bluuebunny/crossref_metadata_2025 huggingface dataset:
Function of leukemogenic mixed lineage leukemia 1 (MLL) fusion proteins through distinct partner protein complexes
Authors: Biswas Debabrata , Milne Thomas A. , Basrur Venkatesha , Kim Jaehoon , Elenitoba-Johnson Kojo S. J. , Allis C. David , Roeder Robert G.
Published: September 2011

A number of acute leukemias arise from fusion of the mixed lineage leukemia 1 protein (MLL) N terminus to a variety of fusion partners that have been reported to reside in one or more poorly defined complexes linked to transcription elongation through interactions with the histone H3-K79 methyltransferase DOT1 and positive transcription elongation factor b (P-TEFb). Here we first identify natural complexes (purified through fusion partners AF9, AF4, and ELL) with overlapping components, different elongation activities, and different cofactor associations that suggest dynamic interactions. Then, through reconstitution of defined, functionally active minimal complexes, we identify stable subcomplexes that, through newly defined protein-protein interactions, form distinct higher order complexes. These definitive analyses show, for example, that (
i
) through direct interactions with AF9 and cyclinT1, family members AF4 and AFF4 independently mediate association of P-TEFb with AF9, (
ii
) P-TEFb, through direct interactions, provides the link for association of ELL and ELL-associated factors 1 and 2 (EAF1 and EAF2) with AF4, and (
iii
) in the absence of other factors, DOT1 forms a stable complex with AF9 and does not interact with AF9•AF4•P-TEFb complexes. Finally, we show the importance of defined higher order complex formation in MLL–AF9-mediated transcriptional up-regulation and cell immortalization potential in vivo. Thus, our study provides direct mechanistic insight into the role of fusion partners in MLL fusion-mediated leukemogenesis.
A special pair of phytohormones controls excitability, slow closure, and external stomach formation in the Venus flytrap
Authors: Escalante-Pérez María , Krol Elzbieta , Stange Annette , Geiger Dietmar , Al-Rasheid Khaled A. S. , Hause Bettina , Neher Erwin , Hedrich Rainer
Published: September 2011

Venus flytrap's leaves can catch an insect in a fraction of a second. Since the time of Charles Darwin, scientists have struggled to understand the sensory biology and biomechanics of this plant,
Dionaea muscipula
. Here we show that insect-capture of
Dionaea
traps is modulated by the phytohormone abscisic acid (ABA) and jasmonates. Water-stressed
Dionaea
, as well as those exposed to the drought-stress hormone ABA, are less sensitive to mechanical stimulation. In contrast, application of 12-oxo-phytodienoic acid (OPDA), a precursor of the phytohormone jasmonic acid (JA), the methyl ester of JA (Me-JA), and coronatine (COR), the molecular mimic of the isoleucine conjugate of JA (JA-Ile), triggers secretion of digestive enzymes without any preceding mechanical stimulus. Such secretion is accompanied by slow trap closure. Under physiological conditions, insect-capture is associated with Ca
2+
signaling and a rise in OPDA, Apparently, jasmonates bypass hapto-electric processes associated with trap closure. However, ABA does not affect OPDA-dependent gland activity. Therefore, signals for trap movement and secretion seem to involve separate pathways. Jasmonates are systemically active because application to a single trap induces secretion and slow closure not only in the given trap but also in all others. Furthermore, formerly touch-insensitive trap sectors are converted into mechanosensitive ones. These findings demonstrate that prey-catching
Dionaea
combines plant-specific signaling pathways, involving OPDA and ABA with a rapidly acting trigger, which uses ion channels, action potentials, and Ca
2+
signals.
Sound symbolic naming of novel objects is a graded function
Authors: Thompson Patrick D. , Estes Zachary
Published: September 2011

Although linguistic traditions of the last century assumed that there is no link between sound and meaning (i.e., arbitrariness), recent research has established a nonarbitrary relation between sound and meaning (i.e., sound symbolism). For example, some sounds (e.g., /u/ as in took) suggest bigness whereas others (e.g., /i/ as in tiny) suggest smallness. We tested whether sound symbolism only marks contrasts (e.g., small versus big things) or whether it marks object properties in a graded manner (e.g., small, medium, and large things). In two experiments, participants viewed novel objects (i.e., greebles) of varying size and chose the most appropriate name for each object from a list of visually or auditorily presented nonwords that varied incrementally in the number of “large” and “small” phonemes. For instance, “wodolo” contains all large-sounding phonemes, whereas “kitete” contains all small-sounding phonemes. Participants' choices revealed a graded relationship between sound and size: The size of the object linearly predicted the number of large-sounding phonemes in its preferred name. That is, small, medium, and large objects elicited names with increasing numbers of large-sounding phonemes. The results are discussed in relation to cross-modal processing, gesture, and vocal pitch.
The tumor suppressor adenomatous polyposis coli controls the direction in which a cell extrudes from an epithelium
Authors: Marshall Thomas W. , Lloyd Isaac E. , Delalande Jean Marie , Näthke Inke , Rosenblatt Jody
Published: September 2011

