Systemic Capillary Leak Syndrome Secondary to Coronavirus Disease 2019

Systemic capillary leak syndrome is a rare disorder characterized by dysfunctional inflammatory response, endothelial dysfunction, and extravasation of fluid from the vascular space to the interstitial space leading to shock, hemoconcentration, hypoalbuminemia, and subsequent organ failure. The condition may be idiopathic or secondary to an underlying cause, which can include viral infections. Here we describe a patient with acute coronavirus disease 2019 (COVID-19) infection who presented with hemoconcentration, shock, and hypoalbuminemia. The patient subsequently developed rhabdomyolysis and compartment syndrome of all four extremities, requiring fasciotomies. This is the first reported case of systemic capillary leak syndrome associated with COVID-19 infection. This case adds to the evolving spectrum of inflammatory effects associated with this viral infection.

Enumeration of Probiotic Pediococci in Animal Feed: Interlaboratory Study

An enumeration method to be used as official control under Council Directive 70/524/EEC for probiotic pediococci used as feed additives was validated for consideration for adoption as Comitée Européen de Normalisation (CEN) and ISO standards. Seventeen laboratories in 11 European countries carried out an interlaboratory study. A spread plate method following BS ISO 15214:1998 using 4 different agars [MRS, acidified MRS, MRS with triphenyl tetrazolium chloride (TTC), and a newly developed pediococci selective medium (PSM)] was validated. Precision data in terms of repeatability (r) and reproducibility (R) of the method for each medium using different feeding stuffs with a high and a low inoculation level were determined. Pediococci were present in the samples in mixtures with other probiotics. The enumeration of pediococci on all agars showedan RSDr value of 0.4–3.1% and an RSDR of 1.3–4.8%. MRS agar was preferred, followed by acidified MRS and MRS + TTC agar. All 4 media gave similar counts. Depending on the presence and concentration of other probiotic, such as enterococci, lactobacilli, and yeast, acidified MRS or MRS + TTC agar are recommended. The PSM was selective for pediococci and can be used if this species is present at a concentration more than 10-fold lower than other species that can grow on the MRS agars. The methodology with all 4 media is not applicable to mineral feed.

It's time to recognise self care as an integral component of health systems

Empowering and supporting people to manage their own health benefits everyone

[Guidelines for Accurate and Transparent Health Estimates Reporting: the GATHER Statement]

Measurements of health indicators are rarely available for every population and period of interest, and available data may not be comparable. The Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER) define best reporting practices for studies that calculate health estimates for multiple populations (in time or space) using multiple information sources. Health estimates that fall within the scope of GATHER include all quantitative population-level estimates (including global, regional, national, or subnational estimates) of health indicators, including indicators of health status, incidence and prevalence of diseases, injuries, and disability and functioning; and indicators of health determinants, including health behaviours and health exposures. GATHER comprises a checklist of 18 items that are essential for best reporting practice. A more detailed explanation and elaboration document, describing the interpretation and rationale of each reporting item along with examples of good reporting, is available on the GATHER website (http://gather-statement.org).

Guidelines for Accurate and Transparent Health Estimates Reporting: the GATHER statement

Measurements of health indicators are rarely available for every population and period of interest, and available data may not be comparable. The Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER) define best reporting practices for studies that calculate health estimates for multiple populations (in time or space) using multiple information sources. Health estimates that fall within the scope of GATHER include all quantitative population-level estimates (including global, regional, national, or subnational estimates) of health indicators, including indicators of health status, incidence and prevalence of diseases, injuries, and disability and functioning; and indicators of health determinants, including health behaviours and health exposures. GATHER comprises a checklist of 18 items that are essential for best reporting practice. A more detailed explanation and elaboration document, describing the interpretation and rationale of each reporting item along with examples of good reporting, is available on the GATHER website.

Correction: Guidelines for Accurate and Transparent Health Estimates Reporting: the GATHER statement

[This corrects the article DOI: 10.1371/journal.pmed.1002056.].

Guidelines for Accurate and Transparent Health Estimates Reporting: the GATHER statement

Gretchen Stevens and colleagues present the GATHER statement, which seeks to promote good practice in the reporting of global health estimates.

Surgical site infections (SSIs) after stoma reversal (SR): risk factors, implications, and protective strategies

BACKGROUND

Stoma reversals (SRs) are commonly performed with potentially significant postoperative complications including surgical site infections (SSIs). Our aim was to determine the incidence and risk factors for SSIs in a large cohort of SR patients.

DESIGN

We reviewed our institutional 2006-2011 American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database for 30-day SSIs in patients undergoing SR. Records were additionally reviewed for 10 non-ACS-NSQIP variables. The primary outcome was SSI after SR. Secondary outcomes were additional 30-day postoperative complications and length-of-stay. Predictors of SSIs were identified using multivariable logistic regression.

RESULTS

From 528 SR patients, 36 patients developed a SSI (6.8 %). Most patients underwent SR for loop ileostomies (76.5 %) after index operations for ulcerative colitis (38.6 %) and colorectal cancer (27.8 %). SSI patients had fewer subcutaneous drains compared to patients with no SSI and had significantly higher rates of smoking, ASA 3-4 classification and laparotomies at SR (p < 0.05). Patients with SSI had increased length-of-stay and 30-day morbidities including sepsis and returns to the operating room (p < 0.05) compared to no-SSI patients. On multivariable analysis, subcutaneous drain placement was suggestive of SSI protection (odds ratio [OR] 0.52, 95 % confidence interval [CI] 0.2-1.1), but only smoking was significantly associated with an increased risk for SSI (OR 2.4, 95 % CI 1.1-5.4).

CONCLUSIONS

Smoking increased the risk of SR SSIs in patients by over twofold, and SR SSIs are associated with additional significant morbidities. Smoking cessation should be an important part of any SSI risk-reduction strategy.

Milk-derived bioactive peptides inhibit human endothelial-monocyte interactions via PPAR-γ dependent regulation of NF-κB

Background

Milk-derived bioactive peptides retain many biological properties and have therapeutic effects in cardiovascular disorders such as atherosclerosis. Under inflammatory conditions the expression of endothelial cells adhesion molecules is induced, increasing monocyte adhesion to human vessel wall, a critical step in the pathogenesis of atherosclerosis. In the present work we explored the effects of milk-derived bioactive peptides on the expression of the inflammatory phenotype of human endothelial cells and their effects on monocyte adherence to endothelial cells.

