Fecal DNA analysis coupled with the sighting records re-expanded a known distribution of dugongs in Ryukyu Islands after half a century.

DNA analysis of large herbivore feces samples collected from seagrass beds at two distant sites (Irabu Island in Miyako Islands and Kushi in Okinawa Island) in the Ryukyu Islands proved that some of these feces were from dugongs, which had been treated in recent studies as extinct in this region since the last stranding of a deceased individual in 2019. In addition, local knowledge of sightings of animals thought to be dugongs and confirmed cases of dugong feeding trails since 2010 were compiled to estimate its recent distribution. This is the first scientific report on the presence of this mammal in the Ryukyu Islands within the last four years, and particularly in the Miyako Islands within the last half-century. As the Ryukyu Islands are known to be the northern limit of the dugong's fragmented distribution in East Asia, conservation efforts are therefore needed.

Method for obtaining reliable R-waves in fish electrocardiograms by utilizing conductivity of seawater.

A simple method for measuring bioelectric signals of fish in seawater is expected for managing the health of farmed fish and clarifying the ecophysiology of natural fish. We previously proposed a simple and unique method for measuring bioelectric signals of fish by inserting only one special internal electrode (which can be isolated from seawater) into the fish's body and by sinking an external electrode in seawater (for utilizing the conductivity of seawater). However, the proposed method could not obtain fish electrocardiograms (ECGs) with reliable R-waves in the same manner as the conventional method. In this study, we thus experimentally investigated whether the R-waves of ECGs could be observed by optimizing the insertion position of the internal electrode into the fish's body. The results of the experiment show that for four species of fish (each slightly longer than 10 cm) with different body shapes, reliable R-waves could be observed by inserting the internal electrode near the heart. We also investigated the possibility of simultaneously measuring ECGs of multiple fish by the proposed method. The results of the investigation show that the fish ECGs with R-waves of three fish could be observed simultaneously even when one single common external electrode replaced multiple external electrodes. This result indicates the advantage of the proposed method in reducing the total number of bioelectrodes compared to the conventional method for ECG measurements of multiple fish.

Fumagillin inhibits growth of the enteric protozoan parasite Entamoeba histolytica by covalently binding to and selectively inhibiting methionine aminopeptidase 2.

Amebiasis is an important cause of morbidity and mortality worldwide, and caused by infection with the protozoan parasite Entamoeba histolytica. Metronidazole is currently the first-line drug despite adverse effects and concerns on the emergence of drug resistance. Fumagillin, a fungal metabolite from Aspergillus fumigatus, and its structurally related natural and synthetic compounds have been previously explored as potential anti-angiogenesis inhibitors for cancers, anti-microbial, and anti-obese compounds. Although fumagillin was used for human amebiasis in clinical trials in 1950s, the mode of action of fumagillin remains elusive until now. In this report, we showed that fumagillin covalently binds to methionine aminopeptidase 2 (MetAP2) and non-covalently but abundantly binds to patatin family phospholipase A (PLA). Susceptibility against fumagillin of the amebic strains in which expression of E. histolytica MetAP2 (EhMetAP2) gene was silenced increased compared to control strain. Conversely, overexpression of EhMetAP2 mutants that harbors amino acid substitutions responsible for resistance to ovalicin, a fumagillin analog, in human MetAP2, also resulted in decrease in fumagillin susceptibility. In contrast, neither gene silencing nor overexpression of E. histolytica PLA (EhPLA) affected fumagillin susceptibility. These data suggest that EhPLA is not essential and not the target of fumagillin for its amebicidal activity. Taken together, our data have demonstrated that EhMetAP2 is the primary target for amebicidal activity of fumagillin, and EhMetAP2 represents a rational explorable target for the development of alternative therapeutic agents against amebiasis.

Origin of Homochirality in Amino Acids Induced by Lyman-α Irradiation in the Early Stage of the Milky Way.

