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1.  Service Priorities and Unmet Service Needs Among People Living with HIV/AIDS: Results from a Nationwide Interview of HIV/AIDS Housing Organizations 
AIDS care  2013;25(9):1083-1091.
Housing for people living with HIV/AIDS has been linked to a number of positive physical and mental health outcomes, in addition to decreased sexual and drug-related risk behavior. The current study identified service priorities for people living with HIV/AIDS, services provided by HIV/AIDS housing agencies, and unmet service needs for people living with HIV/AIDS through a nationwide telephone survey of HIV/AIDS housing agencies in the United States. Housing, alcohol/drug treatment, and mental health services were identified as the three highest priorities for people living with HIV/AIDS and assistance finding employment, dental care, vocational assistance, and mental health services were the top needs not being met. Differences by geographical region were also examined. Findings indicate that while housing affords people living with HIV/AIDS access to services, there are still areas (e.g., mental health services) where gaps in linkages to care exist.
PMCID: PMC4271631  PMID: 23305552
2.  NET23/STING Promotes Chromatin Compaction from the Nuclear Envelope 
PLoS ONE  2014;9(11):e111851.
Changes in the peripheral distribution and amount of condensed chromatin are observed in a number of diseases linked to mutations in the lamin A protein of the nuclear envelope. We postulated that lamin A interactions with nuclear envelope transmembrane proteins (NETs) that affect chromatin structure might be altered in these diseases and so screened thirty-one NETs for those that promote chromatin compaction as determined by an increase in the number of chromatin clusters of high pixel intensity. One of these, NET23 (also called STING, MITA, MPYS, ERIS, Tmem173), strongly promoted chromatin compaction. A correlation between chromatin compaction and endogenous levels of NET23/STING was observed for a number of human cell lines, suggesting that NET23/STING may contribute generally to chromatin condensation. NET23/STING has separately been found to be involved in innate immune response signaling. Upon infection cells make a choice to either apoptose or to alter chromatin architecture to support focused expression of interferon genes and other response factors. We postulate that the chromatin compaction induced by NET23/STING may contribute to this choice because the cells expressing NET23/STING eventually apoptose, but the chromatin compaction effect is separate from this as the condensation was still observed when cells were treated with Z-VAD to block apoptosis. NET23/STING-induced compacted chromatin revealed changes in epigenetic marks including changes in histone methylation and acetylation. This indicates a previously uncharacterized nuclear role for NET23/STING potentially in both innate immune signaling and general chromatin architecture.
PMCID: PMC4227661  PMID: 25386906
3.  Eosinophilic Appendicitis Attributable to Strongyloides Infection in a Pediatric Renal Transplant Patient 
PMCID: PMC3761319  PMID: 24009985
Pediatrics; Kidney Transplantation; Strongyloidiasis; Appendicitis; Eosinophilia
4.  It takes two to tango: two TatA paralogues and two redox enzyme-specific chaperones are involved in the localization of twin-arginine translocase substrates in Campylobacter jejuni 
Microbiology  2014;160(Pt 9):2053-2066.
The food-borne zoonotic pathogen Campylobacter jejuni has complex electron transport chains required for growth in the host, many of which contain cofactored periplasmic enzymes localized by the twin-arginine translocase (TAT). We report here the identification of two paralogues of the TatA translocase component in C. jejuni strain NCTC 11168, encoded by cj1176c (tatA1) and cj0786 (tatA2). Deletion mutants constructed in either or both of the tatA1 and tatA2 genes displayed distinct growth and enzyme activity phenotypes. For sulphite oxidase (SorAB), the multi-copper oxidase (CueO) and alkaline phosphatase (PhoX), complete dependency on TatA1 for correct periplasmic activity was observed. However, the activities of nitrate reductase (NapA), formate dehydrogenase (FdhA) and trimethylamine N-oxide reductase (TorA) were significantly reduced in the tatA2 mutant. In contrast, the specific rate of fumarate reduction catalysed by the flavoprotein subunit of the methyl menaquinone fumarate reductase (MfrA) was similar in periplasmic fractions of both the tatA1 and the tatA2 mutants and only the deletion of both genes abolished activity. Nevertheless, unprocessed MfrA accumulated in the periplasm of the tatA1 (but not tatA2) mutant, indicating aberrant signal peptide cleavage. Surprisingly, TatA2 lacks two conserved residues (Gln8 and Phe39) known to be essential in Escherichia coli TatA and we suggest it is unable to function correctly in the absence of TatA1. Finally, only two TAT chaperones (FdhM and NapD) are encoded in strain NCTC 11168, which mutant studies confirmed are highly specific for formate dehydrogenase and nitrate reductase assembly, respectively. Thus, other TAT substrates must use general chaperones in their biogenesis.
