Phylogenetic uncertainty revisited: Implications for ecological analyses

Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify the effects of phylogenetic uncertainty in ecological analyses. We propose here a novel analytical strategy to maximize the use of incomplete phylogenetic information, while simultaneously accounting for several sources of phylogenetic uncertainty that may distort statistical inferences about evolutionary processes. We illustrate the approach using a clade‐wide analysis of the hummingbirds, evaluating how different sources of uncertainty affect several phylogenetic comparative analyses of trait evolution and biogeographic patterns. Although no statistical approximation can fully substitute for a complete and robust phylogeny, the method we describe and illustrate enables researchers to broaden the number of clades for which studies informed by evolutionary relationships are possible, while allowing the estimation and control of statistical error that arises from phylogenetic uncertainty. Software tools to carry out the necessary computations are offered.     

Working through polytomies: Auklets revisited

Polytomies, or phylogenetic “bushes”, are the result of a series of internodes occurring in a short period of evolutionary time (which can result in data that do not contain enough information), or data that have too much homoplasy to resolve a bifurcating branching pattern. In this study we used the Aethia auklet polytomy to explore the effectiveness of different methods for resolving polytomies: mitochondrial DNA gene choice, number of individuals per species sampled, model of molecular evolution, and AFLP loci. We recovered a fully-resolved phylogeny using NADH dehydrogenase subunit 2 (ND2) sequence data under two different Bayesian models. We were able to corroborate this tree under one model with an expanded mtDNA dataset. Effectiveness of additional intraspecific sampling varied with node, and fully 20% of the subsampled datasets failed to return a congruent phylogeny when we sampled only one or two individuals per species. We did not recover a resolved phylogeny using AFLP data. Conflict in the AFLP dataset showed that nearly all possible relationships were supported at low levels of confidence, suggesting that either AFLPs are not useful at the genetic depth of the Aethia auklet radiation (7–9% divergent in the mtDNA ND2 gene), perhaps resulting in too much homoplasy, or that the Aethia auklets have experienced incomplete lineage sorting at many nuclear loci.     

Diagnostic criteria for diabetes revisited: making use of combined criteria

Background  

Existing cut-offs for fasting plasma glucose (FPG) and post-load glucose (2hPG) criteria are not equivalent in the diagnosis of diabetes and glucose intolerance. Adjusting cut-offs of single measurements have not helped so we undertook this project to see if they could be complementary.     

假说检验和科学方法

本文的意图是让研究者审视研究方法,并在研究设计中充分使用假说检验,并在选择模式物种时充分理解其自然史.我们的总前提是,按照"强推论"(指假定拒绝某一假说而不是支持某一偏爱假说)的逻辑,科学能够进展得更快、更可观、更有确定性.我们强调并提供了符合逻辑的一系列步骤,即确定科学问题或确定具有未知生物学意义的问题;列出所有可靠的、能解释所观察现象的假说,每个假说列出其可检验的、可证明其无根据的预测;然后是符合预测检验的实验或研究设计.我们也强调,模式物种对于解决科学的理论问题以及得出推论是很重要的.本文所展示的不是新思想,只是提醒研究者要注意遵循的基本研究途径.     

Lambda excision revisited: testing a model for synapsis of prophage ends

Excision of lambda prophage was reexamined to test a model for prophage end synapsis. The model proposes that, during in situ prophage replication, following induction, the diverging replication forks are held together. Consequently, prophage DNA is spooled through the replication machinery, drawing the prophage ends together and facilitating synapsis. The model predicts that excision will be slowed if in situ lambda replication is inhibited, and the predicted low rate of excision of a nonreplicating prophage was observed after thermoinduction. However, excision was rapid if additional Int protein was supplied or if the temperature was reduced after induction, showing that (i) Int is partially thermosensitive for excision at 42 degrees C and (ii) in situ replication is not required for rapid excision, a finding that is inconsistent with the model.     

