Bacterial pili,with emphasis on Mycobacterium tuberculosis curli pili: potential biomarkers for point-of care tests and therapeutics

Context: Novel biomarkers are essential for developing rapid diagnostics and therapeutic interventions

Objective: This review aimed to highlight biomarker characterisation and assessment of unique bacterial pili.

Methods: A PubMed search for bacterial pili, diagnostics, vaccine and therapeutics was performed, with emphasis on the well characterised pili.

Results: In total, 46 papers were identified and reviewed.

Conclusion: Extensive analyses of pili enabled by advanced nanotechnology and whole genome sequencing provide evidence that they are strong biomarker candidates. Mycobacterium tuberculosis curli pili are emphasised as important epitopes for the development of much needed point-of-care diagnostics and therapeutics.     

The role of progesterone metabolites in breast cancer: potential for new diagnostics and therapeutics

Proliferative changes in the normal breast are known to be controlled by female sex steroids. However, only a portion of all breast cancer patients respond to current estrogen based endocrine therapy, and with continued treatment nearly all will become unresponsive and experience relapse. Therefore, ultimately for the majority of breast carcinomas, explanations and treatments based on estrogen are inadequate. Recent observations indicate that 5α-pregnane and 4-pregnene progesterone metabolites may serve as regulators of estrogen-responsive as well as unresponsive human breast cancers. The conversion of progesterone to the 5α-pregnanes is increased while conversion to the 4-pregnenes is decreased in breast carcinoma tissue, as a result of changes in progesterone metabolizing 5α-reductase, 3α-hydroxysteroid oxidoreductase (3α-HSO) and 20α-HSO activities and gene expression. The 5α-pregnane, 5α-pregnane-3,20-dione (5αP) stimulates, whereas the 4-pregnene, 3α-hydroxy-4-pregnen-20-one (3αHP), inhibits cell proliferation and detachment, by modulation of cytoskeletal and adhesion plaque molecules via the MAP kinase pathway and involving separate and specific plasma membrane-based receptors. The promotion of breast cancer appears to be related to changes in in situ concentrations of cancer-inhibiting and cancer-promoting progesterone metabolites. New diagnostic and therapeutic possibilities for breast cancer are suggested.     

The electrochemical modification of clenbuterol for biosensors of dopamine, norepinephrine, adrenalin, ascorbic acid and uric acid at paraffin-impregnated graphite electrode

The electrochemical modification of clenbuterol (CLB) was studied at paraffin-impregnated graphite electrode (WGE) in two potential ranges of 0.0-1.6V and -1.2 to 1.2V. Various methods including X-ray photoelectron spectroscopy (XPS), UV-spectroelectrochemistry, infrared (IR) spectra and electrochemical techniques have been used to characterizing the modification. Clenbuterol can be modified at the electrode surface by carbon-nitrogen linkage or carbon-carbon linkage in 0.0-1.6V or -1.2 to 1.2V, respectively. The electrochemical behaviors of dopamine (DA), norepinephrine (NE), adrenalin (EP), ascorbic acid (AA) and uric acid (UA) were studied at clenbuterol-modified paraffin-impregnated graphite electrode (CLB/WGE), and it was found that all these compounds could be detected successfully.     

Multi‐omics of the expression and clinical outcomes of TMPRSS2 in human various cancers: A potential therapeutic target for COVID‐19

Growing evidence has shown that Transmembrane Serine Protease 2 (TMPRSS2) not only contributes to the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection, but is also closely associated with the incidence and progression of tumours. However, the correlation of coronavirus disease (COVID‐19) and cancers, and the prognostic value and molecular function of TMPRSS2 in various cancers have not been fully understood. In this study, the expression, genetic variations, correlated genes, immune infiltration and prognostic value of TMPRSS2 were analysed in many cancers using different bioinformatics platforms. The observed findings revealed that the expression of TMPRSS2 was considerably decreased in many tumour tissues. In the prognostic analysis, the expression of TMPRSS2 was considerably linked with the clinical consequences of the brain, blood, colorectal, breast, ovarian, lung and soft tissue cancer. In protein network analysis, we determined 27 proteins as protein partners of TMPRSS2, which can regulate the progression and prognosis of cancer mediated by TMPRSS2. Besides, a high level of TMPRSS2 was linked with immune cell infiltration in various cancers. Furthermore, according to the pathway analysis of differently expressed genes (DEGs) with TMPRSS2 in lung, breast, ovarian and colorectal cancer, 160 DEGs genes were found and were significantly enriched in respiratory system infection and tumour progression pathways. In conclusion, the findings of this study demonstrate that TMPRSS2 may be an effective biomarker and therapeutic target in various cancers in humans, and may also provide new directions for specific tumour patients to prevent SARS‐CoV‐2 infection during the COVID‐19 outbreak.     

