Recombination in HIV and the evolution of drug resistance: for better or for worse?

The rapid evolution of drug resistance remains a major obstacle for HIV therapy. The capacity of the virus for recombination is widely believed to facilitate the evolution of drug resistance. Here, we challenge this intuitive view. We develop a population genetic model of HIV replication that incorporates the processes of mutation, cellular superinfection, and recombination. We show that cellular superinfection increases the abundance of low fitness viruses at the expense of the fittest strains due to the mixing of viral proteins during virion assembly. Moreover, we argue that whether recombination facilitates the evolution of drug resistance depends critically on how resistance mutations interact to determine viral fitness. Contrary to the commonly held belief, we find that, under the most plausible biological assumptions, recombination is expected to slow down the rate of evolution of multi-drug-resistant virus during therapy.     

Blood biomarkers role in acute ischemic stroke patients: higher is worse or better?

Background

Thrombolytic therapy (TT) for acute ischemic stroke (AIS) can provoke bleeding’s complication depending on the ischemic lesion (IL) dimension. Inflammation involved in the setting of acute ischaemic stroke, is associated with infarct size. We aimed to study the independent correlation and association between clinical panel of routinely identified biomarkers, including inflammatory parameters, and cerebral IL dimension and site.

Results

We evaluated eleven biomarkers in 105 unrelated patients during their hospitalization after acute stroke event. Our data indicate a significant association of: a) confluent IL size with 4th quartile of Erythrocyte Sedimentation Rate (ESR) (OR = 5.250; 95% CI, 1.002 to 27.514) and an independent correlation with sex; b) confluent IL size with 3rd quartile of fibrinogen (OR = 5.5; 95% CI, 1.027 to 29.451); c) confluent IL size with 3rd quartile of platelets (OR= 0.059; 95% CI, 0.003 to 1.175) and independent correlation with sex; d) smaller IL size (OR = 5.25; 95% CI, 1.351 to 20.396) with 3rd quartile of albumin levels and nodular and parenchimal IL size with 2nd (OR = 0.227; 95% CI, 0.053 to 0.981), 3rd (OR = 0.164; 95% CI, 0.038 to 0.711) and 4th (OR = 0.205; 95% CI, 0.048 to 0.870) quartiles albumin levels; e) smaller IL size with 3rd quartile triglycerides (TG) levels (OR = 9; 95% CI, 2.487 to 32.567) and an independent correlation with anterior location. Smaller IL size, anterior AIS turned out to be independently correlated with high serum albumin levels. Finally, high INR and PTT values were associated with worse NIHSS clinical outcomes in contrast to that observed with higher albumin level.

Conclusions

We provide evidence of routine biomarkers levels correlation with acute IL size, independently of age and sex. In addition, we highlight the importance of differentiation of biomarkers normal interval levels for further improvement not only of the clinical decision making but also in post-acute clinical outcome management.

     

Mitigating the impacts of rainforest roads in Queensland’s Wet Tropics: Effective or are further evaluations and new mitigation strategies required?

Summary Research into mitigation of the ecological impacts of rainforest roads in North Queensland has a long history, commencing during the formative years of Australian road ecology. In Queensland’s Wet Tropics and throughout Australia, installation of engineered structures to ameliorate ecological road impacts is now common during larger construction projects, but unusual in smaller road projects. Retro‐fitting of engineering solutions to roads that are causing obvious impacts is also uncommon. Currently, Australian mitigation measures concentrate on two important impacts: road mortality and terrestrial habitat fragmentation. Unfortunately, other important ecological impacts of roads are seldom addressed. These include edge effects, traffic disturbance, exotic invasions and fragmentation of stream habitats. In North Queensland, faunal underpasses and canopy bridges across rainforest roads have been monitored over long periods. These structures are used frequently by multiple individuals of various species, implying effectiveness for movements and dispersal of many generalist and specialised rainforest animals. However, without addressing population and genetic implications, assessment of effectiveness of these connectivity structures is not holistic. These aspects need sufficient long‐term funding to allow similar systematic monitoring before and after construction. Throughout Australia, more holistic approaches to mitigation of road impacts would routinely examine population and genetic connectivity, consider mitigation against more ecological impacts where appropriate and include landscape‐scale replication.     

