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  • 1. Addario, Barbara
    et al.
    Sandblad, Linda
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Persson, Karina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Backman, Lars
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Characterisation of Schizosaccharomyces pombe alpha-actinin2016Inngår i: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, artikkel-id e1858Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The actin cytoskeleton plays a fundamental role in eukaryotic cells. Its reorganization is regulated by a plethora of actin-modulating proteins, such as a-actinin. In higher organisms, alpha-actinin is characterized by the presence of three distinct structural domains: an N-terminal actin-binding domain and a C-terminal region with EF-hand motif separated by a central rod domain with four spectrin repeats. Sequence analysis has revealed that the central rod domain of alpha-actinin from the fission yeast Schizosaccharomyces pombe consists of only two spectrin repeats. To obtain a firmer understanding of the structure and function of this unconventional alpha-actinin, we have cloned and characterized each structural domain. Our results show that this alpha-actinin isoform is capable of forming dimers and that the rod domain is required for this. However, its actin-binding and cross-linking activity appears less efficient compared to conventional alpha-actinins. The solved crystal structure of the actin-binding domain indicates that the closed state is stabilised by hydrogen bonds and a salt bridge not present in other a-actinins, which may reduce the affinity for actin.

  • 2.
    Backman, Lars
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Alpha-actinin of the chlorarchiniophyte Bigelowiella natans2018Inngår i: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, artikkel-id e4288Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The genome of the chlorarchiniophyte Bigelowiella natans codes for a protein annotated as an α-actinin-like protein. Analysis of the primary sequence indicate that this protein has the same domain structure as other α-actinins, a N-terminal actin-binding domain and a C-terminal calmodulin-like domain. These two domains are connected by a short rod domain, albeit long enough to form a single spectrin repeat. To analyse the functional properties of this protein, the full-length protein as well as the separate domains were cloned and isolated. Characerisation showed that the protein is capable of cross-linking actin filaments into dense bundles, probably due to dimer formation. Similar to human α-actinin, calcium-binding occurs to the most N-terminal EF-hand motif in the calmodulin-like C-terminal domain. The results indicate that this Bigelowiella protein is a proper α-actinin, with all common characteristics of a typical α-actinin.

  • 3.
    Karlsson, Edvin
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden.
    Johansson, Anna-Mia
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Ahlinder, Jon
    Lundkvist, Moa J.
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Singh, Navinder J.
    Brodin, Tomas
    Forsman, Mats
    Stenberg, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Biological Agents, Division of CBRN Defense and Security, Swedish Defense Research Agency, Umeå, Sweden.
    Airborne microbial biodiversity and seasonality in Northern and Southern Sweden2020Inngår i: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 8, artikkel-id e8424Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microorganisms are essential constituents of ecosystems. To improve our understanding of how various factors shape microbial diversity and composition in nature it is important to study how microorganisms vary in space and time. Factors shaping microbial communities in ground level air have been surveyed in a limited number of studies, indicating that geographic location, season and local climate influence the microbial communities. However, few have surveyed more than one location, at high latitude or continuously over more than a year. We surveyed the airborne microbial communities over two full consecutive years in Kiruna, in the Arctic boreal zone, and Ljungbyhed, in the Southern nemoral zone of Sweden, by using a unique collection of archived air filters. We mapped both geographic and seasonal differences in bacterial and fungal communities and evaluated environmental factors that may contribute to these differences and found that location, season and weather influence the airborne communities. Location had stronger influence on the bacterial community composition compared to season, while location and season had equal influence on the fungal community composition. However, the airborne bacterial and fungal diversity showed overall the same trend over the seasons, regardless of location, with a peak during the warmer parts of the year, except for the fungal seasonal trend in Ljungbyhed, which fluctuated more within season. Interestingly, the diversity and evenness of the airborne communities were generally lower in Ljungbyhed. In addition, both bacterial and fungal communities varied significantly within and between locations, where orders like Rhizobiales, Rhodospirillales and Agaricales dominated in Kiruna, whereas Bacillales, Clostridiales and Sordariales dominated in Ljungbyhed. These differences are a likely reflection of the landscape surrounding the sampling sites where the landscape in Ljungbyhed is more homogenous and predominantly characterized by artificial and agricultural surroundings. Our results further indicate that local landscape, as well as seasonal variation, shapes microbial communities in air.

