Publications by authors named "Magnus Andersson"

163 Publications

Laser induced degradation of bacterial spores during micro-Raman spectroscopy.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Sep 12;265:120381. Epub 2021 Sep 12.

Dept of Physics, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå, Sweden. Electronic address:

Micro-Raman spectroscopy combined with optical tweezers is a powerful method to analyze how the biochemical composition and molecular structures of individual biological objects change with time. In this work we investigate laser induced effects in the trapped object. Bacillus thuringiensis spores, which are robust organisms known for their resilience to light, heat, and chemicals are used for this study. We trap spores and monitor the Raman peak from CaDPA (calcium dipicolinic acid), which is a chemical protecting the spore core. We see a correlation between the amount of laser power used in the trap and the release of CaDPA from the spore. At a laser power of 5 mW, the CaDPA from spores in water suspension remain intact over the 90 min experiment, however, at higher laser powers an induced effect could be observed. SEM images of laser exposed spores (after loss of CaDPA Raman peak was confirmed) show a notable alteration of the spores' structure. Our Raman data indicates that the median dose exposure to lose the CaDPA peak was ∼60 J at 808 nm. For decontaminated/deactivated spores, i.e., treated in sodium hypochlorite or peracetic acid solutions, the sensitivity on laser power is even more pronounced and different behavior could be observed on spores treated by the two chemicals. Importantly, the observed effect is most likely photochemical since the increase of the spore temperature is in the order of 0.1 K as suggested by our numerical multiphysics model. Our results show that care must be taken when using micro-Raman spectroscopy on biological objects since photoinduced effects may substantially affect the results.
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http://dx.doi.org/10.1016/j.saa.2021.120381DOI Listing
September 2021

Synthetic NAC 71-82 Peptides Designed to Produce Fibrils with Different Protofilament Interface Contacts.

Int J Mol Sci 2021 Aug 28;22(17). Epub 2021 Aug 28.

Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden.

Alpha-synucleinopathies are featured by fibrillar inclusions in brain cells. Although α-synuclein fibrils display structural diversity, the origin of this diversity is not fully understood. We used molecular dynamics simulations to design synthetic peptides, based on the NAC 71-82 amino acid fragment of α-synuclein, that govern protofilament contacts and generation of twisted fibrillar polymorphs. Four peptides with structures based on either single or double fragments and capped or non-capped ends were selected for further analysis. We determined the fibrillar yield and the structures from these peptides found in the solution after fibrillisation using protein concentration determination assay and circular dichroism spectroscopy. In addition, we characterised secondary structures formed by individual fibrillar complexes using laser-tweezers Raman spectroscopy. Results suggest less mature fibrils, based on the lower relative β-sheet content for double- than single-fragment peptide fibrils. We confirmed this structural difference by TEM analysis which revealed, in addition to short protofibrils, more elongated, twisted and rod-like fibril structures in non-capped and capped double-fragment peptide systems, respectively. Finally, time-correlated single-photon counting demonstrated a difference in the Thioflavin T fluorescence lifetime profiles upon fibril binding. It could be proposed that this difference originated from morphological differences in the fibril samples. Altogether, these results highlight the potential of using peptide models for the generation of fibrils that share morphological features relevant for disease, e.g., twisted and rod-like polymorphs.
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http://dx.doi.org/10.3390/ijms22179334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8431055PMC
August 2021

A review of 28 free animal-tracking software applications: current features and limitations.

Lab Anim (NY) 2021 09 29;50(9):246-254. Epub 2021 Jul 29.

Department of Physics, Umeå University, Umeå, Sweden.

Well-quantified laboratory studies can provide a fundamental understanding of animal behavior in ecology, ethology and ecotoxicology research. These types of studies require observation and tracking of each animal in well-controlled and defined arenas, often for long timescales. Thus, these experiments produce long time series and a vast amount of data that require the use of software applications to automate the analysis and reduce manual annotation. In this review, we examine 28 free software applications for animal tracking to guide researchers in selecting the software that might best suit a particular experiment. We also review the algorithms in the tracking pipeline of the applications, explain how specific techniques can fit different experiments, and finally, expose each approach's weaknesses and strengths. Our in-depth review includes last update, type of platform, user-friendliness, off- or online video acquisition, calibration method, background subtraction and segmentation method, species, multiple arenas, multiple animals, identity preservation, manual identity correction, data analysis and extra features. We found, for example, that out of 28 programs, only 3 include a calibration algorithm to reduce image distortion and perspective problems that affect accuracy and can result in substantial errors when analyzing trajectories and extracting mobility or explored distance. In addition, only 4 programs can directly export in-depth tracking and analysis metrics, only 5 are suited for tracking multiple unmarked animals for more than a few seconds and only 11 have been updated in the period 2019-2021.
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http://dx.doi.org/10.1038/s41684-021-00811-1DOI Listing
September 2021

Andrological and cytogenetic investigations of an infertile Przewalski's stallion.

Acta Vet Hung 2021 Jul 22. Epub 2021 Jul 22.

9Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, Hungary.

