Clades of huge phages from across Earth's ecosystems.

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

[Surgical Techniques for Microvascular Decompression in Hemifacial Spasm].

This study discusses the key microvascular decompression(MVD)techniques for the treatment of hemifacial spasm(HFS). The author's experience is based on their institution's cases, highlighting three critical techniques. (1)Vertebral artery(VA)repositioning: Repositioning the VA is essential in challenging cases. This article focuses on the relocation of the proximal portion of the VA and the importance of careful dissection. (2)Relocating vessels compressing the peripheral branches of the facial nerve: HFS can result from nerve compression at various locations, including the cisternal portion. This study addressed cisternal compression and considered the nearby nerves. (3)Considering the perforating branches during repositioning, cases may involve complex branching of the perforating arteries. This paper describes an approach that carefully repositions the vessels without damaging the perforating branches. The results from 100 VA-involved cases showed excellent outcomes, with 91.2% of patients experiencing T0(excellent)results. This study emphasized the need to adapt the surgical approach to each unique case to ensure the safety and effectiveness of MVD. This study provides insights into the critical MVD techniques for HFS, emphasizing the importance of continuous experience and knowledge accumulation. These techniques can be learned by other neurosurgeons, thereby expanding the availability of safe and successful MVD procedures for HFS.

[A Case of Rhabdomyolysis Caused by Oxaliplatin during Postoperative Adjuvant Chemotherapy].

The patient was a 50-year-old male. At the age of 48 years, he had undergone total gastrectomy and right hemicolectomy simultaneously for gastric and ascending colon cancers. Since adjuvant chemotherapy has become common practice for patients with ascending colon cancer, capecitabine was administered for 6 months. One year and 6 months after the surgery, he was diagnosed with recurrence of the ascending colon cancer at the anastomotic site and underwent local colectomy. Considering he was pathologically diagnosed as pT4a, mFOLFOX6 therapy was prescribed as postoperative adjuvant chemotherapy. On the day the 11th course of treatment was initiated, the patient complained of weakness; however, his blood test results showed no abnormalities; therefore, he was followed-up as an outpatient. Three days later, he presented to the hospital with exacerbated symptoms and was diagnosed with rhabdomyolysis due to a marked increase in CK(2,031 U/L). Rhabdomyolysis was determined to be the adverse effect of oxaliplatin because out of all the drugs prescribed to the patient, this condition is listed as a side effect only in oxaliplatin's package insert. Fortunately, outpatient treatment was enough to alleviate rhabdomyolysis. Subsequently, adjuvant chemotherapy was completed without oxaliplatin. The patient has been followed-up without recurrence for 9 months after the surgery.

Cisplatin-Chelated Iminodiacetic Acid-Conjugated Hyaluronic Acid Nanogels for the Treatment of Malignant Pleural Mesothelioma in Mice.

Malignant pleural mesothelioma (MPM) is one of the intractable cancers that require a more effective therapeutic strategy for clinical practice. Hyaluronic acid (HA) nanogels were prepared by the chelation of cisplatin (CDDP) with different molecular weights of iminodiacetic acid-conjugated hyaluronic acid (HA-IDA). The sizes of the 100, 850, and 2000 kDa HA nanogels were 33, 43, and 44 nm, respectively. MSTO-211H, a human MPM cell line, was more effective in taking up all three HA nanogels compared to AB22, a mouse MPM cell line. In addition, the 850 kDa HA nanogel showed higher anticancer activity against AB22 and MSTO-211H than 100 and 2000 kDa HA nanogels. Furthermore, all the HA nanogels showed a milder cytotoxic effect on normal Met-5A mesothelial cells compared to that exhibited by free CDDP. Finally, the 850 kDa HA nanogel was administrated intrapleurally into both the MSTO-211H xenograft and AB22 allograft mouse models of MPM using an injectable HA-based hydrogel. HA nanogels showed a significant therapeutic effect in both the xenograft and allograft models.

[A Case of Extramural Growth-Type Ileocecal Colon Cancer].

A woman in her 80s was diagnosed with an abdominal mass during physical examination. Contrast-enhanced computed tomography(CT)revealed a tumor with contrast enhancement outside the ileocecal region of the intestine, and the ileocolic artery penetrated the tumor. No tumor was detected by colonoscopy. An endoscope could not be passed through due to an ileocecal valve stenosis. A biopsy of the ileocecal valve revealed only lymphocyte hyperplasia without adenocarcinoma components. Barium enema examination demonstrated no influx of the contrast medium from the cecum into the oral side of the intestine. Since a gastrointestinal stromal tumor in the ileocecal region was suspected, laparotomy was performed in the ileocecal region owing to the preoperative diagnosis of suspected malignant lymphoma, revealing a 5-cm elastic hard tumor outside the ileocecal wall. The tumor could not be separated from the intestinal tract. Histopathological examination revealed no lesion on the mucosal surface, although poorly differentiated adenocarcinoma infiltrated from the submucosa to the serosa. Thus, the patient was diagnosed with extramural growth-type ileocecal colon cancer. This disease is relatively rare but need to be kept in mind.

