Incomplete proteasomal degradation of green fluorescent proteins in the context of tandem fluorescent protein timers

Tandem fluorescent protein timers (tFTs) report on protein age through time-dependent change in color, which can be exploited to study protein turnover and trafficking. Each tFT, composed of two fluorescent proteins (FPs) that differ in maturation kinetics, is suited to follow protein dynamics within a specific time range determined by the maturation rates of both FPs. So far, tFTs have been constructed by combining slower-maturing red fluorescent proteins (redFPs) with the faster-maturing superfolder green fluorescent protein (sfGFP). Toward a comprehensive characterization of tFTs, we compare here tFTs composed of different faster-maturing green fluorescent proteins (greenFPs) while keeping the slower-maturing redFP constant (mCherry). Our results indicate that the greenFP maturation kinetics influences the time range of a tFT. Moreover, we observe that commonly used greenFPs can partially withstand proteasomal degradation due to the stability of the FP fold, which results in accumulation of tFT fragments in the cell. Depending on the order of FPs in the timer, incomplete proteasomal degradation either shifts the time range of the tFT toward slower time scales or precludes its use for measurements of protein turnover. We identify greenFPs that are efficiently degraded by the proteasome and provide simple guidelines for the design of new tFTs.     

Estimation of Box's ε for low‐ and high‐dimensional repeated measures designs with unequal covariance matrices

We present new inference methods for the analysis of low‐ and high‐dimensional repeated measures data from two‐sample designs that may be unbalanced, the number of repeated measures per subject may be larger than the number of subjects, covariance matrices are not assumed to be spherical, and they can differ between the two samples. In comparison, we demonstrate how crucial it is for the popular Huynh‐Feldt (HF) method to make the restrictive and often unrealistic or unjustifiable assumption of equal covariance matrices. The new method is shown to maintain desired α‐levels better than the well‐known HF correction, as demonstrated in several simulation studies. The proposed test gains power when the number of repeated measures is increased in a manner that is consistent with the alternative. Thus, even increasing the number of measurements on the same subject may lead to an increase in power. Application of the new method is illustrated in detail, using two different real data sets. In one of them, the number of repeated measures per subject is smaller than the sample size, while in the other one, it is larger.     

Madagascar Fish Eagle productivity in the Tsimembo-Manambolomaty Protected Area and surrounding habitat of western Madagascar

We monitored the productivity of the critically endangered Madagascar Fish Eagle Haliaeetus vociferoides inside and outside of the Tsimembo-Manambolomaty Protected Area (T-M PA), western Madagascar from 2010 to 2015. We recorded 14 breeding pairs inside and 13 outside T-M PA. The T-M PA and surrounding habitat hosted respectively 10 and six breeding polyandrous pairs, composed of one adult female and two adult males. During the six-year study period, 101 eggs were laid in nests in T-M PA of which 60 hatched and 58 young fledged. We recorded 62 eggs laid in nests outside the T-M PA of which 39 hatched and 36 young fledged. Productivity was similar at both sites, inside and outside T-M PA, with 0.84 (58/69) and 0.76 (36/47) fledgling per nesting attempt and 0.69 (58/84) and 0.5 (36/72) fledglings per territorial pair, respectively. Polyandrous pairs have higher productivity compared with normal pairs. Threats to Madagascar Fish Eagles and their habitat were low due to the existence of a community-based resource management system called the Local Management Secured System (GELOSE) inside and outside the T-M PA. This system is based on strengthening local traditional customs and rules, and involving local people in managing their natural resources sustainably along with biodiversity conservation.     

Late Eocene sea retreat from the Tarim Basin (west China) and concomitant Asian paleoenvironmental change

The Paleogene sediments of the southwest Tarim Basin along the West Kunlun Shan in western China include the remnants of the easternmost extent of a large epicontinental sea. This shallow sea once extended across the Eurasian continent before it retreated westward and eventually separated as the Paratethys Sea. Climate modeling results suggest that this sea retreat is an equally important forcing mechanism as the Tibetan plateau uplift in the aridification of the Asian continental interior and the intensification of the Asian monsoon system. The age and paleogeography of the retreat are poorly constrained, hindering the understanding of its cause and paleoenvironmental impacts. This study reports litho- and biostratigraphic results from two sections recording the last major regression out of the Tarim Basin that is expressed by a regional transition from marine clastics and limestones to continental red-beds. Rich micro- and macrofossil assemblages, including benthic foraminifera, ostracods, bivalves, calcareous nannofossils and organic walled dinoflagellate cysts (dinocysts), indicate a shallow, proximal and marine environment. Strong similarity to assemblages known from Central Asia and Europe confirms that surface–ocean connections extended across Eurasia from the Tarim Basin to the western Tethys during the latest Eocene. Moreover, the recovered fossil associations date the last marine sediments as earliest Priabonian in age (~ 37 Ma; overlap between dinoflagellate Mps Interval Zone and calcareous nannofossil Zone CP 14). The retreat of the sea from the Tarim Basin is time-equivalent with the sea level lowstand at the Bartonian–Priabonian boundary but pre-dates both the Oligocene–Miocene regional uplift of the Pamir mountains and Kunlun Shan and the major eustatic sea-level falls of the Eocene–Oligocene Transition (~ 34 Ma) and mid-Oligocene (~ 30 Ma), which are usually held responsible for the sea retreat. Furthermore, a concomitant and significant aridification step occurs at ~ 36.6 Ma (top of chron C17n.1n) as recorded by regional sedimentary records of the Xining Basin along the northeastern Tibetan Plateau, suggesting that the Tarim Sea served as a significant moisture contributor for the Asian interior.     

