Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.

The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.

Validation of open-path dual-comb spectroscopy against an O2 background: erratum.

This erratum corrects errors that appear in Opt. Express31, 5042 (2023).10.1364/OE.480301.

Removing biases in dual frequency comb spectroscopy due to digitizer nonlinearity.

Operation of any dual-comb spectrometer requires digitization of the interference signal before further processing. Nonlinearities in the analog-to-digital conversion can alter the apparent gas concentration by multiple percent, limiting both precision and accuracy of this technique. This work describes both the measurement of digitizer nonlinearity and the development of a model that quantitatively describes observed concentration bias over a range of conditions. We present hardware methods to suppress digitizer-induced bias of concentration retrievals below 0.1%.

Validation of open-path dual-comb spectroscopy against an O2 background.

Dual-comb spectroscopy measures greenhouse gas concentrations over kilometers of open air with high precision. However, the accuracy of these outdoor spectra is challenging to disentangle from the absorption model and the fluctuating, heterogenous concentrations over these paths. Relative to greenhouse gases, O2 concentrations are well-known and evenly mixed throughout the atmosphere. Assuming a constant O2 background, we can use O2 concentration measurements to evaluate the consistency of open-path dual-comb spectroscopy with laboratory-derived absorption models. To this end, we construct a dual-comb spectrometer spanning 1240 nm to 1700nm, which measures O2 absorption features in addition to CO2 and CH4. O2 concentration measurements across a 560 m round-trip outdoor path reach 0.1% precision in 10 minutes. Over seven days of shifting meteorology and spectrometer conditions, the measured O2 has -0.07% mean bias, and 90% of the measurements are within 0.4% of the expected hemisphere-average concentration. The excursions of up to 0.4% seem to track outdoor temperature and humidity, suggesting that accuracy may be limited by the O2 absorption model or by water interference. This simultaneous O2, CO2, and CH4 spectrometer will be useful for measuring accurate CO2 mole fractions over vertical or many-kilometer open-air paths, where the air density varies.

Mandibular muscle troponin of the Florida carpenter ant Camponotus floridanus: extending our insights into invertebrate Ca2+ regulation.

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.

Fabrication and characterization of short acetylene-filled photonic microcells.

We have developed short (6-10 cm), connectorized acetylene-filled photonic microcells (PMCs) from photonic bandgap fibers that may replace near-IR frequency references for certain applications based on gas-filled glass cells. By using a tapering technique to seal the microcells, we were able to achieve a high transmission efficiency of 80% and moderate line center accuracy of 10 MHz (1σ). This approaches the National Institute of Standard Technology Standard Reference Material 2517a 10 MHz (2σ) accuracy. Using an earlier Q-tipping technique, 37% off-resonant transmission and 5 MHz accuracy were achieved in finding the line center, but a large 13% etalon-like effect appears on the wings of the optical depth. The etalon-like effect is reduced to less than 1% by using the tapering method. In both cases, the microcells could be connectorized, albeit with a reduction in off-resonant transmission efficiency, for integration into multimode fibers or free-space optical systems. Although contamination is introduced during both fabrication techniques, the P13 PMC line center shifts are small with respect to the sub-Doppler line center. This shows that the PMC can be used for moderate-accuracy frequency measurements. Finally, repeatable measurements show that PMCs are stable in terms of total pressure over approximately one year.

Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome.

Bacteriophages of nitrogen-fixing rhizobial bacteria are revealing a wealth of novel structures, diverse enzyme combinations and genomic features. Here we report the cryo-EM structure of the phage capsid at 4.9-5.7Å-resolution, the phage particle proteome, and the genome of the Sinorhizobium meliloti-infecting Podovirus ΦM5. This is the first structure of a phage with a capsid and capsid-associated structural proteins related to those of the LUZ24-like viruses that infect Pseudomonas aeruginosa. Like many other Podoviruses, ΦM5 is a T=7 icosahedron with a smooth capsid and short, relatively featureless tail. Nonetheless, this group is phylogenetically quite distinct from Podoviruses of the well-characterized T7, P22, and epsilon 15 supergroups. Structurally, a distinct bridge of density that appears unique to ΦM5 reaches down the body of the coat protein to the extended loop that interacts with the next monomer in a hexamer, perhaps stabilizing the mature capsid. Further, the predicted tail fibers of ΦM5 are quite different from those of enteric bacteria phages, but have domains in common with other rhizophages. Genomically, ΦM5 is highly mosaic. The ΦM5 genome is 44,005bp with 357bp direct terminal repeats (DTRs) and 58 unique ORFs. Surprisingly, the capsid structural module, the tail module, the DNA-packaging terminase, the DNA replication module and the integrase each appear to be from a different lineage. One of the most unusual features of ΦM5 is its terminase whose large subunit is quite different from previously-described short-DTR-generating packaging machines and does not fit into any of the established phylogenetic groups.

