Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective.

Intense X-rays available at powerful synchrotron beamlines provide macromolecular crystallographers with an incomparable tool for investigating biological phenomena on an atomic scale. The resulting insights into the mechanism's underlying biological processes have played an essential role and shaped biomedical sciences during the last 30 years, considered the "golden age" of structural biology. In this review, we analyze selected aspects of the impact of synchrotron radiation on structural biology. Synchrotron beamlines have been used to determine over 70% of all macromolecular structures deposited into the Protein Data Bank (PDB). These structures were deposited by over 13,000 different research groups. Interestingly, despite the impressive advances in synchrotron technologies, the median resolution of macromolecular structures determined using synchrotrons has remained constant throughout the last 30 years, at about 2 Å. Similarly, the median times from the data collection to the deposition and release have not changed significantly. We describe challenges to reproducibility related to recording all relevant data and metadata during the synchrotron experiments, including diffraction images. Finally, we discuss some of the recent opinions suggesting a diminishing importance of X-ray crystallography due to impressive advances in Cryo-EM and theoretical modeling. We believe that synchrotrons of the future will increasingly evolve towards a life science center model, where X-ray crystallography, Cryo-EM, and other experimental and computational resources and knowledge are encompassed within a versatile research facility. The recent response of crystallographers to the COVID-19 pandemic suggests that X-ray crystallography conducted at synchrotron beamlines will continue to play an essential role in structural biology and drug discovery for years to come.

80 Years of the Medicine and Tropical Hygiene Center in Gdynia (1937-2017): The Pioneer Pre-War Years 1937-1939.

The present Interdepartmental Institute of Maritime and Tropical Medicine in Gdynia of the Medical University of Gdansk was formally established in 1939 by the Order of June 5, 1939, of the Minister of Social Welfare, Marian Zyndram-Koscialkowski. However, the Branch of the National Institute of Hygiene in Gdynia was founded 2 years earlier, in 1937 (the first head was Dr. Med. Jerzy Jakóbkiewicz [1892-1953]), and its fruitful activity was ennobled 2 years later by increasing its rank and adding the name "Marine and Tropical Hygiene Institute". These facts are very little known, and therefore worth presenting in the jubilee years of the 80th anniversary of the institution.

Sulfurous Balneotherapy in Poland: A Vignette on History and Contemporary Use.

Balneotherapy experiences a sharp increase in popularity during recent years. The present paper gives a perspective on the therapeutic use of mineral baths in the town of Solec-Zdroj in southeastern Poland, an old time spa endowed with rich natural sulfurous water resources. Historical aspects of the formation and development of the spa are presented, along with the contemporary insights into the plausible mechanisms and benefits of sulfide treatment, not only in otherwise hardly treatable chronic skin disorders but also in a variety of disease processes in organ systems. Sulfurous balneotherapy is not without potential risks, particularly for the skin, a tissue it is considered the most viable treatment for. The healing effect of sulfide waters does not increase in proportion to the sulfur content. As in every stimulus-based treatment, the stimulant strength should not go beyond the favorable hormetic boundaries of safety. Although the exact bioproperties of a high content of hydrogen sulfide in natural mineral springs are yet to be fully unraveled and understood in the context of healing capability, sulfide bath treatment is capable of growing and developing. It remains a cost-effective alternative to pharmaceutical products in a variety of disorders.

The Lethal Spanish Influenza Pandemic in Poland.

