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Genome architecture has proven to be critical in determining gene regulation across almost all domains of life. While many of the key components and mechanisms of eukaryotic genome organization have been described, the interplay between bacterial DNA organization and gene regulation is only now being fully appreciated. An increasing pool of evidence has demonstrated that the bacterial chromosome can reasonably be thought of as chromatin, and that bacterial chromosomes contain transcriptionally silent and transcriptionally active regions analogous to heterochromatin and euchromatin, respectively. The roles played by histones in eukaryotic systems appear to be shared across a range of nucleoid-associated proteins (NAPs) in bacteria, which function to compact, structure, and regulate large portions of bacterial chromosomes. The broad range of extant NAPs, and the extent to which they differ from species to species, has raised additional challenges in identifying and characterizing their roles in all but a handful of model bacteria. Here we review the regulatory roles played by NAPs in several well-studied bacteria and use the resulting state of knowledge to provide a working definition for NAPs, based on their function, binding pattern, and expression levels. We present a screening procedure which can be applied to any species for which transcriptomic data are available. Finally, we note that NAPs tend to play two major regulatory roles – xenogeneic silencers and developmental regulators – and that many unrecognized potential NAPs exist in each bacterial species examined.

There is increasing evidence that prokaryotes maintain chromosome structure, which in turn impacts gene expression. We recently characterized densely occupied, multi-kilobase regions in the E. coli genome that are transcriptionally silent, similar to eukaryotic heterochromatin. These extended protein occupancy domains (EPODs) span genomic regions containing genes encoding metabolic pathways as well as parasitic elements such as prophages. Here, we investigate the contributions of nucleoid-associated proteins (NAPs) to the structuring of these domains, by examining the impacts of deleting NAPs on EPODs genome-wide in E. coli and B. subtilis. We identify key NAPs contributing to the silencing of specific EPODs, whose deletion opens a chromosomal region for RNA polymerase binding at genes contained within that region. We show that changes in E. coli EPODs facilitate an extra layer of transcriptional regulation, which prepares cells for exposure to exotic carbon sources. Furthermore, we distinguish novel xenogeneic silencing roles for the NAPs Fis and Hfq, with the presence of at least one being essential for cell viability in the presence of domesticated prophages. Our findings reveal previously unrecognized mechanisms through which genomic architecture primes bacteria for changing metabolic environments and silences harmful genomic elements.

Heterochromatin is most often associated with eukaryotic organisms. Yet, bacteria also contain areas with densely protein-occupied chromatin that appear to silence gene expression. One nucleoid-associated silencing factor is the conserved protein Hfq. Although seemingly nonspecific in its DNA binding properties, Hfq is strongly enriched at AT-rich DNA regions, characteristic of prophages and mobile genetic elements. Here, we demonstrate that polyphosphate (polyP), an ancient and highly conserved polyanion, is essential for the site-specific DNA binding properties of Hfq in bacteria. Absence of polyP markedly alters the DNA binding profile of Hfq, causes unsolicited prophage and transposon mobilization, and increases mutagenesis rates and DNA damage–induced cell death. In vitro reconstitution of the system revealed that Hfq and polyP interact with AT-rich DNA sequences and form phase-separated condensates, a process that is mediated by the intrinsically disordered C-terminal extensions of Hfq. We propose that polyP serves as a newly identified driver of heterochromatin formation in bacteria.

Eukaryotes maintain hundreds of copies of ribosomal DNA (rDNA), many more than required for ribosome biogenesis, suggesting a yet undefined role for large rDNA arrays outside of ribosomal RNA synthesis. We demonstrate that reducing the Saccharomyces cerevisiae rDNA array to 35 copies, which is sufficient for ribosome function, shifts rDNA from being the latest replicating region in the genome to one of the earliest. This change in replication timing results in delayed genome-wide replication and classic replication defects. We present evidence that the requirement for rDNA to replicate late, which is conserved among eukaryotes, also coordinates the completion of genome replication with anaphase entry through the proper sequestration of the mitotic exit regulator Cdc14p in the rDNA-containing nucleolus. Our findings suggest that, instead of being a passive repetitive element, the large late-replicating rDNA array plays an active role in genome replication and cell cycle control.

