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Studies are urgently needed to characterize immunogenicity, efficacy, and safety of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccines in kidney transplant (KT) recipients, excluded from major clinical trials. Complex ELISPOT and other cellular response techniques have been applied, but simpler tools are needed. An easy-to-use real-world monitoring of SARS-CoV-2 IgG antibodies against the Spike protein and QuantiFERON® SARS-CoV-2 IFNI³ release assay (IGRA) were performed at baseline and 28 days after the second dose in KT recipients and controls (dialysis patients and healthy ones). All healthy controls and >95% dialysis controls became positive for anti-S IgG antibodies, while only 63.3% of KT patients seroconverted with a very low antibody level. A positive IGRA was documented in 96.9% of controls, 89.3% peritoneal dialysis, 77.6% hemodialysis, 61.3% of KT patients transplanted more than 1 year ago and only 36% of those transplanted within the previous 12 months. Overall, 100% of healthy controls, 95.4% of dialysis patients and 78.8% KT recipients developed any immune response (humoral and/or cellular) against SARS-CoV-2. KT patients showed low rates of immune responses to mRNA Coronavirus infectious disease 2019 vaccines, especially those with recent transplantations. Simple humoral and cellular monitoring is advisable, so that repeated doses may be scheduled according to the results.

The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.

Assignment of Morelet's crocodile Crocodylus moreletii individuals into size groups or classes based on ecological and morphological similarities has not yet been associated with species-specific ontogeny related changes. Age or size of first reproductive behavior is not precisely known for C. moreletii, but differences in allometric patterns and relative cranial size between juveniles and adults might be used as an indicator of sexual maturity. In this study, a regression tree analysis was used to investigate the relationship between age and body size in 1266 crocodiles by using both simple and generalized linear models, with gender and origin (captivity or wild) as factors. Total length (TL), snout–vent length (SVL) and cranial length (CL) were used as predictor variables and the logarithm of body mass as the response variable. Four length intervals with well-defined thresholds (514, 899 and 1497 mm of TL) were established using all three predictors (TL, SVL and CL). Relationship between SVL and TL was described, and a strong positive relationship (r2 = 0.98), unaffected by crocodile gender, was observed. The observed CL–TL and CL–SVL relationships were also positive but significantly different between males and females (p < 0.001) and length interval classes (p = 0.01). These results suggest that our estimated size thresholds seem to correspond to important ontogenetic changes in C. moreletii and that sexual maturity is closely related to size in this species, where sexual dimorphism in body length occurs, particularly in large individuals (size group IV).

This research aimed to improve dairy production and increase the income of dairy farmers using locally available feed resources. Small-scale milk producers rely heavily on available feed resources in the locality which are either indigenous in the area or introduced species for feed and nutrition of their dairy cattle and buffalos. Their milk output depends mainly on seasonal fluctuations in the quality and quantity of natural forage. Crop residues such as corn stover and rice straw which are high in fiber but low in nutrients serve as a feed supplement and filler to the daily diets of dairy cattle and buffalos. Cagayan Valley is an ear of top corn and rice-producing region. The potential of crop residues as feed supplements or raw materials of dairy cattle/buffalo feed mix is great. But dairy farmers still face the scarcity problem of quality feed resources for dairy animals especially during the dry season. The supply of forage is very low during the dry spell. Inadequate feed mix and low nutritive value of feed mix result in low or no milk production. Producing green corn and ensiling it to produce green corn silage preserves and prolong the storage life of forages. In this way, a stable supply of feed mix for dairy animals is assured year-round. Type of Paper: Empirical. Keywords: adoption and commercialization, dairy industry, financial viability, green-corn silage production, indigenous grasses, smallholder farmers.

In vivo diagnostic imaging of bacterial infections is currently reliant on targeting their metabolic pathways, an ineffective method to identify microbial species with low metabolic activity. Here, we establish HS-198 as a small-molecule fluorescent conjugate that selectively targets the highly conserved bacterial protein HtpG (high-temperature protein G), within Borrelia burgdorferi, the bacterium responsible for Lyme disease. We describe the use of HS-198 to target morphologic forms of B. burgdorferi in both the logarithmic growth phase and the metabolically dormant stationary phase as well as in inactivated spirochetes. Furthermore, in a murine infection model, systemically injected HS-198 identified B. burgdorferi as revealed by imaging in postnecropsy tissue sections. These findings demonstrate how small-molecule probes directed at conserved bacterial protein targets can function to identify the microbe using noninvasive imaging and potentially as scaffolds to deliver antimicrobial agents to the pathogen.

The nuclear lamina supports many functions, including maintaining nuclear structure and gene expression control, and correct spatio-temporal assembly is vital to meet these activities. Recently, multiple lamina systems have been described that, despite independent evolutionary origins, share analogous functions. In trypanosomatids the two known lamina proteins, NUP-1 and NUP-2, have molecular masses of 450 and 170 kDa, respectively, which demands a distinct architecture from the ∼60 kDa lamin-based system of metazoa and other lineages. To uncover organizational principles for the trypanosome lamina we generated NUP-1 deletion mutants to identify domains and their arrangements responsible for oligomerization. We found that both the N- and C-termini act as interaction hubs, and that perturbation of these interactions impacts additional components of the lamina and nuclear envelope. Furthermore, the assembly of NUP-1 terminal domains suggests intrinsic organizational capacity. Remarkably, there is little impact on silencing of telomeric variant surface glycoprotein genes. We suggest that both terminal domains of NUP-1 have roles in assembling the trypanosome lamina and propose a novel architecture based on a hub-and-spoke configuration., Summary: The arrangement of the lamina in trypanosomatids has architectural differences to the metazoan system.