[A Case of Transverse Colon Cancer Complicated by Eosinophilic Granulomatosis with Polyangiitis].

A man in his 50s had undergone steroid therapy for eosinophilic granulomatosis with polyangiitis(EGPA). Since an examination for malignant tumors revealed type 0-Ⅰsp(cT1aN0M0)and type 2(cT2N0M0)lesions in the proximal and mid- transverse colon, respectively, he was referred to our department. Endoscopic resection was performed on the proximal lesion. After the confirmation of curative resection, laparoscopic partial colectomy(transverse colon)and D3 lymph node dissection were performed on the mid-transverse lesion. Because of the patient's favorable postoperative course, he was discharged from the hospital on POD17. Since steroids and immunosuppressants may cause immunological abnormalities and malignant tumors, such patients should be strictly followed up.

Desulfovibrio subterraneus sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation.

A novel mesophilic sulfate-reducing bacterium, strain HN2T, was isolated from groundwater sampled from the subsurface siliceous mudstone of the Wakkanai Formation located in Horonobe, Hokkaido, Japan. The bacterium was Gram-negative and vibrio-shaped, and its motility was conferred by a single polar flagellum. Cells had desulfoviridin. Catalase and oxidase activities were not detected. It grew in the temperature range of 25-40 °C (optimum, 35 °C) and pH range of 6.3-8.1 (optimum, pH 7.2-7.6). It used sulfate, thiosulfate, dimethyl sulfoxide, anthraquinone-2,6-disulfonate, Fe3+, and manganese oxide, but not elemental sulfur, nitrite, nitrate, or fumarate as electron acceptors. The strain showed weak growth with sulfite as the electron acceptor. Fermentative growth with pyruvate, lactate and cysteine was observed in the absence of sulfate, but not with malate or fumarate. NaCl was not required, but the strain tolerated up to 40 g l-1. Strain HN2T did not require vitamins. The major cellular fatty acids were iso-C15 : 0 (23.8 %), C18 : 1 ω9t (18.4 %), C18 : 0 (15.0 %), C16 : 0 (14.5 %), and anteiso-C17 :0 (10.1 %). The major respiratory quinone was menaquinone MK-6(H2). The G+C content of the genomic DNA was 56.7 mol%. Based on 16S rRNA gene sequence analysis, the closest phylogenetic relative of strain HN2T is Desulfovibrio psychrotolerans JS1T (97.0 %). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of the strains HN2T and D. psychrotolerans JS1T were 22.2 and 79.8 %, respectively. Based on the phenotypic and molecular genetic evidence, we propose a novel species, D. subterraneus sp. nov. with the type strain HN2T (=DSM 101010T=NBRC 112213T).

Influence of light-dark cycle on delayed recovery from isoflurane anesthesia induced by hypnotics in mice.

We previously reported that brotizolam, but not suvorexant, delayed recovery from isoflurane anesthesia in mice. However, the effects of hypnotics may be altered by the circadian rhythm. Locomotor activity was measured using sighted (ICR and C57BL/6J) and blind (FVB/N and C3H/HeN) mice, and the effects of hypnotics on isoflurane anesthesia were compared during the light and dark periods. In sighted mice, recovery induced by brotizolam was delayed in the light period, while that by suvorexant was delayed in the dark period. In C57BL/6J mice, delayed recovery induced by brotizolam was marked, and that by suvorexant was observed in the light and dark periods. Locomotor activity was low in the last 6 h of the dark period in blind mice, and was similar to that in the light period. In blind mice, delayed recovery induced by brotizolam was identical in both periods, while suvorexant did not influence recovery from isoflurane anesthesia. These results suggest that the effects of hypnotics on isoflurane anesthesia are altered by the circadian rhythm and that daily light-dark stimuli may be required for the chronopharmacological effects of hypnotics.

[A Case of Unresectable Gastric Cancer Who Underwent Conversion Surgery after SP Therapy and Achieved Long-Term Survival].

