Wolfberry genome database: integrated genomic datasets for studying molecular biology

Wolfberry, also known as goji berry or Lycium barbarum, is a highly valued fruit with significant health benefits and nutritional value. For more efficient and comprehensive usage of published L. barbarum genomic data, we established the Wolfberry database. The utility of the Wolfberry Genome Database (WGDB) is highlighted through the Genome browser, which enables the user to explore the L. barbarum genome, browse specific chromosomes, and access gene sequences. Gene annotation features provide comprehensive information about gene functions, locations, expression profiles, pathway involvement, protein domains, and regulatory transcription factors. The transcriptome feature allows the user to explore gene expression patterns using transcripts per kilobase million (TPM) and fragments per kilobase per million mapped reads (FPKM) metrics. The Metabolism pathway page provides insights into metabolic pathways and the involvement of the selected genes. In addition to the database content, we also introduce six analysis tools developed for the WGDB. These tools offer functionalities for gene function prediction, nucleotide and amino acid BLAST analysis, protein domain analysis, GO annotation, and gene expression pattern analysis. The WGDB is freely accessible at https://cosbi7.ee.ncku.edu.tw/Wolfberry/. Overall, WGDB serves as a valuable resource for researchers interested in the genomics and transcriptomics of L. barbarum. Its user-friendly web interface and comprehensive data facilitate the exploration of gene functions, regulatory mechanisms, and metabolic pathways, ultimately contributing to a deeper understanding of wolfberry and its potential applications in agronomy and nutrition.

[The Breast Cancer Cohort Study in Chinese Women: research design and preliminary results of clinical multi-center cohort]

Objective: The incidence of breast cancer in Chinese women continues to rise. The large breast cancer cohort studies in China are relatively scarce. There are many bottlenecks in the construction of large clinical cohort for breast cancer diagnosis, treatment, and prognoses, such as inconsistent standards, high rates of lost follow-up, repeated construction, and inability to share. To better solving the difficulties and problems faced by large-scale clinical cohort research in China, this project will cooperate with several tertiary A hospitals to establish a breast cancer cohort in Chinese women. It also provides a data platform and technical support for breast cancer multi-center clinical cohort research. Methods: Based on the evidence-based medicine and expert opinion and consensus, we established a breast cancer cohort standardized indicator set-recording baseline information, diagnosis and treatment-related information of the enrolled patients, and collecting biological specimens. According to the technical specification of long-term follow-up for the endpoint, data management, and data security and in the large population-based cohort study, a standardized follow-up system for the diagnosis, treatment, and prognosis of breast cancer prospective cohorts is formed. Results: Based on standardized data sets and the computer discipline's advantage from the University of Science and Technology Beijing, we integrate the new information technology methods, including dynamic information collection terminals and social networks. Thus, the quality of control programs on compliance and intelligence data was improved, and a Chinese women breast cancer cohort database was developed. By February 2020, 12 147 patients were included in the clinical cohort database. Biological specimens'resources in cohort construction were collected and cooperated with Shandong University to research the multi-center quality control system and shared evaluation system of biobanks. Building an open and shared biobank network and forming a full chain of breast cancer research platform. Conclusion: With the implementation of the "13(th) Five-Year Plan" precision medicine research, this study provides a research foundation for precision diagnosis and treatment of breast cancer and provides data support for the country to formulate relevant medical policies.

Effects of isobutyrate supplementation on ruminal microflora, rumen enzyme activities and methane emissions in Simmental steers