The enantiomeric excess (ee) of l-form amino acids found in the Murchison meteorite poses some issues about the cosmic origin of their chirality. Circular dichroism (CD) spectra of amino acids in the far-ultraviolet (FUV) at around 6.8 eV (182 nm) indicate that the circularly polarized light can induce ee through photochemical reactions. Here, we resort to ab initio calculations to extract the CD spectra up to the vacuum-ultraviolet (VUV) region (∼11 eV), and we propose a novel equation to compute the ee applicable to a wider range of light frequency than what is available to date. This allows us to show that the strength of the induced ee (|ee|) in the 10 eV VUV region is comparable to the one in the 6.8 eV FUV region. This feature is common for some key amino acids (alanine, 2-aminobutyric acid, and valine). In space, intense Lyman-α (Lyα) light of 10.2 eV is emitted from star forming regions. This study provides a theoretical basis that Lyα emitter from an early starburst in the Milky Way plays a crucial role in initiating the ee of amino acids.

Enantioselective amino acid interactions in solution.

Enantiomeric excesses (ee) of L-amino acids in meteorites are higher than 10%, especially for isovaline (Iva). This suggests the existence of some kind of triggering mechanism responsible for the amplification of the ee from an initial small value. Here, we investigate the dimeric molecular interactions of alanine (Ala) and Iva in solution as an initial nucleation step of crystals at an accurate first-principles level. We find that the dimeric interaction of Iva is more chirality-dependent than that of Ala, thus providing a clear molecular-level insight into the enantioselectivity of amino acids in solution.

Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theory.

Aldehydes and carboxylic acids are widely used as catalysts for efficient racemization process of amino acids. However, the detailed reaction mechanism remains unclear. This work aims to clarify the racemization mechanism of aspartic acid (Asp) catalyzed by salicylaldehyde and acetic acid by using computational approaches. Density functional theory was used to obtain the structures and relative energies of 10 intermediates and five transition states, thus characterizing the main stages of the reaction. The calculated energy diagram shows that the dehydration step has the highest energy barrier, followed by the reaction step to change the chirality of Asp, which is a crucial process for racemization. In the dehydration reaction, water molecules can induce a remarkable decrease in the required energy.

Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids.

High enantiomeric excesses (ee's) of l-amino acids, including non-proteinogenic amino acid isovaline (Iva), were discovered in the Murchison meteorite, but the detailed molecular mechanism responsible for the observed ee of amino acids remains elusive and inconsistent, because Iva has an inverted circular dichroism (CD) spectrum with respect to α-H amino acids, e.g., alanine. To address this issue, we resort to accurate ab initio calculations for amino acids and their precursors in the Strecker synthesis. We evaluated their photolysis-induced ee in the range 5-11 eV including the Lyman alpha emission line (Lyα), the typical intensive 10.2 eV radiation ascribed to the early phase of galactic evolution. We show that only the aminonitrile precursors are characterized by positive ee in the Lyα region, explaining why right-handed circularly polarized Lyα (R-CP-Lyα) induces homologous l-amino acids. This study shows that the homochirality of amino acids is produced at the aminonitrile precursors stage.

Determination of the reference range for semi-quantified elasticity of healthy supraspinatus muscles using real-time tissue elastography and its clinical use in patients after rotator cuff repair.

BACKGROUND: The quantitative assessment of healthy supraspinatus muscle elasticity may provide clinically useful preliminary information after rotator cuff repairs. We aimed to determine the reference range for supraspinatus muscle semi-quantified elasticity and describe how it can be used clinically after rotator cuff repair. METHODS: The elasticity of healthy bilateral supraspinatus muscles in 43 participants aged between 24 and 75 years (categorized into two subgroups: <50 and ≥ 50 years) was measured as a strain ratio at 0° and 60° of shoulder abduction using real-time tissue elastography. The reference and modified reference ranges calculated by excluding outliers for elasticity were determined using normal distribution methods for logarithmically transformed data. The modified reference range was applied to eight cases of rotator cuff repair. FINDINGS: Strain ratios under and over 50 years of age were 1.63 vs. 2.21 at 0° of shoulder abduction (P = 0.028) and 0.92 vs. 1.29 at 60° of shoulder abduction (P = 0.002), respectively. Modified reference ranges for under and over 50 years of age were 0.72-4.17 and 0.98-4.50 at 0° of shoulder abduction and 0.38-1.95 and 0.56-2.76 at 60° of shoulder abduction, respectively. Among eight cases, two showed strain ratios above the reference range at 1 month postoperatively, and rehabilitation protocols were adjusted. INTERPRETATION: A strain ratio above the reference range, especially above the upper limit at 0° of shoulder abduction, may indicate increased passive stiffness of the musculotendinous unit. Clinically, the reference range has the potential to be used as a baseline after rotator cuff repairs.

