Biology subjects

Kraft, B.

Publications and source records attributed to Kraft, B..

7 recordsLinked to original sources

bioRxiv2026

Effects of sulfide on the activity of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1

Ammonia-oxidizing archaea (AOA) are frequently found in oxygen-depleted marine environments with permanent or temporal presence of sulfide (HS-). However, it remains unexplored how sulfide affects the activity of ammonia-oxidizing archaea. We studied the capability of Nitrosopumilus maritimus SCM1 to oxidize ammonia when exposed to HS-. Ammonia oxidation remained active even after exposure to sulfidic spikes in the lower micromolar range, albeit at reduced rates compared to the absence of HS-. However, 90 {micro}M HS- completely inhibited ammonia oxidation. We found no evidence of NO-dismutation under oxygen depletion and presence of HS- (20 {micro}M): the formation of O2, N2O and N2 did not occur. All in all, we confirmed ammonia oxidation in N. maritimus SCM1 under oxic conditions after sulfide additions, but no evidence of NO-dismutation under sulfidic conditions. Our findings suggest that AOA can recover ammonia-oxidation activity after oxygen re-exposure in regions with periodic sulfide accumulation. However, in permanently sulfidic areas, ammonia oxidation recovery seems unlikely, as NO-dismutation does not appear to be a viable mechanism.

microbiology↗

bioRxiv2023

STIL overexpression shortens lifespan and reduces tumor formation in mice

Centrosomes are the major microtubule organizing centers of animal cells. Supernumerary centrosomes are a common feature of human tumors and associated with karyotype abnormalities and aggressive disease, but whether they are cause or consequence of cancer remains controversial. Here, we analyzed the consequences of centrosome amplification by generating transgenic mice in which centrosome numbers can be increased by overexpression of the structural centrosome protein STIL. We show that STIL overexpression induces centrosome amplification and aneuploidy, leading to senescence, apoptosis, and impaired proliferation in mouse embryonic fibroblasts, and microcephaly with increased perinatal lethality and shortened lifespan in mice. Importantly, both overall tumor formation in mice with constitutive, global STIL overexpression and chemical skin carcinogenesis in animals with inducible, skin-specific STIL overexpression were reduced, an effect that was not rescued by concomitant p53 inactivation. These results suggest that supernumerary centrosomes impair proliferation in vitro as well as in vivo, resulting in reduced lifespan and spontaneous as well as carcinogen-induced tumor formation.

cancer biology↗

bioRxiv2023

Oxygen production via NO dismutation in different ammonia oxidizers.

Ammonia oxidizing archaea (AOA) are widespread and highly abundant in nature. Despite their typical aerobic metabolism, they can be abundant in ecosystems where oxygen is scarce. Recent observations revealed that the AOA isolate Nitrosopumilus maritimus produces oxygen and dinitrogen at nanomolar concentrations, upon oxygen depletion through nitric oxide (NO) dismutation. Here, we explore NO dismutation capability in other ammonia oxidizers with different phylogenetic affinities and from different environmental settings. The organisms explored include three marine AOA, one soil AOA and two soil ammonia-oxidizing bacteria (AOB). Upon oxygen depletion all isolates accumulated oxygen. In incubations with 15N tracers with ongoing oxygen accumulation, the AOA strains Nitrosopumilus adriaticus and Nitrosopumilus viennensis produced 46N2O from nitrite. Transient 46N2O accumulation followed by 30N2 production was detected in the AOA strains Nitrosopumilus piranensis and Nitrosopumilus sp. CCS1, supporting the earlier observation that NO-dismutation is a common metabolism in AOA, albeit with physiological variations between different strains. An important physiological variable is the capability to reduce N2O to N2. The finding of oxygen production in several AOA, as well as AOB, indicates that this process is widely distributed among the tree of life and adds an explanation for their abundance in oxygen-depleted environments.

microbiology↗

bioRxiv2023

Transcriptomic responses of sponge holobionts to in situ, seasonal anoxia and hypoxia

