HIV versus the Terminator: Drug resistance of HIV reverse transcriptase with mutations at the connection subdomain

Abstract only availableAntiretroviral drug therapy can prolong the life of an HIV-infected individual, but this treatment also promotes drug-resistance mutations. The replicative enzyme of HIV, reverse transcriptase (RT), is a primary target for anti-HIV drug therapy because it is responsible for converting the single stranded RNA genome of HIV into double stranded DNA for integration into the host genome. Many current anti-HIV drugs belong to two classes of inhibitors that target RT: nucleoside reverse transcriptase inhibitors (NRTIs) incorporate into and chain-terminate nascent transcription products of RT, whereas non-nucleoside reverse transcriptase inhibitors (NNRTIs) alter enzyme-nucleic acid interactions, thereby affecting the efficiency of DNA polymerization. Here, we focus on NRTI resistance mutations that are located at the connection subdomain of the enzyme in the presence and absence of thymidine analog associated mutations (TAMs). TAMs cause resistance to the commonly prescribed chain terminator 3'-azido-3'-deoxythymidine (AZT) through excision of the incorporated AZT-monophosphate. Mutations in the connection domain, such as N348I, confer resistance to NRTIs and NNRTIs and augment AZT resistance when present in combination with TAMs. Although the underlying mechanism of N348I resistance remains elusive, it has been suggested that the mutation compromises ribonuclease (RNase) H activity, which is responsible for cleaving the viral genomic RNA of the RNA/DNA heterodimeric intermediate. Changes in RNase H cleavage affect the availability of AZT-terminated primers to be excised, thereby increasing the unblocking of template/primer and NRTI resistance. Our investigation attempts to determine if AZT-resistance mutations affect resistance to other commonly prescribed NRTIs, as well as to competitive substrate inhibitors currently in development, through changes in template/primer processing. In addition, we are examining the effects of NRTI and NNRTI cocktails on the RNase H activity of RT possessing connection domain mutations. Our findings should provide insight for screening novel inhibitors for their efficacy against emergent strains of drug-resistant HIV.Life Sciences Undergraduate Research Opportunity Progra

Uncertainties in steric sea level change estimation during the satellite altimeter era: concepts and practices

This article presents a review of current practice in estimating steric sea level change, focussed on the treatment of uncertainty. Steric sea level change is the contribution to the change in sea level arising from the dependence of density on temperature and salinity. It is a significant component of sea level rise and a reflection of changing ocean heat content. However tracking these steric changes remains still a significant challenge for the scientific community. We review the importance of understanding the uncertainty in estimates of steric sea level change. Relevant concepts of uncertainty are discussed and illustrated with the example of observational uncertainty propagation from a single profile of temperature and salinity measurements to steric height. We summarise and discuss the recent literature on methodologies and techniques used to estimate steric sea level in the context of the treatment of uncertainty. Our conclusions are that progress in quantifying steric sea level uncertainty will benefit from: greater clarity and transparency in published discussions of uncertainty, including exploitation of international standards for quantifying and expressing uncertainty in measurement; and the development of community ‘recipes’ for quantifying the error covariances in observations and from sparse sampling, and for estimating and propagating uncertainty across spatio-temporal scales

Scientific Case for Avoiding Dangerous Climate Change to Protect Young People and Nature

28 pages, 6 figures; version submitted to Proceedings of the National Academy of SciencesGlobal warming due to human-made gases, mainly CO2, is already 0.8{\deg}C and deleterious climate impacts are growing worldwide. More warming is 'in the pipeline' because Earth is out of energy balance, with absorbed solar energy exceeding planetary heat radiation. Maintaining a climate that resembles the Holocene, the world of stable shorelines in which civilization developed, requires rapidly reducing fossil fuel CO2 emissions. Such a scenario is economically sensible and has multiple benefits for humanity and other species. Yet fossil fuel extraction is expanding, including highly carbon-intensive sources that can push the climate system beyond tipping points such that amplifying feedbacks drive further climate change that is practically out of humanity's control. This situation raises profound moral issues as young people, future generations, and nature, with no possibility of protecting their future well-being, will bear the principal consequences of actions and inactions of today's adults

Scientific case for avoiding dangerous climate change to protect young people and nature

