FAST (Flexible Analysis by Software Tool) and CHAMP (CHemico-physical AMinoacidic Parameter data bank): a new tool to investigate protein structure

A flexible package designed to study protein structure is described.The package is devoted to the analysis of protein sequencesby drawing structural profiles of specific structure-relatedamino acid parameters. An Aminoacidic Parameters Data Bank (CHAMP)containing 32 different series of physico-chemical parametersof amino acids is available. Sequences can be loaded from anyASCII format data bank or from keyboard. The program possessesa routine which enables easy updating of the protein data bankand CHAMP Data Bank. FAST reads statistical correlations betweentwo plots in order to identify structural similarities. Plotscan be printed, saved or used for correlation, comparison orgraph overlap by using common spreadsheets (e.g. Lotus 123).Plots can be smoothed by a running mean or a running median.The program also has a special feature—a global flexibilityanalysis of proteins. The package runs on IBM or compatiblesand requires DOS 3.0 or later. Received on June 20, 1989; accepted on August 2, 1989     

Integrated cultivation of salmonids and seaweeds in open systems

Bacterial abundance and production in a vertical profile in Lake Kariba (17dgS), Zimbabwe, were affected by solar irradiance. At the surface, 1.87 × 10⁹ bacteria 1^–1 were found and abundance peaked at 10 m (2.5 × 10⁹ bacteria l^-1), then decreasing with depth. Bacterial reproduction at the surface(0.145 µg C1^–1 h^–1) was nearly four times less than the production at 10 m although bacterial numbers were only 26% less. Thus, bacterial production per cell was lower at the surface than deeper down, suggesting that bacterial production is inhibited at the surface.Bacterial production in GF/F filtered lake water in Whirl Pack bags showed an exponential decrease down to 3 m depth. The inhibition was well in accordance with light extinction in the UV region. Phosphatase activity was low in light exposed bags compared to dark, indicating photolysis of extracellular enzymes, or phototransformation of recalcitrant DOM, which substitutes enzyme activity. Hypolimnetic enzyme activity was less affected by solar light than epilimnetic.     

Influence of nitrate on uptake of ammonium by nitrogen-depleted soybean: is the effect located in roots or shoots?

In non-nodulated soybean [Glycine max (L.) Merrill cv. Ransom]plants that were subjected to 15 d of nitrogen deprivation inflowing hydroponic culture, concentrations of nitrogen declinedto 1.0 and 1.4mmol Ng^–1 dry weight in shoots and roots,respectively, and the concentration of soluble amino acids (determinedas primary amines) declined to 40µmol g^–1 dry weightin both shoots and roots. In one experiment, nitrogen was resuppliedfor 10 d to one set of nitrogen-depleted plants as 1.0 mol m^–3NH₄⁺ to the whole root system, to a second set as 0.5 mol m^–3NH₄⁺ plus 0.5 mol m^–3 NO₃^– to the whole root system,and to a third set as 1.0 mol m^–3 NH₄⁺ to one-half ofa split-root system and 1.0 mol m^–3 NO₃^– to theother half. In a second experiment, 1.0 mol m^–3 of nitrogenwas resupplied for 4 d to whole root systems in NH₄⁺ : NO₃^–ratios of 1:0, 9:1, and 1:1. Nutrient solutions were maintainedat pH 6.0. When NH₄⁺ was resupplied in combination with NO₃^– to thewhole root system in Experiment I, cumulative uptake of NH₄⁺for the 10 d of resupply was about twice as great as when NH₄⁺was resupplied alone. Also, about twice as much NH₄⁺ as NO₃^–was taken up when both ions were resupplied to the whole rootsystem. When NH₄⁺ and NO₃^– were resupplied to separatehalves of a split-root system, however, cumulative uptake ofNH₄⁺ was about half that of NO₃^–. The uptake of NH₄⁺,which is inhibited in nitrogen-depleted plants, thus is facilitatedby the presence of exogenous NO₃^–, and the stimulatingeffect of NO₃^– on uptake of NH₄⁺ appears to be confinedto processes within root tissues. In Experiment II, resupplyof nitrogen as both NH₄⁺ and NO₃^– in a ratio of either1:1 or 9:1 enhanced the uptake of NH₄⁺. The enhancement of NH₄⁺uptake was 1.8-fold greater when the NH₄⁺: NO₃^–-resupplyratio was 1:1 than when it was 9:1; however, only 1.3 timesas much NO₃^– was taken up by plants resupplied with the1 :1 exogenous ratio. The effect of NO₃^– on enhancementof uptake of NH₄⁺ apparently involves more than net uptake ofNO₃^– itself and perhaps entails an effect of NO₃^–uptake on maintenance of K⁺ availability within the plant. Theconcentration of K⁺ in plants declined slightly during nitrogendeprivation and continued to decline following resupply of nitrogen.The greatest decline in K⁺ concentration occurred when nitrogenwas resupplied as NH₄⁺ alone. It is proposed that decreasedavailability of K⁺ within the NH₄⁺-resup-plied plants inhibitedNH₄⁺ uptake through restricted transfer of amino acids fromthe root symplasm into the xylem. Key words: Ammonium, Glycine max, nitrate, nitrogen-nutrition, nitrogen stress, split-root cultures     

Mice lacking the mitochondrial exonuclease MGME1 develop inflammatory kidney disease with glomerular dysfunction

Mitochondrial DNA (mtDNA) maintenance disorders are caused by mutations in ubiquitously expressed nuclear genes and lead to syndromes with variable disease severity and tissue-specific phenotypes. Loss of function mutations in the gene encoding the mitochondrial genome and maintenance exonuclease 1 (MGME1) result in deletions and depletion of mtDNA leading to adult-onset multisystem mitochondrial disease in humans. To better understand the in vivo function of MGME1 and the associated disease pathophysiology, we characterized a Mgme1 mouse knockout model by extensive phenotyping of ageing knockout animals. We show that loss of MGME1 leads to de novo formation of linear deleted mtDNA fragments that are constantly made and degraded. These findings contradict previous proposal that MGME1 is essential for degradation of linear mtDNA fragments and instead support a model where MGME1 has a critical role in completion of mtDNA replication. We report that Mgme1 knockout mice develop a dramatic phenotype as they age and display progressive weight loss, cataract and retinopathy. Surprisingly, aged animals also develop kidney inflammation, glomerular changes and severe chronic progressive nephropathy, consistent with nephrotic syndrome. These findings link the faulty mtDNA synthesis to severe inflammatory disease and thus show that defective mtDNA replication can trigger an immune response that causes age-associated progressive pathology in the kidney.     

