Net greenhouse gas balance of fibre wood plantation on peat in Indonesia.

Tropical peatlands cycle and store large amounts of carbon in their soil and biomass1-5. Climate and land-use change alters greenhouse gas (GHG) fluxes of tropical peatlands, but the magnitude of these changes remains highly uncertain6-19. Here we measure net ecosystem exchanges of carbon dioxide, methane and soil nitrous oxide fluxes between October 2016 and May 2022 from Acacia crassicarpa plantation, degraded forest and intact forest within the same peat landscape, representing land-cover-change trajectories in Sumatra, Indonesia. This allows us to present a full plantation rotation GHG flux balance in a fibre wood plantation on peatland. We find that the Acacia plantation has lower GHG emissions than the degraded site with a similar average groundwater level (GWL), despite more intensive land use. The GHG emissions from the Acacia plantation over a full plantation rotation (35.2 ± 4.7 tCO2-eq ha-1 year-1, average ± standard deviation) were around two times higher than those from the intact forest (20.3 ± 3.7 tCO2-eq ha-1 year-1), but only half of the current Intergovernmental Panel on Climate Change (IPCC) Tier 1 emission factor (EF)20 for this land use. Our results can help to reduce the uncertainty in GHG emissions estimates, provide an estimate of the impact of land-use change on tropical peat and develop science-based peatland management practices as nature-based climate solutions.

Modeled production, oxidation, and transport processes of wetland methane emissions in temperate, boreal, and Arctic regions.

Wetlands are the largest natural source of methane (CH4 ) to the atmosphere. The eddy covariance method provides robust measurements of net ecosystem exchange of CH4 , but interpreting its spatiotemporal variations is challenging due to the co-occurrence of CH4 production, oxidation, and transport dynamics. Here, we estimate these three processes using a data-model fusion approach across 25 wetlands in temperate, boreal, and Arctic regions. Our data-constrained model-iPEACE-reasonably reproduced CH4 emissions at 19 of the 25 sites with normalized root mean square error of 0.59, correlation coefficient of 0.82, and normalized standard deviation of 0.87. Among the three processes, CH4 production appeared to be the most important process, followed by oxidation in explaining inter-site variations in CH4 emissions. Based on a sensitivity analysis, CH4 emissions were generally more sensitive to decreased water table than to increased gross primary productivity or soil temperature. For periods with leaf area index (LAI) of ≥20% of its annual peak, plant-mediated transport appeared to be the major pathway for CH4 transport. Contributions from ebullition and diffusion were relatively high during low LAI (<20%) periods. The lag time between CH4 production and CH4 emissions tended to be short in fen sites (3 ± 2 days) and long in bog sites (13 ± 10 days). Based on a principal component analysis, we found that parameters for CH4 production, plant-mediated transport, and diffusion through water explained 77% of the variance in the parameters across the 19 sites, highlighting the importance of these parameters for predicting wetland CH4 emissions across biomes. These processes and associated parameters for CH4 emissions among and within the wetlands provide useful insights for interpreting observed net CH4 fluxes, estimating sensitivities to biophysical variables, and modeling global CH4 fluxes.

Synthesis and anti-tumor activities in human leukemia-derived cells of polyenylpyrroles with a methyl group at the conjugated polyene terminus.

To develop novel drugs for treating T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML) which are highly malignant hematological tumors, a series of analogs having a polyenylpyrrole structure of natural compounds (rumbrin and auxarconjugatin B) were synthesized and investigated their structure-activity relationships (SAR) of in vitro anti-T-ALL and anti-AML activities. We obtained three findings: (1) introduction of a methyl group at the conjugated polyene terminus enhanced anti-T-ALL activity, (2) analogs with a 3-chloropyrrole moiety had even higher selectivity for T-ALL cells, and (3) some analogs were effective against AML-derived cells. Among the studied compounds, 3-chloro-2-(8-ethoxycarbonylnona-1,3,5,7-tetraenyl) pyrrole 4e was the most promising candidate of T-ALL- and AML-treating drug. This study provides useful structural information for designing novel drugs treating T-ALL and AML.

S-Series Coelenterazine-Driven Combinatorial Bioluminescence Imaging Systems for Mammalian Cells.

