Miracle-dz/UniFAR-FTUs huggingface dataset:
Kidney retransplantation after anti–programmed cell death‐1 (PD‐1)–related allograft rejection

In this report, we describe the first kidney retransplantation performed after anti–programmed cell death‐1 (PD‐1)–related allograft rejection. In 2014, we administered pembrolizumab (anti–PD‐1) for ~9 months to a 57‐year‐old kidney transplant recipient with metastatic cutaneous squamous cell carcinoma (CSCC). The patient experienced both a complete antitumor response and T cell–mediated allograft rejection requiring reinitiation of hemodialysis. Four‐and‐a‐half years after initiating pembrolizumab, the patient remained without evidence of CSCC relapse and received a kidney transplant from a living‐unrelated donor. Ten‐and‐a‐half months after kidney retransplantation, the allograft is functioning well and the patient's CSCC remains in remission. This case illustrates the potential for PD‐1 blockade to bring about durable immune‐mediated tumor control in chronically immunosuppressed patients, and begins to address the feasibility of kidney retransplantation in patients who have previously received immune checkpoint inhibitor therapy for cancer. Results from this and future cases may help elucidate mechanisms of antitumor immunity and allograft tolerance, and inform updates to transplant decision models. Our report also underscores the need for clinical trials testing novel immunotherapy combinations in solid organ transplant recipients designed to uncouple antitumor and anti‐allograft immunity.
Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage.

The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce the hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, several advances have provided an understanding into the origin and evolution of this protein family. Here, we report the most comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences centralized in a dedicated database, we have deepened our understanding of the evolutionary process underlying non-animal peroxidases diversification through phylogenetic reconstructions. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlate with the presence or absence of certain organelles or with specific biological processes. Scrutinizing in near 2000 organisms, we confirmed that ascorbate peroxidases (APx) and cytochromes c peroxidases (CcP) were detected respectively in chloroplast and mitochondria containing organisms. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prx) only found in fungi with wood decay abilities and plant degradation and Class III peroxidases (CIII Prx) only detected in both streptophyte algae and land plants, have been subjected to large family expansion in the latter group. Moreover, we demonstrate that biochemical activities (APx, CcP and CIII Prx) assayed with protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of non-animal peroxidase encoding sequences.
Effects of Conventional Surfactants on the Activity of Designed Antimicrobial Peptide.

In this paper, the interaction between a designed antimicrobial peptide (AMP) G(IIKK)3I-NH2 (G3) and four typical conventional surfactants (SDS, C16TAB, C12EO23 and C14DMAO) have been studied through surface tension measurement, circular dichroism (CD) spectroscopy. The antimicrobial activities of AMP/surfactant mixtures have also been studied with gram-negative E. coli, gram-positive S. aureus, and fungus C. albicans. The cytotoxicity of the AMP/surfactant mixtures has also been assessed with NIH 3T3 and HSF cells. The surface tension data showed that AMP/SDS mixture was much more surface active than SDS alone. CD results showed that G3 conformation changed from random coil, to -sheet, then to α-helix with increasing SDS concentration, showing a range of structural transformation driven by the different interactions with SDS. The antimicrobial activity of G3 to gram-negative and gram-positive bacteria decreased in the presence of SDS due to the strong interaction of electrostatic attraction between peptide and surfactant. The interaction between G3 and C16TAB, C12EO23, C14DMAO were much weaker than SDS. As a result, the surface tension of surfactants with G3 did not change much, neither were the secondary structures of G3. The antimicrobial activities of G3 were little affected in presence of C12EO23, slightly improved by C14DMAO and clearly enhanced by cationic surfactant C16TAB due to its strong cationic and antimicrobial nature, consistent with their surface physical activities as binary mixtures. Although AMP G3 didn't show activity to fungus, the mixtures of AMP/C16TAB and AMP/C14DMAO could kill C. albicans at high surfactant concentration. The mixtures had rather high cytotoxicity to NIH 3T3 and HSF cells although G3 is nontoxic to cells. Cationic AMPs can be formulated with nonionic, cationic and zwitterionic surfactants during product development, but care must be taken when AMPs are formulated with anionic surfactants, as the strong electrostatic interaction may undermine their antimicrobial activity.
Gender Parity at Work and Its Association With Workplace Sexual Harassment