The case of an 8-year-old, sexually active but infertile Przewalski's stallion (Equus ferus przewalskii) was studied. Besides the infertility, the stallion also showed permanent problems with its body condition, being obviously weaker than all the other group members. The horse was kept in a separate place for two years with 12 mares in its harem group (six mares had foals earlier); however, none of the mares covered got pregnant. Andrological and cytogenetic investigations revealed underdeveloped testes, arrested spermatogenesis, azoospermia, and XY/XXY/X0 mosaicism. We classify the case as a mosaic Klinefelter syndrome, the first reported case in Przewalski's horse.
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http://dx.doi.org/10.1556/004.2021.00027DOI Listing
July 2021

Optical design for laser tweezers Raman spectroscopy setups for increased sensitivity and flexible spatial detection.

Appl Opt 2021 Jun;60(16):4519-4523

We demonstrate a method to double the collection efficiency in laser tweezers Raman spectroscopy (LTRS) by collecting both the forward-scattered and backscattered light in a single-shot multitrack measurement. Our method can collect signals at different sample volumes, granting both the pinpoint spatial selectivity of confocal Raman spectroscopy and the bulk sensitivity of non-confocal Raman spectroscopy simultaneously. Further, we display that our approach allows for reduced detector integration time and laser power. To show this, we measure the Raman spectra of both polystyrene beads and bacterial spores. For spores, we can trap them at 2.5 mW laser power and acquire a high signal-to-noise ratio power spectrum of the calcium-dipicolinic acid peaks using an integration time of ${2} \times {30}\;{\rm s}$. Thus, our method will enable the monitoring of biological samples sensitive to high intensities for longer times. Additionally, we demonstrate that by a simple modification, we can add polarization sensitivity and retrieve extra biochemical information.
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http://dx.doi.org/10.1364/AO.424595DOI Listing
June 2021

Impact of an alpha helix and a cysteine-cysteine disulfide bond on the resistance of bacterial adhesion pili to stress.

Proc Natl Acad Sci U S A 2021 May;118(21)

Department of Physics, Umeå University, Umeå 90187, Sweden;

express adhesion pili that mediate attachment to host cell surfaces and are exposed to body fluids in the urinary and gastrointestinal tracts. Pilin subunits are organized into helical polymers, with a tip adhesin for specific host binding. Pili can elastically unwind when exposed to fluid flow forces, reducing the adhesin load, thereby facilitating sustained attachment. Here we investigate biophysical and structural differences of pili commonly expressed on bacteria that inhabit the urinary and intestinal tracts. Optical tweezers measurements reveal that class 1a pili of uropathogenic (UPEC), as well as class 1b of enterotoxigenic (ETEC), undergo an additional conformational change beyond pilus unwinding, providing significantly more elasticity to their structure than ETEC class 5 pili. Examining structural and steered molecular dynamics simulation data, we find that this difference in class 1 pili subunit behavior originates from an α-helical motif that can unfold when exposed to force. A disulfide bond cross-linking β-strands in class 1 pili stabilizes subunits, allowing them to tolerate higher forces than class 5 pili that lack this covalent bond. We suggest that these extra contributions to pilus resiliency are relevant for the UPEC niche, since resident bacteria are exposed to stronger, more transient drag forces compared to those experienced by ETEC bacteria in the mucosa of the intestinal tract. Interestingly, class 1b ETEC pili include the same structural features seen in UPEC pili, while requiring lower unwinding forces that are more similar to those of class 5 ETEC pili.
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http://dx.doi.org/10.1073/pnas.2023595118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166124PMC
May 2021

Step-by-step guide to 3D print motorized rotation mounts for optical applications.

Appl Opt 2021 May;60(13):3764-3771

Motorized rotation mounts and stages are versatile instruments that introduce computer control to optical systems, enabling automation and scanning actions. They can be used for intensity control, position adjustments, etc. However, these rotation mounts come with a hefty price tag, and this limits their use. This work shows how to build two different types of motorized rotation mounts for $1^{\prime \prime}$ optics, using a 3D printer and off-the-shelf components. The first is intended for reflective elements, such as mirrors and gratings, and the second for transmissive elements, such as polarizers and retarders. We evaluate and compare their performance to commercial systems based on velocity, resolution, precision, backlash, and axis wobble. Also, we investigate the angular stability using Allan variance analysis. The results show that our mounts perform similarly to systems costing as much as $\$ 2500\,\rm USD $, while also being quick to build and costing less than $\$ 220\,\rm USD$. As a proof of concept, we show how to control lasers used in an optical tweezers and Raman spectroscopy setup. When used for this, the 3D printed motorized rotational mounts provide intensity control with a resolution of 0.03 percentage points or better.
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http://dx.doi.org/10.1364/AO.422695DOI Listing
May 2021

[Spinal cord infarction - a rare condition and a diagnostic challenge].

Lakartidningen 2021 02 5;118. Epub 2021 Feb 5.

specialistläkare, Neurologiska kliniken, Karolinska Universitetssjukhuset Solna , Institutionen för klinisk neurovetenskap, Karolinska Institutet.

