αC including a novel three- component non-heme diiron monooxygenase system

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Development of P450-BM3 using molecular dynamics simulations- A tribute to the late Professor Hideaki Yamada

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Autonomous mobile robot for outdoor slope using 2D LiDAR with uniaxial gimbal mechanism

The Nakanoshima Challenge is a contest for developing sophisticated navigation systems of robots for collecting garbage in outdoor public spaces. In this study, a robot named Navit(oo)n is designed, and its performance in public spaces such as city parks is evaluated. Navit(oo)n contains two 2D LiDAR scanners with uniaxial gimbal mechanism, improving self-localization robustness on a slope. The gimbal mechanism adjusts the angle of the LiDAR scanner, preventing erroneous ground detection. We evaluate the navigation performance of Navit(oo)n in the Nakanoshima and its Extra Challenges

A three-component monooxygenase from Rhodococcus wratislaviensis may expand industrial applications of bacterial enzymes

地球外有機化合物に対する微生物代謝の解明から全く新規な酵素系を発見 --生命分子進化の理解や産業応用に期待--. 京都大学プレスリリース. 2021-01-20.The high-valent iron-oxo species formed in the non-heme diiron enzymes have high oxidative reactivity and catalyze difficult chemical reactions. Although the hydroxylation of inert methyl groups is an industrially promising reaction, utilizing non-heme diiron enzymes as such a biocatalyst has been difficult. Here we show a three-component monooxygenase system for the selective terminal hydroxylation of α-aminoisobutyric acid (Aib) into α-methyl-D-serine. It consists of the hydroxylase component, AibH1H2, and the electron transfer component. Aib hydroxylation is the initial step of Aib catabolism in Rhodococcus wratislaviensis C31-06, which has been fully elucidated through a proteome analysis. The crystal structure analysis revealed that AibH1H2 forms a heterotetramer of two amidohydrolase superfamily proteins, of which AibHm2 is a non-heme diiron protein and functions as a catalytic subunit. The Aib monooxygenase was demonstrated to be a promising biocatalyst that is suitable for bioprocesses in which the inert C–H bond in methyl groups need to be activated

Mitochondrial DNA as a biomarker for acute central serous chorioretinopathy: A case-control study

The literature suggests that stress may play a pivotal role in the precipitation of acute central serous chorioretinopathy (CSC) because chorioretinal integrity can be affected by the psychosocial state of the patient, indicating the need for a biomarker. Not only physical stress but also psychological stress causes many types of physical disorders. However, little is known about the pathophysiology of stress-induced disease. The objective of this study was to investigate whether serum factors might be involved in the development of stress-induced ocular diseases. Methods: This observational case series included 33 eyes of 33 consecutive patients with treatment-naïve acute CSC. Fifty eyes of 50 age-matched healthy volunteers were included in this study as non-CSC controls. Serum samples were collected from all participants, and the levels of mitochondrial DNA (mtDNA) were measured by quantitative real-time (RT)-PCR. Serum levels of high-mobility group box (HMGB) 1 and 8-hydroxy-2′-deoxyguanosine (8-OHdG), biological markers of acute/chronic inflammation and oxidative stress, were also measured. The relationships between serum mtDNA, 8-OHdG, and HMGB1 concentrations were investigated by multivariate regression analysis, alongside an assessment of clinical data. Results: In the treatment-naïve acute CSC group, the serum mtDNA levels (36.5 ± 32.4 ng/mL) were significantly higher than the levels in the control group (7.4 ± 5.9 ng/mL; p < 0.001). Serum levels of 8-OHdG and HMGB1 in treatment-naïve acute CSC patients measured 0.12 ± 0.08 ng/mL and 18.1 ± 35.0 ng/mL, respectively, indicating that HMGB1 levels were elevated in CSC compared with the control group. Multivariable regression analysis demonstrated that increased serum mtDNA levels were significantly associated with the height of serous retinal detachment. Conclusion: We showed serum mtDNA and HMGB1 level elevation and its relation to the clinical activities of CSC, indicating that serum mtDNA and HMGB1 could serve as biomarkers for the acute phase of the disease. The use of these biomarkers makes it possible to predict disease onset and determine disease severity