Despite high rates of cell death, epithelia maintain intact barriers by squeezing dying cells out using a process termed cell extrusion. Cells can extrude apically into the lumen or basally into the tissue the epithelium encases, depending on whether actin and myosin contract at the cell base or apex, respectively. We previously found that microtubules in cells surrounding a dying cell target p115 RhoGEF to the actin cortex to control where contraction occurs. However, what controls microtubule targeting to the cortex and whether the dying cell also controls the extrusion direction were unclear. Here we find that the tumor suppressor adenomatous polyposis coli (APC) controls microtubule targeting to the cell base to drive apical extrusion. Whereas wild-type cells preferentially extrude apically, cells lacking APC or expressing an oncogenic APC mutation extrude predominantly basally in cultured monolayers and zebrafish epidermis. Thus APC is essential for driving extrusion apically. Surprisingly, although APC controls microtubule reorientation and attachment to the actin cortex in cells surrounding the dying cell, it does so by controlling actin and microtubules within the dying cell. APC disruptions that are common in colon and breast cancer may promote basal extrusion of tumor cells, which could enable their exit and subsequent migration.
Correlated evolution of transcription factors and their binding sites
Authors: Yang Shu , Yalamanchili Hari Krishna , Li Xinran , Yao Kwok-Ming , Sham Pak Chung , Zhang Michael Q. , Wang Junwen
Published: September 2011

Motivation:The interaction between transcription factor (TF) and transcription factor binding site (TFBS) is essential for gene regulation. Mutation in either the TF or the TFBS may weaken their interaction and thus result in abnormalities. To maintain such vital interaction, a mutation in one of the interacting partners might be compensated by a corresponding mutation in its binding partner during the course of evolution. Confirming this co-evolutionary relationship will guide us in designing protein sequences to target a specific DNA sequence or in predicting TFBS for poorly studied proteins, or even correcting and rescuing disease mutations in clinical applications.

Results: Based on six, publicly available, experimentally validated TF–TFBS binding datasets for the basic Helix–Loop–Helix (bHLH) family, Homeo family, High-Mobility Group (HMG) family and Transient Receptor Potential channels (TRP) family, we showed that the evolutions of the TFs and their TFBSs are significantly correlated across eukaryotes. We further developed a mutual information-based method to identify co-evolved protein residues and DNA bases. This research sheds light on the dynamic relationship between TF and TFBS during their evolution. The same principle and strategy can be applied to co-evolutionary studies on protein–DNA interactions in other protein families.

Availability: All the datasets, scripts and other related files have been made freely available at: http://jjwanglab.org/co-evo.

Contact:  junwen@uw.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Nonhost Resistance of Rice to Rust Pathogens
Authors: Ayliffe Michael , Devilla Rosangela , Mago Rohit , White Rosemary , Talbot Mark , Pryor Anthony , Leung Hei
Published: September 2011

Rice is atypical in that it is an agricultural cereal that is immune to fungal rust diseases. This report demonstrates that several cereal rust species (Puccinia graminis f. sp tritici, P. triticina, P. striiformis, and P. hordei) can infect rice and produce all the infection structures necessary for plant colonization, including specialized feeding cells (haustoria). Some rust infection sites are remarkably large and many plant cells are colonized, suggesting that nutrient uptake occurs to support this growth. Rice responds with an active, nonhost resistance (NHR) response that prevents fungal sporulation and that involves callose deposition, production of reactive oxygen species, and, occasionally, cell death. Genetic variation for the efficacy of NHR to wheat stem rust and wheat leaf rust was observed. Unlike cereal rusts, the rust pathogen (Melampsora lini) of the dicotyledenous plant flax (Linum usitatissimum) rarely successfully infects rice due to an apparent inability to recognize host-derived signals. Morphologically abnormal infection structures are produced and appressorial-like structures often don't coincide with stomata. These data suggest that basic compatibility is an important determinate of nonhost infection outcomes of rust diseases on cereals, with cereal rusts being more capable of infecting a cereal nonhost species compared with rust species that are adapted for dicot hosts.
Agroinoculation of Citrus tristeza virus Causes Systemic Infection and Symptoms in the Presumed Nonhost Nicotiana benthamiana
Authors: Ambrós Silvia , El-Mohtar Choaa , Ruiz-Ruiz Susana , Peña Leandro , Guerri José , Dawson William O. , Moreno Pedro
Published: September 2011

Citrus tristeza virus (CTV) naturally infects only some citrus species and relatives and within these it only invades phloem tissues. Failure to agroinfect citrus plants and the lack of an experimental herbaceous host hindered development of a workable genetic system. A full-genome cDNA of CTV isolate T36 was cloned in binary plasmids and was used to agroinfiltrate Nicotiana benthamiana leaves, with or without coinfiltration with plasmids expressing different silencing-suppressor proteins. A time course analysis in agroinfiltrated leaves indicated that CTV accumulates and moves cell-to-cell for at least three weeks postinoculation (wpi), and then, it moves systemically and infects the upper leaves with symptom expression. Silencing suppressors expedited systemic infection and often increased infectivity. In systemically infected Nicotiana benthamiana plants, CTV invaded first the phloem, but after 7 wpi, it was also found in other tissues and reached a high viral titer in upper leaves, thus allowing efficient transmission to citrus by stem-slash inoculation. Infected citrus plants showed the symptoms, virion morphology, and phloem restriction characteristic of the wild T36 isolate. Therefore, agroinfiltration of Nicotiana benthamiana provided the first experimental herbaceous host for CTV and an easy and efficient genetic system for this closterovirus.
HflB Gene-Based Phytopathogenic Classification of ‘Candidatus Phytoplasma mali’ Strains and Evidence that Strain Composition Determines Virulence in Multiply Infected Apple Trees
Authors: Seemüller Erich , Kampmann Maren , Kiss Emese , Schneider Bernd
Published: September 2011