Results

Treatment of endothelial cells with milk-derived hydrolysate inhibited their production of inflammatory proteins MCP-1 and IL-8 and expression of VCAM-1, ICAM-1 and E-selectin. Milk derived hydrolysate also attenuated the adhesion of human monocytes to activated endothelial cells. The effect was similar to that obtained in endothelial cells treated with troglitazone, a ligand of peroxisome proliferators-activator receptor-gamma (PPAR-γ). PPAR-γ is a transcription factor which when activated antagonises the pro-inflammatory capability of nuclear factor κB (NF-κB). We further examined whether the effects of milk-derived hydrolysates on endothelial cells may be mediated through NF-κB activation via a PPAR-γ dependent mechanism. The specific PPAR-γ inhibitor, GW9662 blocked the effects of the hydrolysate on the NF-κB-mediated chemokines and adhesion molecules expression in endothelial cells.

Conclusions

These results suggest that milk-derived bioactive peptides work as anti-atherogenic agents through the inhibition of endothelial-dependent adhesive interactions with monocytes by inhibiting the NF-κB pathway through a PPAR-γ dependent mechanism.

Electronic supplementary material

The online version of this article (doi:10.1186/s12950-014-0044-1) contains supplementary material, which is available to authorized users.

Characterization of two novel aldo-keto reductases from Arabidopsis: expression patterns, broad substrate specificity, and an open active-site structure suggest a role in toxicant metabolism following stress

Aldo-keto reductases (AKRs) are widely distributed in nature and play numerous roles in the metabolism of steroids, sugars, and other carbonyls. They have also frequently been implicated in the metabolism of exogenous and endogenous toxicants, including those stimulated by stress. Although the Arabidopsis genome includes at least 21 genes with the AKR signature, very little is known of their functions. In this study, we have screened the Arabidopsis thaliana genomic sequence for genes with significant homology to members of the mammalian AKR1 family and identified four homologues for further study. Following alignment of the predicted protein sequences with representatives from the AKR superfamily, the proteins were ascribed not to the AKR1 family but to the AKR4C subfamily, with the individual designations of AKR4C8, AKR4C9, AKR4C10, and AKR4C11. Expression of two of the genes, AKR4C8 and AKR4C9, has been shown to be coordinately regulated and markedly induced by various forms of stress. The genes have been overexpressed in bacteria, and recombinant proteins have been purified and crystallized. Both enzymes display NADPH-dependent reduction of carbonyl compounds, typical of the superfamily, but will accept a very wide range of substrates, reducing a range of steroids, sugars, and aliphatic and aromatic aldehydes/ketones, although there are distinct differences between the two enzymes. We have obtained high-resolution crystal structures of AKR4C8 (1.4 A) and AKR4C9 (1.25 A) in ternary complexes with NADP(+) and acetate. Three extended loops, present in all AKRs and responsible for defining the cofactor- and substrate-binding sites, are shorter in the 4C subfamily compared to other AKRs. Consequently, the crystal structures reveal open and accommodative substrate-binding sites, which correlates with their broad substrate specificity. It is suggested that the primary role of these enzymes may be to detoxify a range of toxic aldehydes and ketones produced during stress, although the precise nature of the principal natural substrates remains to be determined.

Malonyl-CoA decarboxylase inhibition is selectively cytotoxic to human breast cancer cells

Fatty acid synthase (FAS) inhibition initiates selective apoptosis of cancer cells both in vivo and in vitro, which may involve malonyl-CoA metabolism. These findings have led to the exploration of malonyl-CoA decarboxylase (MCD) as a potential novel target for cancer treatment. MCD regulates the levels of cellular malonyl-CoA through the decarboxylation of malonyl-CoA to acetyl-CoA. Malonyl-CoA is both a substrate for FAS and an inhibitor of fatty acid oxidation acting as a metabolic switch between anabolic fatty acid synthesis and catabolic fatty acid oxidation. We now report that the treatment of human breast cancer (MCF7) cells with MCD small interference RNA (siRNA) reduces MCD expression and activity, reduces adenosine triphosphate levels, and is cytotoxic to MCF7 cells, but not to human fibroblasts. In addition, we synthesized a small-molecule inhibitor of MCD, 5-{(Morpholine-4-carbonyl)-[4-(2,2,2-trifluoro-1-hydroxy-1-trifluoromethyl-ethyl)-phenyl]-amino}-pentanoic acid methyl ester (MPA). Similar to MCD siRNA, MPA inhibits MCD activity in MCF7 cells, increases cellular malonyl-CoA levels and is cytotoxic to a number of human breast cancer cell lines in vitro. Taken together, these data indicate that MCD-induced cytotoxicity is likely mediated through malonyl-CoA metabolism. These findings support the hypothesis that MCD is a potential therapeutic target for cancer therapy.

Does the use of nizatidine, as a pro-kinetic agent, improve gastric emptying in patients post-oesophagectomy?

PURPOSE

Delayed gastric emptying following oesophagectomy is common and can often lead to weight loss, malnutrition and a poor quality of life. Animal models have shown that nizatidine, a histamine H2-receptor antagonist, has pro-kinetic properties and can accelerate gastric emptying. Patients post-oesophagectomy require long-term acid suppression medication; if nizatidine can improve gastric emptying, it can be adopted for its dual pharmacological actions.

METHODOLOGY

Twenty consecutive patients were prospectively enrolled in this trial following oesophagectomy. All patients were more than 6 months post-surgery and had no evidence of recurrent cancer. A baseline nuclear medicine scan following a radiolabelled meal was conducted and then repeated after 1 week of nizatidine (150 mg bd) treatment. Quality of life and eating comfort data were collected.

RESULTS

Oesophagectomy causes a significant delay in gastric emptying. Early satiety (80%) and reflux (65%) were the most common post-operative complaints. The percentage of food remaining in the stomach at 60 min post-meal was significantly more than normal values in both the pre- and post-nizatidine studies. There is no advantage in using nizatidine as a pro-kinetic agent.