Background: Gender parity in the workplace—and increased representation of women at work—may reduce workplace sexual harassment, but research on this is unclear. This study assessed the associations between gender parity at work and workplace sexual harassment. Methods: We analyzed data from an online sexual harassment survey conducted with a nationally representative sample of U.S. adults in 2018 (N = 2,009; response rate 29%); current analyses were restricted to employed participants (women n = 610, men n = 690). Data on occupation and industry were each categorized as female-dominant (61%–100% female), male-dominant (0%–39% female), or at parity (40%–60% female). We used sex-stratified logistic regression models to assess associations between gender parity in industry and occupation and workplace sexual harassment. Findings: Our study of employed adults in the U.S. found that 42% women and 15% men had experienced workplace sexual harassment. Logistic regression analyses indicated that women employed in female-dominated industries (adjusted odds ratio [AOR] = 0.52; 95% confidence interval [CI] = [0.33, 0.81]) and men employed in male-dominated occupations (AOR = 0.55; 95% CI = [0.33, 0.91]) were less likely to have experienced workplace sexual harassment. Women in male-dominated occupations were more likely to report harassment or assault by a supervisor (AOR = 2.41, 95% CI = [1.00, 5.80]), and men in male-dominated occupations were less likely to report harassment or assault by a supervisor (AOR = 0.26, 95% CI = [0.08, 0.89]). Conclusion/Application to Practice: Women in female-dominated industries and men in male-dominated occupations, relative to those with workplace gender parity, are at lower risk for harassment. Women in male-dominated occupations are at greater risk for harassment from supervisors. Gender parity at work is not sufficient on its own to address workplace sexual harassment; normative changes are needed.
Understanding the Response of Nitrifying Communities to Disturbance in the McMurdo Dry Valleys, Antarctica

Polar ecosystems are generally limited in nitrogen (N) nutrients, and the patchy availability of N is partly determined by biological pathways, such as nitrification, which are carried out by distinctive prokaryotic functional groups. The activity and diversity of microorganisms are generally strongly influenced by environmental conditions. However, we know little of the attributes that control the distribution and activity of specific microbial functional groups, such as nitrifiers, in extreme cold environments and how they may respond to change. To ascertain relationships between soil geochemistry and the ecology of nitrifying microbial communities, we carried out a laboratory-based manipulative experiment to test the selective effect of key geochemical variables on the activity and abundance of ammonia-oxidizing communities in soils from the McMurdo Dry Valleys of Antarctica. We hypothesized that nitrifying communities, adapted to different environmental conditions within the Dry Valleys, will have distinct responses when submitted to similar geochemical disturbances. In order to test this hypothesis, soils from two geographically distant and geochemically divergent locations, Miers and Beacon Valleys, were incubated over 2 months under increased conductivity, ammonia concentration, copper concentration, and organic matter content. Amplicon sequencing of the 16S rRNA gene and transcripts allowed comparison of the response of ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) to each treatment over time. This approach was combined with measurements of 15NH4+ oxidation rates using 15N isotopic additions. Our results showed a higher potential for nitrification in Miers Valley, where environmental conditions are milder relative to Beacon Valley. AOA exhibited better adaptability to geochemical changes compared to AOB, particularly to the increase in copper and conductivity. AOA were also the only nitrifying group found in Beacon Valley soils. This laboratorial manipulative experiment provided new knowledge on how nitrifying groups respond to changes on key geochemical variables of Antarctic desert soils, and we believe these results offer new insights on the dynamics of N cycling in these ecosystems.
Tracking the cargo of extracellular symbionts into host tissues with correlated electron microscopy and nanoscale secondary ion mass spectrometry imaging

