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1.  Extracellular Onchocerca-derived small RNAs in host nodules and blood 
Parasites & Vectors  2015;8:58.
Background
microRNAs (miRNAs), a class of short, non-coding RNA can be found in a highly stable, cell-free form in mammalian body fluids. Specific miRNAs are secreted by parasitic nematodes in exosomes and have been detected in the serum of murine and dog hosts infected with the filarial nematodes Litomosoides sigmodontis and Dirofilaria immitis, respectively. Here we identify extracellular, parasite-derived small RNAs associated with Onchocerca species infecting cattle and humans.
Methods
Small RNA libraries were prepared from total RNA extracted from the nodule fluid of cattle infected with Onchocerca ochengi as well as serum and plasma from humans infected with Onchocerca volvulus in Cameroon and Ghana. Parasite-derived miRNAs were identified based on the criteria that sequences unambiguously map to hairpin structures in Onchocerca genomes, do not align to the human genome and are not present in European control serum.
Results
A total of 62 mature miRNAs from 52 distinct pre-miRNA candidates were identified in nodule fluid from cattle infected with O. ochengi of which 59 are identical in the genome of the human parasite O. volvulus. Six of the extracellular miRNAs were also identified in sequencing analyses of serum and plasma from humans infected with O. volvulus. Based on sequencing analysis the abundance levels of the parasite miRNAs in serum or plasma range from 5 to 127 reads/per million total host miRNA reads identified, comparable to our previous analyses of Schistosoma mansoni and L. sigmodontis miRNAs in serum. All six of the O. volvulus miRNAs identified have orthologs in other filarial nematodes and four were identified in the serum of mice infected with L. sigmodontis.
Conclusions
We have identified parasite-derived miRNAs associated with onchocerciasis in cattle and humans. Our results confirm the conserved nature of RNA secretion by diverse nematodes. Additional species-specific small RNAs from O. volvulus may be present in serum based on the novel miRNA sequences identified in the nodule fluid. In our analyses comparison to European control serum illuminates the scope for false-positives, warranting caution in criteria that should be applied to identification of biomarkers of infection.
Electronic supplementary material
The online version of this article (doi:10.1186/s13071-015-0656-1) contains supplementary material, which is available to authorized users.
doi:10.1186/s13071-015-0656-1
PMCID: PMC4316651  PMID: 25623184
microRNAs; Extracellular RNA; Filarial nematode; Onchocerciasis; Host-pathogen
2.  Genome and Phylogenetic Analyses of Trypanosoma evansi Reveal Extensive Similarity to T. brucei and Multiple Independent Origins for Dyskinetoplasty 
Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.
Author Summary
The single-cell parasite Trypanosoma evansi is the disease-causing trypanosome with the widest geographical distribution. The disease, called surra, has significant economic impact primarily due to infections of cattle, horses, and camels. Morphologically the parasite is indistinguishable from bloodstream stage T. brucei, a parasite causing sleeping sickness in humans and the disease nagana in animals. T. brucei, however, is strictly bound to sub-Saharan Africa where its obligate vector, the tsetse fly, resides. The lack of a complete mitochondrial genome in T. evansi further distinguishes this parasite from T. brucei. Important questions regarding the biology of T. evansi include how it escaped from Africa, whether this has happened more than once, and how exactly it is related to T. brucei. To help answer these questions we have sequenced the T. evansi nuclear genome. Our phylogenetic analysis demonstrates that T. evansi, and the closely related horse parasite T. equiperdum, evolved more than once from T. brucei. We also demonstrate extensive similarity to T. brucei, including the maintenance of numerous genes that T. evansi no longer requires. Therefore, despite the significant functional and pathological differences between T. evansi and T. brucei, our analysis supports the notion that T. evansi is not an independent species.
doi:10.1371/journal.pntd.0003404
PMCID: PMC4288722  PMID: 25568942
3.  Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity 
Nature Communications  2014;5:5488.
In mammalian systems RNA can move between cells via vesicles. Here we demonstrate that the gastrointestinal nematode Heligmosomoides polygyrus, which infects mice, secretes vesicles containing microRNAs (miRNAs) and Y RNAs as well as a nematode Argonaute protein. These vesicles are of intestinal origin and are enriched for homologues of mammalian exosome proteins. Administration of the nematode exosomes to mice suppresses Type 2 innate responses and eosinophilia induced by the allergen Alternaria. Microarray analysis of mouse cells incubated with nematode exosomes in vitro identifies Il33r and Dusp1 as suppressed genes, and Dusp1 can be repressed by nematode miRNAs based on a reporter assay. We further identify miRNAs from the filarial nematode Litomosoides sigmodontis in the serum of infected mice, suggesting that miRNA secretion into host tissues is conserved among parasitic nematodes. These results reveal exosomes as another mechanism by which helminths manipulate their hosts and provide a mechanistic framework for RNA transfer between animal species.
Mammalian cell-derived exosomes can carry RNA and proteins from cell to cell, but this mode of transport has not been shown in nematodes. Here the authors show that a gastrointestinal parasite secretes exosomes that transfer microRNAs to mammalian cells and regulate innate immunity.
doi:10.1038/ncomms6488
PMCID: PMC4263141  PMID: 25421927
4.  Strain Classification of Mycobacterium tuberculosis Isolates in Brazil Based on Genotypes Obtained by Spoligotyping, Mycobacterial Interspersed Repetitive Unit Typing and the Presence of Large Sequence and Single Nucleotide Polymorphism 
PLoS ONE  2014;9(10):e107747.
Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as “LAM-like”, 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.
doi:10.1371/journal.pone.0107747
PMCID: PMC4196770  PMID: 25314118
6.  Changes in hemodynamic responses in chronic stroke survivors do not affect fMRI signal detection in a block experimental design 
Magnetic resonance imaging  2013;31(7):10.1016/j.mri.2013.02.009.
The use of canonical functions to model BOLD-fMRI data in people post-stroke may lead to inaccurate descriptions of task-related brain activity. The purpose of this study was to determine whether the spatiotemporal profile of hemodynamic responses (HDRs) obtained from stroke survivors during an event-related experiment could be used to develop individualized HDR functions that would enhance BOLD-fMRI signal detection in block experiments. Our long term goal was to use this information to develop individualized HDR functions for stroke survivors that could be used to analyze brain activity associated with locomotor-like movements. We also aimed to examine the reproducibility of HDRs obtained across two scan sessions in order to determine whether data from a single event-related session could be used to analyze block data obtained in subsequent sessions. Results indicate that the spatiotemporal profile of HDRs measured with BOLD-fMRI in stroke survivors was not the same as that observed in individuals without stroke. We observed small between-group differences in the rates of rise and decline of HDRs that were more apparent in individuals with cortical as compared to subcortical stroke. There were no differences in the peak or time to peak of HDRs in people with and without stroke. Of interest, differences in HDRs were not as substantial as expected from previous reports and were not large enough to necessitate the use of individualized HDR functions to obtain valid measures of movement-related brain activity. We conclude that all strokes do not affect the spatiotemporal characteristics of HDRs in such a way as to produce inaccurate representations of brain activity as measured by BOLD-fMRI. However, care should be taken to identify individuals whose BOLD-fMRI data may not provide an accurate representation of underlying brain activation when canonical models are used. Examination of HDRs need not be done for each scan session, as our data suggest that the characteristics of HDRs in stroke survivors are reproducible across days.
doi:10.1016/j.mri.2013.02.009
PMCID: PMC3822766  PMID: 23642802
Stroke; CVA; fMRI; Hemodynamic response function; Locomotion; Methods
7.  Genome wide dissection of the quorum sensing signaling pathway in Trypanosoma brucei 
Nature  2013;505(7485):681-685.
The protozoan parasites Trypanosoma brucei spp. cause important human and livestock diseases in sub Saharan Africa. In the mammalian blood, two developmental forms of the parasite exist: proliferative ‘slender’ forms and arrested ‘stumpy’ forms that are responsible for transmission to tsetse flies. The slender to stumpy differentiation is a density-dependent response that resembles quorum sensing (QS) in microbial systems and is crucial for the parasite life cycle, ensuring both infection chronicity and disease transmission1. This response is triggered by an elusive ‘stumpy induction factor’ (SIF) whose intracellular signaling pathway is also uncharacterized. Laboratory-adapted (monomorphic) trypanosome strains respond inefficiently to SIF but can generate forms with stumpy characteristics when exposed to cell permeable cAMP and AMP analogues. Exploiting this, we have used a genome-wide RNAi library screen to identify the signaling components driving stumpy formation. In separate screens, monomorphic parasites were exposed to 8-(4-chlorophenylthio)-cAMP (pCPTcAMP) or 8-pCPT-2′-O-Me-5′-AMP to select cells that were unresponsive to these signals and hence remained proliferative. Genome-wide ion torrent-based RNA interference Target sequencing identified cohorts of genes implicated in each step of the signaling pathway, from purine metabolism, through signal transducers (kinases, phosphatases) to gene expression regulators. Genes at each step were independently validated in cells naturally capable of stumpy formation, confirming their role in density sensing in vivo, whilst the putative RNA-binding protein, RBP7, was required for normal QS and promoted cell-cycle arrest and transmission competence when overexpressed. This study reveals that QS signaling in trypanosomes shares similarities to fundamental quiescence pathways in eukaryotic cells, its components providing targets for QS-interference based therapeutics.
doi:10.1038/nature12864
PMCID: PMC3908871  PMID: 24336212
8.  Low frequency depression of H-reflexes in humans with acute and chronic spinal-cord injury 
Experimental brain research  2000;133(2):233-241.
We measured low-frequency depression of soleus H-reflexes in individuals with acute (n=5) and chronic (n=7) spinal-cord injury and in able-bodied controls (n=7). In one acute subject, we monitored longitudinal changes in low-frequency depression of H-reflexes over 44 weeks and examined the relationship between H-reflex depression and soleus-muscle fatigue properties. Soleus H-reflexes were elicited at 0.1, 0.2, 1, 5, and 10 Hz. The mean peak-to-peak amplitude of ten reflexes at each frequency was calculated, and values obtained at each frequency were normalized to 0.1 Hz. H-reflex amplitude decreased with increasing stimulation frequency in all three groups, but H-reflex suppression was significantly larger in the able-bodied and acute groups than in the chronic group. The acute subject who was monitored longitudinally displayed reduced low-frequency depression with increasing time post injury. At 44 weeks post injury, the acute subject’s H-reflex depression was similar to that of chronic subjects, and his soleus fatigue index (assessed with a modified Burke fatigue protocol) dropped substantially, consistent with transformation to faster muscle. There was a significant inverse correlation over the 44 weeks between the fatigue index and the mean normalized H-reflex amplitude at 1, 5, and 10 Hz. We conclude that: (1) the chronically paralyzed soleus muscle displays impaired low-frequency depression of H-reflexes, (2) attenuation of rate-sensitive depression in humans with spinal-cord injury occurs gradually, and (3) changes in H-reflex excitability are generally correlated with adaptation of the neuromuscular system. Possible mechanisms underlying changes in low-frequency depression and their association with neuromuscular adaptation are discussed.
