Nitrifying microbial community analysis of nitrite accumulating biofilm reactor by fluorescence in situ hybridization

Biological nitrogen removal via nitrite pathway in wastewater treatment is very important especially in the cost of aeration and as an electron donor for denitrification. Wastewater nitrification and nitrite accumulations were carried out in a biofilm reactor. The biofilm reactor showed almost complete nitrification and most of the oxidized ammonium was present as nitrite at the ammonium load of 1.2 kg N/m3/d. Nitrite accumulation was achieved by the selective inhibition of nitrite oxidizers by free ammonia and oxygen limitation. Nitrite oxidation activity was recovered as soon as the inhibition factor was removed. Fluorescence in situ hybridization studies of the nitrite accumulating biofilm system have shown that genus Nitrosomonas which is specifically hybridized with probe NSM 156 was the dominant nitrifying bacteria while Nitrospira was less abundant than those of normal nitrification systems. Further FISH analysis showed that the combinations of Nitrosomonas and Nitrospira cells were identified as important populations of nitrifying bacteria in an autotrophic nitrifying biofilm system.

Fate of nitrogen in bioreactor landfills: lab-scale in situ aeration in well decomposed MSW

Dissertação para obtenção do Grau de Mestre em Engenharia do ambiente, perfil de engenharia sanitária

Assessing the sources and magnitude of diurnal nitrate variability in the San Joaquin River (California) with an in-situ optical nitrate sensor and dual nitrate isotopes

We investigated diurnal nitrate (NO3-) concentration variability in the San Joaquin River using an in situ optical NO3- sensor and discrete sampling during a 5-day summer period characterized by high algal productivity. Dual NO3- isotopes (delta N-15(NO3) and delta O-18(NO3)) and dissolved oxygen isotopes (delta O-18(DO)) were measured over 2 days to assess NO3- sources and biogeochemical controls over diurnal time-scales. Concerted temporal patterns of dissolved oxygen (DO) concentrations and delta O-18(DO) were consistent with photosynthesis, respiration and atmospheric O-2 exchange, providing evidence of diurnal biological processes independent of river discharge. Surface water NO3- concentrations varied by up to 22% over a single diurnal cycle and up to 31% over the 5-day study, but did not reveal concerted diurnal patterns at a frequency comparable to DO concentrations. The decoupling of delta N-15(NO3) and delta O-18(NO3) isotopes suggests that algal assimilation and denitrification are not major processes controlling diurnal NO3- variability in the San Joaquin River during the study. The lack of a clear explanation for NO3- variability likely reflects a combination of riverine biological processes and time-varying physical transport of NO3- from upstream agricultural drains to the mainstem San Joaquin River. The application of an in situ optical NO3- sensor along with discrete samples provides a view into the fine temporal structure of hydrochemical data and may allow for greater accuracy in pollution assessment.

Charakterisierung von optischen Partikelspektrometern und in-situ Messungen zur Mikrophysik der polaren Stratosphärenwolken

