Sample treatment for tissue proteomics in cancer, toxicology, and forensics

Since the birth of proteomics science in the 1990, the number of applications and of sample preparation methods has grown exponentially, making a huge contribution to the knowledge in life science disciplines. Continuous improvements in the sample treatment strategies unlock and reveal the fine details of disease mechanisms, drug potency, and toxicity as well as enable new disciplines to be investigated such as forensic science. This chapter will cover the most recent developments in sample preparation strategies for tissue proteomics in three areas, namely, cancer, toxicology, and forensics, thus also demonstrating breath of application within the domain of health and well-being, pharmaceuticals, and secure societies. In particular, in the area of cancer (human tumor biomarkers), the most efficient and multi-informative proteomic strategies will be covered in relation to the subsequent application of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid extraction surface analysis (LESA), due to their ability to provide molecular localization of tumor biomarkers albeit with different spatial resolution. With respect to toxicology, methodologies applied in toxicoproteomics will be illustrated with examples from its use in two important areas: the study of drug-induced liver injury (DILI) and studies of effects of chemical and environmental insults on skin, i.e., the effects of irritants, sensitizers, and ionizing radiation. Within this chapter, mainly tissue proteomics sample preparation methods for LC-MS/MS analysis will be discussed as (i) the use of LC-MS/MS is majorly represented in the research efforts of the bioanalytical community in this area and (ii) LC-MS/MS still is the gold standard for quantification studies. Finally, the use of proteomics will also be discussed in forensic science with respect to the information that can be recovered from blood and fingerprint evidence which are commonly encountered at the scene of the crime. The application of proteomic strategies for the analysis of blood and fingerprints is novel and proteomic preparation methods will be reported in relation to the subsequent use of mass spectrometry without any hyphenation. While generally yielding more information, hyphenated methods are often more laborious and time-consuming; since forensic investigations need quick turnaround, without compromising validity of the information, the prospect to develop methods for the application of quick forensic mass spectrometry techniques such as MALDI-MS (in imaging or profiling mode) is of great interest

Rarity of monodominance in hyperdiverse Amazonian forests.

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors

Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study

Background Early mobilisation (EM) is an intervention that may improve the outcome of critically ill patients. There is limited data on EM in COVID-19 patients and its use during the first pandemic wave. Methods This is a pre-planned subanalysis of the ESICM UNITE-COVID, an international multicenter observational study involving critically ill COVID-19 patients in the ICU between February 15th and May 15th, 2020. We analysed variables associated with the initiation of EM (within 72 h of ICU admission) and explored the impact of EM on mortality, ICU and hospital length of stay, as well as discharge location. Statistical analyses were done using (generalised) linear mixed-effect models and ANOVAs. Results Mobilisation data from 4190 patients from 280 ICUs in 45 countries were analysed. 1114 (26.6%) of these patients received mobilisation within 72 h after ICU admission; 3076 (73.4%) did not. In our analysis of factors associated with EM, mechanical ventilation at admission (OR 0.29; 95% CI 0.25, 0.35; p = 0.001), higher age (OR 0.99; 95% CI 0.98, 1.00; p ≤ 0.001), pre-existing asthma (OR 0.84; 95% CI 0.73, 0.98; p = 0.028), and pre-existing kidney disease (OR 0.84; 95% CI 0.71, 0.99; p = 0.036) were negatively associated with the initiation of EM. EM was associated with a higher chance of being discharged home (OR 1.31; 95% CI 1.08, 1.58; p = 0.007) but was not associated with length of stay in ICU (adj. difference 0.91 days; 95% CI − 0.47, 1.37, p = 0.34) and hospital (adj. difference 1.4 days; 95% CI − 0.62, 2.35, p = 0.24) or mortality (OR 0.88; 95% CI 0.7, 1.09, p = 0.24) when adjusted for covariates. Conclusions Our findings demonstrate that a quarter of COVID-19 patients received EM. There was no association found between EM in COVID-19 patients' ICU and hospital length of stay or mortality. However, EM in COVID-19 patients was associated with increased odds of being discharged home rather than to a care facility. Trial registration ClinicalTrials.gov: NCT04836065 (retrospectively registered April 8th 2021)