The expression profiling of circulating miR-204, miR-182, and lncRNA H19 as novel potential biomarkers for the progression of peptic ulcer to gastric cancer

Deregulation of noncoding RNAs, microRNAs (miRNAs) and long noncoding RNA (lncRNA), are implicated in the initiation and progression of gastric cancer (GC). This study is a pilot case-control study carried out on 75 subjects, 40 of them were Helicobacter pylori-gastric ulcer patients and 35 were GC patients recruited from the Gastrointestinal Endoscopy Unit in Al-Kasr Al-Aini Hospital, Cairo University in Egypt. Real-time PCR was performed to evaluate the expression level of serum miR-204, miR-182, and lncRNA H19 in patients with peptic ulcer-progressed GC vs nonprogressed peptic ulcer patients. Fibroblast growth factor 18 (FGF-18)/FGF receptor 2 (FGFR2) expression and their downstream immunological and inflammatory signaling markers were assessed and their association with the addressed noncoding RNAs investigated. As regards miR-204 and miR-182, they were significantly increased (12.5 and 2.6 folds, respectively) in GU samples, compared with those of healthy control levels. The elevated levels of these miRNAs were significantly de-escalated in GC samples compared with GU and the fold decrease valued 2.2 fold for miR-204 and 1.8 folds for miR-182. On the other hand, the significant escalation in the level of lnRNA H19 in GU recorded a 16.6 fold increase and further elevation in its levels was evident in GC samples. The herein assessed miRNAs are correlated with disease duration and FGFR2 with miR-182 being significantly correlated with all inflammatory markers, TAC, INF-γ, matrix metallopeptidase 9, and FGF-18. In terms of diagnostic accuracy of assessed miRNAs (stages III to IV), the receiver operating characteristic analysis indicated that serum lncRNA H19 showed the highest diagnostic accuracy (95.5%), specificity (100%), and sensitivity (90.9%), compared with miR-204 and miR-182, which showed the same specificity (60%), sensitivity (72.7%), and diagnostic accuracy (68.8%). Our findings conclude that lnRNA H19, miR-204, and miR-182 may function as novel prospective plasma biomarkers to detect GC and its progression from H. pylori-peptic ulcer, which would be helpful to improve the theranostics of GC.     

Bioremediation of cyanide‐containing wastes: The potential of systems and synthetic biology for cleaning up the toxic leftovers from mining

Synthetic biology could harness the ability of microorganisms to use highly toxic cyanide compounds for growth applied to bioremediation of cyanide‐contaminated mining wastes and areas. Subject Categories: Biotechnology & Synthetic Biology, Evolution & Ecology, Metabolism

Cyanide is a highly toxic chemical produced in large amounts by the mining and jewellery industries, steel manufacturing, coal coking, food processing and chemical synthesis (Luque‐Almagro et al, 2011). The mining industry uses so‐called cyanide leaching to extract gold and other precious metals from ores, which leaves large amounts of cyanide‐containing liquid wastes with arsenic, mercury, lead, copper, zinc and sulphuric acid as cocontaminants.Although these techniques are very efficient, they still produce about one million tonnes of toxic wastewaters each year, which are usually stored in artificial ponds that are prone to leaching or dam breaks and pose a major threat to the environment and human health (Luque‐Almagro et al, 2016). In 2000, a dam burst in Baia Mare, Romania, caused one of the worst environmental disasters in Europe. Liquid waste from a gold mining operation containing about 100 tonnes of cyanide spilled into the Somes River and eventually reached the Danube, killing up to 80% of wildlife in the affected areas. A more recent spill was caused by a blast furnace at Burns Harbor, IN, USA, which released 2,400 kg of ammonia and 260 kg of cyanide at concentrations more than 1,000 times over the legal limit into Calumet River and Lake Michigan, severely affecting wildlife. Notwithstanding the enormous damage such major spills cause, industrial activities that continuously release small amounts of waste are similarly dangerous for human and environmental health.The European Parliament, as part of its General Union Environment Action Programme, has called for a ban on cyanide in mining activities to protect water resources and ecosystems against pollution. Although several EU member states have joined this initiative, there is still no binding legislation. Similarly, there are no general laws in the USA to prevent cyanide spills, and former administration even authorized the use of cyanide for control predators in agriculture.     