Polare Stratosphärenwolken (PSC), die unterhalb einer Temperatur von etwa -78 °C in polaren Regionen auftreten, üben einen starken Einfluss auf die stratosphärische Ozonschicht aus. Dieser Einfluss erfolgt größtenteils über heterogene chemische Reaktionen, die auf den Oberflächen von Wolkenpartikeln stattfinden. Chemische Reaktionen die dabei ablaufen sind eine Voraussetzung für den späteren Ozonabbau. Des Weiteren verändert die Sedimentation der Wolkenpartikel die chemische Zusammensetzung bzw. die vertikale Verteilung der Spurengase in der Stratosphäre. Für die Ozonchemie spielt dabei die Beseitigung von reaktivem Stickstoff durch Sedimentation Salpetersäure-haltiger Wolkenpartikeln (Denitrifizierung) eine wichtige Rolle. Durch gleichen Sedimentationsprozess von PSC Elementen wird der Stratosphäre des weiteren Wasserdampf entzogen (Dehydrierung). Beide Prozesse begünstigen einen länger andauernden stratosphärischen Ozonabbau im polaren Frühling.rnGerade im Hinblick auf die Denitrifikation durch Sedimentation größerer PSC-Partikel werden in dieser Arbeit neue Resultate von in-situ Messungen vorgestellt, die im Rahmen der RECONCILE-Kampagne im Winter des Jahres 2010 an Bord des Höhenforschungs-Flugzeugs M-55 Geophysica durchgeführt wurden. Dabei wurden in fünf Flügen Partikelgrößenverteilungen in einem Größenbereich zwischen 0,5 und 35 µm mittels auf der Lichtstreuung basierender Wolkenpartikel-Spektrometer gemessen. Da polare Stratosphärenwolken in Höhen zwischen 17 und 30 km auftreten, sind in-situ Messungen vergleichsweise selten, so dass noch einige offene Fragen bestehen bleiben. Gerade Partikel mit optischen Durchmessern von bis zu 35µm, die während der neuen Messungen detektiert wurden, müssen mit theoretischen Einschränkungen in Einklang gebracht werden. Die Größe der Partikel wird dabei durch die Verfügbarkeit der beteiligten Spurenstoffe (Wasserdampf und Salpetersäure), die Sedimentationsgeschwindigkeit, Zeit zum Anwachsen und von der Umgebungstemperatur begrenzt. Diese Faktoren werden in der vorliegenden Arbeit diskutiert. Aus dem gemessenen Partikelvolumen wird beispielsweise unter der Annahme der NAT-Zusammensetzung (Nitric Acid Trihydrate) die äquivalente Konzentration des HNO 3 der Gasphase berechnet. Im Ergebnis wird die verfügbare Konzentration von Salpetersäure der Stratosphäre überschritten. Anschließend werden Hypothesen diskutiert, wodurch das gemessene Partikelvolumen überschätzt worden sein könnte, was z.B. im Fall einer starken Asphärizität der Partikel möglich wäre. Weiterhin wurde eine Partikelmode unterhalb von 2-3µm im Durchmesser aufgrund des Temperaturverhaltens als STS (Supercooled Ternary Solution droplets) identifiziert.rnUm die Konzentration der Wolkenpartikel anhand der Messung möglichst genau berechnen zu können, muss das Messvolumen bzw. die effektive Messfläche der Instrumente bekannt sein. Zum Vermessen dieser Messfläche wurde ein Tröpfchengenerator aufgebaut und zum Kalibrieren von drei Instrumenten benutzt. Die Kalibration mittels des Tröpfchengenerators konzentrierte sich auf die Cloud Combination Probe (CCP). Neben der Messfläche und der Größenbestimmung der Partikel werden in der Arbeit unter Zuhilfenahme von Messungen in troposphärischen Wolken und an einer Wolkensimulationskammer auch weitere Fehlerquellen der Messung untersucht. Dazu wurde unter anderem die statistische Betrachtung von Intervallzeiten einzelner Messereignisse, die in neueren Sonden aufgezeichnet werden, herangezogen. Letzteres ermöglicht es, Messartefakte wie Rauschen, Koinzidenzfehler oder „Shattering“ zu identifizieren.rn

Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community

A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO3-.N mg of mixed-liquor volatile suspended solids (MLVSS)(-1) h(-1) to a steady-state value of 0.06 mg of NO3-.N mg of MLVSS-1 h(-1) over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [C-13] methanol to biomark the DNA of the denitrifiers. The extracted [C-13]DNA and [C-12]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [C-13]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [C-12]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [C-14] methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.

Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography

The acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (SIP). [C-13]acetate was used in SIP to label the DNA of the denitrifiers. The [C-13]DNA fraction that was extracted was subjected to a full-cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the C-13 library were closely related to the bacterial families Comamonadaceae and Rhodocyclaceae in the class Betaproteobacteria. Seven oligonucleotide probes for use in fluorescent in situ hybridization (FISH) were designed to specifically target these clones. Application of these probes to the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated for 16 days revealed that there was a significant positive correlation between the CFDSBR denitrification rate and the relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH-microautoradiography demonstrated that the DEN581 and DEN124 probe-targeted cells that dominated the CFDSBR were capable of taking Up [C-14] acetate under anoxic conditions. Initially, DEN444 and DEN1454 probe-targeted bacteria also dominated the CFDSBR biomass, but eventually DEN581 and DEN124 probe-targeted bacteria were the dominant bacterial groups. All probe-targeted bacteria assessed in this study were denitrifiers capable of utilizing acetate as a source of carbon. The rapid increase in the number of organisms positively correlated with the immediate increase in denitrification rates observed by plant operators when acetate is used as an external source of carbon to enhance denitrification. We suggest that the impact of bacteria on activated sludge subjected to intermittent acetate supplementation should be assessed prior to the widespread use of acetate in the waste-water industry to enhance denitrification.