A unique combinatorial bioluminescence (BL) imaging system was developed for determining molecular events in mammalian cells with various colors and BL intensity patterns. This imaging system consists of one or multiple reporter luciferases and a series of novel coelenterazine (CTZ) analogues named "S-series". For this study, ten kinds of novel S-series CTZ analogues were synthesized and characterized concerning the BL intensities, spectra, colors, and specificity of various marine luciferases. The characterization revealed that the S-series CTZ analogues luminesce with blue-to-orange-colored BL spectra with marine luciferases, where the most red-shifted BL spectrum peaked at 583 nm. The colors completed a visible light color palette with those of our precedent C-series CTZ analogues. The synthesized substrates S1, S5, S6, and S7 were found to have a unique specificity with marine luciferases, such as R86SG, NanoLuc (shortly, NLuc), and ALuc16. They collectively showed unique BL intensity patterns to identify the marine luciferases together with colors. The marine luciferases, R86SG, NLuc, and ALuc16, were multiplexed into multi-reporter systems, the signals of which were quantitatively unmixed with the specific substrates. When the utility was applied to a single-chain molecular strain probe, the imaging system simultaneously reported three different optical indexes for a ligand, i.e., unique BL intensity and color patterns for identifying the reporters, together with the ligand-specific fold intensities in mammalian cells. This study directs a new combinatorial BL imaging system to specific image molecular events in mammalian cells with multiple optical indexes.

C-Series Coelenterazine-Driven Bioluminescence Signature Imaging.

The present study introduces a unique BL signature imaging system with novel CTZ analogues named "C-series." Nine kinds of C-series CTZ analogues were first synthesized, and BL intensity patterns and spectra were then examined according to the marine luciferases. The results show that the four CTZ analogues named C3, C4, C6, and C7, individually or collectively luminesce with completely distinctive BL spectral signatures and intensity patterns according to the luciferases: Renilla luciferase (RLuc), NanoLuc, and artificial luciferase (ALuc). The signatural reporters were multiplexed into a multi-reporter system comprising RLuc8.6-535SG and ALuc16. The usefulness of the signatural reporters was further determined with a multi-probe system that consists of two single-chain probes embedding RLuc8 and ALuc23. This study is a great addition to the study of conventional bioassays with a unique methodology, and for the specification of each signal in a single- or multi-reporter system using unique BL signatures and patterns of reporter luciferases.

Identifying dominant environmental predictors of freshwater wetland methane fluxes across diurnal to seasonal time scales.

While wetlands are the largest natural source of methane (CH4 ) to the atmosphere, they represent a large source of uncertainty in the global CH4 budget due to the complex biogeochemical controls on CH4 dynamics. Here we present, to our knowledge, the first multi-site synthesis of how predictors of CH4 fluxes (FCH4) in freshwater wetlands vary across wetland types at diel, multiday (synoptic), and seasonal time scales. We used several statistical approaches (correlation analysis, generalized additive modeling, mutual information, and random forests) in a wavelet-based multi-resolution framework to assess the importance of environmental predictors, nonlinearities and lags on FCH4 across 23 eddy covariance sites. Seasonally, soil and air temperature were dominant predictors of FCH4 at sites with smaller seasonal variation in water table depth (WTD). In contrast, WTD was the dominant predictor for wetlands with smaller variations in temperature (e.g., seasonal tropical/subtropical wetlands). Changes in seasonal FCH4 lagged fluctuations in WTD by ~17 ± 11 days, and lagged air and soil temperature by median values of 8 ± 16 and 5 ± 15 days, respectively. Temperature and WTD were also dominant predictors at the multiday scale. Atmospheric pressure (PA) was another important multiday scale predictor for peat-dominated sites, with drops in PA coinciding with synchronous releases of CH4 . At the diel scale, synchronous relationships with latent heat flux and vapor pressure deficit suggest that physical processes controlling evaporation and boundary layer mixing exert similar controls on CH4 volatilization, and suggest the influence of pressurized ventilation in aerenchymatous vegetation. In addition, 1- to 4-h lagged relationships with ecosystem photosynthesis indicate recent carbon substrates, such as root exudates, may also control FCH4. By addressing issues of scale, asynchrony, and nonlinearity, this work improves understanding of the predictors and timing of wetland FCH4 that can inform future studies and models, and help constrain wetland CH4 emissions.

