CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing

Gene editing characterization with currently available tools does not always give precise relative proportions among the different types of gene edits present in an edited bulk of cells. We have developed CRISPR-Analytics, CRISPR-A, which is a comprehensive and versatile genome editing web application tool and a nextflow pipeline to give support to gene editing experimental design and analysis. CRISPR-A provides a robust gene editing analysis pipeline composed of data analysis tools and simulation. It achieves higher accuracy than current tools and expands the functionality. The analysis includes mock-based noise correction, spike-in calibrated amplification bias reduction, and advanced interactive graphics. This expanded robustness makes this tool ideal for analyzing highly sensitive cases such as clinical samples or experiments with low editing efficiencies. It also provides an assessment of experimental design through the simulation of gene editing results. Therefore, CRISPR-A is ideal to support multiple kinds of experiments such as double-stranded DNA break-based engineering, base editing (BE), primer editing (PE), and homology-directed repair (HDR), without the need of specifying the used experimental approach.

Monitoring cytosolic H2O2 fluctuations arising from altered plasma membrane gradients or from mitochondrial activity

Genetically encoded probes monitoring H₂O₂ fluctuations in living organisms are key to decipher redox signaling events. Here we use a new probe, roGFP2-Tpx1.C169S, to monitor pre-toxic fluctuations of peroxides in fission yeast, where the concentrations linked to signaling or to toxicity have been established. This probe is able to detect nanomolar fluctuations of intracellular H₂O₂ caused by extracellular peroxides; expression of human aquaporin 8 channels H₂O₂ entry into fission yeast decreasing membrane gradients. The probe also detects H₂O₂ bursts from mitochondria after addition of electron transport chain inhibitors, the extent of probe oxidation being proportional to the mitochondrial activity. The oxidation of this probe is an indicator of steady-state levels of H₂O₂ in different genetic backgrounds. Metabolic reprogramming during growth in low-glucose media causes probe reduction due to the activation of antioxidant cascades. We demonstrate how peroxiredoxin-based probes can be used to monitor physiological H₂O₂ fluctuations.

Reliable methods of measuring intracellular H₂O₂ fluctuations are necessary to advance redox biology. Here the authors design a H₂O₂ sensor based on the fission yeast peroxiredoxin Tpx1 to sense nanomolar fluctuations of intracellular H₂O₂ in response to genetic and environmental perturbations.

Boring sponges, an increasing threat for coral reefs affected by bleaching events

Coral bleaching is a stress response of corals induced by a variety of factors, but these events have become more frequent and intense in response to recent climate-change-related temperature anomalies. We tested the hypothesis that coral reefs affected by bleaching events are currently heavily infested by boring sponges, which are playing a significant role in the destruction of their physical structure. Seventeen reefs that cover the entire distributional range of corals along the Mexican Pacific coast were studied between 2005/2006, and later between 2009/2010. Most of these coral reefs were previously impacted by bleaching events, which resulted in coral mortalities. Sponge abundance and species richness was used as an indicator of bioerosion, and coral cover was used to describe the present condition of coral reefs. Coral reefs are currently highly invaded (46% of the samples examined) by a very high diversity of boring sponges (20 species); being the coral reef framework the substrate most invaded (56%) followed by the rubbles (45%), and the living colonies (36%). The results also indicated that boring sponges are promoting the dislodgment of live colonies and large fragments from the framework. In summary, the eastern coral reefs affected by bleaching phenomena, mainly provoked by El Niño, present a high diversity and abundance of boring sponges, which are weakening the union of the colony with the reef framework and promoting their dislodgment. These phenomena will probably become even more intense and severe, as temperatures are projected to continue to rise under the scenarios for future climate change, which could place many eastern coral reefs beyond their survival threshold.

Recovery of proteins from wastewater of tannery beamhouse operations: influence on the main pollution parameters

The recovery of proteins from effluents of beamhouse operations in a hair-pulping process of hides is proposed. Precipitation with sulphuric acid at the isoelectric pH was chosen for protein recovery. The precipitates were characterized in order to study their potential uses. Apart from the protein nitrogen, the precipitate also contained a considerable content of fats resulting from the co-precipitation of natural fat of the hide in the wastewaters. The precipitation of the protein fraction resulted in a reduction of 80-85% of COD, whereas the protein content decreased 68-78%. This diminution of the contamination load led to a notable reduction of the tax on wastewater. The content of protein material in the precipitate varied from 15 to 44%. As expected, the protein in the precipitate did not result from the collagen decomposition of the hide but from soluble proteins such as albumin and globulin and remains of keratin. The precipitates obtained met the maximum limits of heavy metals according to legislation on organic fertilizers. The potential uses of the protein fraction recovered from tannery wastewaters are currently being investigated.

