Macroecology of methane-oxidizing bacteria: the β-diversity of pmoA genotypes in tropical and subtropical rice paddies

Studies addressing microbial biogeography have increased during the past decade, but research on microbial distribution patterns is still in its infancies, and many aspects are only poorly understood. Here, we compared the methanotroph community in paddy soils sampled in Indonesia, Vietnam, China and Italy, focusing on the distance-decay relationship. We used the pmoA gene as marker for methanotroph diversity in terminal restriction fragment length polymorphism, microarray and pyrosequencing approaches. We could observe a significant increase of -diversity with geographical distance across continents (12000km). Measured environmental parameters explained only a small amount of data variation, and we found no evidence for dispersal limitation. Thus, we propose historical contingencies being responsible for the observed patterns. Furthermore, we performed an in-depth analysis of type II methanotroph pmoA distribution at the sequence level. We used ordination analysis to project sequence dissimilarities into a three-dimensional space (multidimensional scaling). The ordination suggests that type II methanotrophs in paddy fields can be divided into five major groups. However, these groups were found to be distributed in all soils independent of the geographic origin. By including tropical field sites (Indonesia and Vietnam) into the analysis, we further observed the first paddy fields harbouring a methanotroph community depleted in type II methanotrophs

Structural disorder promotes assembly of protein complexes

<p>Abstract</p> <p>Background</p> <p>The idea that the assembly of protein complexes is linked with protein disorder has been inferred from a few large complexes, such as the viral capsid or bacterial flagellar system, only. The relationship, which suggests that larger complexes have more disorder, has never been systematically tested. The recent high-throughput analyses of protein-protein interactions and protein complexes in the cell generated data that enable to address this issue by bioinformatic means.</p> <p>Results</p> <p>In this work we predicted structural disorder for both <it>E. coli </it>and <it>S. cerevisiae</it>, and correlated it with the size of complexes. Using IUPred to predict the disorder for each complex, we found a statistically significant correlation between disorder and the number of proteins assembled into complexes. The distribution of disorder has a median value of 10% in yeast for complexes of 2–4 components (6% in <it>E. coli</it>), but 18% for complexes in the size range of 11–100 proteins (12% in <it>E. coli</it>). The level of disorder as assessed for regions longer than 30 consecutive disordered residues shows an even stronger division between small and large complexes (median values about 4% for complexes of 2–4 components, but 12% for complexes of 11–100 components in yeast). The predicted correlation is also supported by experimental evidence, by observing the structural disorder in protein components of complexes that can be found in the Protein Data Bank (median values 1. 5% for complexes of 2–4 components, and 9.6% for complexes of 11–100 components in yeast). Further analysis shows that this correlation is not directly linked with the increased disorder in hub proteins, but reflects a genuine systemic property of the proteins that make up the complexes.</p> <p>Conclusion</p> <p>Overall, it is suggested and discussed that the assembly of protein-protein complexes is enabled and probably promoted by protein disorder.</p

Automatisierte Klassifikation nach WRB 2015 mit KA 5-konformen Daten – Qualität der Ableitung bei beschränkten Daten

Zur Verwendung in großen Profildatenbanken wurde eine Datenbankanwendung erstellt, die Bodennamen nach World Reference Base for Soil Resources 2014, update 2015 (WRB) automatisiert aus Profilbeschrieben nach Bodenkundlicher Kartieranleitung und Labordaten ableitet. Mit einem Datensatz von 201 gut beschriebenen Profilen aus Deutschland, Österreich und der Schweiz wurden die Auswirkungen von fehlenden Daten auf die Qualität der Ableitung geprüft. Insbesondere sind Ableitungen allein aus dem Horizontsymbol ebenso wenig erfolgversprechend wie Ableitungen ohne Horizontsymbolinformation. Wir schließen daraus, dass Bodenmerkmale ohne eine grundsätzliche Einordnung in einen genetischen Zusammenhang nicht im Nachhinein genetisch interpretierbar sind. Da die Auswertungen sehr komplex sind, kann dies auch für andere Datenauswertungen als gültig angenommen werden

Utahns are Becoming More Likely to Say Human-Caused Climate Change is Happening

Scientists who study the earth’s climate overwhelmingly agree that human activities are causing rapid change1 . Most Americans also agree that global warming is happening (74%) and caused by humans (61%)2 . However, the same research finds that about one in eight (12%) of Americans do not think global warming is happening. This indicates that despite scientific consensus, some Americans remain skeptical about whether climate change is real and if humans are the cause

