Demography of an invading forest insect reunited with hosts and parasitoids from its native range

SUPPLEMENTARY MATERIALS : Explanation note: This file includes demographic data from native Sirex nigricornis woodwasps that were collected during our study. TABLE S1. Correlation matrix of bolt-level variables for P. resinosa and P. sylvestris. TABLE S2. Review of 10th and 90th percentile female body mass from insect species estimated from source paper cited, showing comparatively higher female S. noctilio body size variation. FIGURE S1. Examples of S. noctilio oviposition sites, lesion formation and emergence holes in the field. FIGURE S2. Top panels show a typical bolt from P. sylvestris with bark removed and S. noctilio emergence holes and oviposition sites identified. FIGURE S3. The number of S. noctilio emerging per tree was best described by a zero inflated negative binomial distribution (dotted line) with proportion of excess zeroes Φ = 0.32, μ = 75.39 and overdispersion parameter k = 0.35. FIGURE S4. Allometric relationships for S. noctilio in the Central NY data set: number of eggs and adult female mass (a; quantile regression), adult female mass and adult female length (b; fitted power function) and adult length and width of adult head capsule (c; linear regression).The Sirex woodwasp Sirex noctilio Fabricius (Hymenoptera: Siricidae), a widespread invasive pest of pines in the Southern Hemisphere, was first detected in North America in 2004. This study assessed the impacts of life history traits, host resistance and species interactions on the demography of S. noctilio in New York, Pennsylvania and Vermont, then compared key metrics to those found in the native range in Galicia, Spain. Many trees naturally attacked by S. noctilio in North America produced no adult woodwasps, with 5 of 38 infested trees (13%) sampled across six sites yielding 64% of emerging insects. Reproductive success was highest in the introduced host scots pine, Pinus sylvestris, but native red pine, Pinus resinosa, produced larger insects. Sirex noctilio required one or sometimes two years to develop and sex ratios were male biased, 1:2.98 ♀:♂. Body size and fecundity were highly variable, but generally lower than observed in non-native populations in the Southern Hemisphere. Hymenopteran parasitoids killed approximately 20% of S. noctilio larvae and 63% of emerging adults were colonized by the parasitic nematode Deladenus siricidicola, although no nematodes entered eggs. Demographic models suggested that S. noctilio in the northeastern USA have a higher potential for population growth than populations in the native range: estimated finite factor of increase, λ, was 4.17–4.52 (depending on tree species colonized), compared to λ = 1.57 in Spain.USDA Forest Service International Programs and OP RDE.https://neobiota.pensoft.netam2023Forestry and Agricultural Biotechnology Institute (FABI)Zoology and Entomolog

Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma

Abstract: The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy

Exploring meaningful nature experience, connectedness with nature and the revitalization of transformative education for sustainability