Relevant and impactful mentors are essential to a graduate student’s career. Finding mentors can be challenging in umbrella programs with hundreds of faculty members. To foster connections between potential mentors and students with similar research interests, we created a Matchathon event, which has successfully enabled students to find mentors. We developed an easy-to-use R Shiny app (https://github.com/UM-OGPS/matchathon/) to facilitate matching and organizing the event that can be used at any institution. It is our hope that this resource will improve the environment and retention rates for students in the academy.The open source app is publicly available on the web (app: https://UM-OGPS.shinyapps.io/matchathon/; source code: https://github.com/UM-OGPS/matchathon/).

Free-living bacteria adapt to environmental change by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. A predictive understanding of bacterial physiology requires us to globally monitor all such protein–DNA interactions across a range of environmental and genetic perturbations. Here, we show that such global observations are possible using an optimized version of in vivo protein occupancy display technology (in vivo protein occupancy display—high resolution, IPOD-HR) and present a pilot application to Escherichia coli. We observe that the E. coli protein–DNA interactome organizes into 2 distinct prototypic features: (1) highly dynamic condition-dependent transcription factor (TF) occupancy; and (2) robust kilobase scale occupancy by nucleoid factors, forming silencing domains analogous to eukaryotic heterochromatin. We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium. Beyond discovery of previously hidden regulatory logic, we show that these observations can be utilized to computationally determine sequence specificity models for the majority of active TFs. Our study demonstrates that global observations of protein occupancy combined with statistical inference can rapidly and systematically reveal the transcriptional regulatory and structural features of a bacterial genome. This capacity is particularly crucial for non-model bacteria that are not amenable to routine genetic manipulation., This study uses a novel technology (IPOD-HR) to quantify the protein occupancy of an entire bacterial chromosomes at high-resolution; in addition to enabling the monitoring of global transcriptional regulatory dynamics, IPOD-HR reveals densely occupied silencing domains akin to eukaryotic heterochromatin.

A form of dwarfism known as Meier-Gorlin syndrome (MGS) is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5). These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase. Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45). The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty. Since the site of one of the missense mutations in the human ORC4 alleles is conserved between humans and yeast, we sought to determine in what way this single amino acid change affects the process of chromosome replication, by introducing the comparable mutation into yeast (orc4Y232C). We find that yeast cells with the orc4Y232C allele have a prolonged S-phase, due to compromised replication initiation at the ribosomal DNA (rDNA) locus located on chromosome XII. The inability to initiate replication at the rDNA locus results in chromosome breakage and a severely reduced rDNA copy number in the survivors, presumably helping to ensure complete replication of chromosome XII. Although reducing rDNA copy number may help ensure complete chromosome replication, orc4Y232C cells struggle to meet the high demand for ribosomal RNA synthesis. This finding provides additional evidence linking two essential cellular pathways—DNA replication and ribosome biogenesis., Author summary The origin recognition complex (ORC) is essential for licensing replication origins during M/G1 for their firing in the subsequent S phase. Individuals with a rare form of dwarfism called Meier-Gorlin syndrome (MGS) have mutations in proteins required for origin activation, including various subunits of ORC. To better understand the molecular and cellular consequences of these mutations, we introduced an equivalent MGS mutation in ORC4 into yeast. We find that origin activity in the ribosomal DNA (rDNA) repeats is severely compromised in yeast that harbor the MGS allele. Consequently, cells that have reduced their rDNA copy number from ~150 to fewer than 30 copies overtake the culture. Although the loss of rDNA repeats helps ensure the complete replication of chromosome XII during S phase, cells with fewer rDNA repeats struggle to meet the high demand for ribosomal RNA.

