Microbiological insights into anaerobic phenol degradation mechanisms and bulking phenomenon in a mesophilic upflow anaerobic sludge blanket reactor in long-term operation.

In this study, a long-term operation of 2,747 days was conducted to evaluate the performance of the upflow anaerobic sludge blanket (UASB) reactor and investigated the degradation mechanisms of high-organic loading phenol wastewater. During the reactor operation, the maximum chemical oxygen demand (COD) removal rate of 6.1 ± 0.6 kg/m3/day under 1,680 mg/L phenol concentration was achieved in the mesophilic UASB reactor. After a significant change in the operating temperature from 24.0 ± 4.1 °C to 35.9 ± 0.6 °C, frequent observations of floating and washout of the bloated granular sludge (novel types of the bulking phenomenon) were made in the UASB reactor, suggesting that the change in operating temperature could be a trigger for the bulking phenomenon. Through the metagenomic analysis, phenol degradation mechanisms were predicted that phenol was converted to 4-hydroxybenzoate via two possible routes by Syntrophorhabdaceae and Pelotomaculaceae bacteria. Furthermore, the degradation of 4-hydroxybenzoate to benzoyl-CoA was carried out by members of Syntrophorhabdaceae and Smithellaceae. In the bulking sludge, a predominant presence of Nanobdellota, belonging to DPANN archaea, was detected. The metagenome-assembled genome of the Nanobdellota lacks many biosynthetic pathways and has several genes for the symbiotic lifestyle such as trimeric autotransporter adhesin-related protein. Furthermore, the Nanobdellota have significant correlations with several methanogenic archaea that are predominantly present in the UASB reactor. Considering the results of this study, the predominant Nanobdellota may negatively affect the growth of the methanogens through the parasitic lifestyle and change the balance of microbial interactions in the granular sludge ecosystem.

Structural insights into the rational design of a nanobody that binds with high affinity to the SARS-CoV-2 spike variant.

The continuous emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants associated with the adaptive evolution of the virus is prolonging the global coronavirus disease 2019 (COVID-19) pandemic. The modification of neutralizing antibodies based on structural information is expected to be a useful approach to rapidly combat emerging variants. A dimerized variable domain of heavy chain of heavy chain antibody (VHH) P17 that has highly potent neutralizing activity against SARS-CoV-2 has been reported but the mode of interaction with the epitope remains unclear. Here, we report the X-ray crystal structure of the complex of monomerized P17 bound to the SARS-CoV-2 receptor binding domain (RBD) and investigated the binding activity of P17 toward various variants of concern (VOCs) using kinetics measurements. The structure revealed details of the binding interface and showed that P17 had an appropriate linker length to have an avidity effect and recognize a wide range of RBD orientations. Furthermore, we identified mutations in known VOCs that decrease the binding affinity of P17 and proposed methods for the acquisition of affinity toward the Omicron RBD because Omicron is currently the most predominant VOC. This study provides information for the rational design of effective VHHs for emerging VOCs.

Intratracheal trimerized nanobody cocktail administration suppresses weight loss and prolongs survival of SARS-CoV-2 infected mice.

BACKGROUND: SARS-CoV-2 Omicron variants are highly resistant to vaccine-induced immunity and human monoclonal antibodies. METHODS: We previously reported that two nanobodies, P17 and P86, potently neutralize SARS-CoV-2 VOCs. In this study, we modified these nanobodies into trimers, called TP17 and TP86 and tested their neutralization activities against Omicron BA.1 and subvariant BA.2 using pseudovirus assays. Next, we used TP17 and TP86 nanobody cocktail to treat ACE2 transgenic mice infected with lethal dose of SARS-CoV-2 strains, original, Delta and Omicron BA.1. RESULTS: Here, we demonstrate that a novel nanobody TP86 potently neutralizes both BA.1 and BA.2 Omicron variants, and that the TP17 and TP86 nanobody cocktail broadly neutralizes in vitro all VOCs as well as original strain. Furthermore, intratracheal administration of this nanobody cocktail suppresses weight loss and prolongs survival of human ACE2 transgenic mice infected with SARS-CoV-2 strains, original, Delta and Omicron BA.1. CONCLUSIONS: Intratracheal trimerized nanobody cocktail administration suppresses weight loss and prolongs survival of SARS-CoV-2 infected mice.