Cladistic analysis and description of three new species of the Chilean genus Nanophareus (Opiliones: Gonyleptidae: Pachylinae)

Hara, Marcos Ryotaro (2016): Cladistic analysis and description of three new species of the Chilean genus Nanophareus (Opiliones: Gonyleptidae: Pachylinae). Zootaxa 4105 (2): 101-123, DOI: http://doi.org/10.11646/zootaxa.4105.2.

Iandumoema setimapocu Hara & Pinto-Da-Rocha, 2008, sp. n.

Iandumoema setimapocu sp. n. Figs 1–3 Type material: Brazil, Minas Gerais, Coração de Jesus, Lapa do Zu, 3.IX. 2004, M.E. Bichuette & E. Trajano leg., male holotype, one female and one male paratypes (MZSP- 28536). Etymology: The name (from “sëtymã” = animal leg, and “poku”= long; a noun in apposition) is taken from the language of the indigenous Tupi people and refers to the characteristic legs of this species. Diagnosis: The new species differs from I. uai by the male femur IV being straight (curved laterally and dorsally in the basal part in I. uai), the male apophysis on coxa IV directed obliquely backwards (basal-half laterad), eyes depigmented (reduced black pigmentation); tubercles on femur IV close to each other, separated by about one diameter (tubercles much more widely spaced); pedipalpal tibia with ectal setae IiiIi (ectal and mesal setae IiIi). See also Table 2. Description: Male (holotype): Dorsum (Fig. 1 A): Measurements: Dorsal scute length 3.7; prosoma length 1.4; opisthosoma maximum width 3.3; prosoma width 2.2. Measurements of legs: Table 1. Frontal hump with 4 tubercles, anterior margin with 4 tubercles on each side. Ocularium with reduced and depigmented eyes; with high upwardly directed spine, apex curved backwards (Fig. 1 C). Each side of ocularium with 7–8 tubercles; 6 tubercles posterior to ocularium. Area I divided, with 5 tubercles on each side; II with two transversal rows of 5–7 tubercles each; III with 9 tubercles; IV with 8 tubercles. Lateral margin with two rows of tubercles from sulci I to III. Posterior margin of dorsal scute with 9 tubercles. Free tergite I with 13 tubercles; II with 10; III with 10. Anal opercle irregularly tuberculate. Venter (Fig. 1 B): Coxa I with 17 tubercles; II with 22; III with 12 tubercles; IV and stigmatic area irregularly tuberculate. Posterior margin and free sternites with a row of low tubercles. Chelicera: Segment I elongated, bulla with 5 tubercles. Fixed finger with 5 equal-sized teeth on the edge; movable finger with 3 teeth. Pedipalps (Fig. 1 A,E): Slightly elongated. Coxa with 1 dorsal tubercle. Trochanter with 2 dorsal and 2 ventral (ventral mesal largest) tubercles. Femur with 1 ventro-basal followed by 3 small and 1 mesal subapical tubercles. Patella smooth; tibial spination: Ectal IiiIi, mesal IiIi; tarsal spination: Ectal and mesal IiIi. Legs (Figs 1 C–D, 2 A–C): Coxa I with 2 stout tubercles; II with 1 stout anterior tubercle and 1 posterior, the latter largely fused with anterior tubercle of III; IV with scattered tubercles and with dorso-apical, slightly sigmoid, backwards-directed apophysis. Trochanter I with 4 dorsal, 1 prolateral, 1 retrolateral and 3 ventral tubercles; II with 3 dorsal, 1 prolateral, 1 retrolateral and 3 ventral tubercles; III with 4 dorsal and 3 ventral tubercles; IV with large basal prolateral apophysis, wide and low median apophysis, and with 4 retrolateral (apical one largest), 2 dorsal and 9 ventral tubercles. Femur–tibia III with small tubercles. Femur IV straight, with 2 irregular rows of dorsal tubercles, 2 ventral rows of higher (twice as long as wide) tubercles on apex, 1 retrolateral row of irregular-sized tubercles, 1 prolateral row of small tubercles, 3 larger (median one largest) dorso-apical tubercles. Tibia IV with 2 rows of ventral tubercles (one higher than the other) in distal 1 / 3. Basitarsus I slightly swollen. Tarsal segmentation: 6 (3), 11 (3), 6, 6. Penis (Fig. 3 A–B): Ventral plate