The objective of this study was to evaluate the effects of isobutyrate supplementation on rumen microflora, enzyme activities and methane emissions in Simmental steers consuming a corn stover-based diet. Eight ruminally cannulated Simmental steers were used in a replicated 4 × 4 Latin square experiment. The treatments were control (without isobutyrate), low isobutyrate (LIB), moderate isobutyrate (MIB) and high isobutyrate (HIB) with 8.4, 16.8 and 25.2 g isobutyrate per steer per day respectively. Isobutyrate was hand-mixed into the concentrate portion. Diet consisted of 60% corn stover and 40% concentrate [dry matter (DM) basis]. Dry matter intake (averaged 9 kg/day) was restricted to a maximum of 90% of ad libitum intake. Population of total bacteria, cellulolytic bacteria and anaerobic fungi were linearly increased, whereas that of protozoa and total methanogens was linearly reduced with increasing isobutyrate supplementation. Real-time PCR quantification of population of Ruminococcus albus, Ruminococcus flavefaciens, Butyrivibrio fibrisolvens and Fibrobacter succinogenes was linearly increased with increasing isobutyrate supplementation. Activities of carboxymethyl cellulase, xylanase and β-glucosidase were linearly increased, whereas that of protease was linearly reduced. Methane production was linearly decreased with increasing isobutyrate supplementation. Effective degradabilities of cellulose and hemicellulose of corn stover were linearly increased, whereas that of crude protein in diet was linearly decreased with increasing isobutyrate supplementation. The present results indicate that isobutyrate supplemented improved microflora, rumen enzyme activities and methane emissions in steers. It was suggested that the isobutyrate stimulated the digestive micro-organisms or enzymes in a dose-dependent manner. In the experimental conditions of this trial, the optimum isobutyrate dose was approximately 16.8 g isobutyrate per steer per day.

Effects of amyloid β-peptide fragment 31-35 on the BK channel-mediated K⁺ current and intracellular free Ca²⁺ concentration of hippocampal CA1 neurons

The present study characterizes the effects of Aβ31-35, a short active fragment of amyloid β-peptide (Aβ), upon the BK channel-mediated K⁺ current and intracellular free Ca²⁺ concentration ([Ca²⁺]i) of freshly dissociated pyramidal cells from rat CA1 hippocampus by using whole-cell patch-clamp recording and single cell Ca²⁺ imaging techniques. The results show that: (1) in the presence of voltage- and ATP-gated K⁺ channel blockers application of 5.0 μM Aβ31-35 significantly diminished transient outward K⁺ current amplitudes at clamped voltages between 0 and 45mV; (2) under the same conditions [Ca²⁺]i was minimally affected by 5.0 μM but significantly increased by 12.5 μM and 25 μM Aβ31-35; and (3) when 25 μM of a larger fragment of the amyloid β-peptide, Aβ25-35, was applied, the results were similar to those obtained with the same concentration of Aβ31-35. These results indicate that Aβ31-35 is likely to be the shortest active fragment of the full Aβ sequence, and can be as effectively as the full-length Aβ peptide in suppressing BK-channel mediated K⁺ currents and significantly elevating [Ca²⁺]i in hippocampal CA1 neurons.

Effect of recombinant bactericidal/permeability-increasing protein on endotoxin translocation and lipopolysaccharide-binding protein/CD14 expression in rats after thermal injury

OBJECTIVE

To investigate the potential mechanisms underlying the in vivo effect of recombinant bactericidal/permeability-increasing protein (rBPI21) on endogenous bacteria or endotoxin translocation and lipopolysaccharide-binding protein/CD14 expression secondary to thermal injury.

DESIGN

Prospective, randomized, controlled animal study.

SETTING

College hospital animal research laboratory.

SUBJECTS

Thirty-six male Wistar rats weighing 250-300 g.

INTERVENTIONS

The rats were anesthetized, and a 35% total body surface area full-thickness burn was created. Animals were randomized to receive treatment with either rBPI21 or the control protein (albumin). rBPI21 (2 mg/kg body wt, BPI group) or a protein control preparation (burn group) in the same dose was administered in an intravenous bolus at 30 mins and 4 hrs after thermal injury. All animals were killed at 12 and 24 hrs postburn (six to ten rats for each interval). In addition, eight rats were taken as normal controls.

MEASUREMENT AND MAIN RESULTS

Our data showed that treatment with rBPI21 was effective in preventing endotoxin translocation secondary to severe burns. Meanwhile, tissue lipopolysaccharide-binding protein, CD14, and tumor necrosis factor-alpha mRNA expression in various organs were inhibited markedly by rBPI21 secondary to acute insults (p <.05-.01). Furthermore, significant reduction in serum aminoleucine transferase concentrations and elevation in intestinal diamine oxidase activities in the rBPI21-treated group were found compared with controls (p <.05-.01).