COVID‐19 and the opportunities for research: The lockdowns’ impacts on wildlife,ecology and conservation biology,and the humanities

The ongoing lockdowns provide ideal conditions to study the relationship between wildlife and humans but among humans themselves. Subject Categories: Ecology, S&S: History & Philosophy of Science

Almost all research has been affected in some way or another by the COVID‐19 pandemic, at the very least by challenging collaboration and interaction. But some areas have been affected more than others. Ecology and conservation biology experience a real boon as ongoing lockdowns have presented unique opportunities to study the impact of human activities on animals and ecosystems. This has not just galvanised research but also promises to leave a legacy of networks and collaborations to explore means to reduce negative human impacts on biodiversity long after the pandemic has subsided. In the social sciences and humanities, however, the pandemic is raising fundamental questions about their ability to contribute meaningfully to inform policy and public health responses.

In the social sciences and humanities […] the pandemic is raising fundamental questions about their ability to contribute meaningfully to inform policy and public health responses.

     

Psychotherapies for depression: a network meta‐analysis covering efficacy,acceptability and long‐term outcomes of all main treatment types

The effects of psychotherapies for depression have been examined in several hundreds of randomized trials, but no recent network meta‐analysis (NMA) has integrated the results of these studies. We conducted an NMA of trials comparing cognitive behavioural, interpersonal, psychodynamic, problem‐solving, behavioural activation, life‐review and “third wave” therapies and non‐directive supportive counseling with each other and with care‐as‐usual, waiting list and pill placebo control conditions. Response (50% reduction in symptoms) was the primary outcome, but we also assessed remission, standardized mean difference, and acceptability (all‐cause dropout rate). Random‐effects pairwise and network meta‐analyses were conducted on 331 randomized trials with 34,285 patients. All therapies were more efficacious than care‐as‐usual and waiting list control conditions, and all therapies – except non‐directive supportive counseling and psychodynamic therapy – were more efficacious than pill placebo. Standardized mean differences compared with care‐as‐usual ranged from –0.81 for life‐review therapy to –0.32 for non‐directive supportive counseling. Individual psychotherapies did not differ significantly from each other, with the only exception of non‐directive supportive counseling, which was less efficacious than all other therapies. The results were similar when only studies with low risk of bias were included. Most therapies still had significant effects at 12‐month follow‐up compared to care‐as‐usual, and problem‐solving therapy was found to have a somewhat higher long‐term efficacy than some other therapies. No consistent differences in acceptability were found. Our conclusion is that the most important types of psychotherapy are efficacious and acceptable in the acute treatment of adult depression, with few significant differences between them. Patient preference and availability of each treatment type may play a larger role in the choice between types of psychotherapy, although it is possible that a more detailed characterization of patients with a diagnosis of depression may lead to a more precise matching between individual patients and individual psychotherapies.     

Oxidative chemistry of 2-nitro and 4-nitroestradiol: Dichotomous behavior of radical intermediates and novel potential routes for oxyfunctionalization and B-ring fission of steroidal scaffolds

Oxidation of 4-nitro-17beta-estradiol (1) with the peroxidase/H(2)O(2) system gave the symmetric C(2)-linked dimer (3) through phenoxy radical coupling. Similar oxidation of 2-nitro-17beta-estradiol (2), in which the nitro group is coplanar with the aromatic ring, yielded 9alpha- and 9beta-hydroxy-2-nitro-17beta-estradiol (4a,b), (17beta)-2-nitroestra-1(10),2,4,9(11)-tetraene-3,17-diol (5), and (12alpha,17beta)-2-nitroestra-1(10),2,4,9(11)-tetraene-3,12,17-triol (6). With higher concentrations of H(2)O(2), the novel secoestra-1(10),2,4-trien-9-one derivative 7 was obtained from 2. Theoretical calculations suggested that the peculiar behavior of 2 may be due to the generation of a relatively stable radical intermediate at C(9), which would then be converted to the reactive quinone methide 8. The chemistry described in this paper appears to be an intriguing example of control of the site of substitution over evolution of phenoxy radicals, and opens new vistas toward selective oxyfunctionalization of the estrane skeleton.     