Utahns\u27 Perceptions of Climate Change and Disaster Vulnerabilities

Climate change increases the frequency and severity of extreme weather events, making people more vulnerable in a variety of ways1-2. It is essential to determine if individuals believe they are susceptible to the effects of climate change in order to develop effective adaptation strategies. Climate change has contributed to extreme weather occurrences in Utah in recent years. For instance, in the summer of 2022, there was a severe or extreme drought in all of Utah\u27s counties3. Health effects of drought vary with intensity4 and can cause climate related deaths directly and indirectly, such as by worsening air quality which can increase cardiovascular and pulmonary disease5-8. According to most climate models, such events are likely to continue as temperature is expected to increase and snowpack to decrease in the western U.S. and Utah9. A recent statewide survey found that Utahns are concerned about various environmental and climatic issues including increased temperature, poor air quality, drought/lack of water etc10. Moreover, since 2020, more Utahns agree with the scientific consensus that human activities are causing climate change11. This research brief uses representative statewide survey data from the 2023 Utah People and Environment Poll (UPEP) to understand how Utah residents consider themselves vulnerable to climate change, how prepared they think they are for climate change, and if they believe they need to plan or prepare for climate change

Bodenklassifizierung nach WRB mit Bodendaten nach Kartieranleitung

Die internationale Bodenklassifikation World Reference Base for Soil Resources (WRB) wird in der internationalen fachlichen wie administrativen Arbeit zur Benennung von Böden verwendet. Die Klassifizierung erfolgt nicht wie in der deutschen Bodensystematik aufgrund der Folge der im Profil vorkommenden morphogenetischen Horizonte, sondern durch Betrachtung des Gesamtprofils hinsichtlich unterschiedlicher Eigenschaften. Dies führt zu Problemen mit in Datenbanken abgelegten Bodendaten, die allgemein neben den Profilmerkmalen morphogenetische Horizonte beschreiben. Einige dieser Probleme werden beispielhaft vorgestellt, darunter die Festlegung der Grenzen diagnostischer Horizonte, sei es wegen der Art der Beschreibung der Horizontgrenzen, unscharfer Definitionen in der WRB oder wegen der Datenstrukturen der Bodendatenbanken, und die Problematik des abrupten Bodenartenwechsels. Es wird ein algorithmen-basierter Ansatz vorgestellt, mit dem die diagnostischen Horizonte, Materialien und Eigenschaften der WRB sowie die für die Benennung benötigten Namensbestandteile Referenzbodengruppe, Qualifier und Specifier aus den Profilbeschrieb-Daten nach KA5 und Labordaten ermittelt werden können. Die Algorithmen sind so angelegt, dass die Einzelparameter in absteigender Reihenfolge der Zuverlässigkeit für die Ableitung abgefragt werden. Mithilfe von im Gelände nach KA5 beschriebenen und nach WRB klassifizierten Fahlerdeprofilen aus Brandenburg wird die Zuverlässigkeit der Ableitungen geprüft. In einem Ausblick sollen mögliche Konsequenzen der Arbeiten für eine Verbesserung der Klassifikation ebenso diskutiert werden wie Vorschläge zur Verbesserung der Datenaufnahme, um eine Klassifizierung nach WRB zu vereinfachen

Ableitungsschlüssel WRB 2007 aus Bodendaten nach KA 5

Bodennamen nach World Reference Base for Soil Resources (WRB) werden automa-tisiert aus Profilbeschrieben nach Boden-kundlicher Kartieranleitung (Ad-hoc AG BODEN 2005, weiter als KA 5) und Labor-daten abgeleitet. Die Datenbankanwen-dung wurde mit einen umfangreichen Pro-fildatensatz aus dem Fachinformations-system Bodengeologie des Landesamtes für Bergbau, Geologie und Rohstoffe Bran-denburg getestet. Über 90 Prozent richtig erkannte Diagnostika und Namenselemen-te der WRB zeigen das Potential des im-plementierten Verfahrens. Die MS Access-Anwendung ist frei zugänglich unter: www.bgr.bund.de/uebersetzungsschluessel

Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14.

Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins, there are a number of intrinsically disordered proteins (IDPs) that can also serve as highly effective protecting agents in the cells. One of the largest groups of disordered chaperones is the group of dehydrins, proteins that are expressed at high levels under different abiotic stress conditions, such as drought, high temperature, or osmotic stress. Dehydrins are characterized by the presence of different conserved sequence motifs that also serve as the basis for their categorization. Despite their accepted importance, the exact role and relevance of the conserved regions have not yet been formally addressed. Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana's Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of different regions of ERD14