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Understanding the molecular mechanisms that underpin diverse vaccination responses is a critical step toward developing efficient vaccines. Molecular subtyping approaches can offer valuable insights into the heterogeneous nature of responses and aid in the design of more effective vaccines. In order to explore the molecular signatures associated with the vaccine response, we analyzed baseline transcriptomics data from paired samples of whole blood, proteomics and glycomics data from serum, and metabolomics data from urine, obtained from influenza vaccine recipients (2019-2020 season) prior to vaccination. After integrating the data using a network-based model, we performed a subtyping analysis. The integration of multiple data modalities from 62 samples resulted in five baseline molecular subtypes with distinct molecular signatures. These baseline subtypes differed in the expression of pre-existing adaptive or innate immunity signatures, which were linked to significant variation across subtypes in baseline immunoglobulin A (IgA) and hemagglutination inhibition (HAI) titer levels. It is worth noting that these significant differences persisted through day 28 post-vaccination, indicating the effect of initial immune state on vaccination response. These findings highlight the significance of interpersonal variation in baseline immune status as a crucial factor in determining vaccine response and efficacy. Ultimately, incorporating molecular profiling could enable personalized vaccine optimization.

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

Background: Tryptophan synthase consists of two subunits, alpha and beta. Two distinct subgroups of beta chain exist. The major group (TrpEb_1) includes the well-studied beta chain of Salmonella typhimurium. The minor group of beta chain (TrpEb_2) is most frequently found in the Archaea. Most of the amino-acid residues important for catalysis are highly conserved between both TrpE subfamilies., Results: Conserved amino-acid residues of TrpEb_1 that make allosteric contact with the TrpEa subunit (the alpha chain) are absent in TrpEb_2. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. In those prokaryotes where two trpEb genes coexist, one is usually trpEb_1 and is adjacent to trpEa, whereas the second is trpEb_2 and is usually unlinked with other tryptophan-pathway genes., Conclusions: TrpEb_1 is nearly always partnered with TrpEa in the tryptophan synthase reaction. However, by default at least six lineages of the Archaea are likely to use TrpEb_2 as the functional beta chain, as TrpEb_1 is absent. The six lineages show a distinctive divergence within the overall TrpEa phylogenetic tree, consistent with the lack of selection for amino-acid residues in TrpEa that are otherwise conserved for interfacing with TrpEb_1. We suggest that the standalone function of TrpEb_2 might be to catalyze the serine deaminase reaction, an established catalytic capability of tryptophan synthase beta chains. A coincident finding of interest is that the Archaea seem to use the citramalate pathway, rather than threonine deaminase (IlvA), to initiate the pathway of isoleucine biosynthesis.

GH and IGF-I secretion decrease with age. The decline in serum GH with age appears to be associated with menopause. Prior studies of GH release before and after oral and transdermal hormonal replacement in the postmenopausal patient have shown no change or an increase in GH secretion. To distinguish the somatotropic axis effects of aging from those of estrogen deficiency, we compared eight prematurely menopausal women, aged 25-40 yr, with eight postmenopausal women, aged 51-70 yr, both before and after estradiol replacement. All women had a body mass index below 28 kg/m2. All were evaluated twice with frequent blood sampling every 10 min for 24 h. Studies were performed in the absence of exogenous hormones and 6-8 wk after transdermal estradiol replacement, targeted to achieve a serum estradiol level of 367 pmol/liter. GH pulsatility was analyzed. Variables tested included mean GH levels, interpulse baseline mean, pulse frequency per 24 h, and pulse amplitude. Transdermal estrogen replacement had a significant effect on mean GH levels and mean basal GH levels in both the premature ovarian failure and the age-appropriate postmenopausal group. No differences were noted in GH pulse frequency, GH pulse amplitude, IGF-I, IGF-binding protein-1, and IGF-binding protein-3 before and after treatment. A pronounced age effect was noted between the two groups. The premature ovarian failure women secreted significantly greater mean GH than the age-appropriate postmenopausal group regardless of treatment, with a significance level of P = 0.026. Interpulse baseline GH means were greater in the premature ovarian failure women than in the age-appropriate postmenopausal group, but the significance of this relationship was obliterated after adjustment for body mass index. Pulse amplitude was significantly increased in the premature ovarian failure women compared with age-appropriate postmenopausal women (P = 0.006). No significant changes were detected in the GH pulse frequency between the premature ovarian failure and postmenopausal groups. We conclude that moderate doses of transdermal estradiol supplementation do not exert a great effect on the somatotropic axis in women. Age and body composition appear to be the predominant influences on GH activity in women.

