Eco-evolutionary feedbacks in the human gut microbiome.

Gut microbiota can evolve within their hosts on human-relevant timescales, but little is known about how these changes influence (or are influenced by) the composition of their local community. Here, by combining ecological and evolutionary analyses of a large cohort of human gut metagenomes, we show that the short-term evolution of the microbiota is linked with shifts in its ecological structure. These correlations are not simply explained by expansions of the evolving species, and often involve additional fluctuations in distantly related taxa. We show that similar feedbacks naturally emerge in simple resource competition models, even in the absence of cross-feeding or predation. These results suggest that the structure and function of host microbiota may be shaped by their local evolutionary history, which could have important implications for personalized medicine and microbiome engineering.

Small bowel diverticulosis: imaging appearances, complications, and pitfalls.

Diverticula of the small bowel can be categorised as true, with Meckel's being the only example, or false. False small bowel diverticula (SBD) are acquired through herniation of the internal layers of the bowel wall through the muscularis propria. Peri-ampullary duodenal diverticula are a well-recognised example; however, the importance of more distal SBD in the jejunum and ileum is underappreciated, and they are under-reported on cross-sectional imaging. SBD are a known cause of anaemia, malabsorption, and diarrhoea, and there are myriad complications of SBD and Meckel's diverticula, which range in severity from inflammation and perforation to haemorrhage, tumour formation, and obstruction. Before the advent of computed tomography (CT), SBD were readily diagnosed on fluoroscopic oral contrast studies; however, radiologists are less comfortable with their cross-sectional imaging appearances. This imaging review combines our experience of multiple proven cases, with illustrative diagrams and radiological images of SBD to provide distinct imaging characteristics, allowing for confident diagnosis of SBD and their numerous complications. We discuss the importance of SBD as a cause of benign, non-surgical pneumoperitoneum. We additionally provide important pitfalls to be aware of such as SBD masquerading as other abnormalities.

A fully automatic system to assess foot collapse on lateral weight-bearing foot radiographs: A pilot study.

BACKGROUND: Foot collapse is primarily diagnosed and monitored using lateral weight-bearing foot x-ray images. There are several well-validated measurements which aid assessment. However, these are subject to inter- and intra-user variability. OBJECTIVE: To develop and validate a software system for the fully automatic assessment of radiographic changes associated with foot collapse; automatically generating measurements for calcaneal tilt, cuboid height and Meary's angle. METHODS: This retrospective study was approved by the Health Research Authority (IRAS 244852). The system was developed using lateral weight-bearing foot x-ray images, and evaluated against manual measurements from five clinical experts. The system has two main components: (i) a Random Forest-based point-finder to outline the bones of interest; and (ii) a geometry-calculator to generate the measurements based on the point positions from the point-finder. The performance of the point-finder was assessed using the point-to-point error (i.e. the mean absolute distance between each found point and the equivalent ground truth point, averaged over all points per image). For assessing the performance of the geometry-calculator, linear mixed models were fitted to estimate clinical inter-observer agreement and to compare the performance of the software system to that of the clinical experts. RESULTS: A total of 200 images were collected from 79 subjects (mean age: 56.4 years ±12.9 SD, 30/49 females/males). There was good agreement among all clinical experts with intraclass correlation estimates between 0.78 and 0.86. The point-finder achieved a median point-to-point error of 2.2 mm. There was no significant difference between the clinical and automatically generated measurements using the point-finder points, suggesting that the fully automatically obtained measurements are in agreement with the manually obtained measurements. CONCLUSIONS: The proposed system can be used to support and automate radiographic image assessment for diagnosing and managing foot collapse, saving clinician time, and improving patient outcomes.

Enterococcus species distribution among human and animal hosts using multiplex PCR.

AIMS: This study evaluated the use of Enterococcus species differentiation as a tool for microbial source tracking (MST) in recreational waters. METHODS AND RESULTS: Avian, mammalian and human faecal samples were screened for the occurrence of Enterococcus avium, Enterococcus casseliflavus, Enterococcus durans, Enterococcus gallinarum, Enterococcus faecium, Enterococcus faecalis, Enterococcus hirae and Enterococcus saccharolyticus using multiplex PCR. Host-specific patterns of Enterococcus species presence were observed only when data for multiple Enterococcus species were considered in aggregate. CONCLUSIONS: The results suggest that no single Enterococcus species is a reliable indicator of the host faecal source. However, Enterococcus species composite 'fingerprints' may offer auxiliary evidence for bacterial source identification. SIGNIFICANCE AND IMPACT OF STUDY: This study presents novel information on the enterococci species assemblages present in avian and mammalian hosts proximate to the nearshore ocean. These data will aid the development of appropriate MST strategies, and the approach used in this study could potentially assist in the identification of faecal pollution sources.

