Climate‐driven rampant speciation of the Cape flora

Aim To test whether the radiation of the extremely rich Cape flora is correlated with marine‐driven climate change. Location Middle to Late Miocene in the south‐east Atlantic and the Benguela Upwelling System (BUS) off the west coast of South Africa. Methods We studied the palynology of the thoroughly dated Middle to Late Miocene sediments of Ocean Drilling Program (ODP) Site 1085 retrieved from the Atlantic off the mouth of the Orange River. Both marine upwelling and terrestrial input are recorded at this site, which allows a direct correlation between changes in the terrestrial flora and the marine BUS in the south‐east Atlantic. Results Pollen types from plants of tropical affinity disappeared, and those from the Cape flora gradually increased, between 10 and 6 Ma. Our data corroborate the inferred dating of the diversification in Aizoaceae c. 8 Ma. Main conclusions Inferred vegetation changes for the Late Miocene south‐western African coast are the disappearance of Podocarpus‐dominated Afromontane forests, and a change in the vegetation of the coastal plain from tropical grassland and thicket to semi‐arid succulent vegetation. These changes are indicative of an increased summer drought, and are in step with the development of the southern BUS. They pre‐date the Pliocene uplift of the East African escarpment, suggesting that this did not play a role in stimulating vegetation change. Some Fynbos elements were present throughout the recorded period (from 11 Ma), suggesting that at least some elements of this vegetation were already in place during the onset of the BUS. This is consistent with a marine‐driven climate change in south‐western Africa triggering substantial radiation in the terrestrial flora, especially in the Aizoaceae.     

Four genes in two diverged subfamilies encode the ribulose-1,5-bisphosphate carboxylase small subunit polypeptides of Arabidopsis thaliana

The multigene family encoding the small subunit polypeptides of ribulose-1,5-bisphosphate carboxylase/oxygenase in the crucifer Arabidopsis thaliana has been isolated and the organization and structure of the individual members determined. The family consists of four genes which have been divided into two subfamilies on the basis of linkage and DNA and amino acid sequence similarities. Three of the genes, designated ats1B, ats2B, and ats3B, reside in tandem on an 8 kb stretch of the chromosome. These genes share greater than 95% similarity in DNA sequence and encode polypeptides identical in length and 96.7% similar in amino acid sequence. The fourth gene, ats1A, is at least 10 kb removed from, or completely unlinked to the B subfamily. The B subfamily genes are more similar to each other than to ats1A in nucleotide and amino acid sequence. All four genes are interupted by two introns whose placement within the coding region of the genes is conserved. The introns of the B subfamily genes are similar in length and nucleotide sequence, but show no similarity to the introns of ats1A. Comparison of the DNA sequences within the immediate 5 and 3 flanking sequences among the genes revealed only limited regions of homology. S1 analysis shows that all four genes are expressed.     

Availability of water controls Crassulacean acid metabolism in succulents of the Richtersveld (Namib desert,South Africa)

Features of Crassulacean acid metabolism (CAM) were studied in a variety of different succulents in response to climatic conditions between March 1977 and October 1983 in the southern Namib desert (Richtersveld). A screening in 1977 and 1978 revealed that nearly all investigated succulents performed a CAM, but overnight accumulation of malate declined gradually with decreasing soil water potential, tissue osmotic potential, and leaf water content. This was further substantiated by an extended period of insufficient rainfall in 1979 and 1980 which damaged the evergreen CAM succulents between 80 and 100%. In most of the species still living, neither CO₂-gas exchange nor diurnal acid fluctuation, indicative of CAM, could be detected unless an abundant rainfall restored both CAM features. Plants persisted in a stage of latent life.Water supply is one necessary prerequisite for CAM in the Richtersveld. But even well-watered plants with CAM were sensitive to short-term water stress caused by high water-vapour partialpressure deficit (VPD) in the night, which reduced or prevented CO₂ uptake and resulted in a linear relation between overnight accumulated malate and VPD. The results do not support the opinion that, for the Namib succulents, CAM is an adaptive mechanism to water stress since long-term and short-term water stress stopped nocturnal malate synthesis, but instead lead to the conclusion that nocuturnal CO₂ fixation is only performed when the water status of the plant can be improved simultaneously.Abbreviations CAM Crassulacean acid metabolism - VPD water vapour pressure deficit Dedicated to Professor H. Ziegler on the occasion of his 60th birthday     

The BIORACK facility and its performance during the IML-2 Spacelab mission

The configuration and performance of the Biorack facility during the Second International Microgravity Laboratory mission (IML-2; 8-23 July 1995) is described in detail. During this Spacelab mission, Biorack flew with two incubators (22 degrees C and 37 degrees C), glovebox, cooler (5 degrees C) and four passive thermal conditioning units (PTCU; 5 degrees C and 10 degrees C) in the stowage. The crew worked more than 40 h to perform 19 Biorack experiments originating from seven European countries. Almost 200 Biorack experiment containers had to be translocated in about 1500 predetermined steps before the Space Shuttle Columbia returned after nearly 14 days: 18 h or 236 orbits in space to Kennedy Space Center, Florida.     

