Pre-Commercial Thinning Increases the Profitability of Norway Spruce Monoculture and Supports Norway Spruce-Birch Mixture over Full Rotations

Pre-commercial thinning (PCT) is a common measure in Norway spruce (Picea abies L. Karst.) stands but the profitability of doing PCT and timing of PCT has not been fully investigated over a full rotation. Further, limited knowledge is available for mixed forest management compared to monocultures. In this study, different PCT strategies were tested to investigate the effect of PCT and timing of PCT on the production and profitability of Norway spruce monocultures and mixed Norway spruce-birch stands. A forest decision support system was used to simulate stand development during the whole rotation. Our study findings show that there is a positive effect of PCT on Norway spruce plantations' long-term profitability but that the timing of PCT has little effect on profitability. However, site variation might influence the effect of PCT timing on the profitability of Norway spruce stands. Moreover, we also found that retaining 1000 Norway spruce ha(-1) and 1000 birch ha(-1) after PCT supports a mixture of Norway spruce and birch over a full rotation, with little or no economic loss compared to pure Norway spruce stands. Therefore, such a mixture can lead to profitable production while still providing other ecosystem services

The Regulation of Commodity Options

To outline further genetic mechanisms of transformation from follicular lymphoma (FL) to diffuse large B-cell lymphoma (DLBCL), we have performed whole genome array-CGH in 81 tumors from 60 patients [29 de novo DLBCL (dnDLBCL), 31 transformed DLBCL (tDLBCL), and 21 antecedent FL]. In 15 patients, paired tumor samples (primary FL and a subsequent tDLBCL) were available, among which three possessed more than two subsequent tumors, allowing us to follow specific genetic alterations acquired before, during, and after the transformation. Gain of 2p15-16.1 encompassing, among others, the REL, BCL11A, USP34, COMMD1, and OTX1 genes was found to be more common in the tDLBCL compared with dnDLBCL (P < 0.001). Furthermore, a high-level amplification of 2p15-16.1 was also detected in the FL stage prior to transformation, indicating its importance during the transformation event. Quantitative real-time PCR showed a higher level of amplification of REL, USP34, and COMMD1 (all involved in the NF kappa B-pathway) compared with BCL11A, which indicates that the altered genes disrupting the NF kappa B pathway may be the driver genes of transformation rather than the previously suggested BCL11A. Moreover, a 17q21.33 amplification was exclusively found in tDLBCL, never in FL (P < 0.04) or dnDLBCL, indicating an upregulation of genes of importance during the later phase of transformation. Taken together, our study demonstrates potential genomic markers for disease progression to clinically more aggressive forms. We also confirm the importance of the TP53-, CDKN2A-, and NF kappa B-pathways for the transformation from FL to DLBCL

Pre-commercial thinning in Norway spruce-birch mixed stands can provide abundant forage for ungulates without losing volume production

Mixed stands of Norway spruce and birch have the potential to simultaneously produce timber and provide large ungulates with a significant amount of forage during the regeneration phase. While the growth and yield of such mixtures are well studied, little is known about potential trade-offs between timber and forage production and which management techniques are suitable for meeting both goals. In this study, four different pre-commercial thinning (PCT) strategies were used to study the trade-offs between production and available forage for free-ranging ungulates in a Norway spruce-birch mixture. The four PCT strategies were: 1) retaining 2000 birch stems ha(-1) with 2000 Norway spruce ha(-1), 2) removing all birches within a 0.75 m radius around Norway spruce stems, 3) removing all birches and other broadleaves, and 4) no PCT (control). Growth of Norway spruce was higher in the 2000 birch ha(-1) and full removal treatments compared to the untreated control, but these two treatments did not differ from one another in volume production of Norway spruce. We found a negative effect of PCT on forage availability but no effect on ungulate browsing. Therefore, PCT strategies that provide both sufficient birch forage and maximize volume production of Norway spruce can be implemented

Clonal spread of carbapenem-resistant Klebsiella pneumoniae among patients at admission and discharge at a Vietnamese neonatal intensive care unit

Background The increasing prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is a growing problem globally, particularly in low- to middle-income countries (LMICs). Previous studies have shown high rates of CRE colonisation among patients at hospitals in LMICs, with increased risk of hospital-acquired infections. Methods We isolated carbapenem-resistant Klebsiella pneumoniae (CRKP) from faecal samples collected in 2017 from patients at admission and discharge at a Vietnamese neonatal intensive care unit (NICU). 126 CRKP were whole-genome sequenced. The phylogenetic relationship between the isolates and between clinical CRKP isolates collected in 2012-2018 at the same hospital were investigated. Results NDM-type carbapenemase-(61%) and KPC-2-encoding genes (41%) were the most common carbapenem resistance genes observed among the admission and discharge isolates. Most isolates (56%) belonged to three distinct clonal clusters of ST15, carrying bla(KPC-2), bla(NDM-1) and bla(NDM-4), respectively. Each cluster also comprised clinical isolates from blood collected at the study hospital. The most dominant ST15 clone was shown to be related to isolates collected from the same hospital as far back as in 2012. Conclusions Highly resistant CRKP were found colonising admission and discharge patients at a Vietnamese NICU, emphasising the importance of continued monitoring. Whole-genome sequencing revealed a population of CRKP consisting mostly of ST15 isolates in three clonally related clusters, each related to blood isolates collected from the same hospital. Furthermore, clinical isolates collected from previous years (dating back to 2012) were shown to likely be clonally descended from ST15 isolates in the largest cluster, suggesting a successful hospital strain which can colonise inpatients

Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the mode and strength of selection. To control for regional variation in substitution rates, the proportionate number of nonsynonymous differences (dN) is divided by the proportionate number of synonymous differences (dS). The resulting ratio (dN/dS) is a widely used indicator for functional divergence to identify particular genes that underwent positive selection. With the ever-growing amount of genome data, summary statistics like mean dN/dS allow gathering information on the mode of evolution for entire species. Both applications hinge on the assumption that dS and mean dS (∼branch length) are neutral and adequately control for variation in substitution rates across genes and across organisms, respectively. We here explore the validity of this assumption using empirical data based on whole-genome protein sequence alignments between human and 15 other vertebrate species and several simulation approaches. We find that dN/dS does not appropriately reflect the action of selection as it is strongly influenced by its denominator (dS). Particularly for closely related taxa, such as human and chimpanzee, dN/dS can be misleading and is not an unadulterated indicator of selection. Instead, we suggest that inconsistencies in the behavior of dN/dS are to be expected and highlight the idea that this behavior may be inherent to taking the ratio of two randomly distributed variables that are nonlinearly correlated. New null hypotheses will be needed to adequately handle these nonlinear dynamics

The genetic history of Scandinavia from the Roman Iron Age to the present

The authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We used resources from projects SNIC 2022/23-132, SNIC 2022/22-117, SNIC 2022/23-163, SNIC 2022/22-299, and SNIC 2021-2-17. This research was supported by the Swedish Research Council project ID 2019-00849_VR and ATLAS (Riksbankens Jubileumsfond). Part of the modern dataset was supported by a research grant from Science Foundation Ireland (SFI), grant number 16/RC/3948, and co-funded under the European Regional Development Fund and by FutureNeuro industry partners.Peer reviewedPublisher PD

DNA repair genes are selectively mutated in diffuse large B cell lymphomas

DNA repair mechanisms are fundamental for B cell development, which relies on the somatic diversification of the immunoglobulin genes by V(D)J recombination, somatic hypermutation, and class switch recombination. Their failure is postulated to promote genomic instability and malignant transformation in B cells. By performing targeted sequencing of 73 key DNA repair genes in 29 B cell lymphoma samples, somatic and germline mutations were identified in various DNA repair pathways, mainly in diffuse large B cell lymphomas (DLBCLs). Mutations in mismatch repair genes (EXO1, MSH2, and MSH6) were associated with microsatellite instability, increased number of somatic insertions/deletions, and altered mutation signatures in tumors. Somatic mutations in nonhomologous end-joining (NHEJ) genes (DCLRE1C/ARTEMIS, PRKDC/DNA-PKcs, XRCC5/KU80, and XRCC6/KU70) were identified in four DLBCL tumors and cytogenetic analyses revealed that translocations involving the immunoglobulin-heavy chain locus occurred exclusively in NHEJ-mutated samples. The novel mutation targets, CHEK2 and PARP1, were further screened in expanded DLBCL cohorts, and somatic as well as novel and rare germline mutations were identified in 8 and 5% of analyzed tumors, respectively. By correlating defects in a subset of DNA damage response and repair genes with genomic instability events in tumors, we propose that these genes play a role in DLBCL lymphomagenesis

Infection and growth of Heterobasidion spp. in Picea abies

In economical terms, species of Heterobasidion are among the most severe fungal pests in coniferous forests of the northern hemisphere. The fungi cause interior decay in the stem of trees and trees may also die as a cause of infection. Two species of Heterobasidion have been identified in Sweden, Heterobasidion annosum s.s. (Fr.) Bref. and Heterobasidion parviporum Niemelä & Korhonen. The former has been identified from southern to central Sweden whereas the latter is present throughout the whole country. Stump treatment, using chemical or biological treatment agents, is the most widely used silvicultural method to prevent infection by Heterobasidion. This thesis mainly focuses on different aspects of biological stump treatment using Phlebiopsis gigantea (Fr.) Jül. The effectiveness of stump treatment against air-borne Heterobasidion spores with P. gigantea, when applied at different rates of stump coverage was investigated in southern Sweden. The results showed that, in order to achieve the best control, the aim should be to cover the complete stump surface with the treatment agent. In another field experiment in southern Sweden the effectiveness of Finish and Swedish strains of P. gigantea was compared. Two formulations containing two species of Trichoderma were also included in the study. Two of the Swedish P. gigantea strains showed the best control against air-borne Heterobasidion spores. None of the Trichoderma formulations significantly reduced Heterobasidion infection. The effect of stump treatment using P. gigantea on stumps from trees that were already infected by H. parviporum at the time of felling was studied in south-western Sweden. It was hypothesized that P. gigantea may restrict the growth of Heterobasidion in the root system of treated stumps. However, no such effect was observed and treatment of stumps from already infected trees can, based on this study, not be recommended as a means of restricting the spread of the pathogen. In the last study, the ability of inoculated H. annosum s.s. to establish and grow in trees and stumps in northern Sweden (outside its natural range of distribution) was compared with the ability to establish and grow in southern Sweden. In the trees, H. annosum s.s. established in almost as many trees in the north as in the south of Sweden. However, spores of H. annosum s.s. showed an inability to establish on stumps, in both parts of the country. This indicates that routes of infection, other than through fresh stump surfaces may be involved in the disease cycle of H. annosum s.s. in Norway spruce

Historielärarens uppdrag : en studie om skolans möjlighet att motverka fördomar och främlingsfientlighet

Validerat; 20101217 (root