CONCLUSIONS

Impaired gastric emptying post-surgery causes a change in eating habits. Patients in this study did not lose a significant amount of weight despite all indicating worse eating comfort. Patients required more regular meals or snacks throughout the day and avoid foods that are difficult to swallow. It is likely that gastric motility only plays a small role in the emptying process and gravity combined with appropriate drainage procedures (pyloroplasty/pyloromyotomy) at the time of surgery are more important.

Defect studies of ZnSe nanowires

During the synthesis of ZnSe nanowires various point and extended defects can form, leading to observed stacking faults and twinning defects, and strong defect related emission in photoluminescence spectra. In this paper, we report on the development of a simple thermodynamic model for estimating the defect concentration in ZnSe nanowires grown under varying Se vapour pressure and for explaining the results of our experimental findings. Positron annihilation spectroscopy was used successfully for the first time for nanowires and the results support predictions from the defect model as well as agreeing well with our structural and optical characterization results. Under very high Se vapour pressure, Se nodules were observed to form on the sidewalls of the nanowire, indicating that beyond a limit, excess Se will begin to precipitate out of the liquid alloy droplet in the vapour-liquid-solid growth of nanowires.

Serial Memory for Sound-Specified Locations: Effects of Spatial Uncertainty and Motor Suppression

According to Parmentier and Jones (2000), serial recall of locations that are specified by a sequence of sounds is prone to temporal error and is unaffected by motor suppression during retention. Experiments are reported here that show that with increased spatial uncertainty at recall (Experiment 1) and presentation (Experiment 2), spatial rather than temporal errors predominate. This is also the case when serial recall of sound-specified locations is subject to interference from a motor suppression task (Experiment 3). Contrary to Parmentier and Jones's (2000) original report, these results suggest that the memory representation for location is not necessarily amodal but is influenced by the representational requirements of the task being performed. This is consistent with recent findings that provide evidence for a distinct spatial working memory.

pEOC01: A plasmid from Pediococcus acidilactici which encodes an identical streptomycin resistance (aadE) gene to that found in Campylobacter jejuni

The complete nucleotide sequence of pEOC01, a plasmid (11,661 bp) from Pediococcus acidilactici NCIMB 6990 encoding resistance to clindamycin, erythromycin, and streptomycin was determined. The plasmid, which also replicates in Lactococcus and Lactobacillus species contains 16 putative open reading frames (ORFs), including regions annotated to encode replication, plasmid maintenance and multidrug resistance functions. Based on an analysis the plasmid replicates via a theta replicating mechanism closely related to those of many larger Streptococcus and Enterococcus plasmids. Interestingly, genes homologous to a toxin/antitoxin plasmid maintenance system are present and are highly similar to the omega-epsilon-zeta operon of Streptococcus plasmids. The plasmid contains two putative antibiotic resistance homologs, an ermB gene encoding erythromycin and clindamycin resistance, and a streptomycin resistance gene, aadE. Of particular note is the aadE gene which holds 100% identity to an aadE gene found in Campylobacter jejuni plasmid but which probably originated from a Gram-positive source. This observation is significant in that it provides evidence for recent horizontal transfer of streptomycin resistance from a lactic acid bacterium to a Gram-negative intestinal pathogen and as such infers a role for such plasmids for dissemination of antibiotic resistance genes possibly in the human gut.

Susceptibility of Pediococcus spp. to antimicrobial agents

AIM

To investigate the susceptibility of Pediococcus species to antimicrobial agents.

METHODS AND RESULTS

The susceptibility to 14 antimicrobial agents of 31 genotypically distinct strains of six Pediococcus species was assessed by using Etests on ISO-sensitest agar supplemented with horse blood. The species included were Pediococcus acidilactici, Pediococcus damnosus, Pediococcus dextrinicus, Pediococcus inopinatus, Pediococcus parvulus and Pediococcus pentosaceus. For several antimicrobial agents, some species were more susceptible than others. The two industrially important species, P. acidilactici and P. pentosaceus, differed with respect to erythromycin and trovafloxacin susceptibility, and in general both species had higher minimum inhibitory concentrations than the other species. In an erythromycin-resistant P. acidilactici, an erythromycin resistance methylase B [erm(B)] gene was identified by PCR. Using a plasmid preparation from strain P. acidilactici 6990, a previously erythromycin-sensitive Lactococcus lactis strain was made resistant. Transformants harboured a single plasmid, sized at 11.6 kb through sequence analysis. In addition, the erm(B) gene was identified within the plasmid sequence.

CONCLUSIONS

The phenotypic test indicated the absence of acquired antimicrobial resistance genes in 30 of the strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results will help in selection of the best Pediococcus strains for use as starter cultures.

Intrinsic tolerance of Bifidobacterium species to heat and oxygen and survival following spray drying and storage

AIMS

This study examined the tolerance of various species of the genus Bifidobacterium to heat and oxygen and evaluated the survival of selected strains following spray drying and during storage.

METHODS AND RESULTS

Nine Bifidobacterium species were considered to be relatively tolerant to both heat and oxygen and mostly segregated into two clusters within the 16S rDNA phylogenetic tree. Four species were tolerant to oxygen and 12 species were considered sensitive to oxygen and heat. Using a skimmed milk-based carrier good survival following spray drying and storage at 4 degrees C correlated with tolerance to heat and oxygen. Viability was inversely related to storage temperature and at 15 degrees C and 25 degrees C, a significant decline was observed for all species. The inclusion of gum acacia had no significant affect on survival or viability. However, using a fluidized-bed spray dryer viability was greatly improved.

CONCLUSIONS

A group of closely related species tolerant to heat and oxygen had high survival following spray drying and maintained viability during prolonged storage at 4 degrees C.

SIGNIFICANCE AND IMPACT OF THE STUDY

Spray drying is a suitable method for the production of skimmed milk powder enriched with high numbers of viable bifidobacteria.