Spinal cord infarction (SCI) causes acute spinal cord dysfunction with high morbidity. Without an inciting event such as a surgical procedure, a definitive diagnosis may be challenging. Thus, patients with a spontaneous (i e, non-traumatic, non-surgical) SCI are often misdiagnosed and the radiological distinction between SCI and other conditions with similar symptoms is more difficult than in cerebral infarction. Compared to cerebral infarction, SCI is rare and only accounts for approximately 1.2% of all strokes. SCI is usually localized to the anterior spinal artery area, causing the anterior spinal artery syndrome. Misdiagnosis may lead to unnecessary and possibly deleterious treatments as well as missed secondary stroke prevention. In this review, a typical case, an overview of the disease and newly proposed diagnostic criteria are presented.
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February 2021

Mode of Action of Disinfection Chemicals on the Bacterial Spore Structure and Their Raman Spectra.

Anal Chem 2021 02 1;93(6):3146-3153. Epub 2021 Feb 1.

Department of Physics, Umeå University, Umeå, 901 87 Sweden.

Contamination of toxic spore-forming bacteria is problematic since spores can survive a plethora of disinfection chemicals and it is hard to rapidly detect if the disinfection chemical has inactivated the spores. Thus, robust decontamination strategies and reliable detection methods to identify dead from viable spores are critical. In this work, we investigate the chemical changes of spores treated with sporicidal agents such as chlorine dioxide, peracetic acid, and sodium hypochlorite using laser tweezers Raman spectroscopy. We also image treated spores using SEM and TEM to verify if we can correlate structural changes in the spores with changes to their Raman spectra. We found that over 30 min, chlorine dioxide did not change the Raman spectrum or the spore structure, peracetic acid showed a time-dependent decrease in the characteristic DNA/DPA peaks and ∼20% of the spores were degraded and collapsed, and spores treated with sodium hypochlorite showed an abrupt drop in DNA and DPA peaks within 20 min and some structural damage to the exosporium. Structural changes appeared in spores after 10 min, compared to the inactivation time of the spores, which is less than a minute. We conclude that vibrational spectroscopy provides powerful means to detect changes in spores but it might be problematic to identify if spores are live or dead after a decontamination procedure.
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http://dx.doi.org/10.1021/acs.analchem.0c04519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893628PMC
February 2021

Correction to: Characterization of anisotropic turbulence behavior in pulsatile blood flow.

Biomech Model Mechanobiol 2021 Apr;20(2):507-508

Department of Management and Engineering, Linköping University, SE-581 83, Linköping, Sweden.

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http://dx.doi.org/10.1007/s10237-020-01404-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8182884PMC
April 2021

Tracking Membrane Protein Dynamics in Real Time.

J Membr Biol 2021 02 7;254(1):51-64. Epub 2021 Jan 7.

Department of Chemistry, Umeå University, Umeå, Sweden.

Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by the vast ranges of structural dynamics-both in the spatial and time regime-displayed in the protein and surrounding membrane. The membrane lipids have emerged as allosteric modulators of membrane protein function, which further adds to the complexity. In this review, we discuss several examples of membrane dependency. A particular focus is on how molecular dynamics (MD) simulation have aided to map membrane protein dynamics and how enhanced sampling methods can enable observing the otherwise inaccessible biological time scale. Also, time-resolved X-ray scattering in solution is highlighted as a powerful tool to track membrane protein dynamics, in particular when combined with MD simulation to identify transient intermediate states. Finally, we discuss future directions of how to further develop this promising approach to determine structural dynamics of both the protein and the surrounding lipids.
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http://dx.doi.org/10.1007/s00232-020-00165-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7936944PMC
February 2021

[email protected]: a team-based, person-centred intervention for rehabilitation after stroke supported by information and communication technology - a feasibility study.

BMC Neurol 2020 Oct 23;20(1):387. Epub 2020 Oct 23.

Division of Physiotherapy, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden.

Background: Globally, there is a growing use of Information and Communication Technology (ICT), including mobile phones, tablets and computers, which are being integrated into people's daily activities. An ICT-based intervention called [email protected] was developed in order to provide a structure for the process in stroke rehabilitation and facilitate change by integrating a global problem-solving strategy using SMS alerts. The aim of the study was to evaluate the feasibility of i) [email protected] within in-patient and primary care rehabilitation after stroke, ii) the study design and outcome measures used, and iii) the fidelity, adherence and acceptability of the intervention.

Methods: Three teams comprising occupational therapists and physiotherapists who work in neurological rehabilitation participated in a preparatory workshop on [email protected] and then enrolled 10 persons with stroke to participate in the intervention. Goals were set using the Canadian Occupational Performance Measure (COPM) and the participants with stroke rated their performance and satisfaction with the activities associated with the three goals every day for 8 weeks. Data were collected at inclusion, at four and 8 weeks, using the COPM, Stroke Impact Scale, Frenchay Activities Index, Life Satisfaction Checklist, Self-Efficacy Scale, Hospital Anxiety and Depression Scale, Fatigue Severity Scale, follow-up survey, daily ratings on the web platform and logbooks.