Antibodies are made by the immune system to identify and inactivate infectious agents such as viruses. Alpacas produce a simple type of antibodies called nanobodies. We previously developed two nanobodies named P17 and P86 that inactivate SARS-CoV-2. In this study, we modified these nanobodies to create two nanobodies named TP17 and TP86. The cocktail of these nanobodies inactivated different types of SARS-CoV-2 viruses including Omicron BA.1 and BA.2. The cocktail also prolonged survival of mice infected with lethal doses of SARS-CoV-2.

A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.

We are amid the historic coronavirus infectious disease 2019 (COVID-19) pandemic. Imbalances in the accessibility of vaccines, medicines, and diagnostics among countries, regions, and populations, and those in war crises, have been problematic. Nanobodies are small, stable, customizable, and inexpensive to produce. Herein, we present a panel of nanobodies that can detect the spike proteins of five SARS-CoV-2 variants of concern (VOCs) including Omicron. Here we show via ELISA, lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays that our nanobodies can quantify the spike variants. This panel of nanobodies broadly neutralizes viral infection caused by pseudotyped and authentic SARS-CoV-2 VOCs. Structural analyses show that the P86 clone targets epitopes that are conserved yet unclassified on the receptor-binding domain (RBD) and contacts the N-terminal domain (NTD). Human antibodies rarely access both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins that go undetected by conventional antibodies.

Investigating the Therapeutic Potential of LSD1 Enzyme Activity-Specific Inhibition by TAK-418 for Social and Memory Deficits in Rodent Disease Models.

Inhibition of lysine-specific demethylase 1 (LSD1) enzyme activity is a promising approach to treat diseases associated with epigenetic dysregulation, such as neurodevelopmental disorders. However, this concept has not been fully validated because genetic LSD1 deletion causes embryonic lethality and conventional LSD1 inhibitors cause thrombocytopenia via the dissociation of LSD1-cofactor complex. To characterize the therapeutic potential of LSD1 enzyme inhibition, we used TAK-418 and T-448, the LSD1 enzyme activity-specific inhibitors with minimal impact on the LSD1-cofactor complex. TAK-418 and T-448, by inhibiting brain LSD1 enzyme activity, consistently improved social deficits in animal models of neurodevelopmental disorders without causing thrombocytopenia. Moreover, TAK-418 improved memory deficits caused by aging or amyloid precursor protein overexpression. In contrast, TAK-418 did not improve memory deficits caused by miR-137 overexpression. Thus, miR-137 modulation may be involved in memory improvement by LSD1 inhibition. TAK-418 warrants further investigation as a novel therapeutic agent for diseases with epigenetic dysregulation.

Reduction of Thermal Conductivity for Icosahedral Al-Cu-Fe Quasicrystal through Heavy Element Substitution.

Icosahedral Al-Cu-Fe quasicrystal (QC) shows moderate electrical conductivity and low thermal conductivity, and both p- and n-type conduction can be controlled by tuning the sample composition, making it potentially suited for thermoelectric materials. In this work, we investigated the effect of introducing chemical disorder through heavy element substitution on the thermal conductivity of Al-Cu-Fe QC. We substituted Au and Pt elements for Cu up to 3 at% in a composition of Al63Cu25Fe12, i.e., Al63Cu25-x(Au,Pt)xFe12 (x = 0, 1, 2, 3). The substitutions of Au and Pt for Cu reduced the phonon thermal conductivity at 300 K (κph,300K) by up to 17%. The reduction of κph,300K is attributed to a decrease in the specific heat and phonon relaxation time through heavy element substitution. We found that increasing the Pt content reduced the specific heat at high temperatures, which may be caused by the locked state of phasons. The observed glass-like low values of κph,300K (0.9-1.1 W m-1 K-1 at 300 K) for Al63Cu25-x(Au,Pt)xFe12 are close to the lower limit calculated using the Cahill model.

The conducting fibrillar networks of a PEDOT:PSS hydrogel and an organogel prepared by the gel-film formation process.

Poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) is a practical conducting polymer. The gel-film formation process produces a PEDOT:PSS organogel with a structure between a PEDOT:PSS water dispersion and a dried film. We found that this film has a high water-swelling ratio and thickens by a hitherto unreported factor of approximately 6600% as its swells to form a hydrogel. In this study, we investigated the drying behaviour of a hydrogel and an organogel with electrical properties to elucidate the internal structures of the gel responsible for the swelling and shrinkage behaviour with high expansion and contraction ratios. SEM revealed that the gel is composed of a 3D fibrillar network consisting of fibrils that are 4.6 ± 1.6 µm long and 0.63 ± 0.29 µm in diameter. This network plays a pivotal role in the conduction of electricity and swelling behaviour with high expansion ratios. The thickness of the gel decreased to 1/66 of its original value after drying on a substrate, while the total electrical resistance decreased by only 20%. The organogel exhibited the same drying behaviour as the hydrogel, which indicates that the network forms first in the organogel and is maintained in the subsequent swelling and drying processes. The electrical conductivity of the hydrogel increased from 9.0 ± 0.1 to 346.4 ± 1.2 S cm-1 under anisotropic shrinking from 3.1 ± 0.2 mm to 77.4 ± 3.3 µm. The network plays an important role as an enhanced swelling framework by providing effective pathways for the conduction of electricity.

Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3.

Polypeptide GalNAc-transferase T3 (GalNAc-T3) regulates fibroblast growth factor 23 (FGF23) by O-glycosylating Thr178 in a furin proprotein processing motif RHT178R↓S. FGF23 regulates phosphate homeostasis and deficiency in GALNT3 or FGF23 results in hyperphosphatemia and familial tumoral calcinosis. We explored the molecular mechanism for GalNAc-T3 glycosylation of FGF23 using engineered cell models and biophysical studies including kinetics, molecular dynamics and X-ray crystallography of GalNAc-T3 complexed to glycopeptide substrates. GalNAc-T3 uses a lectin domain mediated mechanism to glycosylate Thr178 requiring previous glycosylation at Thr171. Notably, Thr178 is a poor substrate site with limiting glycosylation due to substrate clashes leading to destabilization of the catalytic domain flexible loop. We suggest GalNAc-T3 specificity for FGF23 and its ability to control circulating levels of intact FGF23 is achieved by FGF23 being a poor substrate. GalNAc-T3's structure further reveals the molecular bases for reported disease-causing mutations. Our findings provide an insight into how GalNAc-T isoenzymes achieve isoenzyme-specific nonredundant functions.

Dephosphorylation of protamine 2 at serine 56 is crucial for murine sperm maturation in vivo.

The posttranslational modification of histones is crucial in spermatogenesis, as in other tissues; however, during spermiogenesis, histones are replaced with protamines, which are critical for the tight packaging of the DNA in sperm cells. Protamines are also posttranslationally modified by phosphorylation and dephosphorylation, which prompted our investigation of the underlying mechanisms and biological consequences of their regulation. On the basis of a screen that implicated the heat shock protein Hspa4l in spermatogenesis, we generated mice deficient in Hspa4l (Hspa4l-null mice), which showed male infertility and the malformation of sperm heads. These phenotypes are similar to those of Ppp1cc-deficient mice, and we found that the amount of a testis- and sperm-specific isoform of the Ppp1cc phosphatase (Ppp1cc2) in the chromatin-binding fraction was substantially less in Hspa4l-null spermatozoa than that in those of wild-type mice. We further showed that Ppp1cc2 was a substrate of the chaperones Hsc70 and Hsp70 and that Hspa4l enhanced the release of Ppp1cc2 from these complexes, enabling the freed Ppp1cc2 to localize to chromatin. Pull-down and in vitro phosphatase assays suggested the dephosphorylation of protamine 2 at serine 56 (Prm2 Ser56) by Ppp1cc2. To confirm the biological importance of Prm2 Ser56 dephosphorylation, we mutated Ser56 to alanine in Prm2 (Prm2 S56A). Introduction of this mutation to Hspa4l-null mice (Hspa4l -/-; Prm2 S56A/S56A) restored the malformation of sperm heads and the infertility of Hspa4l -/- mice. The dephosphorylation signal to eliminate phosphate was crucial, and these results unveiled the mechanism and biological relevance of the dephosphorylation of Prm2 for sperm maturation in vivo.

Mouse macrophages show different requirements for phosphatidylserine receptor Tim4 in efferocytosis.