28 pages, 6 figures; version submitted to Proceedings of the National Academy of SciencesPeer reviewe

Associations of statins and diabetes with diagnosis of ulcerated cutaneous melanoma

Ulcerated primary melanomas are associated with an inflammatory tumor microenvironment. We hypothesized that systemic proinflammatory states and anti-inflammatory medications are also associated with a diagnosis of ulcerated melanoma. In a cross-sectional study of 787 patients with newly diagnosed clinical stage IB or II melanoma, we estimated odds ratios for the association of proinflammatory factors (high body mass index, diabetes, cardiovascular disease, hypertension, and smoking) or the use of anti-inflammatory medications (statins, aspirin, corticosteroids, and nonsteroidal anti-inflammatory drugs), with ulcerated primary melanoma using regression models and subgroup analyses to control for melanoma thickness and mitotic rate. On the basis of information from 194 patients with ulcerated and 593 patients with nonulcerated primary melanomas, regular statin users had lower likelihood of a diagnosis of ulcerated primary melanoma (odds ratio 0.67, 95% confidence interval 0.45-0.99), and this association remained after adjusting for age, sex, thickness, and mitosis. When analysis was limited to melanomas that wer

A review of global ocean temperature observations: Implications for ocean heat content estimates and climate change

The evolution of ocean temperature measurement systems is presented with a focus on the development and accuracy of two critical devices in use today (expendable bathythermographs and conductivity‐temperature‐depth instruments used on Argo floats). A detailed discussion of the accuracy of these devices and a projection of the future of ocean temperature measurements are provided. The accuracy of ocean temperature measurements is discussed in detail in the context of ocean heat content, Earth's energy imbalance, and thermosteric sea level rise. Up‐to‐date estimates are provided for these three important quantities. The total energy imbalance at the top of atmosphere is best assessed by taking an inventory of changes in energy storage. The main storage is in the ocean, the latest values of which are presented. Furthermore, despite differences in measurement methods and analysis techniques, multiple studies show that there has been a multidecadal increase in the heat content of both the upper and deep ocean regions, which reflects the impact of anthropogenic warming. With respect to sea level rise, mutually reinforcing information from tide gauges and radar altimetry shows that presently, sea level is rising at approximately 3 mm yr−1 with contributions from both thermal expansion and mass accumulation from ice melt. The latest data for thermal expansion sea level rise are included here and analyzed

Heat stored in the Earth system 1960–2020: where does the energy go?

The Earth climate system is out of energy balance, and heat has accumulated continuously over the past decades, warming the ocean, the land, the cryosphere, and the atmosphere. According to the Sixth Assessment Report by Working Group I of the Intergovernmental Panel on Climate Change, this planetary warming over multiple decades is human-driven and results in unprecedented and committed changes to the Earth system, with adverse impacts for ecosystems and human systems. The Earth heat inventory provides a measure of the Earth energy imbalance (EEI) and allows for quantifying how much heat has accumulated in the Earth system, as well as where the heat is stored. Here we show that the Earth system has continued to accumulate heat, with 381±61 ZJ accumulated from 1971 to 2020. This is equivalent to a heating rate (i.e., the EEI) of 0.48±0.1 W m−2. The majority, about 89 %, of this heat is stored in the ocean, followed by about 6 % on land, 1 % in the atmosphere, and about 4 % available for melting the cryosphere. Over the most recent period (2006–2020), the EEI amounts to 0.76±0.2 W m−2. The Earth energy imbalance is the most fundamental global climate indicator that the scientific community and the public can use as the measure of how well the world is doing in the task of bringing anthropogenic climate change under control. Moreover, this indicator is highly complementary to other established ones like global mean surface temperature as it represents a robust measure of the rate of climate change and its future commitment. We call for an implementation of the Earth energy imbalance into the Paris Agreement's Global Stocktake based on best available science. The Earth heat inventory in this study, updated from von Schuckmann et al. (2020), is underpinned by worldwide multidisciplinary collaboration and demonstrates the critical importance of concerted international efforts for climate change monitoring and community-based recommendations and we also call for urgently needed actions for enabling continuity, archiving, rescuing, and calibrating efforts to assure improved and long-term monitoring capacity of the global climate observing system. The data for the Earth heat inventory are publicly available, and more details are provided in Table 4