Made available in DSpace on 2021-06-25T10:24:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Coffee berry borer—CBB (Hypothenemus hampei) is a globally important economic pest of coffee (Coffea spp.). Despite current insect control methods for managing CBB, development of future control strategies requires a better understanding of its biology and interaction with its host plant. Towards this objective, we performed de novo CBB genome and transcriptome sequencing, improved CBB genome assembly and predicted 18,765 protein-encoding genes. Using genome and transcriptome data, we annotated the genes associated with chemosensation and found a reduced gene repertoire composed by 67 odorant receptors (ORs), 62 gustatory receptors (GRs), 33 ionotropic receptors (IRs) and 29 odorant-binding proteins (OBPs). In silico transcript abundance analysis of these chemosensory genes revealed expression enrichment in CBB adults compared with larva. Detection of differentially expressed chemosensory genes between males and females is likely associated with differences in host-finding behavior between sexes. Additionally, we discovered male-specific genome content and identified candidate male-specific expressed genes on these scaffolds, suggesting that a Y-like chromosome may be involved in the CBB’s functional haplodiploid mechanism of sex determination. National Coffee Research Center-CENICAFE Estadual Paulista UNESP-Univ Manaaki Whenua–Landcare Research, PO Box 69040 Department of Entomology Pennsylvania State University Department of Biology Duke University Instituto de Investigación en Microbiología Y Biotecnología Agroindustrial Universidad Católica de Manizales Department of Entomology Purdue University Estadual Paulista UNESP-Univ

In vivo diagnostic imaging of bacterial infections is currently reliant on targeting their metabolic pathways, an ineffective method to identify microbial species with low metabolic activity. Here we establish HS-198 as a small molecule-fluorescent conjugate that selectively targets the highly conserved bacterial protein, HtpG (High temperature protein G), within B. burgdorferi, the bacteria responsible for Lyme Disease. We describe the use of HS-198 to target morphologic forms of B. burgdorferi in both the logarithmic growth phase and the metabolically dormant stationary phase. Furthermore, in a murine infection model, systemically injected HS-198 identified B. burgdorferi as revealed by imaging in post necropsy tissue sections. These findings demonstrate how small molecule probes directed at conserved bacterial protein targets can function to identify the microbe using non-invasive imaging and potentially as scaffolds to deliver antimicrobial agents to the pathogen.

This study determines the suitability of using blood plasma and dermal scute samples as a non-destructive technique for monitoring the health of Morelet’s crocodiles and the presence of organochlorine pesticides (OCPs) in the environment. We collected samples (blood plasma and caudal scutes) from 30 Morelet’s crocodiles (C. moreletii); 16 were wild, and 14 were captive. The 30 samples were analyzed for 24 different OCPs and compared in 10 groups based on chemical affinities (isomers and degradation products). Endrin and Chlordane were the most frequent OCP groups detected, found in 63% and 57% of the samples, respectively. We did not find significant differences in OCP concentrations in tissues (plasma and scutes) between wild and captive crocodiles; there were also no significant correlations among concentrations in tissues. Blood plasma and scutes are good indicators of OCP body burdens in Morelet’s crocodiles for monitoring the presence and fluctuation of toxicity in the environment; however, it is not possible to infer the concentrations in one tissue from the concentrations detected in the other tissue. Selecting which tissues to use for OCP analyses depends on the specific objectives of the researcher. For research, on individual health and local exposure to contaminants, plasma is suitable. For evaluating the presence over time of OCPs in the environment, the caudal dermal scutes are the most appropriate tissue. Overall, it is important to take into account the body condition to avoid biases due to bioamplification effects.

Maternal nutritional challenges during fetal and neonatal development result in developmental programming of multiple offspring organ systems including brain maturation and function. A maternal low-protein diet during pregnancy and lactation impairs associative learning and motivation. We evaluated effects of a maternal low-protein diet during gestation and/or lactation on male offspring spatial learning and hippocampal neural structure. Control mothers (C) ate 20% casein and restricted mothers (R) 10% casein, providing four groups: CC, RR, CR, and RC (first letter pregnancy, second lactation diet). We evaluated the behavior of young adult male offspring around postnatal day 110. Corticosterone and ACTH were measured. Males were tested for 2 days in the Morris water maze (MWM). Stratum lucidum mossy fiber (MF) area, total and spine type in basal dendrites of stratum oriens in the hippocampal CA3 field were measured. Corticosterone and ACTH were higher in RR vs. CC. In the MWM acquisition test CC offspring required two, RC three, and CR seven sessions to learn the maze. RR did not learn in eight trials. In a retention test 24 h later, RR, CR, and RC spent more time locating the platform and performed fewer target zone entries than CC. RR and RC offspring spent less time in the target zone than CC. MF area, total, and thin spines were lower in RR, CR, and RC than CC. Mushroom spines were lower in RR and RC than CC. Stubby spines were higher in RR, CR, and RC than CC. We conclude that maternal low-protein diet impairs spatial acquisition and memory retention in male offspring, and that alterations in hippocampal presynaptic (MF), postsynaptic (spines) elements and higher glucocorticoid levels are potential mechanisms to explain these learning and memory deficits.

SUMMARYEukaryotic 5S rRNA, synthesized by RNA polymerase III (Pol III), is an essential component of the large ribosomal subunit. Most organisms contain hundreds of 5S rRNA genes organized into tandem arrays. However, the genome of the protozoan parasiteLeishmania majorcontains only 11 copies of the 5S rRNA gene, which are interspersed and associated with other Pol III-transcribed genes. Here we report that, in general, the number and order of the 5S rRNA genes is conserved between different species ofLeishmania. While in most organisms 5S rRNA genes are normally associated with the nucleolus, combined fluorescentin situhybridization and indirect immunofluorescence experiments showed that 5S rRNA genes are mainly located at the nuclear periphery inL. major. Similarly, the tandemly repeated 5S rRNA genes inTrypanosoma cruziare dispersed throughout the nucleus. In contrast, 5S rRNA transcripts inL. majorwere localized within the nucleolus, and scattered throughout the cytoplasm, where mature ribosomes are located. Unlike other rRNA species, stable antisense RNA complementary to 5S rRNA is not detected inL. major.

Analysis of external injuries in captive and free-ranging Morelet's crocodiles Crocodylus moreletii was performed in the northern wetlands of Campeche, Mexico. From March to September of 2007, a total of 52 free-ranging and 51 captive Morelet's crocodiles were studied. Captive crocodiles presented significantly more injuries. Sixteen free-ranging crocodiles presented some type of lesion, mostly superficial abrasions. Nineteen captive crocodiles presented lesions, mostly incisions from agonistic interactions. Overall, the injuries with highest prevalence were the incisions. The tail was the most frequently injured body region. Injuries were more common in adults than in other size classes. Conversely, the presence of lesions caused by the parasite Paratrichosoma spp. was greater in crocodiles captured in the coastal channels (mangrove habitat). The information presented here is important to understand some of the effects of individual interactions and to foresee and manage the consequences of conservation and management activities of crocodile populations.

DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.

Surveillance for evidence of West Nile virus (WNV) infection in Morelet’s crocodiles (Crocodylus moreletii) was conducted in Campeche State, Mexico, in 2007. Sera from 62 crocodiles (32 free-ranging and 30 captive) were assayed for antibodies to WNV by epitope-blocking enzyme-linked immunosorbent assay. Antibodies to WNV were detected in 13 (41%) wild and nine (30%) captive crocodiles, and the overall antibody prevalence was 35%. Although evidence of WNV infection in captive crocodiles has been reported in Mexico, we provide the first evidence of WNV exposure in wild crocodiles in Mexico.