Manipulating flux through plant metabolic pathways

The past two years have seen a marked increase in patent applications for novel methods of altering the level and spectrum of commercially important products in plants. Results from these studies have proven surprising, showing that in many cases those enzymes traditionally thought of as flux-controlling have no impact on product formation when they are directly altered by genetic manipulation. In many cases, successful induction of increased flux throughout an entire pathway has been achieved by targeting one of the terminal enzymes in the pathway.     

Diagnostic testing holds the key to NTD elimination

“Fit-for-purpose” diagnostic tests have emerged as a prerequisite to achieving global targets for the prevention, control, elimination, and eradication of neglected tropical diseases (NTDs), as highlighted by the World Health Organization’s (WHO) new roadmap. There is an urgent need for the development of new tools for those diseases for which no diagnostics currently exist and for improvement of existing diagnostics for the remaining diseases. Yet, efforts to achieve this, and other crosscutting ambitions, are fragmented, and the burden of these 20 debilitating diseases immense. Compounded by the Coronavirus Disease 2019 (COVID-19) pandemic, programmatic interruptions, systemic weaknesses, limited investment, and poor commercial viability undermine global efforts—with a lack of coordination between partners, leading to the duplication and potential waste of scant resources. Recognizing the pivotal role of diagnostic testing and the ambition of WHO, to move forward, we must create an ecosystem that prioritizes country-level action, collaboration, creativity, and commitment to new levels of visibility. Only then can we start to accelerate progress and make new gains that move the world closer to the end of NTDs.

Ahead of the second-ever World Neglected Tropical Disease (NTD) Day in January 2021, and amid the global Coronavirus Disease 2019 (COVID-19) crisis, the World Health Organization (WHO) launched a new roadmap for the prevention, control, elimination, and eradication of NTDs—a group of 20 diseases affecting more than one billion people worldwide [1]. Diagnostic testing is central to safeguarding decades of progress in NTDs and must be strategically leveraged to reach the goals laid out in the new NTD roadmap.Stepping back, we recognize the massive progress that has been made to combat NTDs. Today, 500 million fewer people need treatment for these debilitating diseases than in 2010, and 40 countries or areas have eliminated at least one of the 20 [1]. Yet, despite these gains, NTDs continue to impose a devastating human, social, and economic toll on the world’s poorest and most vulnerable communities [2–6]. COVID-19 is compounding the situation by wreaking havoc on health systems, which impacts progress on NTDs: this includes interruptions to mass treatment campaigns for diseases controlled through preventive chemotherapy (PCT) or individual case management interventions, as well as rerouting the already sparse available funding and resources [7].Diagnostic testing has been central to the COVID-19 response even with the introduction of vaccines. The rapid ramp up of research and development (R&D), the scaling up of low-cost and decentralized testing, and country-led approaches to tailored testing strategies for COVID-19, as well as lessons learned, can also provide new thinking around testing for NTDs. The new NTD roadmap offers a series of multisectoral actions and intensified, cross-cutting approaches to get us back on track—with diagnostics central to unlocking and accelerating this progress [1].However, the NTD roadmap shows that, of all 20 diseases or disease groups, just 2 (yaws and snakebite envenoming) are supported by adequate and accessible diagnostic tools. Six have no diagnostic tests available at all, with tools for each of the remaining conditions in urgent need of adaptation, modification, and/or improved accessibility (likely a more cost-effective option than the development of new diagnostics for these NTDs) [1]. This has to change. NTDs cannot continue to be neglected in favor of other competing priorities, or we risk losing the progress made to date.Until the COVID-19 pandemic thrust testing into the spotlight, diagnostics have been a “silent partner” in healthcare, receiving little by way of international attention and funding, specific country strategies, and dedicated budget lines. NTDs are no exception. Just 5% of the (limited) funding made available to NTDs has been invested in new diagnostics, compared with 44% and 39% on basic research and medicines and vaccines, respectively [1]. For most NTDs, diagnostics are a market failure situation, and as such, are not commercially viable enough to attract private investment. Consequently, very few diagnostic developers engage in this area—contrary, for example, to COVID-19, where developers are in the hundreds. Furthermore, as some diseases approach the last mile of elimination, falling infection rates precipitate the need for increasingly sensitive tests [1]. But progress in R&D is slow and fragmented, with a lack of engagement and coordination between governments, industry, donors, and development actors, leading to the duplication—and potential waste—of scant resources. While serial testing using multiple diagnostic tools or techniques can compensate for low sensitivity [8], such approaches are associated with increased costs of testing, sample collection, and transportation.Closing the diagnostic gap then, is a prerequisite to achieving the global ambition for NTDs, with the new NTD roadmap giving a blueprint for action. It is for this reason that we call on governments, industry, donors, and development actors to

