The population biology of the living coelacanth studied over 21 years

Between 1986 and 2009 nine submersible and remote-operated vehicle expeditions were carried out to study the population biology of the coelacanth Latimeria chalumnae in the Comoro Islands, located in the western Indian Ocean. Latimeria live in large overlapping home ranges that can be occupied for as long as 21 years. Most individuals are confined to relatively small home ranges, resting in the same caves during the day. One hundred and forty five coelacanths are individually known, and we estimate the total population size of Grande Comore as approximately 300–400 adult individuals. The local population inhabiting a census area along an 8-km section of coastline remained stable for at least 18 years. Using LASER-assisted observations, we recorded length frequencies between 100 and 200 cm total length and did not encounter smaller-bodied individuals (\100 cm total length). It appears that coelacanth recruitment in the observation areas occur mainly by immigrating adults. We estimate that the mean numbers of deaths and newcomers are 3–4 individuals per year, suggesting that longevity may exceed 100 years. The domestic fishery represents a threat to the long-term survival of coelacanths in the study area. Recent changes in the local fishery include a decrease in the abundance of the un-motorized canoes associated with exploitation of coelacanths and an increase in motorized canoes. Exploitation rates have fallen in recent years, and by 2000, had fallen to lowest ever reported. Finally, future fishery developments are discussed

Comment on “The extent of forest in dryland biomes”

This is the author accepted manuscript. The final version is available from American Association for the Advancement of Science via the DOI in this record.Bastin et al. (Reports, 12 May 2017, p. 635) infer forest as more globally extensive than previously estimated using tree cover data. However, their forest definition does not reflect ecosystem function or biotic composition. These structural and climatic definitions inflate forest estimates across the tropics and undermine conservation goals, leading to inappropriate management policies and practices in tropical grassy ecosystems

Fire History from Life-History: Determining the Fire Regime that a Plant Community Is Adapted Using Life-Histories

Wildfire is a fundamental disturbance process in many ecological communities, and is critical in maintaining the structure of some plant communities. In the past century, changes in global land use practices have led to changes in fire regimes that have radically altered the composition of many plant communities. As the severe biodiversity impacts of inappropriate fire management regimes are recognized, attempts are being made to manage fires within a more ‘natural’ regime. In this aim, the focus has typically been on determining the fire regime to which the community has adapted. Here we take a subtly different approach and focus on the probability of a patch being burnt. We hypothesize that competing sympatric taxa from different plant functional groups are able to coexist due to the stochasticity of the fire regime, which creates opportunities in both time and space that are exploited differentially by each group. We exploit this situation to find the fire probability at which three sympatric grasses, from different functional groups, are able to co-exist. We do this by parameterizing a spatio-temporal simulation model with the life-history strategies of the three species and then search for the fire frequency and scale at which they are able to coexist when in competition. The simulation gives a clear result that these species only coexist across a very narrow range of fire probabilities centred at 0.2. Conversely, fire scale was found only to be important at very large scales. Our work demonstrates the efficacy of using competing sympatric species with different regeneration niches to determine the probability of fire in any given patch. Estimating this probability allows us to construct an expected historical distribution of fire return intervals for the community; a critical resource for managing fire-driven biodiversity in the face of a growing carbon economy and ongoing climate change

Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses

The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates pose significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. Simultaneously, product toxicity must also be overcome to allow for efficient production of next generation biofuels such as n-butanol, isopropanol, and others from these low cost feedstocks.This study explores the high ferulic acid and n-butanol tolerance in Lactobacillus brevis, a lactic acid bacterium often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis reveals that the presence of ferulic acid triggers the expression of currently uncharacterized membrane proteins, possibly in an effort to counteract ferulic acid induced changes in membrane fluidity and ion leakage. In contrast to the ferulic acid stress response, n-butanol challenges to growing cultures primarily induce genes within the fatty acid synthesis pathway and reduced the proportion of 19:1 cyclopropane fatty acid within the L. brevis membrane. Both inhibitors also triggered generalized stress responses. Separate attempts to alter flux through the Escherichia coli fatty acid synthesis by overexpressing acetyl-CoA carboxylase subunits and deleting cyclopropane fatty acid synthase (cfa) both failed to improve n-butanol tolerance in E. coli, indicating that additional components of the stress response are required to confer n-butanol resistance.Several promising routes for understanding both ferulic acid and n-butanol tolerance have been identified from L. brevis gene expression data. These insights may be used to guide further engineering of model industrial organisms to better tolerate both classes of inhibitors to enable facile production of biofuels from lignocellulosic biomass

Sequencing technologies and genome sequencing

The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research

Cognitive Neuropsychology of HIV-Associated Neurocognitive Disorders

Advances in the treatment of the human immunodeficiency virus (HIV) have dramatically improved survival rates over the past 10 years, but HIV-associated neurocognitive disorders (HAND) remain highly prevalent and continue to represent a significant public health problem. This review provides an update on the nature, extent, and diagnosis of HAND. Particular emphasis is placed on critically evaluating research within the realm of cognitive neuropsychology that aims to elucidate the component processes of HAND across the domains of executive functions, motor skills, speeded information processing, episodic memory, attention/working memory, language, and visuoperception. In addition to clarifying the cognitive mechanisms of HAND (e.g., impaired cognitive control), the cognitive neuropsychology approach may enhance the ecological validity of neuroAIDS research and inform the development of much needed novel, targeted cognitive and behavioral therapies

