Guidelines for Authors

ScopeCell Research is an international journal publishing peer-reviewed original articles,invited reviews,commentaries,and letters to the editor.Original articles report significantoriginal basic research that describe novel molecular andcellular processes and events and/or address the underlyingbiological mechanisms.Reviews and Commentaries reviewor comment on current progress in any field covered by thejournal.Reviews are generally invited in advance by the edi-tors.Letters to the editor report novel findings that have animmediate major impact on current biological research withonly one figure and less than 10 references.     

Replication Origins: Why Do We Need So Many?

During the G1 phase of the cell cycle, replication origins are prepared to fire, a process that is referred to as origin licensing. It was often pondered what a cell’s fate would be if not all of its replication origins were licensed and subsequently activated during S phase. One obvious prediction was that S phase would simply be prolonged. As it turns out, however, the consequences are much more complex. A short G1 phase enforced by premature entry into S phase, or other events that negatively affect origin licensing, will ultimately compromise the cell’s ability to complete DNA replication before entering mitosis. As a result, the cell becomes genomically unstable when it attempts to repair unreplicated DNA during anaphase. Thus, the density of active replication origins in the chromosomes of eukaryotic cells determines S phase dynamics and chromosome stability during mitosis.     

Characterizing Protease Specificity: How Many Substrates Do We Need?

Calculation of cleavage entropies allows to quantify, map and compare protease substrate specificity by an information entropy based approach. The metric intrinsically depends on the number of experimentally determined substrates (data points). Thus a statistical analysis of its numerical stability is crucial to estimate the systematic error made by estimating specificity based on a limited number of substrates. In this contribution, we show the mathematical basis for estimating the uncertainty in cleavage entropies. Sets of cleavage entropies are calculated using experimental cleavage data and modeled extreme cases. By analyzing the underlying mathematics and applying statistical tools, a linear dependence of the metric in respect to 1/n was found. This allows us to extrapolate the values to an infinite number of samples and to estimate the errors. Analyzing the errors, a minimum number of 30 substrates was found to be necessary to characterize substrate specificity, in terms of amino acid variability, for a protease (S4-S4’) with an uncertainty of 5 percent. Therefore, we encourage experimental researchers in the protease field to record specificity profiles of novel proteases aiming to identify at least 30 peptide substrates of maximum sequence diversity. We expect a full characterization of protease specificity helpful to rationalize biological functions of proteases and to assist rational drug design.     

Vaccines against Tuberculosis: Where Are We and Where Do We Need to Go?

In this review we discuss recent progress in the development, testing, and clinical evaluation of new vaccines against tuberculosis (TB). Over the last 20 years, tremendous progress has been made in TB vaccine research and development: from a pipeline virtually empty of new TB candidate vaccines in the early 1990s, to an era in which a dozen novel TB vaccine candidates have been and are being evaluated in human clinical trials. In addition, innovative approaches are being pursued to further improve existing vaccines, as well as discover new ones. Thus, there is good reason for optimism in the field of TB vaccines that it will be possible to develop better vaccines than BCG, which is still the only vaccine available against TB.     

Evaluating Tropical Biodiversity: Do We Need a More Refined Approach?

The exceptional biodiversity of tropical forests inspired the earliest ecologists such as H. W. Bates. Today we still strive to quantify and understand this diversity. Drawing on our own experience of Mamirauá reserve in Amazonas, which is located in an area that Bates explored, we argue that the emphasis of research in tropical ecosystems should shift away from species richness as an end in itself, and focus instead on other fundamental, but more tractable, questions that will increase our ecological understanding of these systems, support conservation management, and appeal to policy makers and society in general.     

Refilling of Embolized Vessels in Young Stems of Laurel. Do We Need a New Paradigm?

Recovery of hydraulic conductivity after the induction of embolisms was studied in woody stems of laurel (Laurus nobilis). Previous experiments confirming the recovery of hydraulic conductivity when xylem pressure potential was less than −1 MPa were repeated, and new experiments were done to investigate the changes in solute composition in xylem vessels during refilling. Xylem sap collected by perfusion of excised stem segments showed elevated levels of several ions during refilling. Stem segments were frozen in liquid N₂ to view refilling vessels using cryoscanning electron microscopy. Vessels could be found in all three states of presumed refilling: (a) mostly water with a little air, (b) mostly air with a little water, or (c) water droplets extruding from vessel pits adjacent to living cells. Radiographic probe microanalysis of refilling vessels revealed nondetectable levels of dissolved solutes. Results are discussed in terms of proposed mechanisms of refilling in vessels while surrounding vessels were at a xylem pressure potential of less than −1 MPa. We have concluded that none of the existing paradigms explains the results.     