First Occurrence of Laurel Wilt Disease Caused by Raffaelea lauricola on Redbay Trees in Mississippi.

Laurel wilt is a lethal, nonnative vascular wilt disease of redbay (Persea borbonia), sassafras (Sassafras albidum), and other trees in the Lauraceae (1,4). It is caused by a fungus (Raffaelea lauricola) and transmitted by the redbay ambrosia beetle (Xyleborus glabratus), a nonnative insect first detected in Georgia in 2002 (1,2). Since introduction of the pathogen and vector (presumably from Asia), laurel wilt has caused extensive mortality to redbays in Georgia, Florida, and South Carolina (1). In June 2009, a landowner in Gautier, MS reported dead redbay trees. Signs and symptoms were identical to those reported for laurel wilt along the Atlantic Coast (wilted, bronze red foliage, and dark gray-to-black vascular discoloration) (1). Infected trees have subsequently been confirmed in and near the Pascagoula River Basin. Size of infected redbays ranged from 5 to 20 cm (diameter at breast height). No heavily decomposed or fallen redbays were noted. Many individual specimens exhibited extensive drying of stem wood and dry, wilted, light brown foliage. This indicates that introduction to the area may have occurred within the last 3 years. X. glabratus adults were collected (30°26'44.45″N, 88°39'41.83″W) in a Lindgren funnel trap baited with phoebe and manuka oil lures. Beetle identification was confirmed by USDA-APHIS, and voucher specimens were submitted to the Smithsonian National Museum of Natural History and the Mississippi Entomological Museum. Symptomatic redbay wood chips from the same location were surface sterilized and plated on cycloheximide-streptomycin malt agar and R. lauricola was isolated. A 1,026-bp portion of 18S rDNA (GenBank No. GQ996063) was amplified by PCR and sequenced using primers NS1 and NS4. BLASTn searches revealed perfect homology to R. lauricola isolate PL 697 (GQ329704). Two isolates of R. lauricola were recovered and prepared into separate spore suspensions (1 × 108 CFU/ml). Each isolate was inoculated into two healthy redbays. The inoculated redbays were placed in a growth chamber with two water-only controls. All inoculated plants, and none of the controls, exhibited wilt symptoms and died within 20 days. R. lauricola was recovered from the discolored sapwood of the inoculated plants, completing Koch's postulates. A model prediction for the natural dispersion of X. glabratus and R. lauricola estimated that these organisms may not reach Mississippi for 10 to 15 years (3). The current detection of laurel wilt in Mississippi is substantially ahead of this estimate. Currently, no records of laurel wilt have been reported from western Georgia, all of Alabama, or the panhandle of Florida. Confirmed locations in Mississippi are in Jackson County, along the Interstate 10 corridor and the Pascagoula River drainage. Due to the relatively large extent of the infestation (~64 km2, including hundreds of infected trees) eradication is not being attempted. Surveys, remote sensing, and phylogeographic analysis are underway to delineate the extent of infestation and discover the mode of introduction. The current outbreak of laurel wilt in Mississippi is likely the result of human transport of infested wood, either from Asia as a separate, new introduction or from previously infested areas in the southeastern United States. References: (1) S. W Fraedrich et al. Plant Dis. 92:215, 2008. (2) T. C. Harrington et al. Mycotaxon 104:399, 2008. (3) F. Koch and W. Smith. Environ. Entomol. 37:442, 2008. (4) J. A. Smith et al. Plant Dis. 93:198, 2009.

Distribution and diversity of the enterococcal surface protein (esp) gene in animal hosts and the Pacific coast environment.

AIMS: This study sought to evaluate the distribution of the enterococcal surface protein (esp) gene in Enterococcus faecium in the Pacific coast environment as well as the distribution and diversity of the gene in Northern California animal hosts. METHODS AND RESULTS: Over 150 environmental samples from the Pacific coast environment (sand, surf zone, fresh/estuarine, groundwater, and storm drain) were screened for the esp gene marker in E. faecium, and the marker was found in 37% of the environmental samples. We examined the host specificity of the gene by screening various avian and mammalian faecal samples, and found the esp gene to be widespread in nonhuman animal faeces. DNA sequence analysis performed on esp polymerase chain reaction amplicons revealed that esp gene sequences were not divergent between hosts. CONCLUSIONS: Our data confirm recent findings that the E. faecium variant of the esp gene is not human-specific. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results suggest that the use of the esp gene for microbial source tracking applications may not be appropriate at all recreational beaches.