Molecular Dissection of Phagocytosis by Proteomic Analysis in Entamoeba histolytica.

Entamoeba histolytica is the enteric protozoan parasite responsible for amebiasis. Trophozoites of E. histolytica ingest human cells in the intestine and other organs, which is the hallmark of its pathogenesis. Phagocytosis and trogocytosis are pivotal biological functions for its virulence and also contribute to the proliferation of nutrient uptake from the environment. We previously elucidated the role of a variety of proteins associated with phagocytosis and trogocytosis, including Rab small GTPases, Rab effectors, including retromer, phosphoinositide-binding proteins, lysosomal hydrolase receptors, protein kinases, and cytoskeletal proteins. However, a number of proteins involved in phagocytosis and trogocytosis remain to be identified, and mechanistic details of their involvement must be elucidated at the molecular level. To date, a number of studies in which a repertoire of proteins associated with phagosomes and potentially involved in phagocytosis have been conducted. In this review, we revisited all phagosome proteome studies we previously conducted in order to reiterate information on the proteome of phagosomes. We demonstrated the core set of constitutive phagosomal proteins and also the set of phagosomal proteins recruited only transiently or in condition-dependent fashions. The catalogs of phagosome proteomes resulting from such analyses can be a useful source of information for future mechanistic studies as well as for confirming or excluding a possibility of whether a protein of interest in various investigations is likely or is potentially involved in phagocytosis and phagosome biogenesis.

Providing safe and effective rehabilitation by assessing supraspinatus muscle elasticity using ultrasound real-time tissue elastography after rotator cuff repair: A case series.

INTRODUCTION: Although surgical techniques have advanced to avoid a postoperative re-tear after rotator cuff surgery, it remains unclear how to directly evaluate the risk of a re-tear. OBJECTIVE: To describe how muscle elasticity with real-time tissue elastography could be used to avoid re-tear in individual cases after rotator cuff repair. CASE DESCRIPTION: This case series included four patients, two per tear size (small and large/massive), with contrasting changes in muscle elasticity of the supraspinatus muscle. All patients underwent primary arthroscopic or open rotator cuff repair. The elasticity of the supraspinatus muscle was evaluated at relaxed and elongated positions of 0° and 60° shoulder abduction angles, respectively. The change in muscle elasticity at 1 month after surgery was characteristically different, and we predicted that a greater elasticity in the elongated position indicated a higher risk of re-tear. The cases with high risk underwent careful rehabilitation to avoid re-tear, and no re-tears were recorded in this report. CONCLUSION: Our findings suggested that evaluation of muscle elasticity using real-time tissue elastography, which provides an indication of the risk of re-tear, in the clinical setting might be useful for therapists, who could adjust the intensity of rehabilitation, and for patients.

Proteomic analysis of Atg8-dependent recruitment of phagosomal proteins in the enteric protozoan parasite Entamoeba histolytica.