CONCLUSIONS

These findings indicate that endotoxin accumulated in local sites after thermal injury can markedly up-regulate lipopolysaccharide-binding protein/CD14 and tumor necrosis factor-alpha mRNA expression in various organs. Meanwhile, up-regulation of lipopolysaccharide-binding protein/CD14 expression would be the major molecular mechanism of increasing sensitivity to endogenous endotoxin response after burns. Early treatment with rBPI21may be effective in attenuating multiple organ damage resulting from gut-origin endotoxin translocation. This might be associated with the down-regulation effects of tissue lipopolysaccharide-binding protein and CD14 gene expression by the use of rBPI21.

[The biological effect of tetrahydrobiopterin and its potential role in sepsis]

It is well known that overproduction of nitric oxide (NO) is the final common pathway in septic shock. Tetrahydrobiopterin (BH4), a low molecular weight pterdine, is an essential cofactor required for the activity of NO synthase (NOS). Existing evidences show that lipopolysaccharide and proinflammatory cytokines can cause significant rises in bipoterin levels, which in turn augments the synthesis of NO. Also inhibition of biosynthesis of BH4 can decrease NO formation, implying that BH4 may be involved in the pathophysiological alterations of sepsis. However, the precise mechanisms of BH4 in regulating NO formation are not yet fully understood. In this review, we focus on the biological effects and regulation of BH4, as well as its potential role in sepsis. The therapeutic significance of biopterin synthesis inhibitors in septic symptoms is also discussed.

Influence of selective decontamination of the digestive tract on cell-mediated immune function and bacteria/endotoxin translocation in thermally injured rats

OBJECTIVE

To determine the influence of pretreatment with selective decontamination of the digestive tract (SDD) on systemic immunosuppression, and the relationship between bacteria/endotoxin translocation and abnormalities of immune function in thermally injured rats.

DESIGN, MATERIALS, AND METHODS

Animals were subjected to a 40% full-thickness scald injury, and divided into SDD-treated and control groups. The treatment group received SDD (polymyxin E, tobramycin, and 5-flucytosine) by gavage twice daily for 3 days before the experiment and continued for 5 days after thermal injury. The control group was given the same amount of water. The parameters reflecting cell-mediated immunity, including splenocyte proliferation in response to mitogens, interleukin 2 (IL-2) production, and lymphocyte subpopulation, were measured before injury and 1 and 5 days after burn, respectively.

MEASUREMENTS AND MAIN RESULTS

Thermal injury resulted in marked reduction in splenocyte proliferative response to T-cell mitogens, IL-2 production, and T-helper/suppressor cells (CD4/CD8) ratio. Prophylactic treatment with SDD significantly decreased the incidences of bacterial translocation and endotoxemia, prevented suppressive mitogenic response and inadequate IL-2 production (p < 0.05-0.01) but did not affect the abnormal ratio of CD4 to CD8 T lymphocytes in blood (p > 0.05).

CONCLUSIONS

These results suggest that bacteria/endotoxin translocation from the gut appears to be involved in cell-mediated immune dysfunction as a consequence of thermal injury. Pretreatment with SDD might attenuate postburn immunosuppression by preventing translocation events.

Reduction of circulating prostaglandin E2 level by antiserum against core lipopolysaccharide in a rabbit model of multiple organ failure

OBJECTIVE

To determine the potential role of prostaglandin E2 (PGE2) in the development of multiple organ dysfunction or failure (MOF), the possible effects of antiserum directed against Re chemotype lipopolysaccharide (LPS, from Re mutant of Escherichia coli F515) on circulating PGE2 level and survival rate, and whether there is an elevation in the plasma LPS concentration that could account for the induction of arachidonic acid metabolite in a rabbit model of MOF caused by acute hypovolemic insult.

DESIGN, MATERIALS, AND METHODS

An animal model of MOF in rabbits, engendered by feeding live Escherichia coli O111:B4 before hemorrhagic shock (35-40 mm Hg for 60 min), was used in the present study. Re-LPS antiserum was given intravenously in the treatment group at the onset of hemorrhage and 4 hours after resuscitation. The animals that received equal volumes of normal rabbit serum and antiserum served as the control group.

MEASUREMENTS AND MAIN RESULTS

The circulating PGE2 level was not increased at the end of shock (p > 0.05), but it was found to be significantly elevated 24 hours after hemorrhage and resuscitation in both groups. However, Re-LPS antiserum administration markedly decreased peak PGE2 level (p < 0.05) and attenuated multiple organ damage caused by acute insult. Concomitantly, there were also lower LPS concentrations in the treatment group as compared with the control group (p < 0.05-0.01). The survival rate was significantly increased in antiserum-treated rabbits 96 hours postinjury (treatment vs. control: 58.0% vs. 11.1%, p < 0.01).

