processes: leukocyte migration/infiltration to the site of cancer cells and recognition of common surface properties on cancer cells. The infiltration of SR/CR leukocytes was based on both the innate ability of leukocytes to respond to chemotactic signals produced by cancer cells and on whether cancer cells produced these chemotactic signals. We found that some cancer cells could escape from SR/CR resistance because they did not induce infiltration of SR/CR leukocytes. However, if infiltration of leukocytes was induced by co-injection with chemotactic factors, these same cancer cells could be effectively recognized and killed by SR/CR leukocytes.
doi:10.1186/1471-2407-10-179
PMCID: PMC2875217  PMID: 20438640
16.  Cancer resistance of SR/CR mice in the genetic knockout backgrounds of leukocyte effector mechanisms: determinations for functional requirements 
BMC Cancer  2010;10:121.
Background
Spontaneous Regression/Complete Resistant (SR/CR) mice are a colony of cancer-resistant mice that can detect and rapidly destroy malignant cells with innate cellular immunity, predominately mediated by granulocytes. Our previous studies suggest that several effector mechanisms, such as perforin, granzymes, or complements, may be involved in the killing of cancer cells. However, none of these effector mechanisms is known as critical for granulocytes. Additionally, it is unclear which effector mechanisms are required for the cancer killing activity of specific leukocyte populations and the survival of SR/CR mice against the challenges of lethal cancer cells. We hypothesized that if any of these effector mechanisms was required for the resistance to cancer cells, its functional knockout in SR/CR mice should render them sensitive to cancer challenges. This was tested by cross breeding SR/CR mice into the individual genetic knockout backgrounds of perforin (Prf-/-), superoxide (Cybb-/), or inducible nitric oxide (Nos2-/).
Methods
SR/CR mice were bred into individual Prf-/-, Cybb-/-, or Nos2-/- genetic backgrounds and then challenged with sarcoma 180 (S180). Their overall survival was compared to controls. The cancer killing efficiency of purified populations of macrophages and neutrophils from these immunodeficient mice was also examined.
Results
When these genetically engineered mice were challenged with cancer cells, the knockout backgrounds of Prf-/-, Cybb-/-, or Nos2-/- did not completely abolish the SR/CR cancer resistant phenotype. However, the Nos2-/- background did appear to weaken the resistance. Incidentally, it was also observed that the male mice in these immunocompromised backgrounds tended to be less cancer-resistant than SR/CR controls.
Conclusion
Despite the previously known roles of perforin, superoxide or nitric oxide in the effector mechanisms of innate immune responses, these effector mechanisms were not required for cancer-resistance in SR/CR mice. The resistance was functional when any one of these effector mechanisms was completely absent, except some noticeably reduced penetrance, but not abolishment, of the phenotype in the male background in comparison to female background. These results also indicate that some other effector mechanism(s) of granulocytes may be involved in the killing of cancer cells in SR/CR mice.
doi:10.1186/1471-2407-10-121
PMCID: PMC2861034  PMID: 20356394
17.  Phenotypic Plasticity of Leaf Shape along a Temperature Gradient in Acer rubrum 
PLoS ONE  2009;4(10):e7653.
Both phenotypic plasticity and genetic determination can be important for understanding how plants respond to environmental change. However, little is known about the plastic response of leaf teeth and leaf dissection to temperature. This gap is critical because these leaf traits are commonly used to reconstruct paleoclimate from fossils, and such studies tacitly assume that traits measured from fossils reflect the environment at the time of their deposition, even during periods of rapid climate change. We measured leaf size and shape in Acer rubrum derived from four seed sources with a broad temperature range and grown for two years in two gardens with contrasting climates (Rhode Island and Florida). Leaves in the Rhode Island garden have more teeth and are more highly dissected than leaves in Florida from the same seed source. Plasticity in these variables accounts for at least 6–19 % of the total variance, while genetic differences among ecotypes probably account for at most 69–87 %. This study highlights the role of phenotypic plasticity in leaf-climate relationships. We suggest that variables related to tooth count and leaf dissection in A. rubrum can respond quickly to climate change, which increases confidence in paleoclimate methods that use these variables.
doi:10.1371/journal.pone.0007653
PMCID: PMC2764093  PMID: 19893620
18.  Impact of sex, MHC, and age of recipients on the therapeutic effect of transferred leukocytes from cancer-resistant SR/CR mice 
BMC Cancer  2009;9:328.
Background
Spontaneous Regression/Complete Resistant (SR/CR) mice are resistant to cancer through a mechanism that is mediated entirely by leukocytes of innate immunity. Transfer of leukocytes from SR/CR mice can confer cancer resistance in wild-type (WT) recipients in both preventative and therapeutic settings. In the current studies, we investigated factors that may impact the efficacy and functionality of SR/CR donor leukocytes in recipients.
Results
In sex-mismatched transfers, functionality of female donor leukocytes was not affected in male recipients. In contrast, male donor leukocytes were greatly affected in the female recipients. In MHC-mismatches, recipients of different MHC backgrounds, or mice of different strains, showed a greater negative impact on donor leukocytes than sex-mismatches. The negative effects of sex-mismatch and MHC-mismatch on donor leukocytes were additive. Old donor leukocytes performed worse than young donor leukocytes in all settings including in young recipients. Young recipients were not able to revive the declining function of old donor leukocytes. However, the function of young donor leukocytes declined gradually in old recipients, suggesting that an aged environment may contain factors that are deleterious to cellular functions. The irradiation of donor leukocytes prior to transfers had a profound suppressive effect on donor leukocyte functions, possibly as a result of impaired transcription. The cryopreserving of donor leukocytes in liquid nitrogen had no apparent effect on donor leukocyte functions, except for a small loss of cell number after revival from freezing.
Conclusion
Despite the functional suppression of donor leukocytes in sex- and MHC-mismatched recipients, as well as old recipients, there was a therapeutic time period during the initial few weeks during which donor leukocytes were functional before their eventual rejection or functional decline. The eventual rejection of donor leukocytes will likely prevent donor leukocyte engraftment which would help minimize the risk of transfusion-associated graft-versus-host disease. Therefore, using leukocytes from healthy donors with high anti-cancer activity may be a feasible therapeutic concept for treating malignant diseases.
doi:10.1186/1471-2407-9-328
PMCID: PMC2749872  PMID: 19754973
19.  The Acceptability of Online Courses as Criteria for Admission to Medical School 
The Ochsner Journal  2009;9(1):4-10.
A national survey of medical school admissions administrators was used to assess the acceptability of applicants' qualifications that included degrees earned partly online, partly in a community college, or in a traditional program. A questionnaire was sent from The Florida State University in 2007 to admissions administrators in the 125 accredited allopathic medical schools in the United States. In each of three situations, the respondents were asked to select one of two hypothetical applicants to invite for an interview. The applicants with their coursework taken in a traditional-residential setting were overwhelmingly preferred over the applicant holding the degree earned partly online. Further analysis indicated that online courses were perceived as not presenting sufficient opportunity for students to develop important social skills through interaction with other students and mentors.
PMCID: PMC3096245  PMID: 21603401
Graduate school admissions; online degrees; acceptability

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