PMCID: PMC4034370  PMID: 10968224
Spasticity; Paralysis; Plasticity; Muscle; Fatigue
9.  Combinatorial Communication in Bacteria: Implications for the Origins of Linguistic Generativity 
PLoS ONE  2014;9(4):e95929.
Combinatorial communication, in which two signals are used together to achieve an effect that is different to the sum of the effects of the component parts, is apparently rare in nature: it is ubiquitous in human language, appears to exist in a simple form in some non-human primates, but has not been demonstrated in other species. This observed distribution has led to the pair of related suggestions, that (i) these differences in the complexity of observed communication systems reflect cognitive differences between species; and (ii) that the combinations we see in non-human primates may be evolutionary pre-cursors of human language. Here we replicate the landmark experiments on combinatorial communication in non-human primates, but in an entirely different species, unrelated to humans, and with no higher cognition: the bacterium Pseudomonas aeruginosa. Using the same general methods as the primate studies, we find the same general pattern of results: the effect of the combined signal differs from the composite effect of the two individual signals. This suggests that advanced cognitive abilities and large brains do not necessarily explain why some species have combinatorial communication systems and others do not. We thus argue that it is premature to conclude that the systems observed in non-human primates are evolutionarily related to language. Our results illustrate the value of an extremely broad approach to comparative research.
doi:10.1371/journal.pone.0095929
PMCID: PMC3997515  PMID: 24759740
10.  Lower Extremity Passive Range of Motion in Community-Ambulating Stroke Survivors 
Background
Physical therapists may prescribe stretching exercises for individuals with stroke to improve joint integrity and to reduce the risk of secondary musculoskeletal impairment. While deficits in passive range of motion (PROM) exist in stroke survivors with severe hemiparesis and spasticity, the extent to which impaired lower extremity PROM occurs in community-ambulating stroke survivors remains unclear. This study compared lower extremity PROM in able-bodied individuals and independent community-ambulatory stroke survivors with residual stroke-related neuromuscular impairments. Our hypothesis was that the stroke group would show decreased lower extremity PROM in the paretic but not the nonparetic side and that decreased PROM would be associated with increased muscle stiffness and decreased muscle length.
Methods
Individuals with chronic poststroke hemiparesis who reported the ability to ambulate independently in the community (n = 17) and age-matched control subjects (n = 15) participated. PROM during slow (5 degrees/sec) hip extension, hip flexion, and ankle dorsiflexion was examined bilaterally using a dynamometer that measured joint position and torque. The maximum angular position of the joint (ANGmax), torque required to achieve ANGmax (Tmax), and mean joint stiffness (K) were measured. Comparisons were made between able-bodied and paretic and able-bodied and nonparetic limbs.
Results
Contrary to our expectations, between-group differences in ANGmax were observed only during hip extension in which ANGmax was greater bilaterally in people post-stroke compared to control subjects (P ≤ 0.05; stroke = 13 degrees, able-bodied = −1 degree). Tmax, but not K, was also significantly higher during passive hip extension in paretic and nonparetic limbs compared to control limbs (P ≤ 0.05; stroke = 40 Nm, able-bodied = 29 Nm). Compared to the control group, Tmax was increased during hip flexion in the paretic and nonparetic limbs of post-stroke subjects (P ≤ 0.05, stroke = 25 Nm, able-bodied = 18 Nm). K in the nonparetic leg was also increased during hip flexion (P ≤ 0.05, nonparetic = 0.52 Nm/degree, able-bodied = 0.37 Nm/degree.)
Conclusion
This study demonstrates that community-ambulating stroke survivors with residual neuromuscular impairments do not have decreased lower extremity PROM caused by increased muscle stiffness or decreased muscle length. In fact, the population of stroke survivors examined here appears to have more hip extension PROM than age-matched able-bodied individuals. The clinical implications of these data are important and suggest that lower extremity PROM may not interfere with mobility in community-ambulating stroke survivors. Hence, physical therapists may choose to recommend activities other than stretching exercises for stroke survivors who are or will become independent community ambulators.
doi:10.1097/NPT.0b013e31816594ea
PMCID: PMC3963266  PMID: 18463552
cerebral vascular accident (CVA); hemiparesis; muscle; range of motion (ROM); spasticity
11.  High-Throughput Chemical Screening for Antivirulence Developmental Phenotypes in Trypanosoma brucei 
Eukaryotic Cell  2014;13(3):412-426.