Thesis (PhD)--Stellenbosch University, 2014.ENGLISH ABSTRACT: Humanity‘s growing separation from nature is central to the convergent social and ecological crises facing earth. This is both a psychological (e.g. perceptual, emotional) and physical (e.g. experiential) disconnect and is therefore better understood as a crisis in consciousness. This research arises out of an intense interest in how to alleviate humanity‘s fading connectedness with nature and, specifically, if meaningful nature experience is capable of healing the divisive ways in which humans tend to think, see and act in the world. This study brings together four core themes: connectedness with nature (CWN), invasive alien species (IAS), and education for sustainability (EfS); each of which are explored around - and in relationship to - the core concept of meaningful nature experience (MNE).1 In doing so, this transdisciplinary research utilizes a theory of complexity to integrate diverse disciplinary perspectives by drawing upon: (conservation) ecology; (environmental-/eco-) psychology; (sustainability) education; and phenomenology as a guiding philosophy. Adopting an interpretivist and pragmatic approach, this research employs mixed methods (quantitative and qualitative/phenomenological analysis) to, firstly, uncover the essences which help describe what MNE feels like (how it appears in consciousness) and that which makes MNE what it is. Secondly, the study explores the relationship between MNE and CWN; the extent to which MNE is perceived to influence attitudes and environmentally responsible behaviour (ERB); and whether ecological change as experienced through IAS may affect MNE or, in turn, how MNE and CWN influence perceptions on IAS. Thirdly, the research examines the implications of the above for EfS: is there merit for integrating MNE and CWN in EfS? What would such a process look like and how can it be applied in a way which revitalizes EfS? Finally, as a form of heuristic inquiry, this study represents my process of conscious transformative learning. Reflective narratives are dispersed throughout this dissertation to capture this enriching personal journey. Research findings draw on over 200 unique accounts of MNEs which were elicited from: online and public questionnaires; in-depth interviews, email submissions and complemented by in-situ field observation and participation. The questionnaires and in-depth interviews also elicited responses on CWN, IAS and EfS. The research finds that a MNE is triggered by an unexpected encounter with the 'non-ordinary‘ in nature. It is characterized by heightened sensory awareness (e.g. the beauty and detail of natural phenomena arrest our attention), intensified emotional (e.g. awe, amazement) and physiological responses (e.g. a 'rush‘). If an animal is involved, close proximity, extended length of time and reciprocity are key themes. For a MNE not involving an animal, perceived aliveness, vibrancy and energy pervading the land-/ sea-/ sky-scape is primary. As mind meets matter, one feels interrelatedness and a diminished sense of self. The privilege to commune with an 'other‘ (re)defines a person‘s being and belonging in the world. Synchronicity as a MNE is distinctive as an uncanny (e.g. numinous) experience of: insight; flow; guidance; a 'knowing‘; and interconnectedness. Respondents who have had a MNE exhibit a higher CWN; a positive correlation exists between frequency of MNE (fMNE) and CWN. Stronger correlations with CWN were found when a wild animal was involved in the MNE. Spiritual / religious practices positively correlate with fMNE and CWN with regular displays of gratitude toward nature returning slightly stronger correlations with CWN. Strongest correlations were found between the experience of synchronicity and CWN. A qualitative analysis of respondents‘ MNEs and their responses on how they perceive their MNE(s) to have changed them, found multiple and diverse mention of (newfound) appreciations of (inter)connectedness. This suggests that MNE acts as a conduit for CWN: one powerful MNE may be sufficient to catalyse the process; however, a higher fMNE increases the likelihood for heightened CWN. Such results affirm the idea that MNEs facilitate a relational worldview necessary for a consciousness attuned to CWN. CWN is considered to be a reliable predictor for ERB. Over 90% agreement was found between respondents on the positive impact of MNEs in: shaping their views on nature and biodiversity; influencing their current behaviour and actions toward nature and the environment; and heavily influencing, changing or transforming their outlooks on life. The most common themes to emerge on how MNE was perceived to have changed respondents related to understanding of (inter)connectedness/interdependence; career choice; respect for nature / life; and new ways of seeing the world. This supports the premise that, by affectively bonding with nature, MNEs can motivate: ERB; life paths into conservation-minded careers; and serve as catalysts for personal growth and transformation, particularly when complemented with reflection, social (guided) facilitation and ecological literacy. The presence of IAS in landscape is likely to adversely affect MNE for stated reasons of ecological impacts, diminished 'naturalness‘, destructiveness and reduced diversity. Those viewing IAS as potentially enhancing their MNEs cite reasons of beauty, novelty and enjoyment. Respondents‘ CWN does not appear to affect perceptions of IAS; however, elevated CWN may invoke empathy, a sense of relatedness and appreciation of their intrinsic value as 'life‘. IAS may also feature in MNEs and, through experiential and metaphorical insight, can deliver newfound understandings of social and ecological connections as they relate to IAS. Respondents concur that today‘s education does not prepare society to learn from MNE: overwhelming agreement was found on the societal and ecological benefits of an education that promotes understanding of MNE through a blend of intellectual concepts; experiential activities; values and ethics; and integrated learning approaches. Experiential nature-based activities were encouraged as vital EfS vehicles for enhancing sensory awareness; respect for nature; ecological knowledge and encountering connectedness. In-depth interviewees saw future EfS opportunities and solutions as focusing more on: participating with nature; bridging spirituality and science; facilitating 'openness‘ and shared experience; instilling values reflecting an interconnected reality; mentoring; contemporary rites of passage; and simply learning to live better. The essence of this research is an expanded appreciation of connectedness - embodying Nature, Community, Self, Source - and the manifold ways it is encountered through MNE. Revitalized EfS (realized through Theory edU) invites a consciousness that attends to an enlivening process of connecting, harmonizing