The influence of the non-dialysable sugar-peptide fraction from bovine blood plasma on the amino acid incorporation of BHK-21 normal and RSV transformed cells.

The non-dialysable sugar-peptide rich fraction of bovine blood plasma has been studied with regard to its influence on the amino acid incorporation of BHK-21 and BHK/RSV cells in vitro. The results indicate that the Nsp fraction contains a peptide factor(s) causing changes in activity for the protein and DNA synthethizing system in both the cell cultures examined. The biological activity of the factor(s) is regulated by interaction with blood serum components and this fact may play a leading role in its regulatory function.     

Glucose and glutamate metabolism ofLegionella pneumophila

Two serotype 1 strains ofLegionella pneumophila, Phildelphia 2 and Bellingham, were tested for their ability to metabolize five common substrates by measuring¹⁴CO₂ released and¹⁴C-carbon incorporated into macromolecules. No major differences were noted between the two strains or preparations grown in the yolk sac of chick embryos or agar-broth diphasic medium, following 2 or 14 pasaages on agar. Glutamate was the most actively metabolized substrate, followed by glutamine. Acetate, glucose, and succinate were utilized at much more moderate rates. Changes in cell density and substrate concentration altered the channeling of glutamate and glucose into CO₂ and macromolecules. Specific CO₂ felease from glutamate was greatest at low cell density and high substrate concentration, while carbon incorporation was increased at high substrate concentration. A reciprocal relationship was noted with glucose: the proportion of carbon incorporation was enhanced at low substrate concentration, but CO₂ release paralleled increases in substrate concentration. The pH optimum for glutamate carbon incorporation and CO₂ release was 5.5 and 6.1, respectively, but 25% of both activities were retained at pH 3.1. CO₂ release from glucose was maximal at pH 7.5 with negligible activity at pH 3.1. Pathways of glucose metabolism were explored by employing glucose, glucose-1-phosphate, and glucose-6-phosphate labeled in various carbon positions. The glycolytic pathway appeared to play a lesser role than the pentose phosphate and/or Entner-Doudoroff pathways. Glucose-1-phosphate was metabolized at a much higher rate than glucose or glucose-6-phosphate. We conclude that glutamate is utilized primarily as an energy source while glucose may serve as an important metabolite for the nutrition ofL. pneumophila.     

Force variability depends on core and muscle temperature

The aim of this study was to investigate if voluntary activation and force variability during maximal voluntary contraction (MVC) depends more on muscle (local) or body (core) temperature. Ten volunteers performed a 2-min MVC of the knee extensors under the control (CON) conditions (ambient temperature (21 °C), relative humidity (30%), and air velocity (∼0.1 m/s)) as well as after heating (HT) and cooling (CL) of the lower body. During water manipulation procedure lower body was immersed up to the waist in a water bath at ∼44 °C for 45 min for HT experiment, and ∼15 °C for 30 min for CL experiment. Peak torque, torque variability, muscle voluntary activation and half-relaxation time were assessed during the exercise. HT increased muscle (2.8±0.2 °C) and rectal (1.9±0.1 °C) temperatures while CL lowered muscle (2.2±0.2 °C) temperature, but did not affect rectal temperature. During 2-min MVC, peak torque decreased (P<0.05; SP>90%) and to a lower level in HT compared to CON and CL experiments (52.6±2.3% versus 69.0±2.3% and 65.6±1.9% MVC, respectively, P<0.05; SP>90%). Torque variability increased significantly during exercise and was significantly larger in HT and lower in CL compared to CON experiment. Voluntary activation of exercising muscle was more depressed in HT (i.e. greater central fatigue) and the smallest effect was found in CL compared to CON. In conclusion increased core and muscle temperature impairs voluntary activation and increases force variability of the exercising muscles while a local muscle cooling decrease force variability but has a small effect on central fatigue.