Protein S (ProS) and growth arrest-specific 6 (Gas6) bind to phosphatidylserine (PtdSer) and induce efferocytosis upon binding TAM-family receptors (Tyro3, Axl, and Mer). Here, we produced mouse ProS, Gas6, and TAM-receptor extracellular region fused to IgG fragment crystallizable region in HEK293T cells. ProS and Gas6 bound Ca2+ dependently to PtdSer (Kd 20-40 nM), Mer, and Tyro3 (Kd 15-50 nM). Gas6 bound Axl strongly (Kd < 1.0 nM), but ProS did not bind Axl. Using NIH 3T3-based cell lines expressing a single TAM receptor, we showed that TAM-mediated efferocytosis was determined by the receptor-binding ability of ProS and Gas6. Tim4 is a membrane protein that strongly binds PtdSer. Tim4 alone did not support efferocytosis, but enhanced TAM-dependent efferocytosis. Resident peritoneal macrophages, Kupffer cells, and CD169+ skin macrophages required Tim4 for TAM-stimulated efferocytosis, whereas efferocytosis by thioglycollate-elicited peritoneal macrophages or primary cultured microglia was TAM dependent, but not Tim4 dependent. These results indicate that TAM and Tim4 collaborate for efficient efferocytosis in certain macrophage populations.

Single administration of a novel γ-secretase modulator ameliorates cognitive dysfunction in aged C57BL/6J mice.

Mutations in presenilin 1 (PS1) and presenilin 2 (PS2) are known to cause early onset of Alzheimer's disease (AD). These proteins comprise the catalytic domain of γ-secretase, which catalyzes the cleavage of ß-amyloid (Aß) from amyloid precursor protein (APP). In recent reports, PS1 and PS2 were linked to the modulation of intracellular calcium ion (Ca(2+)) dynamics, a key regulator of synaptic function. Ca(2+) dysregulation and synaptic dysfunction are leading hypothesis of cognitive dysfunctions during aging and AD progression. Accordingly, manipulations of presenilins by small molecules may have therapeutic potential for the treatment of cognitive dysfunction. In an accompanying report, we showed that chronic treatment with compound-1, a novel γ-secretase modulator (GSM), reduced Aß production and ameliorated cognitive dysfunction in Tg2576 APP transgenic mice. Accordingly, in the present study we showed that single oral administration of compound-1 at 1 and 3mg/kg ameliorated cognitive dysfunction in aged non-transgenic mice. Moreover, compound-1 enhanced synaptic plasticity in hippocampal slices from aged C57BL/6J mice and increased messenger RNA (mRNA) expression of the immediate early gene c-fos, which has been shown to be related to synaptic plasticity in vivo. Finally, compound-1 modulated Ca(2+) signals through PS1 in mouse embryonic fibroblast cells. Taken together, compound-1 ameliorates both Aß pathology and age-related cognitive dysfunctions. Hence, compound-1 may have potential as an early intervention for the cognitive declines that are commonly diagnosed in aged subjects, such as mild cognitive impairment (MCI) and prodromal AD.

Complex regulation and diverse functions of alpha-klotho.

It has been understood that the α-klotho gene, first identified as an aging-related gene, is actually necessary for regulating mineral homeostasis in vertebrates. All vertebrates, including humans, actively maintain calcium and phosphate ions in bones, circulating blood, and cerebrospinal fluid. Therefore, disruptions in homeostasis cause osteoporosis, ectopic calcification, and epilepsy. Vitamin D and parathyroid hormone are well-known hormones for maintaining calcium and phosphate balance. Synthesis of vitamin D, secretion of parathyroid hormone, and absorption of calcium and phosphate ions are all finely controlled by α-Klotho-dependent machineries. However, the precise molecular mechanisms and functions of α-Klotho are still unclear. In this article, we present an overview of recent progress in α-klotho research, with a main focus on molecular aspects.

[Anesthetic management of a patient with multiple system atrophy undergoing adrenal gland tumor surgery].

