Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing.

Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.

Charge microheterogeneity of the beta-trace proteins (lipocalin-type prostaglandin D synthase) in the cerebrospinal fluid of patients with neurological disorders analyzed by capillary isoelectrofocusing.

Charge microheterogeneity of the beta-trace protein (beta-TP = lipocalin-type prostaglandin D synthase) in the cerebrospinal fluid (CSF) of patients with various neurological disorders was analyzed by capillary isoelectric focusing (CIEF). Under the conditions employed, beta-TP in the low-molecular-weight protein fraction of CSF was separated into at least four isoforms with different p/ values. An isoform with the pl value of 4.6-4.8 was usually the most abundant. The total beta-TP level in the CSF was determined by enzyme-linked immunosorbent assay (ELISA) to be elevated in patients recovering from organic damage to the CNS and those with pathological brain atrophy. Changes in the total beta-TP level in the CSF were occasionally accompanied by those in its charge microheterogeneity, as revealed by CIEF. Such quantitative and qualitative changes in beta-TP in human CSF indicated changes in its pathophysiological roles in association with various neurological disorders.

Urinary prostaglandin D synthase (beta-trace) excretion increases in the early stage of diabetes mellitus.

OBJECTIVE: Circulating levels of lipocalin-type prostaglandin D synthase (L-PGDS)/beta-trace reportedly increase in renal failure as well as in cardiovascular injuries. We investigated the alterations of L-PGDS in urine and plasma in the early stage of type-2 diabetic patients. METHOD: Thirty-six type-2 diabetic patients and 29 normal subjects were studied. Overnight spot urine and plasma samples were obtained in the morning. L-PGDS was measured by ELISA method using anti-L-PGDS antibody. Variables indicating renal function were determined. RESULTS: Plasma L-PGDS concentration was slightly higher in the patients with diabetes mellitus than in the control subjects, whereas the urinary L-PGDS excretion almost doubled in the diabetic patients as compared with that in the control subjects. Plasma L-PGDS was determined by plasma creatinine (Cr) concentration while urinary L-PGDS excretion was correlated solely with urinary protein excretion. There was no relationship between plasma L-PGDS concentration and urinary L-PGDS excretion. The averaged plasma concentration of L-PGDS in the diabetics with a normal Cr level in plasma, corresponding to that in the controls, was determined by the plasma Cr concentration. On the other hand, the urinary L-PGDS excretion was determined by the amount of proteinuria and greater in the diabetics with a normal Cr level in plasma than in the controls even when the patients exhibited urinary protein excretion equal to that in the control subjects. CONCLUSIONS: Urinary L-PGDS excretion increased in the early stage of kidney injury in patients with type-2 diabetes mellitus. The urinary excretion was correlated independently with urinary protein excretion even when there was no difference in urinary protein or albumin excretions, thereby suggesting that urinary L-PGDS excretion is possibly a more sensitive indicator of renal injuries than proteinuria. Urinary L-PGDS may thus predict the progression of renal injuries in diabetic patients.

Serum prostaglandin D synthase level after coronary angioplasty may predict occurrence of restenosis.

Lipocalin-type prostaglandin D synthase (L-PGDS), which is responsible for the biosynthesis of PGD2, has recently been found to be present in the atherosclerotic plaque of the human coronary artery and also to be secreted in human serum. We measured the serum L-PGDS level and compared it with the expressions of the platelet membrane surface glycoprotein and neutrophil adhesion molecule in patients undergoing PTCA. The L-PGDS level significantly decreased (P < 0.01) and the platelet surface expression of CD62P (P-selectin) significantly increased (P < 0.01) immediately after PTCA in the coronary sinus blood. Both changes were inversely correlated (R = -0.72, P < 0.001). Although the L-PGDS level in the coronary sinus blood remained equivalent to the baseline level in patients who experienced restenosis, the level increased over the baseline level (P < 0.01) at 48 h after PTCA in patients without restenosis. Neutrophil surface expression of CD11b (alpha subunit of Mac-1) significantly increased at 24 h (P < 0.01) to 48 h (P < 0.001) after PTCA in the coronary sinus blood in patients with restenosis but the change showed less significant in patients without restenosis. The changes in the L-PGDS level and the CD11b expression at 48 h after PTCA were inversely correlated (R = -0.55, P < 0.05). An increased serum L-PGDS level at 48 h after PTCA possibly predicts the avoidance of late restenosis. It is suggested that reduction in PGD2 synthesis triggers platelet activation and that a subsequent increase in the PGD2 synthesis suppresses inflammatory reaction at the intervention site indicated by neutrophil activation and inhibits development of restenosis. Pharmacological or biological intervention that increases endogenous PGD2 synthesis should be tested as a new strategy to prevent restenosis.