Results: All of the participants showed increased scores in the primary outcome (COPM) and a clinically meaningful improvement of ≥2 points was found in four participants regarding performance and in six participants regarding satisfaction. Overall fidelity to the components of [email protected] was good. The response rates to the [email protected] web platform were 44-100% (mean 78%). All of the participants stated that [email protected] had supported their rehabilitation.

Conclusion: The results indicate that the most beneficial part of [email protected] was the person-centred, goal-setting process and SMS alerts. All participants were satisfied with [email protected] and highlighted the benefits of receiving daily alerts about their goals. This encouraged them to be more active. The only downside mentioned was that they felt under an obligation to practice, although this was described as "a positive obligation".
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http://dx.doi.org/10.1186/s12883-020-01968-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7583214PMC
October 2020

Characterization of anisotropic turbulence behavior in pulsatile blood flow.

Biomech Model Mechanobiol 2021 Apr 22;20(2):491-506. Epub 2020 Oct 22.

Department of Management and Engineering, Linköping University, SE-581 83, Linköping, Sweden.

Turbulent-like hemodynamics with prominent cycle-to-cycle flow variations have received increased attention as a potential stimulus for cardiovascular diseases. These turbulent conditions are typically evaluated in a statistical sense from single scalars extracted from ensemble-averaged tensors (such as the Reynolds stress tensor), limiting the amount of information that can be used for physical interpretations and quality assessments of numerical models. In this study, barycentric anisotropy invariant mapping was used to demonstrate an efficient and comprehensive approach to characterize turbulence-related tensor fields in patient-specific cardiovascular flows, obtained from scale-resolving large eddy simulations. These techniques were also used to analyze some common modeling compromises as well as MRI turbulence measurements through an idealized constriction. The proposed method found explicit sites of elevated turbulence anisotropy, including a broad but time-varying spectrum of characteristics over the flow deceleration phase, which was different for both the steady inflow and Reynolds-averaged Navier-Stokes modeling assumptions. Qualitatively, the MRI results showed overall expected post-stenotic turbulence characteristics, however, also with apparent regions of unrealizable or conceivably physically unrealistic conditions, including the highest turbulence intensity ranges. These findings suggest that more detailed studies of MRI-measured turbulence fields are needed, which hopefully can be assisted by more comprehensive evaluation tools such as the once described herein.
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http://dx.doi.org/10.1007/s10237-020-01396-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7979666PMC
April 2021

Absence of Neuronal Autoantibodies in Neuropsychiatric Systemic Lupus Erythematosus.

Ann Neurol 2020 12 6;88(6):1244-1250. Epub 2020 Oct 6.

Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.

This study aimed to characterise both neuronal autoantibodies and levels of interferon α, two proposed causative agents in neuropsychiatric systemic lupus erythematosus (NPSLE). Cerebrospinal fluid (CSF) and plasma from 35 patients with systemic lupus erythematosus (SLE; 15 with NPSLE) showed no antibodies against natively expressed N-methyl-D-aspartate receptors (NMDARs), or the surface of live hippocampal neurons. By comparison to controls (n = 104), patients with SLE had antibodies that bound to a peptide representing the extracellular domain of NMDARs (p < 0.0001), however, binding was retained against both rearranged peptides and no peptide (r = 0.85 and r = 0.79, respectively, p < 0.0001). In summary, neuronal-surface reactive antibodies were not detected in NPSLE. Further, while interferon α levels were higher in SLE (p < 0.0001), they lacked specificity for NPSLE. Our findings mandate a search for novel biomarkers in this condition. ANN NEUROL 2020;88:1244-1250.
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http://dx.doi.org/10.1002/ana.25908DOI Listing
December 2020

Tracking Ca ATPase intermediates in real time by x-ray solution scattering.

Sci Adv 2020 03 20;6(12):eaaz0981. Epub 2020 Mar 20.

Department of Chemistry, Umeå University. Linnaeus Väg 10, 901 87 Umeå, Sweden.

Sarco/endoplasmic reticulum Ca ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca]E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release of caged ATP, a 1.5-ms intermediate was formed that showed closure of the cytoplasmic domains typical of E1 states with bound Ca and ATP. A subsequent 13-ms transient state showed a previously unresolved actuator (A) domain arrangement that exposed the ADP-binding site after phosphorylation. Hence, the obtained TR-XSS models determine the relative timing of so-far elusive domain rearrangements in a native environment.
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http://dx.doi.org/10.1126/sciadv.aaz0981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7083613PMC
March 2020

Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis.

Curr Biol 2020 02 16;30(3):455-464.e7. Epub 2020 Jan 16.

Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden. Electronic address:

Plant organ growth is widely accepted to be determined by cell division and cell expansion, but, unlike that in animals, the contribution of cell elimination has rarely been recognized. We investigated this paradigm during Arabidopsis lateral root formation, when the lateral root primordia (LRP) must traverse three overlying cell layers within the parent root. A subset of LRP-overlying cells displayed the induction of marker genes for cell types undergoing developmental cell death, and their cell death was detected by electron, confocal, and light sheet microscopy techniques. LRP growth was delayed in cell-death-deficient mutants lacking the positive cell death regulator ORESARA1/ANAC092 (ORE1). LRP growth was restored in ore1-2 knockout plants by genetically inducing cell elimination in cells overlying the LRP or by physically killing LRP-overlying cells by ablation with optical tweezers. Our results support that, in addition to previously discovered mechanisms, cell elimination contributes to regulating lateral root emergence.
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http://dx.doi.org/10.1016/j.cub.2019.11.078DOI Listing
February 2020

Prophylactic Mastectomy: Postoperative Skin Flap Thickness Evaluated by MRT, Ultrasound and Clinical Examination.

Ann Surg Oncol 2020 Jul 6;27(7):2221-2228. Epub 2020 Jan 6.

Department of Surgical and Perioperative Sciences, Plastic Surgery and Surgery, Umeå University, Umeå, Sweden.

Background: Women with an increased hereditary risk of breast cancer can undergo prophylactic mastectomy (PM), which provides a significant, but not total, risk reduction. There is an ongoing discussion about how much skin and subcutaneous tissue should be resected to perform an adequate PM while leaving viable skin flaps.

Methods: Forty-five women who had undergone PM were examined with magnetic resonance tomography (MRT), ultrasound (US) and clinical examination (CE) by a plastic surgeon and a general surgeon to estimate skin flap thickness.

Results: The estimated mean skin flap thickness after PM was 13.3 (± 9.6), 7.0 (± 3.3), 6.9 (± 2.8) and 7.4 (± 2.8) mm following MRT, US, and CE performed by a plastic surgeon and a general surgeon, respectively. The mean difference in estimated skin flap thickness was significant between MRT and the other measuring methods, while there was no significant difference between US and CE, nor between CE performed by the surgeons. The mean skin flap thickness was significantly affected by the age at PM. Following PM, necrosis was detected in 7/23 (30.4%) of the breasts in skin flaps ≤ 5 mm and in 5/46 (10.9%) of the breasts in skin flaps > 5 mm (OR 6.29; CI 1.20-32.94; p = 0.03).

Conclusion: The odds of getting postoperative necrosis was > 6 times higher in skin flaps ≤ 5 mm. Thus, if the degree of remaining glandular tissue is acceptably low, it is desirable to create skin flaps thicker than 5 mm to prevent wound healing problems after the PM procedure.
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http://dx.doi.org/10.1245/s10434-019-08157-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311506PMC
July 2020

Cryo-EM structure of the CFA/I pilus rod.

IUCrJ 2019 Sep 9;6(Pt 5):815-821. Epub 2019 Jul 9.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.

Enterotoxigenic (ETEC) are common agents of diarrhea for travelers and a major cause of mortality in children in developing countries. To attach to intestinal cells ETEC express colonization factors, among them CFA/I, which are the most prevalent factors and are the archetypical representative of class 5 pili. The helical quaternary structure of CFA/I can be unwound under tensile force and it has been shown that this mechanical property helps bacteria to withstand shear forces from fluid motion. We report in this work the CFA/I pilus structure at 4.3 Å resolution from electron cryomicroscopy (cryo-EM) data, and report details of the donor strand complementation. The CfaB pilins modeled into the cryo-EM map allow us to identify the buried surface area between subunits, and these regions are correlated to quaternary structural stability in class 5 and chaperone-usher pili. In addition, from the model built using the EM structure we also predicted that residue 13 (proline) of the N-terminal β-strand could have a major impact on the filament's structural stability. Therefore, we used optical tweezers to measure and compare the stability of the quaternary structure of wild type CFA/I and a point-mutated CFA/I with a propensity for unwinding. We found that pili with this mutated CFA/I require a lower force to unwind, supporting our hypothesis that Pro13 is important for structural stability. The high-resolution CFA/I pilus structure presented in this work and the analysis of structural stability will be useful for the development of novel antimicrobial drugs that target adhesion pili needed for initial attachment and sustained adhesion of ETEC.
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http://dx.doi.org/10.1107/S2052252519007966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6760452PMC
September 2019

An atypical Bacillus anthracis infection in a bull-A potential occupational health hazard.

Reprod Domest Anim 2019 Sep 10;54(9):1279-1283. Epub 2019 Aug 10.

Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.

Bacillus anthracis infecting cattle is usually identified based on the typical symptom: sudden death. Bacillus anthracis causing atypical symptoms may remain undiagnosed and represent a potential occupational health hazard for, that is veterinarians and producers, butchers and tanners. In the year 2004, one case of sudden death in a dairy farm in southern Finland was diagnosed as bovine anthrax. Four years later 2008, an atypical case of anthrax was diagnosed in the same holding. The bull was taken to the Production Animal Hospital of the Faculty of Veterinary Medicine, University of Helsinki because of fever, loss of appetite and a symmetrically swollen scrotal sac. Penicillin treatment cured the fever but not the swollen scrotum. Before the intended therapeutic castration, a punctuate consisting of 10 ml fluid collected into a syringe from the scrotal sac was cultivated on blood agar at 37°C. After 24 hr, an almost pure culture of a completely non-hemolytic Bacillus cereus-like bacteria was obtained. The strain was identified as B. anthracis using Ba-specific primers by the Finnish Food Safety Authority (RUOKAVIRASTO). After the diagnosis, the bull was euthanized and destroyed, the personnel were treated with prophylactic antibiotics and the clinic was disinfected. In this particular case, treatment with water, Virkon S and lime seemed to be effective to eliminate endospores and vegetative cells since no relapses of anthrax have occurred in 10 years. This case is the last reported anthrax case in Finland.
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http://dx.doi.org/10.1111/rda.13532DOI Listing
September 2019

Structure of the human ClC-1 chloride channel.