PMCID: PMC4148689  PMID: 24961951
5.  Intestinal Epithelial Apoptosis initiates Gut Mucosal Injury during Extracorporeal Membrane Oxygenation in the Newborn Piglet 
Neonates and young infants exposed to extracorporeal circulation during extracorporeal membrane oxygenation (ECMO) and cardiopulmonary bypass (CPB) are at risk of developing a systemic inflammatory response syndrome (SIRS) with multi-organ dysfunction. We used a piglet model of ECMO to investigate the hypothesis that epithelial apoptosis is an early event that precedes villous damage during ECMO-related bowel injury.
Healthy 3-week-old piglets were subjected to ECMO for up to 8h. Epithelial apoptosis was measured in histopathological analysis, nuclear imaging, and terminal deoxynucleotidyl transferase dUTP nick end labeling. Plasma intestinal-fatty acid-binding protein (I-FABP) levels were measured by enzyme immunoassay. Intestinal mast cells were isolated by fluorescence-assisted cell sorting. Cleaved caspase-8, caspase-9, phospho-p38 MAPK, and fas ligand expression was investigated by immunohistochemistry, Western blots, and reverse transcriptase-quantitative polymerase chain reaction.
Piglet ECMO was associated with increased gut epithelial apoptosis. Extensive apoptotic changes were noted on villus tips and in scattered crypt cells after 2h of ECMO. After 8h, the villi were denuded and apoptotic changes were evident in a majority of crypt cells. Increased circulating I-FABP levels, a marker of gut epithelial injury, showed that epithelial injury occurred during ECMO. We detected increased cleaved caspase-8, but not cleaved caspase-9, in epithelial cells indicating that the extrinsic apoptotic pathway was active. ECMO was associated with increased fas ligand expression in intestinal mast cells, which was induced through activation of the p38 mitogen-activated protein kinase.
Epithelial apoptosis is an early event that initiates gut mucosal injury in a piglet model of ECMO.
PMCID: PMC3946757  PMID: 24365747
extracorporeal circulation; mucosal injury; apoptotic; neonate; ECMO
6.  Molecular and Phenotypic Data Support the Recognition of the Wakatobi Flowerpecker (Dicaeum kuehni) from the Unique and Understudied Sulawesi Region 
PLoS ONE  2014;9(6):e98694.
Accurate estimates of species richness are essential to macroecological and macroevolutionary research, as well as to the effective management and conservation of biodiversity. The resolution of taxonomic relationships is therefore of vital importance. While molecular methods have revolutionised taxonomy, contemporary species delimitation requires an integrative, multi-disciplinary approach. Despite boasting a remarkably high level of endemism, the avifauna of the Sulawesi region of Indonesia remains poorly studied. Previous studies of avian diversity in Sulawesi have focussed predominantly on phenotypic characteristics, thus potentially overlooking any genetically distinct lineages. Grey-sided Flowerpecker Dicaeum celebicum populations from the Wakatobi archipelago were originally described as a separate species from those on nearby mainland Sulawesi. However, for reasons that remain unknown, the Wakatobi populations were reclassified as a subspecies of the mainland form. Combining estimates of genetic divergence with phylogenetic and morphological analyses, we reassessed the status of Wakatobi populations. Our results describe the Wakatobi populations as a separate species to those on mainland Sulawesi; reproductively isolated, genetically and morphologically distinct. We therefore recommend the reclassification of these populations to their original status of Dicaeum kuehni and propose the vernacular name ‘Wakatobi Flowerpecker’. In consideration of our findings and the lack of integrative ornithological research within the Sulawesi region, we believe species richness and avian endemism within the region are underestimated.
PMCID: PMC4045762  PMID: 24896822
7.  Nutritional and Metabolic Requirements for the Infection of HeLa Cells by Salmonella enterica Serovar Typhimurium 
PLoS ONE  2014;9(5):e96266.