subrectangular, with concave base, distal margin straight; apex with an apical and a basal group of 4 long and straight setae on each side, without small intermediary setae. Glans enlarged in basal half, stylus short and thick; ventral process of stylus with serrate distal margin, not reaching apex of stylus. Coloration: Depigmented, uniformly light brown. Pedipalps, legs I–III and tibia–tarsus IV lighter. Eyes depigmented. Female (paratype; Figs 1 F–G, 2 D–E): Measurements: Dorsal scute length 3.2; prosoma length 1.8; opisthosoma maximum width 2.6; prosoma width 1.9. Only characteristics different from those of males are mentioned. Anterior margin of dorsal scute with 1–3 tubercles on each side. Area I with 3–7 tubercles on each side; II with 17; III with 11; IV with 10 tubercles. Posterior margin with 12 tubercles. Free tergite I with 12; II with 11; III with 12 tubercles. Pedipalpal tibia spination: Ectal and mesal IiIi. Coxa IV with a shorter dorsal apophysis (half as long) than in male; trochanter IV with basal and median apophyses half as long or less than in male; tubercles on legs smaller than in male; femur IV with 2 larger dorso-apical tubercles. Detailed comparison between Iandumoema uai and I. setimapocu sp. n.: A brief summary of the morphological comparison is presented in table 2. In general I. uai has proportionally longer appendages, whereas I. setimapocu has proportionally smaller eyes. It is noteworthy to mention that the female of I. setimapocu possesses a dorso-apical apophysis on coxa IV which is proportionally larger than in females of other genera of Pachylinae (usually with a larger, pointed tubercle dorso-apically on coxa IV). Other relatively similar conditions, i.e. females which have legs with spines and apophyses as long as those of males, are exhibited in some species of Caelopyginae (see illustrations in Pinto-da-Rocha 2002) and Progonyleptoidellinae (Kury & Pinto-da-Rocha 1997). The presence of spines and apophyses on coxa IV of females that are as long as in males indicates paternal care (Machado & Macías-Ordóñez 2007). However, there is no reported case of paternal care in Pachylinae and the reproductive biology of I. setimapocu is unknown. Nonetheless, it is worth investigating their reproductive biology to test the hypothesis that paternal care is connected to coxa IV armature in females and to provide additional data for conservation management of the cave and its surroundings. Distribution: Known only from the type locality. Biological notes: The Lapa do Zu Cave is 3 km long, traversed by a stream which carries considerable amounts of leaves, tree branches and trunks into the aphotic zone. The air temperature was around 24 °C during colleting. The animals were captured 200–300 m from the main cave entrance, on plant debris close to the stream and on the cave walls, in a very humid place. I. setimapocu sp. n. shows the following troglomorphism: Body depigmented, appendages elongated, eyes reduced and depigmented. Biogeographical remarks: The genus Iandumoema encompasses only two species, I. uai and I. setimapocu sp. n., each restricted to a single cave in the State of Minas Gerais. These caves are about 170 km apart in a straight line, with the São Francisco river between them. Dispersion across the subterranean habitat by a common ancestor, now extinct, seems to be unlikely, since these caves are located at different margins of the large São Francisco river. Even if there is a lithographic continuity beneath the river, the limestone spaces would be filled with water (A. Auler pers. comm.), thus precluding the dispersion of terrestrial cave animals. An independent colonization of both caves by an epigeic ancestor, which then was widely distributed in northwestern Minas Gerais, followed by isolation and speciation, seems to be more reasonable. Terrestrial subterranean animal species