Comparative study of the asparagine-linked sugar chains of human lipocalin-type prostaglandin D synthase purified from urine and amniotic fluid, and recombinantly expressed in Chinese hamster ovary cells.

Lipocalin-type prostaglandin D synthase (L-PGDS) is a highly glycosylated member of the lipocalin gene family and is secreted into various human body fluids. We comparatively analyzed the structures of asparagine-linked sugar chains of human L-PGDS produced by recombinant Chinese hamster ovary cells and naturally occurring human urine and amniotic fluid. After the sugar chains were liberated by hydrazinolysis followed by N-acetylation, they were derivatized with 2-aminobenzamide. All of the sugar chains of three L-PGDSs occur as biantennary complex-type sugar chains. Most of the sugar chains of three samples were fucosylated on the inner most N-acetylglucosamine residue. Although the sugar chains of the recombinant L-PGDS do not contain any bisecting N-acetylglucosamine residues, 58% and 34% of the fucosylated-sugar chains of amniotic fluid and urine L-PGDSs, respectively, contain bisecting N-acetylglucosamine residues. The sialic acid residues occur solely as Siaalpha2-->3Gal groups of the recombinant L-PGDS; the sialic acid residues of other L-PGDS occur as both Siaalpha2-->3Gal and Siaalpha2-->6Gal groups. Variations in L-PGDS glycosylation may prove useful as markers to further elucidate the role of L-PGDS glycoforms in different tissues.

Reinsertion of stimulated nucleus pulposus cells retards intervertebral disc degeneration: an in vitro and in vivo experimental study.

Reinsertion of autogenous nucleus pulposus, an innovative method to delay further disc degeneration, has been proved with an experimental animal model. This study examined whether coculture of nucleus pulposus cells with annulus fibrosus cells (a) activates annulus fibrosus cells and (b) retards disc degeneration when reinserted into the disc in a rabbit model of disc degeneration. Coculture of the two cell types stimulated proliferation of each, as indicated by increased DNA synthesis measured by increases in DNA polymerase alpha expression and uptake of 5-bromo-2'deoxy-uridine assessed by an enzyme-linked immunosorbent assay. In a model of disc degeneration in rabbits, reinsertion of activated nucleus pulposus cells delayed the formation of clusters of chondrocyte-like cells, the destruction of disc architecture, and the elaboration of type-II collagen as measured immunohistochemically compared with no treatment. The direct reinsertion of activated nucleus pulposus cells into the disc offers a promising line of investigation for delaying intervertebral disc degeneration, although these results obtained with notochordal cells may not necessarily apply when mature central nucleus pulposus cells are used.

Acute and transient increase of lipocalin-type prostaglandin D synthase (beta-trace) level in cerebrospinal fluid of patients with aneurysmal subarachnoid hemorrhage.

We measured the concentration of lipocalin-type prostaglandin D synthase (PGDS) in cerebrospinal fluid (CSF) and serum in patients 1, 3, 5, 7, 9, 11, 14 and 17 days after subarachnoid hemorrhage (SAH) due to ruptured cerebral aneurysms. The PGDS level in lumbar CSF increased about two-fold at day 3 (20.85 +/- 2.71 microg/ml, mean +/- SE) and at day 5 (25.24 +/- 3.76), as compared with the level at day 1 (11.25 +/- 1.07). The CSF level gradually decreased and returned to the day 1 level at day 17. The serum PGDS level was much lower than the CSF level (0.39 +/- 0.06 at day 1) and almost unchanged until day 17. The neuron-specific enolase level in CSF, as an index of brain damage, was maximum at day 1 (29.83 +/- 7.32 ng/ml) and decreased at day 3 and at day 5 (18.28 +/- 2.65 and 11.95 +/- 1.82, respectively). These results suggest that the transient and delayed increase in the PGDS level in CSF is due to its induction of PGDS in the arachnoid membrane after SAH.

Life-threatening hemorrhage in a patient with gastric cancer and acquired hemophilia.