The Spanish influenza pandemic in the years 1918-1920 was the largest and most tragic pandemic of infectious disease in human history. Deciphering the structure of the virus (including the determination of complete genome sequence) of this pandemic and the phylogenetic analysis and explanation of its virulence became possible thanks to molecular genetic analysis of the virus isolated from the fixed and frozen lung tissue of influenza victims who died in 1918 and were buried frozen in Alaska and Spitsbergen. Epidemiological data from the course of this pandemic in Poland have not been previously published. For analysis, we used source materials such as clinical studies and case reports of doctors fighting against the pandemic and registries of influenza cases in units of the Polish Army and military hospitals. Clinically, the pandemic of 1918 was characterized by the same symptoms and course as influenza in other years. Pathologically, the disease was similar to the other pandemic, in that the destruction was mostly limited to the respiratory tract. The "Spanish" influenza pandemic of 1918-1920 took place in Poland in 3 epidemic waves. The peaks of morbidity and mortality occurred in the capital, Warsaw, in December 1918 and in December 1919 to January 1920. It is estimated that throughout the pandemic period of 1918-1920 in Poland, 200 000 to 300 000 people died.

Evolution of sanitary-epidemiological services in Poland in the years 1944-2014.

This paper presents the history of sanitary-epidemiological services in the context of the health, economic and socio-political situation in Poland in the years 1944-2014, with a critical analysis of legal restraints, efficiency and achievements. Polish Sanitary Services, established in 1919, as a state service, have preserved for more than 95 years (also during World War II and the occupation) the continuity of its structures and essential objectives to enable their implementation in the field of public health protection. The unique effectiveness of actions was recorded in the years 1954-1998 and 2002-2009 in the time of central (vertical) subordination of sanitary-epidemiological services. The pre-accession preparation to the European Union (EU) strongly accelerated the development of sanitary-epidemiological services in Poland. Polish accession to the European Union has promoted the implementation of the WHO document "Health for All in the 21st Century" and the reduction of "health inequalities".

A new option for definitive burn wound closure - pair matching type of retrospective case-control study of hand burns in the hospitalised patients group in the Dr Stanislaw Sakiel Centre for Burn Treatment between 2009 and 2015.

Nearly 80% of all burns include the hands of affected individuals. Skin grafting is the gold standard in burns treatment, but in the case of the burn wound bed, it may require the necessity of utilising skin substitutes to facilitate closure. The aim of this study is to assess the impact of a porcine-derived wound dressing (Oasis™) for application to hand burns compared to a synthetic dressing (Suprathel™). Comparative assessments were made, including the time to heal, quality of healing and pain intensity. A retrospective, unblinded, matching pair case-control of hand burns was performed. A control group of 24 patients was treated with Suprathel dressing, and a study group of six patients underwent application of the Oasis dressing. The wound healing process was evaluated by taking histopathological specimens and also utilising the Bates-Jensen Wound Assessment Tool. A 10-cm Visual Analogue Scale (VAS) was used for pain assessment. Other parameters measured included dressing loss because of infection and the need of rehabilitation. The progress of wound healing on the fourth day in the study group was 30%. A decrease in the level of pain was recorded on the fourth day after surgery. There was a decrease of 5% in the risk of rehabilitation in the treatment group.

The impact of structural genomics: the first quindecennial.

The period 2000-2015 brought the advent of high-throughput approaches to protein structure determination. With the overall funding on the order of $2 billion (in 2010 dollars), the structural genomics (SG) consortia established worldwide have developed pipelines for target selection, protein production, sample preparation, crystallization, and structure determination by X-ray crystallography and NMR. These efforts resulted in the determination of over 13,500 protein structures, mostly from unique protein families, and increased the structural coverage of the expanding protein universe. SG programs contributed over 4400 publications to the scientific literature. The NIH-funded Protein Structure Initiatives alone have produced over 2000 scientific publications, which to date have attracted more than 93,000 citations. Software and database developments that were necessary to handle high-throughput structure determination workflows have led to structures of better quality and improved integrity of the associated data. Organized and accessible data have a positive impact on the reproducibility of scientific experiments. Most of the experimental data generated by the SG centers are freely available to the community and has been utilized by scientists in various fields of research. SG projects have created, improved, streamlined, and validated many protocols for protein production and crystallization, data collection, and functional analysis, significantly benefiting biological and biomedical research.

Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures.