If we are to significantly increase the transmission speed of optical networks, the impact of higher order dispersion must be clarified. This paper gives general expressions that describe pulse broadening due to even and odd higher order dispersion in a single-mode fiber. The intrinsic impulsive responses for even order dispersion (beyond the second order) are characterized by symmetrical waveforms with long trailing skirts, whereas the responses for odd orders show asymmetrical strongly oscillating waveforms. The transmission limits are also analytically obtained for each higher nth order that induces intersymbol interference. Transmission lengths are limited by the factor of 1/B/sub 0//sup n/ where B/sub 0/ is the bit rate and n is the dispersion order.

To continue and improve the earlier studies by different authors [1-4], in 2011 the BIPM launched a pilot study on the accurate calibration for the UTC time links [5]. The goal is to unify the UTC time link calibration uncertainties ≤ 2 ns. This is attainable with the ‘one for all’ METODE scheme and a dedicatedly designed travelling calibrator (StdB). The METODE calibration result (CM) can be easily converted to the classic equipment internal delays INTDLY(P1/P2). Nine laboratories participated in the project [6-16]. An operational guideline is drafted and used to guide the calibration tours and data processing. This paper reviews the status of the study and gives the preliminary calibration results of the UTC time link calibrations of GNSS PPP, P3, L1C, TWSTFT and TWOTFT.

The FSA submarine optical amplifier system developed for commercial use is designed to transmit 2.5 and 10 Gb/s signals flexibly; its repeater spacing is 90 km. It contains six line pairs to yield a maximum transmission capacity of 60 Gb/s. Its system configuration, and the characteristics of its fibers and optical amplifiers, which realize effective dispersion and optical passband management, are introduced. We discuss its performance with regard to the parameters significant in optically amplified transmission: evolution of zero dispersion wavelength (ZDW), polarization mode dispersion (PMD), and fiber nonlinearity induced impairments. Signal-to-noise ratios (SNR's) for 2.5 and 10 Gb/s signal transmission are measured and the improvements offered by polarization scrambling are also discussed. Finally, ZDW, PMD, and SNR characteristics of the system after installation are reported.

Changes in dietary acid and blood pH lead to adaptations in key enzymes and transport proteins of the renal proximal tubule that tend to return blood pH to normal. The mechanisms responsible, as well as acid-regulated signaling pathways that may effect these responses, are reviewed.

It has long been known that excess intracellular fatty acids cause impaired insulin secretion, referred to as beta-cell lipotoxicity. Sterol regulatory element-binding protein (SREBP)-1c is a transcription factor that controls hepatic fatty acid synthesis. Activation of SREBP-1c by overnutrition also inhibits insulin receptor substrate-2 (IRS-2) and induces insulin resistance in the liver. As SREBP-1c is also expressed in beta cells, we hypothesized that activation of SREBP-1c could be a part of the mechanism by which saturated fatty acids induce beta-cell lipotoxicity. We found that nuclear SREBP-1c has a negative impact on both glucose- and potassium-stimulated insulin secretion as determined in islets from beta-cell-specific SREBP-1c transgenic mice as well as SREBP-1c knockout mice. This effect of SREBP-1c involves multiple functional pathways required for insulin secretion from beta cells: (i) decreased ATP caused by energy consumption through lipogenesis and uncoupling protein-2 (UCP-2) activation; (ii) repressed IRS-2 and pancreas duodenum homeobox 1 (PDX1) expression, leading to impaired beta-cell mass; and (iii) impaired post-ATP membrane voltage-dependent steps of the insulin secretion pathway caused by upregulated granuphilin and other ion channel proteins. Saturated fatty acids, such as palmitic acid (PA), impair insulin secretion through SREBP-1c activation, whereas polyunsaturated fatty acids including eicosapentaenoic acid (EPA) restore PA-suppressed insulin secretion through suppression of SREBP-1c. These data implicate a therapeutic potential of EPA against insulin secretion defects caused by lipotoxicity.