Deoxygenation can be fatal for many marine animals; however, some sponge species are tolerant of hypoxia and anoxia. Indeed, two sponge species, Eurypon sp. 2 and Hymeraphia stellifera, survive seasonal anoxia for months at a time. To understand their tolerance mechanisms, we performed differential gene expression analyses on the sponges, their mitochondria and their microbial symbionts under in situ conditions of normoxia, hypoxia and anoxia. Each species possessed a unique microbiome, but the microbiomes of each species were dominated by a species-specific Thaumarchaeon and a Gammaproteobacterium. Holobiont gene expression was species-and oxygen-level dependent, though there were some shared interspecific responses to deoxygenation. In general, few changes occurred in the expression of sponge metabolic genes as a function of oxygenation level, indicating that they may remain metabolically active under anoxia. However, ATP synthesis genes were significantly upregulated under hypoxia when compared to normoxia, and genes for DNA replication were downregulated. Mitochondrial gene expression was effectively unchanged under both hypoxia and anoxia. Nevertheless, both anoxia and hypoxia caused upregulation of heat shock proteins (HSPs), indicating cellular level adaptations to deoxygenation stress. A meta-analysis demonstrated that sponge transcriptional responses to anoxia were distinct from those displayed by other invertebrates while dormant, and the hypothesis of sponge dormancy under anoxia was not supported. Thaumarchaeota symbionts also upregulated stress response genes in hypoxia, while maintaining expression of oxygen-dependent metabolic pathways under hypoxia and anoxia. Gammaproteobacteria symbionts showed relatively few noteworthy changes in gene expression in response to anoxia but decreased metabolic gene expression in hypoxia. There was no clear evidence of upregulated anaerobic respiration in the transcriptomes of the sponge holobionts under anoxia or hypoxia. The tolerance of some sponges to prolonged anoxia warrants further investigation and could give them an advantage in future oceans following climate change as well as in ancient oceans when oxygen concentrations were lower than at present.

ecology↗

bioRxiv2021

Oxygen production by an ammonia-oxidizing archaeon

Ammonia-oxidizing archaea (AOA) are one of the most abundant groups of microbes in the worlds oceans and are key players in the nitrogen cycle. Their energy metabolism, the oxidation of ammonia to nitrite, requires oxygen. Nevertheless, AOA are abundant in environments where oxygen is undetectable. In incubation experiments, where oxygen concentrations were resolved to the nanomolar range, we show that Nitrosopumilus maritimus produces oxygen (O2) and dinitrogen (N2). The pathway is not completely resolved, but it has nitric oxide as a key intermediate. Part of the oxygen produced is directly used for ammonia oxidation, while some accumulates in the surrounding environment. N. maritimus joins a small handful of organisms known to produce oxygen in the dark, and based on this ability, we re-evaluate their role in oxygen-depleted marine environments.

microbiology↗

bioRxiv2019

Exploring the Links between Specific Depression Symptoms and Brain Structure: A Network Study

The network approach to psychopathology has recently received considerable attention, and is as a novel way of conceptualizing mental disorders as causally interacting symptoms. In this study, we modeled a joint network of depression symptoms and depression-related brain structures, using 21 symptoms and five regional brain measures. We used a mixed sample of 268 individuals previously treated for one or more major depressive episodes and never depressed individuals. The network revealed associations between brain structure and unique depressive symptoms, which may clarify relationships regarding symptomatic and biological heterogeneity in depression.

neuroscience↗

bioRxiv2018

Effects of Attentional Bias Modification on Residual Symptoms in depression. A Randomized Controlled Trial.

BackgroundFollowing treatment, many depressed patients have significant residual symptoms. However, large randomised controlled trials (RCT) in this population are lacking. When Attention bias modification training (ABM) leads to more positive emotional biases, associated changes in clinical symptoms have been reported. A broader and more transparent picture of the true advantage of ABM based on larger and more stringent clinical trials have been requested.\n\nAimsTo evaluate the early effect of two weeks ABM training on blinded clinician-rated and self-reported residual symptoms, and whether changes towards more positive attentional biases (AB) would be associated with symptom reduction.\n\nMethodA total of 321 patients with a history of depression were included in a preregistered randomized controlled double-blinded trial. Patients were randomised to an emotional ABM paradigm over fourteen days or a closely matched control condition. Symptoms based on the Hamilton Rating Scale for Depression (HRSD) and Beck Depression Inventory II (BDI-II) were obtained at baseline and after ABM training.\n\nResultsABM training led to significantly greater decrease in clinician-rated symptoms of depression as compared to the control condition. No differences between ABM and placebo were found for self-reported symptoms. ABM induced a change of AB towards relatively more positive stimuli associated with greater symptom reduction.\n\nConclusionThe current study demonstrates that ABM produces early changes in both AB and blinded clinician-rated depressive symptoms. ABM may have practical potential in the treatment of residual depression.\n\nClinicalTrials.gov ID: NCT02658682

clinical trials↗