Paleodistributions and Comparative Molecular Phylogeography of Leafcutter Ants (Atta spp.) Provide New Insight into the Origins of Amazonian Diversity

The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses. Recent advances in the fields of phylogeography and species-distribution modeling permit a modern re-evaluation of these hypotheses. Our approach combines comparative, molecular phylogeographic analyses using mitochondrial DNA sequence data with paleodistribution modeling of species ranges at the last glacial maximum (LGM) to test these hypotheses for three co-distributed species of leafcutter ants (Atta spp.). The cumulative results of all tests reject every prediction of the riverine barrier hypothesis, but are unable to reject several predictions of the Pleistocene refugia and marine incursion hypotheses. Coalescent dating analyses suggest that population structure formed recently (Pleistocene-Pliocene), but are unable to reject the possibility that Miocene events may be responsible for structuring populations in two of the three species examined. The available data therefore suggest that either marine incursions in the Miocene or climate changes during the Pleistocene—or both—have shaped the population structure of the three species examined. Our results also reconceptualize the traditional Pleistocene refugia hypothesis, and offer a novel framework for future research into the area

Publisher Correction: A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients

The original version of this Article contained an error in the title, which was incorrectly given as 'APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients'. This has now been corrected in both the PDF and HTML versions of the Article to read 'A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients'

Genome-Wide Signatures of ‘Rearrangement Hotspots’ within Segmental Duplications in Humans

The primary objective of this study was to create a genome-wide high resolution map (i.e., .100 bp) of ‘rearrangement hotspots’ which can facilitate the identification of regions capable of mediating de novo deletions or duplications in humans. A hierarchical method was employed to fragment segmental duplications (SDs) into multiple smaller SD units. Combining an end space free pairwise alignment algorithm with a ‘seed and extend’ approach, we have exhaustively searched 409 million alignments to detect complex structural rearrangements within the reference-guided assembly of the NA18507 human genome (186 coverage), including the previously identified novel 4.8 Mb sequence from de novo assembly within this genome. We have identified 1,963 rearrangement hotspots within SDs which encompass 166 genes and display an enrichment of duplicated gene nucleotide variants (DNVs). These regions are correlated with increased nonallelic homologous recombination (NAHR) event frequency which presumably represents the origin of copy number variations (CNVs) and pathogenic duplications/deletions. Analysis revealed that 20% of the detected hotspots are clustered within the proximal and distal SD breakpoints flanked by the pathogenic deletions/duplications that have been mapped for 24 NAHR-mediated genomic disorders. FISH Validation of selected complex regions revealed 94% concordance with in silico localization of the highly homologous derivatives. Other results from this study indicate that intra-chromosomal recombination is enhanced in genic compared with agenic duplicated regions, and that gene desert regions comprising SDs may represent reservoirs for creation of novel genes. The generation of genome-wide signatures of ‘rearrangement hotspots’, which likely serve as templates for NAHR, may provide a powerful approach towards understanding the underlying mutational mechanism(s) for development of constitutional and acquired diseases

Laboratory experience with radiometric detection of bacteremia with three culture media

In two long-term studies, the BACTEC radiometric system for detection of bacteremia was evaluated with three culture media each: (i) BACTEC media 6A (for aerobes) and 7B (for anaerobes) plus a thioglycolate medium and (ii) BACTEC media 6A, 7B, and 8A (hypertonic). In study 1, clinically significant isolates were identified in 1,873 (13.9%) of 13,432 blood cultures with all three media. The thioglycolate medium revealed 143 (1.1%) organisms not recovered from the 6A and 7B media. In study 2, isolates were identified in 1,135 (12.9%) of 8,759 cultures with all three media; 104 (1.2%) organisms were isolated only from the hypertonic medium. The increased yield of positive cultures in the three-medium system is likely due to the larger volume of blood cultured.</jats:p

Addi-Chek filtration, BACTEC, and 10-ml culture methods for recovery of microorganisms from dialysis effluent during episodes of peritonitis

The Addi-Chek (filtration; Millipore Corp., Bedford, Mass.) and BACTEC (radiometric detection of growth in culture media; Johnston Laboratories, Inc., Towson, Md.) systems were compared with the 10-ml culture (centrifugation) method for the recovery of microorganisms from peritoneal dialysate collected from patients with clinical evidence of peritonitis and containing greater than or equal to 200 leukocytes per mm3. Both alternate methods were comparable, and results were not significantly different from those of the conventional 10-ml culture method. All systems were adversely affected in their capacity to recover organisms when dialysates had been collected during periods of antimicrobial therapy.</jats:p