Synthesis of polyenylpyrrole derivatives with selective growth inhibitory activity against T-cell acute lymphoblastic leukemia cells.

T-cell acute lymphoblastic leukemia (T-ALL) is a hardly curable disease with a high relapse rate. 20 analogs were synthesized based on the structures of two kinds of fungi-derived polyenylpyrrole products (rumbrin (1) and auxarconjugatin-B (2)) to suppress the growth of T-ALL-derived cell line CCRF-CEM and tested for growth-inhibiting activity. The octatetraenylpyrrole analog gave an IC50 of 0.27 µM in CCRF-CEM cells, while it did not affect Burkitt lymphoma-derived cell line Raji and the cervical cancer cell line HeLa, or the oral cancer cell line HSC-3 (IC50 > 10 µM). This compound will be a promising compound for developing T-ALL-specific drugs.

COSORE: A community database for continuous soil respiration and other soil-atmosphere greenhouse gas flux data.

Globally, soils store two to three times as much carbon as currently resides in the atmosphere, and it is critical to understand how soil greenhouse gas (GHG) emissions and uptake will respond to ongoing climate change. In particular, the soil-to-atmosphere CO2 flux, commonly though imprecisely termed soil respiration (RS ), is one of the largest carbon fluxes in the Earth system. An increasing number of high-frequency RS measurements (typically, from an automated system with hourly sampling) have been made over the last two decades; an increasing number of methane measurements are being made with such systems as well. Such high frequency data are an invaluable resource for understanding GHG fluxes, but lack a central database or repository. Here we describe the lightweight, open-source COSORE (COntinuous SOil REspiration) database and software, that focuses on automated, continuous and long-term GHG flux datasets, and is intended to serve as a community resource for earth sciences, climate change syntheses and model evaluation. Contributed datasets are mapped to a single, consistent standard, with metadata on contributors, geographic location, measurement conditions and ancillary data. The design emphasizes the importance of reproducibility, scientific transparency and open access to data. While being oriented towards continuously measured RS , the database design accommodates other soil-atmosphere measurements (e.g. ecosystem respiration, chamber-measured net ecosystem exchange, methane fluxes) as well as experimental treatments (heterotrophic only, etc.). We give brief examples of the types of analyses possible using this new community resource and describe its accompanying R software package.

Analysis of the Diversity of the AvBD Gene Region in Japanese Quail.

The avian ß-defensin (AvBD) gene region is an important component of the innate immune system, encoding a variety of antimicrobial peptides. The AvBD region forms a multigene cluster in a specific chromosomal region. Comparison of the AvBD region among various birds suggests the presence of defects, duplications, and pseudogenization at many loci. The AvBD region in certain galliform birds, namely chicken, turkey, and bobwhite quail, includes AvBD3, -6, and -7, with the latter exhibiting copy number variants (CNVs) in chickens. DNA for genomic analysis was extracted from the peripheral blood of 99 randomly selected quail (Coturnix japonica) from 6 inbred lines. Nine CjAvBD1 and 8 CjAvBD12 alleles were detected. Ten haplotypes, including three that were strain specific, were found in alleles from the quail AvBD1 (CjAvBD1) and -12 (CjAvBD12) loci. Next-generation sequencing was used to determine the nucleotide sequences of the CjAvBD gene region (56-70 kb) for 7 homozygous diplotypes of these 10 haplotypes. These 7 haplotypes contained between 12 and 16 CjAvBD genes and were composed of 11 common loci: CjAvBD1, -2, -4, -5, -8, -9, -10, -11, -12, -13, and -14, but lacked CjAvBD3 and -7. Furthermore, up to 5 CjAvBD101 (AvBD6 ortholog) CNVs were observed among the 7 haplotypes. In addition, we detected amino acid substitutions causing net charge mutations that could affect antimicrobial activity in CjAvBD4, -13, -14, and -101. These results suggest that the CjAvBD region is unique among the Galliformes and that its diversity results in potential functional variation in innate immunity.

Development of near-infrared firefly luciferin analogue reacted with wild-type and mutant luciferases.