We report a case of a patient with life-threatening hemorrhage caused by the presence of acquired factor VIII inhibitors after gastrectomy for signet-ring cell carcinoma of the stomach. Acquired factor VIII inhibitors should be taken into consideration as a cause of acquired bleeding tendency among patients with gastrointestinal malignancies especially when the coagulation tests are unusual.

Sex hormones and the thymus in relation to thymocyte proliferation and maturation.

This paper reviews the mechanism of sex hormone actions on the thymus, presenting mainly our data obtained at the cellular and molecular levels. First, data supporting the "genomic" action via the nuclear sex hormone receptor complexes are as follows: 1) sex hormone receptors and the thymic factor (thymulin) are co-localized in thymic epithelial cells, but not in T cells; 2) production/expression of thymic factors (thymulin, thymosin alpha 1) are remarkably inhibited by sex hormone treatment; 3) sex hormones cause changes in T cell subpopulations in the thymus; and 4) sex hormones strongly influence the development of thymus tumors in spontaneous thymoma BUF/Mna rats through their receptor within the tumor cells. Secondly, data indicating the "non-genomic" action of sex hormones via a membrane signal-generating mechanism are as follows: 1) the proliferation/maturation of thymic epithelial cells is mediated through protein kinase C activity introduced by sex hormones; 2) sex hormones directly influence DNA synthesis and cdc2 kinase (cell cycle-promoting factor) activity.

Expression of lipocalin-type prostaglandin D synthase (beta-trace) in human heart and its accumulation in the coronary circulation of angina patients.

Lipocalin-type prostaglandin D synthase (L-PGDS) is localized in the central nervous system and male genital organs of various mammals and is secreted as beta-trace into the closed compartment of these tissues separated from the systemic circulation. In this study, we found that the mRNA for the human enzyme was expressed most intensely in the heart among various tissues examined. In human autopsy specimens, the enzyme was localized immunocytochemically in myocardial cells, atrial endocardial cells, and a synthetic phenotype of smooth muscle cells in the arteriosclerotic intima, and accumulated in the atherosclerotic plaque of coronary arteries with severe stenosis. In patients with stable angina (75-99% stenosis), the plasma level of L-PGDS was significantly (P < 0.05) higher in the great cardiac vein (0.694 +/- 0.054 microg/ml, n = 7) than in the coronary artery (0.545 +/- 0.034 microg/ml), as determined by a sandwich enzyme immunoassay. However, the veno-arterial difference in the plasma L-PGDS concentration was not observed in normal subjects without stenosis. After a percutaneous transluminal coronary angioplasty was performed to compress the stenotic atherosclerotic plaques, the L-PGDS concentration in the cardiac vein decreased significantly (P < 0.05) to 0.610 +/- 0.051 microg/ml at 20 min and reached the arterial level within 1 h. These findings suggest that L-PGDS is present in both endocardium and myocardium of normal subjects and the stenotic site of patients with stable angina and is secreted into the coronary circulation.

Autonomous control of expression of genes for insulin-like growth factors during the proliferation and differentiation of C2C12 mouse myoblasts in serum-free culture.

The proliferation and differentiation of skeletal muscle cells in culture are usually controlled by serum components, and the differentiation can be induced by a reduction in the serum concentration. Insulin-like growth factors (IGFs) play a critical role in stimulating myoblast differentiation, and the expression of their genes is controlled by serum factors. We have found that C2C12 myoblasts are capable of proliferation and differentiation even in serum-free medium that does not contain peptide mitogens. During these processes in serum-free medium, the accumulation of mRNAs for IGFs in the cells was observed; and their levels increased with concomitant increases in creatine kinase activity and myotube formation and a decrease in DNA synthesis. Thus, the present results suggest that proliferation and differentiation of C2C12 cells are autonomously controlled and that the increase in the expression of the IGFs may be independent of exogenous components.

Female sex hormone stimulates cultured human keratinocyte proliferation and its RNA- and protein-synthetic activities.

