Effects of physical factors on photosynthesis by the Antarctic liverwort Marchantia berteroana

 Effects of irradiance, temperature and water availability on respiration and photosynthesis in a maritime Antarctic liverwort, Marchantia berteroana, were investigated. Carbon dioxide exchange was measured using an infra-red gas analysis system under controlled conditions. The relationships between respiration, photosynthesis, irradiance and temperature were modelled. Application of these models to year-round micro-climate data provided an estimate of yearly net productivity of 823 (SE=75) mg C⋅g^-1 ash-free dry weight. year^-1; this is somewhat higher than figures obtained for other Antarctic cryptogams. Desiccation had a highly adverse affect on Marchantia. Photosynthetic capacity was reduced below a water content of 12 g⋅g^-1 afdw, and there was only a limited recovery (ca. 10%) after dehydration. Freezing also caused a great reduction in photosynthesis, although the model suggested that photosynthesis at sub-zero temperatures is likely. It is suggested that seasonality in the photosynthetic capacity and the survival of sub-zero temperatures might be important. It is concluded that Marchantia is a relatively productive Antarctic cryptogam that may dominate favourable areas, but that its low tolerance of environmental stress, particularly desiccation, limits its distribution to relatively mild habitats. Received: 8 January 1996/Accepted: 12 May 1996     

Fast atom bombardment mass spectrometry as a tool for the rapid determination of enantioselective binding of methylated cyclodextrins

The first FABMS study of the enantioselectivity shown during complex formation between per-methylated cyclodextrins and pairs of enantiomeric guest molecules is described. The 1:1 mixtures of the cyclodextrins, both α- and β-, with the guests, the methyl esters of the amino acids tryptophan and phenylalanine, were studied in a 100:50:1 glycerol-thioglycerol-trifluoro-acetic acid matrix. The uncomplexed cyclodextrin peaks were then used as internal standards to determine the preference of the cavity for one or other of the enantiomers. A clear trend for the preferential binding, greater than 5:1 in each case, of the d-enantiomers of the amino acid esters was observed in agreement with literature ¹H NMR experiments. This methodology provides a rapid route to assessing the enantioselectivity shown by the widely used cyclodextrins towards pairs of enantiomeric guests.     

The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30

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Endoplasmic reticulum-associated protein degradation

The quality control system in the endoplasmic reticulum of eukaryotic cells ensures that newly synthesized proteins that fail to fold into the correct conformation or unassembled orphan subunits of oligomeric proteins are rapidly eliminated by proteolytic degradation. This entails the export of proteins from the endoplasmic reticulum to the cytosol followed by their destruction by the cytosolic ubiquitin/proteasome pathway. While this mechanism effectively prevents the cellular accumulation of non-functional or unwanted endogenous proteins, it renders the cell vulnerable to certain viruses and toxins that are able to subvert this degradative mechanism for their own advantage.     

Nucleosome positioning signals in the DNA sequence of the human and mouse H19 imprinting control regions

We have investigated the sequences of the mouse and human H19 imprinting control regions (ICRs) to see whether they contain nucleosome positioning information pertinent to their function as a methylation-regulated chromatin boundary. Positioning signals were identified by an in vitro approach that employs reconstituted chromatin to comprehensively describe the contribution of the DNA to the most basic, underlying level of chromatin structure. Signals in the DNA sequence of both ICRs directed nucleosomes to flank and encompass the short conserved sequences that constitute the binding sites for the zinc finger protein CTCF, an essential mediator of insulator activity. The repeat structure of the human ICR presented a conserved array of strong positioning signals that would preferentially flank these CTCF binding sites with positioned nucleosomes, a chromatin structure that would tend to maintain their accessibility. Conversely, all four CTCF binding sites in the mouse sequence were located close to the centre of positioning signals that were stronger than those in their flanks; these binding sites might therefore be expected to be more readily incorporated into positioned nucleosomes. We found that CpG methylation did not effect widespread repositioning of nucleosomes on either ICR, indicating that allelic methylation patterns were unlikely to establish allele-specific chromatin structures for H19 by operating directly upon the underlying DNA-histone interactions; instead, epigenetic modulation of ICR chromatin structure is likely to be mediated principally at higher levels of control. DNA methylation did, however, both promote and inhibit nucleosome positioning at several sites in both ICRs and substantially negated one of the strongest nucleosome positioning signals in the human sequence, observations that underline the fact that this epigenetic modification can, nevertheless, directly and decisively modulate core histone-DNA interactions within the nucleosome.     