Near diffraction-limited performance of an OPA pumped acetylene-filled hollow-core fiber laser in the mid-IR.

We investigate the mid-IR laser beam characteristics from an acetylene-filled hollow-core optical fiber gas laser (HOFGLAS) system. The laser exhibits near-diffraction limited beam quality in the 3 µm region with M2 = 1.15 ± 0.02 measured at high pulse energy, and the highest mid-IR pulse energy from a HOFGLAS system of 1.4 µJ is reported. Furthermore, the effects of output saturation with pump pulse energy are reduced through the use of longer fibers with low loss. Finally, the slope efficiency is shown to be nearly independent of gas pressure over a wide range, which is encouraging for further output power increase.

Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid.

UNLABELLED: Relatively little is known about the phages that infect agriculturally important nitrogen-fixing rhizobial bacteria. Here we report the genome and cryo-electron microscopy structure of the Sinorhizobium meliloti-infecting T4 superfamily phage ΦM9. This phage and its close relative Rhizobium phage vB_RleM_P10VF define a new group of T4 superfamily phages. These phages are distinctly different from the recently characterized cyanophage-like S. meliloti phages of the ΦM12 group. Structurally, ΦM9 has a T=16 capsid formed from repeating units of an extended gp23-like subunit that assemble through interactions between one subunit and the adjacent E-loop insertion domain. Though genetically very distant from the cyanophages, the ΦM9 capsid closely resembles that of the T4 superfamily cyanophage Syn9. ΦM9 also has the same T=16 capsid architecture as the very distant phage SPO1 and the herpesviruses. Despite their overall lack of similarity at the genomic and structural levels, ΦM9 and S. meliloti phage ΦM12 have a small number of open reading frames in common that appear to encode structural proteins involved in interaction with the host and which may have been acquired by horizontal transfer. These proteins are predicted to encode tail baseplate proteins, tail fibers, tail fiber assembly proteins, and glycanases that cleave host exopolysaccharide. IMPORTANCE: Despite recent advances in the phylogenetic and structural characterization of bacteriophages, only a small number of phages of plant-symbiotic nitrogen-fixing soil bacteria have been studied at the molecular level. The effects of phage predation upon beneficial bacteria that promote plant growth remain poorly characterized. First steps in understanding these soil bacterium-phage dynamics are genetic, molecular, and structural characterizations of these groups of phages. The T4 superfamily phages are among the most complex phages; they have large genomes packaged within an icosahedral head and a long, contractile tail through which the DNA is delivered to host cells. This phylogenetic and structural study of S. meliloti-infecting T4 superfamily phage ΦM9 provides new insight into the diversity of this family. The comparison of structure-related genes in both ΦM9 and S. meliloti-infecting T4 superfamily phage ΦM12, which comes from a completely different lineage of these phages, allows the identification of host infection-related factors.

Carrier-envelope offset frequency linewidth narrowing in a Cr:forsterite laser-based frequency comb.

Cr:forsterite laser-based frequency combs are useful for spectroscopic purposes in the near-IR wavelength region. However, self-referenced Cr:forsterite combs tend to exhibit wide carrier-envelope offset frequency (f0) linewidths, which result in broad comb teeth. This can be attributed to significant frequency noise across the comb's spectral bandwidth. We have stabilized a prism-based Cr:forsterite laser comb and observed narrowing of the f0 linewidth from ∼1.4 MHz down to ∼100 kHz by changing only the prism insertion, and to 23 kHz by inserting a knife edge into the intracavity beam while keeping the same prism insertion. The noise dynamics of the Cr:forsterite laser frequency comb are investigated with the goal of explaining this f0 narrowing phenomenon.