The present study was carried out to assess the effect of female sex hormones, i.e., estrogen and progesterone, on human keratinocyte proliferation, and its RNA- and protein-synthetic activities in a culture system. The presence of receptors for estrogen and progesterone and their messenger ribonucleic acids (mRNAs) in the cultured cells was also investigated. Human keratinocytes were cultured in the experimental DMEM-Ham's F12 medium containing various concentrations of estrogen or progesterone, which was followed by determining cell yields and [3H]thymidine incorporation. The keratinocytes were also tested for RNA- and protein-synthetic activities by measuring [3H]uridine and [3H]leucine incorporation. Both estrogen and progesterone receptors were determined by the enzyme immunoassay method using monoclonal antibodies, and mRNA expression for these hormone receptors was detected by in situ hybridization. Cell yields and [3H]thymidine incorporation increased gradually until 3 x 10(-10) M of both estrogen and progesterone, decreased thereafter until 3 x 10(-7) M, and peaked at 3 x 10(-10) M. [3H]Uridine and [3H]leucine uptake followed almost the same pattern as the cell proliferation, peaking at 3 x 10(-10) M of both hormones. Small amounts of estrogen and progesterone receptors were present in the cultured cells, and their mRNAs were found to be present in the cell cytoplasm. These results clearly suggest that sex hormones play an important role in human keratinocyte proliferation, and its RNA- and protein-synthetic activities, at least in part, via their hormone receptors.

Effects of sex steroids on the proliferation of thymic epithelial cells in a culture model: a role of protein kinase C.

Using a rat thymic epithelial cell line (TEC; IT-45R1), the present study attempted to elucidate the mechanism of action of sex steroid hormones (SH) on the proliferation of TEC. The findings were as follows: (a) the proliferation of TEC in response to SH was mediated through protein kinase C activity introduced as a result of interaction between SH and plasma-borne inhibitors; (b) the strong inhibitory effect of SH on TEC proliferation might be mediated through the SH receptor pathway because the proliferative response was triggered by progesterone (P) and androgen (A), whereas the inhibitory response was triggered by P, A and oestrogen. These results clearly suggest that the control of TEC proliferation is a 'shut-off' mechanism triggered by high plasma levels of SH. This further refers to the speculation that the development of the normal thymus may be due to a lack of this 'shut-off' mechanism so that development occurs at the adequate plasma SH levels that are often observed before puberty. However, this development is inhibited at the high plasma SH levels after puberty and/or during pregnancy.

Synthetic boundary cell in an analytical ultracentrifuge to determine the flotation coefficient of human serum lipoproteins.

Human serum lipoproteins were analyzed by a new modified synthetic boundary cell using an analytical ultracentrifuge. This cell allows the formation of the synthetic boundary at the bottom level of the cell with self-adjusting meniscus and baseline. Thus, the total amount of lipoproteins was seen as a single peak at first. During centrifugation, each component of the lipoproteins was separated according to its flotation characteristics. It was, therefore, possible to determine precisely all lipoprotein components, especially high-density lipoproteins, in the presence of a more rapidly migrating species and to calculate the flotation coefficient of each lipoprotein using the formula for sedimentation coefficient reported by Svedberg (Svedberg, T. (1925) Kolloid-Z. 36, 53-64.

Chemocoagulation of metastatic lymph nodes using a suspension of mitomycin C-adsorbing activated carbon particles in 80% ethanol.

Chemocoagulation therapy was evaluated in an experimental model of metastasis of murine lymph nodes following injection of a suspension of mitomycin C--containing activated carbon particles in 80% ethanol (MMC-CH-ET) into the popliteal lymph node. Lymph node metastasis was induced in the left popliteal and the lumbar lymph nodes 8 days after injection of mouse leukemia P388 cells into the footpad of the left hindleg of BDF1 mice. When MMC-CH-ET was injected into the left popliteal lymph node, it immediately left this site and entered the lumbar lymph node via lymphatic vessels. When compared with tissue concentrations of mitomycin C following injection of an aqueous solution of this drug, the mitomycin C concentration of MMC-CH-ET was maintained at significantly higher levels for 2 hr following injection both at the site of injection and at secondary lymph nodes. Furthermore, coagulative necrosis was identified histologically throughout the injected lymph node and the secondary lymph node, including the metastatic site. The mortality of mice treated with MMC-CH-ET injection was significantly reduced and lymph node metastasis was controlled with MMC-CH-ET when compared with the results for mice treated with an aqueous solution of mitomycin C or treated by surgical lymph node dissection. In this report, we suggest that the use of MMC-CH-ET as a therapeutic agent may be useful in targeting lymph node metastasis.