The use of fluorescence in situ hybridization in the diagnosis of hidden mosaicism: apropos of three cases of sex chromosome anomalies

FISH has been used as a complement to classical cytogenetics in the detection of mosaicism in sex chromosome anomalies. The aim of this study is to describe three cases in which the final diagnosis could only be achieved by FISH. Case 1 was an 8-year-old 46,XY girl with normal female genitalia referred to our service because of short stature. FISH analysis of lymphocytes with probes for the X and Y centromeres identified a 45,X/46,X,idic(Y) constitution, and established the diagnosis of Turner syndrome. Case 2 was a 21-month-old 46,XY boy with genital ambiguity (penile hypospadias, right testis, and left streak gonad). FISH analysis of lymphocytes and buccal smear identified a 45,X/46,XY karyotype, leading to diagnosis of mixed gonadal dysgenesis. Case 3 was a 47,XYY 19-year-old boy with delayed neuromotor development, learning disabilities, psychological problems, tall stature, small testes, elevated gonadotropins, and azoospermia. FISH analysis of lymphocytes and buccal smear identified a 47,XYY/48,XXYY constitution. Cases 1 and 2 illustrate the phenotypic variability of the 45,X/46,XY mosaicism, and the importance of detection of the 45,X cell line for proper management and follow-up. In case 3, abnormal gonadal function could be explained by the 48,XXYY cell line. The use of FISH in clinical practice is particularly relevant when classical cytogenetic analysis yields normal or uncertain results in patients with features of sex chromosome aneuploidy. Arq Bras Endocrinol Metab. 2012;56(8):545-51

Scanning electron microscopic study of the in situ effect of salivary stimulation on erosion and abrasion in human and bovine enamel

This in situ study investigated, using scanning electron microscopy, the effect of stimulated saliva on the enamel surface of bovine and human substrates submitted to erosion followed by brushing abrasion immediately or after one hour. During 2 experimental 7-day crossover phases, 9 previously selected volunteers wore intraoral palatal devices, with 12 enamel specimens (6 human and 6 bovine). In the first phase, the volunteers immersed the device for 5 minutes in 150 ml of a cola drink, 4 times a day (8h00, 12h00, 16h00 and 20h00). Immediately after the immersions, no treatment was performed in 4 specimens (ERO), 4 other specimens were immediately brushed (0 min) using a fluoride dentifrice and the device was replaced into the mouth. After 60 min, the other 4 specimens were brushed. In the second phase, the procedures were repeated but, after the immersions, the volunteers stimulated the salivary flow rate by chewing a sugar-free gum for 30 min. Enamel superficial alterations of all specimens were then evaluated using a scanning electron microscope. Enamel prism core dissolution was seen on the surfaces submitted to erosion, while on those submitted to erosion and to abrasion (both at 0 and 60 min) a more homogeneous enamel surface was observed, probably due to the removal of the altered superficial prism layer. For all the other variables - enamel substrate and salivary stimulation -, the microscopic pattern of the enamel specimens was similar.

The influence of residual salivary fluoride from dentifrice on enamel erosion: an in situ study