Molecular modeling of the axial and circumferential elastic moduli of tubulin.

Microtubules play a number of important mechanical roles in almost all cell types in nearly all major phylogenetic trees. We have used a molecular mechanics approach to perform tensile tests on individual tubulin monomers and determined values for the axial and circumferential moduli for all currently known complete sequences. The axial elastic moduli, in vacuo, were found to be 1.25 GPa and 1.34 GPa for alpha- and beta-bovine tubulin monomers. In the circumferential direction, these moduli were 378 MPa for alpha- and 460 MPa for beta-structures. Using bovine tubulin as a template, 269 homologous tubulin structures were also subjected to simulated tensile loads yielding an average axial elastic modulus of 1.10 +/- 0.14 GPa for alpha-tubulin structures and 1.39 +/- 0.68 GPa for beta-tubulin. Circumferentially the alpha- and beta-moduli were 936 +/- 216 MPa and 658 +/- 134 MPa, respectively. Our primary finding is that that the axial elastic modulus of tubulin diminishes as the length of the monomer increases. However, in the circumferential direction, no correlation exists. These predicted anisotropies and scale dependencies may assist in interpreting the macroscale behavior of microtubules during mitosis or cell growth. Additionally, an intergenomic approach to investigating the mechanical properties of proteins may provide a way to elucidate the evolutionary mechanical constraints imposed by nature upon individual subcellular components.

Differences between collagen morphologies, properties and distribution in diabetic and normal biobreeding and Sprague-Dawley rat sciatic nerves.

Both structural and functional differences between normal and diabetic nerve have been observed, in human patients and animal models. We hypothesize that these structural differences are quantifiable, morphologically and mechanically, with the ultimate aim of understanding the contribution of these differences to permanent nerve damage. The outer collagenous epineurial and perineurial tissues of mammalian peripheral nerves mechanically and chemically shield the conducting axons. We have quantified differences in these collagens, using whole-nerve uniaxial testing, and immunohistochemistry of collagens type I, III, and IV in diabetic and normal nerves. We present results of two studies, on normal and diabetic BioBreeding (BB), and normal, diabetic and weight-controlled Sprague-Dawley (SD) rats, respectively. Overall, we measured slightly higher uniaxial moduli (e.g. 5.9 MPa vs. 3.5 MPa, BB; 10.7 MPa vs. 10.0 MPa, SD at 40% strain) in whole nerves as well as higher peak stresses (e.g. 0.99 MPa vs. 0.74 MPa, BB; 2.16 MPa vs. 1.94 MPa, SD at 40% strain) in the diabetics of both animal models. We measured increased concentrations of types III and IV collagens in the diabetics of both models and mixed upregulation results were observed in type I protein levels. We detected small differences in mechanical properties at the tissue scale, though we found significant structural and morphometric differences at the fibril scale. These findings suggest that whole-tissue mechanical testing is not a sufficient assay for collagen glycation, and that fibrillar and molecular scale assays are needed to detect the earliest stages of diabetic protein glycation.

Nanomanipulation and characterization of structural proteins.

A methodology is presented for simultaneous mechanical testing and atomic force microscopy imaging of single collagen fibrils under load. This method holds the promise for determining single-fibril modulus and strength in various experimental preparations. Examples of this utility include characterization of deformation and failure modes of naturally occurring and engineered structural proteins. Additional promise of this technique is robotic surgery at the submicron scale for repairing neuronal tracts and capillaries with structural proteins. A series of algorithms for tying knots at the nanoscale in single fibrils is also presented.

A mechanical model for collagen fibril load sharing in peripheral nerve of diabetic and nondiabetic rats.

Peripheral neuropathy affects approximately 50% of the 15 million Americans with diabetes. It has been suggested that mechanical effects related to collagen glycation are related to the permanence of neuropathy. In the present paper, we develop a model for load transfer in a whole nerve, using a simple pressure vessel approximation, in order to assess the significant of stiffening of the collagenous nerve sheath on endoneurial fluid pressure. We also develop a fibril-scale mechanics model for the nerve, to model the straightening of wavy fibrils, producing the toe region observed in nerve tissue, and also to interrogate the effects of interfibrillar crosslinks on the overall properties of the tissue. Such collagen crosslinking has been implicated in complications in diabetic tissues. Our fibril-scale model uses a two-parameter Weibull model for fibril strength, in combination with statistical parameters describing fibril modulus, angle, wave-amplitude, and volume fraction to capture both toe region and failure region behavior of whole rat sciatic nerve. The extrema of equal and local load-sharing assumptions are used to map potential differences in diabetic and nondiabetic tissues. This work may ultimately be useful in differentiating between the responses of normal and heavily crosslinked tissue.