In the bloodstream of mammalian hosts, the sleeping sickness parasite, Trypanosoma brucei, exists as a proliferative slender form or a nonproliferative, transmissible, stumpy form. The transition between these developmental forms is controlled by a density-dependent mechanism that is important for the parasite's infection dynamics, immune evasion via ordered antigenic variation, and disease transmissibility. However, stumpy formation has been lost in most laboratory-adapted trypanosome lines, generating monomorphic parasites that proliferate uncontrolled as slender forms in vitro and in vivo. Nonetheless, these forms are readily amenable to cell culture and high-throughput screening for trypanocidal lead compounds. Here, we have developed and exploited a high-throughput screen for developmental phenotypes using a transgenic monomorphic cell line expressing a reporter under the regulation of gene control signals from the stumpy-specific molecule PAD1. Using a whole-cell fluorescence-based assay to screen over 6,000 small molecules from a kinase-focused compound library, small molecules able to activate stumpy-specific gene expression and proliferation arrest were assayed in a rapid assay format. Independent follow-up validation identified one hit able to induce modest, yet specific, changes in mRNA expression indicative of a partial differentiation to stumpy forms in monomorphs. Further, in pleomorphs this compound induced a stumpy-like phenotype, entailing growth arrest, morphological changes, PAD1 expression, and enhanced differentiation to procyclic forms. This not only provides a potential tool compound for the further understanding of stumpy formation but also demonstrates the use of high-throughput screening in the identification of compounds able to induce specific phenotypes, such as differentiation, in African trypanosomes.
doi:10.1128/EC.00335-13
PMCID: PMC3957582  PMID: 24442893
12.  Parasite-Derived MicroRNAs in Host Serum As Novel Biomarkers of Helminth Infection 
Background
MicroRNAs (miRNAs) are a class of short non-coding RNA that play important roles in disease processes in animals and are present in a highly stable cell-free form in body fluids. Here, we examine the capacity of host and parasite miRNAs to serve as tissue or serum biomarkers of Schistosoma mansoni infection.
Methods/Principal Findings
We used Exiqon miRNA microarrays to profile miRNA expression in the livers of mice infected with S. mansoni at 7 weeks post-infection. Thirty-three mouse miRNAs were differentially expressed in infected compared to naïve mice (>2 fold change, p<0.05) including miR-199a-3p, miR-199a-5p, miR-214 and miR-21, which have previously been associated with liver fibrosis in other settings. Five of the mouse miRNAs were also significantly elevated in serum by twelve weeks post-infection. Sequencing of small RNAs from serum confirmed the presence of these miRNAs and further revealed eleven parasite-derived miRNAs that were detectable by eight weeks post infection. Analysis of host and parasite miRNA abundance by qRT-PCR was extended to serum of patients from low and high infection sites in Zimbabwe and Uganda. The host-derived miRNAs failed to distinguish uninfected from infected individuals. However, analysis of three of the parasite-derived miRNAs (miR-277, miR-3479-3p and bantam) could detect infected individuals from low and high infection intensity sites with specificity/sensitivity values of 89%/80% and 80%/90%, respectively.
Conclusions
This work identifies parasite-derived miRNAs as novel markers of S. mansoni infection in both mice and humans, with the potential to be used with existing techniques to improve S. mansoni diagnosis. In contrast, although host miRNAs are differentially expressed in the liver during infection their abundance levels in serum are variable in human patients and may be useful in cases of extreme pathology but likely hold limited value for detecting prevalence of infection.
Author Summary
Schistosomiasis is a chronic disease caused by blood flukes that affects over 200 million people worldwide, of which 90% live in Sub-Saharan Africa. In the field setting schistosomiasis caused by S. mansoni is diagnosed by detection of parasite eggs in stool samples using microscopic techniques. Here we investigate the potential of microRNAs (miRNAs), a class of short noncoding RNAs, to act as biomarkers of S. mansoni infection. We have identified a specific subset of murine miRNAs whose expression is significantly altered in the liver between 6–12 weeks post infection. However their abundance in serum is not significantly different between naïve and S. mansoni-infected mice until twelve weeks post infection and they do not display consistent differential abundance in the serum of infected versus uninfected humans. In contrast, three parasite-derived miRNAs (miR-277, bantam and miR-3479-3p) were detected in the serum of infected mice and human patients and the combined detection of these miRNAs could distinguish S. mansoni infected from uninfected individuals from low and high infection intensity areas with 89%/80% or 80%/90% specificity/sensitivity, respectively. These results demonstrate that miRNAs of parasite origin are a new class of serum biomarker for detecting S. mansoni and likely other helminth infections.
doi:10.1371/journal.pntd.0002701
PMCID: PMC3930507  PMID: 24587461
13.  EEG during pedaling: Evidence for cortical control of locomotor tasks 
Objective
This study characterized the brain electrical activity during pedaling, a locomotor-like task, in humans. We postulated that phasic brain activity would be associated with active pedaling, consistent with a cortical role in locomotor tasks.
Methods
Sixty four channels of electroencephalogram (EEG) and 10 channels of electromyogram (EMG) data were recorded from 10 neurologically-intact volunteers while they performed active and passive (no effort) pedaling on a custom-designed stationary bicycle. Ensemble averaged waveforms, 2 dimensional topographic maps and amplitude of the β (13–35 Hz) frequency band were analyzed and compared between active and passive trials.