Salmonella is the causative agent of a spectrum of human and animal diseases ranging from gastroenteritis to typhoid fever. It is a food - and water - borne pathogen and infects via ingestion followed by invasion of intestinal epithelial cells and phagocytic cells. In this study we employed a mutational approach to define the nutrients and metabolic pathways required by Salmonella enterica serovar Typhimurium during infection of a human epithelial cell line (HeLa). We deleted the key glycolytic genes, pfkA and pfkB to show that S. Typhimurium utilizes glycolysis for replication within HeLa cells; however, glycolysis was not absolutely essential for intracellular replication. Using S. Typhimurium strains deleted for genes encoding components of the phosphotransferase system and glucose transport, we show that glucose is a major substrate required for the intracellular replication of S. Typhimurium in HeLa cells. We also deleted genes encoding enzymes involved in the utilization of gluconeogenic substrates and the glyoxylate shunt and show that neither of these pathways were required for intracellular replication of S. Typhimurium within HeLa cells.
PMCID: PMC4010460  PMID: 24797930
8.  Metabolomic analysis of the food-borne pathogen Campylobacter jejuni: application of direct injection mass spectrometry for mutant characterisation 
Metabolomics  2014;10(5):887-896.
Campylobacter jejuni is the most frequent cause of human food-borne bacterial gastroenteritis but its physiology and biochemistry are poorly understood. Only a few amino-acids can be catabolised and these are known to be important for host colonization. Here we have established methods for rapid high throughput analyses of global metabolism in C. jejuni using direct injection mass spectrometry (DIMS) to compare metabolite fingerprints of wild-type and mutant strains. Principal component analyses show that the metabolic fingerprint of mutants that have a genomic deletion in genes for key amino-acid catabolic enzymes (either sdaA, serine dehydratase; aspA, aspartase or aspB, aspartate:glutamate transaminase) can easily be distinguished from the isogenic parental strain. Assignment of putative metabolites showed predictable changes directly associated with the particular metabolic lesion in these mutants as well as more extensive changes in the aspA mutant compared to the sdaA or aspB strains. Further analyses of a cj0150c mutant strain, which has no obvious phenotype, suggested a role for Cj0150 in the conversion of cystathionine to homocysteine. Our results show that DIMS is a useful technique for probing the metabolism of this important pathogen and may help in assigning function to genes encoding novel enzymes with currently unknown metabolic roles.
Electronic supplementary material
The online version of this article (doi:10.1007/s11306-014-0644-z) contains supplementary material, which is available to authorized users.
PMCID: PMC4145198  PMID: 25177231
Campylobacter jejuni; DIMS; Metabolism; aspA; aspB; sdaA
9.  Structural and functional characterization of NanU, a novel high-affinity sialic acid-inducible binding protein of oral and gut-dwelling Bacteroidetes species 
Biochemical Journal  2014;458(Pt 3):499-511.
Many human-dwelling bacteria acquire sialic acid for growth or surface display. We identified previously a sialic acid utilization operon in Tannerella forsythia that includes a novel outer membrane sialic acid-transport system (NanOU), where NanO (neuraminate outer membrane permease) is a putative TonB-dependent receptor and NanU (extracellular neuraminate uptake protein) is a predicted SusD family protein. Using heterologous complementation of nanOU genes into an Escherichia coli strain devoid of outer membrane sialic acid permeases, we show that the nanOU system from the gut bacterium Bacteroides fragilis is functional and demonstrate its dependence on TonB for function. We also show that nanU is required for maximal function of the transport system and that it is expressed in a sialic acid-responsive manner. We also show its cellular localization to the outer membrane using fractionation and immunofluorescence experiments. Ligand-binding studies revealed high-affinity binding of sialic acid to NanU (Kd ~400 nM) from two Bacteroidetes species as well as binding of a range of sialic acid analogues. Determination of the crystal structure of NanU revealed a monomeric SusD-like structure containing a novel motif characterized by an extended kinked helix that might determine sugar-binding specificity. The results of the present study characterize the first bacterial extracellular sialic acid-binding protein and define a sialic acid-specific PUL (polysaccharide utilization locus).
We biochemically and structurally characterize a novel inducible surface-associated sialic acid-binding protein present in human-dwelling Bacteroidetes species that represents a novel type of sialic acid-specific polysaccharide utilization locus.
