Immunoreactive pattern of Staphylococcus epidermidis biofilm against human whole saliva

Saliva is essential to interact with microorganisms in the oral cavity. Therefore, the interest in saliva antimicrobial properties is on the rise. Here, we used an immunoproteomic approach, based on protein separation of Staphylococcus epidermidis biofilms by 2DE, followed by Western-blotting, to compare human serum and saliva reactivity profile. A total of 17 proteins were identified by MALDI-TOF/TOF. Serum and saliva presented a distinct pattern of immunoreactive proteins. Our results suggest that saliva seems to have higher propensity to react against S. epidermidis proteins with oxidoreductase activity and proteins involved with L-serine metabolic processes. We show that saliva was a powerful tool for the identification of potential S. epidermidis biofilms proteins.V.C. had an individual FCT fellowship (SFRH/BD/78235/2011). N.C. is an Investigator FCT. This work was funded by Fundacao para a Ciencia e a Tecnologia (FCT) and COMPETE grants PTDC/BIA-MIC/113450/2009, FCOMP-01-0124-FEDER-014309, QOPNA research unit (project PEst-C/QUI/UI0062/2013), RNEM (National Mass Spetrometry Network), and CENTRO-07-ST24-FEDER-002034. The authors also thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013 and the Project "BioHealth - Biotechnology and Bioengineering approaches to improve health quality", Ref. NORTE-07-0124-FEDER-000027, co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER. The authors also acknowledge the project "Consolidating Research Expertise and Resources on Cellular and Molecular Biotechnology at CEB/IBB", Ref. FCOMP-01-0124-FEDER-027462

A novel spliced fusion of MLL with CT45A2 in a pediatric biphenotypic acute leukemia

Background: Abnormalities of 11q23 involving the MLL gene are found in approximately 10% of human leukemias. To date, nearly 100 different chromosome bands have been described in rearrangements involving 11q23 and 64 fusion genes have been cloned and characterized at the molecular level. In this work we present the identification of a novel MLL fusion partner in a pediatric patient with de novo biphenotypic acute leukemia. Methods: Cytogenetics, fluorescence in situ hybridization (FISH), molecular studies (RT-PCR and LDI-PCR), and bioinformatic sequence analysis were used to characterize the CT45A2 gene as novel MLL fusion partner in pediatric acute leukemia. Results: Fluorescence in situ hybridization of the patient G-banded metaphases demonstrated a cryptic insertion of 11q23 in Xq26.3 involving the MLL gene. Breakpoint fusion analysis revealed that a DNA fragment of 653 kb from 11q23, containing MLL exons 1-9 in addition to 16 other 11q23 genes, was inserted into the upstream region of the CT45A2 gene located at Xq26.3. In addition, a deletion at Xq26.3 encompassing the 3' region of the DDX26B gene (exons 9-16) and the entire CT45A1 gene was identified. RNA analysis revealed the presence of a novel MLL-CT45A2 fusion transcript in which the first 9 exons of the MLL gene were fused in-frame to exon 2 of the CT45A2 gene, resulting in a spliced MLL fusion transcript with an intact open reading frame. The resulting chimeric transcript predicts a fusion protein where the N-terminus of MLL is fused to the entire open reading frame of CT45A2. Finally, we demonstrate that all breakpoint regions are rich in long repetitive motifs, namely LINE/L1 and SINE/Alu sequences, but all breakpoints were exclusively identified outside these repetitive DNA sequences. Conclusion: We have identified CT45A2 as a novel spliced MLL fusion partner in a pediatric patient with de novo biphenotypic acute leukemia, as a result of a cryptic insertion of 11q23 in Xq26.3. Since CT45A2 is the first Cancer/Testis antigen family gene found fused with MLL in acute leukemia, future studies addressing its biologic relevance for leukemogenesis are warranted