Autophagy is one of the bulk degradation systems and is conserved throughout eukaryotes. In the enteric protozoan parasite Entamoeba histolytica, the causative agent of human amebiasis, Atg8 is not exclusively involved in autophagy per se but also in other membrane traffic-related pathways such as phagosome biogenesis. We previously reported that repression of atg8 gene expression by antisense small RNA-mediated transcriptional gene silencing (gs) resulted in growth retardation, delayed endocytosis, and reduced acidification of endosomes and phagosomes. In this study, to better understand the role of Atg8 in phagocytosis and trogocytosis, we conducted a comparative proteomic analysis of phagosomes isolated from wild type and atg8-gs strains. We found that 127 and 107 proteins were detected >1.5-fold less or more abundantly, respectively, in phagosomes isolated from the atg8-gs strain, compared to the control strain. Among 127 proteins whose abundance was reduced in phagosomes from atg8-gs, a panel of proteins related to fatty acid metabolism, phagocytosis, and endoplasmic reticulum (ER) homeostasis was identified. Various lysosomal hydrolases and their receptors also tend to be excluded from phagosomes by atg8-gs, reinforcing the notion that Atg8 is involved in phagosomal acidification and digestion. On the contrary, among 107 proteins whose abundance increased in phagosomes from atg8-gs strain, ribosome-related proteins and metabolite interconversion enzymes are enriched. We further investigated the localization of several representative proteins, including adenylyl cyclase-associated protein and plasma membrane calcium pump, both of which were demonstrated to be recruited to phagosomes and trogosomes via an Atg8-dependent mechanism. Taken together, our study has provided the basis of the phagosome proteome to further elucidate molecular events in the Atg8-dependent regulatory network of phagosome/trogosome biogenesis in E. histolytica.

Theoretical Investigation into a Possibility of Formation of Propylene Oxide Homochirality in Space.

The preferential synthesis or destruction of a single enantiomer by ultraviolet circularly polarized light (UV-CPL) has been proposed as a possible triggering mechanism for the extraterrestrial origin of homochirality. Herein, we investigate the photoabsorption property of propylene oxide (c-C3H6O) for UV-CPL in the Lyman-α region. Our calculations show that c-C3H6O was produced by CH3+ and CH3CH(OH)CH3 or C3H7• and O (triplet). The computed electronic circular dichroism spectra show that c-C3H6O and the intermediate (CH3CH(OH)CH2+) could absorb the UV-CPL originating from the Lyman-α emitter spectrum, suggesting that the photolysis of c-C3H6O or CH3CH(OH)CH2+ upon irradiation could induce chiral symmetry breakage.

Site-specific differences in T lymphocyte composition of the gastric mucosa after Helicobacter pylori eradication.

In our earlier work, we revealed that inflammation of the lesser curvature of the gastric body and antrum could constitute independent risk factors for gastric cancer development, while inflammation of the greater curvature was not. The aims of this study were as follows: first, to reveal the differences between T lymphocyte populations of the gastric antrum and the greater and lesser curvatures of the gastric body in patients after Helicobacter pylori eradication; second, to analyze the correlation between the composition of the stomach-resident T lymphocytes and time from H. pylori eradication; and third, to evaluate the sex differences in T lymphocyte subsets after H. pylori eradication. To investigate site-specific differences in stomach-resident T lymphocytes after H. pylori eradication, we performed flow cytometry analysis on samples taken from the gastric antrum, greater curvature of the gastric body, and lesser curvature of the gastric body of 20 patients. We also analyzed the correlation between the composition of the stomach-resident T lymphocytes and the time from H. pylori eradication. The lymphocyte subsets of the antrum and lesser curvature of the body were similar. In contrast, compared to those in the greater curvature of the gastric body, CD4+/CD3+ lymphocyte subsets (43.8 ± 19.4% vs 31.7 ± 14.6%) were elevated in the lesser curvature of the body, whereas CD8+/CD3+ (67.1 ± 21.3% vs 80.4 ± 12.0%), CD7+/CD3+ (91.2 ± 4.6% vs 93.7 ± 3.8%), CCR4+/CD3+ (7.7 ± 8.1% vs 10.4 ± 7.0%), CD45RA+/CD3+CD4+ (27.2 ± 24.8% vs 39.5 ± 20.8%), and CD45RA+/CD3+CD4- (14.2 ± 11.1% vs 18.7 ± 11.5) were lower. Linear regression analysis showed a negative correlation between the time after H. pylori eradication and CD4+/CD3+ (P < .05, R2 = 0.198). There were no significant differences between men and women with respect to the lymphocyte populations. These results indicate that there are site-specific differences in lymphocyte composition in the stomach after H. pylori eradication.

Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses.