A Comparison of Step-Detection Methods: How Well Can You Do?

Many biological machines function in discrete steps, and detection of such steps can provide insight into the machines’ dynamics. It is therefore crucial to develop an automated method to detect steps, and determine how its success is impaired by the significant noise usually present. A number of step detection methods have been used in previous studies, but their robustness and relative success rate have not been evaluated. Here, we compare the performance of four step detection methods on artificial benchmark data (simulating different data acquisition and stepping rates, as well as varying amounts of Gaussian noise). For each of the methods we investigate how to optimize performance both via parameter selection and via prefiltering of the data. While our analysis reveals that many of the tested methods have similar performance when optimized, we find that the method based on a chi-squared optimization procedure is simplest to optimize, and has excellent temporal resolution. Finally, we apply these step detection methods to the question of observed step sizes for cargoes moved by multiple kinesin motors in vitro. We conclude there is strong evidence for sub-8-nm steps of the cargo’s center of mass in our multiple motor records.     

Vitiligo: Where Do We Stand?

Vitiligo is a puzzling disorder characterized by a disappearance of epidermal and/or follicular melanocytes by unknown mechanisms. This very common disorder involving 1–4% of the world population is thus of great importance for the practicing dermatologist. The cellular and molecular mechanisms leading to the destruction of melanocytes in this disorder have not yet been elucidated, making it of major interest for the cell biologist involved in melanocyte research. Recent advances in this field, due largely to the availability of techniques for culturing normal human melanocytes, opened new perspectives in the understanding of vitiligo. Although vitiligo has long been considered a disorder confined to the skin, there is now good evidence that it also involves the extracutaneous compartment of the “melanocyte organ.” It is also clear that vitiligo is not only a melanocyte disorder, but that it also involves cells, such as keratinocytes and Langerhans cells, found in the epidermis and follicular epithelium. The three prevailing theories of the pathogenesis of vitiligo are the immune hypothesis, the neural hypothesis, and the self-destruct hypothesis. New hypotheses suggest that vitiligo may be due to (1) a deficiency in an unidentified melanocyte growth factor, (2) an intrinsic defect of the structure and function of the rough endoplasmic reticulum in vitiligo melanocytes, (3) abnormalities in a putative melatonin receptor on melanocytes and (4) a breakdown in free radical defense in the epidermis. None of these hypotheses has been demonstrated, and according to the available data, it is likely that the loss of epidermal and follicular melanocytes in vitiligo may be the result of several different pathogenetic mechanisms.     

What Affects Authors’ and Editors’ Use of Reporting Guidelines? Findings from an Online Survey and Qualitative Interviews

Objectives

To identify and understand, through data from multiple sources, some of the factors that affect authors’ and editors’ decisions to use reporting guidelines in the publication of health research.

Design

Mixed methods study comprising an online survey and semi-structured interviews with a sample of authors (online survey: n = 56; response rate = 32%; semi-structured interviews: n = 5) and journal editors (online survey: n = 43; response rate = 27%; semi-structured interviews: n = 6) involved in publishing health and medical research. Participants were recruited from an earlier study examining the effectiveness of the TREND reporting guideline.

Results

Four types of factors interacted to affect authors’ and editors’ likelihood of reporting guideline use; individual (e.g. having multiple reasons for use of reporting guidelines); the professional culture in which people work; environmental (e.g. policies of journals); and, practical (e.g. having time to use reporting guidelines). Having multiple reasons for using reporting guidelines was a particularly salient factor in facilitating reporting guidelines use for both groups of participants.

Conclusions

Improving the completeness and consistency of reporting of research studies is critical to the integrity and synthesis of health research. The use of reporting guidelines offers one potentially efficient and effective means for achieving this, but decisions to use (or not use) reporting guidelines take many factors into account. These findings could be used to inform future studies that might, for example, test the factors that we have identified within a wider theoretical framework for understanding changes in professional practices. The use of reporting guidelines by senior professionals appears to shape the expectations of what constitutes best practice and can be assimilated into the culture of a field or discipline. Without evidence of effectiveness of reporting guidelines, and sustained, multifaceted efforts to improve reporting, little progress seems likely to be made.