Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems

Bacteria have adaptive immunity against viruses (phages) in the form of CRISPR-Cas immune systems. Currently, 6 types of CRISPR-Cas systems are known and the molecular study of three of these has revealed important molecular differences. It is unknown if and how these molecular differences change the outcome of phage infection and the evolutionary pressure the CRISPR-Cas systems faces. To determine the importance of these molecular differences, we model a phage outbreak entering a population defending exclusively with a type I/II or a type III CRISPR-Cas system. We show that for type III CRISPR-Cas systems, rapid phage extinction is driven by the probability to acquire at least one resistance spacer. However, for type I/II CRISPR-Cas systems, rapid phage extinction is characterized by an a threshold-like behaviour: any acquisition probability below this threshold leads to phage survival whereas any acquisition probability above it, results in phage extinction. We also show that in the absence of autoimmunity, high acquisition rates evolve. However, when CRISPR-Cas systems are prone to autoimmunity, intermediate levels of acquisition are optimal during a phage outbreak. As we predict an optimal probability of spacer acquisition 2 factors of magnitude above the one that has been measured, we discuss the origin of such a discrepancy. Finally, we show that in a biologically relevant parameter range, a type III CRISPR-Cas system can outcompete a type I/II CRISPR-Cas system with a slightly higher probability of acquisition.     

Translational repression of MCL-1 couples stress-induced eIF2 alpha phosphorylation to mitochondrial apoptosis initiation

The integrated stress response (ISR) integrates a broad range of environmental and endogenous stress signals to the phosphorylation of the alpha-subunit of eukaryotic translation initiation factor 2 (eIF2 alpha). Although intense or prolonged activation of this pathway is known to induce apoptosis, the molecular mechanisms coupling stress-induced eIF2 alpha phosphorylation to the cell death machinery have remained incompletely understood. In this study, we characterized apoptosis initiation in response to classical activators of the ISR (tunicamycin, UVC, elevated osmotic pressure, arsenite). We found that all applied stress stimuli activated a mitochondrial pathway of apoptosis initiation. Rapid and selective down-regulation of the anti-apoptotic BCL-2 family protein MCL-1 preceded the activation of BAX, BAK, and caspases. Stabilization of MCL-1 blocked apoptosis initiation, while cells with reduced MCL-1 protein content were strongly sensitized to stress-induced apoptosis. Stress-induced elimination of MCL-1 occurred with unchanged protein turnover and independently of MCL-1 mRNA levels. In contrast, stress-induced phosphorylation of eIF2 alpha at Ser(51) was both essential and sufficient for the down-regulation of MCL-1 protein in stressed cells. These findings indicate that stress-induced phosphorylation of eIF2 alpha is directly coupled to mitochondrial apoptosis regulation via translational repression of MCL-1. Down-regulation of MCL-1 enables but not enforces apoptosis initiation in stressed cells.     

Forecasting Environmental Responses to Restoration of Rivers Used as Log Floatways: An Interdisciplinary Challenge

Log floating in the 19th to mid 20th centuries has profoundly changed the environmental conditions in many northern river systems of the world. Regulation of flow by dams, straightening and narrowing of channels by various piers and wing dams, and homogenization of bed structure are some of the major impacts. As a result, the conditions for many riverine organisms have been altered. Removing physical constructions and returning boulders to the channels can potentially restore conditions for these organisms. Here we describe the history of log driving, review its impact on physical and biological conditions and processes, and predict the responses to restoration. Reviewing the literature on comparable restoration efforts and building upon this knowledge, using boreal Swedish rivers as an example, we address the last point. We hypothesize that restoration measures will make rivers wider and more sinuous, and provide rougher bottoms, thus improving land-water interactions and increasing the retention capacity of water, sediment, organic matter and nutrients. The geomorphic and hydraulic/hydrologic alterations are supposed to favor production, diversity, migration and reproduction of riparian and aquatic organisms. The response rates are likely to vary according to the types of processes and organisms. Some habitat components, such as beds of very large boulders and bedrock outcrops, and availability of sediment and large woody debris are believed to be extremely difficult to restore. Monitoring and evaluation at several scales are needed to test our predictions.     