A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis

<p>Abstract</p> <p>Background</p> <p>The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal treatment is chosen. However, the available methodologies to detect such fusions all have their distinct short-comings.</p> <p>Results</p> <p>We describe a novel oligonucleotide microarray strategy whereby one can screen for all known oncogenic fusion transcripts in a single experiment. To accomplish this, we combine measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners. To demonstrate the usefulness of the approach, we designed a DNA microarray containing 68,861 oligonucleotide probes that includes oligos covering all combinations of chimeric exon-exon junctions from 275 pairs of fusion genes, as well as sets of oligos internal to all the exons of the fusion partners. Using this array, proof of principle was demonstrated by detection of known fusion genes (such as <it>TCF3:PBX1</it>, <it>ETV6:RUNX1</it>, and <it>TMPRSS2:ERG</it>) from all six positive controls consisting of leukemia cell lines and prostate cancer biopsies.</p> <p>Conclusion</p> <p>This new method bears promise of an important complement to currently used diagnostic and research tools for the detection of fusion genes in neoplastic diseases.</p

Negative MR4·0 chronic myeloid leukaemia and its possible implications for treatment-free remission

© 2019 British Society for Haematology and John Wiley & Sons Ltd.ABL1 tyrosine kinase inhibitors (TKI) have dramatically improved the outcome for chronic myeloid leukaemia (CML) patients, resulting in a life expectancy that approaches that of the general population. Nevertheless, lifelong TKI therapy may have consequences, including chronic adverse events that can substantially impact patients’ quality of life, adherence to therapy and treatment success. Recently, several clinical discontinuation trials have demonstrated that 40–60% of chronic phase CML patients (CP-CML) who have achieved a stable deep molecular response (DMR) can stop therapy without relapsing (Breccia & Foà, 2018). Laboratory recommendations for scoring DMR were previously defined as MR4·0 [either detectable disease ⩽0·01% BCR-ABLIS (MR4·0 positive) or undetectable disease in cDNA with 10 000–31 999 ABL1 transcripts or 24 000–76 999 GUSB transcripts (MR4·0 negative)], MR4·5 [either detectable disease ⩽0·0032% BCR-ABLIS (MR4·5 positive) or undetectable disease in cDNA with 32 000–99 999 ABL1 transcripts or 77 000–239 999 GUSB transcripts (MR4·5 negative)], and MR5·0 [either detectable disease ⩽0·001% BCR-ABLIS (MR5·0 positive) or undetectable disease in cDNA with ⩾100 000 ABL1 transcripts or ⩾240 000 GUSB transcripts (MR5·0 negative)] (Cross et al, 2015).info:eu-repo/semantics/publishedVersio

Natural regeneration of cork oak forests under climate change: a case study in Portugal

The sustainability of forest species is directly related to the success of stand regeneration. Assuring success is particularly critical in stands where perpetuity relies on natural regeneration, as is often the case with cork oak forests. However, 59% of the stand in Portugal have no natural regeneration, and climate change could further worsen the sustainability of the system. The study summarizes the factors that affect the natural regeneration of cork oak (Quercus suber L.) based on current knowledge and presents a case study on a forest in Northeast Portugal, where the natural regeneration of Quercus suber under the effect of climate change have been monitored and analyzed. The present work focuses on the effect of stand density, i.e., tree cover, on the production of acorns, the establishment and survival of seedlings, and the impact of the summer season on seedling mortality. The monitoring was carried out in February, June, September 2022, and January 2023 in two stands with distinct stand canopy cover, when the region was under extreme drought. Data analysis was performed using the analysis of variance for repeated measures and the Mann–Whitney-Wilcoxon test. The study showed that cork oak regeneration is influenced by stand density, which promoted the establishment success and survival of natural regeneration in a period of reduced precipitation, despite possible competition for water resources. The mean number of seedlings differed significantly between the two stands. However, there were no significant differences in the mean number of seedlings throughout the field measurements. Additionally, the percentage of dead seedlings was low even after the summer season (9.5% of the total seedlings) in the denser stand. These results indicate that high canopy cover can have a protective effect for extreme climatic events and should be considered in forestry management to promote regeneration of the cork oak forests

Both SEPT2 and MLL are down-regulated in MLL-SEPT2 therapy-related myeloid neoplasia

