Local use of metrics for the research assessment of academics: The case of Poland

This article discusses the use of bibliometric indicators for the assessment of individual academics. We focused on national indicators for the assessment of productivity in Polish higher education institutions. We analysed whether institutions (N = 768) adopted national templates for their own sets of criteria for intra-institutional evaluations. This study combined an analysis of internal policy documents with semi-structured interviews with deans from institutions in different fields of science. Our findings showed that, despite their high levels of institutional autonomy, the majority of institutions adopted the national criteria for the evaluation of individual academics. This article concludes with recommendations for reducing the negative consequences of local use of national indicators for the assessment of researchers.This work was financially supported by the National Science Centre in Poland (Grant Number UMO-2017/26/E/HS2/00019)

Preservation of fish male germplasm in Poland

The natural resources of a country, including ichthyofauna, constitute a vital aspect of its national heritage. Fish populations are threatened with loss of biodiversity as a result of human activity (anthropopressure), resulting in water pollution, habitat destruction and overfishing. Additionally, the escalating threat is exacerbated by climate change, primarily manifested in periodic reservoir and watercourse desiccation. Genetic variability of captive is also threated as fish raised in hatcheries are susceptible to bacterial and viral diseases. Therefore, methodologies for fish sperm cryopreservation aimed at safeguarding the gene pool of both natural and captive fish populations assume paramount importance for their conservation and mitigation of irreversible losses, particularly crucial in light of increasing ecological disasters. This paper offers an overview of cryopreservation research in Poland, tracing back to early initiatives in the 1970s concerning carp (Cyprinus carpio) semen and culminating in recent advancements, where standardized cryopreservation methodologies were developed. We delve into the freezing results of semen of various fish species, encompassing both wild specimens like whitefish (Coregonus lavaretus) and lake minnows (Eupallasella percnurus), and farmed species such as sturgeons, carp, and numerous salmonid species. Additionally, we delineate projects that support such endeavors. Recent milestones in the establishment of fish sperm cryobanks in Poland catering to both wild and farmed species, including carp and rainbow trout (Oncorhynchus mykiss) – the most economically significant fish in Poland were presented. We also expound on the implementation of cryopreserved semen from sex-reversed rainbow trout in hatchery practices. Furthermore, we discuss significant challenges pertaining to sperm banking, particularly concerning funding and the practical utilization of cryostored semen samples for egg fertilization under hatchery conditions

Characterization of carp seminal plasma Wap65-2 and its participation in the testicular immune response and temperature acclimation

International audienceTwo functionally distinct isoforms of warm-temperature acclimation related 65-kDa protein (Wap65-1 and Wap65-2) with a role in the immune response are present in fish. To our knowledge, contrary to Wap65-1, Wap65-2 has neither been isolated nor functionally characterized in carp especially in reproductive system. The aim of this study was to characterize Wap65-2 and ascertain its functions in immune response and temperature acclimation within reproductive system. Wap65-2 corresponded to one of the most abundant proteins in carp seminal plasma, with a high immunologic similarity to their counterparts in seminal plasma of other fish species and a wide tissue distribution, with predominant expression in the liver. The immunohistochemical localization of Wap65-2 to spermatogonia, Leydig cells, and the epithelium of blood vessels within the testis suggests its role in iron metabolism during spermatogenesis and maintenance of blood-testis barrier integrity. Wap65-2 secretion by the epithelial cells of the spermatic duct and its presence around spermatozoa suggests its involvement in the protection of spermatozoa against damage caused by heme released from erythrocytes following hemorrhage and inflammation. Our results revealed an isoform-specific response of Wap65 to temperature acclimation and Aeromonas salmonicida infection which alters blood-testis barrier integrity. Wap65-2 seems to be related to the immune response against bacteria, while Wap65-1 seems to be involved in temperature acclimation. This study expands the understanding of the mechanism of carp testicular immunity against bacterial challenge and temperature changes, in which Wap65-2 seems to be involved and highlights their potential usefulness as biomarkers of inflammation and temperature acclimation

Secreted novel AID/APOBEC-like deaminase 1 (SNAD1) – a new important player in fish immunology