Composition and Diversity of Avian Communities Using a New Urban Habitat: Green Roofs.

Green roofs on buildings are becoming popular and represent a new component of the urban landscape. Public benefits of green roof projects include reduced stormwater runoff, improved air quality, reduced urban heat island effects, and aesthetic values. As part of a city-wide plan, several green roofs have been constructed at Chicago's O'Hare International Airport (ORD). Like some other landscaping features, green roofs on or near an airport might attract wildlife and thus increase the risk of bird-aircraft collisions. During 2007-2011, we conducted a series of studies to evaluate wildlife use of newly constructed green roofs and traditional (gravel) roofs on buildings at ORD. These green roofs were 0.04-1.62 ha in area and consisted of primarily stonecrop species for vegetation. A total of 188 birds were observed using roofs during this research. Of the birds using green roofs, 66, 23, and 4 % were Killdeer, European Starlings, and Mourning Doves, respectively. Killdeer nested on green roofs, whereas the other species perched, foraged, or loafed. Birds used green roofs almost exclusively between May and October. Overall, avian use of the green roofs was minimal and similar to that of buildings with traditional roofs. Although green roofs with other vegetation types might offer forage or cover to birds and thus attract potentially hazardous wildlife, the stonecrop-vegetated green roofs in this study did not increase the risk of bird-aircraft collisions.

Stretched-pulse and solitonic operation of an all-fiber thulium/holmium-doped fiber laser.

Stretched-pulse operation of a mode-locked thulium/holmium-doped fiber laser has been demonstrated using a high numerical aperture (NA) fiber inside the laser cavity for intracavity dispersion compensation. The high NA fiber exhibits normal group-velocity dispersion allowing for the net-cavity dispersion to be positive. We experimentally investigate the laser dynamics as a function of the net-cavity dispersion, observing the transition from stretched-pulse to solitonic operation as the length of high NA fiber was reduced. In the stretched-pulse regime the laser produced pulses with a bandwidth of 30 nm and duration of 450 fs. Methods for compensating the third-order dispersion using high NA fibers are proposed.

Direct fiber comb stabilization to a gas-filled hollow-core photonic crystal fiber.

We have isolated a single tooth from a fiber laser-based optical frequency comb for nonlinear spectroscopy and thereby directly referenced the comb. An 89 MHz erbium fiber laser frequency comb is directly stabilized to the P(23) (1539.43 nm) overtone transition of (12)C(2)H(2) inside a hollow-core photonic crystal fiber. To do this, a single comb tooth is isolated and amplified from 20 nW to 40 mW with sufficient fidelity to perform saturated absorption spectroscopy. The fractional stability of the comb, ~7 nm away from the stabilized tooth, is shown to be 6 × 10(-12) at 100 ms gate time, which is over an order of magnitude better than that of a comb referenced to a GPS-disciplined Rb oscillator.

Effect of temperature on structural configuration and immunoreactivity of pH-stressed soybean (Glycine max) agglutinin.

Soybean agglutinin (SBA) was purified using ammonium sulfate precipitation and liquid chromatography. Purified SBA was used to produce monoclonal antibodies through hybridoma technology. SBA secondary structure was studied using circular dichroism. pH-stressed (pHs 3.0, 7.2, 8.5, and 9.6) SBA physical properties (particle size, ζ-potential, and aggregation temperature) were investigated. Gel electrophoresis (non-native and native) was used to study heat-induced structural configuration changes in SBA. The effect of pH and temperature on the immunoreactivity of SBA was analyzed using enzyme-linked immunosorbent assay and immunoblots probed with two anti-SBA monoclonal antibodies with either linear or conformational epitopes. The hemagglutinating activity of heated SBA was measured by hemagglutination assay. Our results indicated that SBA had the least thermostability at pH 3.0 and the highest at pH 8.5. Temperature-induced structural configuration change on pH-stressed SBA led to immunoreactivity change. Heat-induced (70 and 80 °C) soluble SBA aggregation was proportionally related to hemagglutinating activity reduction.

The succinoglycan endoglycanase encoded by exoK is required for efficient symbiosis of Sinorhizobium meliloti 1021 with the host plants Medicago truncatula and Medicago sativa (Alfalfa).

