Phylogenomic species delimitation and host‐symbiont coevolution in the fungus‐farming ant genus Sericomyrmex Mayr (Hymenoptera: Formicidae): ultraconserved elements (UCEs) resolve a recent radiation

Ants in the Neotropical genus Sericomyrmex Mayr cultivate fungi for food. Both ants and fungi are obligate, coevolved symbionts. The taxonomy of Sericomyrmex is problematic because the morphology of the worker caste is generally homogeneous across all of the species within the genus, species limits are vague, and the relationships between them are unknown. We used ultraconserved elements (UCEs) as genome‐scale markers to reconstruct evolutionary history and to infer species boundaries in Sericomyrmex. We recovered an average of ～990 UCE loci for 88 Sericomyrmex samples from across the geographical range of the genus as well as for five outgroup taxa. Using maximum likelihood and species‐tree approaches, we recovered nearly identical topologies across datasets with 50–95% matrix completeness. We identify nine species‐level lineages in Sericomyrmex, including two new species. This is less than the previously described 19 species, even accounting for two species for which we had no UCE samples, which brings the total number of Sericomyrmex species to 11. Divergence‐dating analyses recovered 4.3 Ma as the crown‐group age estimates for Sericomyrmex, indicating a recent, rapid radiation. We also sequenced mitochondrial cytochrome oxidase subunit I (COI) for 125 specimens. Resolution and support for clades in our COI phylogeny are weak, indicating that COI is not an appropriate species‐delimitation tool. However, taxa within species consistently cluster together, suggesting that COI is useful as a species identification (‘DNA barcoding’) tool. We also sequenced internal transcribed spacer (ITS) and large subunit (LSU) for 32 Sericomyrmex fungal cultivars. The fungal phylogeny confirms that Sericomyrmex fungi are generalized higher‐attine cultivars, interspersed with Trachymyrmex‐associated fungal species, indicating cultivar sharing and horizontal transfer between these two genera. Our results indicate that UCEs offer immense potential for delimiting and resolving relationships of problematic, recently diverged species.     

Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae

Background  

Methylation of lysine 79 on histone H3 by Dot1 is required for maintenance of heterochromatin structure in yeast and humans. However, this histone modification occurs predominantly in euchromatin. Thus, Dot1 affects silencing by indirect mechanisms and does not act by the recruitment model commonly proposed for histone modifications. To better understand the role of H3K79 methylation gene silencing, we investigated the silencing function of Dot1 by genetic suppressor and enhancer analysis and examined the relationship between Dot1 and other global euchromatic histone modifiers.     

Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics

During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule‐mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes. The resulting ortholog sets imply that the last eukaryotic common ancestor (LECA) possessed a complex kinetochore and highlight that current‐day kinetochores differ substantially. These kinetochores diverged through gene loss, duplication, and, less frequently, invention and displacement. Various kinetochore components co‐evolved with one another, albeit in different manners. These co‐evolutionary patterns improve our understanding of kinetochore function and evolution, which we illustrated with the RZZ complex, TRIP13, the MCC, and some nuclear pore proteins. The extensive diversity of kinetochore compositions in eukaryotes poses numerous questions regarding evolutionary flexibility of essential cellular functions.     

Adult peripheral nerve disorders: nerve entrapment, repair, transfer, and brachial plexus disorders

LEARNING OBJECTIVES: After reading this article, the participant should be able to: 1. Describe the pathophysiologic bases for nerve injury and how they apply to patient evaluation and management. 2. Recognize the wide variety of injury patterns and associated patient complaints and physical findings associated with peripheral nerve pathology. 3. Evaluate and recommend further tests to aid in defining the diagnosis. 4. Specify treatment options and potential risks and benefits. SUMMARY: Peripheral nerve disorders comprise a gamut of problems, ranging from entrapment neuropathy to direct open traumatic injury and closed brachial plexus injury. The pathophysiology of injury defines the patient's symptoms, examination findings, and treatment options and is critical to accurate diagnosis and treatment. The goals of treatment include management of the often associated pain and improvement of sensory and motor function. Understanding peripheral nerve anatomy is critical to adopting novel nerve transfer procedures, which may provide superior options for a variety of injury patterns.     

Sex attractants in nematodes

Nematodes communicate with each other using pheromones - chemicals secreted by one individual that affect the behaviour of others of the same species. Chemicals secreted into the environment are known to influence host location, dormancy (dauer-larva formation), competitive interactions and mate detection; they benefit the nematode by reducing energy expenditure on less orientated movements. Of these chemicals, sex pheromones associated with mate detection and attraction are of particular interest as potential biological control agents. Here, Barbara MacKinnon discusses these developments.     