The AID/APOBECs are a group of zinc-dependent cytidine deaminases that catalyse the deamination of bases in nucleic acids, resulting in a cytidine to uridine transition. Secreted novel AID/APOBEC-like deaminases (SNADs), characterized by the presence of a signal peptide are unique among all of intracellular classical AID/APOBECs, which are the central part of antibody diversity and antiviral defense. To date, there is no available knowledge on SNADs including protein characterization, biochemical characteristics and catalytic activity. We used various in silico approaches to define the phylogeny of SNADs, their common structural features, and their potential structural variations in fish species. Our analysis provides strong evidence of the universal presence of SNAD1 proteins/transcripts in fish, in which expression commences after hatching and is highest in anatomical organs linked to the immune system. Moreover, we searched published fish data and identified previously, “uncharacterized proteins” and transcripts as SNAD1 sequences. Our review into immunological research suggests SNAD1 role in immune response to infection or immunization, and interactions with the intestinal microbiota. We also noted SNAD1 association with temperature acclimation, environmental pollution and sex-based expression differences, with females showing higher level. To validate in silico predictions we performed expression studies of several SNAD1 gene variants in carp, which revealed distinct patterns of responses under different conditions. Dual sensitivity to environmental and pathogenic stress highlights its importance in the fish and potentially enhancing thermotolerance and immune defense. Revealing the biological roles of SNADs represents an exciting new area of research related to the role of DNA and/or RNA editing in fish biology

Cryoprotectant-specific alterations in the proteome of Siberian sturgeon spermatozoa induced by cryopreservation

Cryopreservation is crucial for conserving genetic diversity in endangered species including the critically endangered group of sturgeons (Acipenseridae), but it can compromise sperm quality and protein profiles. Although cryopreservation with dimethyl sulfoxide (DMSO) and methanol (MeOH) results in the recovery of good post-thaw motility, DMSO-preserved sperm show reduced fertilization ability. This study was conducted in Siberian sturgeon as a model for Acipenserid fishes to explore the effects of DMSO and MeOH on the proteome of semen using advanced proteomics methods—liquid chromatography‒mass spectrometry and two-dimensional difference gel electrophoresis. We analyzed the proteomic profiles of fresh and cryopreserved spermatozoa and their extracellular medium and showed that cryopreservation decreases motility and viability and increases reactive oxygen species levels, membrane fluidity, and acrosome damage. Despite having similar post-thaw semen motility, sperm treated with DMSO had significantly lower fertilization success (6.2%) than those treated with MeOH (51.2%). A total of 224 and 118 differentially abundant proteins were identified in spermatozoa preserved with MeOH and DMSO, respectively. MeOH-related proteins were linked to chromosomal structure and mitochondrial functionality, while DMSO-related proteins impacted fertilization by altering the acrosome reaction and binding of sperm to the zona pellucida and nuclear organization. Additionally, cryopreservation led to alterations in the proacrosin/acrosin system in both cryoprotectants. This study provides the first comprehensive proteomic characterization of Siberian sturgeon sperm after cryopreservation, offering insights into how cryoprotectants impact fertilization ability

Jak rozpoznać recenzowane publikacje – o etykietach z otwartymi danymi recenzentów w monografiach naukowych