• Prioritize country-level diagnostic action: As we enter a new era in NTD management and control, we need to shift from traditional, donor-led models to country-driven initiatives. Government ministries must engage with, and advocate on behalf of, their poorest and most vulnerable populations so that no one is left behind. Political frameworks should prioritize diagnostics for NTDs in line with local disease burdens, and as part of fully funded, national health action plans that include a commitment to seeing the process through. Capacity building for diagnostics is also essential at country, sub-regional, and regional levels, including the establishment of laboratory networks, so that testing can be implemented in field settings.
• Collaborate and create: There is never going to be a one-size-fits-all for NTD diagnostics. If targets are to be achieved, we need global frameworks that enable industry, manufacturers, and pharmaceutical companies to engage in the whole process, from R&D to supply chain logistics. Companies need to share knowledge, learnings, and innovation across multiple diseases. This will mean breaking silos and finding new ways to harness the power of existing products, technologies, and infrastructures. Further, it will mean creating economies of scale through regional manufacturing hubs and finding new, cross-cutting approaches to drive systemic change. To obtain the maximum access to technology and relevant intellectual property rights for NTD diagnostics, it is important to ensure that such rights are broadly available (non-exclusively) in NTD-endemic countries and are affordable (e.g., zero royalty rights).
• Commit to new levels of visibility: The resources needed to realize that this ambition is limited, with a lack of visibility around the diagnostic landscape undermining progress in NTD management and control. Creating an ecosystem with visibility, transparency, and integration at its core will help streamline programmatic action, reduce the risk of duplication, and leverage the full potential from this limited pool. To do this, industry, donors, and other development actors must provide the information needed to map both funding and product landscapes. Using this information to create a virtual product pipeline will bring an unprecedented level of transparency to diagnostic developments—harmonizing multisectoral efforts and creating a robust information platform from which new collaborations, synergies, and innovation can grow. Developing an online open-access diagnostic pipeline for WHO NTD roadmap priority pathogens would serve multiple purposes: (i) drive advocacy to address critical product and funding gaps; and (ii) reduce the likelihood of duplication of efforts. Together, this would strengthen partnerships across all stakeholders, from donors to industry partners, to accelerate development, evaluation, and adoption of diagnostic solutions for NTDs. The newly established NTD Diagnostic Technical Advisory Group (DTAG) to WHO NTD department has already identified the priority diagnostic needs for NTD programs not only in terms of developing new tools, but also the accessibility of existing tools [9]. Several sub-groups that focus more narrowly on single diseases or specific topics (i.e., skin NTDs or cross-cutting) have been established and have been tasked to develop tool and biomarker agnostic target product profiles (TPPs), which are now available (for the most part) on WHO website for use by any diagnostic manufacturer to support development of their specific technology. Alignment with these diagnostic priorities by all stakeholders is strongly recommended to facilitate attainment of WHO 2030 NTD roadmap goals.