Analysis of pathological and molecular data of ‘Candidatus Phytoplasma mali’ accessions from 27 apple trees differing considerably in symptomatology was used to molecularly characterize and classify strains of the infecting apple proliferation phytoplasma. Single-strand conformation polymorphism and sequence analysis of a variable fragment of ATP00464-type hflB gene revealed that these sources consisted of single-strain and multiple-strain accessions that occurred in similar numbers. The latter group was composed of two to five distinct strains. Analysis of cloned sequences of mild and severe single-strain accessions resulted in two groups of reads that clustered, according to their virulence, distantly in the phylogram. Based on this data, the clustering patterns of multiple-strain accession sequences indicated that nearly all of them were composed of mild and severe strains. The distinct clustering of sequences representing mild and severe strains was associated with a range of molecular markers at the nucleotide and amino acid level. Data indicate that the virulence of multiple-strain accessions is determined by the ratio of the occurring mild and severe strains in that mild accessions were characterized by the predominance of sequences representing mild strains and vice versa. There is evidence that shifts in the population and other events may occur that drastically alter virulence of multiple-strain accessions.
Assessment of Application Timing of Bacillus spp. to Suppress Pre- and Postharvest Diseases of Apple
Authors: Poleatewich Anissa M. , Ngugi Henry K. , Backman Paul A.
Published: September 2011

Four isolates of Bacillus spp. were tested in a 2-year field study for biological control of pre- and postharvest diseases of apple. For the preharvest test, bacteria were applied to ‘Golden Delicious’ and ‘Rome Beauty’ trees in May or May and June. Foliar apple scab severity was assessed weekly. After harvest, fruit were wounded and then either left untreated or given a postharvest application of the bacteria. Wounded fruit were then inoculated with the bitter rot pathogen and lesion size was measured over 8 days. Bacillus megaterium isolate A3-6, B. mycoides isolate A1-1, and B. cereus isolate FLS-5 applied in May or May and June significantly reduced fruit and foliar apple scab severity in both years. A postharvest application of the bacteria (alone or in combination with a preharvest application) resulted in the greatest suppression of bitter rot on both cultivars (P < 0.04). The May + June + postharvest application of isolate A3-6 resulted in the greatest suppression of bitter rot, with an average of 45 and 95% reduction in lesion size compared with nontreated controls on ‘Golden Delicious’ and ‘Rome Beauty’ fruit, respectively. Results from this study indicate that preharvest applications of the bacteria were able to reduce foliar and fruit scab and an additional postharvest application was effective in reducing bitter rot severity.
Early Blight Control in Potato Using Disease-Orientated Threshold Values
Authors: Leiminger J. H. , Hausladen H.
Published: September 2011

Epidemics of early blight caused by Alternaria spp. can cause significant economic damage to potato production if not adequately controlled. In order to improve control of Alternaria spp. in potato, studies were conducted to identify the optimal fungicide strategy and, if possible, to reduce the number of fungicide applications per growing season. Therefore, a disease-threshold-based framework was tested to define the optimal timing of fungicide application. The initiation and subsequent applications of fungicides were based on increases in disease incidence or severity. Adequate disease control was achieved by a three-time application with azoxystrobin, given that the applications were carried out at pivotal times in the epidemic. Targeted applications of fungicides reduced the number of sprayings required to protect starch yield. Results indicate that early blight can be effectively managed by using fungicide application thresholds based on disease progress.
First Report of Damping-Off of Rhodiola sachalinensis Caused by Rhizoctonia solani AG-4 HG-II in China
Authors: Bai Q. , Xie Y. , Wang X. , Li Y. , Gao J. , Li J. , Li Z. , Li G. , Li H.
Published: September 2011