W tym artykule omawiamy etykiety z otwartymi danymi recenzentów, czyli praktykę ujawniania danych recenzentów w monografiach naukowych, która jest powszechna w krajach Europy Środkowej i Wschodniej. Celem badania było sprawdzenie, czy etykieta z otwartymi danymi recenzentów jest rodzajem etykiety z informacją o recenzowaniu (na podobieństwo tej stosowanej w Finlandii i Flandrii, tj. we flamandzkiej części Belgii), i, czy jako taka, może być używana jako kryterium w różnych systemach wykorzystywanych do oceny publikacji naukowych. Przeprowadziliśmy dwufazowe badanie z wykorzystaniem sekwencyjnej strategii eksploracyjnej. W pierwszej fazie przeprowadziliśmy wywiady z reprezentantami dwudziestu spośród czterdziestu największych polskich wydawnictw naukowych w celu zbadania, w jaki sposób polscy wydawcy kontrolują proces recenzowania oraz czy można wykorzystać etykiety z otwartymi danymi recenzentów do identyfikacji monografii recenzowanych. W drugiej fazie przeprowadziliśmy dwie ankiety mające na celu analizę postrzegania procesu recenzowania oraz etykiet z otwartymi danymi recenzentów przez autorów (n = 600) oraz recenzentów (n = 875) książek opublikowanych przez dwadzieścia poddanych badaniu wydawnictw. Zintegrowane wyniki pozwoliły nam zweryfikować stwierdzenia wydawców dotyczące ich praktyk związanych z procesem recenzowania. Nasze wyniki wskazują, że wydawcy rzeczywiście kontrolują proces recenzowania poprzez dostarczanie recenzentom kryteriów oceny oraz przesyłanie recenzji autorom. Wydawcy rzadko proszą o pozwolenie na ujawnienie nazwisk recenzentów, ale dla recenzentów oczywistym jest, że umieszczanie ich danych w monografii jest częścią procesu recenzowania. Badanie pokazuje również, że ujawniane są dane tylko tych recenzentów, którzy przyjęli manuskrypt do publikacji. A zatem, co najważniejsze, nasza analiza wykazała, że etykieta z otwartymi danymi recenzentów, której używają polscy wydawcy, jest rodzajem etykiety z informacją o recenzowaniu, takiej jak ta stosowana we Flandrii i Finlandii, i, jako taka, może być stosowana do identyfikacji recenzowanych monografii naukowych.This article discusses the open-identity label, i.e., the practice of disclosing reviewers’ names in published scholarly books, a common practice in Central and Eastern European countries. This study’s objective is to verify whether the open-identity label is a type of peer-review label (like those used in Finland and Flanders, i.e., the Flemish part of Belgium), and as such, whether it can be used as a delineation criterion in various systems used to evaluate scholarly publications. We have conducted a two-phase sequential explanatory study. In the first phase, interviews with 20 of the 40 largest Polish publishers of scholarly books were conducted to investigate how Polish publishers control peer reviews and whether the open-identity label can be used to identify peer-reviewed books. In the other phase, two questionnaires were used to analyze perceptions of peer-review and open-identity labelling among authors (n = 600) and reviewers (n = 875) of books published by these 20 publishers. Integrated results allowed us to verify publishers’ claims concerning their peer-review practices. Our findings reveal that publishers actually control peer reviews by providing assessment criteria to reviewers and sending reviews to authors. Publishers rarely ask for permission to disclose reviewers’ names, but it is obvious to reviewers that this practice of disclosing names is part of peer reviewing. This study also shows that only the names of reviewers who accepted manuscripts for publication are disclosed. Thus, most importantly, our analysis shows that the open-identity label that Polish publishers use is a type of peer-review label like those used in Flanders and Finland, and as such, it can be used to identify peer-reviewed scholarly books

Proteomic analysis of carp seminal plasma provides insights into the immune response to bacterial infection of the male reproductive system

Aeromonas salmonicida is recognized as a significant bacterial pathogen in ulcerative disease of cyprinid fish. However, the mechanism of immunity to these bacteria in common carp is still not well understood, especially the immune regulation in the gonad to bacterial infection. The aims of our study were to analyze changes in the seminal plasma proteome following A. salmonicida infection in carp males. The observed pathological changes in the tissue (liver, spleen, kidney and testis) morphology and upregulation of immune-related genes (tnfa2, il6a) confirmed the successful infection challenge. Using mass spectrometry-based label-free quantitative proteomics, we identified 1402 seminal plasma proteins, and 44 proteins (20 up- and 24 downregulated) were found to be differentially abundant between infected and control males. Most differentially abundant proteins were involved in the immune response mechanisms, such as acute phase response, complement activation and coagulation, inflammation, lipid metabolism, cell-cell and cell-matrix adhesion, creatine-phosphate biosynthesis and germ cell-Sertoli cell junction signaling. Bacterial infection also caused profound changes in expression of selected genes in the testis and hematopoietic organs, which contributed to changes in seminal proteins. The altered seminal proteins and bacterial proteins in seminal plasma may serve as valuable markers of infection in the testis