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Background We have used the genomic data in the Integrated Microbial Genomes system of the Department of Energy’s Joint Genome Institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. The genomic data was screened by searching for ORFs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria. Results Using this approach, we identified many genes known to be involved in nodulation or nitrogen fixation, as well as several new candidate genes. We knocked out selected new genes and assayed for the presence of nodulation phenotypes and/or nodule-specific expression. One of these genes, SMc00911, is strongly expressed by bacterial cells within host plant nodules, but is expressed minimally by free-living bacterial cells. A strain carrying an insertion mutation in SMc00911 is not defective in the symbiosis with host plants, but in contrast to expectations, this mutant strain is able to out-compete the S. meliloti 1021 wild type strain for nodule occupancy in co-inoculation experiments. The SMc00911 ORF is predicted to encode a “SodM-like” (superoxide dismutase-like) protein containing a rhodanese sulfurtransferase domain at the N-terminus and a chromate-resistance superfamily domain at the C-terminus. Several other ORFs (SMb20360, SMc01562, SMc01266, SMc03964, and the SMc01424-22 operon) identified in the screen are expressed at a moderate level by bacteria within nodules, but not by free-living bacteria. Conclusions Based on the analysis of ORFs identified in this study, we conclude that this comparative genomics approach can identify rhizobial genes involved in the nitrogen-fixing symbiosis with host plants, although none of the newly identified genes were found to be essential for this process.

The Ume6 transcription factor in yeast is known to both repress and activate expression of diverse genes during growth and meiotic development. To obtain a more complete profile of the functions regulated by this protein, microarray analysis was used to examine transcription in wild-type and ume6Δ diploids during vegetative growth in glucose and acetate. Two different genetic backgrounds (W303 and SK1) were examined to identify a core set of strain-independent Ume6-regulated genes. Among genes whose expression is controlled by Ume6 in both backgrounds, 82 contain homologies to the Ume6-binding site (URS1) and are expected to be directly regulated by Ume6. The vast majority of those whose functions are known participate in carbon/nitrogen metabolism and/or meiosis. Approximately half of the Ume6 direct targets are induced during meiosis, with most falling into the early meiotic expression class (cluster 4), and a smaller subset in the middle and later classes (clusters 5-7). Based on these data, we propose that Ume6 serves a unique role in diploid cells, coupling metabolic responses to nutritional cues with the initiation and progression of meiosis. Finally, expression patterns in the two genetic backgrounds suggest that SK1 is better adapted to respiration and W303 to fermentation, which may in part account for the more efficient and synchronous sporulation of SK1.

Ants use their mandibles for a variety of functions and behaviors. We investigated mandibular muscle structure and function from major workers of the Florida carpenter ant Camponotus floridanus: force-pCa relation and velocity of unloaded shortening of single, permeabilized fibres, primary sequences of troponin subunits (TnC, TnI and TnT) from a mandibular muscle cDNA library, and muscle fibre ultrastructure. From the mechanical measurements, we found Ca2+-sensitivity of isometric force was markedly shifted rightward compared with vertebrate striated muscle. From the troponin sequence results, we identified features that could explain the rightward shift of Ca2+-activation: the N-helix of TnC is effectively absent and three of the four EF-hands of TnC (sites I, II and III) do not adhere to canonical sequence rules for divalent cation binding; two alternatively spliced isoforms of TnI were identified with the alternatively spliced exon occurring in the region of the IT-arm α-helical coiled-coil, and the N-terminal extension of TnI may be involved in modulation of regulation, as in mammalian cardiac muscle; and TnT has a Glu-rich C-terminus. In addition, a structural homology model was built of C. floridanus troponin on the thin filament. From analysis of electron micrographs, we found thick filaments are almost as long as the 6.8 μm sarcomeres, have diameter of ~ 16 nm, and typical center-to-center spacing of ~ 46 nm. These results have implications for the mechanisms by which mandibular muscle fibres perform such a variety of functions, and how the structure of the troponin complex aids in these tasks.

