Regulationseinheiten in Evolution, Entwicklung und humaner Krankheit

Misregulation of gene expression can result in broad types of diseases and abnormalities. For elucidating the molecular mechanisms underlying evolution, development and disease, the 2% protein-coding regions in the human genome have been studied for decades, but the the 98% non-coding regions remain less understood. Many studies have revealed that evolutionary conserved non-coding elements (CNEs) act as cis-regulatory elements (CREs). Nevertheless, not all CREs are evolutionary conserved and, hence, the identification of CREs has proved challenging. Some CREs work cooperatively to regulate gene expression. Together with their target gene(s), these CREs form regulatory units. For instance, topologically associating domains (TADs) are large regulatory units in the genome, controlling and restricting the interactions between genes and CREs. Many studies have found the disruption of TADs can lead to gene expression misregulation. This thesis aimed at characterizing regulatory units. In particular, we explored the mechanisms by which regulatory unit disruption can lead to changes in gene expression in evolution, development, and disease. The first part of this thesis focused on the identification and characterization of small regulatory units consisting of two CREs. We identified 5,500 pairs of adjacent CNEs (to which we further refer as “CNE-CNE pairs”) in the human genome with either expanded, conserved or contracted inter-CNE sequences compared to the common mammalian ancestor. Particularly, the CNEs in CNE-CNE pairs with conserved and mildly contracted inter-CNEs sequences were most likely to perform as active or poised enhancers; in addition, both CNEs of the pairs exhibited similar epigenetic profiles, suggesting that the CNE-CNE pairs tend to act as small regulatory units. Furthermore, transposon deletions and insertions were associated with the contraction or expansion of inter-CNE sequences, indicating that transposon activity might disrupt the link between the two CNEs in the CNE-CNE pairs, leading to a loss of cis-regulatory function. Our study identified novel regulatory units, and highlighted the existence of cooperative interaction between adjacent CREs in the regulatory units that are distance-sensitive and can be disrupted by transposon activity. Our findings contribute to understanding the mechanism by which selective forces act on CREs in the context of evolution and human genetic diseases. The second part of this thesis investigated the mechanisms by which regulatory units can be disrupted, leading to gene expression misregulation in disease. To address this, we first constructed 1,467 consensus TADs in the “normal genome” and 1,622 consensus TADs in the “cancer genome”. To evaluate the prognosis value of knowing the location of structural variants such as copy number variants (CNVs) within the TADs in cancer patient survival outcome, we applied Cox regression analysis. In this manner, we identified 35 prognostic TADs; 54% of these TADs did not contain any genes with a known association to cancer causality, indicating that a large fraction of the TADs have prognostic value independently of coding variants. Furthermore, 34% of the 35 prognostic TADs underwent strong structural perturbations in the cancer genome. Hence, the prognostic value of at least a fraction of the 35 TADs appeared to be associated with the disruption of normal CRE interactions. Our study emphasized the importance of identifying perturbed regulatory units in monitoring cancer development and progression. Understanding the molecular mechanisms regulating gene expression will help us to understand the formation and evolution of life and to find cures for diseases.Eine fehlerhafte Regulation der Genexpression kann zu einem breiten Spektrum an Krankheiten und Abnormitäten führen. Zur Aufklärung der molekularen Mechanismen, die Evolution, Entwicklung und Krankheit zugrunde liegen, werden die 2% protein-kodierenden Regionen im menschlichen Genom seit