CONCLUSIONS

The results suggest that an excessive generation and release of PGE2 may be involved in the pathogenesis of immunosuppression and MOF following hemorrhage and resuscitation. Re-LPS antiserum has an inhibitory effect on overproduction of circulating PGE2 and the ability to improve survival with MOF. Gut-derived endotoxemia, bacterial translocation, or both, could account, at least in part, for the PGE2 formation and release in animals response to acute hypovolemic insult.

[An experimental study of the mechanism of shock-induced enterogenic infection after long-term standard total parenteral nutrition]

In this study, gnotobiotic rats were subjected to total parenteral nutrition (TPN) and subsequent hemorrhagic shock to study the mechanism of enterogenic infection in these circumstances. (1) Long-term (8-12 days) TPN induced impairment of gut barrier function, evidenced by atrophy of intestinal mucosa, significant decrease in diamine oxidase activity of intestinal mucosa and blood, and marked micro-ecologic imbalance of the intestinal mucosa flora with dominant growth of aerobes and relative decrease in anaerobes. The degree of mucosal damage were proportional to the duration of TPN. (2) In TPN+shock groups, further damage was found in the mucosa, with a large number of invading gram-negative organisms and a significant decrease in DAO activity as compared to that with TPN only groups. These changes were significantly correlated with enhanced bacterial translocation, elevation of LPS and MDA levels in the plasma. These findings suggested that long term TPN impairing gut barrier function, precipitated posttraumatic gut barrier failure. The determination of plasma DAO activity may help in the early diagnosis of gut injury during TPN and after trauma.

Protective effect of Re-LPS antiserum on experimental multiple system organ failure

This study examines the possible beneficial effect of Re-LPS (F515) antiserum on experimental multiple system organ failure (MSOF) in rabbits. The results showed that the plasma LPS level was significantly decreased, and it took a shorter period to clear up LPS in experimental than in control rabbits after receiving Re-LPS antiserum. Pretreatment with antiserum can markedly improve the function of the liver, lungs, kidneys, blood and gastrointestinal tract. The MSOF incidence in the group of rabbits receiving immune sera was only 11.2% and the survival rate was raised by about 40.0%. The results suggest that early passive immunotherapy may neutralize gut-derived endotoxin, inhibit endotoxin-induced mediators release and prevent development of severe complications due to sepsis. It is therefore postulated that LPS core antiserum may provide a prophylactic effect on the development of experimental MSOF.

Active oxygen in neuromuscular disorders

Although muscle and nerve are reasonably well protected against active oxygen and related free radicals, environmental or inherited malfunctions can overpower their defences. Active oxygen is involved in many neuropathies and myopathies. In every case the damage is caused by agents which exert effects disproportionately greater than the quantities encountered, through a variety of amplification mechanisms. We can categorize these amplification mechanisms as follows: (a) non-replacement of targets (e.g. loss of genetic information, ataxia telangectasia being an hereditary ataxia in which an oxygen mediated chromosomal instability is apparent), (b) non-removal of unwanted materials (e.g. lipofuscin accumulation in brain and heart), (c) redox cycling, usually involving catalysis by trace-metal ions (e.g. some forms of Parkinsonism), (d) non-redox catalysis (e.g. toxicity in cardiac muscle or brain due to vanadium or aluminium respectively), (e) modification of ion transport (e.g. calcium ionophore or acrylamide induce histopathological changes in muscle, similar in some respects to those seen in Duchenne muscular dystrophy), (f) compromised defences (e.g. muscle and nerve become particularly susceptible to free radical damage after loss of the protective actions of vitamin E), and (g) amplification by inflammatory and immune responses (e.g. multiple sclerosis, reperfusion injury to brain and heart, and traumatic injury to nervous tissue). Unfortunately, a variety of therapeutic agents which might be expected to protect against almost every conceivable form of oxygen mediated damage have proved clinically ineffective in most of these disorders. The reasons for this will be explored with an emphasis on common features, differences, mechanisms, and potential therapeutic approaches.