Results
The peak-to-peak amplitude (peak positive–peak negative) of the EEG waveform recorded at the Cz electrode was higher in the passive than the active trials (p < 0.01). β-band oscillations in electrodes overlying the leg representation area of the cortex were significantly desynchronized during active compared to the passive pedaling (p < 0.01). A significant negative correlation was observed between the average EEG waveform for active trials and the composite EMG (summated EMG from both limbs for each muscle) of the rectus femoris (r = −0.77, p < 0.01) the medial hamstrings (r = −0.85, p < 0.01) and the tibialis anterior (r = −0.70, p < 0.01) muscles.
Conclusions
These results demonstrated that substantial sensorimotor processing occurs in the brain during pedaling in humans. Further, cortical activity seemed to be greatest during recruitment of the muscles critical for transitioning the legs from flexion to extension and vice versa.
Significance
This is the first study demonstrating the feasibility of EEG recording during pedaling, and owing to similarities between pedaling and bipedal walking, may provide valuable insight into brain activity during locomotion in humans.
doi:10.1016/j.clinph.2012.08.021
PMCID: PMC3912946  PMID: 23036179
Electroencephalography; Pedaling; Brain activity
14.  Direction-Dependent Phasing of Locomotor Muscle Activity Is Altered Post-Stroke 
Journal of neurophysiology  2004;92(4):2207-2216.
A major contributor to impaired locomotion post-stroke is abnormal phasing of muscle activity. While inappropriate paretic muscle phasing adapts to changing body orientation, load, and speed, it remains unclear whether paretic muscle phasing adapts to reversal of locomotor direction. We examined muscle phasing in backward pedaling, a task that requires shifts in biarticular but not uniarticular muscle phasing relative to forward pedaling. We hypothesized that if paretic and neurologically intact muscle phasing adapt similarly, then paretic biarticular but not paretic uniarticular muscles would shift phasing in backward pedaling. Paretic and neurologically intact individuals pedaled forward and backward while recording electromyograms (EMGs) from vastus medialis (VM), soleus (SOL), rectus femoris (RF), semimembranosus (SM), and biceps femoris (BF). Changes in muscle phasing were assessed by comparing the probability of muscle activity in forward and backward pedaling throughout 18 pedaling cycles. Paretic uniarticular muscles (VM and SOL) showed phase-advanced activity in backward versus forward pedaling, whereas the corresponding neurologically intact muscles showed little to no phasing change. Paretic biarticular muscles were less likely than neurologically intact biarticular muscles to display phasing changes in backward pedaling. Paretic RF displayed no phase change during backward pedaling, and paretic BF displayed no consistent adaptation to backward pedaling. Paretic SM was the only muscle to display backward/forward phase changes that were similar to the neurologically intact group. We conclude that paretic uniarticular muscles are more susceptible and paretic biarticular muscles are less susceptible to direction-dependent phase shifts, consistent with altered sensory integration and impaired cortical control of locomotion.
doi:10.1152/jn.01207.2003
PMCID: PMC3912995  PMID: 15175363
15.  Is the ICU staff satisfied with the computerized physician order entry? A cross-sectional survey study 
Objective
To evaluate the satisfaction of the intensive care unit staff with a computerized physician order entry and to compare the concept of the computerized physician order entry relevance among intensive care unit healthcare workers.
Methods
We performed a cross-sectional survey to assess the satisfaction of the intensive care unit staff with the computerized physician order entry in a 30-bed medical/surgical adult intensive care unit using a self-administered questionnaire. The questions used for grading satisfaction levels were answered according to a numerical scale that ranged from 1 point (low satisfaction) to 10 points (high satisfaction).
Results
The majority of the respondents (n=250) were female (66%) between the ages of 30 and 35 years of age (69%). The overall satisfaction with the computerized physician order entry scored 5.74±2.14 points. The satisfaction was lower among physicians (n=42) than among nurses, nurse technicians, respiratory therapists, clinical pharmacists and diet specialists (4.62±1.79 versus 5.97±2.14, p<0.001); satisfaction decreased with age (p<0.001). Physicians scored lower concerning the potential of the computerized physician order entry for improving patient safety (5.45±2.20 versus 8.09±2.21, p<0.001) and the ease of using the computerized physician order entry (3.83±1.88 versus 6.44±2.31, p<0.001). The characteristics independently associated with satisfaction were the system's user-friendliness, accuracy, capacity to provide clear information, and fast response time.
Conclusion
Six months after its implementation, healthcare workers were satisfied, albeit not entirely, with the computerized physician order entry. The overall users' satisfaction with computerized physician order entry was lower among physicians compared to other healthcare professionals. The factors associated with satisfaction included the belief that digitalization decreased the workload and contributed to the intensive care unit quality with a user-friendly and accurate system and that digitalization provided concise information within a reasonable time frame.
doi:10.5935/0103-507X.20140001
PMCID: PMC4031891  PMID: 24770682
Medical order entry system; Physician practice patterns; Health care surveys; Attitude of health personnel; Job satisfaction
17.  Lifetime Paid Work and Mental Health Problems among Poor Urban 9-to-13-Year-Old Children in Brazil 
The Scientific World Journal  2013;2013:815218.