Enumeration and identification of pediococci in powder-based products using selective media and rapid PFGE

In this study, pediococci selective medium (PSM) was evaluated for the enumeration of Pediococcus acidilactici and Pediococcus pentosaceus from probiotic animal feed and silage inoculants. PSM is based on the complex basal medium MRS supplemented with cysteine hydrochloride, novobiocin, vancomycin, and nystatin. No significant change in electivity was observed when pediococci where recovered from culture or powder-based products following incubation at 37 degrees C under anaerobic conditions for 24 h. The medium was suitable for the enumeration of pediococci in samples also containing bacilli, bifidobacteria, enterococci, lactobacilli, lactococci, propionibacteria, streptococci, and yeast components. However, to inhibit Lactobacillus plantarum and Lactobacillus casei, ampicillin was added and the revised medium, termed PSM+A, was also considered to be suitably elective for pediococci recovered from powder. In addition, a rapid PFGE protocol is presented, which allows Pediococcus species and strain verification from colonies in less than 3 days.

Tryptase inhibitors: a novel class of anti-inflammatory drugs

Tryptase, a serine protease released from mast cell secretory granules, is found at elevated levels in pathophysiologic conditions associated with allergic inflammation. The in vitro and in vivo biological activities of tryptase strongly suggest that tryptase influences lung function, inflammation, matrix degradation, and tissue remodelling. The pathophysiologic role for tryptase in diseases of airway inflammation such as asthma has been confirmed from studies using the selective tryptase inhibitor APC 366 in the allergic sheep model. APC 366 inhibited the allergen-induced early and late airway responses, blocked postchallenge airway hyperresponsiveness, and reduced airway inflammation. A pilot clinical trial with mild to moderate asthmatics also showed that APC 366 protected against allergen-induced early and late responses and reduced airway hyperresponsiveness. Current data provide compelling evidence that tryptase plays a fundamental role in allergic inflammation, and selective tryptase inhibitors may represent a novel class of anti-inflammatory therapeutics for treating asthma and other mast cell-mediated diseases.

Binocular cues and the control of prehension

The present study was designed to assess the importance of binocular information (i.e. binocular disparity and angle of convergence) in the control of prehension. Previous studies which have addressed this question have typically used the same experimental manipulation: comparing prehensile movements executed either under binocular conditions to those executed when one eye was occluded (monocular). However this may not be the correct comparison as in addition to depriving the subject of binocular depth cues. it also deprives the subject of any visual information in one eye. Therefore we determined the prehensile performance when the subject viewed the target object and scene with either (i) two different views (binocular), (ii) two identical views (bi-ocular), or (iii) one view only (monocular). Overall, the qualitative and quantitative performance in the bi-ocular and monocular control conditions was very similar on all the main measures (and different from the performance in the binocular condition). We conclude that the deficits in performance observed found for 'monocular' reaches should be attributed to the lack of local depth information specified by the binocular cues. In addition we speculate that convergence angle and binocular disparity, although involved in both the pre-movement and movement-execution phases of the reach, the cues may be weighted differently in both phases of a prehension movement depending on the behavioural strategy involved.

The evaluation of a mupirocin-based selective medium for the enumeration of bifidobacteria from probiotic animal feed

In this study, MRS medium supplemented with cysteine hydrochloride and mupirocin, termed Bifidobacterium selective medium (BSM) was found to be elective for bifidobacteria but inhibitory to a wide range of non-bifidobacteria strains commonly included in probiotic animal feed. Bacilli, lactobacilli, lactococci and streptococci failed to form colonies on BSM and enterococci, pediococci and propionibacteria formed colonies <0.5 mm in diameter. Bifidobacteria formed colonies >1 mm in size and could be readily distinguished. The addition of nystatin to BSM further inhibited Saccharomyces cerevisiae. BSM was successfully used to enumerate the bifidobacteria components, confirmed through fructose-6-phophate-phosphoketolase detection, present in two commercial probiotic feeds. The medium is recommended for the enumeration of bifidobacteria from animal feeds especially when not a numerically dominant component.

Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum

In a previous study that was based primarily on 16S rDNA sequencing, two groups of bifidobacteria that had been recovered from a pig caecum were proposed to belong to two novel species, termed ‘Bifidobacterium pyschroaerophilum’ and ‘Bifidobacterium aerophilum’. In this study, based on DNA G+C content and partial heat-shock protein 60 (HSP60) gene sequences, the assignment of ‘B. pyschroaerophilum’, corrected to Bifidobacterium pyschraerophilum, to the genus Bifidobacterium was confirmed. The DNA G+C content of ‘B. aerophilum’ was relatively low, which was consistent with its segregation into subcluster II of the 16S rDNA phylogenetic tree. Based on partial 16S rDNA and HSP60 gene sequences, the species was transferred to a novel genus and reclassified as Aeriscardovia aeriphila gen. nov., sp. nov. Biochemical profiles and growth parameters were established for both novel species. Interestingly, each had a high tolerance to oxygen and grew on agar media under aerobic conditions, a trait that may relate to their caecal habitat. Under aerobic growth conditions, the short-rod morphology of A. aeriphila lengthened considerably. This appeared to arise from incomplete cell division. In addition, B. pyschraerophilum was unusual in that it grew at temperatures as low as 4 °C. On the basis of genetic, phylogenetic and phenotypic data, the identities of Bifidobacterium pyschraerophilum sp. nov. (type strain, T16T=LMG 21775T=NCIMB 13940T) and Aeriscardovia aeriphila gen. nov., sp. nov. (type strain, T6T=LMG 21773T=NCIMB 13939T) are confirmed.

Enumeration of probiotic pediococci in animal feed: interlaboratory study

An enumeration method to be used as official control under Council Directive 70/524/EEC for probiotic pediococci used as feed additives was validated for consideration for adoption as Comitée Européen de Normalisation (CEN) and ISO standards. Seventeen laboratories in 11 European countries carried out an interlaboratory study. A spread plate method following BS ISO 15214:1998 using 4 different agars [MRS, acidified MRS, MRS with triphenyl tetrazolium chloride (TTC), and a newly developed pediococci selective medium (PSM)] was validated. Precision data in terms of repeatability (r) and reproducibility (R) of the method for each medium using different feeding stuffs with a high and a low inoculation level were determined. Pediococci were present in the samples in mixtures with other probiotics. The enumeration of pediococci on all agars showed an RSDr value of 0.4-3.1% and an RSDR of 1.3-4.8%. MRS agar was preferred, followed by acidified MRS and MRS + TTC agar. All 4 media gave similar counts. Depending on the presence and concentration of other probiotic, such as enterococci, lactobacilli, and yeast, acidified MRS or MRS + TTC agar are recommended. The PSM was selective for pediococci and can be used if this species is present at a concentration more than 10-fold lower than other species that can grow on the MRS agars. The methodology with all 4 media is not applicable to mineral feed.