Horizontal gene transfer (HGT) involves the nonsexual transmission of genetic material across species boundaries. Although often detected in prokaryotes, examples of HGT involving animals are relatively rare, and any evolutionary advantage conferred to the recipient is typically obscure. We identified a gene ( HhMAN1 ) from the coffee berry borer beetle, Hypothenemus hampei , a devastating pest of coffee, which shows clear evidence of HGT from bacteria. HhMAN1 encodes a mannanase, representing a class of glycosyl hydrolases that has not previously been reported in insects. Recombinant HhMAN1 protein hydrolyzes coffee berry galactomannan, the major storage polysaccharide in this species and the presumed food of H. hampei . HhMAN1 was found to be widespread in a broad biogeographic survey of H. hampei accessions, indicating that the HGT event occurred before radiation of the insect from West Africa to Asia and South America. However, the gene was not detected in the closely related species H. obscurus (the tropical nut borer or “false berry borer”), which does not colonize coffee beans. Thus, HGT of HhMAN1 from bacteria represents a likely adaptation to a specific ecological niche and may have been promoted by intensive agricultural practices.

In situ hybridization methods enable the mapping of mRNA expression within intact biological samples. With current approaches, it is challenging to simultaneously map multiple target mRNAs within whole-mount vertebrate embryos, representing a significant limitation in attempting to study interacting regulatory elements in systems most relevant to human development and disease. Here, we report a multiplexed fluorescent in situ hybridization method based on orthogonal amplification with hybridization chain reactions (HCR). With this approach, RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. The programmability and sequence specificity of these amplification cascades enable multiple HCR amplifiers to operate orthogonally at the same time in the same sample. Robust performance is achieved when imaging five target mRNAs simultaneously in fixed whole-mount and sectioned zebrafish embryos. HCR amplifiers exhibit deep sample penetration, high signal-to-background ratios and sharp signal localization.

Aims: To study how the antimicrobial and antioxidant activities of Lippia graveolens essential oils with different composition are affected after the microencapsulation process with β-cyclodextrin (βCD). Methods and results: Three Mexican oregano essential oils (EOs) with different carvacrol/thymol/p-cymene ratios (38 : 3 : 32, 23 : 2 : 42, 7 : 19 : 35) were used in this study. Microencapsulation was carried out by spray-drying. Antimicrobial activities were measured as MBC (minimal bactericidal concentration) using 0·05%/0·10%/0·20% (w/v) dilutions of EOs against Escherichia coli ATCC 11229, Pseudomonas aeruginosa ATCC 9027 and Staphylococcus aureus ATCC 6538. Antioxidant activities were determined by the 2,2′-diphenyl-1-picrylhydrazil (DPPH) method. EOs showed antimicrobial and antioxidant activity, but microencapsulation preserved the antimicrobial activity in all cases and increased the antioxidant activity from four- to eightfold. Conclusions: Although the Lippia essential oils were from the same species, their composition affects the biological activities before and after the microencapsulation process, as well as encapsulation efficiency. Our study supports the fact that microencapsulation of EOs in β-cyclodextrin preserves the antimicrobial activity, improves the antioxidant activity and acts as a protection for EOs main compounds. Significance and Impact of the Study: Microencapsulation affects positively EOs main compounds, improves antioxidant activity and retains antimicrobial activity, enhancing the quality of the oils.

Neuropeptide signaling at the cell surface is regulated by metalloendopeptidases, which degrade peptides in the extracellular fluid, and β-arrestins, which interact with G protein-coupled receptors (GPCRs) to mediate desensitization. β-Arrestins also recruit GPCRs and mitogen-activated protein kinases to endosomes to allow internalized receptors to continue signaling, but the mechanisms regulating endosomal signaling are unknown. We report that endothelin-converting enzyme-1 (ECE-1) degrades substance P (SP) in early endosomes of epithelial cells and neurons to destabilize the endosomal mitogen-activated protein kinase signalosome and terminate signaling. ECE-1 inhibition caused endosomal retention of the SP neurokinin 1 receptor, β-arrestins, and Src, resulting in markedly sustained ERK2 activation in the cytosol and nucleus, whereas ECE-1 overexpression attenuated ERK2 activation. ECE-1 inhibition also enhanced SP-induced expression and phosphorylation of the nuclear death receptor Nur77, resulting in cell death. Thus, endosomal ECE-1 attenuates ERK2-mediated SP signaling in the nucleus to prevent cell death. We propose that agonist availability in endosomes, here regulated by ECE-1, controls β-arrestin-dependent signaling of endocytosed GPCRs.

Agonist-induced internalization of somatostatin receptors (ssts) determines subsequent cellular responsiveness to peptide agonists and influences sst receptor scintigraphy. To investigate sst2A trafficking, rat sst2A tagged with epitope was expressed in human embryonic kidney cells and tracked by antibody labeling. Confocal microscopical analysis revealed that stimulation with sst and octreotide induced internalization of sst2A. Internalized sst2A remained sequestrated within early endosomes, and 60 min after stimulation, internalized sst2A still colocalized with β-arrestin1-enhanced green fluorescence protein (EGFP), endothelin-converting enzyme-1 (ECE-1), and rab5a. Internalized 125I-Tyr11-SST-14 was rapidly hydrolyzed by endosomal endopeptidases, with radioactive metabolites being released from the cell. Internalized 125I-Tyr1-octreotide accumulated as an intact peptide and was released from the cell as an intact peptide ligand. We have identified ECE-1 as one of the endopeptidases responsible for inactivation of internalized SST-14. ECE-1-mediated cleavage of SST-14 was inhibited by the specific ECE-1 inhibitor, SM-19712, and by preventing acidification of endosomes using bafilomycin A1. ECE-1 cleaved SST-14 but not octreotide in an acidic environment. The metallopeptidases angiotensin-1 converting enzyme and ECE-2 did not hydrolyze SST-14 or octreotide. Our results show for the first time that stimulation with SST-14 and octreotide induced sequestration of sst2A into early endosomes and that endocytosed SST-14 is degraded by endopeptidases located in early endosomes. Furthermore, octreotide was not degraded by endosomal peptidases and was released as an intact peptide. This mechanism may explain functional differences between octreotide and SST-14 after sst2A stimulation. Moreover, further investigation of endopeptidase-regulated trafficking of neuropeptides may result in novel concepts of neuropeptide receptor inactivation in cancer diagnosis.