Interestingly, only the D-form of firefly luciferin produces light by luciferin-luciferase (L-L) reaction. Certain firefly luciferin analogues with modified structures maintain bioluminescence (BL) activity; however, all L-form luciferin analogues show no BL activity. To this date, our group has developed luciferin analogues with moderate BL activity that produce light of various wavelengths. For in vivo bioluminescence imaging, one of the important factors for detection sensitivity is tissue permeability of the number of photons emitted by L-L reaction, and the wavelengths of light in the near-infrared (NIR) range (700-900 nm) are most appropriate for the purpose. Some NIR luciferin analogues by us had performance for in vivo experiments to make it possible to detect photons from deep target tissues in mice with high sensitivity, whereas only a few of them can produce NIR light by the L-L reactions with wild-type luciferase and/or mutant luciferase. Based on the structure-activity relationships, we designed and synthesized here a luciferin analogue with the 5-allyl-6-dimethylamino-2-naphthylethenyl moiety. This analogue exhibited NIR BL emissions with wild-type luciferase (λmax = 705 nm) and mutant luciferase AlaLuc (λmax = 655 nm).

A Very Bright Far-Red Bioluminescence Emitting Combination Based on Engineered Railroad Worm Luciferase and 6'-Amino-Analogs for Bioimaging Purposes.

Beetle luciferases produce bioluminescence (BL) colors ranging from green to red, having been extensively used for many bioanalytical purposes, including bioimaging of pathogen infections and metastasis proliferation in living animal models and cell culture. For bioimaging purposes in mammalian tissues, red bioluminescence is preferred, due to the lower self-absorption of light at longer wavelengths by hemoglobin, myoglobin and melanin. Red bioluminescence is naturally produced only by Phrixothrix hirtus railroad worm luciferase (PxRE), and by some engineered beetle luciferases. However, Far-Red (FR) and Near-Infrared (NIR) bioluminescence is best suited for bioimaging in mammalian tissues due to its higher penetrability. Although some FR and NIR emitting luciferin analogs have been already developed, they usually emit much lower bioluminescence activity when compared to the original luciferin-luciferases. Using site-directed mutagenesis of PxRE luciferase in combination with 6'-modified amino-luciferin analogs, we finally selected novel FR combinations displaying BL ranging from 636-655 nm. Among them, the combination of PxRE-R215K mutant with 6'-(1-pyrrolidinyl)luciferin proved to be the best combination, displaying the highest BL activity with a catalytic efficiency ~2.5 times higher than the combination with native firefly luciferin, producing the second most FR-shifted bioluminescence (650 nm), being several orders of magnitude brighter than commercial AkaLumine with firefly luciferase. Such combination also showed higher thermostability, slower BL decay time and better penetrability across bacterial cell membranes, resulting in ~3 times higher in vivo BL activity in bacterial cells than with firefly luciferin. Overall, this is the brightest FR emitting combination ever reported, and is very promising for bioimaging purposes in mammalian tissues.

X-ray optics for advanced ultrafast pump-probe X-ray experiments at SACLA.

X-ray optics were implemented for advanced ultrafast X-ray experiments with different techniques at the hard X-ray beamline BL3 of SPring-8 Ångstrom Compact free-electron LAser. A double channel-cut crystal monochromator (DCCM) and compound refractive lenses (CRLs) were installed to tailor the beam conditions. These X-ray optics can work simultaneously with an arrival-timing monitor that compensates for timing jitter and drift. Inner-walls of channel-cut crystals (CCs) in the DCCM were processed by plasma chemical vaporization machining to remove crystallographic damage. Four-bounced reflection profiles of the CCs were investigated and excellent diffraction qualities were achieved. The use of CRLs enabled two-dimensional X-ray focusing with a spot size of ∼1.5 µm × 1.5 µm full width at half-maximum, while keeping reasonable throughputs for a wide photon energy range of 5-15 keV.

A micro channel-cut crystal X-ray monochromator for a self-seeded hard X-ray free-electron laser.

A channel-cut Si(111) crystal with a channel width of 90 µm was developed for achieving reflection self-seeding in hard X-ray free-electron lasers (XFELs). With the crystal a monochromatic seed pulse is produced from a broadband XFEL pulse generated in the first undulator section with an optical delay of 119 fs at 10 keV. The small optical delay allows a temporal overlap between the seed optical pulse and the electron bunch by using a small magnetic chicane for the electron beam placed between two undulator sections. Peak reflectivity reached 67%, which is reasonable compared with the theoretical value of 81%. By using this monochromator, a monochromatic seed pulse without broadband background in the spectrum was obtained at SACLA with a conversion efficiency from a broadband XFEL pulse of 2 × 10-2, which is ∼10 times higher than the theoretical efficiency of transmission self-seeding using a thin diamond (400) monochromator.