Extracellular bacterial symbionts communicate biochemically with their hosts to establish niches that foster the partnership. Using quantitative ion microprobe isotopic imaging (nanoscale secondary ion mass spectrometry [NanoSIMS]), we surveyed localization of 15N‐labelled molecules produced by the bacterium Vibrio fischeri within the cells of the symbiotic organ of its host, the Hawaiian bobtail squid, and compared that with either labelled non‐specific species or amino acids. In all cases, two areas of the organ's epithelia were significantly more 15N enriched: (a) surface ciliated cells, where environmental symbionts are recruited, and (b) the organ's crypts, where the symbiont population resides in the host. Label enrichment in all cases was strongest inside host cell nuclei, preferentially in the euchromatin regions and the nucleoli. This permissiveness demonstrated that uptake of biomolecules is a general mechanism of the epithelia, but the specific responses to V. fischeri cells recruited to the organ's surface are due to some property exclusive to this species. Similarly, in the organ's deeper crypts, the host responds to common bacterial products that only the specific symbiont can present in that location. The application of NanoSIMS allows the discovery of such distinct modes of downstream signalling dependent on location within the host and provides a unique opportunity to study the microbiogeographical patterns of symbiotic dialogue.
Mitophagy in the Retinal Pigment Epithelium of Dry Age-Related Macular Degeneration Investigated in the NFE2L2/PGC-1α-/- Mouse Model

Increased oxidative stress and mitochondrial damage are observed in protein aggregation diseases, such as age-related macular degeneration (AMD). We have recently reported elevated levels of oxidative stress markers, damaged mitochondria, accumulating lysosomal lipofuscin and extracellular drusen-like structures in the retinal pigment epithelial cells (RPE) of the dry AMD-resembling NFE2L2/PGC1α double knockout (dKO) mouse model. Here, we provide evidence of a disturbance in the autolysosomal machinery handling mitochondrial clearance in the RPE cells of one-year-old NFE2L2/PGC1α-deficient mice. Confocal immunohistochemical analysis revealed an upregulation of autophagosome marker microtubule-associated proteins 1A/1B light chain 3B (LC3B) as well as numerous mitophagy markers, such as PTE-induced putative kinase 1 (PINK1) and E3 ubiquitin ligase (PARKIN) together with damaged mitochondria. However, we detected no evidence of increased autolysosome formation in transmission electron micrographs or of colocalization of lysosomal marker LAMP2 (lysosome-associated membrane protein 2) and the mitochondrial marker ATP synthase β in confocal micrographs. Interestingly, we observed an upregulation of late autolysosomal fusion Ras-related protein (Rab7) in the perinuclear space of RPE cells together with autofluorescence aggregates. Our results reveal that there is at least a relative decrease of mitophagy in the RPE cells of NFE2L2/PGC1α dKO mice. This further supports the hypothesis that mitophagy is a putative therapy target in AMD-like pathology.
Maternal Fat-1 Transgene Protects Offspring from Excess Weight Gain, Oxidative Stress, and Reduced Fatty Acid Oxidation in Response to High-Fat Diet

Overweight and obesity accompanies up to 70% of pregnancies and is a strong risk factor for offspring metabolic disease. Maternal obesity-associated inflammation and lipid profile are hypothesized as important contributors to excess offspring liver and skeletal muscle lipid deposition and oxidative stress. Here, we tested whether dams expressing the fat-1 transgene, which endogenously converts omega-6 (n-6) to omega-3 (n-3) polyunsaturated fatty acid, could protect wild-type (WT) offspring against high-fat diet induced weight gain, oxidative stress, and disrupted mitochondrial fatty acid oxidation. Despite similar body mass at weaning, offspring from fat-1 high-fat-fed dams gained less weight compared with offspring from WT high-fat-fed dams. In particular, WT males from fat-1 high-fat-fed dams were protected from post-weaning high-fat diet induced weight gain, reduced fatty acid oxidation, or excess oxidative stress compared with offspring of WT high-fat-fed dams. Adult offspring of WT high-fat-fed dams exhibited greater skeletal muscle triglycerides and reduced skeletal muscle antioxidant defense and redox balance compared with offspring of WT dams on control diet. Fat-1 offspring were protected from the reduced fatty acid oxidation and excess oxidative stress observed in offspring of WT high-fat-fed dams. These results indicate that a maternal fat-1 transgene has protective effects against offspring liver and skeletal muscle lipotoxicity resulting from a maternal high-fat diet, particularly in males. Altering maternal fatty acid composition, without changing maternal dietary composition or weight gain with high-fat feeding, may highlight important strategies for n-3-based prevention of developmental programming of obesity and its complications.
The Min System Disassembles FtsZ Foci and Inhibits Polar Peptidoglycan Remodeling in Bacillus subtilis