  • 4. Lindström, Stafva
    et al.
    Rowe, Owen F.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF). Department of Microbiology, University of Helsinki, Helsinki, Finland.
    Timonen, Sari
    Sundström, Liselotte
    Johansson, Helena
    Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques-validity and compatibility in ecological studies2018Inngår i: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, artikkel-id e5289Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the ant Formica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.

  • 5.
    Ström, Morgan
    et al.
    Umeå universitet, Samhällsvetenskapliga fakulteten, Institutionen för psykologi.
    Uckelstam, Carl-Johan
    Umeå universitet, Samhällsvetenskapliga fakulteten, Institutionen för psykologi.
    Andersson, Gerhard
    Hassmén, Peter
    Umeå universitet, Samhällsvetenskapliga fakulteten, Institutionen för psykologi.
    Umefjord, Göran
    Umeå universitet, Medicinska fakulteten, Institutionen för folkhälsa och klinisk medicin, Allmänmedicin.
    Carlbring, Per
    Internet-delivered therapist-guided physical activity for mild to moderate depression: a randomized controlled trial2013Inngår i: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 1, artikkel-id e178Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Objective. The main hypothesis, and the objective of the study, was to test if the participants allocated to the treatment group would show a larger reduction in depressive symptoms than those in the control group. Methods. This study was a randomized nine week trial of an Internet-administered treatment based on guided physical exercise for Major Depressive Disorder (MDD). A total of 48 participants with mild to moderate depression, diagnosed using the Structured Clinical Interview for DSM-IV Axis I Disorders, were randomized either to a treatment intervention or to a waiting-list control group. The main outcome measure for depression was the Beck Depression Inventory-II (BDI-II), and physical activity level was measured using the International Physical Activity Questionnaire (IPAQ). The treatment program consisted of nine text modules, and included therapist guidance on a weekly basis. Results. The results showed significant reductions of depressive symptoms in the treatment group compared to the control group, with a moderate between-group effect size (Cohen's d = 0.67; 95% confidence interval: 0.09-1.25). No difference was found between the groups with regards to increase of physical activity level. For the treatment group, the reduction in depressive symptoms persisted at six months follow-up. Conclusions. Physical activity as a treatment for depression can be delivered in the form of guided Internet-based self-help.

  • 6. Zhang, Xiangwei
    et al.
    Wang, Yang
    Li, Cheng
    Helmersson, Jing
    Umeå universitet, Medicinska fakulteten, Institutionen för folkhälsa och klinisk medicin, Epidemiologi och global hälsa.
    Jiang, Yuanzhu
    Ma, Guoyuan
    Wang, Guanghui
    Dong, Wei
    Sang, Shaowei
    Du, Jiajun
    The prognostic value of tumor length to resectable esophageal squamous cell carcinoma: a retrospective study2017Inngår i: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, artikkel-id e2943Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The current TNM classification system does not consider tumor length for patients with esophageal carcinoma (EC). This study explored the effect of tumor length, in addition to tumor depth and lymph node involvement, on survival in patients with esophageal squamous cell carcinoma (ESCC).

    Methods: A total of 498 ESCC patients who underwent surgical resection as the primary treatment were selected in the retrospective study. Pathological details were collected, which included tumor type, TNM stage, differentiation. Other collected information were: the types of esophageal resection, ABO blood group, family history and demographic and lifestyle factors. A time-dependent receiver operating characteristic (ROC) curve and a regression tree for survival were used to identify the cut-off point of tumor length, which was 3 cm. Univariate and multivariate Cox proportional hazard regression models were used to identify the prognostic factors to ESCC.

    Results & Discussion: The 1-, 3-, 5-year overall survival rates were found to be 82.5%, 55.6%, and 35.1%, respectively. Patients who had larger tumor length (>3 cm) had a higher risk for death than the rest patients. From the univariate Cox proportional hazards regression model, the overall survival rate was significantly influenced by the depth of the tumor and lymph node involvement (either as dummy or continuous variables), Sex, and tumor length. Using these four variables in the multivariate Cox proportional hazard regression model, we found that the overall survival was significantly influenced by all variables except Sex. Therefore, in addition to the depth of the tumor and lymph node involvement (as either dummy or continuous variables), the tumor length is also an independent prognostic factor for ESCC. The overall survival rate was higher in a group with smaller tumor length (≤3 cm) than those patients with larger tumor length (>3 cm), no matter what the tumor stage was.

    Conclusion: The tumor length was found to be an important prognostic factor for ESCC patients without receiving neoadjuvant therapy. The modification of EC staging system may consider tumor length to better predict ESCC survival and identify higher risk patients for postoperative therapy.

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