Genomic diversity and relatedness of bifidobacteria isolated from a porcine cecum

This study initially involved the isolation of a number of bifidobacteria from either the lumen or the epithelium of a porcine cecum. A total of 160 isolates were selected at random on MRS plates containing cysteine hydrochloride (0.5 g/liter) and mupirocin (50 mg/liter). All were identified as bifidobacteria based on fructose-6-phosphate phosphoketolase activity. Following genomic digestion with the restriction enzyme XbaI and pulsed-field gel electrophoresis (PFGE), the isolates produced 15 distinct macro-restriction patterns. Several of the PFGE patterns differed by only 1, 2, or 3 DNA fragments and were grouped as related patterns into seven PFGE types, termed A through G. The related patterns appeared to show genomic plasticity within the isolates arising from chromosomal mutations or possibly horizontal transfer of plasmids. The relative frequency of each PFGE type was maintained within each cecal sample, with PFGE type E representing approximately 50% of the isolates. Randomly amplified polymorphic DNA PCR, cell morphology, whole-cell protein profiling, 16S ribosomal DNA sequencing, and DNA-DNA hybridization were used to determine if the seven apparently unrelated PFGE types represented genetically distinct isolates. Four groups were identified: PFGE types A, C/D/G, B/E, and F, and these appeared to represent Bifidobacterium minimum, Bifidobacterium pseudolongum subsp. pseudolongum, and Bifidobacterium pseudolongum subsp. globosum and two new species, respectively. The data demonstrate the presence of considerable genomic diversity within a relatively simple bifidobacteria population, consisting of 15 distinct strains representing four groups, which was maintained throughout the porcine cecal contents and epithelial layer.

The stereoscopic anisotropy affects manual pointing

Although binocular disparity can in principle provide absolute depth information, perceived stereoscopic depth depends on the relative disparities between points and their spatial arrangement. An example of this is the stereoscopic anisotropy--observers typically perceive less depth for stereoscopic surfaces when depth varies in the horizontal direction than in the vertical direction. We investigated whether this anisotropy also affects manual pointing. Participants were presented with stereograms depicting surfaces that were slanted in depth about either a horizontal axis (inclination) or a vertical axis (slant), and were asked either to point to the edge of a surface, or to estimate its inclination or slant. For both tasks, a clear anisotropy was observed, with participants perceiving greater depth, and also pointing out steeper surfaces, for inclined surfaces than for slanted surfaces. We conclude that both perception and the control of action are subject to a similar stereoscopic anisotropy, and that performance on the two tasks relies on similar depth processing mechanisms.

Genomic diversity within the genus Pediococcus as revealed by randomly amplified polymorphic DNA PCR and pulsed-field gel electrophoresis

The genomic diversity of 33 previously assigned strains from six species within the genus Pediococcus was assessed by randomly amplified polymorphic DNA (RAPD) PCR and pulsed-field-gel electrophoresis (PFGE). The RAPD PCR patterns produced by two separate random primers, termed P1 (ACGCGCCCT) and P2 (ATGTAACGCC), were compared by the Pearson correlation coefficient and the unweighted pair group method with arithmetic averages clustering algorithm. Pattern variations between repeat samples set a strain discrimination threshold of less than 70% similarity. P1 and P2 primers alone and in combination produced 14, 21, and 28 distinct patterns, respectively. When each strain was assigned with a type strain with which it shared the highest level of similarity, both primers grouped 17 of the 27 strains to their proposed species. PFGE following genomic digestion with the restriction enzymes ApaI, NotI, and AscI produced 30, 32, and 28 distinct macrorestriction patterns, respectively. Specific DNA fragments within the NotI and AscI macrorestriction patterns for each strain were observed that allowed 27 of the 33 strains to be assigned to their proposed species. For example, following digestion with AscI, all Pediococcus parvulus strains were characterized by two DNA fragments, one of approximately 220 kb and another between 700 and 800 kb. The exceptions correlated with those observed with both RAPD PCR primers and included three P. damnosus and two P. pentosaceus strains that grew at temperatures regarded as nonpermissive for their proposed species but not for those with which they grouped.

Reflexive shifts of covert attention operate in an egocentric coordinate frame

Covert shifts of attention have been shown to improve detection and discrimination thresholds for a range of visual stimuli. Although there is some evidence to suggest that the allocation of attention to a particular region of interest occurs in a retinotopic frame of reference, the importance of an allocentric, or object-based, framework has gained widespread empirical support. The current experiment investigates the nature of the spatial representation in which covert shifts of attention occur in response to a reflexive prime. Primes and targets were presented in four conditions designed to vary systematically the validity of the spatial relationship between the prime and target in egocentric or allocentric coordinate frameworks. A significant advantage, in terms of reaction time and correct identification, was found for targets located in positions previously primed in an egocentric (but not allocentric) framework whereas there was no advantage for locations primed in an allocentric (but not egocentric) framework. These results suggest that the allocation of covert spatial attention within an egocentric framework may be more important than previously thought.

Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding

The majority of plant cell wall hydrolases are modular enzymes which, in addition to a catalytic module, possess one or more carbohydrate-binding modules (CBMs). These carbohydrate-active enzymes and their constituent modules have been classified into a number of families based upon amino acid sequence similarity. The Clostridium thermocellum xylanase, Xyn10B, contains two CBMs that belong to family 22 (CBM22). The crystal structure of the C-terminal CBM22 (CBM22-2) was determined in a previous study [Charnock, S. J., et al. (2000) Biochemistry 39, 5013--5021] and revealed a surface cleft which presents several conserved residues that are implicated in ligand binding. These amino acids have been substituted and the structure and biochemical properties of the mutants analyzed. The data show that R25A, W53A, Y103A, Y136A, and E138A exhibit greatly reduced affinity for xylotetraose relative to that of the wild-type protein. Conversely, mutations Y103F and Y136F have little effect on ligand binding. Using thermodynamic, X-ray, and NMR measurements on the mutants, we show that the cleft of CBM22-2 does indeed form the ligand-binding site. Trp 53 and Tyr 103 most likely participate in hydrophobic stacking interactions with the ligand, while Glu 138 makes one or more important hydrogen bonds with the tetrasaccharide. Although Arg 25 and Tyr 136 are likely to form hydrogen bonds with the ligand, they are also shown to play a critical role in maintaining the structural integrity of the binding cleft.

Role of hydrogen bonding in the interaction between a xylan binding module and xylan

NMR studies of the internal family 2b carbohydrate binding module (CBM2b-1) of Cellulomonas fimi xylanase 11A have identified six polar residues and two aromatic residues that interact with its target ligand, xylan. To investigate the importance of the various interactions, free energy and enthalpy changes have been measured for the binding of xylan to native and mutant forms of CBM2b-1. The data show that the two aromatic residues, Trp 259 and Trp 291, play a critical role in the binding, and similarly that mutants N264A and T316A have no affinity for the xylose polymer. Interestingly, mutations E257A, Q288A, N292A, E257A/Q288A, E257A/N292A, and E257A/N292A/Q288A do not significantly diminish the affinity of CBM2b-1 for the xylose polymers, but do influence the thermodynamics driving the protein-carbohydrate interactions. These thermodynamic parameters have been interpreted in light of a fresh understanding of enthalpy-entropy compensation and show the following. (1) For proteins whose ligands are bound on an exposed surface, hydrogen bonding confers little specificity or affinity. It also displays little cooperativity. Most specificity and affinity derive from binding between the face of sugar rings and aromatic rings. (2) Loss of hydrogen bonding interactions leads to a redistribution of the remaining bonding interactions such that the entropic mobility of the ligand is maximized, at the expense (if necessary) of enthalpically favorable bonds. (3) Changes in entropy and enthalpy in the binding between polysaccharide and a range of mutants can be interpreted by considering changes in binding and flexibility, without any need to consider solvent reorganization.

Corynebacterium mooreparkense sp. nov. and Corynebacterium casei sp. nov., isolated from the surface of a smear-ripened cheese

Ten isolates each of two different bacterial species isolated from the surface of a smear-ripened cheese were found to exhibit many characteristics of the genus Corynebacterium. The isolates were Gram-positive, catalase-positive, non-spore-forming rods that did not undergo a rod/coccus transformation when grown on complex media. Chemotaxonomic investigation revealed that the strains belonged unambiguously to the genus Corynebacterium. Their cell walls contained arabinose, galactose and short-chain mycolic acids (C22 to C36) and their peptidoglycan contained meso-diaminopimelic acid. The G+C content of the DNA was 51-60 mol%. MK-9 (H2) was the principal menaquinone. The 16S rDNA sequences of four isolates of each bacterium were determined and aligned with those of other members of the coryneform group. Phylogenetic analysis showed that the strains represented two new sublines within the genus Corynebacterium; Corynebacterium variabile and Corynebacterium ammoniagenes were their nearest known phylogenetic neighbours. Corynebacterium variabile and Corynebacterium ammoniagenes showed the highest levels of sequence homology with the isolates; however, DNA-DNA hydridization studies indicated that the Corynebacterium strains isolated from the cheese smear did not belong to either Corynebacterium variabile or Corynebacterium ammoniagenes (26 and 46% chromosomal similarity, respectively). On the basis of the phylogenetic and phenotypic distinctiveness of the unknown isolates, it is proposed that the bacteria be classified as two new Corynebacterium species, for which the names Corynebacterium mooreparkense sp. nov. and Corynebacterium casei sp. nov. are proposed. Type strains have been deposited in culture collections as Corynebacterium mooreparkense LMG S-19265T (= NCIMB 30131T) and Corynebacterium casei LMG S-19264T (= NCIMB 30130T).

Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A

Glycoside hydrolases often contain multiple copies of noncatalytic carbohydrate binding modules (CBMs) from the same or different families. Currently, the functional importance of this complex molecular architecture is unclear. To investigate the role of multiple CBMs in plant cell wall hydrolases, we have determined the polysaccharide binding properties of wild type and various derivatives of Cellulomonas fimi xylanase 11A (Cf Xyn11A). This protein, which binds to both cellulose and xylan, contains two family 2b CBMs that exhibit 70% sequence identity, one internal (CBM2b-1), which has previously been shown to bind specifically to xylan and the other at the C-terminus (CBM2b-2). Biochemical characterization of CBM2b-2 showed that the module bound to insoluble and soluble oat spelt xylan and xylohexaose with K(a) values of 5.6 x 10(4), 1.2 x 10(4), and 4.8 x 10(3) M(-1), respectively, but exhibited extremely weak affinity for cellohexaose (<10(2) M(-1)), and its interaction with insoluble cellulose was too weak to quantify. The CBM did not interact with soluble forms of other plant cell wall polysaccharides. The three-dimensional structure of CBM2b-2 was determined by NMR spectroscopy. The module has a twisted "beta-sandwich" architecture, and the two surface exposed tryptophans, Trp 570 and Trp 602, which are in a perpendicular orientation with each other, were shown to be essential for ligand binding. In addition, changing Arg 573 to glycine altered the polysaccharide binding specificity of the module from xylan to cellulose. These data demonstrate that the biochemical properties and tertiary structure of CBM2b-2 and CBM2b-1 are extremely similar. When CBM2b-1 and CBM2b-2 were incorporated into a single polypeptide chain, either in the full-length enzyme or an artificial construct comprising both CBM2bs covalently joined via a flexible linker, there was an approximate 18-20-fold increase in the affinity of the protein for soluble and insoluble xylan, as compared to the individual modules, and a measurable interaction with insoluble acid-swollen cellulose, although the K(a) (approximately 6.0 x 10(4) M(-1)) was still much lower than for insoluble xylan (K(a) = approximately 1.0 x 10(6) M(-1)). These data demonstrate that the two family 2b CBMs of Cf Xyn11A act in synergy to bind acid swollen cellulose and xylan. We propose that the increased affinity of glycoside hydrolases for polysaccharides, through the synergistic interactions of CBMs, provides an explanation for the duplication of CBMs from the same family in some prokaryotic cellulases and xylanases.