Do Alix and ALG‐2 really control endosomes for better or for worse?

Alix/AIP1 (ALG-2-interacting protein X/apoptosis-linked-gene-2-interacting protein 1) is an adaptor protein that was first described for its capacity to bind to the calcium-binding protein ALG-2 (apoptosis-linked gene 2), the expression of which seemed necessary for cell death. Over-expression of truncated forms of Alix blocks caspase-dependent and -independent mechanisms of cell death. Numerous observations in yeast and in mammalian cells suggest that Alix controls the making of and trafficking through endosomes called MVBs (multivesicular bodies), which are crucial intermediates within the endolysosomal system. In particular, deletion of Bro1, one of the yeast homologues of Alix, leads to an impairment in the function of MVBs, leading to mis-sorting of proteins normally destined to the vacuole. Mammalian Alix may have a similar function and has been shown to bind to lyso(bis)phosphatidic acid, ESCRT (endosomal sorting complex required for transport) proteins, endophilins and CIN85 (Cbl-interacting protein of 85 kDa), which are all main regulators of the endosomal system. EIAV (equine infectious anaemia virus) and HIV late domains use Alix to recruit the ESCRT machinery in order to bud from the cell surface, underscoring the crucial role of the protein in orchestrating membrane deformation. In this review I develop the hypothesis that the normal function of Alix in the endolysosomal system may be deviated by ALG-2 towards a destructive role during active cell death.     

Pines and oaks in the restoration of Mediterranean landscapes of Spain: New perspectives for an old practice — a review

Pines have been extensively used for land restoration in the Mediterranean basin and in other parts of the world, since the late 19^th century. The theoretical basis supporting pine utilisation was its stress-tolerant and pioneer features, and their attributed role of facilitating the development of late-successional hardwoods in the long-term. In the present work, the use of pines and hardwoods in forest restoration is discussed in the frame of the current disturbance regime and social demands for Mediterranean forests. Large pine plantations have recently disappeared because of their sensitivity to fire (e.g., Pinus nigra) or because of the short fire-intervals (e.g., Pinus halepensis). Combined pine and oak plantations are proposed for degraded land restoration on the basis of the complementary features of both groups of species. Seeding and containerised seedling plantation, soil amendments and plantation techniques to reduce transplant shock are evaluated for reforestation under water-stressing conditions, on the basis of several experiments performed in eastern Spain. Both P. halepensis and Quercus ilex are tested.     

Tree-shrub interactions in a subtropical savanna parkland: competition or facilitation?

Abstract. Prosopis glandulosa var. glandulosa has played a central role in the encroachment of woody plants in southern Texas, grasslands and savannas by acting as a nurse plant for various shrubs that establish in its understory. To test for continued facilitation of established understory shrubs by Prosopis and to determine if established shrubs compete with the Prosopis nucleus, selective removal experiments were conducted and monitored over a 2–5 yr period. Short-term (1–3 days) and long-term (2 yr) growth and physiological activities (midday net photosynthesis and leaf/shoot water potential) of two common understory shrubs, Zanthoxylum fagara and Berberis trifoliolata, growing with Prosopis, were generally comparable to those of individuals occurring in clusters where Prosopis was removed. Shrubs growing with an intact Prosopis occasionally showed significantly higher leaf-[N] and pre-dawn water potentials than those in clusters lacking a live Prosopis, especially under drought conditions; however, these differences did not translate into greater midday leaf gas exchange or shoot growth. By comparison, removal of understory shrubs elicited large increases in Prosopis net photosynthesis, annual trunk growth in each of the 5 yr monitored, and seed pod production in three of the four years monitored. Seven of 26 Prosopis plants in experimental clusters with an intact understory died over a 5-yr period, compared to only two of the 26 plants in clusters with the cleared understory. Results indicate that (1) the founding overstory Prosopis plant may continue to facilitate understory shrubs following their establishment, but these beneficial effects appear to be small and transitory, and (2) the understory shrubs have a pronounced negative effect on Prosopis, such that competition between overstory and understory woody plants is strongly asymmetrical. These findings suggest that understory shrubs will likely persist despite changes in microclimate and soils (potentially) that occur after the Prosopis plant, which facilitated their ingress or establishment, has died. Soil resource depletion by shallow-rooted understory shrubs appears to be a primary factor contributing to the demise of the deeply rooted, overstory Prosopis plants, especially on upland sites with duplex soils where below-ground competition is accentuated.     