Regulation of somatic cell reprogramming through inducible mir-302 expression

Global demethylation is required for early zygote development to establish stem cell pluripotency, yet our findings reiterate this epigenetic reprogramming event in somatic cells through ectopic introduction of mir-302 function. Here, we report that induced mir-302 expression beyond 1.3-fold of the concentration in human embryonic stem (hES) H1 and H9 cells led to reprogramming of human hair follicle cells (hHFCs) to induced pluripotent stem (iPS) cells. This reprogramming mechanism functioned through mir-302-targeted co-suppression of four epigenetic regulators, AOF2 (also known as KDM1 or LSD1), AOF1, MECP1-p66 and MECP2. Silencing AOF2 also caused DNMT1 deficiency and further enhanced global demethylation during somatic cell reprogramming (SCR) of hHFCs. Re-supplementing AOF2 in iPS cells disrupted such global demethylation and induced cell differentiation. Given that both hES and iPS cells highly express mir-302, our findings suggest a novel link between zygotic reprogramming and SCR, providing a regulatory mechanism responsible for global demethylation in both events. As the mechanism of conventional iPS cell induction methods remains largely unknown, understanding this microRNA (miRNA)-mediated SCR mechanism may shed light on the improvements of iPS cell generation.     

Causal inference for heritable phenotypic risk factors using heterogeneous genetic instruments

Over a decade of genome-wide association studies (GWAS) have led to the finding of extreme polygenicity of complex traits. The phenomenon that “all genes affect every complex trait” complicates Mendelian Randomization (MR) studies, where natural genetic variations are used as instruments to infer the causal effect of heritable risk factors. We reexamine the assumptions of existing MR methods and show how they need to be clarified to allow for pervasive horizontal pleiotropy and heterogeneous effect sizes. We propose a comprehensive framework GRAPPLE to analyze the causal effect of target risk factors with heterogeneous genetic instruments and identify possible pleiotropic patterns from data. By using GWAS summary statistics, GRAPPLE can efficiently use both strong and weak genetic instruments, detect the existence of multiple pleiotropic pathways, determine the causal direction and perform multivariable MR to adjust for confounding risk factors. With GRAPPLE, we analyze the effect of blood lipids, body mass index, and systolic blood pressure on 25 disease outcomes, gaining new information on their causal relationships and potential pleiotropic pathways involved.     

A Uve1p-Mediated Mismatch Repair Pathway in Schizosaccharomyces pombe

UV damage endonuclease (Uve1p) from Schizosaccharomyces pombe was initially described as a DNA repair enzyme specific for the repair of UV light-induced photoproducts and proposed as the initial step in an alternative excision repair pathway. Here we present biochemical and genetic evidence demonstrating that Uve1p is also a mismatch repair endonuclease which recognizes and cleaves DNA 5' to the mispaired base in a strand-specific manner. The biochemical properties of the Uve1p-mediated mismatch endonuclease activity are similar to those of the Uve1p-mediated UV photoproduct endonuclease. Mutants lacking Uve1p display a spontaneous mutator phenotype, further confirming the notion that Uve1p plays a role in mismatch repair. These results suggest that Uve1p has a surprisingly broad substrate specificity and may function as a general type of DNA repair protein with the capacity to initiate mismatch repair in certain organisms.