PMCID: PMC3969230  PMID: 24351045
Bacteroides fragilis; carbohydrate; nanOU; outer membrane; sialic acid; transport; BF, Bacteroides fragilis; FA, fastidious anaerobe; HRP, horseradish peroxidase; ManNAc, N-acetyl mannosamine; NAM, N-acetylmuramic acid; NanO, neuraminate outer membrane permease; NanU, extracellular neuraminate uptake protein; Neu5Ac, 5-N-acetylneuraminic acid; Neu5Ac2en, 2-deoxy-2,3-didehydro-Neu5Ac; Neu5Gc, N-glycolylneuraminic acid; PUL, polysaccharide utilization locus; TBDR, TonB-dependent receptor; TCA, trichloroacetic acid; TF, Tannerella forsythia; TPR, tetratricopeptide repeat
10.  Shugoshin biases chromosomes for biorientation through condensin recruitment to the pericentromere 
eLife  2014;3:e01374.
To protect against aneuploidy, chromosomes must attach to microtubules from opposite poles (‘biorientation’) prior to their segregation during mitosis. Biorientation relies on the correction of erroneous attachments by the aurora B kinase, which destabilizes kinetochore-microtubule attachments that lack tension. Incorrect attachments are also avoided because sister kinetochores are intrinsically biased towards capture by microtubules from opposite poles. Here, we show that shugoshin acts as a pericentromeric adaptor that plays dual roles in biorientation in budding yeast. Shugoshin maintains the aurora B kinase at kinetochores that lack tension, thereby engaging the error correction machinery. Shugoshin also recruits the chromosome-organizing complex, condensin, to the pericentromere. Pericentromeric condensin biases sister kinetochores towards capture by microtubules from opposite poles. Our findings uncover the molecular basis of the bias to sister kinetochore capture and expose shugoshin as a pericentromeric hub controlling chromosome biorientation.
eLife digest
When a cell divides to create two new daughter cells, it must produce a copy of each of its chromosomes. It is important that each daughter cell gets just one copy of each chromosome. If an error occurs and one cell gets two copies of a single chromosome, it can lead to cancer or birth defects. Fortunately, there are multiple checks to ensure that this does not happen.
During cell division the chromosomes line up in a way that increases the likelihood that each daughter cell will have one copy of each chromosome. After this process—which is called biorientation—is completed, microtubules pull the chromosomes to opposite ends of the cell, which then divides.
Proteins called shugoshin proteins are known to be involved in biorientation in many organisms. These proteins are found in a region called the pericentromere, which surrounds the area on the chromosomes that the microtubules attach to, but the details of their involvement in biorientation are not fully understood. Now Verzijlbergen et al. have exploited sophisticated genetic techniques in yeast to explore how shugoshin proteins work.
These experiments showed that the shugoshin protein helps to recruit condensin—a protein that keeps the DNA organized within the chromosome—to the pericentromere to assist with biorientation. It also keeps aurora B kinase—one of the enzymes that helps to correct errors during cell division—in the pericentromere when a microtubule attaches to the wrong chromosome. These results help us understand how a ‘hub’ in the pericentromere ensures biorientation. The next challenge will be to understand how this hub is disassembled after biorientation to allow error-free cell division to proceed. As shugoshins have been found to be damaged in some cancers, understanding the workings of this hub could also shed new light on how they contribute to disease.
PMCID: PMC3910079  PMID: 24497542
mitosis; biorientation; shugoshin; condensin; aurora B; S. cerevisiae
11.  Do Globins in Microaerophilic Campylobacter jejuni Confer Nitrosative Stress Tolerance Under Oxygen Limitation? 
Antioxidants & Redox Signaling  2013;18(4):424-431.