The novel guanylyl cyclase MsGC-I is strongly expressed in higher-order neuropils in the brain of Manduca sexta

Guanylyl cyclases are usually characterized as being either soluble (sGCs) or receptor (rGCs). We have recently cloned a novel guanylyl cyclase, MsGC-I, from the developing nervous system of the hawkmoth Manduca sexta that cannot be classified as either an sGC or an rGC. MsGC-I shows highest sequence identity with receptor guanylyl cyclases throughout its catalytic and dimerization domains, but does not contain the ligand-binding, transmembrane or kinase-like domains characteristic of receptor guanylyl cyclases. In addition, MsGC-I contains a C-terminal extension of 149 amino acid residues. In this paper, we report the expression of MsGC-I in the adult. Northern blots show that it is expressed preferentially in the nervous system, with high levels in the pharate adult brain and antennae. In the antennae, immunohistochemical analyses show that it is expressed in the cell bodies and dendrites, but not axons, of olfactory receptor neurons. In the brain, it is expressed in a variety of sensory neuropils including the antennal and optic lobes. It is also expressed in structures involved in higher-order processing including the mushroom bodies and central complex. This complicated expression pattern suggests that this novel guanylyl cyclase plays an important role in mediating cyclic GMP levels in the nervous system of Manduca sexta.

The structural basis for the ligand specificity of family 2 carbohydrate-binding modules

The interactions of proteins with polysaccharides play a key role in the microbial hydrolysis of cellulose and xylan, the most abundant organic molecules in the biosphere, and are thus pivotal to the recycling of photosynthetically fixed carbon. Enzymes that attack these recalcitrant polymers have a modular structure comprising catalytic modules and non-catalytic carbohydrate-binding modules (CBMs). The largest prokaryotic CBM family, CBM2, contains members that bind cellulose (CBM2a) and xylan (CBM2b), respectively. A possible explanation for the different ligand specificity of CBM2b is that one of the surface tryptophans involved in the protein-carbohydrate interaction is rotated by 90 degrees compared with its position in CBM2a (thus matching the structure of the binding site to the helical secondary structure of xylan), which may be promoted by a single amino acid difference between the two families. Here we show that by mutation of this single residue (Arg-262-->Gly), a CBM2b xylan-binding module completely loses its affinity for xylan and becomes a cellulose-binding module. The structural effect of the mutation has been revealed using NMR spectroscopy, which confirms that Trp-259 rotates 90 degrees to lie flat against the protein surface. Except for this one residue, the mutation only results in minor changes to the structure. The mutated protein interacts with cellulose using the same residues that the wild-type CBM2b uses to interact with xylan, suggesting that the recognition is of the secondary structure of the polysaccharide rather than any specific recognition of the absence or presence of functional groups.

Random breakage and reunion chromosome aberration formation model; an interaction-distance version based on chromatin geometry

PURPOSE

Using published FISH data for chromosome aberration production in human fibroblasts by hard X-rays to test a breakage-and-reunion model.

METHODS

The model assumed pairwise misrejoining, random apart from proximity effects, of DNA double-strand break (DSB) free ends. CAS (chromosome aberration simulator) Monte Carlo computer software implementing the model was modified to use a distance algorithm for misrejoining instead of using DSB interaction sites. The modification (called CAS2) allowed a somewhat more realistic approach to large-scale chromatin geometry, chromosome territories and proximity effects. It required adding a third adjustable parameter, the chromosome territory intersection factor, quantifying the amount of intertwining among different chromosomes.

RESULTS

CAS2 gave somewhat better results than CAS. A reasonable fit with a few discrepancies was obtained for the frequencies at three different radiation doses of many different aberration types and of aberrations involving various specific chromosomes in a large data set using one-paint FISH scoring. The optimal average chromosome territory intersection factor was approximately 1.1, indicating that, for an arbitrarily chosen location in the nucleus, on average slightly more than two chromosomes have very nearby loci. Without changing the three parameter values, a fit was also obtained for a corresponding, smaller, two-paint data set.

CONCLUSIONS

A random breakage-and-reunion model incorporating proximity effects by using a distance algorithm gave acceptable approximations for many details of hard X-ray aberration patterns. However, enough discrepancies were found that the possibility of an additional or alternate formation mechanism remains.

Dibasic inhibitors of human mast cell tryptase. Part 2: structure-activity relationships and requirements for potent activity

Detailed structure activity relationships (SARs) for a series of dibasic human tryptase inhibitors are presented. The structural requirements for potent inhibitory activity are remarkably broad with a range of core template modifications being well tolerated. Optimized inhibitors demonstrate potent anti-asthmatic activity in a sheep model of allergic asthma. APC-2059, a dibasic tryptase inhibitor with subnanomolar activity, has been advanced to phase II clinical trials for the treatment of both psoriasis and ulcerative colitis.

Mammalian recombination-repair genes XRCC2 and XRCC3 promote correct chromosome segregation

Growth and development are dependent on the faithful duplication of cells. Duplication requires accurate genome replication, the repair of any DNA damage, and the precise segregation of chromosomes at mitosis; molecular checkpoints ensure the proper progression and fidelity of each stage. Loss of any of these highly conserved functions may result in genetic instability and proneness to cancer. Here we show that highly significant increases in chromosome missegregation occur in cell lines lacking the RAD51-like genes XRCC2 and XRCC3. This increased missegregation is associated with fragmentation of the centrosome, a component of the mitotic spindle, and not with loss of the spindle checkpoint. Our results show that unresolved DNA damage triggers this instability, and that XRCC2 and XRCC3 are potential tumour-suppressor genes in mammals.