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Effect of rotational harvesting on the size composition of Cape rock oysters Striostrea margaritacea on the east coast of South Africa

A commercial fishery for the Cape rock oyster Striostrea margaritacea along the north coast of KwaZulu-Natal, South Africa (western Indian Ocean), follows a 4-year rotational cycle, with each harvest year followed by 3 fallow years across four harvest zones. We analysed reported harvesting effort and catch information, and fishery-independent oyster size composition data collected over 18 years (Feb 2003-Feb 2020), to investigate the sustainability of rotational harvesting. Total harvesting effort and catches declined over the study period, but on average, the number of oysters collected per outing increased. Fewer outings in recent years were attributed to incomplete reporting and a progressive loss of access to harvest sites. Generalised linear mixed models were used to estimate trends in oyster mean size in relation to fishing method (divers and intertidal collectors), harvest zone, 4-year rotational cycles, and months spent in a zone. Oyster mean size increased from north to south along the coast. Oysters caught by divers on newly exploited deeper reefs were initially larger than those caught by intertidal collectors. Mean oyster size decreased monthly during 1-year harvest periods but recovered to pre-harvest size over 3 fallow years. The results confirmed that the current rotational harvest strategy is well-suited to oyster biology and is sustainable at the present level of effort. Improved reporting on harvesting effort and catch are required to verify longer-term spatiotemporal trends in this fishery. More effective stakeholder communication is needed to resolve potential user conflict

The colloidal fraction of dissolved organic matter extracted from a forest soil persists microbial decomposition

We have investigated the bacterial decomposition of dissolved organic matter (DOM) extracted from the organic layer of a boreal forest soil and filtered at a pore size of 0.2 mu m. This DOM source has previously been extensively characterized and contains approximately equal amounts by carbon of a colloidal fraction, mainly composed of carbohydrates, and a fraction of molecularly dissolved DOM. Here, extracts were inoculated with soil bacteria and the decomposition of DOM was followed over a period of 2 months, during which it was analyzed with scattering methods and H-1 NMR, and by measuring the concentration of total organic carbon. A comparison was also made with dialyzed extract. Results showed that while the bacteria fully decomposed the molecular fraction within approximately two weeks, the colloidal fraction was stable with no visible decomposition within the 2 months. The results indicate the importance of distinguishing small molecules from colloidal aggregates in decomposition studies, and demonstrate the usefulness of combining scattering methods with 1H NMR for this purpose

Trends in a recreational fishery for mussels in eastern South Africa, based on postal, telephone and online surveys

The intertidal brown mussel Perna perna is targeted by recreational and subsistence fisheries in KwaZulu-Natal, South Africa. The recreational mussel fishery is monitored by off-site postal, telephone and online questionnaire surveys, assessed in this study. Trends in fisher avidity (proportion of permit holders that went fishing), mean number of outings undertaken per quarter year and catch per unit effort (CPUE, as numbers of mussels collected per outing) between 2002 and 2015 were investigated, based on survey responses and available permit sales data. Fisher avidity was greater during summer, for fishers <30 y old, and for residents of coastal districts. Spring low tide windows limited the number of outings to an average of 3–4 per quarter, during which most fishers collected close to the allowed daily bag limit of 30 mussels. The CPUE trend was constrained by the bag limit, and censored regression models were unable to trace the relative abundance of mussels at the spatio-temporal scale investigated. Despite low response rates and changes in survey strategy, trends based on off-site survey data were broadly consistent, providing the only long-term record of the fishery. Survey response rates, costs and logistical constraints were compared, to develop an optimal survey strategy. We suggest a mixed-mode strategy, increased use of online resources, greater representativity, improved outreach and feed-back of survey results. On-site information is required to verify data from off-site surveys