Investigation of serum cortisol concentration as a potential prognostic marker in hospitalized dogs: a prospective observational study in a primary care animal hospital.

BACKGROUND: Dogs with various medical diseases are usually treated at hospitals; however, the prognostic markers in dogs remain unknown. The aim of this study was to investigate the ability of serum cortisol concentration (SCC) to predict the prognosis of dogs with medical diseases. At 0 and 24 h after hospitalization, the neutrophil count, lymphocyte count, blood glucose concentration, and SCC were measured. Survival for 30 days from the time of hospitalization was investigated, and the dogs were divided into a survivor group and a non-survivor group. RESULTS: The neutrophil count at 24 h, SCC at 24 h, increase in SCC from 0 to 24 h (Inc-SCC), and the rate of increase in SCC from 0 to 24 h (R-Inc-SCC) were significantly higher in the non-survivor group than in the survivor group. The area under the receiver operating characteristic (ROC) curve values for the neutrophil count at 24 h, SCC at 24 h, Inc-SCC, and R-Inc-SCC were 0.695, 0.72, 0.63, and 0.66, respectively. Using the highest area under the ROC curve value, the sensitivity and specificity of SCC at a cutoff level of 6.6 µg/dL for predicting mortality were 89.5 and 61.9%, respectively. Moreover, the Kaplan-Meier curves confirmed the significant prognostic influence of SCC at 24 h. CONCLUSIONS: SCC as a marker of stress is a useful biomarker for predicting the prognosis of dogs with medical diseases requiring hospital treatment.

The development of diffuse panbronchiolitis during the treatment with long-term, low-dose clarithromycin for chronic sinusitis.

Diffuse panbronchiolitis (DPB) is a progressive inflammatory airway disease characterized by a chronic cough, copious sputum expectation, dyspnea, and chronic sinusitis. Owing to the long-term treatment of low-dose macrolides, the prognosis has been remarkably improved. However, in some cases, patients are refractory to macrolides, and the subsequent treatment strategies are controversial. We herein present a patient with the onset of DPB during treatment with long-term, low-dose clarithromycin (CAM) for chronic sinusitis who was successfully treated by switching to long-term treatment with normal-dose CAM. We should recognize that DPB may develop in patients with chronic sinusitis despite treatment with a long-term, low-dose macrolide. We also propose that increasing the dose of macrolide may be a useful strategy for treating refractory patients.

Recurrence of Biphenotypic Sinonasal Sarcoma With Cerebral Hemorrhaging.

Biphenotypic sinonasal sarcoma (BSNS) is a newly classified tumor that is characterized by neural and myogenic differentiation. The authors herein report a rare patient of the recurrence of BSNS with intracranial hemorrhaging and a review of the literature. A 70-year-old man presented with disturbance of consciousness and vomiting blood. He had undergone resection of a sinonasal tumor 11 years earlier and shown no recurrence at his last follow-up 4 years ago. Computed tomography showed cerebral hemorrhaging around a low-density mass that occupied the left frontal base and left ethmoid sinus. Total resection was performed. A histological examination of tumor specimens obtained from the first and the second resections revealed almost the same characteristic morphological features and the patient was diagnosed with BSNS. The lesion was negative for any fusion genes, as previously reported. The long-term progression of BSNS is not clear. This case appears to be the first reported recurrence of BSNS with cerebral hemorrhaging. Biphenotypic sinonasal sarcoma should be considered to need long-term follow-up.

Performance of a hard X-ray split-and-delay optical system with a wavefront division.