Objective. To verify if emotional/behavioral problems are associated with lifetime paid work in poor urban children, when taking into account other potential correlates. Methods. Cross-sectional study focused on 9-to-13-year-old children (n = 212). In a probabilistic sample of clusters of eligible households (women 15–49 years and son/daughter <18 years), one mother-child pair was randomly selected per household (n = 813; response rate = 82.4%). CBCL/6-18 identified child emotional/behavioral problems. Potential correlates include child gender and age, socioeconomic status/SES, maternal education, parental working status, and family social isolation, among others. Multivariate analysis examined the relationship between emotional/behavioral problems and lifetime paid work in the presence of significant correlates. Findings. All work activities were non-harmful (e.g., selling fruits, helping parents at their small business, and baby sitting). Children with lower SES and socially isolated were more involved in paid work than less disadvantaged peers. Children ever exposed to paid work were four times more likely to present anxiety/depression symptoms at a clinical level compared to non-exposed children. Multivariate modeling identified three independent correlates: child pure internalizing problems, social isolation, and low SES. Conclusion. There is an association between lifetime exposure to exclusively non-harmful paid work activities and pure internalizing problems even when considering SES variability and family social isolation.
doi:10.1155/2013/815218
PMCID: PMC3834988  PMID: 24302872
18.  Secretion of Protective Antigens by Tissue-Stage Nematode Larvae Revealed by Proteomic Analysis and Vaccination-Induced Sterile Immunity 
PLoS Pathogens  2013;9(8):e1003492.
Gastrointestinal nematode parasites infect over 1 billion humans, with little evidence for generation of sterilising immunity. These helminths are highly adapted to their mammalian host, following a developmental program through successive niches, while effectively down-modulating host immune responsiveness. Larvae of Heligmosomoides polygyrus, for example, encyst in the intestinal submucosa, before emerging as adult worms into the duodenal lumen. Adults release immunomodulatory excretory-secretory (ES) products, but mice immunised with adult H. polygyrus ES become fully immune to challenge infection. ES products of the intestinal wall 4th stage (L4) larvae are similarly important in host-parasite interactions, as they readily generate sterile immunity against infection, while released material from the egg stage is ineffective. Proteomic analyses of L4 ES identifies protective antigen targets as well as potential tissue-phase immunomodulatory molecules, using as comparators the adult ES proteome and a profile of H. polygyrus egg-released material. While 135 proteins are shared between L4 and adult ES, 72 are L4 ES-specific; L4-specific proteins correspond to those whose transcription is restricted to larval stages, while shared proteins are generally transcribed by all life cycle forms. Two protein families are more heavily represented in the L4 secretome, the Sushi domain, associated with complement regulation, and the ShK/SXC domain related to a toxin interfering with T cell signalling. Both adult and L4 ES contain extensive but distinct arrays of Venom allergen/Ancylostoma secreted protein-Like (VAL) members, with acetylcholinesterases (ACEs) and apyrase APY-3 particularly abundant in L4 ES. Serum antibodies from mice vaccinated with L4 and adult ES react strongly to the VAL-1 protein and to ACE-1, indicating that these two antigens represent major vaccine targets for this intestinal nematode. We have thus defined an extensive and novel repertoire of H. polygyrus proteins closely implicated in immune modulation and protective immunity.
Author Summary
Intestinal helminth parasites are highly prevalent in humans and animals, and survive for long periods by deviating the host immune system. No vaccines are currently available to control these infections. Many helminths invade through barrier surfaces (such as the skin or the digestive tract) and develop through tissue larval stages before reaching their final niche such as the intestinal lumen. We studied the tissue larval stage of a mouse parasite, Heligmosomoides polygyrus, to test whether proteins released by this stage could elicit protective immunity, and found that they indeed constitute very effective vaccine antigens. Proteomic analysis to identify the individual proteins released by the larvae demonstrated that while many products are shared between tissue-dwelling larvae and adults occupying the intestinal lumen, larvae express higher levels of two gene families linked to immunomodulation, namely the Sushi protein family and the ShK toxin family. Antibody analysis of serum from vaccinated mice identified two major antigens recognised by the protective immune response as VAL-1 and ACE-1, which are respectively members of the venom allergen and acetylcholinesterase families. This work establishes that tissue larvae are the source of protective antigens for future vaccines, and highlights their production of two potentially immunomodulatory gene families.
doi:10.1371/journal.ppat.1003492
PMCID: PMC3744408  PMID: 23966853
19.  Clinically Relevant Mutant DNA Gyrase Alters Supercoiling, Changes the Transcriptome, and Confers Multidrug Resistance 
mBio  2013;4(4):e00273-13.
ABSTRACT
Bacterial DNA is maintained in a supercoiled state controlled by the action of topoisomerases. Alterations in supercoiling affect fundamental cellular processes, including transcription. Here, we show that substitution at position 87 of GyrA of Salmonella influences sensitivity to antibiotics, including nonquinolone drugs, alters global supercoiling, and results in an altered transcriptome with increased expression of stress response pathways. Decreased susceptibility to multiple antibiotics seen with a GyrA Asp87Gly mutant was not a result of increased efflux activity or reduced reactive-oxygen production. These data show that a frequently observed and clinically relevant substitution within GyrA results in altered expression of numerous genes, including those important in bacterial survival of stress, suggesting that GyrA mutants may have a selective advantage under specific conditions. Our findings help contextualize the high rate of quinolone resistance in pathogenic strains of bacteria and may partly explain why such mutant strains are evolutionarily successful.
