'Proteomineering': has the mine been excavated?

Evaluation of: Di Girolamo F, Boschetti E, Chung MC, Guadagni F, Righetti PG. 'Proteomineering' or not? The debate on biomarker discovery in sera continues. J. Proteomics 74(5), 589-594 (2011). The combinatorial peptide ligand library in association with mass spectrometry can greatly enhance the dynamic range of the analysis of low- and very low-abundance proteins constituting the vast majority of species in any sample. When compared with untreated samples, the increment in detection of low-abundance species appears to be at least fourfold. Recently, the combinatorial peptide ligand library has been challenged; however, it has been clearly demonstrated in the evaluated paper that the protocols for elution of the captured polypeptides make the difference. Therefore, the solid-phase ligand library made of hexapeptides remains a promising and unique tool for biomarker discovery.     

“Biofilmology”: a multidisciplinary review of the study of microbial biofilms

The observation of biofilm formation is not a new phenomenon. The prevalence and significance of biofilm and aggregate formation in various processes have encouraged extensive research in this field for more than 40 years. In this review, we highlight techniques from different disciplines that have been used to successfully describe the extracellular, surface and intracellular elements that are predominant in understanding biofilm formation. To reduce the complexities involved in studying biofilms, researchers in the past have generally taken a parts-based, disciplinary specific approach to understand the different components of biofilms in isolation from one another. Recently, a few studies have looked into combining the different techniques to achieve a more holistic understanding of biofilms, yet this approach is still in its infancy. In order to attain a global understanding of the processes involved in the formation of biofilms and to formulate effective biofilm control strategies, researchers in the next decade should recognise that the study of biofilms, i.e. biofilmology, has evolved into a discipline in its own right and that mutual cooperation between the various disciplines towards a multidisciplinary research vision is vital in this field.     

Organ transplantation--how much of the promise has been realized?

Since the introduction of organ transplantation into medical practice, progress and optimism have been abundant. Improvements in immunosuppressive drugs and ancillary care have led to outstanding short-term (1--3-year) patient and graft survival rates. This success is mitigated by several problems, including poor long-term (>5-year) graft survival rates, the need for continual immunosuppressive medication and the discrepancy between the demand for organs and the supply. Developing methods to induce transplant tolerance, as a means to improve graft outcomes and eliminate the requirement for immunosuppression, and expanding the pool of organs for transplantation are the major challenges of the field.     

Alpine treelines as ecological indicators of global climate change: Who has studied? What has been studied?

As the “front line” of coping with global climate change, the alpine treeline has been widely investigated by ecologists for a long time. In this study, 3180 articles in the Web of Science database from 2000 to 2021 are visualized by using CiteSpace bibliometric software from the perspectives of basic literature features (volume, discipline, journal, author, institution, and country), academic layout, research hotspot, and research frontier to have a deeper understanding of the development laws and hot spots in the alpine treeline. Results show that: (1) The number of papers published in alpine treeline research field is increasing annually, and the professional degree of papers (Sp) is 0.13–0.14, it is lower than that in other fields, implying a tendency of multi-disciplinary integration . (2) The core journals are headed by Arctic and Alpine Research, and J. Julio Camarero is the most prolific author in the field. (3) From the analysis of countries and institutions, the United States and the Chinese Academy of Sciences have leading positions in this research field. (4) Over the last 20 years, alpine treeline researchers have primarily focused on three key words (climate change, environmental characteristics, interspecific interactions, etc.), research sites (National Glacier Parks, the Alps, the Sygera Mountains, etc.), and research species (Norway spruce, European spruce, Abies georgei, etc.). (5) The first phase (2000–2009) focuses on the formation and changes of the alpine treeline in the context of climate change, and the second phase (2010−2021) focuses on the driving mechanisms of climatic factors, physiological change of tree species and grasslands on the treeline ecotones, and the influence of human activities (logging, grazing, etc.) on the alpine treeline. (6) Academic publications in this discipline have a short half-life (3.85 ± 1.70 years), and the aging rate is high and changing quickly. In the coming years, more research on alpine treeline will be devoted to explain the mechanism of tree species limitation in alpine treeline under climate change, influence of treeline changes the carbon and water cycles. There is a press need to explore the driving mechanism for treeline shift from the perspectives of plant physiology and soil carbon and nitrogen cycles.     