• Establish NTD biobanks: Biobanks are required for the clinical evaluation and validation of new diagnostic tests. Establishing local biobanks would support a country-driven approach as well as allowing for head-to-head comparisons between tests and assessments of cross-reactivity across different NTDs.
• Invest in existing diagnostics: The development of new diagnostics is a complex process, and the time from development to implementation can be lengthy. Training laboratory staff in the use of existing diagnostics and the establishment of robust quality control systems are effective approaches to achieving shorter-term improvements.

There is a long road ahead, but the past 10 years have shown us what can be achieved when governments, industry, donors, and development actors are bound by a shared, global goal. As we look forward to the next decade, we must prioritize country-level action, collaboration, creativity, and commitment to new levels of visibility, if we are to finally end the neglect of NTDs.     

The multiple functions of the thiol-based electron flow pathways of Escherichia coli: Eternal concepts revisited

Electron flow via thiols is a theme with many variations in all kingdoms of life. The favourable physichochemical properties of the redox active couple of two cysteines placed in the optimised environment of the thioredoxin fold allow for two electron transfers in between top biological reductants and ultimate oxidants. The reduction of ribonucleotide reductases by thioredoxin and thioredoxin reductase of Escherichia coli (E. coli) was one of the first pathways to be elucidated. Diverse functions such as protein folding in the periplasm, maturation of respiratory enzymes, detoxification of hydrogen peroxide and prevention of oxidative damage may be based on two electron transfers via thiols. A growing field is the relation of thiol reducing pathways and the interaction of E. coli with different organisms. This concept combined with the sequencing of the genomes of different bacteria may allow for the identification of fine differences in the systems employing thiols for electron flow between pathogens and their corresponding mammalian hosts. The emerging possibility is the development of novel antibiotics.     

Water transport through plant tissue: the apoplasm and symplasm pathways

A detailed quantitative analysis of water flow through the apoplasm and symplasm of plant tissue is presented. The analysis results in two coupled diffusion equations which describe water transport in the two pathways. Various parameters entering the analysis identify the physical properties of the tissue which control the transport process as the resistance to water flow per cell in the two parallel pathways, the resistance per cell between pathways, and the water capacity per cell in the two pathways. Values for the several resistances and water capacities are estimated from available data, and a model problem is solved wherein a sheet of tissue at an initial water potential of — δ bars is immersed in a container of water. The resulting solutions show that depending on the values assigned to the controlling parameters, local water potential equilibrium between each cell and its cell wall may or may not obtain. In the special case of local equilibrium (water potential in the symplasm and apoplasm pathways essentially equal), the transport process can be described by a single diffusion equation which is derived along with an expression for the tissue diffusivity. It is concluded that the weakest link in the analysis is the estimated value for the permeability of the plasmodesma membrane, and that a logical extension of the theory would be to include the effects of a diffusable solute.     

Drosophila wing modularity revisited through a quantitative genetic approach

To predict the response of complex morphological structures to selection it is necessary to know how the covariation among its different parts is organized. Two key features of covariation are modularity and integration. The Drosophila wing is currently considered a fully integrated structure. Here, we study the patterns of integration of the Drosophila wing and test the hypothesis of the wing being divided into two modules along the proximo‐distal axis, as suggested by developmental, biomechanical, and evolutionary evidence. To achieve these goals we perform a multilevel analysis of covariation combining the techniques of geometric morphometrics and quantitative genetics. Our results indicate that the Drosophila wing is indeed organized into two main modules, the wing base and the wing blade. The patterns of integration and modularity were highly concordant at the phenotypic, genetic, environmental, and developmental levels. Besides, we found that modularity at the developmental level was considerably higher than modularity at other levels, suggesting that in the Drosophila wing direct developmental interactions are major contributors to total phenotypic shape variation. We propose that the precise time at which covariance‐generating developmental processes occur and/or the magnitude of variation that they produce favor proximo‐distal, rather than anterior‐posterior, modularity in the Drosophila wing.