Although cell surface metalloendopeptidases degrade neuropeptides in the extracellular fluid to terminate signaling, the function of peptidases in endosomes is unclear. We report that isoforms of endothelin-converting enzyme-1 (ECE-1a-d) are present in early endosomes, where they degrade neuropeptides and regulate post-endocytic sorting of receptors. Calcitonin gene-related peptide (CGRP) co-internalizes with calcitonin receptor-like receptor (CLR), receptor activity-modifying protein 1 (RAMP1), beta-arrestin2, and ECE-1 to early endosomes, where ECE-1 degrades CGRP. CGRP degradation promotes CLR/RAMP1 recycling and beta-arrestin2 redistribution to the cytosol. ECE-1 inhibition or knockdown traps CLR/RAMP1 and beta-arrestin2 in endosomes and inhibits CLR/RAMP1 recycling and resensitization, whereas ECE-1 overexpression has the opposite effect. ECE-1 does not regulate either the resensitization of receptors for peptides that are not ECE-1 substrates (e.g., angiotensin II), or the recycling of the bradykinin B(2) receptor, which transiently interacts with beta-arrestins. We propose a mechanism by which endosomal ECE-1 degrades neuropeptides in endosomes to disrupt the peptide/receptor/beta-arrestin complex, freeing internalized receptors from beta-arrestins and promoting recycling and resensitization.

Calcitonin receptor-like receptor (CLR) and the receptor activity-modifying protein 1 (RAMP1) comprise a receptor for calcitonin gene-related peptide (CGRP). Although CGRP induces endocytosis of CLR/RAMP1, little is known about post-endocytic sorting of these proteins. We observed that the duration of stimulation with CGRP markedly affected post-endocytic sorting of CLR/RAMP1. In HEK and SK-N-MC cells, transient stimulation (10(-7) M CGRP, 1 h), induced CLR/RAMP1 recycling with similar kinetics (2-6 h), demonstrated by labeling receptors in living cells with antibodies to extracellular epitopes. Recycling of CLR/RAMP1 correlated with resensitization of CGRP-induced increases in [Ca(2+)](i). Cycloheximide did not affect resensitization, but bafilomycin A(1), an inhibitor of vacuolar H(+)-ATPases, abolished resensitization. Recycling CLR and RAMP1 were detected in endosomes containing Rab4a and Rab11a, and expression of GTPase-defective Rab4aS22N and Rab11aS25N inhibited resensitization. After sustained stimulation (10(-7) M CGRP, >2 h), CLR/RAMP1 trafficked to lysosomes. RAMP1 was degraded approximately 4-fold more rapidly than CLR (RAMP1, 45% degradation, 5 h; CLR, 54% degradation, 16 h), determined by Western blotting. Inhibitors of lysosomal, but not proteasomal, proteases prevented degradation. Sustained stimulation did not induce detectable mono- or polyubiquitination of CLR or RAMP1, determined by immunoprecipitation and Western blotting. Moreover, a RAMP1 mutant lacking the only intracellular lysine (RAMP1K142R) internalized and was degraded normally. Thus, after transient stimulation with CGRP, CLR and RAMP1 traffic from endosomes to the plasma membrane, which mediates resensitization. After sustained stimulation, CLR and RAMP1 traffic from endosomes to lysosomes by ubiquitin-independent mechanisms, where they are degraded at different rates.

Little is known about nucleosome structure and epigenetic regulation of transcription of rRNA genes in early-branched eukaryotes. Here we analyze the chromatin architecture and distribution of some histone modifications in the rRNA genes in the parasitic protozoon Leishmania major. Southern blots of MNase-partially-digested chromatin with DNA probes spanning the whole rRNA gene repeat showed that the intergenic spacer presents a tight nucleosomal structure, whereas the promoter region is practically devoid of nucleosomes. Intermediate levels of nucleosomes were found in the rRNA coding regions. ChIP assays allowed us to determine that H3K14ac, H3K23ac and H3K27ac, epigenetics marks that are generally associated with activation of transcription, are enriched in the promoter region. In contrast, H4K20me3, which is generally related to transcriptional silencing, was absent from the promoter region and intergenic spacer and enriched in the coding region. Interestingly, the distribution pattern for H3K9me3, generally linked to heterochromatin formation, was very similar to the distribution observed with the euchromatin marks, suggesting that this modification could be involved in transcriptional activation of rRNA genes in L. major.

The search for better surgical repair of nerve injuries should be aimed at uncovering alternatives that not only are efficient, but also enhance nerve growth. The purpose of this study was to compare functional nerve responses following repair with either a traditional microsuture technique or Quixil human fibrin sealant. Thirty female Lewis rats received transection of the right sciatic nerve. Nerve repair was achieved with either epineurial microsuture (n = 15) or Quixil fibrin glue (n = 15). Functional results were assessed at 2, 6, and 12 weeks postoperatively with walking-track analysis. Electrophysiologic nerve recordings were also performed 12 weeks postoperatively. Rats receiving Quixil nerve repair returned to baseline performance on the walking-track analysis significantly faster than those with microsuture repairs (6 and 12 weeks postoperatively; p < 0.0001). Recovery of nerve conduction velocities and wave amplitudes was also significantly better in the nerves repaired with Quixil than in those repaired with microsuture (p's < 0.0001). Quixil human fibrin sealant is a good alternative to traditional microsuture nerve repair techniques.

A study was performed to diagnose tuberculosis by smear, culture, and nucleic acid amplification. The study was comprised of two independent arms. Each arm used a different specimen processing method; in one arm, all specimens were processed with N -acetyl- l -cysteine-sodium hydroxide, and in the other arm, all specimens were processed with C 18 -carboxypropylbetaine and lytic enzymes. In each arm, all processed sediments were split for analysis by auramine smear, by culture using the MB/BacT liquid culture system and solid media, and by nucleic acid amplification using the COBAS AMPLICOR MTB test. In the N -acetyl- l -cysteine-sodium hydroxide arm, 1,468 specimens were analyzed: 65 were smear positive; 88 and 42 were culture positive for Mycobacterium tuberculosis and nontuberculous mycobacteria, respectively; and 103 were PCR positive. Relative to cultures positive for M. tuberculosis , the sensitivity and specificity of the smear were 68.2% and 99.6%, respectively, and those of PCR were 75.0% and 97.3%, respectively. In the C 18 -carboxypropylbetaine study arm, 1,423 specimens were analyzed: 44 were smear positive; 82 and 31 were culture positive for M. tuberculosis and nontuberculous mycobacteria, respectively; and 91 were PCR positive. The sensitivity and specificity of the smear were 48.8% and 99.7%, respectively, and those of PCR were 78.0% and 98.0%, respectively. When the two arms were compared, C 18 -carboxypropylbetaine specimen processing significantly increased the number of smear-negative and culture-positive specimens and significantly increased the PCR sensitivity among this same group of specimens while at the same time significantly reducing the inhibition rate.