Evaluation of a novel, integrated approach using functionalized magnetic beads, bench-top MALDI-TOF-MS with prestructured sample supports, and pattern recognition software for profiling potential biomarkers in human plasma.

The advantage of using proteins and peptides as biomarkers is that they can be found readily in blood, urine, and other biological fluids. Such sample types are easily obtained and represent a potentially rich palette of biologically informative molecules. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) represents a key tool for rapidly interrogating such sample types. The goal of clinical proteomics is to harness the power of this tool for identifying novel, condition-specific protein fingerprints that may, in turn, lead to the elucidation and use of diseasespecific biomarkers that may be used to diagnose disease as well as to evaluate disease severity, disease progression, and intervention efficacy. Here we have evaluated a simple, affordable bench-top MALDI-TOF mass spectrometer to generate protein profiles from human plasma samples of asthma patients and healthy individuals. We achieve this profiling by using C8-functionalized magnetic beads that enrich a specific subset of plasma proteins based on their absorption by this resin. This step is followed by elution, transfer onto a prestructured sample support (AnchorChip technology), and analysis in a bench-top MALDI-TOF mass spectrometer (OmniFLEX) with AutoXecute acquisition control which enables automated operation with reproducible results. Resulting spectra are compiled and analyzed through the pattern recognition component of ClinProTools software. This approach in combination with ClinProTools software permits the investigator to rapidly scan for potential biomarker peptides/proteins in human plasma. The reproducibility of plasma profiles within and between days has been evaluated. The results show that the novel and facile approach with manual magnetic-bead sample preparation and a low-cost bench-top MALDI-TOF mass spectrometer is suitable for preliminary biomarker discovery studies.     

A reaction cycle for cytochrome c oxidase as an electron-transport-driven proton pump: The effect of electrochemical potential and slips

A detailed reaction cycle for cytochrome oxidase, an electron-transport-driven proton pump, has been presented earlier by our research group. The essential feature of the model is that both cytochrome a and Cu_A must be reduced in order to allow the transition from the electron and proton input state to the output state. The model is thus based on an indirect coupling between electron transfer and proton translocation.In this study, the same model is examined with respect to (1) intrinsic electron and proton leaks and (2) the effect of applying an electrochemical potential gradient on the pump incorporated in a membrane, both with respect to the electrical and chemical components.The model is successfully used to simulate various experimental results. Comparisons of experimental results with simulations based on the model support the existence of electron and proton leaks. The analysis of electron leaks suggests that electron gating is best achieved by varying the reorganization energy rather than by varying the reduction potentials.It is also suggested that both the electrical and chemical components of the electrochemical potential gradient are responsible for the regulation of the enzyme activity. Furthermore, an attempt is made to interpret the seemingly contradictory results obtained when measuring the pH dependence of the reduction potential of cytochrome a. In addition, the simulations support the assumption that protons are pumped by a mechanism that combines a membrane Bohr effect with the transition-state mechanism.Abbreviations R molar gas constant - k _B Boltzmann contant - F Faraday constant - e elementary charge - T absolute temperature - transmembrane electrochemical potential gradient - pH transmembrane pH difference - pH₁ and pH₂ inside (matrix) and outside (cytosol) pH, respectively - transmembrane electrical potential - E _m midpoint potential     

The influence of the biological pump on ocean chemistry: implications for long‐term trends in marine redox chemistry,the global carbon cycle,and marine animal ecosystems