We have tried to detect changes of affects by measuring accelerated plethysmogram. We gave 9 kinds of mental stimuli to 22 subjects and measured their accelerated plethysinograms. We chose the power spectrum of a-wave intervals of accelerated plethysmogram as an index to detect changes of affects. The accumulated powers in a low frequency region measured in many kinds of stimuli were significantly smaller than that measured in the light chatting condition which we assume as a base condition in this research, whereas the accumulated powers in a high frequency region measured in some passive kinds of stimuli were significantly bigger than that measured in the base condition. We also analyzed the correlations of the accumulated powers between measured in the different stimuli. The correlation coefficients of the powers between almost all stimuli in the low frequency region are high, whereas these in the high frequency are high between some kinds of similar stimuli.

The purpose of this study was to examine the age-related difference in oral sensory function by testing oral stereognostic ability (OSA) and to determine the effect of wearing complete dentures on OSA. Subjects were 20 dentate and 30 edentulous elderly patients free from oral symptoms and pathologies, and 30 younger dentate students as controls. The OSA tests were conducted with test pieces of 12 shaped forms. The duration time for recognition was noted and the answers were recorded using a three-point scale. anova and paired t-tests were used to examine significant differences. P-values

In the time and frequency transfer and dissemination field, it is important to provide cost effective remote frequency calibration services with an uncertainty of around 10-12 for end users. It is also required to develop ultra precise transfer methods with an order of 10-15 or better uncertainty for the comparison between ultra stable frequency standards which are under developing. This study shows two methods using optical fiber networks to satisfy these demands. First, it is an economical remote calibration method using existing synchronous optical fiber communication networks. The measured frequency stability (the Allan deviation) of the transmission clock is 2times10-13 for an averaging time of one day. The result indicates the method is promising for the simple remote frequency calibration service. Second, it is an ultra precise two-way optical fiber time and frequency transfer method using a newly proposed bi-directional optical amplifier. In this method, wavelength division multiplexing (WDM) signals are transmitted along a single optical fiber. The preliminary measured frequency stability is less than 1015 (tau =104 s) for a 100-km-long fiber with the bi-directional amplifier. It suggests that the method has capability for improving TAI (International Atomic Time) and UTC (Coordinated Universal Time)

The authors present an electrical signal to noise ratio (SNR) formula considering intersymbol interference of transmitter/receiver pairs, which yield measurement error in SNR measurement of long haul optical amplifier systems. Experimental results confirm the validity of the formula.

The authors report 2.5 and 10 Gbit/s transoceanic distance transmission in a commercial FSA optical amplifier system which has 90 km repeater spacing. The unique fibre dispersion management technique and amplifier passband management scheme used in the system are successfully demonstrated. The SNR improvement achieved with polarisation scrambling is also reported.

The authors describe the design of a 1.55 mu m gigabit/s submarine repeatered transmission system. A repeater spacing of approximately 100 km with a small dispersion penalty in the gigabit/s region is achieved by combining 1.55- mu m distributed-feedback lasers with zero-dispersion-shifted fibers. In addition, the reliability requirement and jitter accumulation performance for long-haul repeatered transmission are discussed. A 1.8 Gb/s submarine repeatered transmission system is simulated. >

It is important to realize an economical optical access system that can provide various multimedia services as well as conventional telephone services. We introduce a cost effective system design and a flexible layer structure for a passive double star (PDS) system based on time compression multiplexing/time division multiple access (TCM/TDMA) technologies, a single fiber, and a single wavelength. This optical access system can be upgraded to support high-speed services with the introduction of the WDM technique. Performance evaluation results of the developed system show the validity of the system design. This PDS system will contribute to the development of optical access systems for FTTH (fiber-to-the-home).