In vitro culture and conservation of microalgae: Applications for aquaculture, biotechnology and environmental research

Summary Microalgae are a highly diverse group of unicellular organisms comprising the eukaryotic protists and the prokaryotic cyanobacteria or blue-green algae. The microalgae have a unique environmental status; being virtually ubiquitous in euphotic aquatic niches, they can occupy extreme habitats ranging from tropical coral reefs to the polar regions, and they contribute to half of the globe’s photosynthetic activity. Furthermore, they form the basis of the food chain for more than 70% of the world’s biomass. Microalgae are a valuable environmental and biotechnological resource, and the aim of this review is to explore the use of in vitro technologies in the conservation and sustainable exploitation of this remarkable group of organisms. The first part of the review evaluates the importance of in vitro methods in the maintenance and conservation of microalgae and describes the central role of culture collections in applied algal research. The second part explores the application of microalgal in vitro technologies, particularly in the context of the aquaculture and biotechnology industries. Emphasis is placed upon the exploitation of economically important algal products including aquaculture feed, biomass production for the health care sector, green fertilizers, pigments, vitamins, antioxidants, and antimicrobial agents. The contribution that microalgae can make to environmental research is also appraised; for example, they have an important role as indicator organisms in environmental impact assessments. Similarly, designated culture collection strains of microalgae are used for ecotoxicity testing. Throughout the review, emphasis is placed on the application of in vitro techniques for the continued advancement of microalgal research. The paper concludes by assessing future perspectives for the novel application of microalgae and their products.     

Regulation of Pi,uptake by Acer pseudoplatanus cells

In view of the importance of P_i in the control of cell metabolism, it was of interest to study the mechanism and regulation of P_i uptake by Acer pseudoplatanus cells grown as cell suspensions. At low external P_i concentrations up to 10 mm, sycamore cells incorporate phosphate against a concentration gradient, by a process which is energy dependent. Under these conditions the intracellular P_i concentration is maintained constant (2–3 mm). On the contrary at high external P_i concentrations, higher than that which counterpoises the cytoplasmic P_i concentration (approximately 10 mm), P_i enters the cell by slow diffusion and the intracellular P_i concentration increases continuously as the extracellular P_i concentration increases from 15 to 50 mm. When sycamore cells are transferred to a phosphate-deficient medium, growth slows down considerably and ceases after 4–5 days. During this time, intracellular P_i concentration falls from 3 to 0.1 mm and phosphate esters from 8 to 2 mm. Phosphate starvation stimulates the uptake indicating that phosphate uptake depends on the intracellular phosphate and/or cytoplasmic ester-P pool. P_i uptake by P_i-starved cells is strongly dependent on the pH of the medium.     

Spatial p21 expression profile in the mid-term mouse embryo

Throughout development cells make the decision to proliferate, arrest or die. Control of this process is essential for normal development, with unrestrained cell proliferation and cell death underling the origin and progression of disease. The cell-cycle is tightly regulated by a number of factors including the cyclin-dependent kinase inhibitor 1A (Cdkn1a), termed p21 (or Cip1 or WAF1). p21 acts as a negative regulator of cell-cycle progression by binding and inhibiting complexes formed between the cyclin-dependent kinases and their catalytic partners the cyclins. In this report we identify the temporal spatial expression profile of p21 in the developing mid-term mouse embryo using a p21-LacZ reporter mouse line. Expression of p21 was restricted to specific regions with a correspondence to both areas of terminal differentiation and active remodelling. A complex temporal and spatial relationship between p21 expression and regions of apoptosis was evident. A protective role with regard to apoptosis for p21 is proposed.     

Factors shaping community patterns of protists and bacteria on a European scale

Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.     