Nerve collagens from diabetic and nondiabetic Sprague-Dawley and biobreeding rats: an atomic force microscopy study.

BACKGROUND: Alterations in rat's nerve collagens due to diabetes may be related to the permanence of damage due to diabetic neuropathy. We (1) provide a methodology for determining the diameters of collagen fibers accounting for atomic force microscope (AFM) imaging artifacts, (2) present data on structural differences in sciatic nerve endoneurial, epineurial and tail tendon collagens of control and diabetic Sprague-Dawley and BioBreeding rats, and (3) compare results with literature values. METHODS: We measured collagen diameters and band spacing on endoneurial and epineurial sciatic nerve tissue, and tail tendon, in control and diabetic rats (STZ-induced 12-week diabetic SD and 16-week spontaneously diabetic BB rats). We also developed a model to interpret the raw AFM data. RESULTS: All types of fibrillar collagen diameters studied became larger for diabetic versus control animals. Values for diabetic and control collagen fiber diameters in SD rats were 78 nm and 72 nm for SN epineurium, and 49 nm and 43 nm for SN endoneurium. For diabetic and control BB rats, these values were 83 nm and 77 nm (SN epineurium) and 49 nm and 43 nm (SN endoneurium). Values of 161 nm and 125 nm were found for diabetic and control tail tendon of BB rats. No significant changes were observed in any of the five comparisons made in D-band spacings that ranged from 63 to 69 nm. CONCLUSIONS: The best means we have found to reduce raw AFM data is to measure several diameters with a single scan, using valley-to-valley measurements. Structural, fibrillar collagens of the nerve and tendon become larger in rats exposed to prolonged diabetes.

Are aphasic patients who fail the GOAT in PTA? A modified Galveston Orientation and Amnesia Test for persons with aphasia.

Because the Galveston Orientation and Amnesia Test (GOAT) requires oral or written response, it risks misclassifying as amnestic aphasic patients who are not, in fact, amnestic. To correct for possible classification errors due to anomia, a modified multiple-choice format of the GOAT (AGOAT) was developed. The average GOAT score of 10 control nonaphasic head-injured patients suggested that an AGOAT score of 90 corresponds to the standard GOAT cutoff of 75 for resolution of posttraumatic amnesia (PTA). Using this criterion, 8 of 15 aphasic head-injured patients who technically were classified as amnestic on the GOAT were classified as nonamnestic on the AGOAT.

Urinary myelin basic protein-like material in patients with multiple sclerosis during interferon beta-1b treatment.

OBJECTIVES: To determine levels of urinary myelin basic protein-like material (MBPLM) in patients with multiple sclerosis (MS) openly treated with interferon beta-1b and to correlate these with clinical changes. BACKGROUND: Levels of urinary MBPLM correlate with the presence of the progressive phase of MS and with the disease burden detected on T2-weighted, cranial magnetic resonance imaging. Measurement of urinary MBPLM level may be a feasible test for monitoring or predicting response to therapeutic measures. DESIGN AND METHODS: In a prospective study at one site, 166 patients with MS (131 with relapsing-remitting [RR] and 35 with secondary progressive [SP] disease) were treated for a minimum of 1 year and up to 3 years with interferon beta-1b and underwent assessment for neurologic disability (Expanded Disability Status Scale and Scripps Neurological Rating Scale) and change in disease subtype. Urine samples were obtained at 1219 of 1378 clinic visits, and urinary MBPLM level was determined and related to creatinine level to adjust for renal function. RESULTS: Statistical analysis using the general linear models procedure confirmed previous findings that the level of urinary MBPLM related to urinary creatinine level (MBPLM/creatinine) was higher (P<.001) in patients with SP than RR MS. Of the 131 patients with RR MS, SP disease developed in 13 during the observation period. Compared with those in the RR group, the RR to SP group had a higher level (P<.001) of urinary MBPLM and did not differ from the SP group. CONCLUSIONS: The level of urinary MBPLM is higher in SP MS than RR MS but not in RR MS that converts to SP MS. Level of urinary MBPLM may permit the examination of treatment tested to prevent RR disease from becoming progressive.

Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene.

Mutations of the gene Lps selectively impede lipopolysaccharide (LPS) signal transduction in C3H/HeJ and C57BL/10ScCr mice, rendering them resistant to endotoxin yet highly susceptible to Gram-negative infection. The codominant Lpsd allele of C3H/HeJ mice was shown to correspond to a missense mutation in the third exon of the Toll-like receptor-4 gene (Tlr4), predicted to replace proline with histidine at position 712 of the polypeptide chain. C57BL/10ScCr mice are homozygous for a null mutation of Tlr4. Thus, the mammalian Tlr4 protein has been adapted primarily to subserve the recognition of LPS and presumably transduces the LPS signal across the plasma membrane. Destructive mutations of Tlr4 predispose to the development of Gram-negative sepsis, leaving most aspects of immune function intact.

Implicit memory in posttraumatic stress disorder with amnesia for the traumatic event.

This report documents a case of posttraumatic stress disorder (PTSD) following psychological trauma with cerebral insult and amnesia for the traumatic event. The case history demonstrates the role of implicit memory in PTSD and indicates that the mechanisms of psychopathology are one-trial sensitization and conditioned emotional responses.

Urinary myelin basic protein-like material as a correlate of the progression of multiple sclerosis.

In the multicenter, randomized, placebo-controlled trial of alternate-day injections of recombinant interferon beta-1b in relapsing-remitting multiple sclerosis (MS), urine specimens were collected periodically from all patients (n = 64) in two of the clinical test sites over the 2 years of the study. Urine specimens were also collected over two consecutive 24-hour periods from 43 patients from a third center. Urine samples were assayed for their content of myelin basic protein-like material (MBPLM), the level of which was correlated with clinical changes, cranial magnetic resonance imaging results, and the development of progressive disease. Concordant changes in creatinine values affected some of the relationships of MBPLM. The level of urinary MBPLM correlated with a chronic progressive course and with the number of lesions and the total lesion area on cranial magnetic resonance images. A rise in the level of urinary MBPLM appeared to antedate the clinical transition from a relapsing-remitting to a chronic progressive course. By chance, the randomized entry of patients led to significant differences in urinary MBPLM levels among the three treatment groups, thus precluding correlation studies of treatment effects. However, the patient group from which 24-hour specimens were collected showed that the patients with relapsing-remitting MS changing to a chronic progressive course, and more specifically, those patients with chronic progressive MS receiving placebo, had the highest values of urinary MBPLM. These findings indicate that urinary MBPLM may offer an objective test and possibly serve as a surrogate marker for detecting or predicting the failure of remission or the transition to a progressive phase of MS.

The librarian as a partner in nursing education.

Welch Medical Library has explored new roles for librarians in knowledge management instruction programs throughout the Johns Hopkins University School of Nursing curricula. These programs have created roles for library staff as both instructors and knowledge management experts. By fostering strong communication and attention to quality instruction, librarians achieved their vision of a program in knowledge management integrated into the curriculum, where they are partners working with nursing faculty to define the students' knowledge management needs and decide how these needs can be met.

Correlation of clinical features and findings on cranial magnetic resonance imaging with urinary myelin basic protein-like material in patients with multiple sclerosis.

Immunoreactive material that appears to be a peptide encompassing all or a portion of residues 80 to 89 of myelin basic protein is present in normal unconcentrated urine and is increased in certain patients with multiple sclerosis (MS). Compared with normal controls, urines collected randomly from 158 MS patients or in a clinical research unit from 8 patients with MS had higher mean values of urinary MBP-like material (MBPLM). The level of MBPLM in urine showed no direct relationship to MBPLM in cerebrospinal fluid and did not correlate with clinical relapses of disease. In the other neurological disease control group (26 patients), some patients with other inflammatory diseases, but not stroke or early phase Guillain-Barré syndrome, also showed elevations. Among the subtypes of MS, those with secondary chronic progressive disease had the highest values. Urinary MBPLM showed no definite correlation with or effect of treatment with glucocorticoids and immunosuppressants except that a lower level of urinary MBPLM showed a weak relationship with improvement following treatment with methylprednisolone/prednisone. In a serial study of 8 patients with unenhanced cranial magnetic resonance imaging and 20 patients with gadolinium-enhanced cranial magnetic resonance imaging, urinary MBPLM did not show a direct correlation with new or enhancing lesions. Urinary MBPLM does not parallel acute myelin damage but appears to reflect an ongoing process, possibly linked to attempted efforts at remyelination.