The INNO-LiPA Mycobacteria Test (Innogenetics, N.V., Belgium) is a PCR-based reverse hybridization assay for the simultaneous identification of several mycobacterial species. We evaluated two simplified lysis methods for mycobacterial DNA release for application in the INNO-LiPA Mycobacteria Test. The two methods were based on either (i) heat treatment or (ii) sonication. Both methods were performed directly on 45 positive liquid cultures (MB-BacT, BioMérieux, Marcy l'Etoile, France) containing 17 different mycobacterial species. These two simple lysis procedures demonstrated similar effectiveness (100%) to that recommended by the manufacturer. They also significantly shortened the time required for mycobacterial DNA release.

Forest cover in the dry zone of southern Honduras has suffered drastic reduction, largely as a result of the marginalisation of small farmers onto formerly wooded hillsides. In four case study communities, the relations between the area's human population and the remaining tree diversity were investigated through a combination of interviews, focus group meetings and inventories. Inventories on 10 farms in 2 communities found an average of 57.6 standing trees (above 2 m in height) and 9388.3 live stumps and seedlings of tree and shrub species (less than 2 m in height) per hectare in recently cropped fields. Tree management practices were found to include the selective promotion of naturally regenerated trees valued by farmers for their products, the elimination of unwanted trees due to competition with crops for light and space, and pruning to reduce competition. Farmers listed 41 species as being actively protected, although protection was largely concentrated on a subset of 5 (Cordia alliodora, Swietenia humilis, Lysiloma spp., Enterolobium cyclocarpum and Albizia saman, in that order); they also described broadening their species preferences in the face of scarcity of preferred species. The study questions the common perception of dry zone farmers as being responsible for continued elimination of tree diversity, and highlights the potential of the management of natural regeneration for meeting the livelihood needs of small farmers.

The MB/BacT (Organon-Teknika, USA) is a fully automated, rapid, nonradiometric system for the culture of mycobacteria from clinical samples. The rate of recovery of mycobacteria and the time to detection obtained with the MB/ BacT were compared with those obtained with Löwenstein-Jensen and Coletsos solid media and Bactec 7H12 (12B) (Becton-Dickinson, USA) broth when 600 processed specimens were inoculated into all media in parallel. Specimens included 383 respiratory samples, 20 urine samples, 23 purulent exudates, 13 stool samples, 103 blood samples, 14 bone marrow aspirates, and 44 body fluid samples or aspirates. Overall, 106 mycobacterial isolates comprising six species were recovered, of which 100 (94.3%) were detected with MB/BacT, 98 (92.5%) with egg-based media, and 96 (90.2%) with Bactec 12B. The recovery rates of Mycobacterium tuberculosis complex with MB/BacT, egg-based media, and Bactec 12B were 98.7%, 93.7, and 89.9%, respectively. The average number of days to detection of single mycobacterial isolates was 14.2 days for MB/BacT, 26.1 days for egg-based media, and 11.7 days for Bactec 12B. The contamination rates were higher in MB/BacT (5%) than in Bactec 12B (1.8%) or egg-based media (1.5%). MB/BacT is a reliable, nonradiometric, less labor-intensive alternative to Bactec 12B for recovery of mycobacteria, but, as with other liquid culture methods, MB/BacT should be used in combination with a solid medium, not on its own.

We evaluated a newly commercial enzyme immunoassay (EIA) (Biotest Legionella Urin Antigen EIA; Biotest AG, Dreieich, Germany) for detection of antigens of all Legionella pneumophila serogroups with a relatively wide spectrum of cross-reactivity as well as antigens of other Legionella spp. by comparing its sensitivity and specificity with those of an EIA for detection of L. pneumophila serogroup 1 antigen ( Legionella urinary antigen EIA; Binax, Portland, Maine). Both tests were performed with both concentrated and nonconcentrated urine samples. We also evaluated the capabilities of both EIAs to detect extracted soluble antigens of American Type Culture Collection (ATCC) Legionella strains ( L. pneumophila serogroups 1 to 14, L. bozemanii , and L. longbeachae ). The sensitivity of the Biotest EIA was 66.66% in nonconcentrated urine and 86.66% in concentrated urine. The sensitivity of the Binax EIA was 63.76% and 88.88% in nonconcentrated and concentrated urine, respectively. The specificity was 100% in nonconcentrated and concentrated urine for both assays. The Binax EIA and Biotest EIA detected extracted soluble antigens of L. pneumophila serogroups 1 to 14 and L. bozemanii ATCC strains. The cross-reactions observed with the Binax EIA were probably due to common epitopes directly related to lipopolysaccharide. Further studies are required to determine the usefulness of the Binax EIA for detection of urinary antigens from Legionella species and serogroups other than L. pneumophila serogroup 1. The Biotest EIA proved to be as rapid, sensitive, and specific as the Binax EIA for the diagnosis of legionellosis. Concentration of antigen present in urine increased the sensitivities of both techniques with no reduction in specificity.

The presence of antibodies against Trichinella spiralis was investigated in a semi-rural county of Mexico using ELISA and electroimmunotransfer blot assay with crude larvae and ES antigens. The association of antibodies to several social, hygienic and dietary factors was also investigated. Antibody prevalences between 1.0 and 1.9% were found. Risk factors associated were gender female and ingestion of moronga, a pork meat sausage-like product. Our results suggest the presence of an endemic, unnoticed form of human trichinellosis. These observations may be relevant for other countries, especially in rural and semi-rural areas, where sylvatic and domestic life-cycles of Trichinella coexist.