The case was a man in his 60s. With a complaint of loss of appetite, a peripheral type 3 lesion was found from the lower body of the stomach to the vestibule, and a biopsy revealed poorly differentiated adenocarcinoma. CT examination revealed that the tumor had invaded the left lobe of the liver and the transverse colon, and that the para-aortic lymph nodes were swollen and multiple nodules of the gastrocolonic mesentery were found. After 6 courses of S-1 plus cisplatin(SP)therapy were performed, the tumor shrank and lymph node swelling and nodule disappearance were observed. Laparotomy and pyloric gastrectomy, partial liver resection, D2 dissection, and Roux-en-Y reconstruction were performed. As a result of histopathological examination, R0 was resected. After the operation, S-1 was taken orally for 1 year, and no recurrence or metastasis has been observed 6 and a half years after the operation. This time, we report a valuable case in which SP therapy was successful for unresectable gastric cancer and long-term survival was obtained by conversion surgery.

Intraperitoneal Delivery of Cisplatin via a Hyaluronan-Based Nanogel/in Situ Cross-Linkable Hydrogel Hybrid System for Peritoneal Dissemination of Gastric Cancer.

Intraperitoneal administration of chemotherapeutics is expected for the treatment of peritoneally disseminated gastric cancer because of poor migration of the drugs from the systemic circulation to the peritoneal cavity. In this study, for intraperitoneal delivery of cisplatin (CDDP), we developed a hyaluronan (HA)-based hybrid system in which CDDP-loaded HA nanogels were either physically encapsulated in or chemically conjugated to injectable HA hydrogels. Physical encapsulation enabled sustained release of HA nanogels from the HA hydrogel matrix for over a week. This was a longer release period than that of encapsulated free CDDP, which released 80% of the drug in 2 days. The longer release was attributed to delayed diffusion of HA nanogels from the hydrogel matrix network. The release profile could be tuned by modifying the chemical conjugation of HA nanogels to the HA hydrogel matrix, as well as the type of chelating ligands used to load CDDP to the nanogel. Furthermore, intraperitoneally administered hybrid had significant antitumor activity in a mouse model of peritoneally disseminated gastric cancer, especially for nodules smaller than 1.0 mm.

Production of Cisplatin-Incorporating Hyaluronan Nanogels via Chelating Ligand-Metal Coordination.

Hyaluronan (HA) is a promising drug carrier for cancer therapy because of its CD44 targeting ability, good biocompatibility, and biodegradability. In this study, cisplatin (CDDP)-incorporating HA nanogels were fabricated through a chelating ligand-metal coordination cross-linking reaction. We conjugated chelating ligands, iminodiacetic acid or malonic acid, to HA and used them as a precursor polymer. By mixing the ligand-conjugated HA with CDDP, cross-linking occurred via coordination of the ligands with the platinum in CDDP, resulting in the spontaneous formation of CDDP-loaded HA nanogels. The nanogels showed pH-responsive release of CDDP, because the stability of the ligand-platinum complex decreases in an acidic environment. Cell viability assays for MKN45P human gastric cancer cells and Met-5A human mesothelial cells revealed that the HA nanogels selectively inhibited the growth of gastric cancer cells. In vivo experiments using a mouse model of peritoneal dissemination of gastric cancer demonstrated that HA nanogels specifically localized in peritoneal nodules after the intraperitoneal administration. Moreover, penetration assays using multicellular tumor spheroids indicated that HA nanogels had a significantly higher ability to penetrate tumors than conventional, linear HA. These results suggest that chelating-ligand conjugated HA nanogels will be useful for targeted cancer therapy.

Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements.

Methane emissions are mitigated by anaerobic methane-oxidizing archaea, including Methanoperedens. Some Methanoperedens host huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is understudied. Here we report small enigmatic linear ECEs, circular viruses and unclassified ECEs that are predicted to replicate within Methanoperedens. Linear ECEs have inverted terminal repeats, tandem repeats and coding patterns that are strongly reminiscent of Borgs, but they are only 52-145 kb in length. As they share proteins with Borgs and Methanoperedens, we refer to them as mini-Borgs. Mini-Borgs are genetically diverse and can be assigned to at least five family-level groups. We identify eight families of Methanoperedens viruses, some of which encode multi-haem cytochromes, and circular ECEs encoding transposon-associated TnpB genes with proximal population-heterogeneous CRISPR arrays. These ECEs exchange genetic information with each other and with Methanoperedens, probably impacting their archaeal host activity and evolution.

A Case of Septic Encephalopathy Diagnosed Following Non-inflammatory Febrile Response in an Elderly Patient After Sepsis.