The microaerophilic pathogen Campylobacter jejuni possesses inducible systems for resisting NO. Two globins—Cgb (a single-domain globin) and Ctb (a truncated globin)—are up-regulated in response to NO via the positively acting transcription factor NssR. Our aims were to determine whether these oxygen-binding globins also function in severely oxygen-limited environments, as in the host. At growth-limiting oxygen transfer rates, bacteria were more S-nitrosoglutathione (GSNO) sensitive, irrespective of the presence of Cgb, Ctb, or NssR. Pregrowth of cells with GSNO enhanced GSNO resistance, even in nssR and cgb mutants, but transcriptomic profiling of oxygen-limited, NO-exposed cells failed to reveal the NssR regulon. Nevertheless, globin expression in an Escherichia coli mutant lacking the NO-detoxifying flavohemoglobin Hmp showed that Cgb and Ctb consume NO aerobically or anoxically and offer some protection to respiratory inhibition by NO. The constitutively expressed nitrite reductase NrfA does not provide resistance under oxygen-limited conditions. We, therefore, hypothesize that, although Cgb and NrfA can detoxify NO, even anoxically, they are neither up-regulated nor functional under physiologically relevant oxygen-limited conditions and, second, responses to NO do not stem from trancriptional regulation. Antioxid. Redox Signal. 18, 424–431.
PMCID: PMC3526894  PMID: 22816769
12.  Correction: Myofibroblast Differentiation and Enhanced Tgf-B Signaling in Cystic Fibrosis Lung Disease 
PLoS ONE  2013;8(8):10.1371/annotation/d0132de3-56ca-4258-9119-bdab0ceb2cff.
PMCID: PMC3765485
13.  Development of the other-race effect during infancy: Evidence toward universality? 
The other-race effect in face processing develops within the first year of life in Caucasian infants. It is currently unknown whether the developmental trajectory observed in Caucasian infants can be extended to other cultures. This is an important issue to investigate because recent findings from cross-cultural psychology have suggested that individuals from Eastern and Western backgrounds tend to perceive the world in fundamentally different ways. To this end, the current study investigated 3-, 6-, and 9-month-old Chinese infants’ ability to discriminate faces within their own racial group and within two other racial groups (African and Caucasian). The 3-month-olds demonstrated recognition in all conditions, whereas the 6-month-olds recognized Chinese faces and displayed marginal recognition for Caucasian faces but did not recognize African faces. The 9-month-olds’ recognition was limited to Chinese faces. This pattern of development is consistent with the perceptual narrowing hypothesis that our perceptual systems are shaped by experience to be optimally sensitive to stimuli most commonly encountered in one’s unique cultural environment.
PMCID: PMC3740564  PMID: 19269649
Face processing; Other-race effect; Development; Infancy; Culture; Perceptual narrowing
14.  Myofibroblast Differentiation and Enhanced Tgf-B Signaling in Cystic Fibrosis Lung Disease 
PLoS ONE  2013;8(8):e70196.
TGF-β, a mediator of pulmonary fibrosis, is a genetic modifier of CF respiratory deterioration. The mechanistic relationship between TGF-β signaling and CF lung disease has not been determined.
To investigate myofibroblast differentiation in CF lung tissue as a novel pathway by which TGF-β signaling may contribute to pulmonary decline, airway remodeling and tissue fibrosis.
Lung samples from CF and non-CF subjects were analyzed morphometrically for total TGF-β1, TGF-β signaling (Smad2 phosphorylation), myofibroblast differentiation (α-smooth muscle actin), and collagen deposition (Masson trichrome stain).
TGF-β signaling and fibrosis are markedly increased in CF (p<0.01), and the presence of myofibroblasts is four-fold higher in CF vs. normal lung tissue (p<0.005). In lung tissue with prominent TGF-β signaling, both myofibroblast differentiation and tissue fibrosis are significantly augmented (p<0.005).
These studies establish for the first time that a pathogenic mechanism described previously in pulmonary fibrosis is also prominent in cystic fibrosis lung disease. The presence of TGF-β dependent signaling in areas of prominent myofibroblast proliferation and fibrosis in CF suggests that strategies under development for other pro-fibrotic lung conditions may also be evaluated for use in CF.
PMCID: PMC3741283  PMID: 23950911
15.  Mitotic chromosomes are compacted laterally by KIF4 and condensin and axially by topoisomerase IIα 
The Journal of Cell Biology  2012;199(5):755-770.
During the shaping of mitotic chromosomes, KIF4 and condensin work in parallel to promote lateral chromatid compaction and in opposition to topoisomerase IIα, which shortens the chromatid arms.