Mangroves: obligate or facultative halophytes? A review

Salinity plays significant roles in regulating the growth and distribution of mangroves, and the salt tolerance mechanisms of mangroves have been the focus of research for several decades. There are contradictory views regarding the relationship between mangroves and salt: (1) Mangroves are facultative halophytes, i.e. freshwater is a physiological requirement and salt water is an ecological requirement for mangroves because they are capable of growing in freshwater. The former prevents excess respiratory losses while the latter prevents invasion and competition from non-halophytes. (2) Mangroves are obligate halophytes, i.e. salt is necessary for their growth. Mangroves cannot survive in freshwater permanently and salt water is a physiological requirement. Up to now, mangroves are usually considered as facultative halophytes. In this review, we provided five lines of evidence to evaluate these two contradictory views: (1) the results of laboratory culture experiments and field investigations; (2) the viviparous nature of mangroves; (3) the salt accumulation of mangroves under freshwater or low salinity; (4) the effect of salinity on the photosynthetic rate and in vitro enzyme activities, and (5) the effects of salinity fluctuation on mangrove growth and physiology. Contrary to widely accepted view, our evaluations of the aforementioned evidence suggest that mangroves are obligate halophytes. Mangroves can grow in freshwater for a limited time by drawing upon the nutrients and salt reserves in their hypocotyls while prolonged culture in freshwater is fatal to them. Mangroves have the ability to absorb Na⁺ and Cl⁻ rapidly and preferentially under low-salinity conditions. Not all of the enzymes in mangroves are sensitive to salt. In fact, the activities of some enzymes are even stimulated by low or moderate salinity. Plants grown under constant salinity in a laboratory setting are unlikely to behave in the same way as those in their natural habitat with fluctuating salinity. Thus, studies on the effects of freshwater or low salinity and salinity fluctuation on mangroves, as well as the physiological mechanisms that allow maintenance of function under fluctuating salinity conditions should be strengthened in future research.     

Nitrite in nitric oxide biology: cause or consequence? A systems-based review

All life requires nitrogen compounds. Nitrite is such a compound that is naturally occurring in nature and biology. Over the years, the pharmacological stance on nitrite has undergone a surprising metamorphosis, from a vilified substance that generates carcinogenic nitrosamines in the stomach to a life-saving drug that liberates a protective agent (nitric oxide or NO) during hypoxic events. Nitrite has been investigated as a vasodilator in mammals for over 125 years and is a known by-product of organic nitrate metabolism. There has been a recent rediscovery of some of the vasodilator actions of nitrite in physiology along with novel discoveries which render nitrite a fundamental molecule in biology. Until recently nitrite was thought to be an inert oxidative breakdown product of endogenous NO synthesis but the past few years have focused on the reduction of nitrite back to NO in the circulation as a possible mechanism for hypoxic vasodilatation. Nitrite has evolved into an endogenous signaling molecule and regulator of gene expression that may not only serve as a diagnostic marker but also find its role as a potential therapeutic agent of cardiovascular disease. These data therefore warrant a reevaluation on the fate and metabolism of nitrite in biological systems. This review serves to encompass the history and recent evolution of nitrite, the compartment-specific metabolism of nitrite and its role in plasma as a biomarker for disease, the role of nitrite as a potential regulator of NO homeostasis, and the future of nitrite-based research.     

Denitrification in pathogenic bacteria: for better or worst?

A large variety of physiological and taxonomic groups have the ability to use nitrogen oxides as alternative electron acceptors. Brucella spp. is an alpha-proteobacteriaceae that induces a persistent disease in some mammals. Recent work has revealed that a denitrifying gene cluster is important in the interaction of Brucella neotomoae with its host.     