PLoS Biol 2019 04 25;17(4):e3000218. Epub 2019 Apr 25.

Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.

ClC-1 protein channels facilitate rapid passage of chloride ions across cellular membranes, thereby orchestrating skeletal muscle excitability. Malfunction of ClC-1 is associated with myotonia congenita, a disease impairing muscle relaxation. Here, we present the cryo-electron microscopy (cryo-EM) structure of human ClC-1, uncovering an architecture reminiscent of that of bovine ClC-K and CLC transporters. The chloride conducting pathway exhibits distinct features, including a central glutamate residue ("fast gate") known to confer voltage-dependence (a mechanistic feature not present in ClC-K), linked to a somewhat rearranged central tyrosine and a narrower aperture of the pore toward the extracellular vestibule. These characteristics agree with the lower chloride flux of ClC-1 compared with ClC-K and enable us to propose a model for chloride passage in voltage-dependent CLC channels. Comparison of structures derived from protein studied in different experimental conditions supports the notion that pH and adenine nucleotides regulate ClC-1 through interactions between the so-called cystathionine-β-synthase (CBS) domains and the intracellular vestibule ("slow gating"). The structure also provides a framework for analysis of mutations causing myotonia congenita and reveals a striking correlation between mutated residues and the phenotypic effect on voltage gating, opening avenues for rational design of therapies against ClC-1-related diseases.
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http://dx.doi.org/10.1371/journal.pbio.3000218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483157PMC
April 2019

A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle.

BMC Genomics 2019 Apr 11;20(1):286. Epub 2019 Apr 11.

Animal Genomics, ETH Zurich, 8001, Zurich, Switzerland.

Background: Cattle populations are highly amenable to the genetic mapping of male reproductive traits because longitudinal data on ejaculate quality and dense microarray-derived genotypes are available for thousands of artificial insemination bulls. Two young Nordic Red bulls delivered sperm with low progressive motility (i.e., asthenospermia) during a semen collection period of more than four months. The bulls were related through a common ancestor on both their paternal and maternal ancestry. Thus, a recessive mode of inheritance of asthenospermia was suspected.

Results: Both bulls were genotyped at 54,001 SNPs using the Illumina BovineSNP50 Bead chip. A scan for autozygosity revealed that they were identical by descent for a 2.98 Mb segment located on bovine chromosome 25. This haplotype was not found in the homozygous state in 8557 fertile bulls although five homozygous haplotype carriers were expected (P = 0.018). Whole genome-sequencing uncovered that both asthenospermic bulls were homozygous for a mutation that disrupts a canonical 5' splice donor site of CCDC189 encoding the coiled-coil domain containing protein 189. Transcription analysis showed that the derived allele activates a cryptic splice site resulting in a frameshift and premature termination of translation. The mutated CCDC189 protein is truncated by more than 40%, thus lacking the flagellar C1a complex subunit C1a-32 that is supposed to modulate the physiological movement of the sperm flagella. The mutant allele occurs at a frequency of 2.5% in Nordic Red cattle.

Conclusions: Our study in cattle uncovered that CCDC189 is required for physiological movement of sperm flagella thus enabling active progression of spermatozoa and fertilization. A direct gene test may be implemented to monitor the asthenospermia-associated allele and prevent the birth of homozygous bulls that are infertile. Our results have been integrated in the Online Mendelian Inheritance in Animals (OMIA) database ( https://omia.org/OMIA002167/9913/ ).
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http://dx.doi.org/10.1186/s12864-019-5628-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460654PMC
April 2019

DSeg: A Dynamic Image Segmentation Program to Extract Backbone Patterns for Filamentous Bacteria and Hyphae Structures.

Microsc Microanal 2019 06 21;25(3):711-719. Epub 2019 Mar 21.

Department of Physics,Umeå University,901 87 Umeå,Sweden.

Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. It is even more problematic if these structures continuously grow when recording a time-series of images. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. The program includes a robust binary level-set algorithm modified to use size constraints, edge intensity, and past information. We verify our algorithms using synthetic data, differential interference contrast images of filamentous prokaryotes, and transmission electron microscopy images of bacterial adhesion fimbriae. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available at Sourceforge.
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http://dx.doi.org/10.1017/S1431927619000308DOI Listing
June 2019

Mass spectrometry-based analysis of cerebrospinal fluid from arthritis patients-immune-related candidate proteins affected by TNF blocking treatment.

Arthritis Res Ther 2019 02 15;21(1):60. Epub 2019 Feb 15.