The induction of preneoplastic and neoplastic lesions by the widely used antiestrogen Tamoxifen was studied in female mice. Outbred CD-1 mice were treated with Tamoxifen (1, 2, 5, 10, 25 or 50 microg/pup/day) for the first 5 days after birth. At 14-17 months, reproductive tract tissues were examined for pathological changes. In the ovary, corpora lutea were lacking while cysts were quite common in Tamoxifen-exposed mice at all doses; cystadenomas were seen in two mice. Structural malformations and epithelial hyperplasia of the oviduct were seen in 100% of the treated mice. Malformations of the uterus, cervix, and vagina were also seen. Excessive vaginal keratinization was not a common feature although vaginal adenosis was observed more often after Tamoxifen treatment than previously reported after similar treatment with diethylstilbestrol (DES). The most striking histological features, however, were seen in the uterus. One hundred percent of the Tamoxifen-treated mice at all doses exhibited uterine hypoplasia with focal areas of basal cell hyperplasia in the lining endometrium. Progressive cellular atypias were seen in the lining endometrium ranging from atypical hyperplasia to uterine adenocarcinoma; the highest incidence of uterine adenocarcinoma was 7/14 (50%) observed in the Tamoxifen 10 microg/pup/day dose group. No similar tumors were observed in corresponding control mice. The induction of atypical uterine hyperplasia and adenocarcinoma combined with other abnormalities observed in genital tract structure following neonatal treatment with Tamoxifen suggests the developing reproductive tract is exquisitely sensitive to perturbation by compounds with hormonal activity. These studies provide the basis for future investigation into the mechanisms of Tamoxifen's carcinogenic effects in experimental animals, and to the risk benefit analysis for the prophylactic use of Tamoxifen in healthy women who are at risk of developing breast cancer.

The prevalence of anti-Borrelia burgdorferi antibodies was studied in Granada, Spain, between January 1991 and November 1993 in 354 patients with suspected Lyme disease (group 1); in 50 patients either with syphilis (n = 32) or without syphilis but with a positive Rapid Plasma Reagin test (n = 18) (group 2); and in 150 healthy subjects (group 3). In addition, intrathecal antibody production was evaluated by EIA in CSF samples obtained from 117 patients in group 1. Anti-Borrelia burgdorferi antibodies were detected by EIA in 58 patients (16.4%) in group 1, 29 (8.2%) of whom were positive by Western blot. Intrathecal antibody production was detected in one patient. In group 2, 8 (16%) patients had a positive EIA result, but none of these was confirmed by Western blot. western blot was negative for all subjects in group 3. The results of this study indicate that anti-Borrelia burgdorferi antibodies are not uncommon in our area, although Lyme disease is rare.

Activated G protein-coupled receptors (GPCRs) are phosphorylated and interact with β-arrestins, which mediate desensitization and endocytosis. Endothelin-converting enzyme-1 (ECE-1) degrades neuropeptides in endosomes and can promote recycling. Although endocytosis, dephosphorylation, and recycling are accepted mechanisms of receptor resensitization, a large proportion of desensitized receptors can remain at the cell surface. We investigated whether reactivation of noninternalized, desensitized (phosphorylated) receptors mediates resensitization of the substance P (SP) neurokinin 1 receptor (NK1R). Herein, we report a novel mechanism of resensitization by which protein phosphatase 2A (PP2A) is recruited to dephosphorylate noninternalized NK1R. A desensitizing concentration of SP reduced cell-surface SP binding sites by only 25%, and SP-induced Ca2+signals were fully resensitized before cell-surface binding sites started to recover, suggesting resensitization of cell-surface-retained NK1R. SP induced association of β-arrestin1 and PP2A with noninternalized NK1R. β-Arrestin1 small interfering RNA knockdown prevented SP-induced association of cell-surface NK1R with PP2A, indicating that β-arrestin1 mediates this interaction. ECE-1 inhibition, by trapping β-arrestin1 in endosomes, also impeded SP-induced association of cell-surface NK1R with PP2A. Resensitization of NK1R signaling required both PP2A and ECE-1 activity. Thus, after stimulation with SP, PP2A interacts with noninternalized NK1R and mediates resensitization. PP2A interaction with NK1R requires β-arrestin1. ECE-1 promotes this process by releasing β-arrestin1 from NK1R in endosomes. These findings represent a novel mechanism of PP2A- and ECE-1-dependent resensitization of GPCRs.

Health surveys and hematologic and plasma biochemical analyses were conducted in 52 free-ranging and 51 captive Morelet's crocodiles (Crocodylus moreletii) in Campeche, Mexico, March-September 2007. Blood samples from 92 crocodiles (45 free-ranging and 47 captive) were collected for hematologic and plasma biochemical analyses. Average values of erythrocytes of free-ranging crocodiles were 1,046,166 cells/μl, and total white cells were 1.03 × 10(4) cells/μl. Captive crocodiles had erythrocyte and leukocyte values of 1,100,416 cells/μl and 8.51 × 10(3) cells/μl, respectively. There were no significant differences in values of erythrocytes or in hematocrit between free-ranging and captive crocodiles, or between sexes, or among size classes. Counts of leukocytes in free-ranging crocodiles were significantly higher than in captive individuals. The mean values of plasma analytes were 69.55 mg/l (glucose), 250.14 mg/l (cholesterol), 3.04 mg/l (uric acid), 2.70 mg/l (creatinine), and 20.20 IU/l (alanine aminotransferase). There were significant differences in cholesterol between free-ranging and captive crocodiles and between sexes.

Although long regarded as a conduit for the degradation or recycling of cell surface receptors, the endosomal system is also an essential site of signal transduction. Activated receptors accumulate in endosomes, and certain signaling components are exclusively localized to endosomes. Receptors can continue to transmit signals from endosomes that are different from those that arise from the plasma membrane, resulting in distinct physiological responses. Endosomal signaling is widespread in metazoans and plants, where it transmits signals for diverse receptor families that regulate essential processes including growth, differentiation and survival. Receptor signaling at endosomal membranes is tightly regulated by mechanisms that control agonist availability, receptor coupling to signaling machinery, and the subcellular localization of signaling components. Drugs that target mechanisms that initiate and terminate receptor signaling at the plasma membrane are widespread and effective treatments for disease. Selective disruption of receptor signaling in endosomes, which can be accomplished by targeting endosomal-specific signaling pathways or by selective delivery of drugs to the endosomal network, may provide novel therapies for disease.