Spo13 is a key meiosis-specific regulator required for centromere cohesion and coorientation, and for progression through two nuclear divisions. We previously reported that it causes a G2/M arrest and may delay the transition from late anaphase to G1, when overexpressed in mitosis. Yet its mechanism of action has remained elusive. Here we show that Spo13, which is phosphorylated and stabilized at G2/M in a Cdk/Clb-dependent manner, acts at two stages during mitotic cell division. Spo13 provokes a G2/M arrest that is reversible and largely independent of the Mad2 spindle checkpoint. Since mRNAs whose induction requires Cdc14 activation are reduced, we propose that its anaphase delay results from inhibition of Cdc14 function. Indeed, the Spo13-induced anaphase delay correlates with Cdc14 phosphatase retention in the nucleolus and with cyclin B accumulation, which both impede anaphase exit. At the onset of arrest, Spo13 is primarily associated with the nucleolus, where Cdc14 accumulates. Significantly, overexpression of separase (Esp1), which promotes G2/M and anaphase progression, suppresses Spo13 effects in mitosis, arguing that Spo13 acts upstream or parallel to Esp1. Given that Spo13 overexpression reduces Pds1 and cyclin B degradation, our findings are consistent with a role for Spo13 in regulating APC, which controls both G2/M and anaphase. Similar effects of Spo13 during meiotic MI may prevent cell cycle exit and initiation of DNA replication prior to MII, thereby ensuring two successive chromosome segregation events without an intervening S phase.

Scuba divers typically rinse equipment in communal tanks. Studies show these tanks are contaminated with bacteria, but the types of bacteria have not been studied. We sought to identify bacteria in rinse tanks at a dive facility at San Pedro, Belize, to determine the origin of the bacteria and determine whether the bacteria represented potential threats to human health. The identity of bacteria was investigated using reverse line blot (RLB) assays based on 28 different rDNA probes designed to detect known pathogens of sepsis, as well as by sequencing 23S rDNA from isolates and performing VITEK identification of several isolates. Based on the identities of bacteria in divers' rinse tanks, many likely originate from the ocean, and others likely originate from the divers themselves. None of the bacteria identified would be considered overt human pathogens. However, some of the bacteria found in the tanks are known to be associated with unsanitary conditions and can cause opportunistic infections, which may pose health problems to some individuals. Rinsing scuba equipment in communal tanks has the potential to transmit disease among some divers. Equipment, especially regulators and masks, should be rinsed/cleaned individually and not be placed in communal tanks.

Fecal glucocorticoid metabolite (FGM) assays are a popular means of monitoring adrenocortical activity (i.e., physiological stress response) in wildlife. Species-specific differences in glucocorticoid metabolism and excretion require assay validation, including both laboratory and biological components, before assay use in new species. We validated a commercially available radioimmunoassay (MP 125I corticosterone RIA kit [MP Biomedicals, Solon, OH]) for measuring FGMs of several South African herbivores, including giraffe (Giraffa camelopardalis), impala (Aepyceros melampus), nyala (Tragelaphus buxtoni), kudu (Tragelaphus strepsiceros), wildebeest (Connochaetes taurinus), and zebra (Equus burchelli). These herbivores are important in South African parks and reserves for ecotourism and as a prey base for predators and serve an integral role in ecosystem processes. Standard biochemical validations (e.g., recovery of exogenous corticosterone, intra- and interassay variation, and parallelism) demonstrated that the assay accurately and precisely measured FGMs of all 6 herbivore species. Our biological validations demonstrated that the assay was sensitive enough to detect changes in FGM production associated with season. Samples collected during the dry season (Jun–Aug) contained higher FGM concentrations than those from the wet season (Dec–Feb) in all species. We established optimal sample dilutions and reference FGM levels for these 6 herbivores, which can now be used to monitor the effects of management and ecotourism activities on the stress responses of these herbivores.