The explosion of the size of the universe of known protein sequences has stimulated two complementary approaches to structural mapping of these sequences: theoretical structure prediction and experimental determination by structural genomics (SG). In this work, we assess the accuracy of structure prediction by two automated template-based structure prediction metaservers (genesilico.pl and bioinfo.pl) by measuring the structural similarity of the predicted models to corresponding experimental models determined a posteriori. Of 199 targets chosen from SG programs, the metaservers predicted the structures of about a fourth of them "correctly." (In this case, "correct" was defined as placing more than 70 % of the alpha carbon atoms in the model within 2 Å of the experimentally determined positions.) Almost all of the targets that could be modeled to this accuracy were those with an available template in the Protein Data Bank (PDB) with more than 25 % sequence identity. The majority of those SG targets with lower sequence identity to structures in the PDB were not predicted by the metaservers with this accuracy. We also compared metaserver results to CASP8 results, finding that the models obtained by participants in the CASP competition were significantly better than those produced by the metaservers.

Rapid response to emerging biomedical challenges and threats.

As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.

Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models.

The COVID-19 pandemic has triggered numerous scientific activities aimed at understanding the SARS-CoV-2 virus and ultimately developing treatments. Structural biologists have already determined hundreds of experimental X-ray, cryo-EM, and NMR structures of proteins and nucleic acids related to this coronavirus, and this number is still growing. To help biomedical researchers, who may not necessarily be experts in structural biology, navigate through the flood of structural models, we have created an online resource, covid19.bioreproducibility.org, that aggregates expert-verified information about SARS-CoV-2-related macromolecular models. In this article, we describe this web resource along with the suite of tools and methodologies used for assessing the structures presented therein.

State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and in Vitro Biochemical Experiments.

Efficient and comprehensive data management is an indispensable component of modern scientific research and requires effective tools for all but the most trivial experiments. The LabDB system developed and used in our laboratory was originally designed to track the progress of a structure determination pipeline in several large National Institutes of Health (NIH) projects. While initially designed for structural biology experiments, its modular nature makes it easily applied in laboratories of various sizes in many experimental fields. Over many years, LabDB has transformed into a sophisticated system integrating a range of biochemical, biophysical, and crystallographic experimental data, which harvests data both directly from laboratory instruments and through human input via a web interface. The core module of the system handles many types of universal laboratory management data, such as laboratory personnel, chemical inventories, storage locations, and custom stock solutions. LabDB also tracks various biochemical experiments, including spectrophotometric and fluorescent assays, thermal shift assays, isothermal titration calorimetry experiments, and more. LabDB has been used to manage data for experiments that resulted in over 1200 deposits to the Protein Data Bank (PDB); the system is currently used by the Center for Structural Genomics of Infectious Diseases (CSGID) and several large laboratories. This chapter also provides examples of data mining analyses and warnings about incomplete and inconsistent experimental data. These features, together with its capabilities for detailed tracking, analysis, and auditing of experimental data, make the described system uniquely suited to inspect potential sources of irreproducibility in life sciences research.

Structural genomics: keeping up with expanding knowledge of the protein universe.

Structural characterization of the protein universe is the main mission of Structural Genomics (SG) programs. However, progress in gene sequencing technology, set in motion in the 1990s, has resulted in rapid expansion of protein sequence space--a twelvefold increase in the past seven years. For the SG field, this creates new challenges and necessitates a re-assessment of its strategies. Nevertheless, despite the growth of sequence space, at present nearly half of the content of the Swiss-Prot database and over 40% of Pfam protein families can be structurally modeled based on structures determined so far, with SG projects making an increasingly significant contribution. The SG contribution of new Pfam structures nearly doubled from 27.2% in 2003 to 51.6% in 2006.

Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy.

Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Herein, we report the first structure of serum albumin in complex with dexamethasone. We show that it binds to Drug Site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with our analysis of publicly available clinical data from Wuhan and suggests that an adjustment of dexamethasone regimen should be considered for patients affected by two major COVID-19 risk-factors: low albumin levels and diabetes.

Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy.

Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Here, the first structure of serum albumin in complex with dexamethasone is reported. Dexamethasone binds to drug site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with an analysis of publicly available clinical data from Wuhan and suggests that an adjustment of the dexamethasone regimen should be further investigated as a strategy for patients affected by two major COVID-19 risk factors: low albumin levels and diabetes.

The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years.

It has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new crystal structure should deposit their primary experimental data (X-ray diffraction images) to one of the dedicated resources created in recent years. Here, we describe our experiences developing the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC) and describe several examples of a crucial role that diffraction data can play in improving previously determined protein structures. In its first four years, several hundred crystallographers have deposited data from over 5200 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing. Preliminary analysis indicates that about 95% of the archived data can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of using the automated metadata extraction and automated processing as a validation step for the deposition of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles.

Solec Spa - worldwide unique properties of Polish health resort in the service of rural medicine.

Solec Spa is health resort in south-eastern Poland. Its unique balneorehabilitation significance worldwide is determined by chloride-iodine-sodium water with a high content of hydrogen sulphide. This water, classified as highly mineralized sodium-chloride (seltzer) sulphide, bromide, iodide, boron water, contains naturally approximately 0.9 g/l divalent sulphur compounds, which is the highest concentration noted among the mineral waters of the world. The effectiveness of the Solec waters is proven in: inflammatory and autoimmunological locomotor system diseases, degenerative joint disorders (osteoarthritis), post-traumatic and post-operative orthopedic diseases, skin diseases and allergic disorders. One of the main indications for balneotherapy in Solec Spa and Busko Spa is chronic brucellosis.

Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels.

Vibrio cholerae, the causative pathogen of the life-threatening infection cholera, encodes two copies of ß-ketoacyl-acyl carrier protein synthase III (vcFabH1 and vcFabH2). vcFabH1 and vcFabH2 are pathogenic proteins associated with fatty acid synthesis, lipid metabolism, and potential applications in biofuel production. Our biochemical assays characterize vcFabH1 as exhibiting specificity for acetyl-CoA and CoA thioesters with short acyl chains, similar to that observed for FabH homologs found in most gram-negative bacteria. vcFabH2 prefers medium chain-length acyl-CoA thioesters, particularly octanoyl-CoA, which is a pattern of specificity rarely seen in bacteria. Structural characterization of one vcFabH1 and six vcFabH2 structures determined in either apo form or in complex with acetyl-CoA/octanoyl-CoA indicate that the substrate-binding pockets of vcFabH1 and vcFabH2 are of different sizes, accounting for variations in substrate chain-length specificity. An unusual and unique feature of vcFabH2 is its C-terminal fragment that interacts with both the substrate-entrance loop and the dimer interface of the enzyme. Our discovery of the pattern of substrate specificity of both vcFabH1 and vcFabH2 can potentially aid the development of novel antibacterial agents against V. cholerae. Additionally, the distinctive substrate preference of FabH2 in V. cholerae and related facultative anaerobes conceivably make it an attractive component of genetically engineered bacteria used for commercial biofuel production.

Sharing Big Data.

Macromolecular Big Data provide numerous challenges and a number of initiatives that are starting to overcome these issues are discussed.

Macroscopic Singlet-Triplet Qubit in Synthetic Spin-One Chain in Semiconductor Nanowires.

We show here how to create macroscopic quantum states in a semiconductor device: a chain of InAs quantum dots embedded in an InP nanowire. Filling the nanowire with 4 electrons per dot creates a synthetic spin-one chain, with four-fold degenerate topological ground state protected by a Haldane gap. The four states correspond to two spin-½ quasiparticles localised at the ends of the macroscopic wire. The quasiparticle spins are mapped onto a robust, macroscopic, singlet-triplet qubit. These predictions are supported by a microscopic theory and extensive numerical simulations.

Databases, Repositories, and Other Data Resources in Structural Biology.

Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and "meta" data with a high demand on data storage and manipulations. Primary data come from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of various biomedical problems. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) Databases, and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, as well as integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive "hubs", or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.