Rhodiola sachalinensis A. Bor (family Crassulaceae), a perennial herbaceous plant, is distributed mainly in the mountainous areas of China, Japan, Korea, and Russia. It is widely used as a traditional Chinese medicine with adaptogenic properties, cardiopulmonary protective effects, and central nervous system activities (3). Currently, it is extensively cultivated in northeastern China. In August 2010, widespread (>60% of plants were symptomatic) damping-off was observed in a seedling field in Linjiang, China. Leaves and stems near the ground were affected first, with dark lesions forming on the stem and the lowest leaves exhibiting wilt. The wilt spread rapidly over the entire plant with leaves becoming grayish brown and water soaked and then turned black and died. Root rot, defoliation, and damping-off were also observed. Six isolates with morphological characteristics of Rhizoctonia solani Kühn were isolated from symptomatic stems when plated on potato dextrose agar (PDA). Mycelium was branched at right angles with a septum near the branch and a slight constriction at the branch base. Fungal colonies were initially white, turned brown with age, and produced irregularly shaped, brown sclerotia after 8 days on PDA. Hyphal cells removed from cultures grown at 25°C on 2% water agar were determined to be multinucleate when stained with 1% safranin O and 3% KOH solution (1) and examined at ×400 magnification. The internal transcribed spacer (ITS) region of the nuclear rDNA was amplified by using the primers ITS4/ITS5 (2). The ITS sequences (715 bp) were identical in these six isolates (GenBank Accession No. FR878087) and had 100% sequence identity with R. solani AG-4 HG-II (GenBank Accession No. HQ629873) along with numerous other accessions from this AG subgroup. Pathogenicity tests were performed on healthy, potted seedlings of R. sachalinensis. Twenty plants were inoculated near the base of the stem with a 0.6-cm-diameter mycelial plug from 3-day-old PDA cultures for each isolate. Twenty plants inoculated with only PDA plugs served as controls. The plants were covered with plastic bags and kept in a greenhouse at 20 to 25°C for 72 h. All inoculated plants showed characteristic symptoms as previously observed in the seedling field 13 days after inoculation, while control plants remained healthy. R. solani AG-4 HG-II was reisolated from symptomatic tissues on inoculated plants. To our knowledge, this is the first report of R. solani AG-4 HG-II causing damping-off on R. sachalinensis in China.

References: (1) R. J. Bandoni. Mycologia 71:873, 1979. (2) D. E. L. Cooke et al. Mycol. Res. 101:667, 1997. (3) T. F. Yan et al. Conserv. Genet. 4:213, 2003.
Systemically Induced Resistance and Microbial Competitive Exclusion: Implications on Biological Control
Authors: Martinuz A. , Schouten A. , Sikora R. A.
Published: September 2011

The root-knot nematode, Meloidogyne incognita, is among the most damaging agricultural pests, particularly to tomato. The mutualistic endophytes Fusarium oxysporum strain Fo162 (Fo162) and Rhizobium etli strain G12 (G12) have been shown to systemically induce resistance toward M. incognita. By using triple-split-root tomato plants, spatially separated but simultaneous inoculation of both endophytes did not lead to additive reductions in M. incognita infection. More importantly, spatially separated inoculation of Fo162 and G12 led to a reduction in Fo162 root colonization of 35 and 39% when G12 was inoculated on a separate root section of the same plant in two independent experiments. In an additional split-root experiment, spatial separation of Fo162 and G12 resulted in a reduction of Fo162 root colonization of approximately 50% over the water controls in two independent experiments. The results suggested that the suppressive activity of G12 on Fo162 and M. incognita is possibly related to the induction of specific plant defense mechanisms. Thus, although Fo162 and G12 have the ability to systemically repress M. incognita infection in tomato, they can be considered incompatible biocontrol agents when both organisms are present simultaneously on the same root system.
The meaning of birth and death (in macroevolutionary birth–death models)
Authors: Ezard Thomas H. G. , Pearson Paul N. , Aze Tracy , Purvis Andy
Published: September 2011

Birth–death models are central to much macroevolutionary theory. The fundamental parameters of these models concern durations. Different species concepts realize different species durations because they represent different ideas of what birth (speciation) and death (extinction) mean. Here, we use Cenozoic macroperforate planktonic foraminifera as a case study to ask: what are the dynamical consequences of changing the definition of birth and death? We show strong evidence for biotic constraints on diversification using evolutionary species, but less with morphospecies. Discussing reasons for this discrepancy, we emphasize that clarity of species concept leads to clarity of meaning when interpreting macroevolutionary birth–death models.
Predicting ecosystem shifts requires new approaches that integrate the effects of climate change across entire systems
Authors: Russell Bayden D. , Harley Christopher D. G. , Wernberg Thomas , Mieszkowska Nova , Widdicombe Stephen , Hall-Spencer Jason M. , Connell Sean D.
Published: September 2011

Most studies that forecast the ecological consequences of climate change target a single species and a single life stage. Depending on climatic impacts on other life stages and on interacting species, however, the results from simple experiments may not translate into accurate predictions of future ecological change. Research needs to move beyond simple experimental studies and environmental envelope projections for single species towards identifying where ecosystem change is likely to occur and the drivers for this change. For this to happen, we advocate research directions that (i) identify the critical species within the target ecosystem, and the life stage(s) most susceptible to changing conditions and (ii) the key interactions between these species and components of their broader ecosystem. A combined approach using macroecology, experimentally derived data and modelling that incorporates energy budgets in life cycle models may identify critical abiotic conditions that disproportionately alter important ecological processes under forecasted climates.
Context-dependent tool use in New Caledonian crows
Authors: Taylor Alex H. , Hunt Gavin R. , Gray Russell D.
Published: September 2011