Mitotic chromosome formation involves a relatively minor condensation of the chromatin volume coupled with a dramatic reorganization into the characteristic “X” shape. Here we report results of a detailed morphological analysis, which revealed that chromokinesin KIF4 cooperated in a parallel pathway with condensin complexes to promote the lateral compaction of chromatid arms. In this analysis, KIF4 and condensin were mutually dependent for their dynamic localization on the chromatid axes. Depletion of either caused sister chromatids to expand and compromised the “intrinsic structure” of the chromosomes (defined in an in vitro assay), with loss of condensin showing stronger effects. Simultaneous depletion of KIF4 and condensin caused complete loss of chromosome morphology. In these experiments, topoisomerase IIα contributed to shaping mitotic chromosomes by promoting the shortening of the chromatid axes and apparently acting in opposition to the actions of KIF4 and condensins. These three proteins are major determinants in shaping the characteristic mitotic chromosome morphology.
PMCID: PMC3514791  PMID: 23166350
16.  The CouPSTU and TarPQM Transporters in Rhodopseudomonas palustris: Redundant, Promiscuous Uptake Systems for Lignin-Derived Aromatic Substrates 
PLoS ONE  2013;8(3):e59844.
The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791–1793), which has previously been implicated in the active transport of this class of aromatic substrate. Here, we show using both intrinsic tryptophan fluorescence and isothermal titration calorimetry that CouP binds a range of phenylpropeneoid ligands with Kd values in the nanomolar range. The crystal structure of CouP with ferulate as the bound ligand shows H-bond interactions between the 4-OH group of the aromatic ring with His309 and Gln305. H-bonds are also made between the carboxyl group on the ferulate side chain and Arg197, Ser222, and Thr102. An additional transport system (TarPQM; RPA1782–1784), a member of the tripartite ATP-independent periplasmic (TRAP) transporter family, is encoded at the same locus as rpa1789 and several other genes involved in coumarate metabolism. We show that the periplasmic binding-protein of this system (TarP; RPA1782) also binds coumarate, ferulate, caffeate, and cinnamate with nanomolar Kd values. Thus, we conclude that R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximise the uptake of lignin-derived aromatic substrates from the environment. Our data provide a detailed thermodynamic and structural basis for understanding the interaction of lignin-derived aromatic substrates with proteins and will be of use in the further exploitation of the flexible metabolism of R. palustris for anaerobic aromatic biotransformations.
PMCID: PMC3610893  PMID: 23555803
17.  Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery 
Genome Biology  2013;14(2):R14.
Different cell types have distinctive patterns of chromosome positioning in the nucleus. Although ectopic affinity-tethering of specific loci can be used to relocate chromosomes to the nuclear periphery, endogenous nuclear envelope proteins that control such a mechanism in mammalian cells have yet to be widely identified.
To search for such proteins, 23 nuclear envelope transmembrane proteins were screened for their ability to promote peripheral localization of human chromosomes in HT1080 fibroblasts. Five of these proteins had strong effects on chromosome 5, but individual proteins affected different subsets of chromosomes. The repositioning effects were reversible and the proteins with effects all exhibited highly tissue-restricted patterns of expression. Depletion of two nuclear envelope transmembrane proteins that were preferentially expressed in liver each reduced the normal peripheral positioning of chromosome 5 in liver cells.
The discovery of nuclear envelope transmembrane proteins that can modulate chromosome position and have restricted patterns of expression may enable dissection of the functional relevance of tissue-specific patterns of radial chromosome positioning.
PMCID: PMC4053941  PMID: 23414781
18.  Trophic Enrichment Factors for Blood Serum in the European Badger (Meles meles) 
PLoS ONE  2012;7(12):e53071.
Ecologists undertaking stable isotopic analyses of animal diets require trophic enrichment factors (TEFs) for the specific animal tissues that they are studying. Such basic data are available for a small number of species, so values from trophically or phylogenetically similar species are often substituted for missing values. By feeding a controlled diet to captive European badgers (Meles meles) we determined TEFs for carbon and nitrogen in blood serum. TEFs for nitrogen and carbon in blood serum were +3.0±0.4‰ and +0.4±0.1‰ respectively. The TEFs for serum in badgers are notably different from those published for the red fox (Vulpes vulpes). There is currently no data for TEFs in the serum of other mustelid species. Our data show that species sharing similar niches (red fox) do not provide adequate proxy values for TEFs of badgers. Our findings emphasise the importance of having species-specific data when undertaking trophic studies using stable isotope analysis.