Intracranial disorders are common in cases of prolonged disturbances of consciousness following sepsis. Among these, investigation of vascular lesions is warranted because only a few patients have encephalitic symptoms. However, the examination may not be comprehensive owing to the lack of rapid changes in the clinical status. This report presents the case of an elderly woman with severe sepsis who experienced prolonged disturbances in consciousness and persistent fever. Lumbar puncture results suggested the possibility of post-sepsis encephalitis. Sepsis induces systemic acute inflammation and activates autoimmune responses, leading to prolonged brain inflammation in some cases. When disturbances in consciousness persist after sepsis, a thorough investigation for the possibility of post-septic encephalitis is imperative.

Long insular artery damage might be a key sign for predicting functional prognosis of putaminal hemorrhage.

OBJECTIVE: Although the putamen is the most common area of spontaneous intracerebral hemorrhage, previous reports about the effects of surgery are limited. We sometimes experience a poor prognosis in patients in whom there is no damage to the internal capsule, but with injury in the long insular artery (LIA) region. The purpose of this study was to confirm the relationship between LIA damage and patient prognosis following surgery for putaminal hemorrhage. METHODS: We retrospectively collected data of 287 surgical cases who presented with putaminal hemorrhage between January 2004 and March 2022. Among them, we chose patients without initial damage to the posterior limb of the internal capsule, and divided these patients into two groups, those without (Group A) and with (Group B) final damage in the LIA region. We compared positivity rates of final manual muscle test (MMT) scores≥3 and related factors. RESULTS: Sixty-three of the 287 patients were included in this study. Of them, 11 cases in Group A were positive for MMT scores≥3 (68.8%) and 9 cases (19.1%) in Group B had MMT scores≥3 seven days after surgery. Group A thus had a significantly higher rate of MMT scores≥3 than group B (p=0.00). CONCLUSION: In patients without initial damage to the internal capsule, LIA injury might be a key sign for predicting the functional prognosis of putaminal hemorrhage.

Significant Correlation between Structural Changes in the Net-like Appearance on Postoperative Cranial Magnetic Resonance Images and Hematoma Recurrence in Cases of Chronic Subdural Hematoma.

Organized hematoma, which exhibits a net-like appearance on imaging studies, is one of the predisposing factors for the recurrence of chronic subdural hematoma. Patients who are positive for the net-like appearance are often treated with only burr hole surgery. We investigated the relationship between postoperative structural changes in the net-like appearance and the recurrence rate of chronic subdural hematoma. Of the 949 patients with chronic subdural hematoma treated with primary burr hole surgery between January 2010 and April 2021 at our hospital, 268 who were considered positive for the net-like appearance on T2- and T2 star-weighted magnetic resonance images were extracted. We followed the structural changes in the net-like appearance postoperatively and subsequently classified the patients into three groups: decreasing type, shifting type, and no change and deterioration type. The relationship between each structural change and the recurrence rate in the three groups was investigated. Postoperative recurrence requiring surgery occurred in 3.5% of the subjects with decreasing type, 0% with shifting type, and 100% with deterioration type of the net-like appearance (P < 0.05), indicating differences in the recurrence rates according to postoperative structural changes in the magnetic resonance images (MRI) features of chronic subdural hematoma. Our results indicate that the risk of postoperative chronic subdural hematoma recurrence can be predicted by focusing on the structural changes in the postoperative net-like appearance on MRI.

Anaerobic methane-oxidizing activity in a deep underground borehole dominantly colonized by Ca. Methanoperedenaceae.

The family Ca. Methanoperedenaceae archaea mediates the anaerobic oxidation of methane (AOM) in different terrestrial environments. Using a newly developed high-pressure laboratory incubation system, we investigated 214- and 249-m deep groundwater samples at Horonobe Underground Research Laboratory, Japan, where the high and low abundances of Ca. Methanoperedenaceae archaea have been shown by genome-resolved metagenomics, respectively. The groundwater samples amended with 13 C-labelled methane and amorphous Fe(III) were incubated at a pressure of 1.6 MPa. After 3-7 days of incubation, the AOM rate was 45.8 ± 19.8 nM/day in 214-m groundwater. However, almost no activity was detected from 249-m groundwater. Based on the results from 16S rRNA gene analysis, the abundance of Ca. Methanoperedenaceae archaea was high in the 214-m deep groundwater sample, whereas Ca. Methanoperedenaceae archaea was undetected in the 249-m deep groundwater sample. These results support the in situ AOM activity of Ca. Methanoperedenaceae archaea in the 214-m deep subsurface borehole interval. Although the presence of Fe-bearing phyllosilicates was demonstrated in the 214-m deep groundwater, it needs to be determined whether Ca. Methanoperedenaceae archaea use the Fe-bearing phyllosilicates as in situ electron acceptors by high-pressure incubation amended with the Fe-bearing phyllosilicates.