Many bacteria grow and divide by binary fission in which a mother cell divides into two identical daughter cells. To produce two equally sized daughters, the division machinery, guided by FtsZ, must dynamically localize to the midcell each cell cycle. Here, we quantitatively analyzed FtsZ dynamics during growth and found that the Min system of Bacillus subtilis is essential to disassemble FtsZ rings after division. Moreover, a failure to efficiently recycle FtsZ results in an increase in cell size. Finally, we show that the Min system has an additional role in inhibiting cell wall turnover and contributes to the “inert” property of cell walls at the poles. ABSTRACT A microfluidic system coupled with fluorescence microscopy is a powerful approach for quantitative analysis of bacterial growth. Here, we measure parameters of growth and dynamic localization of the cell division initiation protein FtsZ in Bacillus subtilis. Consistent with previous reports, we found that after division, FtsZ rings remain at the cell poles, and polar FtsZ ring disassembly coincides with rapid Z-ring accumulation at the midcell. In cells mutated for minD, however, the polar FtsZ rings persist indefinitely, suggesting that the primary function of the Min system is in Z-ring disassembly. The inability to recycle FtsZ monomers in the minD mutant results in the simultaneous maintenance of multiple Z-rings that are restricted by competition for newly synthesized FtsZ. Although the parameters of FtsZ dynamics change in the minD mutant, the overall cell division time remains the same, albeit with elongated cells necessary to accumulate a critical threshold amount of FtsZ for promoting medial division. Finally, the minD mutant characteristically produces minicells composed of polar peptidoglycan shown to be inert for remodeling in the wild type. Polar peptidoglycan, however, loses its inert character in the minD mutant, suggesting that the Min system not only is important for recycling FtsZ but also may have a secondary role in the spatiotemporal regulation of peptidoglycan remodeling. IMPORTANCE Many bacteria grow and divide by binary fission in which a mother cell divides into two identical daughter cells. To produce two equally sized daughters, the division machinery, guided by FtsZ, must dynamically localize to the midcell each cell cycle. Here, we quantitatively analyzed FtsZ dynamics during growth and found that the Min system of Bacillus subtilis is essential to disassemble FtsZ rings after division. Moreover, a failure to efficiently recycle FtsZ results in an increase in cell size. Finally, we show that the Min system has an additional role in inhibiting cell wall turnover and contributes to the “inert” property of cell walls at the poles.
Influence of canopy openness, ungulate exclosure, and low‐intensity fire for improved oak regeneration in temperate Europe

Abstract Failed oak regeneration is widely reported in temperate forests and has been linked in part to changed disturbance regimes and land‐use. We investigated if the North American fire–oak hypothesis could be applicable to temperate European oaks (Quercus robur, Quercus petraea) using a replicated field experiment with contrasting canopy openness, protection against ungulate browsing (fencing/no fencing), and low‐intensity surface fire (burn/no burn). Survival, relative height growth (RGRH), browsing damage on naturally regenerated oaks (≤300 cm tall), and changes in competing woody vegetation were monitored over three years. Greater light availability in canopy gaps increased oak RGRH (p = .034) and tended to increase survival (p = .092). There was also a trend that protection from browsing positively affected RGRH (p = .058) and survival (p = .059). Burning reduced survival (p < .001), nonetheless, survival rates were relatively high across treatment combinations at the end of the experiment (54%–92%). Most oaks receiving fire were top‐killed and survived by producing new sprouts; therefore, RGRH in burned plots became strongly negative the first year. Thereafter, RGRH was greater in burned plots (p = .002). Burning altered the patterns of ungulate browsing frequency on oaks. Overall, browsing frequency was greater during winter; however, in recently burned plots summer browsing was prominent. Burning did not change relative density of oaks, but it had a clear effect on competing woody vegetation as it reduced the number of individuals (p < .001) and their heights (p < .001). Our results suggest that young, temperate European oaks may respond similarly to fire as their North American congeners. However, disturbance from a single low‐intensity fire may not be sufficient to ensure a persistent competitive advantage—multiple fires and canopy thinning to increase light availability may be needed. Further research investigating long‐term fire effects on oaks of various ages, species‐specific response of competitors and implications for biodiversity conservation is needed.
Angiotensin II induces RAW264.7 macrophage polarization to the M1-type through the connexin 43/NF-κB pathway