Ultrasonically nebulized distilled water-induced bronchoconstriction (UNDW-IB) is specific to asthma. The mechanisms underlying UNDW-IB are not fully understood, and no reproducible animal model has been reported. The purpose of this study was to develop a guinea-pig model of UNDW-IB. Ultrasonically nebulized distilled water (UNDW) was inhaled 20 min after an aerosolized antigen challenge in passively sensitized and artificially ventilated guinea-pigs. UNDW was also inhaled 5 and 20 min after 0.1 mg x mL(-1) methacholine inhalation in nonsensitized animals. In addition, 0.1 mg x kg(-1) S-1452, a thromboxane A2 antagonist, or saline was given intravenously 5 min before UNDW inhalation in sensitized animals. The inhalation of UNDW caused bronchoconstriction, when inhaled 20 min after an antigen challenge in sensitized guinea-pigs. UNDW inhalation did not produce bronchoconstriction after saline inhalation in nonsensitized or sensitized guinea-pigs, or after antigen inhalation in nonsensitized animals. Methacholine-induced bronchoconstriction did not evoke UNDW-IB. Neither did S-1452 reduce the UNDW-IB. In conclusion, the guinea-pig model of ultrasonically nebulized distilled water-induced bronchoconstriction developed in this study suggests that allergic reaction, but not bronchoconstriction, can induce bronchial hyperresponsiveness to ultrasonically nebulized distilled water, and that thromboxane A2 is not involved in ultrasonically nebulized distilled water-induced bronchoconstriction.

We reported previously that electroacupuncture (Acu) applied to the acu-point equivalent to GV4 in the mouse just before the 2,4,6-trinitrochlorobenzene (TNCB) challenge suppressed the delayed type hypersensitivity (DTH) through endogenous opioidergic systems in the brain, and the pituitary was pivotal in this immunosuppression. The purpose of the present study was to compare the suppressive effects of Acu with those of single, acute doses of morphine on TNCB-DTH in intact and hypophysectomized (HPX) mice. Subcutaneous morphine 10 mg/kg in ddY mice, 30 mg/kg in BALB/c mice or intracisternal morphine 40 micrograms/mouse in BALB/c mice given just before TNCB challenge suppressed (40-53%) the maximal extent of ear swelling at 24 hrs after challenge in intact mice. In HPX mice, the suppressive effects of intracisternal morphine 10 and 100 micrograms/mouse were less pronounced than those observed in intact mice and there was no significant difference between intact and HPX groups. In addition, suppressive effects observed with Acu or subcutaneous morphine (30 mg/kg) were effectively antagonized by pretreatment with intracisternal naloxone at a dose of as low as 2 micrograms/mouse. Naloxone alone had no effect of its own. These results suggest that 1) the activation of opioid receptor-mediated pathways in the brain, which occurs when opioids are endogenously released (Acu) or exogenously given (morphine), is important in the suppression of TNCB-induced DTH, a cell-mediated immune response, and 2) the pituitary is less pivotal in the suppressive effects of acute morphine than in those of Acu.

Delaminomycins A, B, C and their derivatives were prepared and investigated biological activities of them. Among these compounds, spiro compounds (A2, B2 and C2) showed stronger inhibitory activity than natural products (A1, B1 and C1) on B16 melanoma cells adhesion assay and Con A-induced proliferation of murine splenic lymphocytes assay. In MLCR and antimicrobial assay, however, A1, B1 and C1 showed more potent inhibitory activity than spiro compounds (A2, B2 and C2). On the other hand, as to C-5' substituents of pyrrolidine ring, the order of inhibitory activity was R = OHR = OCH3R = H on Con A-induced proliferation of murine splenic lymphocytes assay. In MLCR and antimicrobial assay, however, the order of inhibitory activities were R = HR = OCH3R = OH. Inhibitory activities of A4 which was lacked pyrrolidine ring were reduced on B16 melanoma cells adhesion assay and on cytotoxicity against tumor cells in vitro in comparison with those of A1.

A simple method which can directly measure the zero dispersion wavelength of a entire optical amplifier transmission system is reported. It is based on dispersion induced phase to amplitude modulation conversion in an optical fibre. The experimental and theoretical results agree for a 2000 km transmission system, and the standard deviation of measured zero dispersion wavelengths is only 0.053 nm.