Microvascular Decompression for Concurrent Trigeminal Neuralgia and Hemi-Laryngopharyngeal Spasm: A Case Report.

BACKGROUND AND IMPORTANCE: Hemi-laryngopharyngeal spasm (HeLPS) may result from vascular compression of the vagus nerve and can be treated using microvascular decompression. We describe the clinical characteristics and surgical treatment in a case of concurrent trigeminal neuralgia (TN) and HeLPS. CLINICAL PRESENTATION: A 44-year-old man presented with a 12-month history of right TN and 8-month history of intermittent episodes of repeated throat contractions associated with a very distressing choking sensation. Preoperative 3-dimensional fusion imaging demonstrated compression of the trigeminal nerve by the superior cerebellar artery and petrosal vein and compression of the vagus nerve by the posterior inferior cerebellar artery and one of its branches. Microvascular decompression was performed by a right standard retrosigmoid approach with enlarged craniotomy. Initially, the compression of the trigeminal nerve was identified by visual inspection. All the offending vessels were wrapped in Teflon felt, transposed away from the trigeminal nerve, and adhered to the tentorial membrane and petrous bone using fibrin glue. Furthermore, observation of the caudal rootlets of the vagus nerve revealed that the posterior inferior cerebellar artery and its branch compressed the ventral side of the nerve. These vessels were displaced antero-caudally with Teflon felt and fibrin glue; no other vessels were found around the trigeminal and vagus nerves. Postoperatively, the patient had immediate and complete resolution of symptoms of TN and HeLPS without recurrence at the 18-month follow-up. CONCLUSION: HeLPS may occur with TN, and neurosurgeons should identify the symptoms suspicious of this disease preoperatively.

Objectively-captured Changes in Trigeminal Fibers before and after Microvascular Decompression Using 3D T2-SPACE MRI Might Relate to Eventual Residual Symptoms.

Although microvascular decompression (MVD) is a reliable treatment for trigeminal neuralgia (TN), neurosurgeons sometimes encounter patients whose symptoms do not improve postoperatively or who experience good treatment efficacy but develop other sensory disturbances. This study aims to objectively identify changes in nerve fibers before and after surgery by MRI and to clarify the relationship between the changes and residual postoperative symptoms. We retrospectively analyzed data from 36 consecutive patients who underwent MVD for classical TN at our hospital between November 2019 and November 2020. Cases that fulfilled the diagnostic criteria for multiple sclerosis were excluded. We confirmed the changes on the brainstem side of the trigeminal nerve preoperatively and at seven days postoperatively using 3D T2-SPACE MRI, in which the patients were divided into three groups: preoperative T2 high intensity positive (A), postoperative T2 high intensity positive (B), and no T2 high-intensity region (C). The primary outcome measures were therapeutic efficacy and frequency of postoperative numbness. The results of MVD surgery were evaluated one year postoperatively. The percentage of cases in which treatment outcomes were rated as excellent or good at one year: group A: 0 (0%), group B: 6 (100%), and group C: 25 (96.2%) (p < 0.05); the frequency of numbness: 2 (50%) in group A, 3 (50%) in group B, and 1 (3.8%) in group C, indicating significant differences between the three groups (p < 0.05). 3D T2-SPACE MRI sequences can be used to identify changes in trigeminal nerve fibers before and after MVD, which might correlate with eventual residual symptoms.

Injectable extracellular matrix hydrogels contribute to native cell infiltration in a rat partial nephrectomy model.

Decellularized extracellular matrix (dECM) hydrogels have cytocompatibility, and are currently being investigated for application in soft tissues as a material that promotes native cell infiltration and tissue reconstruction. A dECM hydrogel has broad potential for application in organs with complex structures or various tissue injury models. In this study, we investigated the practical application of a dECM hydrogel by injecting a kidney-derived dECM hydrogel into a rat partial nephrectomy model. The prepared dECM hydrogel was adjustable in viscosity to allow holding at the excision site, and after gelation, had an elastic modulus similar to that of kidney tissue. In addition, the migration of renal epithelial cells and vascular endothelial cells embedded in dECM hydrogels was observed in vitro. Four weeks after injection of the dECM hydrogel to the partial excision site of the kidneys, infiltration of renal tubular constituent cells and native cells with high proliferative activity, as well as angiogenesis, were observed inside the injected areas. This study is the first to show that dECM hydrogels can be applied to the kidney, one of the most complex structural organs and that they can function as a scaffold to induce angiogenesis and infiltration of organ-specific renal tubular constituent cells, providing fundamental insights for further application of dECM hydrogels.

A predicted CRISPR-mediated symbiosis between uncultivated archaea.

CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.