Biophysical Reviews: 2020—looking back,going forward

After first describing the issue contents (Biophysical Reviews—Volume 12 Issue 6), this Editorial goes on to provide a short round-up of the activities of the journal in 2020. Directly following this Editorial are two obituaries marking the recent deaths of Prof. Fumio Oosawa (Japan) and Dr. Herbert Tabor (USA)—two major figures in Biophysical/Biochemical science from the last 100 years.

With the outbreak of the COVID-19 pandemic, 2020 has been a testing year for all. Filled with a myriad combination of personal tragedies and work/life inconveniences, circumstances have required many difficult decisions to be made at the personal, family, organizational and society levels with the results of these difficult choices amplifying the general level of stress within communities. Scientists have certainly not been immune from such pressures. For working scientists, this year has presented a number of challenges. Those scientists heavily involved in teaching have had to engage with remote teaching methodologies and the necessarily rapid preparation of additional online teaching materials. Research-focused scientists have had to cope with the closing or restriction of work facilities and the loss of personnel, which has certainly impacted (and often disrupted) scientific progress. For the many itinerant working scientists living away from home and family, the restrictions on worldwide travel have caused additional dilemmas and necessitated difficult career decisions. Student scientists have had to deal with other problems. Oftentimes educational institutions have maintained the steep fee requirements associated with enrolment despite the year being a virtual write-off in terms of focusing on academic performance. Overseas students have also faced problems related to maintaining interdependent attendance and residence requirements.Irrespective of the stage of their career progression, scientists (like all members of society) have tried their best to make the most of a bad situation. In 2020, the Biophysical Reviews’ Editorial Board and the specifically dedicated professional officers from Springer-Nature have similarly pushed on with our journal related duties. From 2018, Biophysical Reviews moved to a six Issue per year format. The current Issue (Issue 6) is the last for 2020, and as such, the first duty of this Editorial is to describe the contents of the twelve articles appearing within it. After providing a precis of these articles, we then move on to describe some of the highlights of this year and finish by welcoming some new members to the Editorial Board.     

Distribution of Gastrointestinal Parasitic Infection in Domestic Pigs in the Republic of Korea: Nationwide Survey from 2020–2021

This study aimed to examine the distribution of gastrointestinal parasitic infections in domestic pigs in the Republic of Korea. From May 2020 to October 2021, 364 pig fecal samples were collected from 75 farms in 7 Provinces and microscopically examined. A total of 170 (46.7%) pigs were infected with at least one of the following parasites: Balantioides coli, strongyles, Ascaris suum, Trichuris suis, and coccidia. By parasite species, B. coli, strongyles, A. suum, T. suis, and coccidia oocysts or eggs were detected in 144 (39.6%), 24 (6.6%), 14 (3.8%), 4 (1.1%), and 1 (0.3%) samples, respectively. One hundred fifty-four, 15, and 1 cases showed single, double, and triple infections, respectively. Of the swine fecal samples from 75 farms, 69 specimens (92.0%) were infected with 1 or more parasites. All surveyed farms across the country exhibited a positive rate of over 30%, among which the highest positive rate was 65.0% in Chungcheongnam-do, and Jeollabuk-do was followed by 61.9%. Winter showed a statistically lower prevalence than other seasons. This study showed that gastrointestinal parasites are prevalent in pigs in Korea, although the diversity of parasites is low.     

Ultrastructure of the Invasion of Eimeria magna Sporozoites into Cultured Cells*†‡

SYNOPSIS. Monolayers of bovine kidney cells were overlaid with Eimeria magna sporozoites and observed with phase-contrast optics until penetration of the cells by the parasites had begun. Cells and penetrating parasites were fixed with glutaraldehyde and OsO₄-containing ruthenium red, dehydrated, and embedded in situ. Cells being penetrated were selected for study in the electron microscope. The lack of intracellular staining with ruthenium red and intact plasmalemmas of cells being penetrated, was accepted as evidence that the sporozoites did not disrupt the plasma membranes. The sporozoite caused invagination of the host cell plasmalemma until the parasite was entirely within the cell, after which the invagination was sealed off by short pseudopodia enclosing the sporozoite within a membrane-lined vacuole inside the cell. Often myelin-forms, apparently of host cell origin, were seen in the space between the sporozoite and the cell.     