and becoming.AFRIKAANSE OPSOMMING: Hierdie studie bring vier kern temas na vore: verbintenis met die natuur (VMN), indringende uitheemse spesies (IUS), en opvoeding vir volhoubaarheid (OVV); waarvan elk verken is rondom – en in verhouding is tot die kern konsep van betekenisvolle natuur ervaring 2 (BNE). Deur dit te doen, wend hierdie transdisiplinêre studie 'n teorie van kompleksiteit aan om diverse dissiplinêre perspektiewe te integreer deur gebruik te maak van: bewarings ekologie; omgewings-/eko- sielkunde; onderwys; en femenologie as 'n rigtinggewende filosofie. Deur 'n interpretatiewe en pragmatiese benadering aan te neem, is gemengde metodes (kwantitatief en kwalitatief / femenologiese analise) gebruik om eerstens die essensies wat help om te beskryf hoe BNE voel (hoe dit in die bewussyn voorkom) en dit wat BNE maak wat dit is, te ontbloot. Tweedens verken die studie die verhouding tussen BNE en VMN; die mate waartoe BNE beskou word om houdings en omgewings verantwoordelike gedragte beïnvloed (OVG); en of ekologiese verandering soos deur IUS ervaar word BNE kan affekteer, of, op sy beurt, hoe BNE en VMN persepsies van IUS kan beïnvloed. Derdens bestudeer die navorsing implikasies van die bogenoemde vir OVV: is daar meriete vir die integrasie van BNE en VMN in OVV? Hoe sal so 'n proses lyk en hoe kan dit toegepas word op 'n manier wat OVV weer nuwe lewe sal gee? Ten einde, as 'n vorm van heuristiese ondersoek, stel hierdie studie my proses van bewuste transformatiewe leer voor. Reflektiewe narratiewe is regdeur die proefskrif versprei om hierdie verrykende persoonlike reis vas te lê. Navorsing bevindinge gebruik meer as 200 unieke verklarings van BNE‘s wat aan die lig gebring is deur: aanlyn en publieke vraelyste; in-diepte onderhoude, e-pos indienings en dit is gekomplementeer deur in-situ veld observasie en deelname. Die vraelyste en in-diepte onderhoude het ook reaksies op VMN, IUS en OVV ontlok. Die navorsing het bevind dat 'n BNE word veroorsaak deur 'n onverwagste ontmoeting met die 'nie-gewone‘ in die natuur. Dit word gekarakteriseer deur verhoogde sensoriese bewustheid (bv. die prag en besonderhede van natuurlike verskynsels beset ons aandag), versterkde emosionele (bv. verwondering en verbasing) en psigologiese reaksies (bv. 'n stormloop). Indien 'n dier betrokke is, is nabyheid, verlengde duur van tyd en wederkerigheid sleutel temas. Vir 'n BNE wat nie 'n dier insluit nie, is waarneembare lewendigheid, dinamiek en energie wat die landskap / see / luglandskap deurdring primêr. Soos wat die gees die stof ontmoet, voel 'n mens 'n onderlinge verband en 'n verminderde sin van die self. Die voorreg om in noue aanraking met 'n 'ander‘ te kan wees (her)definieër 'n persoon se wese en behoort in die wêreld. 'Synchronicity‘ as 'n BNE is kenmerkend as 'n ongelooflike (bv. numineuse) ervaring van: insig, vloei, leiding; 'n 'wete‘; en onderlinge verbintenis. Respondente wat 'n BNE gehad het, het 'n hoër VMN getoon; 'n positiewe korrelasie bestaan tussen die frekwensie van BNE (fBNE) en VMN. Sterker korrelasies met VMN was gevind in die geval waar 'n wilde dier in die BNE betrokke was. Geestelike / religieuse praktyke korreleer positief met fBNE en VMN waar gewone openbarings van dankbaarheid tot die natuur effens sterker korrelasies met VMN terugbring. Die sterkste korrelasies was gevind tussen die ervaring van 'synchronicity‘ en VMN. 'n Kwalitatiewe analise van respondente se BNE‘s en hul response van hoe hulle hul BNE(s) as dit wat hul verander het, beskou, het veelvoudige en diverse antwoorde van (nuutgevonde) erkennings van (onderlinge) verbintenis navore gebring. Dit dui daarop dat BNE as 'n toevoerbuis vir VMN optree: een kragtige BNE mag voldoende wees om die proses te kataliseer; aan die anderkant verhoog 'n hoër fBNE die waarskynlikheid vir verhoogde VMN. Sulke resultate bevestig die idee dat BNEs 'n relasionele wêreldbeskouing is wat nodig is vir 'n bewustheid wat ingestel is vir VMN. VMN word as 'n betroubare voorspelling vir OVG beskou. Meer as 90% van respondente was in ooreenstemming ten opsigte van die positiewe impak van BNEs in: die vorming van hul beskouings van die natuur, biodiversiteit; beïnvloeding van hul huidige gedrag en aksies tot die natuur en die omgewing; en hoe dit hul vooruitsigte op die lewe hewig beïnvloed, verander of transformeer. Die meesal gemene temas wat ontluik het, was oor die beskouing van hoe BNE respondente se verstaan aangaande (onderlinge)verbintenis / onafhanklikheid; beroepskeuse; respek vir die natuur / lewe; en nuwe maniere om na die wêreld te kyk, verander het. Dit ondersteun die uitgangspunt, dat deur affektiewelik met die natuur in verbinding te tree, BNEs gemotiveer kan word: OVG; lewens paaie tot bewaring-gesinde beroepe; en as katalisators dien vir persoonlike groei en transformasie, veral as dit met refleksie, sosiale (begeleide) fassilitering en ekologiese geletterdheid gekomplimenteer word. Die teenwoordigheid van IUS in 'n landskap kan waarskynlik BNE nadelig affekteer weens verklaarbare redes van ekologiese impakte, afneembare 'natuurlikheid', verwoestendheid en verminderde diversiteit. Diegene wat IUS as iets positief tot hul ervaring beskou, verskaf redes soos skoonheid, nuutheid en genot. Dit wil voorkom of deelnemers se VMN nie algemene persepsies van IUS affekteer nie; alhoewel, verhoogde VMN empatie, verwantskap en waardering vir hul intrinsieke waarde as 'lewe' mag oproep. IUS mag ook in BNE vertoon en deur ervarings- en metaforiese insig, kan dit waardevolle nuut-bevinde begrippe van sosiale en ekologiese verbande soos wat hulle aansluit by die probleem van IUS, lewer. Respondente is dit eens dat vandag se onderwys nie die samelewing voorberei om te leer van BNE nie: oorweldigende ooreenstemming was gevind aangaande die maatskaplike en ekologiese voordele van onderwys wat die verstaan van BNE bevorder deur middel van 'n vermenging van intellektuele konsepte; ervarings leeraktiwiteite; waardes en etiek; en geïntegreerde leer benaderings. Ervarings leer natuur-gebaseerde aktiwiteite was aangemoedig as essensiële middels vir OVV vir die verhoging van sensoriese bewussyn; respek vir die natuur, ekologiese kennis en die teëkoming van verbintenis. In-diepte ondervraagdes het geleenthede en oplossings vir toekomstige OVV gesien in terme van 'n groter fokus op: deelname aan die natuur; die orbruging van spiritualiteit en wetenskap; fassilitering van 'oopheid‘ en gedeelde ervaring; vestiging van waardes wat 'n onderlinge verbonde realiteit reflekteer; mentorskap; kontemporêre deurgangsrites; en om eenvoudig te leer om beter te lewe. Die kern van hierdie navorsing behels 'n toenemende waardering van verbintenis – beliggaming van die Natuur, Gemeenskap, Self, Bron – en die menigvuldige maniere waar op dit deur BNE ondervind is. Hernude OVV (soos ontdek deur Theory edU) nooi 'n bewustheid uit wat aandag skenk aan 'n verlewendige proses van verbintenis, harmonisering en wording