Evidence against a Looped Structure of the Inactive Human X-Chromosome Territory

Multicolor fluorescencein situhybridization with a whole chromosome composite probe for the X-chromosome and microdissection probes for the Xp and Xq arms, as well as for the Xp terminal, Xq terminal, and X centromer specific subregional probes, was applied to three-dimensional (3D) preserved human female amniotic fluid cell nuclei. Confocal laser scanning microscopy and three-dimensional image analysis demonstrated distinctly separated Xp arm and Xq arm domains. 3D distance measurements revealed a high variability of intrachromosomal distances between Xpter, Xcen, and Xqter specific probes within both X territories. A 3D distance measurement error of ±70 nm was found in control experiments using quartz glass microspheres labeled with different fluorochromes. Our data argue against the hypothesis of Walkeret al.(1991,Proc. Natl. Acad. Sci. USA88, 6191–6195) that a looped structure of the inactive X territory is formed by tight telomere–telomere associations.     

Osteopathy of the pectoral and pelvic limbs including pentadactyly in a young Kestrel (Falco t. tinnunculus)

Summary A five and a half weeks old female Kestrel exhibiting osteopathy of the pectoral and pelvic limbs, including symmetrical hyperdactyly, was investigated in order to clarify the pattern of the involved anatomical alterations and the possible causes of this developmental malformation. In the pectoral limb it consisted of a triplication of the alular digit, in the pelvic limb of a duplication of digit I. The live young Kestrel was observed for a period of two weeks to ascertain that it was unable to fly or procure prey on its own. After its death radiographs were taken and, apart from an eidonomic inspection including the wing claws, a detailed macroscopic dissection of the musculature of the pectoral and pelvic limbs was carried out using the in-water-method. Consecutive dissection steps were documented by a series of photographic slides. The relevant musculature, particularly that of the supernumerary digits, was recorded in proportional drawings. Subsequent to maceration of the limbs the isolated bones were reassembled according to the radiographs and also documented by means of photographs and drawings. This anatomical approach produced a reliable reconstruction of the skeletomuscular apparatus of the hyperdactylous limb parts. The eidonomic inspection revealed that at least young Kestrels may have two (alular and major digit) or even three wing claws per side. The proximal skeletal elements of both pectoral and pelvic limb were more sturdily built than in a typical Kestrel of comparable age. The proximal elements of the pelvic limb, the tarsometatarsus in particular, were shorter than in a typical Kestrel. In addition, the long axis of the tarsometatarsus was laterally bent in the transverse plane so that its proximal articular surfaces were medially inclined. Duplication of the cutaneous and osseous elements in the foot was accompanied by a duplication of some of the muscular and/or tendinous elements supplying digit I proper and the accessory digit I'. There were left-to-right asymmetries of the pedal musculature concerned. In contrast, the two accessory alular digits of each wing were almost completely devoid of musculature. Apart from atypical points of origin or insertion of the remaining distal musculture, left-to-right asymmetries and the two accessory alulae per wing, presumably, affected aerodynamic properties and resulted in flightlessness.A juvenile Kestrel of similar age and without hyperdactyly was dissected for comparison. In addition, the external appearance of the carpometacarpal region of two female Silkies, an obligatory pentadactylous breed of domestic fowl, was inspected and the skeletal parts of their pectoral and pelvic limbs compared with those of the hyperdactylous Kestrel. Our results and a literature review suggest that the symmetrical hyperdactyly in the Kestrel bears striking similarities to the hereditary hyperdactyly observed in certain breeds of domestic fowl. In addition, there is a striking resemblance between the hyperdactyly of the young Kestrel and certain forms of hyperdactyly induced by molecular genetical experiments of other authors on chicks. Comparison with these results taken from the literature suggest that the symmetrical hyperdactyly in the young Kestrel, including the alterations of the proximal skeletal elements, is caused by an unusually early expression of the Hoxd-11 gene group during embryological development. Most likely, this gene group is situated on the 2^nd chromosome in birds just as it is in mammals.