The objective of this study was to assess the salivary residual effect of fluoride dentifrice on human enamel subjected to an erosive challenge. This crossover in situ study was performed in two phases (A and B), involving ten volunteers. In each phase, they wore acrylic palatal appliances, each containing 3 human enamel blocks, during 7 days. The blocks were subjected to erosion by immersion of the appliances in a cola drink for 5 minutes, 4 times a day. Dentifrice was used to brush the volunteers’ teeth, 4 times a day, during 1 minute, before the appliance was replaced into the mouth. In phases A and B the dentifrices used had the same formulation, except for the absence (PD) or presence (FD) of fluoride, respectively. Enamel alterations were determined using profilometry, microhardness (%SMHC), acid- and alkali-soluble F analysis. The data were tested using ANOVA (p < 0.05). The concentrations (mean ± SD) of alkali- and acid-soluble F (µgF/cm²) were, respectively, PD: 1.27ª ± 0.70/2.24A ± 0.36 and FD: 1.49ª ± 0.44/2.24A ± 0.67 (p > 0.05). The mean wear values (± SD, µm) were PD: 3.63ª ± 1.54 and FD: 3.54ª ± 0.90 (p > 0.05). The mean %SMHC values (± SD) were PD: 89.63ª ± 4.73 and FD: 87.28ª ± 4.01 (p > 0.05). Thus, we concluded that the residual fluoride from the fluoride-containing dentifrice did not protect enamel against erosion.

Vertical alveolar crest bone maintenance around implants in two-stage surgery: an in situ study in dogs

The aim of this study was to evaluate in situ changes in the alveolar crest bone height around immediate implant-supported crowns in comparison to tooth-supported crowns (control) with the cervical margins located at the bone crest level, without occlusal load. In Group I, after extraction of 12 mandibular premolars from 4 adult dogs, implants from Branemark System (MK III TiU RP 4.0 x 11.5 mm) were placed to retain complete acrylic crowns. In Group II, premolars were prepared to receive complete metal crowns. Sixteen weeks after placement of the crowns (38 weeks after tooth extraction), the height of the alveolar bone crest was measured with a digital caliper. Data were analyzed statistically by the Mann-Whitney test at 5% significance level. The in situ analysis showed no statistically significant difference (p=0.880) between the implant-supported and the tooth-supported groups (1.528 + 0.459 mm and 1.570 + 0.263 mm, respectively). Based on the findings of the present study, it may be concluded that initial peri-implant bone loss may result from the remodeling process necessary to establish the biological space, similar to which occurs with tooth-supported crowns.

Expressão da proteína erbB-2 e dos receptores de hormônios na transição das regiões in situ para invasora de tumores da mama

OBJETIVOS: avaliar a expressão de erbB-2 e dos receptores hormonais para estrógeno e progesterona (RE/RP) nas regiões de transição entre as frações in situ e invasoras de neoplasias ductais da mama (CDIS e CDI, respectivamente). MÉTODOS: oitenta e cinco casos de neoplasias mamárias, contendo regiões contíguas de CDIS e CDI, foram selecionados. Espécimes histológicos das áreas de CDIS e de CDI foram obtidos através da técnica de tissue microarray (TMA). As expressões da erbB-2 e dos RE/RP foram avaliadas por meio de imunoistoquímica convencional. A comparação da expressão da erbB-2 e dos RE/RP nas frações in situ e invasoras da mama foi realizada com emprego do teste de McNemar. Os intervalos de confiança foram determinados em 5% (p=0,05). Foram calculados coeficientes de correlação intraclasse (ICC) para avaliar a concordância na tabulação cruzada da expressão de erbB-2 e RE/RP nas frações de CDIS e CDI. RESULTADOS: a expressão da erbB-2 não diferiu entre as áreas de CDIS e CDI (p=0,38). Comparando caso a caso suas áreas de CDIS e CDI, houve boa concordância na expressão da erbB-2 (coeficiente de correlação intraclasse, ICC=0,64), dos RP (ICC = 0,71) e dos RE (ICC = 0,64). Considerando apenas tumores cujo componente in situ apresentasse áreas de necrose (comedo), o ICC para erbB-2 foi de 0,4, comparado a 0,6 no conjunto completo de casos. Os ICC não diferiram substancialmente daqueles obtidos com o conjunto completo de espécimes em relação aos RE/RP: para RE, ICC=0,7 (versus 0,7 no conjunto completo), e para RP, ICC=0,7 (versus 0,6 no conjunto completo). CONCLUSÕES: nossos achados sugerem que as expressões de erbB-2 e RE/RP não diferem nos componentes contíguos in situ e invasivo em tumores ductais da mama.