An investigation of spatial-temporal patterns and predictions of the coronavirus 2019 pandemic in Colombia, 2020–2021

Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, 2020. Since then, the country has reported a total of 5,002,387 cases and 127,258 deaths as of October 31, 2021. The aggressive transmission dynamics of SARS-CoV-2 motivate an investigation of COVID-19 at the national and regional levels in Colombia. We utilize the case incidence and mortality data to estimate the transmission potential and generate short-term forecasts of the COVID-19 pandemic to inform the public health policies using previously validated mathematical models. The analysis is augmented by the examination of geographic heterogeneity of COVID-19 at the departmental level along with the investigation of mobility and social media trends. Overall, the national and regional reproduction numbers show sustained disease transmission during the early phase of the pandemic, exhibiting sub-exponential growth dynamics. Whereas the most recent estimates of reproduction number indicate disease containment, with R_t<1.0 as of October 31, 2021. On the forecasting front, the sub-epidemic model performs best at capturing the 30-day ahead COVID-19 trajectory compared to the Richards and generalized logistic growth model. Nevertheless, the spatial variability in the incidence rate patterns across different departments can be grouped into four distinct clusters. As the case incidence surged in July 2020, an increase in mobility patterns was also observed. On the contrary, a spike in the number of tweets indicating the stay-at-home orders was observed in November 2020 when the case incidence had already plateaued, indicating the pandemic fatigue in the country.     

Tracer Experiments in Feeding Littoral Foraminifera*†‡

SYNOPSIS. Tracer technic has proved to be an excellent tool in the study of predator-prey relationships among the foraminifera. More than fifty axenic species of protists including diatoms, dinoflagellates, chlorophytes, chrysophytes, cyanophytes, bacteria and yeasts were tested as potential food for Allogromia sp (NF), A. laticollaris, Am. monia beccarii, Quinqueloculina spp, Rosalina floridana, Anomalina sp, Elphidium sp, Spiroloculina hyalina, Globigerina bulloides, and Globorotalia truncatulinoides. Although many types of potential food are present in the environment, foraminifera select only certain organisms. The yeasts, cyanophytes, dinoflagellates, chrysophytes and most bacteria tested were not eaten. Selected species of diatoms, chlorophytes and bacteria were eaten in large quantity. Three additional factors affect feeding: the “age” of the food organism, the “age” of the foraminifer or its position in the life cycle, and the concentration of the food. Feeding by foraminifera on most food is erratic below a concentration of 10³ organisms and is approximately directly proportional to concentration within a range of 10³-10⁶ organisms per 10 ml experimental tube. A natural bloom of Protelphidium tisburyensis was analyzed. A high concentration of 6 species of diatoms characterized the community. A “bloom”-feeder hypothesis for foraminiferal nutrition is presented.     

Biophysical Reviews ‘Meet the editor series’—Addmore Shonhai

It gives me great pleasure to have the opportunity to introduce myself to the readers of Biophysical Reviews as part of the ‘meet the editors’ series. What follows is a mini-autobiography of my life as it relates to my scientific career and research.

     

Biophysical Reviews— 2021, the year that was

The current issue (volume 13 issue 6, 2021) is a Special Issue jointly dedicated to scientific content presented at the 20th triennial IUPAB Congress that was held in conjunction with both the 45th Annual Meeting of the Brazilian Biophysical Society (Sociedade Brasileira de Biofísica - SBBf) and the 50th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (Sociedade Brasileira de Bioquímica e Biologia Molecular – SBBq). In addition to describing the scientific and nonscientific content arising from the meeting this sub-editorial also provides a look back at some of the high points for Biophysical Reviews in the year 2021 before going on to describe a number of matters of interest to readers of the journal in relation to the coming year of 2022.