Rheumatology Unit, Department of Medicine, Solna, Center of Molecular Medicine (CMM), Karolinska Institutet, Karolinska University Hospital, SE-17176, Stockholm, Sweden.

Background: Signs of inflammation in cerebrospinal fluid (CSF) of rheumatoid arthritis patients correlate positively with fatigue, a central nervous system (CNS)-related symptom that can be partially suppressed by TNF blockade. This suggests a possible role for CNS inflammation in arthritis that may be affected by TNF blockade. We therefore investigated the effects of TNF blockade on the arthritis CSF proteome and how candidate proteins related to clinical measures of disease activity and inflammation.

Methods: Mass spectrometry-based quantitative proteomic analysis was performed on CSF from seven polyarthritis patients before and during infliximab treatment. Treatment-associated proteins were identified using univariate (Wilcoxon signed rank test) and multivariate (partial least squares discriminant analysis (PLS-DA)) strategies. Relations between selected candidate proteins and clinical measures were investigated using the Spearman correlations. Additionally, selected proteins were cross-referenced to other studies investigating human CSF in a thorough literature search to ensure feasibility of our results.

Results: Univariate analysis of arthritis CSF proteome revealed a decrease of 35 proteins, predominantly involved in inflammatory processes, following TNF blockade. Seven candidate proteins, Contactin-1 (CNTN1), fibrinogen gamma chain (FGG), hemopexin (HPX), cell adhesion molecule-3 (CADM3), alpha-1B-glycoprotein (A1BG), complement factor B (CFB), and beta-2-microglobulin (B2M), were selected for further studies based on identification by both univariate and multivariate analyses and reported detection in human CSF and known associations to arthritis. Decreased levels of FGG and CFB in CSF after treatment showed strong correlations with both erythrocyte sedimentation rate and disability scores, while CNTN1 and CADM3 were associated with pain.

Conclusion: Several immune-related proteins in the CSF of arthritis patients decreased during TNF blockade, including FGG and CFB that both correlated strongly with systemic inflammation. Our findings stress that also intrathecal inflammatory pathways are related to arthritis symptoms and may be affected by TNF blockade.
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http://dx.doi.org/10.1186/s13075-019-1846-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377734PMC
February 2019

Characterization and estimation of turbulence-related wall shear stress in patient-specific pulsatile blood flow.

J Biomech 2019 03 19;85:108-117. Epub 2019 Jan 19.

Department of Management and Engineering (IEI), Linköping University, Linköping, Sweden; Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden.

Disturbed, turbulent-like blood flow promotes chaotic wall shear stress (WSS) environments, impairing essential endothelial functions and increasing the susceptibility and progression of vascular diseases. These flow characteristics are today frequently detected at various anatomical, lesion and intervention-related sites, while their role as a pathological determinant is less understood. To present-day, numerous WSS-based descriptors have been proposed to characterize the spatiotemporal nature of the WSS disturbances, however, without differentiation between physiological laminar oscillations and turbulence-related WSS (tWSS) fluctuations. Also, much attention has been focused on magnetic resonance (MR) WSS estimations, so far with limited success; promoting the need of a near-wall surrogate marker. In this study, a new approach is explored to characterize the tWSS, by taking advantage of the tensor characteristics of the fluctuating WSS correlations, providing both a magnitude and an anisotropy measure of the disturbances. These parameters were studied in two patient-specific coarctation models (sever and mild), using large eddy simulations, and correlated against near-wall reciprocal Reynolds stress parameters. Collectively, results showed distinct regions of differing tWSS characteristics, features which were sensitive to changes in flow conditions. Generally, the post-stenotic tWSS was governed by near axisymmetric fluctuations, findings that where not consistent with conventional WSS disturbance predictors. At the 2-3 mm wall-offset range, a strong linear correlation was found between tWSS magnitude and near-wall turbulence kinetic energy (TKE), in contrast to the anisotropy indices, suggesting that MR-measured TKE can be used to assess elevated tWSS regions while tWSS anisotropy estimates request well-resolved simulation methods.
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http://dx.doi.org/10.1016/j.jbiomech.2019.01.016DOI Listing
March 2019

Object plane detection and phase retrieval from single-shot holograms using multi-wavelength in-line holography.

Appl Opt 2018 Nov;57(33):9855-9862

Phase retrieval and the twin-image problem in digital in-line holographic microscopy can be resolved by iterative reconstruction routines. However, recovering the phase properties of an object in a hologram requires an object plane to be chosen correctly for reconstruction. In this work, we present a novel multi-wavelength iterative algorithm to determine the object plane using single-shot holograms recorded at multiple wavelengths in an in-line holographic microscope. Using micro-sized objects, we verify the object positioning capabilities of the method for various shapes and derive the phase information using synthetic and experimental data. Experimentally, we built a compact digital in-line holographic microscopy setup around a standard optical microscope with a regular RGB-CCD camera and acquired holograms of micro-spheres, E. coli, and red blood cells, which are illuminated using three lasers operating at 491 nm, 532 nm, and 633 nm, respectively. We demonstrate that our method provides accurate object plane detection and phase retrieval under noisy conditions, e.g., using low-contrast holograms with an inhomogeneous background. This method allows for automatic positioning and phase retrieval suitable for holographic particle velocimetry, and object tracking in biophysical or colloidal research.
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http://dx.doi.org/10.1364/AO.57.009855DOI Listing
November 2018

High-speed imaging reveals how antihistamine exposure affects escape behaviours in aquatic insect prey.