Enantiomeric excesses of l-amino acids have been detected in meteorites; however, their molecular mechanism and prebiotic syntheses are still a matter of debate. To elucidate the origin of homochirality, alanine and the chiral precursors formed in prebiotic processes were investigated with regard to their stabilities among their isomers by employing the minimum energy principle, namely, the abundancy of a molecule in the interstellar medium is directly correlated to the stability among isomers. To facilitate the search for possible isomers, we developed a new isomer search algorithm, the random connection method, and performed a thorough search for all the stable isomers within a given chemical formula. We found that alanine and most of its precursors are located at higher energy by more than 5.7 kcal mol-1, with respect to the most stable isomer that consists of a linear-chain structure, whereas only the 2-aminopropanenitrile is the most stable isomer among all others possible. The inherent stability of the α-amino nitrile suggests that the 2-aminopropanenitrile is the dominant contribution in the formation of the common enantiomeric excess over α-amino acids.

PTEN differentially regulates endocytosis, migration, and proliferation in the enteric protozoan parasite Entamoeba histolytica.

PTEN is a lipid phosphatase that is highly conserved and involved in a broad range of biological processes including cytoskeletal reorganization, endocytosis, signal transduction, and cell migration in all eukaryotes. Although regulation of phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P3] signaling via PTEN has been well established in model organisms and mammals, it remains elusive in the parasitic protist E. histolytica, which heavily relies on PtdIns phosphate(s)-dependent membrane traffic, migration, and phago- and trogocytosis for its pathogenesis. In this study, we characterized the major PTEN from E. histolytica, EhPTEN1, which shows the highest expression at the transcript level in the trophozoite stage among 6 possible PTENs, to understand the significance of PtdIns(3,4,5)P3 signaling in this parasite. Live imaging of GFP-EhPTEN1 expressing amebic trophozoites showed localization mainly in the cytosol with a higher concentration at pseudopods and the extending edge of the phago- and trogocytic cups. Furthermore, quantitative analysis of phago- and trogocytosis using a confocal image cytometer showed that overexpression of EhPTEN1 caused reduction in trogo- and phagocytosis while transcriptional gene silencing of EhPTEN1 gene caused opposite phenotypes. These data suggest that EhPTEN1 has an inhibitory role in these biological processes. Conversely, EhPTEN1 acts as a positive regulator for fluid-phase and receptor-mediated endocytosis in E. histolytica trophozoites. Moreover, we showed that EhPTEN1 was required for optimal growth and migration of this parasite. Finally, the phosphatase activity of EhPTEN1 towards PtdIns(3,4,5)P3 was demonstrated, suggesting that the biological roles of EhPTEN1 are likely linked to its catalytic function. Taken together, these results indicate that EhPTEN1 differentially regulates multiple cellular activities essential for proliferation and pathogenesis of the organism, via PtdIns(3,4,5)P3 signaling. Elucidation of biological roles of PTEN and PtdIns(3,4,5)P3 signaling at the molecular levels promotes our understanding of the pathogenesis of this parasite.

Enriched CD45RA-CD62L+ central memory T and decreased CD3+CD56+ natural killer T lymphocyte subsets in the rectum of ulcerative colitis patients.

OBJECTIVES: To investigate the distinctive features of lymphocytes promoting inflammation in ulcerative colitis. METHODS: We performed flow cytometric analysis of peripheral blood mononuclear cells (PBMCs) and colorectal mucosa lymphocytes in ulcerative colitis patients (n = 13) and control patients (n = 5). RESULTS: CD62L+/CD3+CD4+ (35.7 ± 14.0% vs. 19.9 ± 6.4%) and CD62L+/CD3+CD4- cells (17.1 ± 17.4% vs. 2.4 ± 3.9%) were higher in the rectum of ulcerative colitis patients than in control patients. Subpopulation analysis revealed that CD45RA-CD62L+/CD3+CD4+, that is, central memory T cell fraction in CD4+ T cells, was significantly increased in the rectum of ulcerative colitis, compared to that in control patients (23.3 ± 10.5% vs. 8.2 ± 4.0%). Comparison of rectum and colon samples in ulcerative colitis patients indicated that CD56+/CD3+ was decreased in the rectum compared to that in the colon (11.3 ± 12.5% vs. 21.3 ± 16.5%). The ratio of CD56+/CD3+ was also decreased in the rectum of active ulcerative colitis patients compared to that in ulcerative colitis patients at the endoscopic remission stages (2.8 ± 1.7% vs. 18.5 ± 13.3%). CONCLUSION: We demonstrated that CD62L+ T lymphocytes, particularly the CD45RA-CD62L+ T cell subset that represents central memory T cells, were increased in the rectum of patients with ulcerative colitis. In addition, the CD56+/CD3+ subset (natural killer T cells) was decreased in the rectum compared to that of less inflamed colonic mucosa. These results suggest that the enrichment of central memory T lymphocytes and the reduction of natural killer T cells in the gut mucosa are involved in the pathogenesis of ulcerative colitis.