IMPORTANCE
Fluoroquinolones are a powerful group of antibiotics that target bacterial enzymes involved in helping bacteria maintain the conformation of their chromosome. Mutations in the target enzymes allow bacteria to become resistant to these antibiotics, and fluoroquinolone resistance is common. We show here that these mutations also provide protection against a broad range of other antimicrobials by triggering a defensive stress response in the cell. This work suggests that fluoroquinolone resistance mutations may be beneficial under a range of conditions.
doi:10.1128/mBio.00273-13
PMCID: PMC3735185  PMID: 23882012
20.  Regulation of Trypanosoma brucei Total and Polysomal mRNA during Development within Its Mammalian Host 
PLoS ONE  2013;8(6):e67069.
The gene expression of Trypanosoma brucei has been examined extensively in the blood of mammalian hosts and in forms found in the midgut of its arthropod vector, the tsetse fly. However, trypanosomes also undergo development within the mammalian bloodstream as they progress from morphologically ‘slender forms’ to transmissible ‘stumpy forms’ through morphological intermediates. This transition is temporally progressive within the first wave of parasitaemia such that gene expression can be monitored in relatively pure slender and stumpy populations as well as during the progression between these extremes. The development also represents the progression of cells from translationally active forms adapted for proliferation in the host to translationally quiescent forms, adapted for transmission. We have used metabolic labelling to quantitate translational activity in slender forms, stumpy forms and in forms undergoing early differentiation to procyclic forms in vitro. Thereafter we have examined the cohort of total mRNAs that are enriched throughout development in the mammalian bloodstream (slender, intermediate and stumpy forms), irrespective of strain, revealing those that exhibit consistent developmental regulation rather than sample specific changes. Transcripts that cosediment with polysomes in stumpy forms and slender forms have also been enriched to identify transcripts that escape translational repression prior to transmission. Combined, the expression and polysomal association of transcripts as trypanosomes undergo development in the mammalian bloodstream have been defined, providing a resource for trypanosome researchers. This facilitates the identification of those that undergo developmental regulation in the bloodstream and therefore those likely to have a role in the survival and capacity for transmission of stumpy forms.
doi:10.1371/journal.pone.0067069
PMCID: PMC3694164  PMID: 23840587
21.  White matter structural connectivity is associated with sensorimotor function in stroke survivors☆ 
NeuroImage : Clinical  2013;2:767-781.
Purpose
Diffusion tensor imaging (DTI) provides functionally relevant information about white matter structure. Local anatomical connectivity information combined with fractional anisotropy (FA) and mean diffusivity (MD) may predict functional outcomes in stroke survivors. Imaging methods for predicting functional outcomes in stroke survivors are not well established. This work uses DTI to objectively assess the effects of a stroke lesion on white matter structure and sensorimotor function.
Methods
A voxel-based approach is introduced to assess a stroke lesion's global impact on motor function. Anatomical T1-weighted and diffusion tensor images of the brain were acquired for nineteen subjects (10 post-stroke and 9 age-matched controls). A manually selected volume of interest was used to alleviate the effects of stroke lesions on image registration. Images from all subjects were registered to the images of the control subject that was anatomically closest to Talairach space. Each subject's transformed image was uniformly seeded for DTI tractography. Each seed was inversely transformed into the individual subject space, where DTI tractography was conducted and then the results were transformed back to the reference space. A voxel-wise connectivity matrix was constructed from the fibers, which was then used to calculate the number of directly and indirectly connected neighbors of each voxel. A novel voxel-wise indirect structural connectivity (VISC) index was computed as the average number of direct connections to a voxel's indirect neighbors. Voxel-based analyses (VBA) were performed to compare VISC, FA, and MD for the detection of lesion-induced changes in sensorimotor function. For each voxel, a t-value was computed from the differences between each stroke brain and the 9 controls. A series of linear regressions was performed between Fugl-Meyer (FM) assessment scores of sensorimotor impairment and each DTI metric's log number of voxels that differed from the control group.
Results
Correlation between the logarithm of the number of significant voxels in the ipsilesional hemisphere and total Fugl-Meyer score was moderate for MD (R2 = 0.512), and greater for VISC (R2 = 0.796) and FA (R2 = 0.674). The slopes of FA (p = 0.0036), VISC (p = 0.0005), and MD (p = 0.0199) versus the total FM score were significant. However, these correlations were driven by the upper extremity motor component of the FM score (VISC: R2 = 0.879) with little influence of the lower extremity motor component (FA: R2 = 0.177).
Conclusion
The results suggest that a voxel-wise metric based on DTI tractography can predict upper extremity sensorimotor function of stroke survivors, and that supraspinal intraconnectivity may have a less dominant role in lower extremity function.
Highlights
•An intrinsic voxel-based structural connectivity metric is proposed.•The metric enhances the impact of stroke lesions on the distant voxels.•Whole-brain extralesional anatomical connectivity predicts functional outcome.•Functional impact of a lesion is determined by residual anatomical connectivity.•Connectivity to the posterior parietal cortex is a key to sensorimotor function.
doi:10.1016/j.nicl.2013.05.009
PMCID: PMC3777792  PMID: 24179827
DTI, diffusion tensor imaging; FA, fractional anisotropy; FOV, field of view; FM, Fugl-Meyer; LDV, log difference volume; LE, lower extremity; MD, mean diffusivity; TE, echo time; TFIRE, Tactful Functional Imaging Research Environment; TR, repetition time; UE, upper extremity; VISC, voxel-wise indirect structural connectivity; Voxel-wise structural connectivity; Tractography; Diffusion tensor imaging; Stroke; Sensorimotor function; Lesion analysis
22.  Choice of Bacterial Growth Medium Alters the Transcriptome and Phenotype of Salmonella enterica Serovar Typhimurium 
PLoS ONE  2013;8(5):e63912.