Epidemic management and control through risk-dependent individual contact interventions

Testing, contact tracing, and isolation (TTI) is an epidemic management and control approach that is difficult to implement at scale because it relies on manual tracing of contacts. Exposure notification apps have been developed to digitally scale up TTI by harnessing contact data obtained from mobile devices; however, exposure notification apps provide users only with limited binary information when they have been directly exposed to a known infection source. Here we demonstrate a scalable improvement to TTI and exposure notification apps that uses data assimilation (DA) on a contact network. Network DA exploits diverse sources of health data together with the proximity data from mobile devices that exposure notification apps rely upon. It provides users with continuously assessed individual risks of exposure and infection, which can form the basis for targeting individual contact interventions. Simulations of the early COVID-19 epidemic in New York City are used to establish proof-of-concept. In the simulations, network DA identifies up to a factor 2 more infections than contact tracing when both harness the same contact data and diagnostic test data. This remains true even when only a relatively small fraction of the population uses network DA. When a sufficiently large fraction of the population (≳ 75%) uses network DA and complies with individual contact interventions, targeting contact interventions with network DA reduces deaths by up to a factor 4 relative to TTI. Network DA can be implemented by expanding the computational backend of existing exposure notification apps, thus greatly enhancing their capabilities. Implemented at scale, it has the potential to precisely and effectively control future epidemics while minimizing economic disruption.     

Spleen immune status is affected after acute handling stress but not regulated by cortisol in Eurasian perch,Perca fluviatilis

The effects of acute stress on immune status and its regulation by cortisol/corticosteroid receptors have received little attention in percids. To address that question, we investigated the physiological and immune responses of Eurasian perch, Perca fluviatilis to acute stress. We exposed immature perch to an 1-min exondation and measured at 1 h, 6 h, 24 h and 72 h post-stress: (1) stress-related parameters including plasma cortisol and glucose levels, (2) immune parameters in the plasma and in the spleen (complement, respiratory burst and lysozyme activity, total immunoglobulins; gene expression of lysozyme, complement unit 3, apolipoprotein A1 and 14 kDa, hepcidin and chemotaxin) (3) the corticosteroid receptors gene expression in the spleen after having cloned them. In addition, the in vitro effects of cortisol on the spleen immune parameters were also investigated.Plasma cortisol and glucose levels increased markedly 1 h post-stress and returned at basal levels after 24 h. P. fluviatilis mineralocorticoid receptor, but not glucocorticoid receptors, was significantly up-regulated both in vivo after the stress and in vitro by cortisol at a physiological concentration (100 ng/ml). The plasma immune parameters were not significantly affected by the stress. In contrast, spleno-somatic index, spleen lysozyme activity, lysozyme and hepcidin gene expression were depleted and total immunoglobulins increased along the whole time-course (1–72 h). But, these immune parameters were not regulated in vitro by cortisol at physiological or supra-physiological doses.Our results indicate that handling stress may affect spleen antibacterial defences without clear effects on circulating immune compounds and that the elevation of plasma cortisol after handling stress may not be related to the regulation of this splenic response.     

ZMAT3 hypomethylation contributes to early senescence of preadipocytes from healthy first‐degree relatives of type 2 diabetics

Senescence of adipose precursor cells (APC) impairs adipogenesis, contributes to the age‐related subcutaneous adipose tissue (SAT) dysfunction, and increases risk of type 2 diabetes (T2D). First‐degree relatives of T2D individuals (FDR) feature restricted adipogenesis, reflecting the detrimental effects of APC senescence earlier in life and rendering FDR more vulnerable to T2D. Epigenetics may contribute to these abnormalities but the underlying mechanisms remain unclear. In previous methylome comparison in APC from FDR and individuals with no diabetes familiarity (CTRL), ZMAT3 emerged as one of the top‐ranked senescence‐related genes featuring hypomethylation in FDR and associated with T2D risk. Here, we investigated whether and how DNA methylation changes at ZMAT3 promote early APC senescence. APC from FDR individuals revealed increases in multiple senescence markers compared to CTRL. Senescence in these cells was accompanied by ZMAT3 hypomethylation, which caused ZMAT3 upregulation. Demethylation at this gene in CTRL APC led to increased ZMAT3 expression and premature senescence, which were reverted by ZMAT3 siRNA. Furthermore, ZMAT3 overexpression in APC determined senescence and activation of the p53/p21 pathway, as observed in FDR APC. Adipogenesis was also inhibited in ZMAT3‐overexpressing APC. In FDR APC, rescue of ZMAT3 methylation through senolytic exposure simultaneously downregulated ZMAT3 expression and improved adipogenesis. Interestingly, in human SAT, aging and T2D were associated with significantly increased expression of both ZMAT3 and the P53 senescence marker. Thus, DNA hypomethylation causes ZMAT3 upregulation in FDR APC accompanied by acquisition of the senescence phenotype and impaired adipogenesis, which may contribute to FDR predisposition for T2D.