Angiotensin II (AngII) serves an important inflammatory role in cardiovascular disease; it can induce macrophages to differentiate into the M1-type, produce inflammatory cytokines and resist pathogen invasion, and can cause a certain degree of damage to the body. Previous studies have reported that connexin 43 (Cx43) and NF-κB (p65) are involved in the AngII-induced inflammatory pathways of macrophages; however, the mechanisms underlying the effects of Cx43 and NF-κB (p65) on AngII-induced macrophage polarization have not been determined. Thus, the present study aimed to investigate the effects of Cx43 and NF-κB (p65) on the polarization process of AngII-induced macrophages. The macrophage polarization-related proteins and mRNAs were examined by flow cytometry, western blotting, immunofluorescence, ELISA and reverse transcription-quantitative PCR analyses. RAW264.7 macrophages were treated with AngII to simulate chronic inflammation and it was subsequently found that AngII promoted RAW 264.7 macrophage polarization towards the M1-type by such effects as the release of inducible nitric oxide synthase (iNOS), tumour necrosis factor (TNF)-α, IL-1β, the secretion of IL-6, and the expression of M1-type indicators, such as CD86. Simultaneously, compared with the control group, the protein expression levels of Cx43 and phosphorylated (p)-p65 were significantly increased following AngII treatment. The M1-related phenotypic indicators, iNOS, TNF-α, IL-1β, IL-6 and CD86, were inhibited by the NF-κB (p65) signalling pathway inhibitor BAY117082. Similarly, the Cx43 inhibitors, Gap26 and Gap19, also inhibited the expression of M1-related factors, and the protein expression levels of p-p65 in the Gap26/Gap19 groups were significantly decreased compared with the AngII group. Altogether, these findings suggested that AngII may induce the polarization of RAW264.7 macrophages to the M1-type through the Cx43/NF-κB (p65) signalling pathway.
Time-Course Transcriptome Study Reveals Mode of bZIP Transcription Factors on Light Exposure in Arabidopsis

The etiolation process, which occurs after germination, is terminated once light is perceived and then de-etiolation commences. During the de-etiolation period, monochromatic lights (blue, red and far-red) induce differences in gene expression profiles and plant behavior through their respective photoreceptors. ELONGATED HYPOCOTYL 5 (HY5), a bZIP-type transcription factor (TF), regulates gene expression in the de-etiolation process, and other bZIP TFs are also involved in this regulation. However, transcriptomic changes that occur in etiolated seedlings upon monochromatic light irradiation and the relationship with the bZIP TFs still remain to be elucidated. Here, we track changes in the transcriptome after exposure to white, blue, red and far-red light following darkness and reveal both shared and non-shared trends of transcriptomic change between the four kinds of light. Interestingly, after exposure to light, HY5 expression synchronized with those of the related bZIP TF genes, GBF2 and GBF3, rather than HY5 HOMOLOG (HYH). To speculate on the redundancy of target genes between the bZIP TFs, we inspected the genome-wide physical binding sites of homodimers of seven bZIP TFs, HY5, HYH, GBF1, GBF2, GBF3, GBF4 and EEL, using an in vitro binding assay. The results reveal large overlaps of target gene candidates, indicating a complicated regulatory literature among TFs. This work provides novel insight into understanding the regulation of gene expression of the plant response to monochromatic light irradiation.