The acidic polysaccharide succinoglycan produced by the nitrogen-fixing rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and to efficiently invade the host plant M. sativa (alfalfa). The ß-glucanase enzyme encoded by exoK has previously been demonstrated to cleave succinoglycan and participate in producing the low molecular weight form of this polysaccharide. Here, we show that exoK is required for efficient S. meliloti invasion of both M. truncatula and alfalfa. Deletion mutants of exoK have a substantial reduction in symbiotic productivity on both of these plant hosts. Insertion mutants of exoK have an even less productive symbiosis than the deletion mutants with the host M. truncatula that is caused by a secondary effect of the insertion itself, and may be due to a polar effect on the expression of the downstream exoLAMON genes.

Acetylene frequency references in gas-filled hollow optical fiber and photonic microcells.

Gas-filled hollow optical fiber references based on the P(13) transition of the ν1+ν3 band of 12C2H2 promise portability with moderate accuracy and stability. Previous realizations are corrected (<1σ) by using proper modeling of a shift due to line-shape. To improve portability, a sealed photonic microcell is characterized on the 12C2H2 ν1+ν3 P(23) transition with somewhat reduced accuracy and stability. Effects of the photonic crystal fiber, including surface modes, are explored. Both polarization-maintaining (PM) and non-PM 7-cell photonic bandgap fiber are shown to be unsuitable for kilohertz-level frequency references.

Open-path measurement of stable water isotopologues using mid-infrared dual-comb spectroscopy.

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 1000s. 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.

Limosilactobacillus reuteri administration alters the gut-brain-behavior axis in a sex-dependent manner in socially monogamous prairie voles.

Research on the role of gut microbiota in behavior has grown dramatically. The probiotic L. reuteri can alter social and stress-related behaviors - yet, the underlying mechanisms remain largely unknown. Although traditional laboratory rodents provide a foundation for examining the role of L. reuteri on the gut-brain axis, they do not naturally display a wide variety of social behaviors. Using the highly-social, monogamous prairie vole (Microtus ochrogaster), we examined the effects of L. reuteri administration on behaviors, neurochemical marker expression, and gut-microbiome composition. Females, but not males, treated with live L. reuteri displayed lower levels of social affiliation compared to those treated with heat-killed L. reuteri. Overall, females displayed a lower level of anxiety-like behaviors than males. Live L. reuteri-treated females had lower expression of corticotrophin releasing factor (CRF) and CRF type-2-receptor in the nucleus accumbens, and lower vasopressin 1a-receptor in the paraventricular nucleus of the hypothalamus (PVN), but increased CRF in the PVN. There were both baseline sex differences and sex-by-treatment differences in gut microbiome composition. Live L. reuteri increased the abundance of several taxa, including Enterobacteriaceae, Lachnospiraceae NK4A136, and Treponema. Interestingly, heat-killed L. reuteri increased abundance of the beneficial taxa Bifidobacteriaceae and Blautia. There were significant correlations between changes in microbiota, brain neurochemical markers, and behaviors. Our data indicate that L. reuteri impacts gut microbiota, gut-brain axis and behaviors in a sex-specific manner in socially-monogamous prairie voles. This demonstrates the utility of the prairie vole model for further examining causal impacts of microbiome on brain and behavior.

A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules.

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.

All-fiber passively mode-locked thulium/holmium laser with two center wavelengths.

We have demonstrated a self-starting, passively mode-locked Tm/Ho codoped fiber laser that lases at one of two center wavelengths. An amplified 1.56 µm distributed feedback laser pumps a ring laser cavity which contains 1 m of Tm/Ho codoped silica fiber. Mode locking is obtained via nonlinear polarization rotation using a c-band polarization sensitive isolator with two polarization controllers. The laser is able to pulse separately at either 1.97 or 2.04 µm by altering the intracavity polarization during the initiation of mode locking. The codoped fiber permits pulsing at one of two wavelengths, where the shorter is due to the Tm(3+) emission and the longer due to the Ho(3+) emission. The laser produces a stable pulse train at 28.4 MHz with 25 mW average power, and a pulse duration of 966 fs with 9 nm bandwidth.