Dating minerals by ID-TIMS geochronology at times of in situ analysis: selected case studies from the CPGeo-IGc-USP laboratory

Since 1964, the Center for Geochronological Research - CPGeo, one of the interdepartmental centers of the Instituto de Geociências (IG) of São Paulo University, has developed studies related to several geological processes associated with different rock types. Thermal Ionization Mass Spectrometry Isotopic Dilution (ID-TIMS) has been the technique widely used in the CPGeo U-Pb Laboratory. It provides reliable and accurate results in age determination of superposed events. However, the open-system behavior such as Pb-loss, the inheritance problem and metamictization processes allow and impel us to a much richer understanding of the power and limitations of U-Pb geochronology and thermochronology. In this article, we present the current methodology used at the CPGeo-IGc-USP U-Pb laboratory, the improvements on ID-TIMS method, and report high-precision U-Pb data from zircon, monazite, epidote, titanite, baddeleyite and rutile from different rock types of several domains of the Brazilian south-southeast area, Argentina and Uruguay.

Sudan Black B treatment reduces autofluorescence and improves resolution of in situ hybridization specific fluorescent signals of brain sections

Interference by autofluorescence is one of the major concerns of immunofluorescence analysis of in situ hybridization-based diagnostic assays. We present a useful technique that reduces autofluorescent background without affecting the tissue integrity or direct immunofluorescence signals in brain sections. Using six different protocols, such as ammonia/ethanol, Sudan Black B (SBB) in 70% ethanol, photobleaching with UV light and different combinations of them in both formalin-fixed paraffin-embedded and frozen human brain tissue sections, we have found that tissue treatment of SBB in a concentration of 0.1% in 70% ethanol is the best approach to reduce/eliminate tissue autofluorescence and background, while preserving the specific fluorescence hybridization signals. This strategy is a feasible, non-time consuming method that provides a reasonable compromise between total reduction of the tissue autofluorescence and maintenance of specific fluorescent labels.

Influence of a polyclonal antibody preparation on the in situ degradability of three energy sources

The objective of this study was to evaluate the effect of a polyclonal antibody preparation (PAP) against specific ruminal bacteria on the in situ degradability of dry-grounded maize grain (DMG), high moisture maize silage (HMMS) starch and citrus pulp (CiPu) pectin. Nine ruminally cannulated cows were used in a 3 x 3 Latin square design, replicated three times in a factorial arrangement of treatments of two rumen modifiers represented by monensin and PAP plus a control group, and the three energy sources (DMG, HMMS and CiPu). Each period had 21 days, where 16 were used for adaptation to treatment and five for data collection. The group treated with PAP showed an effect on the soluble fraction (""a"") of DMG starch, decreasing it by respectively 45.3% and 45.4% compared to the CON and MON groups. No effect of PAP was observed for any in situ degradability parameters of starch from HMMS or pectin of CiPu. It was concluded that the polyclonal antibody preparation had limited effect on the in situ degradability of the tested energy sources.

In situ delivery of bone marrow cells and mesenchymal stem cells improves cardiovascular function in hypertensive rats submitted to myocardial infarction

This work aimed to evaluate cardiac morphology/function and histological changes induced by bone marrow cells (BMCs) and cultured mesenchymal stem cells (MSCs) injected at the myocardium of spontaneously hypertensive rats (SHR) submitted to surgical coronary occlusion. Female syngeneic adult SHR, submitted (MI) or not (C) to coronary occlusion, were treated 24 h later with in situ injections of normal medium (NM), or with MSCs (MSC) or BMCs (BM) from male rats. The animals were evaluated after 1 and 30 days by echocardiography, histology of heart sections and PCR for the Y chromosome. Improved ejection fraction and reduced left ventricle infarcted area were observed in MSC rats as compared to the other experimental groups. Treated groups had significantly reduced lesion tissue score, increased capillary density and normal (not-atrophied) myocytes, as compared to NM and C groups. The survival rate was higher in C, NM and MSC groups as compared to MI and BM groups. In situ injection of both MSCs and BMCs resulted in improved cardiac morphology, in a more physiological model of myocardial infarction represented by surgical coronary occlusion of spontaneously hypertensive rats. Only treatment with MSCs, however, ameliorated left ventricle dysfunction, suggesting a positive role of these cells in heart remodeling in infarcted hypertensive subjects.