Effects of serum amyloid A protein (SAA) on composition, size, and density of high density lipoproteins in subjects with myocardial infarction

The acute phase reactant serum amyloid A protein (SAA) circulates in plasma as a constituent of high density lipoproteins (HDL). Advantage has been taken of the induction of SAA in human subjects with myocardial infarction to study the effect of SAA on the physical and chemical properties of HDL. HDL were isolated by sequential ultracentrifugation and assayed for chemical composition. Apolipoprotein composition was assessed by SDS polyacrylamide gel electrophoresis. Size distribution of HDL was determined by gradient gel electrophoresis and density distribution by density gradient ultracentrifugation. In studies of 18 subjects with myocardial infarction, SAA accounted for 8-87% (median 52%) of the HDL apolipoprotein. These SAA-enriched HDL had a density comparable to that of normal HDL subfraction-3 (HDL3). Their chemical composition differed from normal HDL3, however, with a reduced phospholipid (17% vs 24%) and an increased triglyceride (7.7% vs 1.6%) value. When separated by gradient gel electrophoresis, the SAA-enriched HDL were much larger than normal HDL3, having a radius of 4.5-5.3 nm that extended well into the size range of HDL2; particle size correlated with SAA content. This disassociation between particle density and particle size was also observed with the SAA-enriched HDL isolated from a subject with secondary amyloidosis and also with normal HDL that had been enriched with SAA during incubation in vitro. Thus, the presence of high levels of SAA has been found to be associated with phospholipid-depleted particles of a density comparable to HDL3 but a size larger than normal HDL3.     

The role of primary bone grafting in complex craniomaxillofacial trauma

The role of craniofacial surgical techniques and immediate bone grafting in the management of complex craniofacial trauma has been reviewed. Four hundred and one patients with complex facial injuries have been treated. Two hundred and forty-one primary bone and cartilage grafts have been performed in 66 patients. Complex facial injuries should be managed by direct exposure, reduction, and fixation of all fractures utilizing interfragmentary wiring. Very comminuted or absent bone is replaced by immediate bone grafting, producing a stable skeleton without the need for external fixation devices. Associated mandibular fractures are managed with rigid internal fixation utilizing A-O technique. Results of immediate bone grafting have been excellent, and complications are rare. All deformities should be corrected, whenever possible, during the initial operation. This one-stage reconstruction of even the most complex facial injuries will prevent severe postoperative traumatic deformity and disability that may be extremely difficult or impossible to correct secondarily.     

Assessment of enzyme inhibition or stimulation in plasma membrane preparations

The purity of isolated plasma membranes is routinely judged by the activity of enzymes present both in this membrane and other locations in the cell. However, since enzyme inhibition and/or stimulation often occurs following disruption of the cell, the question as to which enzyme(s) provides a reliable marker of membrane purity should be considered. We have devised a simple method with which to address this problem. Inhibition or stimulation of plasma membrane marker enzymes can be rapidly assessed in cell homogenates and subfractions by mixing both samples, with known enzyme activity, and observing any deviation from the expected combined activity. Should the activity remain constant that enzyme can be used to gauge the purity of the plasma membrane preparation. Of the four putative plasma membrane marker enzymes examined only one, gamma-glutamyltranspeptidase appeared to give a reliable purity measurement in the cell system studied.     

Mapping Quantitative Trait Loci Controlling Milk Production in Dairy Cattle by Exploiting Progeny Testing

We have exploited ``progeny testing' to map quantitative trait loci (QTL) underlying the genetic variation of milk production in a selected dairy cattle population. A total of 1,518 sires, with progeny tests based on the milking performances of > 150,000 daughters jointly, was genotyped for 159 autosomal microsatellites bracketing 1645 centimorgan or approximately two thirds of the bovine genome. Using a maximum likelihood multilocus linkage analysis accounting for variance heterogeneity of the phenotypes, we identified five chromosomes giving very strong evidence (LOD score >/= 3) for the presence of a QTL controlling milk production: chromosomes 1, 6, 9, 10 and 20. These findings demonstrate that loci with considerable effects on milk production are still segregating in highly selected populations and pave the way toward marker-assisted selection in dairy cattle breeding.     

A large-subunit mitochondrial ribosomal DNA sequence translocated to the nuclear genome of two stone crabs (Menippe)

Two DNA sequences that appear to be homologous to large-subunit mitochondrial ribosomal RNA genes have been identified in the stone crabs Menippe mercenaria and M. adina. Amplification from whole genomic DNA by polymerase chain reaction (PCR) with oligonucleotide primers based on conserved portions of large-subunit mitochondrial rRNA genes consistently amplified two products of similar length (565 and 567 bp). These products differed at 3% of their nucleotide bases, and could be distinguished by a HindIII site. Only one of these sequences (designated the A sequence) was detected by PCR in purified mitochondrial DNA. The other (designated the B sequence) hybridized to total genomic DNA at a level consistent with a nuclear genome location. It is unlikely that the type B product would have been recognized as a nuclear copy by examination of its sequence alone. This is the first report of a mitochondrial gene sequence translocated into the nuclear genome of a crustacean.