Humans and chimpanzees both exhibit context-dependent tool use. That is, both species choose to use tools when food is within reach, but the context is potentially hazardous. Here, we show that New Caledonian crows used tools more frequently when food was positioned next to a novel model snake than when food was positioned next to a novel teddy bear or a familiar food bowl. However, the crows showed no significant difference in their neophobic reactions towards the teddy bear and the model snake. Therefore, the crows used tools more in response to a risky object resembling a natural predator than to a less-threatening object that provoked a comparable level of neophobia. These results show that New Caledonian crows, like humans and chimpanzees, are capable of context-dependent tool use.
John Wesley Mitchell. 3 December 1913 — 12 July 2007
Authors: Barber D. J.
Published: September 2011

John (‘Jack’) Mitchell was a New Zealander who came to Oxford University on a scholarship of the Commission of the 1851 Exhibition. Mitchell’s association with Nevill (later Sir Nevill) Mott FRS during World War II, when they both worked at the Armament Research Department, afterwards led Mitchell to join Mott at Bristol University, where he began the research into the photographic process for which he is best known. His pursuit of an understanding of the mechanism through which a latent image forms led to the important discovery of the decoration by silver particles of individual dislocations in silver halide crystals and the mosaic microstructure of them. In turn the decoration technique provided the first clear experimental evidence of the link between plastic deformation and the creation and movement of dislocations. In 1960 Mitchell was appointed as professor in the Physics Department at the University of Virginia, where, apart from a brief spell in England as the Director of the National Chemical Laboratory, he worked happily for some 40 years. During this time his research group published many papers describing and explaining the mechanisms of plastic deformation in metallic alloys, devising and using state-of-the-art methods, thereby adding much to a wider understanding of mechanical properties and strength. All the time, working alone, Mitchell further developed and refined his photoaggregation theory of the photographic process, gaining worldwide recognition and honours for his effort.
Fluid convection, constraint and causation
Authors: Bishop Robert C.
Published: September 2011

Complexity—nonlinear dynamics for my purposes in this essay—is rich with metaphysical and epistemological implications but is receiving sustained philosophical analysis only recently. I will explore some of the subtleties of causation and constraint in Rayleigh–Bénard convection as an example of a complex phenomenon, and extract some lessons for further philosophical reflection on top-down constraint and causation particularly with respect to causal foundationalism.
Biomaterial strategies for alleviation of myocardial infarction
Authors: Venugopal Jayarama Reddy , Prabhakaran Molamma P. , Mukherjee Shayanti , Ravichandran Rajeswari , Dan Kai , Ramakrishna Seeram
Published: September 2011

World Health Organization estimated that heart failure initiated by coronary artery disease and myocardial infarction (MI) leads to 29 per cent of deaths worldwide. Heart failure is one of the leading causes of death in industrialized countries and is expected to become a global epidemic within the twenty-first century. MI, the main cause of heart failure, leads to a loss of cardiac tissue impairment of left ventricular function. The damaged left ventricle undergoes progressive ‘remodelling’ and chamber dilation, with myocyte slippage and fibroblast proliferation. Repair of diseased myocardium within vitro-engineered cardiac muscle patch/injectable biopolymers with cells may become a viable option for heart failure patients. These events reflect an apparent lack of effective intrinsic mechanism for myocardial repair and regeneration. Motivated by the desire to develop minimally invasive procedures, the last 10 years observed growing efforts to develop injectable biomaterials with and without cells to treat cardiac failure. Biomaterials evaluated include alginate, fibrin, collagen, chitosan, self-assembling peptides, biopolymers and a range of synthetic hydrogels. The ultimate goal in therapeutic cardiac tissue engineering is to generate biocompatible, non-immunogenic heart muscle with morphological and functional properties similar to natural myocardium to repair MI. This review summarizes the properties of biomaterial substrates having sufficient mechanical stability, which stimulates the native collagen fibril structure for differentiating pluripotent stem cells and mesenchymal stem cells into cardiomyocytes for cardiac tissue engineering.
Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs
Authors: Bell Rayna C. , MacKenzie Jason B. , Hickerson Michael J. , Chavarría Krystle L. , Cunningham Michael , Williams Stephen , Moritz Craig
Published: September 2011

Though Pleistocene refugia are frequently cited as drivers of species diversification, comparisons of molecular divergence among sister species typically indicate a continuum of divergence times from the Late Miocene, rather than a clear pulse of speciation events at the Last Glacial Maximum. Community-scale inference methods that explicitly test for multiple vicariance events, and account for differences in ancestral effective population size and gene flow, are well suited for detecting heterogeneity of species' responses to past climate fluctuations. We apply this approach to multi-locus sequence data from five co-distributed frog species endemic to the Wet Tropics rainforests of northeast Australia. Our results demonstrate at least two episodes of vicariance owing to climate-driven forest contractions: one in the Early Pleistocene and the other considerably older. Understanding how repeated cycles of rainforest contraction and expansion differentially affected lineage divergence among co-distributed species provides a framework for identifying evolutionary processes that underlie population divergence and speciation.
Mitochondrial DNA data indicate an introduction through Mainland Southeast Asia for Australian dingoes and Polynesian domestic dogs
Authors: Oskarsson Mattias C. R. , Klütsch Cornelya F. C. , Boonyaprakob Ukadej , Wilton Alan , Tanabe Yuichi , Savolainen Peter
Published: September 2011