Measuring global ocean heat content to estimate the earth energy imbalance

The energy radiated by the Earth toward space does not compensate the incoming radiation from the Sun leading to a small positive energy imbalance at the top of the atmosphere (0.4–1 Wm–2). This imbalance is coined Earth’s Energy Imbalance (EEI). It is mostly caused by anthropogenic greenhouse gas emissions and is driving the current warming of the planet. Precise monitoring of EEI is critical to assess the current status of climate change and the future evolution of climate. But the monitoring of EEI is challenging as EEI is two orders of magnitude smaller than the radiation fluxes in and out of the Earth system. Over 93% of the excess energy that is gained by the Earth in response to the positive EEI accumulates into the ocean in the form of heat. This accumulation of heat can be tracked with the ocean observing system such that today, the monitoring of Ocean Heat Content (OHC) and its long-term change provide the most efficient approach to estimate EEI. In this community paper we review the current four state-of-the-art methods to estimate global OHC changes and evaluate their relevance to derive EEI estimates on different time scales. These four methods make use of: (1) direct observations of in situ temperature; (2) satellite-based measurements of the ocean surface net heat fluxes; (3) satellite-based estimates of the thermal expansion of the ocean and (4) ocean reanalyses that assimilate observations from both satellite and in situ instruments. For each method we review the potential and the uncertainty of the method to estimate global OHC changes. We also analyze gaps in the current capability of each method and identify ways of progress for the future to fulfill the requirements of EEI monitoring. Achieving the observation of EEI with sufficient accuracy will depend on merging the remote sensing techniques with in situ measurements of key variables as an integral part of the Ocean Observing System

Heat stored in the Earth system:where does the energy go?

Human-induced atmospheric composition changes cause a radiative imbalance at the top of the atmosphere which is driving global warming. This Earth energy imbalance (EEI) is the most critical number defining the prospects for continued global warming and climate change. Understanding the heat gain of the Earth system – and particularly how much and where the heat is distributed – is fundamental to understanding how this affects warming ocean, atmosphere and land; rising surface temperature; sea level; and loss of grounded and floating ice, which are fundamental concerns for society. This study is a Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory and presents an updated assessment of ocean warming estimates as well as new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period 1960–2018. The study obtains a consistent long-term Earth system heat gain over the period 1971–2018, with a total heat gain of 358±37 ZJ, which is equivalent to a global heating rate of 0.47±0.1 W m−2. Over the period 1971–2018 (2010–2018), the majority of heat gain is reported for the global ocean with 89 % (90 %), with 52 % for both periods in the upper 700 m depth, 28 % (30 %) for the 700–2000 m depth layer and 9 % (8 %) below 2000 m depth. Heat gain over land amounts to 6 % (5 %) over these periods, 4 % (3 %) is available for the melting of grounded and floating ice, and 1 % (2 %) is available for atmospheric warming. Our results also show that EEI is not only continuing, but also increasing: the EEI amounts to 0.87±0.12 W m−2 during 2010–2018. Stabilization of climate, the goal of the universally agreed United Nations Framework Convention on Climate Change (UNFCCC) in 1992 and the Paris Agreement in 2015, requires that EEI be reduced to approximately zero to achieve Earth's system quasi-equilibrium. The amount of CO2 in the atmosphere would need to be reduced from 410 to 353 ppm to increase heat radiation to space by 0.87 W m−2, bringing Earth back towards energy balance. This simple number, EEI, is the most fundamental metric that the scientific community and public must be aware of as the measure of how well the world is doing in the task of bringing climate change under control, and we call for an implementation of the EEI into the global stocktake based on best available science. Continued quantification and reduced uncertainties in the Earth heat inventory can be best achieved through the maintenance of the current global climate observing system, its extension into areas of gaps in the sampling, and the establishment of an international framework for concerted multidisciplinary research of the Earth heat inventory as presented in this study. This Earth heat inventory is published at the German Climate Computing Centre (DKRZ, https://www.dkrz.de/, last access: 7 August 2020) under the DOI https://doi.org/10.26050/WDCC/GCOS_EHI_EXP_v2 (von Schuckmann et al., 2020)