Nocturnal oxygen therapy in patients with the Eisenmenger syndrome

This prospective and controlled pilot study evaluates the long-term effects of nocturnal oxygen therapy (NOT) on exercise endurance, hematology variables, quality of life, and survival of 23 adult patients (mean age, 32 +/- 6 yr) with post-tricuspid congenital heart defects (ventricular septal defect = 10; patent ductus arteriosus = 13) and Eisenmenger Syndrome. All had pulmonary hypertension (mean pulmonary artery pressure = 88 +/- 20 mm Hg), severe hypoxemia (Pa(O(2)) = 44 +/- 5 mm Hg), and secondary erythrocytosis (hematocrit = 61.5 +/- 7%). Exercise endurance (6-min walk test = 380 +/- 88 m) was limited. In a random fashion, NOT was given to one group of patients (n = 12) but withheld from a comparable control group (n = 11). At 2 yr of close follow-up, two patients in the group of control patients, and three in the treatment group died. Mean survival estimates were similar in both groups (20.7 versus 20.8 mo; chi-square log-rank, 0.08; p = NS). Likewise, none of the hematology, exercise capacity, and quality of life variables examined showed statistically significant changes that were dependent on treatment regimen. We conclude that NOT does not modify the natural history of patients with advanced Eisenmenger Syndrome.

[Follicular conjunctivitis due to Chlamydia trachomatis]

During two years (1997-1999) an investigation of possible infections of chlamydial etiology in outpatients with follicular conjunctivitis was carried out, through the use of specific assays. Fifty-seven selected patients with presumptive inclusion conjunctivitis were diagnosed by means of ophthalmoscopic examination and bilateral tarsal-conjunctiva swabbing for microorganisms. The possible presence of Chlamydia trachomatis was tested by immunofluorescence microscopy and isolation in cell culture of McCoy line. Of the 57 conjunctivitis patients screened, 37 (65%) proved to be positive by cell culture (CC) and 27 (47%) by direct immunofluorescence (IFD). A good agreement between the two assays was observed, where the CC was more sensitive than IFD. Of these 37 patients with chlamydial conjunctivitis, 23 (62%) were women, with over one-third of them ranging in age from 45 to 65 years. Their clinical records revealed an evolution period of 1 to 12 months. Eighteen (78%) of these women reported previous genital pathology, while 4 (29%) of the 14 men had a history of urethritis by Chlamydia trachomatis. A high frequency of follicular conjunctivitis by Chlamydia (65%) in the screened patients was observed, without any evidence of urogenital signs and symptoms at the moment of the study.

Exudation of low molecular weight compounds (thiobismethane, methyl isocyanide, and methyl isothiocyanate) as a possible chemical defense mechanism in the marine sponge Ircinia felix

The volatile constituents of the marine sponge Ircinia felix were obtained by dynamic headspace extraction and analyzed by HRGC, HRGC-MS and HRGC-Odor at sniffing port. Fifty-nine volatiles were identified for the first time in the odor of this sponge. Hydrocarbons (32.9%), alcohols (17.8%) and carbonyl compounds (16.0%) predominated in the sponge volatile profile, followed by esters (11.6%), halogen compounds (8.6%), ethers (7.7%), nitrogen and/or sulfur compounds (4.6%) and carboxylic acids (0.8%). Among the identified volatiles, thiobismethane (commonly known as dimethylsulfide), methyl isocyanide and methyl isothiocyanate were found to be responsible for the nauseating and toxic smell emitted by the sponge and for the antimicrobial activity detected in the volatile extract. Exudation experiments in aquarium and in situ conditions revealed that thiobismethane, methyl isocyanide and methyl isothiocyanate are continuously released by the sponge. Upon injury, the concentration of these volatiles increased strongly. Hence, these substances form a chemical protective barrier which may help these sponges avoid fouling, compete for space, prevent infection in the short term, and/or signal generalist predators regarding the existence of other toxic substances in the internal tissues.