In the late stages of the global dispersal of dogs, dingoes appear in the Australian archaeological record 3500 years BP, and dogs were one of three domesticates brought with the colonization of Polynesia, but the introduction routes to this region remain unknown. This also relates to questions about human history, such as to what extent the Polynesian culture was introduced with the Austronesian expansion from Taiwan or adopted en route, and whether pre-Neolithic Australia was culturally influenced by the surrounding Neolithic world. We investigate these questions by mapping the distribution of the mtDNA founder haplotypes for dingoes (A29) and ancient Polynesian dogs (Arc1 and Arc2) in samples across Southern East Asia (n= 424) and Island Southeast Asia (n= 219). All three haplotypes were found in South China, Mainland Southeast Asia and Indonesia but absent in Taiwan and the Philippines, and the mtDNA diversity among dingoes indicates an introduction to Australia 4600–18 300 years BP. These results suggest that Australian dingoes and Polynesian dogs originate from dogs introduced to Indonesia via Mainland Southeast Asia before the Neolithic, and not from Taiwan together with the Austronesian expansion. This underscores the complex origins of Polynesian culture and the isolation from Neolithic influence of the pre-Neolithic Australian culture.
Factors associated with the seroprevalence of 26 cutaneous and two genital human papillomavirus types in organ transplant patients
Authors: Sampogna F. , Bavinck J. N. Bouwes , Pawlita M. , Abeni D. , Harwood C. A. , Proby C. M. , Feltkamp M. C. W. , Euvrard S. , Naldi L. , Neale R. E. , Nindl I. , Pfister H. , Quint W. G. V. , Waterboer T. ,   the EPI-HPV-UV-CA group
Published: September 2011

Viral skin infections are commonly present in organ transplant recipients (OTR). In this study, we aimed to identify factors associated with human papillomavirus (HPV) infections in OTR. Patients with solid-organ transplants were recruited from the outpatient nephrology and dermatology clinics in five European countries. Only patients with no current or past skin cancer were included in this analysis. Serum samples were analysed for antibodies to the L1 proteins of 26 cutaneous and two genital HPV types from five phylogenetic genera (α, β, γ, μ and ν). The most consistent association was found between recreational sun exposure and the seroprevalence of all tested genera, except α. The antibody presence of any β type was higher among people who had been transplanted at least 23 years prior to participation than in those who had been transplanted for less than 7 years. The prevalence of two γ-HPV types (60 and 65) and three β-HPV types (15, 38 and 49) was associated with time since transplantation. The presence of a high number of warts was associated with the presence of any μ-PV or ν-PV types, and having greater than 50 keratotic skin lesions was almost significantly associated with the presence of antibodies to two or more γ-PV. Discrepancies in the results of the present study, as well as in previous reports, may depend on different methodologies and on geographical variations. Our results also indicate that further research with more standardized methods is needed to clarify the role of cutaneous HPV in OTR.
Viruses and microRNAs: RISCy interactions with serious consequences
Authors: Cullen Bryan R.
Published: September 2011

Analyses of small RNA expression profiles have revealed that several DNA viruses—including particularly, herpesviruses—express high levels of multiple viral microRNAs (miRNAs) in infected cells. Here, I review our current understanding of how viral miRNAs influence viral replication and pathogenesis and discuss how viruses reshape the pattern of cellular miRNA expression. Indeed, viruses are now known to both activate and repress the expression of specific cellular miRNAs, and disrupting this process can perturb the ability of viruses to replicate normally. In addition, it is now clear that virally encoded miRNAs play a key role in inhibiting antiviral innate immune responses and can also promote cell transformation in culture. While our understanding of how viruses interact with miRNAs remains somewhat rudimentary, it is nevertheless already clear that these interactions can play a critical role in mediating viral pathogenesis and therefore may represent novel and highly specific targets for therapeutic intervention.
Multiple Lines of Evidence Localize Signaling, Morphology, and Lipid Biosynthesis Machinery to the Mitochondrial Outer Membrane of Arabidopsis
Authors: Duncan Owen , Taylor Nicolas L. , Carrie Chris , Eubel Holger , Kubiszewski-Jakubiak Szymon , Zhang Botao , Narsai Reena , Millar A. Harvey , Whelan James
Published: September 2011

The composition of the mitochondrial outer membrane is notoriously difficult to deduce by orthology to other organisms, and biochemical enrichments are inevitably contaminated with the closely associated inner mitochondrial membrane and endoplasmic reticulum. In order to identify novel proteins of the outer mitochondrial membrane in Arabidopsis (Arabidopsis thaliana), we integrated a quantitative mass spectrometry analysis of highly enriched and prefractionated samples with a number of confirmatory biochemical and cell biology approaches. This approach identified 42 proteins, 27 of which were novel, more than doubling the number of confirmed outer membrane proteins in plant mitochondria and suggesting novel functions for the plant outer mitochondrial membrane. The novel components identified included proteins that affected mitochondrial morphology and/or segregation, a protein that suggests the presence of bacterial type lipid A in the outer membrane, highly stress-inducible proteins, as well as proteins necessary for embryo development and several of unknown function. Additionally, proteins previously inferred via orthology to be present in other compartments, such as an NADH:cytochrome B5 reductase required for hydroxyl fatty acid accumulation in developing seeds, were shown to be located in the outer membrane. These results also revealed novel proteins, which may have evolved to fulfill plant-specific requirements of the mitochondrial outer membrane, and provide a basis for the future functional characterization of these proteins in the context of mitochondrial intracellular interaction.
Functional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Data Sets
Authors: Bassel George W. , Glaab Enrico , Marquez Julietta , Holdsworth Michael J. , Bacardit Jaume
Published: September 2011