The performance of a hard X-ray split-and-delay optical (SDO) system with a wavefront division scheme was investigated at the hard X-ray free-electron laser facility SACLA. For the wavefront division, beam splitters made of edge-polished perfect Si(220) crystals were employed. We characterized the beam properties of the SDO system, and investigated its capabilities for beam manipulation and diagnostics. First, it was confirmed that shot-to-shot non-invasive diagnostics of pulse energies for both branches in the SDO system was feasible. Second, nearly ideal and identical focal profiles for both branches were obtained with a spot size of ∼1.5 µm in full width at half-maximum. Third, a spatial overlap of the two focused beams with a sub-µm accuracy was achieved by fine tuning of the SDO system. Finally, a reliable tunability of the delay time between two pulses was confirmed. The time interval was measured with an X-ray streak camera by changing the path length of the variable-delay branch. Errors from the fitted line were evaluated to be as small as ±0.4 ps over a time range of 60 ps.

Ecosystem-scale methane flux in tropical peat swamp forest in Indonesia.

Data on ecosystem-scale methane (CH4 ) fluxes in tropical peatlands are currently lacking in the global CH4 budget. Although the waterlogged Indonesian peatlands contain the largest share of peat carbon in South-East Asia, ecosystem-scale CH4 budgets have not yet been reported, although these peatlands have the potential to emit CH4 . We observed 1-year variations in the ecosystem-scale CH4 flux in an undrained secondary peat swamp forest in central Kalimantan, Indonesia, using the eddy covariance method. We found that the peat swamp forest switched from being a CH4 sink during the dry season (as low as -8.9 mg C m-2  day-1 ) to a source of CH4 during the wet season (up to 10.7 mg C m-2  day-1 ), and this was dependent on changes in the groundwater level (GWL). The high GWL during the wet season enhanced the anaerobic CH4 production in the surface layer that had more labile organic matter. However, the CH4 emission also increased when the GWL dropped during dry spells in the wet season. The annual CH4 budget in the studied tropical peat swamp forest (0.09-0.17 g C m-2  year-1 ) was much lower than that in northern, temperate, and subtropical wetlands. We found that CH4 fluxes had almost no effect on the global warming gas budget of the peat swamp forest, and values were only a few percent less than the CO2 fluxes at the same site. In addition, we conducted anaerobic soil incubation experiments to examine the effect of land-use change on CH4 production. The results indicated much higher CH4 production potential in undrained forest soil than in drained or drained and burned ex-forest soils. However, although CH4 production decreased in drained soils relative to undrained soils, conserving pristine peat swamp forests with high GWLs is important to suppress global warming because CO2 emissions increase in drained peatlands.

Non-synonymous FGD3 Variant as Positional Candidate for Disproportional Tall Stature Accounting for a Carcass Weight QTL (CW-3) and Skeletal Dysplasia in Japanese Black Cattle.

Recessive skeletal dysplasia, characterized by joint- and/or hip bone-enlargement, was mapped within the critical region for a major quantitative trait locus (QTL) influencing carcass weight; previously named CW-3 in Japanese Black cattle. The risk allele was on the same chromosome as the Q allele that increases carcass weight. Phenotypic characterization revealed that the risk allele causes disproportional tall stature and bone size that increases carcass weight in heterozygous individuals but causes disproportionately narrow chest width in homozygotes. A non-synonymous variant of FGD3 was identified as a positional candidate quantitative trait nucleotide (QTN) and the corresponding mutant protein showed reduced activity as a guanine nucleotide exchange factor for Cdc42. FGD3 is expressed in the growth plate cartilage of femurs from bovine and mouse. Thus, loss of FDG3 activity may lead to subsequent loss of Cdc42 function. This would be consistent with the columnar disorganization of proliferating chondrocytes in chondrocyte-specific inactivated Cdc42 mutant mice. This is the first report showing association of FGD3 with skeletal dysplasia.

Pseudomonas aeruginosa Clinical Isolates in Nepal Coproducing Metallo-ß-Lactamases and 16S rRNA Methyltransferases.

A total of 11 multidrug-resistant Pseudomonas aeruginosa clinical isolates were obtained in Nepal. Four of these isolates harbored genes encoding one or more carbapenemases (DIM-1, NDM-1, and/or VIM-2), and five harbored genes encoding a 16S rRNA methyltransferase (RmtB4 or RmtF2). A novel RmtF variant, RmtF2, had a substitution (K65E) compared with the same gene in RmtF. To our knowledge, this is the first report describing carbapenemase- and 16S rRNA methyltransferase-coproducing P. aeruginosa clinical isolates in Nepal.