The information provided by completely sequenced genomes can yield insights into the multi-level organization of organisms and their evolution. At the lowest level of molecular organization individual enzymes are formed, often through assembly of multiple polypeptides. At a higher level, sets of enzymes group into metabolic networks. Much has been learned about the relationship of species from phylogenetic trees comparing individual enzymes. In this article we extend conventional phylogenetic analysis of individual enzymes in different organisms to the organisms' metabolic networks. For this purpose we suggest a method that combines sequence information with information about the underlying reaction networks. A distance between pathways is defined as incorporating distances between substrates and distances between corresponding enzymes. The new analysis is applied to electron-transfer and amino acid biosynthesis networks yielding a more comprehensive understanding of similarities and differences between organisms.

Objective: To describe the lived experience of women who have been diagnosed with idiopathic premature ovarian failure (POF)., Design: Phenomenology was used to achieve the purpose. Women were asked to share their experiences in living with premature ovarian failure during an approximately 1-hour interview. The interviews were tape-recorded, transcribed, and analyzed for emergent themes., Setting: Interviews were conducted in the participants' homes and in a conference room in a hospital., Participants: The six participants were drawn from a multicultural sample of women with idiopathic POF., Results: The women in this study expressed anger at their health care providers for their perceived lack of quality care they had experienced and at the insurance industry for its lack of reimbursement for fertility interventions; they expressed depression and sadness at the prospective outcome of the diagnosis, mixed emotions regarding their significant others, and sadness and resignation about their menopausal symptoms., Conclusions: Health care providers who create an environment in which women and their significant others will feel supported in asking questions, be assured that their concerns are taken seriously, and be provided with the physical and emotional resources they need can help these women to continue to build and live their lives.

Folding of RNA sequences into secondary structures is viewed as a map that assigns a uniquely defined base pairing pattern to every sequence. The mapping is non-invertible since many sequences fold into the same minimum free energy (secondary) structure or shape. The pre-images of this map, called neutral networks, are uniquely associated with the shapes and vice versa. Random graph theory is used to construct networks in sequence space which are suitable models for neutral networks. The theory of molecular quasispecies has been applied to replication and mutation on single-peak fitness landscapes. This concept is extended by considering evolution on degenerate multi-peak landscapes which originate from neutral networks by assuming that one particular shape is fitter than all the others. On such a single-shape landscape the superior fitness value is assigned to all sequences belonging to the master shape. All other shapes are lumped together and their fitness values are averaged in a way that is reminiscent of mean field theory. Replication and mutation on neutral networks are modeled by phenomenological rate equations as well as by a stochastic birth-and-death model. In analogy to the error threshold in sequence space the phenotypic error threshold separates two scenarios: (i) a stationary (fittest) master shape surrounded by closely related shapes and (ii) populations drifting through shape space by a diffusion-like process. The error classes of the quasispecies model are replaced by distance classes between the master shape and the other structures. Analytical results are derived for single-shape landscapes, in particular, simple expressions are obtained for the mean fraction of master shapes in a population and for phenotypic error thresholds. The analytical results are complemented by data obtained from computer simulation of the underlying stochastic processes. The predictions of the phenomenological approach on the single-shape landscape are very well reproduced by replication and mutation kinetics of tRNA(phe). Simulation of the stochastic process at a resolution of individual distance classes yields data which are in excellent agreement with the results derived from the birth-and-death model.