Impaired hepatic extraction and increased splanchnic production contribute to lactic acidosis in canine sepsis

In septic shock, the extent to which lactic acidosis (LA) is a consequence of splanchnic lactate overproduction (SLP) or impaired hepatic lactate extraction (HLE) is not clear. We examined SLP and HLE in E. coli sepsis in dogs. We further determined the effects of vasopressor treatments, which included phenylephrine, dopamine, norepinephrine, and a combination of dobutamine and norepinephrine treatment, on SLP and HLE in respective groups. The animals were studied while anesthetized and ventilated. During sepsis, SLP increased as compared with presepsis (-0.017 versus 0.07 mmol/min, p < 0.05), but this increase could not be explained by reduced splanchnic oxygen delivery (SOD). During sepsis, HLE increased as compared with baseline (0.8 versus 8%, p < 0.05), but was significantly lower than that found during lactic acid loading in nonseptic dogs. None of the vasopressor treatments had a detrimental effect on SLP. These results indicate that LA in sepsis occurs secondary to an increase in splanchnic lactate production that is not related to reduced splanchnic oxygen delivery, as well as to a decrease in hepatic lactate extraction. Effects of different vasoactive agents did not alter either splanchnic lactate production or hepatic lactate extraction in this sepsis model.

Histamine H3 receptor blockade improves cardiac function in canine anaphylaxis

In anaphylactic shock (AS), the relative effects of the autacoids including histamine, prostaglandins, and leukotrienes on causing cardiovascular collapse and the extent to which receptor blocking agents and pathway inhibitors may prevent this collapse are not clear. In a ragweed model of anaphylaxis, we examined whether pretreatment with H1, H2, H3 receptor blockers, and cyclooxygenase and leukotriene pathway inhibitors was useful in preventing the depression in left ventricular (LV) contractility known to occur in this model. The dose of allergen was varied to produce similar degrees of shock between treatments. The animals were studied under pentobarbital anesthesia in which the treatment studies were approximately 3 wk apart. LV volumes were measured by sonomicrometric techniques. During challenge, mean arterial blood pressure (Pa), cardiac output (Q), and LV end-diastolic pressure (LVEDP) decreased approximately 50% compared with preshock values in all treatments. Histamine H3 receptor blockade was associated with higher heart rates (HR) and higher stroke work (SW) (p < 0.05) as compared with the other treatment studies. We conclude that histamine H3 activation by inhibiting adrenergic neural norepinephrine release contributes to cardiovascular collapse in AS.

[Relationship between discontinuous sucrose gradient and viability of Cryptosporidium sp. oocysts]

Cryptosporidium sp. causes self-limiting gastroenteritis in immunocompetent individuals and can produce a life-threatening chronic diarrhea in immunodeficient patients. In order to obtain populations of selectively infective oocysts for inoculation in biological experiments, we developed an operational protocol for the enrichment of viable oocysts from crude fecal material. Using either fresh or formaldehyde-fixed feces as sources of viable and nonviable oocysts, respectively, we fractionated the samples on parallel discontinuous sucrose gradients and evaluated oocyst viability at different banding densities by an in vitro excystation assay. The formaldehyde-inactivated fecal samples formed no bands after centrifugation and 91.66% of the oocysts became concentrated in the pellet. Fresh fecal samples formed three bands at densities 1.062, 1.092, and 1.121, in addition to a sediment. Here the viability of the gradient-sedimented oocysts was 92.3% overall, and of those in the second band 100%. Modifications in oocyst permeability thus seems to alter their sedimentation characteristics so that consequent distribution on sucrose gradients can be correlated with oocyst viability. Discontinuous sucrose density gradient sedimentation would thus constitute a simple and rapid mean to obtain viable oocysts for use in biological models both in vivo and in vitro.

Antinociceptive and uterine relaxant activities of Viburnum toronis alive (Caprifoliaceae)

Petroleum ether, ethyl acetate and methanolic leaf extracts of Viburnum toronis Killip et Smith were studied. From the petroleum ether extract, fatty acids of methyl esters such as methyl myristate, methyl palmitate, methyl stearate and methyl araquidonate were identified by means of GC-MS. From the ethyl acetate extract, 2-methylbutanoic, 2-methyl-2-butenoic, 3-methylbutanoic acids and 4-hydroxy-4-methylpentanone were identified by means of GC-MS. Through the isolated organ technique, uterine relaxant was verified; and through the method of writhings induced by acetic acid, the antinociceptive activity of methanolic extracts and the extract in ethyl acetate were verified. It was found that the extract in ethyl acetate showed the greatest in both uterine relaxant and antinociceptive activity at doses of 250 mg/kg.