The meta-analysis of large-scale postgenomics data sets within public databases promises to provide important novel biological knowledge. Statistical approaches including correlation analyses in coexpression studies of gene expression have emerged as tools to elucidate gene function using these data sets. Here, we present a powerful and novel alternative methodology to computationally identify functional relationships between genes from microarray data sets using rule-based machine learning. This approach, termed “coprediction,” is based on the collective ability of groups of genes co-occurring within rules to accurately predict the developmental outcome of a biological system. We demonstrate the utility of coprediction as a powerful analytical tool using publicly available microarray data generated exclusively from Arabidopsis thaliana seeds to compute a functional gene interaction network, termed Seed Co-Prediction Network (SCoPNet). SCoPNet predicts functional associations between genes acting in the same developmental and signal transduction pathways irrespective of the similarity in their respective gene expression patterns. Using SCoPNet, we identified four novel regulators of seed germination (ALTERED SEED GERMINATION5, 6, 7, and 8), and predicted interactions at the level of transcript abundance between these novel and previously described factors influencing Arabidopsis seed germination. An online Web tool to query SCoPNet has been developed as a community resource to dissect seed biology and is available at http://www.vseed.nottingham.ac.uk/.
Accessing the hidden lamellar nanostructure of semi-crystalline nascent polymers by small-angle X-ray scattering contrast variation
Authors: Westfahl Jr Harry , Cardoso Mateus Borba
Published: September 2011

Most melt-crystallized polymers present a lamellar nanostructure of alternating crystalline and amorphous lamellae which is coherent enough to display a broad interference peak in small-angle X-ray scattering experiments (SAXS). Nascent semi-crystalline polymers, on the other hand, though highly crystalline, hardly show an interference peak. This has long been attributed either to the formation of extended chain crystals or to a highly incoherent lamellar stacking. Here it is shown that a coherent lamellar order is shaded by a large scattering contribution from the air/grain interface. This is revealed by a SAXS contrast variation technique that suppresses the air/grain interface scattering and leaves only the scattering contribution from the internal lamellae.
Parallel use of by‐passing agents in haemophilia with inhibitors: a critical review
Authors: Ingerslev Jørgen , Sørensen Benny
Published: September 2011

In the absence of new outbreaks of transfusion‐related infections, the occurrence of neutralizing antibodies currently remains the most prominent complication in haemophilia. Coagulation factor products that may circumvent the inadequate activation of factor X in classical haemophilia, often referred to as bypassing agents, have demonstrated a high degree of efficacy. A smaller number of patients have been described in whom either bypassing agent, or both, demonstrate diminished efficacy. In those cases, the use of both bypassing agents in parallel was attempted, either using simultaneous (combined) or alternating (sequential) infusion of the two drugs, reportedly with successful haemostasis. We speculated whether such treatment might cause thromboembolism. A thorough literature search disclosed 17 reports regarding the parallel use of bypassing agents in the same bleeding episode in 49 patients; reporting nine patients with acquired haemophilia and forty patients with congenital haemophilia with inhibitors. Notable incidences of thromboembolic manifestations were observed: in nine patients with acquired haemophilia, five and in 40 patients with congenital haemophilia five suffered from significant thrombotic complications, and overall four cases were fatal. Although efficacy of parallel treatment was reported excellent in most cases, thromboembolism is rare in haemophilia and parallel treatment with activated prothrombin complex concentrate and activated recombinant human factor VII appears to increase the risk of thrombosis in these patients.
An update on mosquito cell expressed dengue virus receptor proteins
Authors: Smith D. R.
Published: September 2011

Dengue is the most important mosquito transmitted viral disease of humans worldwide. Despite intensive study over several decades, many of the fine details of the dengue virus (DENV) replication cycle remain unknown, although generally more is known about the phase of the replication cycle in mammalian cells as compared to the phase in mosquito cells. This results from a combination of less research emphasis on the mosquito stage, as well as fewer tools such as specific antibodies against mosquito proteins and insect informatics databases. The binding of a virus to a host cell is a first and critical stage in the infectious process and the mechanism and identity of cellular proteins involved in this process remains largely unknown. This short review aims to provide an update on our current understanding of the proteins expressed by mosquito cells that mediate DENV binding as a prerequisite to DENV entry and replication.
West to east dispersal and subsequent rapid diversification of the mega‐diverse genusBegonia(Begoniaceae) in the Malesian archipelago
Authors: Thomas D. C. , Hughes M. , Phutthai T. , Ardi W. H. , Rajbhandary S. , Rubite R. , Twyford A. D. , Richardson J. E.
Published: September 2011

Aim The complex palaeogeography of the Malesian archipelago, characterized by the evolution of an ever‐changing mosaic of terrestrial and marine areas throughout the Cenozoic, provides the geographic backdrop for the remarkable diversification of MalesianBegonia(> 450 species). This study aimed to investigate the origin of MalesianBegonia, the directionality of dispersal events within the Malesian archipelago and the impact of ancient water gaps on colonization patterns, and to identify drivers of diversification.