This Editorial marks the last issue for the journal to be published in 2021 – a year that has been characterized by a mixture of hardship, frustration, and of late, (possibly) a slowly developing cautious optimism in relation to the COVID-19 pandemic. Over the last 2 years, the journal has had to rapidly adapt to suddenly altered plans of contributors, as the publication of scientific reviews and organization of conference-based special issues has necessarily taken a back seat to the realities of altered work practices and, in some cases, changed life and career plans. One such major change was directly concerned with the subject of this special issue (SI) on the scientific content associated with the 20th Congress of the IUPAB (International Union for Pure and Applied Biophysics) conducted in concert with the 45th Annual Meeting of the Brazilian Biophysical Society (SBBf) and the 50th Annual Meeting of the Brazilian Biochemical and Molecular Biology Society (SBBq) (Itri et al. 2021). After discussing a few notable features of the SI, this editorial will introduce important developments occurring with the journal that relate to new feature commentaries and Institutional access arrangements. This Editorial will then close with a look back at some of the standout articles of 2021.     

Biophysical Reviews ‘Meet the Editors Series’ — a profile of Sabrina Leslie

It is my pleasure to introduce myself to the readers of Biophysical Reviews as part of the ‘Meet the Editors Series’.     

Severity of COVID-19 among solid organ transplant recipients in Canada, 2020–2021: a prospective,multicentre cohort study

Background:Severe COVID-19 appears to disproportionately affect people who are immunocompromised, although Canadian data in this context are limited. We sought to determine factors associated with severe COVID-19 outcomes among recipients of organ transplants across Canada.Methods:We performed a multicentre, prospective cohort study of all recipients of solid organ transplants from 9 transplant programs in Canada who received a diagnosis of COVID-19 from March 2020 to November 2021. Data were analyzed to determine risk factors for oxygen requirement and other metrics of disease severity. We compared outcomes by organ transplant type and examined changes in outcomes over time. We performed a multivariable analysis to determine variables associated with need for supplemental oxygen.Results:A total of 509 patients with solid organ transplants had confirmed COVID-19 during the study period. Risk factors associated with needing (n = 190), compared with not needing (n = 319), supplemental oxygen included age (median 62.6 yr, interquartile range [IQR] 52.5–69.5 yr v. median 55.5 yr, IQR 47.5–66.5; p < 0.001) and number of comorbidities (median 3, IQR 2–3 v. median 2, IQR 1–3; p < 0.001), as well as parameters associated with immunosuppression. Recipients of lung transplants (n = 48) were more likely to have severe disease with a high mortality rate (n = 15, 31.3%) compared with recipients of other organ transplants, including kidney (n = 48, 14.8%), heart (n = 1, 4.4%), liver (n = 9, 11.4%) and kidney–pancreas (n = 3, 12.0%) transplants (p = 0.02). Protective factors against needing supplemental oxygen included having had a liver transplant and receiving azathioprine. Having had 2 doses of SARS-CoV-2 vaccine did not have an appreciable influence on oxygen requirement. Multivariable analysis showed that older age (odds ratio [OR] 1.04, 95% confidence interval [CI] 1.02–1.07) and number of comorbidities (OR 1.63, 95% CI 1.30–2.04), among other factors, were associated with the need for supplemental oxygen. Over time, disease severity did not decline significantly.Interpretation:Despite therapeutic advances and vaccination of recipients of solid organ transplants, evidence of increased severity of COVID-19, in particular among those with lung transplants, supports ongoing public health measures to protect these at-risk people, and early use of COVID-19 therapies for recipients of solid organ transplants.