To examine the relationship between endometrial histological maturation and reproductive hormones, we studied 11 fertile women, aged 18-37 yr. All participants had had at least 1 previous pregnancy and cycled regularly, every 25-35 days. Women collected daily, first morning voided urine for measurement of estradiol and progesterone metabolite excretion, estrone conjugates (E1c), and pregnanediol glucuronide (Pdg), respectively, throughout the cycle of study. Hormones were normalized for creatinine. Between 7-9 days after home detection of a LH surge (Sure Step), participants underwent an endometrial biopsy using a small bore (Pipelle) catheter. Tissue was prepared for histological and biochemical analyses. The histological analysis is reported herein. Endometrium was dated by 3 authors (N.S., D.H., and S.P.), all of whom were blinded to the participant's identity or timing of biopsy within her cycle. Final dating was agreed upon based upon the method of Noyes et al. E1c and Pdg were integrated throughout the cycle using the trapezoidal rule, and correlations were sought between deviation from expected histology (based upon urinary hormones and LH surge) and integrated hormone values. E1c varied over a 2-fold range in these normal women, from 1196-2040 ng/cycle. Pdg excretion was much more variable, ranging from 22-119 microg/cycle. No relationship could be found between histological lagging of endometrial maturation and lower excretion of E1c. A moderate correlation was observed (Spearman's r = 0.6; P < 0.05) between degree of histological maturation and integrated Pdg. Of two women with evidence of a disparity between gland and stromal development (glands lagging behind stroma by >2 days), one excreted 24 microg Pdg/cycle, the next to lowest value. We conclude that normal fertile women experience a wide range of hormone concentrations in the face of normal endometrial maturation. Progesterone appears to exert a dose-related effect on endometrial maturation, and the techniques we used, although relatively crude clinical measures, appeared to be sufficient to detect this relationship.

In this paper, we consider the evolutionary dynamics of catalytically active species with a distinct genotype-phenotype relationship. Folding landscapes of RNA molecules serve as a paradigm for this relationship with essential neutral properties. The landscape itself is partitioned by phenotypes (realized as RNA secondary structures). To each genotype (represented as a sequence) a structure is assigned in a unique way. The set of all sequences which map into a particular structure is modeled as a random graph in sequence space (the so-called neutral network). A catalytic network is realized as a random digraph with maximal out-degree two and secondary structures as vertex sets. A population of catalytic RNA molecules shows significantly different behavior compared to a deterministic description: hypercycles are able to co-exist and out-compete a parasite with superior catalytic support. A "switching" between different dynamic organizations of the network can be observed, dynamical stability of hypercyclic organizations against errors and the existence of an error-threshold of catalysis can be reported., (Copyright 2000 Academic Press.)

The abundance of information provided by completely sequenced genomes defines a starting point for new insights in the multilevel organization of organisms and their evolution. At the lowest level enzymes and other protein complexes are formed by aggregating multiple polypeptides. At a higher level enzymes group conceptually into metabolic pathways as part of a dynamic information-processing system, and substrates are processed by enzymes yielding other substrates. A method based on a combination of sequence information with graph topology of the underlying pathway is presented. With this approach pathways of different organisms are related to each other by phylogenetic analysis, extending conventional phylogenetic analysis of individual enzymes. The new method is applied to pathways related to electron transfer and to the Krebs citric acid cycle. In addition to providing a more comprehensive understanding of similarities and differences between organisms, this method indicates different evolutionary rates between substrates and enzymes.

We examined the changes that occur in the adenosine receptor system during diabetes mellitus. Experimental diabetes mellitus was induced in male Lewis rats with streptozocin (65 mg/kg), and A(1) adenosine receptor binding was characterized with [(125)I]N (6)-2-(4-aminophenyl) ethyladenosine. In adipocytes, high-affinity A(1) adenosine receptor binding decreased from 1466±228 of protein to 312±123 fmol/mg of protein (p<0.01) following 14 d of untreated diabetes mellitus. Neither the dissociation constant (K (d)=1.3±0.2 nM) nor the basal level of adenylate cyclase activity (2.8±1.1 pmol cAMP/mg of protein/min) was altered by diabetes mellitus. The dose-response curve for the inhibition of adenylate cyclase byN (6)-R-phenylisopropyladenosine (R-PIA), however, did show a rightward shift, indicating that diabetic adipocyte membranes were less sensitive to the effects of adenosine than nondiabetic adipocyte membranes. In contrast, the A(1) adenosine receptor-binding characteristics and adenylate cyclase dose-response curve for cerebral cortical tissue were unchanged by diabetes. These findings suggest that diabetes has tissue-specific effects on the A(1) adenosine receptor system. Furthermore, the decreased sensitivity to adenosine potentially worsens the hyperlipidemia associated with diabetes mellitus. Such alterations in the adenosine receptor system may play a previously undescribed role in the pathophysiology of diabetes mellitus and may help explain why some organs are severely affected by diabetes, but others are relatively spared. Understanding these alterations in adenosine receptor function may lead tonovel therapies of this common metabolic disease.