<p>Abstract</p> <p>Background</p> <p>A relevant role of septins in leukemogenesis has been uncovered by their involvement as fusion partners in <it>MLL</it>-related leukemia. Recently, we have established the <it>MLL-SEPT2 </it>gene fusion as the molecular abnormality subjacent to the translocation t(2;11)(q37;q23) in therapy-related acute myeloid leukemia. In this work we quantified <it>MLL </it>and <it>SEPT2 </it>gene expression in 58 acute myeloid leukemia patients selected to represent the major AML genetic subgroups, as well as in all three cases of <it>MLL-SEPT2</it>-associated myeloid neoplasms so far described in the literature.</p> <p>Methods</p> <p>Cytogenetics, fluorescence in situ hybridization (FISH) and molecular studies (RT-PCR, qRT-PCR and qMSP) were used to characterize 58 acute myeloid leukemia patients (AML) at diagnosis selected to represent the major AML genetic subgroups: <it>CBFB-MYH11 </it>(n = 13), <it>PML-RARA </it>(n = 12); <it>RUNX1-RUNX1T1 </it>(n = 12), normal karyotype (n = 11), and <it>MLL </it>gene fusions other than <it>MLL-SEPT2 </it>(n = 10). We also studied all three <it>MLL-SEPT2 </it>myeloid neoplasia cases reported in the literature, namely two AML patients and a t-MDS patient.</p> <p>Results</p> <p>When compared with normal controls, we found a 12.8-fold reduction of wild-type <it>SEPT2 </it>and <it>MLL-SEPT2 </it>combined expression in cases with the <it>MLL-SEPT2 </it>gene fusion (p = 0.007), which is accompanied by a 12.4-fold down-regulation of wild-type <it>MLL </it>and <it>MLL-SEPT2 </it>combined expression (p = 0.028). The down-regulation of <it>SEPT2 </it>in <it>MLL-SEPT2 </it>myeloid neoplasias was statistically significant when compared with all other leukemia genetic subgroups (including those with other <it>MLL </it>gene fusions). In addition, <it>MLL </it>expression was also down-regulated in the group of <it>MLL </it>fusions other than <it>MLL-SEPT2</it>, when compared with the normal control group (p = 0.023)</p> <p>Conclusion</p> <p>We found a significant down-regulation of both <it>SEPT2 </it>and <it>MLL </it>in <it>MLL-SEPT2 </it>myeloid neoplasias. In addition, we also found that <it>MLL </it>is under-expressed in AML patients with <it>MLL </it>fusions other than <it>MLL-SEPT2</it>.</p

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Mammals in Portugal: a data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n =31,573) has the highest number of records followed by Chiroptera (n = 18,857), Carnivora (n = 18,594), Lagomorpha (n = 17,496), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n = 12,159], Monachus monachus [n = 1,512], and Lynx pardinus [n = 197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications

Structural and expression changes of septins in myeloid neoplasia.

Ciências BiomédicasBiomedical Science

Light pollution: Assessment of sky glow on two dark sky regions of Portugal

Artificial light at night (ALAN), producing light pollution (LP), is not a matter restricted to astronomy anymore. Light is part of modern societies and, as a consequence, the natural cycle day-night (bright-dark) has been interrupted in a large segment of the global population. There is increasing evidence that exposure to certain types of light at night and beyond threshold levels may produce hazardous effects to humans and the environment. The concept of "dark skies reserves" is a step forward in order to preserve the night sky and a means of enhancing public awareness of the problem of spread of light pollution worldwide. The aim of this study was to assess the skyglow at two sites in Portugal, the Peneda-Gerês National Park (PNPG) and the region now known as Dark Sky Alqueva Reserve. The latter site was classified as a "Starlight Tourism Destination" by the Starlight Foundation (the first in the world to achieve this classification) following a series of night sky measurements in situ described herein. The measurements at PNPG also contributed to the new set of regulations concerning light pollution at this national park. This study presents the first in situ systematic measurements of night sky brightness, showing that at the two sites the skies are mostly in levels 3 to 4 of the Bortle 9-level scale (with level 1 being the best achievable). The results indicate that the sources of light pollution and skyglow can be attributed predominantly to contamination from nearby urban regions