Location Asia, Southeast Asia, Malesia.

Methods Plastid DNA sequence data of representatives of all families of the Cucurbitales and Fagales (matK,rbcL,trnL intron,trnL–F spacer, 4076 aligned positions, 92 taxa) and a sample of all major AsianBegoniasections (ndhA intron,ndhF–rpl32 spacer,rpl32–trnL spacer, 4059 aligned positions, 112 taxa) were analysed under an uncorrelated‐rates relaxed molecular clock model to estimate the age of theBegoniacrown group divergence and divergence ages within AsianBegonia. Ancestral areas were reconstructed using a likelihood approach implementing a dispersal–extinction–cladogenesis model, and with a Bayesian approach to dispersal–vicariance analysis.

Results The results indicated an initial diversification of AsianBegoniain continental Asia in the Miocene, and subsequent colonization of Malesia by multiple lineages. There was support for at least six independent dispersal events from continental Asia and western Malesia to Wallacea dating from the late Miocene to the Pleistocene.BegoniasectionPetermannia(> 270 species) originated in Western Malesia, and subsequently dispersed to Wallacea, New Guinea and the Philippines. Lineages within this section diversified rapidly since the Pliocene, coinciding with rapid orogenesis on Sulawesi and New Guinea.

Main conclusions The predominant trend ofBegoniadispersals between continental Asia and Malesia, and also within Malesia, has been from west to east. The water bodies separating the Sunda Shelf region from Wallacea have been porous barriers to dispersal inBegoniafollowing the emergence of substantial land in eastern Malesia from the late Miocene onwards. We hypothesize two major drivers of the diversification of MalesianBegonia: (1) the formation of topographical heterogeneity and the promotion of microallopatry by orogenesis in the Pliocene and Pleistocene; and (2) cyclic vicariance by frequent habitat fragmentations and amalgamations due to climate and sea‐level fluctuations during the Pleistocene.
Range shift promotes the formation of stable range edges
Authors: Phillips Ben L.
Published: September 2011

Aim I investigate the counter‐intuitive possibility that range shift promotes the formation of stable range edges. This might be expected because: (1) range‐shifting populations typically evolve increased dispersal on the expanding range edge; (2) increased dispersal steepens the relative slope of environmental gradients (gradients appear steeper to a more dispersive population); and (3) environmental gradients that are steep relative to dispersal encourage the formation of stable range edges (when gradients appear steep, adaptation on the range edge is swamped by maladapted genes).

Methods I test the idea that populations take longer to evolve across an environmental gradient when those populations have already undergone a period of spread. I do this using an individual‐based coupled map lattice simulation, in which individuals carry heritable traits for dispersal probability and environment‐specific fitness.

Results Numerous simulations across parameter space confirm that a period of range shift almost always results in a longer time to evolve through an environmental gradient. This occurs because of both the mechanism described above and the erosion of adaptive variation resulting from the serial foundering that occurs during range advance.

Main conclusions This result suggests that species may often shift their range due to intrinsic changes in the population rather than extrinsic changes in the environment. The result also suggests a new mechanism regulating the speed of invasion, and sounds a cautionary note for climate change impacts: the longer a species tracks climate change, the less able it may be to track that change into the future.
Ultrasonography in the management of the airway
Authors: KRISTENSEN M. S.
Published: September 2011

In this study, it is described how to use ultrasonography (US) for real‐time imaging of the airway from the mouth, over pharynx, larynx, and trachea to the peripheral alveoli, and how to use this in airway management. US has several advantages for imaging of the airway – it is safe, quick, repeatable, portable, widely available, and it must be used dynamically for maximum benefit in airway management, in direct conjunction with the airway management, i.e. immediately before, during, and after airway interventions. US can be used for direct observation of whether the tube enters the trachea or the esophagus by placing the ultrasound probe transversely on the neck at the level of the suprasternal notch during intubation, thus confirming intubation without the need for ventilation or circulation. US can be applied before anesthesia induction and diagnose several conditions that affect airway management, but it remains to be determined in which kind of patients the predictive value of such an examination is high enough to recommend this as a routine approach to airway management planning. US can identify the croicothyroid membrane prior to management of a difficult airway, can confirm ventilation by observing lung sliding bilaterally and should be the first diagnostic approach when a pneumothorax is suspected intraoperatively or during initial trauma‐evaluation. US can improve percutaneous dilatational tracheostomy by identifying the correct tracheal‐ring interspace, avoiding blood vessels and determining the depth from the skin to the tracheal wall.