This paper describes the performance of a 446-Mbit/s integrated optical repeater which consists of four monolithic-integrated circuits (MIC's) using silicon bipolar-process technology. Repeater sensitivity for a bit error rate of 10-11is -37.5 dBm, and dynamic jitter is less than 0.3 degrees. Decision-level deviation of less than 1 percent caused by an ambient temperature change, and that of less than 4 percent due to a mark-ratio change is achieved by using a monolithic-integrated control system developed for a dc-coupled optical receiver. The degradation of the output optical power is less than 0.5 dB over a temperature range of 0-30\deg C. A power penalty of about 2 dB is observed for a 30°C ambient temperature increase.

It is important to accurately evaluate and reduce jitter accumulation in long-haul digital repeatered lines. Jitter accumulation caused by random pattern signals has already been analyzed. However, periodic pattern signals such as pseudorandom signals are usually used to measure jitter accumulation. This paper describes the difference between the jitter accumulation for both signals and the necessary conditions to accurately estimate jitter accumulation for random pattern signals by using periodic pattern signals. First, it is shown theoretically that systematic jitter for periodic signals saturates, showing a ripple pattern. The limit of increase is determined by the ratio of tank bandwidth and pattern repetition frequency. Up to a certain number of regenerators determined by the ratio, systematic jitter increases in rough proportion to the \sqrt{N} slope. It is also shown that the equation to estimate random pattern jitter accumulation is determined by the measured value for periodic pattern signals. Second, jitter characteristics are simulated by optical signal circulating experiments. The results are in agreement with the analysis. In addition, the reduction effects on periodic signal jitter accumulation caused by timing signal delay and nonlinearity of the limiter in the timing circuit are shown.

Periodic lowering of oxygen content of the soil atmosphere to 13% or less for periods of 2 or 3 days appeared to have no adverse effects on alfalfa growth. If there were any adverse effects, they were entirely masked by the dominating effect of reduced soil moisture stress. When hydraulic moisture stress reached approximately 0.2 atm. at the 10-inch depth, growth rate was greatly curtailed. When combined with the osmotic component of soil moisture stress, 0.2 atm. hydraulic stress resulted in total soil-moisture stresses of about 1.9 and 2.8 atm. on leached and unleached plots, respectively. In one series of irrigations where 17 inches of water were applied, the soil surface was sealed against diffusion of oxygen for at least 8 days. During this time the average oxygen content in the root zone dropped to 6% with individual readings as low as 3%. Alfalfa on these plots grew much better than did alfalfa on adjacent plots which received normal irrigation.

An experiment to determine the feasibility of reclaiming an unproductive saline-alkali calcareous soil (Billings silty clay loam) in the Upper Colorado River Basin was established near Grand Junction, Colo. The effects of leaching and gypsum on the reclamation of this soil, which is typical of the soils of the Upper Colorado River Basin, were followed by periodic soil analysis and by measuring the yield of alfalfa. The amounts of soluble salts and exchangeable sodium in the soil were materially decreased by the leaching treatments. This decrease was a function of the amount of water used to leach the soil. From 4 to 6 feet of water were required to reclaim such soils to a depth of 50 inches. Gypsum application in combination with leaching had little or no effect on reducing exchangeable sodium. After cropping with alfalfa for 1 year, soluble salts and exchangeable sodium adversely affected the yield of alfalfa where only 2 feet of water were used to reclaim. There are indications that salts and exchangeable sodium may be re-accumulating in the profile. Soil differences attributable to different reclamation treatments significantly affected the yield of alfalfa. Plots leached with 6 feet of water yielded 5.15 tons of hay per acre, as compared with 4.37 tons per acre obtained from plots leached with only 2 feet of water. Yield differences were attributed to differences in the chemical and physical properties of the soil which resulted from the reclamation treatments.