The purpose of this study was to determine the effects of portal hypertension on gastrointestinal transit. Portal hypertension was induced in a group of 15 rats by the staged portal vein ligation technique. A control group of 15 rats underwent a sham operation. Ten days later, a 51Cr-labeled Krebs' buffer solution was instilled into the duodenum and the distribution or radioactivity along the length of the small intestine was determined after 15, 30, and 60 minutes. Portal hypertension was consistently established in the study group; splenic pulp pressure (mm Hg, mean +/- SD, portal hypertensive vs. control) was 20.0 +/- 3.9 vs. 12.7 +/- 3.9, P less than 0.002. Various measures of intestinal transit revealed delayed transit in the portal hypertensive group. Retention of radioactivity in the most proximal quartile of the intestine was greater [percentage retained (portal hypertensive vs. control) was 57.9 +/- 17.3 vs. 31.2 +/- 15.3, P less than 0.02, 49.1 +/- 15.5 vs. 28.3 +/- 4.8, P = 0.03, and 42.4 +/- 17.6 vs. 29.0 +/- 8.8, P = 0.08, at 15, 30, and 60 minutes, respectively] and the geometric mean of transit was located more proximally (P less than 0.02) at each study interval in the portal hypertension group. It was concluded that portal hypertension is associated with delayed intestinal transit. This abnormality could predispose to bacterial overgrowth and contribute to altered digestion and absorption.

The effects of portal hypertension on gastric motor function were investigated using the rat staged portal vein ligation model. Gastric emptying of liquids and solids was studied separately following meals labeled with 51Cr or 99Tc by whole stomach scintillation counting. Portal hypertension was consistently established in experimental rats (splenic pulp pressure: mean +/- SEM, portal hypertension versus control, 16.8 +/- 0.7 vs 11.8 +/- 0.7 mm Hg, P less than 0.0001). Although liquids were emptied in an exponential manner and solids in a linear fashion, gastric emptying of both meals was more rapid in the experimental rats. Ten minutes after the liquid meal, more than 50% of the meal had emptied from the stomachs of portal hypertensive rats while only one third of the meal had cleared in the control group (P less than 0.02). Gastric emptying of the solid meal was significantly accelerated in experimental rats at 60 and 120 min (percent meal remaining: portal hypertension versus control, 41.9 +/- 4.0 vs 55.4 +/- 3.5 and 21.5 +/- 4.9 vs 32.6 +/- 4.3, P less than 0.05). Stomachs of portal hypertensive animals were heavier (P less than 0.009) and histologic examination revealed submucosal edema. Thus, a possible mechanism of the disrupted gastric motor function in portal hypertension is decreased gastric wall compliance secondary to edema.

The biochemical and clinical effects of selenium (Na2SeO3) on 1,2-dimethylhydrazine (DMH)-induced colon carcinogenesis in male Sprague-Dawley rats are presented. A 4-ppm selenium supplement to the drinking water was provided before, during, and after 20 weekly injections of 20 mg DMH per kg body weight. Immediately after the 20th DMH injection, part of the rats were sacrificed. The incidences of colon tumors in groups provided selenium before DMH, before and during DMH, and only during DMH treatment were reduced to 39, 43, and 36%, respectively. The incidence in the DMH only control was 63%. Other rats in all treated and control groups were maintained up to 5 months post-DMH treatment. At 10-week intervals throughout the study, selected blood and tissue components were analyzed. The following hematological changes correlated with DMH treatment. (a) Serum glutamic oxalacetic transaminase increased 2-fold (normal, 66 +/- 14 g/dl). (b) Serum alkaline phosphatase increased 24% (normal, 166 +/- 56 units/liter). (c) Serum protein decreased 14% (normal, 6.77 +/- 0.48 g/dl). (d) White blood count increased 2- to 3-fold (normal, 7.7 +/- 2.7 X 10(3)/cu mm). And (e) hemoglobin decreased 67% (normal, 18.1 +/- 1.3 g/dl). The magnitude of these changes varies with each selenium treatment group and with each 10-week analysis period. Provision of 4 ppm selenium doubled both liver and blood selenium levels compared to unsupplemented controls. The effects of selenium and DMH treatments on glutathione peroxidase and beta-glucuronidase activities and on sialic acid are presented. Possible mechanisms by which selenium protects against DMH-induced neoplasia are discussed.