Isolation of lymphocytes from the human gastric mucosa.

Flow cytometry is widely used for lymphocyte immunophenotyping in clinical settings. However, few studies have applied it for analyzing lymphocytes of the gastric mucosa. This review offers an overview of methodologies for isolating lymphocytes from the human stomach. Previously reported articles were reviewed, focusing on procedures for isolating human gastric mucosal lymphocytes. Helicobacter pylori-associated peptic diseases and gastric cancer are two major subjects of research in this field. Enzymatic dissociation, mechanical dissociation, or a combination of the two have been used to isolate lymphocytes from the stomach. Intra-epithelial and lamina propria lymphocytes were separately isolated in several studies. We also summarize the history and present trends in analyzing lymphocytes in patients with gastric disease.

Two StAR-related lipid transfer proteins play specific roles in endocytosis, exocytosis, and motility in the parasitic protist Entamoeba histolytica.

Lipid transfer proteins (LTPs) are the key contributor of organelle-specific lipid distribution and cellular lipid homeostasis. Here, we report a novel implication of LTPs in phagocytosis, trogocytosis, pinocytosis, biosynthetic secretion, recycling of pinosomes, and motility of the parasitic protist E. histolytica, the etiological agent of human amoebiasis. We show that two StAR-related lipid transfer (START) domain-containing LTPs (named as EhLTP1 and 3) are involved in these biological pathways in an LTP-specific manner. Our findings provide novel implications of LTPs, which are relevant to the elucidation of pathophysiology of the diseases caused by parasitic protists.

Diversity of phosphoinositide binding proteins in Entamoeba histolytica.

Phosphatidylinositol phosphates (PIPs, phosphoinositides) are localized to the membranes of all cellular compartments, and play pivotal roles in multiple cellular events. To fulfill their functions, PIPs that are located to specific organelles or membrane domains bind to and recruit various proteins in spatiotemporal specific manner via protein domains that selectively bind to either a single or an array of PIPs. In Entamoeba histolytica, the human intestinal protozoan parasite, PIPs and PIP-binding proteins have been shown to be involved in their virulence-associated mechanisms such as cell motility, vesicular traffic, trogo- and phagocytosis. In silico search of the domains and the signatures implicated in PIP binding in the E. histolytica proteome allows identification of dozens of potential PIP-binding proteins. However, such analysis is often misleading unless the protein domain used as query is cautiously selected and the binding specificity of the proteins are experimentally validated. This is because all the domains initially presumed to bind PIPs in other systems are not always capable of PIP binding, but rather involved in other biological roles. In this review, we carried out in silico survey of proteins which have PIP-binding domains in the E. histolytica genome by utilizing only validated PIP-binding domains that had been experimentally proven to be faithful PIP-binding bioprobes. Our survey has identified that FYVE (Fab1, YOTB1, Vac1, EEA1) and PH (pleckstrin homology) domain containing proteins are the most expanded families in E. histolytica. A few FYVE domain-containing proteins (EhFP4 and 10) and phox homology (PX) domain containing proteins (EhSNX1 and 2) were previously studied in depth in E. histolytica. Furthermore, most of the identified PH domain-containing proteins are annotated as protein kinases and possess protein kinase domains. Overall, PIP-binding domain-containing proteins that can be identified by in silico survey of the genome using the domains from well characterized bioprobes are limited in E. histolytica. However, their domain architectures are often unique, suggesting unique evolution of PIP-binding domain-containing proteins in this organism.