The fruit fly scourge: has Zimbabwe been spared?

We conducted a questionnaire survey to assess fruit growers’ knowledge and practices regarding fruit fly pests and a fruit fly trapping inspection to capture any fruit fly species present at 10 points of 23 wards of Marondera district. Most growers were not aware of the pest, although they had reported that fruits were rotting in orchards. Most growers therefore took no action against fruit flies on their farms. The trapping inspection confirmed that three fruit fly species, Bactrocera, Ceratitis, and Dacus, are already present in Zimbabwe in general and in Marondera district in particular and the Bactrocera species dominates. There is a need for government, through extension agents, and other stakeholders to compile and communicate accurate data on the presence and status of the fruit fly in addition to investing in the continuous monitoring of the pest.     

Is the microbial tree of life verificationist?

The field of microbial phylogenetics has questioned the feasibility of using a tree‐like structure to the describe microbial evolution. This debate centres on two main points. First, because microorganisms are able to transfer genes from one to another in zero generations (horizontal gene transfer, or HGT), the use of molecular characters to perform phylogenetic analyses will yield an erroneous topology and HGT clearly makes the evolution of microorganisms non tree‐like. Second, the use of concatenated gene sequences in a total evidence approach to phylogenetic systematics is a verificationist endeavour, the aim of which is to bolster support. However, the goal of the total evidence approach to phylogenetic research is based in the idea of increasing explanatory power over background knowledge through test and corroboration, rather than to bolster support for nodes in a tree. In this context, the testing of phylogenetic data is a falsificationist endeavour that includes the possibility of not rejecting the null hypothesis that there is no tree‐like structure in molecular phylogenetic data. We discuss several tests that aim to test rigorously the hypothesis that a tree of life exists for microorganisms. We also discuss the philosophical ramifications of background knowledge and corroboration in microbial studies that need to be considered when suggesting that HGT confounds the tree of life. © The Willi Hennig Society 2009.     

The mitochondrial pyruvate carrier: has it been unearthed at last?

The mitochondrial pyruvate carrier (MPC) is essential for several major pathways of carbohydrate, fat, and amino acid metabolism, yet its molecular identity has remained elusive. Two recent papers in Science (Herzig et?al., 2012; Bricker et?al., 2012) implicate three newly identified inner mitochondrial membrane proteins as MPC components.     

The new EU REACH regulation has finally been adopted: is this the end of the campaign trail... or just the beginning?

The final EU REACH legislation has recently been adopted. This article considers the progress that has been made toward reducing the numbers of animals likely to be required to fulfil the testing requirements, and also considers the benefits to animal welfare and science that have arisen since the original REACH system proposals were published in 2003. Several positive changes have been made, including: the use of exposure-based testing; the requirement for scientific justification of any proposed animal testing; mandatory data sharing; and the fact that the EU is to take responsibility for the development and validation of alternative methods. While these changes are to be commended, there is still much room for improvement, particularly with respect to the adoption of integrated testing strategies that make maximum use of non-animal approaches to expedite the risk assessment process of existing chemicals, with the use of refined and updated animal tests only as a last resort.     

Unraveling the story of NGF-mediated sensitization of nociceptive sensory neurons: ON or OFF the Trks?

Nerve Growth Factor (NGF) is produced by and affects a number of immune and inflammatory cells. As part of the inflammatory response, NGF directly or indirectly alters the sensitivity of small diameter sensory neurons that communicate noxious information. The question remains as to the receptors and intracellular signaling cascades that mediate this sensitizing action of NGF. Although the general consensus is that NGF produces peripheral sensitization by activating TrkA, recent work suggests that p75 also contributes. Thus, both NGF receptors appear to contribute to peripheral sensitization although whether they act independently or together remains to be determined. Furthermore, controversy exists as to the downstream signaling pathways involved in NGF-induced peripheral sensitization.     

Is proteomics the new genomics?

Mass spectrometry (MS)-based proteomics has become a formidable tool for the investigation of posttranslational modifications to proteins, protein interactions, and organelles. Is it now ready to tackle comprehensive protein expression analysis?