Previous investigations have shown that animals maintained with enteral nutrition are better able to survive an intraperitoneal bacterial challenge than animals receiving parenteral nutrition. The aim of this study was to assess the effects of enteral and parenteral nutrition on reticuloendothelial function. Eighteen enteral-fed male Sprague-Dawley rats had access to a standard hyperalimentation solution via a sipper tube ad libitum. Seventeen parenteral-fed animals received the same solution at an infusion rate determined by the volume ingested by the pair-fed enteral animals. All animals had central venous catheters. After 12 days, reticuloendothelial function was assessed by measuring the clearance rate (K) and the organ distribution of intravenous 51Cr-labeled sheep red blood cells and by plasma fibronectin levels. Nutritional status was assessed by body weight and nitrogen balance. K values in enteral and parenteral animals were similar (0.110 +/- 0.011 and 0.140 +/- 0.012, respectively, mean +/- SEM) as were plasma fibronectin levels (196 +/- 22 and 228 +/- 15 micrograms, respectively). Organ distribution of the 51Cr-labeled sheep red blood cells was the same in both groups. Nitrogen balance and body weights were also similar in both groups. These data demonstrate that in this experimental model enteral nutrition and parenteral nutrition were equally effective at maintaining reticuloendothelial function and nutritional status.

Se as sodium selenite was administered by gavage (three consecutive times) and as drinking water supplements for 46 d to male and female Swiss mice. With respect to survival in 7-wk-old mice, Se was less toxic in males than in females when gavaged. Drinking water supplements of 1-64 ppm Se resulted in 1 male and 1 female death in mice first given Se at 7 wk of age. Se supplements to the drinking water of adult (18-wk-old) mice was less toxic in females. All young (7-wk-old) and adult (18-wk-old) mice provided 1-16 ppm Se in the drinking water survived the 46-d treatment, but in adult mice 64 ppm Se significantly reduced survival. Only 64 ppm Se supplements caused a sharp reduction in body weight in young and adult mice of both sexes. Supplements of 1-8 ppm Se in all mice elicited growth responses similar to those of untreated controls. Occasional liver and kidney congestion, liver necrosis, parenchymal cell degeneration, and bile duct proliferation were observed in control and treatment groups. Serum alkaline phosphatase and glutamic-oxaloacetic transaminase (SGOT) increased with 32 ppm Se and higher supplements. Survival, growth, serum enzymes, and pathology were normal in untreated controls and in mice of growth ages and sexes give 1, 4, and 8 ppm Se supplements. A chronic toxicity study was conducted in female Swiss mice given 1, 4, and 8 ppm Se supplements for 50 wk. The survival of Se-treated groups was more than 90% and that of controls was only 72% after 50 wk. All mice gained weight, but the group treated with 8 ppm Se gained half as much as other groups. Both liver Se and glutathione peroxidase activity increased in Se-treated mice compared to controls at 25 and 50 wk. A reduced white blood cell count and increased alkaline phosphatase and SGOT suggested a mild toxic effect of the 8 ppm Se supplement in the chronic study.

Acute and chronic effects of Se as sodium selenite given as a supplement in the drinking water of Sprague-Dawley rats for 35 d, 1 yr, and 2 yr are compared. For the 35-d study the experimental groups were untreated controls and rats supplemented with 1, 4, 8, 16, and 64 ppm Se. Survival was 100% in the control and 1 and 4 ppm groups, decreased in the 8 and 16 ppm groups, and was zero in the 64 ppm group. Body weights increased and were equivalent in the control and 1 and 4 ppm groups and substantially decreased in the 16 and 64 ppm groups., Serum alkaline phosphatase and glutamic-oxaloacetic transaminase (SGOT) increased with 16 ppm Se and higher supplements. Se toxicity was apparent in microscopic pathology showing liver congestion, fatty degeneration of parenchymal cells, and necrosis. In the chronic studies untreated controls are compared with rate receiving 4 ppm Se in the drinking water. In general, the weight gains throughout were equivalent for both groups. The 1-yr survival in each was above 90% and the 2-yr survival above 50%. With increased age there was a slight reduction in hemoglobin and white blood cells. The latter effect was greater in Se-treated then in control rats. Several serum components were equivalent in both groups, including alkaline and acid phosphatase, SGOT, protein, glucose, and sialic acid. Liver glutathione peroxidase was half and Se levels in the Se-treated rats were twice those in the controls. Data are presented for male rats in the chronic study with occasional reference to data on females. The parameters measured in the chronic study are highly dependent on the age of the rat when Se-supplemented drinking water is initiated.