---

Osteopathie der Vorder - und Hinterextremitäten, verbunden mit einer symmetrischen Hyperdactylie bei einem jungen Turmfalken (Falco tinnunculus)

Zusammenfassung Ein fünfeinhalb Wochen alter weiblicher Turmfalke mit einer Osteopathie der Vorder- und Hinterextremitäten, verbunden mit einer symmetrischen Hyperdactylie, wurde untersucht, um das Muster der beteiligten anatomischen Veränderungen und die möglichen Ursachen dieser Mißbildung zu erkennen. An der Vorderextremität bestand sie aus einer Verdreifachung des Alula-Fingers, an der Hinterextremität aus einer Verdoppelung der Zehe I. Die Beobachtung des lebenden jungen Turmfalken während eines Zeitraumes von zwei Wochen ergab, dass er flugunfähig war und keine Beute schlagen konnte.Nach seinem Tod und einer Inspektion der Eidonomie, einschließlich der Flügelkrallen, wurden Röntgenaufnahmen angefertigt. Danach folgte eine detaillierte makroskopische Präparation der Flügel- und Beinmuskulatur unter Verwendung der In-Wasser-Methode. Die einzelnen Präparationsschritte wurden anhand von Dia-Serien dokumentiert. Die relevante Muskulatur, insbesondere die der überzähligen Digiti, wurde in proportionsgetreuen Zeichnungen festgehalten. Nach Mazeration der Extremitäten wurden die Einzelknochen, entsprechend den Röntgenbildern, wieder zusammengesetzt und ebenfalls mit Fotografien und Zeichnungen dokumentiert. Dieser anatomische Ansatz lieferte eine zuverlässige Rekonstruktion des Skelett-Muskel-Apparates der hyperdactylen Extremitätenanteile.Die eidonomische Inspektion ergab, dass zumindest junge Turmfalken zwei (Digitus alularis und majoris) oder sogar drei Flügelkrallen haben können. Die proximalen Skelettelemente der Vorder- und Hinterextremität waren deutlich robuster gebaut als bei einem typischen Turmfalken vergleichbaren Alters. Die proximalen Elemente der Hinterextremität, insbesondere der Tarsometatarsus, waren kürzer als bei einem typischen Turmfalken. Darüberhinaus war die Längsachse des Tarsometatarsus in der Transversalebene laterad gekrümmt, so dass sich seine proximalen Gelenkflächen schräg mediad richteten. Entsprechend der kutanen und knöchernen Doppelbildungen des Fußes waren auch einige der Muskeln und Sehnen doppelt vorhanden, welche die eigentliche erste Zehe und die akzessorische erste Zehe versorgten. Es traten Rechts-/Links-Asymmetrien der betreffenden Muskulatur auf. Im Gegensatz dazu waren die beiden akzessorischen Alula-Finger jedes Flügels fast vollständig ohne Muskulatur. Abgesehen von atypischen Ursprungs- und Insertionspunkten der verbleibenden distalen Muskulatur, beeinträchtigten Rechts-/Links-Asymmetrien und die beiden akzessorischen Alulae pro Flügel vermutlich die aerodynamischen Eigenschaften und führten zur Flugunfähigkeit.Ein junger Turmfalke ähnlichen Alters ohne Hyperdactylie wurde zum Vergleich präpariert. Zusätzlich wurde die äußere Erscheinung der Carpometacarpal-Region zweier Seidenhühner, einer obligatorisch pentadactylen Hühnerrasse, inspiziert und die Skelettelemente ihrer Vorder- und Hinterextremitäten mit denen des hyperdactylen Turmfalken verglichen. Unsere Ergebnisse und ein Überblick der Literatur lassen auffallende Übereinstimmungen zwischen der symmetrischen Hyperdactylie des jungen Turmfalken und der erblichen Hyperdactylie bestimmter Hühnerrassen erkennen. Darüberhinaus besteht eine auffallende übereinstimmung zwischen der Hyperdactylie des jungen Turmfalken und bestimmten Formen der Hyperdactylie, welche von anderen Autoren durch molekulargenetische Experimente an Hühnerküken induziert wurden. Ein Vergleich mit diesen Ergebnissen aus der Literatur legt nahe, dass die symmetrische Hyperdactylie des jungen Turmfalken, einschließlich der Veränderungen der proximalen Skelettelemente, durch eine ungewöhnlich frühe Expression der Hoxd-11 Gengruppe im Laufe der Embryonalentwicklung verursacht wurde. Sehr wahrscheinlich ist diese Gengruppe bei Vögeln auf dem zweiten Chromosom lokalisiert — ebenso wie bei Säugetieren.