Localization of estrogen receptors and estrogen receptor-mRNA in female mouse thymus.

The present study was performed to demonstrate estrogen receptor (ER) and ER-mRNA in female mouse thymus. The results are as follows: (i) thymic tissue contains ER in both reticuloepithelial(RE)- and T-cell fractions, the ER level being three-fold higher in the former fraction than in the latter; and (ii) thymic tissue contains ER-mRNA at 6.2 kb, a large amount of which was localized in the RE cells and less in the T cells. From these results it is suggested that estrogen (E) mediates some immune function of the mouse thymus through its receptor within RE cells and/or T cells.

[Intra-lymph nodal injection of OK-432 for treatment of lymph node metastasis].

MH134 (5 x 10(5) in 0.1 ml of normal saline) was inoculated subcutaneously into the hind foot pad of C3H/He mice. The mice were divided into three groups on day 11 after inoculation. Each mouse in the first group (n = 12) received an intra-lymph nodal injection of 5KE of OK-432 in 0.1 ml of normal saline (OK-432 ILN group). The second group (n = 12) underwent subcutaneous injection of OK-432 (of the same dose) into the back (OK-432 SC group). The last group received no OK-432 (untreated group). Three hours after treatment the left popliteal lymph node was excised and the left hind foot at the knee joint was removed in each mouse. The mice were then observed for 90 days after treatment. Mice that died underwent autopsy and the left popliteal, inguinal, lumbar and suprarenal lymph nodes were excised for weighing. The survival rates were 10/12 for the OK-432 ILN group, 2/12 for the OK-432 SC group and 2/12 for the untreated group. The differences between the survival rate of the OK-432 ILN group and those of the other two groups were statistically significant (p less than 0.001). The lymph nodes were heavier in the OK-432 SC group and the untreated group than in the OK-432 ILN group. We concluded that intra-lymph nodal injection of OK-432 is very effective for treating lymph node metastasis.

[Principles of lymphadenectomy for gastric cancer according to depth of wall invasion, tumor site and regional lymphatic flow].

The principles of lymphadenectomy for gastric cancer are discussed based on the 1010 gastric cancer patients who underwent gastrectomy with curative intent between 1970 and 1990. In 147 of these patients, regional lymphatic flow was examined by injecting activated carbon particles CH40. 1) One hundred and ninety patients (19.8%) with cancer invasion confined to the mucosa had lymph node metastases limited to the perigastric nodes (n1). 2) Two hundred and five patients (20.3%) had cancer invasion to the submucosa. For 99.0% of them the lymph node metastases were limited to compartment II (n2). 3) Three hundred and twenty-two patients (31.9%), with cancer invasion to the muscle layer or serosa and limited to the upper or middle third of the stomach, had lymph node metastases in compartment II and No. 12 (n 2 + No. 12). 4) Two hundred and ninety-three patients (29.0%) with cancer invasion to the muscle layer or serosa and limited to lower third of the stomach or to its extension, had lymph nodes metastases in compartment III (n3). 5) Consequent to observations on the regional lymph flow of the stomach by CH40, we now perform paraaortic lymph node dissection, when gastric cancer patients with serosal invasion have metastases lymph nodes No. 2, 7, 8a, 9, 11, 12 or No. 14V.

Lymph nodal vital staining with newer carbon particle suspensions compared with India ink: experimental and clinical observations.

CH40 and CH1500AA are newly prepared carbon suspensions which were examined as vital staining dyes for their usefulness in visualizing lymphatics at operation and to blacken lymph nodes. In mice, these carbon suspensions at 0.001 ml/g of body weight and India ink were injected subcutaneously into the footpad of the right hindpaw. Regional lymph nodes were visualized and were examined stereomicroscopically to determine how intensely these nodes blackened with carbon suspensions. Compared with India ink, CH40 and CH1500AA blackened the regional lymph nodes much faster and more vividly (1-8 min. after subcutaneous injection). As analyzed by centrifugal particle size distribution, CH40 and CH1500AA are narrowly distributed with a small particle size (150 and 167 nm, respectively, in mean diameter). By contrast, India ink is comprised of widely distributed and relatively large particles in suspension (mean diameter--254 nm). In 10 patients undergoing radical gastrectomy for treatment of stomach cancer, CH40 blackened 69% of regional lymph nodes with metastases (38 of 55) and 76% of those nodes without metastases (387 of 512).