The temporal order of DNA replication (replication timing, RT) is highly coupled with genome architecture, but cis-elements regulating spatio-temporal control of replication have remained elusive. We performed an extensive series of CRISPR mediated deletions and inversions and high-resolution capture Hi-C of a pluripotency associated domain (DppA2/4) in mouse embryonic stem cells. Whereas CTCF mediated loops and chromatin domain boundaries were dispensable, deletion of three intra-domain prominent CTCF-independent 3D contact sites caused a domain-wide early to late switch in RT, shift in sub-nuclear chromatin compartment and loss of transcriptional activity, These early replication control elements (ERCEs) display prominent chromatin features resembling enhancers/promoters and individual and pair-wise deletions of the ERCEs confirmed their partial redundancy and interdependency in controlling domain-wide RT and transcription. Our results demonstrate that discrete cis-regulatory elements mediate domain-wide RT, chromatin compartmentalization, and transcription, representing a major advance in dissecting the relationship between genome structure and function.

Avian radar technologies have the potential to serve an important role in the quantification of bird movements and determining patterns of bird use in areas where human–wildlife conflicts might occur (e.g., airports, wind energy facilities). Ground-truthing studies are needed to help wildlife managers understand the biological meaning of radar information, as the capabilities and limitations of these technologies are relatively unknown. We conducted a study to evaluate the efficacy of three X-band marine radar sensors for tracking red-tailed hawks (Buteo jamaicensis) on or near the airfield at Chicago’s O’Hare International Airport from September 2010 to May 2014. Specific information regarding red-tailed hawk locations derived from satellite telemetry was used to determine how frequently the three radar sensors provided corresponding tracks of these avian targets (i.e., synchronized monitoring). We examined various factors (e.g., bird altitude and distance to the radar) to determine if they had any influence on the frequency of synchronicity between satellite telemetry locations and radar tracks. We found evidence that as the distance between a hawk and the radars increased, the radars’ ability to detect and track known avian targets decreased. Overall, the frequency of synchronization events for red-tailed hawks was low. Of the 1977 red-tailed hawk locations that should have been visible to the radar sensors, 51 of these bird movements were tracked by at least one of the radar sensors (2.6%). This study provides a new methodology for evaluating the performance of radar systems for tracking birds and determining what factors might influence overall performance.

Objectives. We assessed the effectiveness of a 5-year trial of a comprehensive school-based program designed to prevent substance use, violent behaviors, and sexual activity among elementary-school students. Methods. We used a matched-pair, cluster-randomized, controlled design, with 10 intervention schools and 10 control schools. Fifth-graders (N = 1714) self-reported on lifetime substance use, violence, and voluntary sexual activity. Teachers of participant students reported on student (N = 1225) substance use and violence. Results. Two-level random-effects count models (with students nested within schools) indicated that student-reported substance use (rate ratio [RR] = 0.41; 90% confidence interval [CI] = 0.25, 0.66) and violence (RR = 0.42; 90% CI = 0.24, 0.73) were significantly lower for students attending intervention schools. A 2-level random-effects binary model indicated that sexual activity was lower (odds ratio = 0.24; 90% CI = 0.08, 0.66) for intervention students. Teacher reports substantiated the effects seen for student-reported data. Dose-response analyses indicated that students exposed to the program for at least 3 years had significantly lower rates of all negative behaviors. Conclusions. Risk-related behaviors were substantially reduced for students who participated in the program, providing evidence that a comprehensive school-based program can have a strong beneficial effect on student behavior.

We present an open-path mid-infrared dual-comb spectroscopy (DCS) system capable of precise measurement of the stable water isotopologues H216O and HD16O. This system ran in a remote configuration at a rural test site for 3.75 months with 60 % uptime and achieved a precision of < 2 ‰ on the normalized ratio of H216O and HD16O (δD) in 1000 s. Here, we compare the δD values from the DCS system to those from the National Ecological Observatory Network (NEON) isotopologue point sensor network. Over the multi-month campaign, the mean difference between the DCS δD values and the NEON δD values from a similar ecosystem is < 2 ‰ with a standard deviation of 18 ‰, which demonstrates the inherent accuracy of DCS measurements over a variety of atmospheric conditions. We observe time-varying diurnal profiles and seasonal trends that are mostly correlated between the sites on daily timescales. This observation motivates the development of denser ecological monitoring networks aimed at understanding regional- and synoptic-scale water transport. Precise and accurate open-path measurements using DCS provide new capabilities for such networks.