An animal model to evaluate the function and regulation of the adaptively evolving stress protein SEP53 in oesophageal bile damage responses

Squamous epithelium in mammals has evolved an atypical stress response involving down-regulation of the classic HSP70 protein and induction of sets of proteins including one named SEP53. This atypical stress response might be due to the unusual environmental pressures placed on squamous tissue. In fact, SEP53 plays a role as an anti-apoptotic factor in response to DNA damage induced by deoxycholic acid stresses implicated in oesophageal reflux disease. SEP53 also has a genetic signature characteristic of an adaptively and rapidly evolving gene, and this observation has been used to imply a role for SEP53 in immunity. Physiological models of squamous tissue are required to further define the regulation and function of SEP53. We examined whether porcine squamous epithelium would be a good model to study SEP53, since this animal suffers from a bile-reflux disease in squamous oesophageal tissue. We have (1) cloned and sequenced the porcine SEP53 locus from porcine bacterial artificial chromosome genomic DNA, (2) confirmed the strikingly divergent nature of the C-terminal portion of the SEP53 gene amongst mammals, (3) discovered that a function of the conserved N-terminal domain of the gene is to maintain cytoplasmic localisation, and (4) examined SEP53 expression in normal and diseased porcine pars oesophagea. SEP53 expression in porcine tissue was relatively confined to gastric squamous epithelium, consistent with its expression in normal human squamous epithelium. Immunohistochemical staining for SEP53 protein in normal and damaged pars oesophagea demonstrated significant stabilisation of SEP53 protein in the injured tissue. These results suggest that porcine squamous epithelium would be a robust physiological model to examine the evolution and function of the SEP53 stress pathway in modulating stress-induced responses in squamous tissue

Multipoint genome-wide linkage scan for nonword repetition in a multigenerational family further supports chromosome 13q as a locus for verbal trait disorders

Verbal trait disorders encompass a wide range of conditions and are marked by deficits in five domains that impair a person’s ability to communicate: speech, language, reading, spelling, and writing. Nonword repetition is a robust endophenotype for verbal trait disorders that is sensitive to cognitive processes critical to verbal development, including auditory processing, phonological working memory, and motor planning and programming. In the present study, we present a six-generation extended pedigree with a history of verbal trait disorders. Using genome-wide multipoint variance component linkage analysis of nonword repetition, we identified a region spanning chromosome 13q14–q21 with LOD = 4.45 between 52 and 55 cM, spanning approximately 5.5 Mb on chromosome 13. This region overlaps with SLI3, a locus implicated in reading disability in families with a history of specific language impairment. Our study of a large multigenerational family with verbal trait disorders further implicates the SLI3 region in verbal trait disorders. Future studies will further refine the specific causal genetic factors in this locus on chromosome 13q that contribute to language traits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00439-016-1717-z) contains supplementary material, which is available to authorized users

Nigeria Anopheles vector database: an overview of 100 years' research.

Anopheles mosquitoes are important vectors of malaria and lymphatic filariasis (LF), which are major public health diseases in Nigeria. Malaria is caused by infection with a protozoan parasite of the genus Plasmodium and LF by the parasitic worm Wuchereria bancrofti. Updating our knowledge of the Anopheles species is vital in planning and implementing evidence based vector control programs. To present a comprehensive report on the spatial distribution and composition of these vectors, all published data available were collated into a database. Details recorded for each source were the locality, latitude/longitude, time/period of study, species, abundance, sampling/collection methods, morphological and molecular species identification methods, insecticide resistance status, including evidence of the kdr allele, and P. falciparum sporozoite rate and W. bancrofti microfilaria prevalence. This collation resulted in a total of 110 publications, encompassing 484,747 Anopheles mosquitoes in 632 spatially unique descriptions at 142 georeferenced locations being identified across Nigeria from 1900 to 2010. Overall, the highest number of vector species reported included An. gambiae complex (65.2%), An. funestus complex (17.3%), An. gambiae s.s. (6.5%). An. arabiensis (5.0%) and An. funestus s.s. (2.5%), with the molecular forms An. gambiae M and S identified at 120 locations. A variety of sampling/collection and species identification methods were used with an increase in molecular techniques in recent decades. Insecticide resistance to pyrethroids and organochlorines was found in the main Anopheles species across 45 locations. Presence of P. falciparum and W. bancrofti varied between species with the highest sporozoite rates found in An. gambiae s.s, An. funestus s.s. and An. moucheti, and the highest microfilaria prevalence in An. gambiae s.l., An. arabiensis, and An. gambiae s.s. This comprehensive geo-referenced database provides an essential baseline on Anopheles vectors and will be an important resource for malaria and LF vector control programmes in Nigeria