PMCID: PMC3531416  PMID: 23300863
19.  Sarcoidosis in a young child with Alagille syndrome: a case report 
We report a now 6-year-old African-American male with both Alagille syndrome and pediatric sarcoidosis. With a prior JAG1 mutation positive diagnosis of Alagille syndrome, he presented to the hospital with a subacute, predominantly respiratory febrile condition, eventually diagnosed as sarcoidosis. A liver biopsy revealed paucity of bile ducts and scattered epithelioid granulomas, while a skin biopsy showed granulomatous angiitis, a manifestation of sarcoidosis not yet reported in a pediatric patient. He has subsequently been treated with corticosteroids, mycophenolate mofetil, and infliximab with clinical response. Alagille syndrome and sarcoidosis have not yet been reported in the medical literature in the same patient to the best of our knowledge. We briefly review these two seemingly unrelated conditions and propose a possible common pathogenic mechanism.
PMCID: PMC3599400  PMID: 22937766
Sarcoidosis; Alagille syndrome; Granulomatous angiitis; Granuloma; JAG1; NOTCH1; T lymphocyte
20.  Health-related quality of life and strain in caregivers of Australians with Parkinson’s disease: An observational study 
BMC Neurology  2012;12:57.
The relationship between health-related quality of life (HRQoL) in people with Parkinson’s disease and their caregivers is little understood and any effects on caregiver strain remain unclear. This paper examines these relationships in an Australian sample.
Using the generic EuroQol (EQ-5D) and disease-specific Parkinson’s Disease Questionnaire-39 Item (PDQ-39), HRQoL was evaluated in a sample of 97 people with PD and their caregivers. Caregiver strain was assessed using the Modified Caregiver Strain Index. Associations were evaluated between: (i) caregiver and care-recipient HRQoL; (ii) caregiver HRQoL and caregiver strain, and; (iii) between caregiver strain and care-recipient HRQoL.
No statistically significant relationships were found between caregiver and care-recipient HRQoL, or between caregiver HRQoL and caregiver strain. Although this Australian sample of caregivers experienced relatively good HRQoL and moderately low strain, a significant correlation was found between HRQoL of people with PD and caregiver strain (rho 0.43, p < .001).
Poor HRQoL in people with PD is associated with higher strain in caregivers. Therapy interventions may target problems reported as most troublesome by people with PD, with potential to reduce strain on the caregiver.
PMCID: PMC3434109  PMID: 22804846
21.  2,3-Substituted quinoxalin-6-amine analogs as antiproliferatives: A structure activity relationship study 
The quinoxaline core is considered a privileged scaffold as it is found in a variety of biologically relevant molecules. Here we report the synthesis of a quinoxalin-6-amine library, screening against a panel of cancer cell lines and a structure activity relationship (SAR). This resulted in the identification of a bisfuranylquinoxalineurea analog (7c) that has low micromolar potency against the panel of cancer cell lines. We also show that cells treated with quinoxalineurea 7c results in caspase 3/7 activation, PARP cleavage and Mcl-1 dependent apoptosis.
PMCID: PMC3063321  PMID: 21376584
Quinoxaline urea; Antiproliferative; Mcl-1 dependent apoptosis
22.  2D-Difference Gel Electrophoretic Proteomic Analysis of a Cell Culture Model of Alveolar Rhabdomyosarcoma 
Journal of proteome research  2011;10(2):624-636.
To evaluate the consequences of expression of the protein encoded by PAX3-FOXO1 (P3F) in the pediatric malignancy alveolar rhabdomyosarcoma (A-RMS), we developed and evaluated a genetically defined in vitro model of A-RMS tumorigenesis. The expression of P3F in cooperation with simian virus 40 (SV40) Large-T (LT) antigen in murine C3H10T1/2 fibroblasts led to robust malignant transformation. Using 2 dimensional difference gel electrophoresis (2D-DIGE) we compared proteomes from lysates from cells that express P3F + LT versus from cells that express LT alone. Analysis of 2D gel spot patterns by DeCyder™ image analysis software indicated 93 spots that were different in abundance. Peptide mass fingerprint analysis of the 93 spots by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis identified 37 non-redundant proteins. 2D DIGE analysis of cell culture media conditioned by cells transduced by P3F + LT versus by LT alone found 29 spots in the P3F + LT cells leading to the identification of 11 non-redundant proteins. A substantial number of proteins with potential roles in tumorigenesis and myogenesis were detected, most of which have not been identified in previous wide-scale expression studies of RMS experimental models or tumors. We validated the 2D gel image analysis findings by western blot analysis and immunohistochemistry (IHC). Thus, the 2D DIGE proteomics methodology described here provided an important discovery approach to the study of RMS biology and complements the findings of previous mRNA expression studies.