Recipients of solid organ transplants take life-long immunosuppressive agents to prevent rejection. In Canada, an estimated 3000 transplant procedures are performed annually and 40 000 people are living with a transplant. Early studies from Europe and the United States suggested that transplant recipients were at greater risk of severe COVID-19, with a two- to fivefold greater mortality than the general population.^1–3 It is unclear whether the increased risk is owing to multiple comorbidities, immunosuppression or a combination of both factors.Initial trials of therapeutics for SARS-CoV-2, including remdesivir, dexamethasone and tocilizumab, did not formally include transplant recipients.^4–6 Similarly, pivotal studies of the SARS-CoV-2 vaccines did not include immunocompromised populations.^7,8 Therefore, the use of COVID-19 therapeutics and SARS-CoV-2 vaccines in the transplant population has been extrapolated from the general population. Commonly used COVID-19 therapies such as dexamethasone and tocilizumab may place transplant recipients at risk of over-immunosuppression, which may result in secondary infections. In addition, withdrawal of standard immunosuppression may result in organ rejection.Previous cohort studies of transplant recipients with COVID-19 have primarily focused on the early phase of the pandemic, when therapeutics and vaccinations were limited.^2,9,10 These have generally been single-centre studies with short-term follow-up. Canadian data may differ from that of other countries owing to differences in timing and strategy of vaccine rollouts, as well as use and availability of certain therapeutics. Moreover, current data are limited with regard to longer-term outcomes of COVID-19 in transplant recipients up to 90 days postinfection, especially for the development of graft rejection.We sought to determine factors associated with severe COVID-19 outcomes, to estimate the impact of available therapeutics on COVID-19 severity and to determine whether disease severity changed over the course of the pandemic among recipients of solid organ transplants from 9 centres in Canada.     

New global targets for NTDs in the WHO roadmap 2021–2030

The second World Neglected Tropical Diseases (NTDs) Day was celebrated on 30 January 2021. To mark the occasion, the World Health Organization (WHO) launched its roadmap for NTDs for the period 2021 to 2030, which is aimed at increasing prevention and control of these too-long neglected diseases. Described here is a global overview on past achievements, current challenges, and future prospects for the WHO NTDs roadmap 2021–2030.     

“Cancer Reviews 2021” series: Cell competition in intratumoral and tumor microenvironment interactions

Tumors are complex cellular and acellular environments within which cancer clones are under continuous selection pressures. Cancer cells are in a permanent mode of interaction and competition with each other as well as with the immediate microenvironment. In the course of these competitive interactions, cells share information regarding their general state of fitness, with less‐fit cells being typically eliminated via apoptosis at the hands of those cells with greater cellular fitness. Competitive interactions involving exchange of cell fitness information have implications for tumor growth, metastasis, and therapy outcomes. Recent research has highlighted sophisticated pathways such as Flower, Hippo, Myc, and p53 signaling, which are employed by cancer cells and the surrounding microenvironment cells to achieve their evolutionary goals by means of cell competition mechanisms. In this review, we discuss these recent findings and explain their importance and role in evolution, growth, and treatment of cancer. We further consider potential physiological conditions, such as hypoxia and chemotherapy, that can function as selective pressures under which cell competition mechanisms may evolve differently or synergistically to confer oncogenic advantages to cancer.     

“Cancer Reviews 2021” series: Dynamic EMT: a multi‐tool for tumor progression

The process of epithelial–mesenchymal transition (EMT) is fundamental for embryonic morphogenesis. Cells undergoing it lose epithelial characteristics and integrity, acquire mesenchymal features, and become motile. In cancer, this program is hijacked to confer essential changes in morphology and motility that fuel invasion. In addition, EMT is increasingly understood to orchestrate a large variety of complementary cancer features, such as tumor cell stemness, tumorigenicity, resistance to therapy and adaptation to changes in the microenvironment. In this review, we summarize recent findings related to these various classical and non‐classical functions, and introduce EMT as a true tumorigenic multi‐tool, involved in many aspects of cancer. We suggest that therapeutic targeting of the EMT process will—if acknowledging these complexities—be a possibility to concurrently interfere with tumor progression on many levels.