Background The protozoan pathogens Leishmania major, Trypanosoma brucei and Trypanosoma cruzi (the Tritryps) are parasites that produce devastating human diseases. These organisms show very unusual mechanisms of gene expression, such as polycistronic transcription. We are interested in the study of tRNA genes, which are transcribed by RNA polymerase III (Pol III). To analyze the sequences and genomic organization of tRNA genes and other Pol III-transcribed genes, we have performed an in silico analysis of the Tritryps genome sequences. Results Our analysis indicated the presence of 83, 66 and 120 genes in L. major, T. brucei and T. cruzi, respectively. These numbers include several previously unannotated selenocysteine (Sec) tRNA genes. Most tRNA genes are organized into clusters of 2 to 10 genes that may contain other Pol III-transcribed genes. The distribution of genes in the L. major genome does not seem to be totally random, like in most organisms. While the majority of the tRNA clusters do not show synteny (conservation of gene order) between the Tritryps, a cluster of 13 Pol III genes that is highly syntenic was identified. We have determined consensus sequences for the putative promoter regions (Boxes A and B) of the Tritryps tRNA genes, and specific changes were found in tRNA-Sec genes. Analysis of transcription termination signals of the tRNAs (clusters of Ts) showed differences between T. cruzi and the other two species. We have also identified several tRNA isodecoder genes (having the same anticodon, but different sequences elsewhere in the tRNA body) in the Tritryps. Conclusion A low number of tRNA genes is present in Tritryps. The overall weak synteny that they show indicates a reduced importance of genome location of Pol III genes compared to protein-coding genes. The fact that some of the differences between isodecoder genes occur in the internal promoter elements suggests that differential control of the expression of some isoacceptor tRNA genes in Tritryps is possible. The special characteristics found in Boxes A and B from tRNA-Sec genes from Tritryps indicate that the mechanisms that regulate their transcription might be different from those of other tRNA genes.

Transient stimulation with substance P (SP) induces endocytosis and recycling of the neurokinin-1 receptor (NK(1)R). The effects of sustained stimulation by high concentrations of SP on NK(1)R trafficking and Ca(2+) signaling, as may occur during chronic inflammation and pain, are unknown. Chronic exposure to SP (100 nm, 3 h) completely desensitized Ca(2+) signaling by wild-type NK(1)R (NK(1)Rwt). Resensitization occurred after 16 h, and cycloheximide prevented resensitization, implicating new receptor synthesis. Lysine ubiquitination of G-protein-coupled receptors is a signal for their trafficking and degradation. Lysine-deficient mutant receptors (NK(1)RDelta5K/R, C-terminal tail lysines; and NK(1)RDelta10K/R, all intracellular lysines) were expressed at the plasma membrane and were functional because they responded to SP by endocytosis and by mobilization of Ca(2+) ions. SP desensitized NK(1)Rwt, NK(1)RDelta5K/R, and NK(1)RDelta10K/R. However, NK(1)RDelta5K/R and NK(1)RDelta10K/R resensitized 4-8-fold faster than NK(1)Rwt by cycloheximide-independent mechanisms. NK(1)RDelta325 (a naturally occurring truncated variant) showed incomplete desensitization, followed by a marked sensitization of signaling. Upon labeling receptors in living cells using antibodies to extracellular epitopes, we observed that SP induced endocytosis of NK(1)Rwt, NK(1)RDelta5K/R, and NK(1)RDelta10K/R. After 4 h in SP-free medium, NK(1)RDelta5K/R and NK(1)RDelta10K/R recycled to the plasma membrane, whereas NK(1)Rwt remained internalized. SP induced ubiquitination of NK(1)Rwt and NK(1)RDelta5K/R as determined by immunoprecipitation under nondenaturing and denaturing conditions and detected with antibodies for mono- and polyubiquitin. NK(1)RDelta10K/R was not ubiquitinated. Whereas SP induced degradation of NK(1)Rwt, NK(1)RDelta5K/R and NK(1)RDelta10K/R showed approximately 50% diminished degradation. Thus, chronic stimulation with SP induces ubiquitination of the NK(1)R, which mediates its degradation and down-regulation.

The results of nerve repair with fibrin glue and microsuture were evaluated in rat nerve transection models. Ninety Wistar-Furth rat median nerves were exposed, transected, and repaired in an end-to-end fashion with one of four substances/techniques: 1) human fibrin sealant (Quixil); 2) autologous graft and human fibrin sealant (Quixil); 3) bovine fibrin sealant (Tissucol); and 4) nylon microsuture, epineurial technique. Histologic analyses were performed at 3-, 6-, and 9-month postoperative intervals, and factors evaluated included: presence of inflammatory cells (i.e., macrophages and T cells); number of Schwann cells at the repair site; number of blood vessels; fibrosis; axonal regeneration; and fiber alignment. An additional group underwent histologic analysis at 3 weeks following repair with Quixil. Surgical time of repair was also measured. Nerve repairs performed with fibrin sealants produced less inflammatory response and fibrosis, and better axonal regeneration and fiber alignment than nerve repairs performed with microsuture. In addition, the fibrin sealant techniques were quicker and easier to use. The authors conclude that fibrin sealant represents a good alternative technique to microsuture for peripheral-nerve repair.

We evaluated a commercially available radioimmunoassay technique for detecting the soluble antigen of Legionella pneumophila serogroup 1 using concentrated and nonconcentrated urine. Concentration was achieved by selective ultrafiltration. The sensitivity of the technique was 60.9% for nonconcentrated urine and 80.4% for concentrated samples, with 100% specificity in both cases.

The performance of two DNA line probe assays, a new version of INNO-LiPA Mycobacteria (Innogenetics, Ghent, Belgium) and the GenoType Mycobacterium (Hain Diagnostika, Nehren, Germany), were evaluated for identification of mycobacterial species isolated from liquid cultures. Both tests are based on a PCR technique and designed for simultaneous identification of different mycobacterial species by reverse hybridization and line probe technology. The INNO-LiPA Mycobacteria v2 targeting the 16S-23S rRNA gene spacer region was developed for the simultaneous identification of 16 different mycobacterial species. The GenoType Mycobacterium, which targets the 23S rRNA gene, allows simultaneous identification of 13 mycobacterial species. Both tests were evaluated on 110 mycobacterial strains belonging to 22 different mycobacterial species (20 reference strains, 83 clinical strains, and 4 Mycobacterium kansasii strains isolated from tap water) that were previously inoculated into MB/BacT bottles. The sensitivity of both methods, defined as the number of positive results obtained with the Mycobacterium genus probe together with an interpretable result on the number of samples tested was 110 of 110 (100%) for INNO-LiPA and 102 of 110 (92.7%) for GenoType. For samples with interpretable results, INNO-LiPA was able to correctly identify 109 of 110 samples (99.1%), whereas the GenoType correctly identified 100 of 102 samples (98.0%). Both tests were easy to perform, rapid, and reliable when applied to mycobacterial identification directly from MB/BacT bottles.