Bisulfite compounds as metabolic inhibitors: nonspecific effects on membranes

Bisulfite compounds are shown to be nonspecific inhibitors ofphotosynthetic processes and of ion transport in green tissues.CO₂ fixation and light-dependent transient changes in externalpH are inhibited about 50% by 5x10^–4 M glyoxal-Na-bisulfite.Chloride uptake in the light and in the dark is inhibited tothe same extent at this concentration. At 5x10^–3 M theinhibitor reduces ATP levels in the light and in the dark, andeffects on glycolate oxidase and PEP carboxylase are observed.The extent of inhibition is dependent on time of treatment withglyoxal-Na-bisulfite and freshly prepared NaHSO₃ is equallyas effective as the addition compound. Possible explanations of the bisulfite effects and the relationshipsto SO₂ effects on photosynthesis are discussed. (Received September 1, 1971; )     

Half a century of Scots pine forest ecosystem monitoring reveals long‐term effects of atmospheric deposition and climate change

At two forest sites in Germany (Pfaffenwinkel, Pustert) stocked with mature Scots pine (Pinus sylvestris L.), we investigated changes of topsoil chemistry during the recent 40 years by soil inventories conducted on replicated control plots of fertilization experiments, allowing a statistical analysis. Additionally, we monitored the nutritional status of both stands from 1964 until 2019 and quantified stand growth during the monitoring period by repeated stand inventories. Moreover, we monitored climate variables (air temperature and precipitation) and calculated annual climatic water balances from 1991 to 2019. Atmospheric nitrogen (N) and sulfur (S) deposition between 1964 and 2019 was estimated for the period 1969–2019 by combining annual deposition measurements conducted in 1985–1987 and 2004 with long‐term deposition records from long‐term forest monitoring stations. We investigated interrelations between topsoil chemistry, stand nutrition, stand growth, deposition, and climate trends. At both sites, the onset of the new millennium was a turning point of important biogeochemical processes. Topsoil acidification turned into re‐alkalinization, soil organic matter (SOM) accumulation stopped, and likely turned into SOM depletion. In the new millennium, topsoil stocks of S and plant‐available phosphorus (P) as well as S and P concentrations in Scots pine foliage decreased substantially; yet, age‐referenced stand growth remained at levels far above those expected from yield table data. Tree P and S nutrition as well as climate change (increased temperature and drought stress) have replaced soil acidification as major future challenges for both forests. Understanding of P and S cycling and water fluxes in forest ecosystems, and consideration of these issues in forest management is important for successfully tackling the new challenges. Our study illustrates the importance of long‐term forest monitoring to identify slow, but substantial changes of forest biogeochemistry driven by natural and anthropogenic global change.     

TRAP assists membrane protein topogenesis at the mammalian ER membrane

Membrane protein insertion and topogenesis generally occur at the Sec61 translocon in the endoplasmic reticulum membrane. During this process, membrane spanning segments may adopt two distinct orientations with either their N- or C-terminus translocated into the ER lumen. While different topogenic determinants in membrane proteins, such as flanking charges, polypeptide folding, and hydrophobicity, have been identified, it is not well understood how the translocon and/or associated components decode them. Here we present evidence that the translocon-associated protein (TRAP) complex is involved in membrane protein topogenesis in vivo. Small interfering RNA (siRNA)-mediated silencing of the TRAP complex in HeLa cells enhanced the topology effect of mutating the flanking charges of a signal-anchor, but not of increasing signal hydrophobicity. The results suggest a role of the TRAP complex in moderating the ‘positive-inside’ rule.     

A heterodimer comprised of two bovine lactoferrin antimicrobial peptides exhibits powerful bactericidal activity against Burkholderia pseudomallei

Melioidosis is a severe infectious disease that is endemic in Southeast Asia and Northern Australia. Burkholderia pseudomallei, the causative agent of this disease, has developed resistance to an increasing list of antibiotics, demanding a search for novel agents. Lactoferricin and lactoferrampin are two antimicrobial domains of lactoferrin with a broad spectrum of antimicrobial activity. A hybrid peptide (LFchimera) containing lactoferrampin (LFampin265–284) and a part of lactoferricin (LFcin17–30) has strikingly higher antimicrobial activities compared to the individual peptides. In this study, the antimicrobial activities of this chimeric construct (LFchimera1), as well as of another one containing LFcin17–30 and LFampin268–284, a shorter fragment of LFampin265–284 (LFchimera2), and the constituent peptides were tested against 7 isolates of B. pseudomallei and compared to the preferential antibiotic ceftazidime (CAZ). All isolates including B. pseudomallei 979b shown to be resistant to CAZ, at a density of 10⁵ CFU/ml, could be killed by 5–10 μM of LFchimera1 within 2 h, while the other peptides as well as the antibiotic CAZ only inhibited the B. pseudomallei strains resulting in an overgrowth in 24 h. These data indicate that LFchimera1 could be considered for development of therapeutic agents against B. pseudomallei.     

A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

Background

Recently, Marcus et al. (Bioinformatics 30:3476–83, 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an \(O(n\log g)\) time algorithm called splitMEM that constructs this graph directly (i.e., without using the uncompressed de Bruijn graph) based on a suffix tree, where n is the total length of the genomes and g is the length of the longest genome. Baier et al. (Bioinformatics 32:497–504, 2016) improved their result.

Results

In this paper, we propose a new space-efficient representation of the compressed de Bruijn graph that adds the possibility to search for a pattern (e.g. an allele—a variant form of a gene) within the pan-genome. The ability to search within the pan-genome graph is of utmost importance and is a design goal of pan-genome data structures.