[Sotos syndrome associated with focal dystonia]

INTRODUCTION

Sotos syndrome is a form of infantile gigantism characterized by excessive body size from the time of birth, particular facies, acromegalic changes and signs of non-progressive cerebral involvement. The etiology is unknown. Diagnosis is based on somatometric data and the particular phenotype traits. Biochemical and endocrine studies are normal. Torticollis is a focal dystonia and therefore more common in adults.

CLINICAL CASE

A 20 year old woman with macrosomic features since birth presented with: weight 104 kg, height 182 cm; prognathism, hypertelorism, a broad over hanging forehead with a high hair line; large ears, hands and feet; torticollis towards the right with elevation and anteroversion of the right shoulder which caused symptomatic scoliosis. She was bradypsychic and rather slow in speech. The complementary tests done (cerebral and cervical CT and MR, bone gammography, evoked potentials, EMG-ENG, sural nerve biopsy, biopsy of skin and muscle, EEG and hormone and biochemistry studies) were normal. The torticollis was treated with botulinus toxin and improved considerably, as did the scoliosis.

CONCLUSIONS

To date, dystonia has not been described in association with Sotos syndrome. This may be a causal association, or even perhaps hereditary, since the patient's mother had dystonia (in the form of blepharospasm).

Symptomatic venous hypertension because of occult iliofemoral deep vein thrombosis: a report of two cases

Two 25-year-old males with symptomatic venous hypertension (venous claudication, n = 1; swollen leg, n = 1) were evaluated for iliofemoral venous occlusive disease. One patient had a common femoral vein/external iliac vein occlusion with no history of deep vein thrombosis or trauma. The second patient had an acute deep vein thrombosis superimposed on a chronic external iliac vein stenosis. No source of extrinsic venous compression was identified in either patient. Venous reconstruction with vein bypass (patient no. 1) and vein patch angioplasty (patient no. 2) led to resolution of their hypertensive symptoms. Intraoperative examination of the involved vein segments revealed chronic changes consistent with a prior occult deep vein thrombosis in both patients. Occult iliofemoral deep vein thrombosis in young healthy males is rarely seen. The acute deep vein thrombosis may manifest minimal or no symptoms but it can lead to chronic venous occlusive disease and serious post-phlebitic morbidity. In this context, these two cases are discussed with a review of the pertinent literature.

Effect of porcine reproductive and respiratory syndrome virus infection on the clearance of Haemophilus parasuis by porcine alveolar macrophages

Porcine reproductive and respiratory syndrome virus (PRRSV) infection in young piglets is frequently associated with secondary infection due to various pathogens, especially those of the respiratory tract. One of the most important mechanisms in respiratory diseases is related to the alteration of function of porcine alveolar macrophages (PAMs). The objective of this study was to determine how PRRS virus infection affects the capabilities of PAMs in the phagocytosis and destruction of Haemophilus parasuis. Phagocytosis percentages were determined in vitro and ex vivo, after collected PAMs were directly exposed to the virus of if PAMs were collected from piglets previously infected with PRRSV. In vitro experiments demonstrated that H. parasuis uptake by PAMs is only increased in the early stages of PRRSV infection (2 h post-infection). In contrast, in the ex vivo experiments it was shown that PAMs from PRRSV-infected piglets do not seem to change in their phagocytic rate until the later stages of infection. Together with a decrease in the phagocytic rate, a marked decrease in the functional ability of PAMs to kill bacteria was observed 7 d post-infection. It is hypothesized that when animals are exposed to PRRSV, there is a marked decrease in the functional ability of PAMs to kill bacteria through the release of superoxide anion, indicating a possible negative effect of the virus, at least at the macrophage level.

Graded balloon dilation atrial septostomy in severe primary pulmonary hypertension. A therapeutic alternative for patients nonresponsive to vasodilator treatment

OBJECTIVES

We sought to investigate the acute hemodynamic effects of graded balloon dilation atrial septostomy (BDAS) and to define the long-term impact of this procedure on New York Heart Association functional class and survival in adult patients with primary pulmonary hypertension (PPH).