The net export of organic matter from the surface ocean and its respiration at depth create vertical gradients in nutrient and oxygen availability that play a primary role in structuring marine ecosystems. Changes in the properties of this ‘biological pump’ have been hypothesized to account for important shifts in marine ecosystem structure, including the Cambrian explosion. However, the influence of variation in the behavior of the biological pump on ocean biogeochemistry remains poorly quantified, preventing any detailed exploration of how changes in the biological pump over geological time may have shaped long‐term shifts in ocean chemistry, biogeochemical cycling, and ecosystem structure. Here, we use a 3‐dimensional Earth system model of intermediate complexity to quantitatively explore the effects of the biological pump on marine chemistry. We find that when respiration of sinking organic matter is efficient, due to slower sinking or higher respiration rates, anoxia tends to be more prevalent and to occur in shallower waters. Consequently, the Phanerozoic trend toward less bottom‐water anoxia in continental shelf settings can potentially be explained by a change in the spatial dynamics of nutrient cycling rather than by any change in the ocean phosphate inventory. The model results further suggest that the Phanerozoic decline in the prevalence ocean anoxia is, in part, a consequence of the evolution of larger phytoplankton, many of which produce mineralized tests. We hypothesize that the Phanerozoic trend toward greater animal abundance and metabolic demand was driven more by increased oxygen concentrations in shelf environments than by greater food (nutrient) availability. In fact, a lower‐than‐modern ocean phosphate inventory in our closed system model is unable to account for the Paleozoic prevalence of bottom‐water anoxia. Overall, these model simulations suggest that the changing spatial distribution of photosynthesis and respiration in the oceans has exerted a first‐order control on Earth system evolution across Phanerozoic time.     

Evaluation of a package of continuum of care interventions for improved maternal,newborn, and child health outcomes and service coverage in Ghana: A cluster-randomized trial

BackgroundIn low- and middle-income countries (LMICs), the continuum of care (CoC) for maternal, newborn, and child health (MNCH) is not always complete. This study aimed to evaluate the effectiveness of an integrated package of CoC interventions on the CoC completion, morbidity, and mortality outcomes of woman–child pairs in Ghana.Methods and findingsThis cluster-randomized controlled trial (ISRCTN: 90618993) was conducted at 3 Health and Demographic Surveillance System (HDSS) sites in Ghana. The primary outcome was CoC completion by a woman–child pair, defined as receiving antenatal care (ANC) 4 times or more, delivery assistance from a skilled birth attendant (SBA), and postnatal care (PNC) 3 times or more. Other outcomes were the morbidity and mortality of women and children. Women received a package of interventions and routine services at health facilities (October 2014 to December 2015). The package comprised providing a CoC card for women, CoC orientation for health workers, and offering women with 24-hour stay at a health facility or a home visit within 48 hours after delivery. In the control arm, women received routine services only. Eligibility criteria were as follows: women who gave birth or had a stillbirth from September 1, 2012 to September 30, 2014 (before the trial period), from October 1, 2014 to December 31, 2015 (during the trial period), or from January 1, 2016 to December 31, 2016 (after the trial period). Health service and morbidity outcomes were assessed before and during the trial periods through face-to-face interviews. Mortality was assessed using demographic surveillance data for the 3 periods above. Mixed-effects logistic regression models were used to evaluate the effectiveness as difference in differences (DiD). For health service and morbidity outcomes, 2,970 woman–child pairs were assessed: 1,480 from the baseline survey and 1,490 from the follow-up survey. Additionally, 33,819 cases were assessed for perinatal mortality, 33,322 for neonatal mortality, and 39,205 for maternal mortality. The intervention arm had higher proportions of completed CoC (410/870 [47.1%]) than the control arm (246/620 [39.7%]; adjusted odds ratio [AOR] for DiD = 1.77; 95% confidence interval [CI]: 1.08 to 2.92; p = 0.024). Maternal complications that required hospitalization during pregnancy were lower in the intervention (95/870 [10.9%]) than in the control arm (83/620 [13.4%]) (AOR for DiD = 0.49; 95% CI: 0.29 to 0.83; p = 0.008). Maternal mortality was 8/6,163 live births (intervention arm) and 4/4,068 live births during the trial period (AOR for DiD = 1.60; 95% CI: 0.40 to 6.34; p = 0.507) and 1/4,626 (intervention arm) and 9/3,937 (control arm) after the trial period (AOR for DiD = 0.11; 95% CI: 0.11 to 1.00; p = 0.050). Perinatal and neonatal mortality was not significantly reduced. As this study was conducted in a real-world setting, possible limitations included differences in the type and scale of health facilities and the size of subdistricts, contamination for intervention effectiveness due to the geographic proximity of the arms, and insufficient number of cases for the mortality assessment.ConclusionsThis study found that an integrated package of CoC interventions increased CoC completion and decreased maternal complications requiring hospitalization during pregnancy and maternal mortality after the trial period. It did not find evidence of reduced perinatal and neonatal mortality.Trial registrationThe study protocol was registered in the International Standard Randomised Controlled Trial Number Registry (90618993).

Akira Shibanuma and co-workers study a package of maternal and child health interventions in a cluster-randomized trial done in Ghana.