In the study presented here, the performance of the S. aureus PNA FISH assay was evaluated using 285 blood cultures (from 104 patients) that had gram-positive cocci resembling staphylococci on Gram stain. The new molecular test is based on a fluorescence in situ hybridization assay using peptide nucleic acid probes targeting Staphylococcus aureus 16S rRNA and is designed for the rapid identification of Staphylococcus aureus directly from positive blood cultures. The sensitivity, specificity, and positive and negative predictive values of the S. aureus PNA FISH for the rapid identification of Staphylococcus aureus directly from positive blood culture bottles were 100, 99.4, 99.2 and 100%, respectively.

A detailed study comparing specimen processing methods for the isolation of mycobacteria was recently reported [1]. In the follow-up study presented here, 1,201 specimens (95% respiratory) were collected and split approximately equally such that one-half of each specimen was processed with 3% sodium dodecyl sulfate-1% sodium hydroxide (SDS-NaOH) [2] and the other half was processed with C18-carboxypropylbetaine (CB-18) followed by lytic enzyme decontamination [3, 4]. All processed specimens were analyzed by culture using the MB/BacT liquid culture system containing the antibiotic supplement MAS (bioM rieux, France). The SDS-NaOHprocessed specimens were also inoculated onto L wenstein-Jensen slants, while the CB-18-processed specimens were also inoculated onto 7H11-selective plates (50 g/ml carbenicillin, 200 U/ml polymyxin B, 10 g/ml amphotericin B, and 20 g/ml trimethoprim lactate). CB-18/lytic enzyme processing increased overall culture sensitivity by approximately 14.1% (P

The ability of a polymerase-chain-reaction-based technique combined with a reverse hybridisation line-probe assay to detect and identify eight of the most clinically significant mycobacterial species directly from cultures in liquid medium was evaluated. The line-probe assay allows simultaneous identification of eight different mycobacterial species. Ninety-seven mycobacterial strains belonging to 22 different species were evaluated. All strains were previously inoculated into MB/BacT bottles (Organon Teknika, USA). The sensitivity and specificity of the test when applied on positive MB/BacT liquid cultures containing isolates from mycobacterial species included as specific probes on the line-probe assay strip was 100% and 100%, respectively. These results further support the potential clinical usefulness of this technique in the diagnosis of mycobacterial infections.

The performance was evaluated of a fluorescence in situ hybridisation assay using peptide nucleic acid probes (Dako Probe MTB Culture Confirmation Test; Dako, Denmark) for identification of Mycobacterium tuberculosis complex (MTC) organisms and differentiation between tuberculous and non-tuberculous mycobacteria (NTM) in material taken directly from Bactec 12B (Becton Dickinson, USA) and MB/BacT (Organon Teknika, USA) bottles. The test was applied to 129 smear-positive (Ziehl-Neelsen stain) clinical specimens, 48 previously identified clinical strains of mycobacteria (12 MTC and 36 NTM), and 51 reference strains (7 MTC and 44 NTM) which were all previously inoculated into Bactec 12B and MB/BacT bottles. The sensitivity and specificity of the assay for MTC-positive cultures was 87.6% and 100%, respectively, for Bactec 12B, and 100%, respectively, for MB/BacT. The sensitivity and specificity of the assay for NTM-positive cultures was 100% for both media.

To improve turnaround time and decrease the cost of the identification of Candida glabrata , we evaluated four methods for the detection of trehalose assimilation or fermentation. These methods were compared with the API 20C method (bioMERIEUX, Hazelwood, Mo.) to determine accuracy. We recommend the use of Remel Rapid Trehalose Assimilation Broth because of its rapid, 3-h results, reasonable sensitivity, and low number of false positives.

Two commercial systems for the amplification and detection of Mycobacterium tuberculosis directly from respiratory samples were compared. The Roche Cobas Amplicor MTB Test and the Roche manual Amplicor MTB Test (Roche Diagnostic Systems, USA) were applied to 755 decontaminated respiratory specimens collected from 470 patients. Results were compared with those of acid-fast staining and culture. A total of 251 specimens were collected from 156 patients diagnosed with pulmonary tuberculosis, including 28 specimens corresponding to 13 patients that were receiving antituberculous treatment. Given the overall positivity rate of 33.2% (251/755), the sensitivity, specificity, and positive and negative predictive values were 92.4, 100, 100, and 96.5%, respectively, for the Cobas Amplicor MTB Test and 90.8, 100, 100, and 95.8%, respectively, for the Amplicor MTB Test. For 204 (81.3%) smear positive specimens and 47 (19.7%) smear negative specimens, the sensitivity values were 100 and 59.6%, respectively, for the Cobas Amplicor MTB Test and 100 and 51%, respectively, for the Amplicor MTB Test. There were no statistically significant differences in sensitivity or specificity between the two assays and culture (p0.05). The overall results of both assays were concordant for 99.5% of the samples. It is concluded that although both nucleic acid amplification methods are rapid and specific for the detection of Mycobacterium tuberculosis complex in respiratory specimens, the Cobas Amplicor MTB Test appears to be slightly more sensitive than the Amplicor MTB Test when smear negative specimens are investigated.

A rapid amplification-based test for the diagnosis of extrapulmonary tuberculosis, the LCx Mycobacterium tuberculosis Assay from Abbott Laboratories, was evaluated. Results from the LCx M. tuberculosis Assay were compared with those from culture and the final clinical diagnosis for each patient. A total of 526 nonrespiratory specimens from 492 patients were tested. The specimens included urine; feces; lymph node exudates; pleural, cerebrospinal, articular, and ascitic fluids; tissue biopsies; gastric aspirates; purulent exudates; blood; and bone marrow aspirates. After combination of the culture results and the patient’s clinical data, a total of 135 specimens were collected from 122 patients with a diagnosis of extrapulmonary tuberculosis. The sensitivity, specificity, and positive and negative predictive values for the LCx M. tuberculosis Assay were 77.7, 98.7, 95.2, and 93.1%, respectively; these values rose in resolved cases of TB to 78.5, 100, 100, and 93.1%, respectively. For 37 (27.4%) specimens from patients smear positive for the disease and 98 (72.6%) specimens from patients smear negative for the disease, the sensitivities of the LCx M. tuberculosis Assay were 100 and 71.1%, respectively. Statistically significant differences ( P < 0.01) in sensitivities were found between culture and the LCx M. tuberculosis Assay. These differences were even greater among smear-negative specimens. The results demonstrate that the LCx M. tuberculosis Assay will provide rapid and valuable information for the diagnosis of extrapulmonary tuberculosis.