in Brazil are believed to be of recent origin (Trajano 1995). The isolation may have occurred in one of the nine Pleistocenic dry phases during the last 210,000 years that were intercalated by short wet phases lasting from several hundred to a few thousand years each, as found for the northern Bahia region (Trajano 2007). The absence of detailed paleoclimatic records from the study site led us to assume a scenario similar to that suggested for northeastern and southeastern Brazil, which showed wet periods with a certain synchronism (Wang et al. 2004; Cruz et al. 2005; Wang et al. 2007). Unfortunately, studies on phylogenetic relationships among Pachylinae species and even Laniatores families are just beginning. Phylogenetic molecular analyses focusing on species closely related to Iandumoema are also not available, thus making it impossible to correlate isolation and speciation to a dated geological or paleoclimatic event. Notes on the distribution of Brazilian cave species: About 800 harvestmen species in 13 families occur in Brazil (Kury 2003). Among them, 30 species in five families (Sclerosomatidae; Escadabiidae; Cosmetidae; Gonyleptidae; and Stygnidae) are associated to a subterranean environment. Some are found close to cave entrances and use caves only as oviposition sites and/or as diurnal shelters. These species belong to the gagrellines (Sclerosomatidae), cosmetines (Cosmetidae), goniosomatines and mitobatines (Gonyleptidae); they are considered to be trogloxenes (Pinto-da-Rocha 1995). Others maintain considerable populations in the interior of caves, but also occur outside. These are Verrucastygnus caliginosus (Pinto-da-Rocha, 1990) (Stygnidae), “ Daguerreia ” inermis Soares & Soares, 1947 (the only species that cannot be placed in the genus Daguerreia after it was synonymized with Pachyloides Holmberg by Acosta (1996); it is currently considered as a species of uncertain taxonomic position), and a few Eusarcus species (both Gonyleptidae). Eleven truly troglobitic harvestmen species belonging to the families Escadabiidae (Spaeleoleptes spaeleus H.Soares, 1966) and Gonyleptidae (remaining species) have been recorded from Brazilian caves. Most troglobitic gonyleptids belong to the Pachylinae (Discocyrtus sp., Eusarcus spp., Giupponia chagasi, Iandumoema uai and two undescribed Pachylinae), others to the Tricommatinae (Spinopilar sp.) and the Pachylospeleinae (Pachylospeleus strinatii). Almost all species live in limestone regions, except for an undescribed Discocyrtus sp. (Kury in press) in a sandstone cave (see Fig. 4). Although most of the diversity of Gonyleptidae (more than one third of the known 800 spp.; see Kury 2003) was recorded from the coastal Atlantic Rain Forest, an area with some isolated limestone lenses (in southern Bahia, from São Paulo to Santa Catarina States), most of the troglobitic species occur in Central Brazil (Bambuí region, Goiás, Minas Gerais and Bahia States; see Fig. 4). There limestone caves are very abundant and covered by the relatively hotter and drier cerrado (Brazilian savanna). Other areas with this kind of rock that is very susceptible to dissolution (and thus to form caves) are Mato Grosso (West of Cuiabá) and the northeastern Brazilian States (approximately at 6 °S). The few surveys conducted there yielded no troglobitic harvestmen up to now. Brazilian troglobitic species are considered by the government as threatened and are listed in a “Red list of threatened species” (Ministério do Meio Ambiente 2003) due to their very restricted distribution (normally only one cave), low population densities and threat by limestone quarrying.Published as part of Hara, Marcos Ryotaro & Pinto-Da-Rocha, Ricardo, 2008, A new species of Brazilian troglobitic harvestman of the genus Iandumoema (Opiliones: Gonyleptidae), pp. 50-58 in Zootaxa 1744 on pages 51-56, DOI: 10.5281/zenodo.18160