The type of bacterial culture medium is an important consideration during design of any experimental protocol. The aim of this study was to understand the impact of medium choice on bacterial gene expression and physiology by comparing the transcriptome of Salmonella enterica SL1344 after growth in the widely used LB broth or the rationally designed MOPS minimal medium. Transcriptomics showed that after growth in MOPS minimal media, compared to LB, there was increased expression of 42 genes involved in amino acid synthesis and 23 genes coding for ABC transporters. Seven flagellar genes had decreased expression after growth in MOPS minimal medium and this correlated with a decreased motility. In both MOPS minimal medium and MEM expression of genes from SPI-2 was increased and the adhesion of S. Typhimurium to intestinal epithelial cells was higher compared to the levels after growth in LB. However, SL1344 invasion was not significantly altered by growth in either MOPs minimal media or MEM. Expression of SPI-2 was also measured using chromosomal GFP reporter fusions followed by flow cytometry which showed, for the first time, that the reduction in SPI-2 transcript after growth in different media related to a reduction in the proportion of the bacterial population expressing SPI-2. These data highlight the profound differences in the global transcriptome after in vitro growth in different media and show that choice of medium should be considered carefully during experimental design, particularly when virulence related phenotypes are being measured.
doi:10.1371/journal.pone.0063912
PMCID: PMC3660369  PMID: 23704954
23.  Sex determination in the social amoeba Dictyostelium discoideum 
Science (New York, N.Y.)  2010;330(6010):1533-1536.
The genetics of sex determination remains mysterious in many organisms including some that are otherwise well-studied. Here we report the discovery and analysis of the mating-type locus of the model organism Dictyostelium discoideum. Three forms of a single genetic locus specifies this species’ three mating-types: two versions of the locus are entirely different in sequence, and the third resembles a composite of the other two. Single, unrelated genes are sufficient to determine two of the mating-types, while homologues of both these genes are required in the composite type. The key genes encode polypeptides that possess no recognisable similarity to established protein families. Sex determination in the social amoebae thus appears to use regulators unrelated to any currently known.
doi:10.1126/science.1197423
PMCID: PMC3648785  PMID: 21148389
24.  Blood–brain barrier breakdown as a novel mechanism underlying cerebral hyperperfusion syndrome 
Journal of neurology  2009;257(4):615-620.
Cerebral hyperperfusion syndrome (CHS) may occur as a severe complication following surgical treatment of carotid stenosis. However, the mechanism inducing neurological symptoms in CHS remains unknown. We describe a patient with CHS presenting with seizures 24 h following carotid endarterectomy. Imaging demonstrated early ipsilateral blood–brain barrier (BBB) breakdown with electroencephalographic evidence of cortical dysfunction preceding brain edema. Using in vitro experiments on rat cortical tissue, we show that direct exposure of isolated brain slices to a serum-like medium induces spontaneous epileptiform activity, and that neuronal dysfunction is triggered by albumin. We propose BBB breakdown and subsequent albumin extravasation as a novel pathogenic mechanism underlying CHS and a potential target for therapy.
doi:10.1007/s00415-009-5384-z
PMCID: PMC3625729  PMID: 20361293
Albumin; Blood–brain barrier; Cerebral hyperperfusion syndrome; Magnetic resonance imaging; Seizure; Astrocytes; TGF-βR
25.  A pilot study to measure upper extremity H-reflexes following neuromuscular electrical stimulation therapy after stroke 
Neuroscience letters  2013;535:1-6.
Upper extremity (UE) hemiparesis persists after stroke, limiting hand function. Neuromuscular electrical stimulation (NMES) is an effective intervention to improve UE recovery, although the underlying mechanisms are not fully understood. Our objective was to establish a reliable protocol to measure UE agonist–antagonist forearm monosynaptic reflexes in a pilot study to determine if NMES improves wrist function after stroke. We established the between-day reliability of the H-reflex in the extensor carpi radialis longus (ECRL) and flexor carpi radialis (FCR) musculature for individuals with prior stroke (n = 18). The same-day generation of ECRL/FCR H-reflex recruitment curves was well tolerated, regardless of age or UE spasticity. The between-day reliability of the ECRL H-reflex was enhanced above FCR, similar to healthy subjects [20], with the Hmax the most reliable parameter quantified in both muscles. H-reflex and functional measures following NMES show the potential for NMES-induced increases in ECRL Hmax, but confirmation requires a larger clinical study. Our initial results support the safe, easy, and efficacious use of in-home NMES, and establish a potential method to measure UE monosynaptic reflexes after stroke.
doi:10.1016/j.neulet.2012.11.063
PMCID: PMC3592334  PMID: 23313593
Stroke; H-reflex; FCR; ECRL; Upper extremity spasticity; Neuromuscular electrical stimulation

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