Impact of the patient population on the risk for heparin-induced thrombocytopenia

The frequency of immune heparin-induced thrombocytopenia (HIT) varies among prospective studies. It is unknown whether this is caused by differences in the heparin preparations, the patient populations, or the types of serologic assay used to confirm the diagnosis. Seven hundred forty-four patients were studied from 3 different clinical treatment settings, as follows: unfractionated heparin (UFH) during or after cardiac surgery (n = 100), UFH after orthopedic surgery (n = 205), and low-molecular-weight heparin (LMWH) after orthopedic surgery (n = 439). Both an activation assay and an antigen assay were used to detect heparin-dependent IgG (HIT-IgG) antibodies. By activation assay, the frequency of HIT-IgG formation ranged from a low of 3.2% in orthopedic patients receiving LMWH to a high of 20% in cardiac patients receiving UFH; by antigen assay, the corresponding frequencies ranged from 7.5% to 50%. Both UFH use (P =.002) and cardiac surgery (P =.01) were more likely to be associated with HIT-IgG formation. However, among patients in whom HIT-IgG formed and who were administered UFH, the probability for HIT was higher among orthopedic patients than among cardiac patients (by activation assay: 52.6% compared with 5%; odds ratio, 21.1 [95% CI, 2.2-962.8]; P =.001; by antigen assay: 34.5% compared with 2.0%; odds ratio, 25.8 [95% CI, 3.2-1141]; P <.001). It is concluded that there is an unexpected dissociation between the frequency of HIT-IgG formation and the risk for HIT that is dependent on the patient population. HIT-IgG antibodies are more likely to form in patients who undergo cardiac surgery than in orthopedic patients, but among patients in whom antibodies do form, orthopedic patients are more likely to develop HIT. (Blood. 2000;96:1703-1708)

Trp22, Trp24, and Tyr8 play a pivotal role in the binding of the family 10 cellulose-binding module from Pseudomonas xylanase A to insoluble ligands

Aromatic amino acids are believed to play a pivotal role in carbohydrate-binding proteins, by forming hydrophobic stacking interactions with the sugar rings of their target ligands. Family 10 cellulose-binding modules (CBM10s), present in a number of cellulases and xylanases expressed by Pseudomonas fluorescens subsp. cellulosa, contain two tyrosine and three tryptophan residues which are highly conserved. To investigate whether these amino acids play an important role in the interaction of CBM10 from P. fluorescens subsp. cellulosa xylanase A (Pf Xyn10A) with cellulose, each of these residues was changed to alanine in CBM10 expressed as a discrete module or fused to the catalytic domain of Pf Xyn10A (CBM10-CD), and the capacity of the mutant proteins of CBM10-CD to bind the polysaccharide was evaluated. The data showed that W22A, W24A, and Y8A bound very weakly to cellulose compared to the wild-type protein, while Y12A retained its capacity to interact with the glucose polymer. When the W7A mutation was introduced into CBM10 the protein domain did not accumulate in Escherichia coli. In contrast, the W7A mutant of CBM10-CD was efficiently expressed in E. coli, although the protein bound very weakly to cellulose. NMR spectra of wild-type CBM10, W22A, and W24A were very similar, suggesting that the mutations did not significantly affect the protein fold. Titration of wild-type CBM10, W22A, and W24A with N-bromosuccinimide indicated that Trp22 and Trp24 were on the surface of the protein, while Trp7 was buried. Collectively, these data indicate that Trp22, Trp24, and Tyr8 play a direct role in the binding of Pf Xyn10A CBM10 to cellulose. The results are discussed in the light of the three-dimensional structure of CBM10 [Raghothama, S., Simpson, P. J., Szabó, L., Nagy, T., Gilbert, H. J., and Williamson, M. P. (2000) Biochemistry 39, 978-984].

Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A

Plant cell wall hydrolases generally have a modular structure consisting of a catalytic domain linked to one or more noncatalytic carbohydrate-binding modules (CBMs), whose common function is to attach the enzyme to the polymeric substrate. Xylanase A from Pseudomonas fluorescens subsp. cellulosa (Pf Xyn10A) consists of a family 10 catalytic domain, an N-terminal family IIa cellulose-binding module, and an internal family 10 cellulose-binding module. The structure of the 45-residue family 10 CBM has been determined in solution using NMR. It consists of two antiparallel beta-sheets, one with two strands and one with three, with a short alpha-helix across one face of the three-stranded sheet. There is a high density of aromatic residues on one side of the protein, including three aromatic residues (Tyr8, Trp22, and Trp24), which are exposed and form a flat surface on one face, in a classical polysaccharide-binding arrangement. The fold is closely similar to that of the oligonucleotide/oligosaccharide-binding (OB) fold, but appears to have arisen by convergent evolution, because there is no sequence similarity, and the presumed binding sites are on different faces.

Underprediction of visibly complex chromosome aberrations by a recombinational-repair ('one-hit') model

PURPOSE

Published low-LET FISH data were used to test two models of chromosome aberration production based on breakage-and-reunion or recombinational repair.

MATERIALS AND METHODS

Randomness of DNA double strand break induction and misrejoining is analyzed comprehensively and adopted as a working hypothesis. Proximity effects are approximated by using interaction sites. Model results are calculated using CAS (chromosome aberration simulator) Monte Carlo computer software with two adjustable parameters. CAS can emulate the specifics of any experimental painting protocol, allowing very detailed tests of the models.

RESULTS

To reasonable approximation, breakage-and-reunion model predictions are consistent with low-LET FISH results, including two large, elaborate, one-paint data sets. An explicitly specified version of the recombinational-repair model severely underpredicts the frequency of the visibly complex aberration patterns most commonly observed with one-paint FISH, and is inconsistent with some observed multi-paint patterns. When high-dose effects (distortion and saturation) are taken into account quantitatively, a dose-response relation for apparently simple interchanges slightly favours the breakage-and-reunion model over the recombinational-repair model, despite being approximately linear over the dose range 2-6 Gy.

CONCLUSIONS

The random breakage-and-reunion model gives comprehensive baseline predictions that are sufficiently accurate for the organization of experimental results. The data speak against complex aberrations being formed by the random recombinational repair pathway discussed here.