Grains of truth or transparent blindfolds? A review of current debates in archaeological phytolith analysis

Phytolith analysis has become an increasingly popular archaeobotanical tool in the past few decades. Phytoliths have been used to support key hypotheses relating to the domestication of several food crops and in the study of ancient diet, and they are of particular importance in contexts where other plant remains are poorly preserved. However, the discipline has also been subject to controversy and debate. This paper gives an overview of the technique and three key case studies covering a range of geographical areas. Some of the problems that are common to each are discussed and suggestions are made for how these problems could be resolved in future research. It is suggested that further caution should be taken during interpretation, and a greater consideration given to taphonomy. Despite these criticisms it is concluded that there is still much potential in the technique, particularly when integrated with other lines of microarchaeological evidence.     

Consciousness in dolphins? A review of recent evidence

For millennia, dolphins have intrigued humans. Scientific study has confirmed that bottlenose dolphins are large-brained, highly social mammals with an extended developmental period, flexible cognitive capacities, and powerful acoustic abilities including a sophisticated echolocation system. These findings have led some to ask if dolphins experience aspects of consciousness. Recent investigations targeting self-recognition/self-awareness and metacognition, constructs tied to consciousness on some accounts, have analyzed the dolphin’s ability to recognize itself in a mirror or on a video as well as to monitor its own knowledge in a perceptual categorization task. The current article reviews this work with dolphins and grapples with some of the challenges in designing, conducting, and interpreting these studies as well as with general issues related to studying consciousness in animals. The existing evidence does not provide a convincing case for consciousness in dolphins. For productive scientific work on consciousness in dolphins (and other animals including humans), we need clearer characterizations of consciousness, better methods for studying it, and appropriate paradigms for interpreting outcomes. A current focus on metamemory in animals offers promise for future discovery in this area.     

Local or global? Biogeography of some primitive Lepidoptera in New Zealand

Abstract

Distribution maps are presented for 30 species of small forest moths representing two genera of Micropterigidae and one genus of Mnesarchaeidae. Evolutionary patterns are interpreted by means of the panbiogeographic method in order to seek a relationship between dispersal patterns within New Zealand and the overseas links of the taxa in question. It is established that different evolutionary lines indeed exhibit different geographic dispersal patterns within New Zealand. Moreover, certain characteristics of these patterns can be attributed to the overseas affinities of the groups, i.e., groups of organisms with New Caledonian or Australian affinities have a western disjunct pattern, whereas those with circum-Pacific affinities have a different pattern in which the taxa occupying a basal position in the phylogeny are to be found in the eastern South Island. However, both groups have overlapping centres of diversity, particularly in NW Nelson.     

Agonistic display or courtship behavior? A review of contests over mating opportunity in butterflies

Male butterflies compete over mating opportunities. Two types of contest behavior are reported. Males of various butterfly species compete over a mating territory via aerial interactions until one of the two contestants retreats. Males of other butterfly species fly around larval food plants to find receptive females. Males of some species among the latter type can find a conspecific pupa, and they gather around it without expelling their rivals. Scramble competition over mating occurs when a female emerges from the pupa. Many studies have been performed on territorial species, and their contest resolution has often been understood from the point of view of contest models based on game theory. However, these models cannot explain why these butterflies perform contest displays despite the fact that they do not have the ability to attack their opponent. A recent study based on Lloyd Morgan’s Canon showed that territorial contests of male butterflies are better understood as erroneous courtship between sexually active males. In this paper, I review research on contests over mating opportunity in butterflies, and show that the erroneous courtship framework can explain not only territorial contests of butterflies but also why males do not determine the owner of a conspecific pupa.     

“How Local Is Local?”—A Review of Practical and Conceptual Issues in the Genetics of Restoration

In plant conservation, restoration (the augmentation or reestablishment of an extinct population or community) is a valuable tool to mitigate the loss of habitat. However, restoration efforts can result in the introduction of novel genes and genotypes into populations when plant materials used are not of local origin. This movement is potentially important because many plant species are subdivided into populations that are adapted to local environmental conditions. Here we focus on genetic concerns arising from ongoing restoration efforts, where often little is known about “How local is local?” (i.e., the geographic or environmental scale over which plant species are adapted). We review the major issues regarding gene flow and local adaptation in the restoration of natural plant populations. Finally, we offer some practical, commonsense guidelines for the consideration of genetic structure when restoring natural plant populations.