We report anesthetic management of a 61-year-old man with multiple system atrophy undergoing adrenal grand tumor surgery. Before surgery, he was sufficiently hydrated and an elastic bandage had been applied to the legs. After epidural catheterization for the postoperative analgesia, general anesthesia was induced with midazolam 7 mg and remifentanil 0.25 microg x kg(-1) x min(-1) and his trachea was intubated. During surgery, general anesthesia was maintained with sevoflurane and remifentanil 0.12-0.25 microg x kg(-1) x min(-1). Hemodynamics was almost stable although transient hypotension occurred during surgery because of bleeding and partial clamping of the inferior vena cava. After surgery, he emerged from anesthesia and tracheal tube was removed uneventfully. However, on the first postoperative day, hypotension and respiratory failure occurred. Noradrenaline infusion was needed to treat hypotension due to vasodilation and reintubation was performed. After several days, hypotension and respiratory failure improved and he was discharged from ICU.

Relevant use of Klotho in FGF19 subfamily signaling system in vivo.

Alpha-Klotho (alpha-Kl) and its homolog, beta-Klotho (beta-Kl) are key regulators of mineral homeostasis and bile acid/cholesterol metabolism, respectively. FGF15/ humanFGF19, FGF21, and FGF23, members of the FGF19 subfamily, are believed to act as circulating metabolic regulators. Analyses of functional interactions between alpha- and beta-Kl and FGF19 factors in wild-type, alpha-kl(-/-), and beta-kl(-/-) mice revealed a comprehensive regulatory scheme of mineral homeostasis involving the mutually regulated positive/negative feedback actions of alpha-Kl, FGF23, and 1,25(OH)(2)D and an analogous regulatory network composed of beta-Kl, FGF15/humanFGF19, and bile acids that regulate bile acid/cholesterol metabolism. Contrary to in vitro data, beta-Kl is not essential for FGF21 signaling in adipose tissues in vivo, because (i) FGF21 signals are transduced in the absence of beta-Kl, (ii) FGF21 could not be precipitated by beta-Kl, and (iii) essential phenotypes in Fgf21(-/-) mice (decreased expressions of Hsl and Atgl in WAT) were not replicated in beta-kl(-/-) mice. These findings suggest the existence of Klotho-independent FGF21 signaling pathway(s) where undefined cofactors are involved. One-to-one functional interactions such as alpha-Klotho/FGF23, beta-Klotho/FGF15 (humanFGF19), and undefined cofactor/FGF21 would result in tissue-specific signal transduction of the FGF19 subfamily.

p97/valosin-containing protein (VCP) is highly modulated by phosphorylation and acetylation.

p97/valosin-containing protein (VCP) is a member of the AAA family proteins, which plays various important roles in cells by using its ATPase activity. But mechanism of regulating its ATPase activity is mostly unknown. We report here that VCP is highly modified throughout the protein via acetylation and phosphorylation. In addition to six previously identified phosphorylation sites, we identified at least 14 serines, 14 threonines, 6 tyrosines and 22 lysines as potential modification sites. Interestingly, these sites included Lys251 and Lys524, which are very critical for the ATP binding in Walker A motif of D1 and D2 domains, respectively. It is notable that 16 sites are in the N-terminal region and 16 sites are clustered in D2alpha domain (from Pro646 to Gly765). Indeed, amino acid substitution of Lys696 and Thr761 profoundly affect VCP ATPase activities. From these results, we propose that D2alpha domain acts as a VCP ATPase Regulatory domain or "VAR domain". VCP modifications including those in this VAR domain may endorse adaptive and multiple functions to VCP in different cell conditions such as in the cell cycle and with abnormal protein accumulation.

alpha-Klotho as a regulator of calcium homeostasis.

alpha-klotho was identified as a gene associated with premature aging-like phenotypes characterized by short lifespan. In mice, we found the molecular association of alpha-Klotho (alpha-Kl) and Na+,K+-adenosine triphosphatase (Na+,K+-ATPase) and provide evidence for an increase of abundance of Na+,K+-ATPase at the plasma membrane. Low concentrations of extracellular free calcium ([Ca2+]e) rapidly induce regulated parathyroid hormone (PTH) secretion in an alpha-Kl- and Na+,K+-ATPase-dependent manner. The increased Na+ gradient created by Na+,K+-ATPase activity might drive the transepithelial transport of Ca2+ in cooperation with ion channels and transporters in the choroid plexus and the kidney. Our findings reveal fundamental roles of alpha-Kl in the regulation of calcium metabolism.