BACKGROUND

Current treatment strategies for patients with severe and refractory PPH are limited by either technical difficulties and high mortality or cost.

METHODS

We studied 15 patients with severe PPH. BDAS was successfully performed in all patients by crossing the interatrial septum with a Brockenbrough needle, followed by progressive dilation of the orifice with a Mansfield balloon in a hemodynamically controlled, step-by-step manner.

RESULTS

BDAS caused an immediate significant fall in right ventricular end-diastolic pressure and in systemic arterial oxygen saturation and an increase in cardiac index. One patient died, and 14 survived the procedure and significantly improved their mean functional class (from 3.57 +/- 0.6 to 2.07 +/- 0.3 [mean +/- SD], p < 0.001). Exercise endurance (6-min test) also improved from 107 +/- 127 to 217 +/- 108 m (p < 0.001). Because of spontaneous closure, BDAS was repeated in four patients. The survival rate among patients who survived the procedure was 92% at 1, 2 and 3 years, which is better than that for historical control PPH patients (73%, 59% and 52%, respectively).

CONCLUSIONS

With careful monitoring, BDAS is a safe and useful palliative treatment for selected patients with severe PPH.

[Factors affecting the in vitro excystation of Cryptosporidium sp]

To assess the viability of the oocysts from Cryptosporidium sp, an in vitro excystation technique was developed and optimized. To this end, oocysts from Cryptosporidium sp were isolated from a sample of fecal material from a child with symptomatic cryptosporidiosis. The specimen was processed by a discontinuous-sucrose-gradient technique yielding a final suspension of purified and concentrated oocysts. The resulting oocysts were quantified by counting an aliquot in a Neubauer hemocytometer chamber and the remainder were preserved in phosphate-buffered saline at pH 7.2 and 4 degrees C. The two protocols tested through the use of 100-microliter aliquots containing 178,000 oocytes/mm3 were: I. Treatment at 37 degrees C for 24 h with 1% (v/v) bile plus 0.44% (w/v) sodium bicarbonate. Group A: pretreated with acidified trypsin (pH 2.75) at 37 degrees C for 1 h; Group B: not pretreated. II. Treatment at 37 degrees C for 24 h with 1% (v/v) bile at pH 6 and at pH 8 either with or without 0.44% (w/v) sodium bicarbonate in air or an atmosphere containing 10% (v/v) CO2. Group 1: bile, pH 6; Group 2: bile, pH 6 plus CO2; Group 3: bile, pH 6 plus bicarbonate; Group 4: bile, pH 8 plus bicarbonate; Group 5: bile, pH 6 plus bicarbonate plus CO2; Group 6: bile, pH 8 plus bicarbonate plus CO2; Group 7: bile, pH 8; and Group 8: bile, pH 8 plus CO2. We then assessed the degree of excystation in all the groups by counting the number of intact oocysts in the hemocytometer. For the first protocol, the oocyst count after excystation revealed an average of 28,000 oocysts/mm3 in Group A and 22,000 in Group B. These values indicate excystation frequencies of 84.3% and 87.6% for these two groups, respectively. The corresponding excystation percentages for groups 1-8 of protocol II were 49.5, 56.7, 83.2, 88.3, 88.3, 92.7, and 94.1, respectively. Preincubation with trypsin failed to augment oocyst excystation in Cryptosporidium in any of these experimental circumstances. The optimal conditions for oocyst excystation in these 24 h incubations were thus seen to be in the presence of 1% (v/v) bile at pH 8, and 37 degrees C under an atmosphere of 10% (v/v) CO2.

A novel experimental model for the study and evaluation of experimental vaccines to Actinobacillus pleuropneumoniae

A novel experimental model to study immune protection to Actinobacillus pleuropneumoniae in the rat is described. One-week-old rats born from immunized mothers were challenged intraperitoneally with a suspension of A. pleuropneumoniae serotype 1 and mortality recorded up to 48 h postinfection. Immunization with inactivated whole cells (IWC) or a whole cell extract (WCE) from A. pleuropneumoniae serotype 1 resulted in protection against an homologous challenge, particularly in the case of WCE where protection was observed at the highest challenge dose of approximately 1000 50% lethal doses.