Jahrzehnten untersucht, die 98% nichtkodierenden Regionen sind bisher deutlich weniger gut verstanden. Viele Studien haben gezeigt, dass evolutionär konservierte nicht-kodierende Elemente (KNEs) als cis-regulatorische Elemente (CREs) fungieren. Jedoch sind nicht alle CREs evolutionär konserviert, weswegen sich die Identifizierung von CREs als schwierig erwiesen hat. Einige CREs regulieren die Genexpression kooperativ. Zusammen mit ihrem Zielgen oder ihren Zielgenen bilden diese CREs Regulationseinheiten. Zum Beispiel sind topologisch assoziierende Domänen (TADs) große Regulationseinheiten im Genom, die die Interaktionen zwischen Genen und CREs kontrollieren und einschränken. Viele Studien haben bestätigt, dass die Störung der TAD-Struktur zu einer fehlerhaften Genexpression führen kann. Diese Arbeit zielte auf die Charakterisierung von Regulationseinheiten ab. Insbesondere hat sie die Mechanismen erforscht, durch die eine Störung von Regulationseinheiten zu Veränderungen der Genexpression führt, im Kontext von Evolution, Entwicklung und Krankheit. Der erste Teil dieser Arbeit hat sich mit der Identifizierung und Charakterisierung kleiner Regulationseinheiten, bestehend aus zwei CREs, befasst. Wir haben 5500 Paare benachbarter KNEs im menschlichen Genom identifiziert (im Folgenden als ”KNE-KNE-Paare” bezeichnet), bei denen die Inter-KNE-Sequenzen im Vergleich zu dem gemeinsamen Vorfahren der Säugetiere entweder expandiert, konserviert, oder kontrahiert sind. Insbesondere die KNEs in KNE-KNE-Paaren mit konservierten oder leicht kontrahierten Inter-KNE-Sequenzen wiesen die größte Wahrscheinlichkeit auf, als aktive Enhancer oder ”poised” Enhancer (d.h., in Bereitschaftsstellung) zu fungieren. Des Weiteren zeigten die zu einem Paar gehörenden KNEs ähnliche epigenetische Profile, was darauf hindeutet, dass die KNE-KNE-Paare als kleine Regulationseinheiten fungieren. Darüber hinaus waren Transposon-Deletionen (respektive Insertionen) mit einer Kontraktion (respektive Expansion) der Inter-KNE-Sequenzen assoziiert. Dies deutet an, dass die Transposonaktivität möglicherweise den funktionellen Zusammenhang zwis chen den beiden KNEs in den KNE-KNE-Paaren stört und so zu einem Verlust ihrer cis-regulatorischen Funktion führt. Unsere Studie hat neue Regulationseinheiten identifiziert und die Existenz kooperativer Interaktionen zwischen benachbarten CREs, die sich in distanzsensitiven und durch Transposonaktivität zerstörbaren Regulationseinheiten befinden, hervorgehoben. Unsere Ergebnisse tragen zum Verständnis des Mechanismus bei, durch den selektive Kräfte auf CREs im Kontext von Evolution und genetisch bedingten Erkrankungen des Menschen wirken. Der zweite Teil dieser Arbeit hat die Mechanismen untersucht, durch die Regulationseinheiten gestört werden können, was zu einer Fehlregulation der Genexpression bei Krankheiten führt. Hierzu haben wir zunächst 1467 Konsensus-TADs im „normalen Genom“ und 1622 Konsensus-TADs im „Krebsgenom“ konstruiert. Um den prognostischen Wert der Kenntnis der Position von Strukturvarianten wie Kopienzahlvarianten (KZVs) innerhalb der TADs bezüglich der Überlebensdauer von Krebspatienten zu ermitteln, haben wir eine Cox-Regressionsanalyse durchgeführt. Auf diese Weise haben wir 35 prognostische TADs identifiziert; 54% dieser TADs enthielten keine Gene mit einem bekannten Zusammenhang mit der Krebsursache, was darauf hinweist, dass ein großer Teil der TADs unabhängig von kodierenden Varianten einen prognostischen Wert hat. Darüber hinaus zeigten 34% der 35 prognostischen TADs starke strukturelle Störungen im Krebsgenom. Daher schien der prognostische Wert von mindestens einem Bruchteil der 35 TADs mit der Störung normaler CRE-Interaktionen verbunden zu sein. Unsere Studie zeigt, wie wichtig es ist, gestörte Regulationseinheiten zur Überwachung der Krebsentwicklung und -progression zu identifizieren. Das Verständnis der molekularen Mechanismen, die die Genexpression regulieren, wird uns helfen die Entstehung und Evolution des Lebens zu verstehen und Heilmittel für Krankheiten zu finden