The enzymatic basis for pesticide bioremediation

Enzymes are central to the biology of many pesticides, influencing their modes of action, environmental fates and mechanisms of target species resistance. Since the introduction of synthetic xenobiotic pesticides, enzymes responsible for pesticide turnover have evolved rapidly, in both the target organisms and incidentally exposed biota. Such enzymes are a source of significant biotechnological potential and form the basis of several bioremediation strategies intended to reduce the environmental impacts of pesticide residues. This review describes examples of enzymes possessing the major activities employed in the bioremediation of pesticide residues, and some of the strategies by which they are employed. In addition, several examples of specific achievements in enzyme engineering are considered, highlighting the growing trend in tailoring enzymatic activity to a specific biotechnologically relevant function

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma

The molecular genetic relationship between esophageal adenocarcinoma (EAC) and its precursor lesion, Barrett's esophagus, is poorly understood. Using whole-genome sequencing on 23 paired Barrett's esophagus and EAC samples, together with one in-depth Barrett's esophagus case study sampled over time and space, we have provided the following new insights: (i) Barrett's esophagus is polyclonal and highly mutated even in the absence of dysplasia; (ii) when cancer develops, copy number increases and heterogeneity persists such that the spectrum of mutations often shows surprisingly little overlap between EAC and adjacent Barrett's esophagus; and (iii) despite differences in specific coding mutations, the mutational context suggests a common causative insult underlying these two conditions. From a clinical perspective, the histopathological assessment of dysplasia appears to be a poor reflection of the molecular disarray within the Barrett's epithelium, and a molecular Cytosponge technique overcomes sampling bias and has the capacity to reflect the entire clonal architecture.</p