PMCID: PMC3071502  PMID: 21110518
23.  A New Method for Inferring Hidden Markov Models from Noisy Time Sequences 
PLoS ONE  2012;7(1):e29703.
We present a new method for inferring hidden Markov models from noisy time sequences without the necessity of assuming a model architecture, thus allowing for the detection of degenerate states. This is based on the statistical prediction techniques developed by Crutchfield et al. and generates so called causal state models, equivalent in structure to hidden Markov models. The new method is applicable to any continuous data which clusters around discrete values and exhibits multiple transitions between these values such as tethered particle motion data or Fluorescence Resonance Energy Transfer (FRET) spectra. The algorithms developed have been shown to perform well on simulated data, demonstrating the ability to recover the model used to generate the data under high noise, sparse data conditions and the ability to infer the existence of degenerate states. They have also been applied to new experimental FRET data of Holliday Junction dynamics, extracting the expected two state model and providing values for the transition rates in good agreement with previous results and with results obtained using existing maximum likelihood based methods. The method differs markedly from previous Markov-model reconstructions in being able to uncover truly hidden states.
PMCID: PMC3256161  PMID: 22247783
24.  TGF-β2 Suppresses Macrophage Cytokine Production and Mucosal Inflammatory Responses in the Developing Intestine 
Gastroenterology  2010;140(1):242-253.
Background & Aims
Premature neonates are predisposed to necrotizing enterocolitis (NEC), an idiopathic, inflammatory bowel necrosis. We investigated the hypothesis that NEC occurs in the preterm intestine due to incomplete ‘non-inflammatory’ differentiation of intestinal macrophages, which increases the risk of a severe mucosal inflammatory response to bacterial products.
We compared inflammatory properties of human/murine fetal, neonatal, and adult intestinal macrophages. To investigate gut-specific macrophage differentiation, we next treated monocyte-derived macrophages with conditioned media from ex planted human fetal and adult intestinal tissues. Transforming growth factor-beta (TGF-β) expression and bioactivity were measured in fetal/adult intestine and in NEC. Finally, we used wild-type and transgenic mice to investigate the effects of deficient TGF-β signaling on NEC-like inflammatory mucosal injury.
Intestinal macrophages in the human preterm intestine (fetus/premature neonate), but not in full-term neonates and adults, expressed inflammatory cytokines. Macrophage cytokine production was suppressed in the developing intestine by TGF-β, particularly the TGF-β2 isoform. NEC was associated with decreased tissue expression of TGF-β2 and decreased TGF-β bioactivity. In mice, disruption of TGF-β signaling worsened NEC-like inflammatory mucosal injury, whereas enteral supplementation with recombinant TGF-β2 was protective.
Intestinal macrophages progressively acquire a non-inflammatory profile during gestational development. TGF-β, particularly the TGF-β2 isoform, suppresses macrophage inflammatory responses in the developing intestine and protects against inflammatory mucosal injury. Enterally-administered TGF-β2 protected mice from experimental NEC-like injury.
PMCID: PMC3008335  PMID: 20875417
necrotizing enterocolitis; macrophage; newborn; inflammation; TGF-β
25.  The Shaping of the Face Space in Early Infancy: Becoming a Native Face Processor 
Child development perspectives  2010;4(3):205-211.
Face perception remains one of the most intensively researched areas in psychology and allied disciplines, and there has been much debate regarding the early origins and experiential determinants of face processing. This article reviews studies, the majority of which have appeared in the past decade, that discuss possible mechanisms underlying face perception at birth and document the prominent role of experience in shaping infants’ face-processing abilities. In the first months of life, infants develop a preference for female and own-race faces and become better able to recognize and categorize own-race and own-species faces. This perceptual narrowing and shaping of the “face space” forms a foundation for later face expertise in childhood and adulthood and testifies to the remarkable plasticity of the developing visual system.
PMCID: PMC3090162  PMID: 21562620
infancy; face perception; neural plasticity; own-race effect; own-species effect; gender preferences; perceptual narrowing

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