Positive periodic solutions of higher-dimensional functional difference equations with a parameter

AbstractBy using Krasnoselskii's fixed point theorem and upper and lower solutions method, we find some sets of positive values λ determining that there exist positive T-periodic solutions to the higher-dimensional functional difference equations of the form x(n+1)=A(n)x(n)+λh(n)fxn−τ(n),n∈Z, where A(n)=diag[a1(n),a2(n),…,am(n)], h(n)=diag[h1(n),h2(n),…,hm(n)], aj,hj:Z→R+, τ:Z→Z are T -periodic, j=1,2,…,m, T⩾1, λ>0, x:Z→Rm, f:R+m→R+m, where R+m={(x1,…,xm)T∈Rm, xj⩾0, j=1,2,…,m}, R+={x∈R,x>0}

7-Piperazine ethyl chrysin inhibits proliferation of lung cancer cells via induction of apoptosis

Purpose: To investigate the effect of 7-piperazine ethyl chrysin (PEC) on A-427 and A-549 lung cancer cell lines.Methods: The cell lines were incubated with PEC at doses of 2, 4, 6, 8 and 10 μM for 24, 48 and 72 h, and their viabilities at each time interval were assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazolium bromide (MTT) assay. Cell apoptosis was evaluated with annexin V fluorescein isothiocyanate/propidium iodide staining, while the expression of ERK1/2 protein was determined using western blot. The involvement of ERK1/2 in the effect of PEC on viability and apoptosis was assessed by incubating the cells with PD98059 (an inhibitor of ERK1/2).Results: Exposure to PEC at doses ≥ 4 μM significantly reduced the viability of A-427 and A-549 cell lines in time- and concentration-dependent manners at 48 h (p < 0.02). The viability of A-427 and A-549 cells was reduced to 21 and 18 %, respectively, on treatment with 8 μM PEC for 48 h. Moreover, PEC treatment induced apoptosis in A-427 (59.67 %) and A-549 (61.37 %) cells after 48 h. Western blot data revealed that PEC also significantly inhibited phosphorylation of ERK1/2 in both cancer cell lines (p < 0.05). Incubation of A-427 and A-549 cells with PD98059 for 48 h also reduced their viability and induced their apoptosis (p < 0.05).Conclusion: These results indicate that PEC inhibits the viability of lung cancer cells via inhibition of ERK1/2 expression. Thus, PEC may be efective for the treatment of lung carcinoma but further studies are required to ascertain this.Keywords: 7-Piperazine ethyl chrysin, Lung cancer cells, Apoptosis, Viability, inhibitio

Exploring Color Invariance through Image-Level Ensemble Learning

In the field of computer vision, the persistent presence of color bias, resulting from fluctuations in real-world lighting and camera conditions, presents a substantial challenge to the robustness of models. This issue is particularly pronounced in complex wide-area surveillance scenarios, such as person re-identification and industrial dust segmentation, where models often experience a decline in performance due to overfitting on color information during training, given the presence of environmental variations. Consequently, there is a need to effectively adapt models to cope with the complexities of camera conditions. To address this challenge, this study introduces a learning strategy named Random Color Erasing, which draws inspiration from ensemble learning. This strategy selectively erases partial or complete color information in the training data without disrupting the original image structure, thereby achieving a balanced weighting of color features and other features within the neural network. This approach mitigates the risk of overfitting and enhances the model's ability to handle color variation, thereby improving its overall robustness. The approach we propose serves as an ensemble learning strategy, characterized by robust interpretability. A comprehensive analysis of this methodology is presented in this paper. Across various tasks such as person re-identification and semantic segmentation, our approach consistently improves strong baseline methods. Notably, in comparison to existing methods that prioritize color robustness, our strategy significantly enhances performance in cross-domain scenarios. The code available at \url{https://github.com/layumi/Person\_reID\_baseline\_pytorch/blob/master/random\_erasing.py} or \url{https://github.com/finger-monkey/Data-Augmentation}

Cancer Is Associated with Alterations in the Three-Dimensional Organization of the Genome

The human genome is organized into topologically associating domains (TADs), which represent contiguous regions with a higher frequency of intra-interactions as opposed to inter-interactions. TADs contribute to gene expression regulation by restricting the interactions between their regulatory elements, and TAD disruption has been associated with cancer. Here, we provide a proof of principle that mutations within TADs can be used to predict the survival of cancer patients. Specifically, we constructed a set of 1467 consensus TADs representing the three-dimensional organization of the human genome and used Cox regression analysis to identify a total of 35 prognostic TADs in different cancer types. Interestingly, only 46% of the 35 prognostic TADs comprised genes with known clinical relevance. Moreover, in the vast majority of such cases, the prognostic value of the TAD was not directly related to the presence/absence of mutations in the gene(s), emphasizing the importance of regulatory mutations. In addition, we found that 34% of the prognostic TADs show strong structural perturbations in the cancer genome, consistent with the widespread, global epigenetic dysregulation often observed in cancer patients. In summary, this study elucidates the mechanisms through which non-coding variants may influence cancer progression and opens new avenues for personalized medicine

Effects of experimental parameters on elemental analysis of coal by laser-induced breakdown spectroscopy

The purpose of this work is to improve the precision of the elemental analysis of coal using laser-induced breakdown spectroscopy (LIBS). The LIBS technique has the ability to allow simultaneous elemental analysis and on-line determination, so it could be used in the elemental analysis of coal. Organic components such as C, H, O, N and inorganic components such as Ca, Mg, Fe, Al, Si, Ti, Na, and K of coal have been identified. The precision of the LIBS technique depends strongly on the experimental conditions, and the choice of experimental parameters should be aimed at optimizing the repeatability of the measurements. The dependences of the relative standard deviation (RSD) of the LIBS measurements on the experimental parameters including the sample preparation parameters, lens-to-sample distance, sample operation mode, and ambient gas have been investigated. The results indicate that the precision of LIBS measurements for the coal sample can be improved by using the optimum experimental parameters