Sci Total Environ 2019 Jan 18;648:1257-1262. Epub 2018 Aug 18.

School of Marine Studies, The University of the South Pacific, Laucala Bay Road, Suva, Fiji.

Aquatic systems receive a wide range of pharmaceuticals that may have adverse impacts on aquatic wildlife. Among these pharmaceuticals, antihistamines are commonly found, and these substances have the potential to influence the physiology of aquatic invertebrates. Previous studies have focused on how antihistamines may affect behaviours of aquatic invertebrates, but these studies probably do not capture the full consequences of antihistamine exposure, as traditional recording techniques do not capture important animal movements occurring at the scale of milliseconds, such as prey escape responses. In this study, we investigated if antihistamine exposure can impact escape responses in aquatic insect, by exposing damselfly (Coenagrion hastulatum) larvae to two environmentally relevant concentrations (0.1 and 1 μg L) of diphenhydramine. Importantly, we used a high-speed imaging approach that with high-time resolution captures details of escape responses and, thus, potential impacts of diphenhydramine on these behaviours. Our results show overall weak effects of antihistamine exposure on the escape behaviours of damselfly larvae. However, at stage 2 of the C-escape response, we found a significant increase in turning angle, which corresponds to a reduced swimming velocity, indicating a reduced success at evading a predator attack. Thus, we show that low concentrations of an antihistamine may affect behaviours strongly related to fitness of aquatic insect prey - effects that would have been overlooked using traditional recording techniques. Hence, to understand the full consequences of pharmaceutical contamination on aquatic wildlife, high-speed imaging should be incorporated into future environmental risk assessments.
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http://dx.doi.org/10.1016/j.scitotenv.2018.08.226DOI Listing
January 2019

miR-31 regulates energy metabolism and is suppressed in T cells from patients with Sjögren's syndrome.

Eur J Immunol 2019 02 22;49(2):313-322. Epub 2018 Oct 22.

Unit of Rheumatology, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine Karolinska University Hospital, Stockholm, Sweden.

Systemic autoimmune diseases are characterized by the overexpression of type I IFN stimulated genes, and accumulating evidence indicate a role for type I IFNs in these diseases. However, the underlying mechanisms for this are still poorly understood. To explore the role of type I IFN regulated miRNAs in systemic autoimmune disease, we characterized cellular expression of miRNAs during both acute and chronic type I IFN responses. We identified a T cell-specific reduction of miR-31-5p levels, both after intramuscular injection of IFNβ and in patients with Sjögren's syndrome (SjS). To interrogate the role of miR-31-51p in T cells we transfected human CD4 T cells with a miR-31-5p inhibitor and performed metabolic measurements. This identified an increase in basal levels of glucose metabolism after inhibition of miR-31-5p. Furthermore, treatment with IFN-α also increased the basal levels of human CD4 T-cell metabolism. In all, our results suggest that reduced levels of miR-31-5p in T cells of SjS patients support autoimmune T-cell responses during chronic type I IFN exposure.
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http://dx.doi.org/10.1002/eji.201747416DOI Listing
February 2019

Cooke-Triplet tweezers: more compact, robust, and efficient optical tweezers.

Opt Lett 2018 May;43(9):1990-1993

We present a versatile three-lens optical design to improve the overall compactness, efficiency, and robustness for optical tweezers based applications. The design, inspired by the Cooke-Triplet configuration, allows for continuous beam magnifications of 2-10×, and axial as well as lateral focal shifts can be realized without switching lenses or introducing optical aberrations. We quantify the beam quality and trapping stiffness and compare the Cooke-Triplet design with the commonly used double Kepler design through simulations and direct experiments. Optical trapping of 1 and 2 μm beads shows that the Cooke-Triplet possesses an equally strong optical trap stiffness compared to the double Kepler lens design but reduces its lens system length by a factor of 2.6. Finally, we demonstrate how a Twyman-Green interferometer integrated in the Cooke-Triplet optical tweezers setup provides a fast and simple method to characterize the wavefront aberrations in the lens system and how it can help in aligning the optical components perfectly.
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http://dx.doi.org/10.1364/OL.43.001990DOI Listing
May 2018

Ejaculated boar spermatozoa displaying a rare multivesicular defect.

Acta Vet Scand 2018 Mar 27;60(1):21. Epub 2018 Mar 27.

Department of Clinical and Experimental Medicine-BKH/O&G, Linköping University, 581 85, Linköping, Sweden.

Two cases of a previously unreported sperm defect appearing in boar studs in Finland are presented. Spermatozoa showed small particles scattered on their surface with a prevalence decreasing with boar age. Semen samples, either stained with eosin-nigrosin or examined with phase contrast optics on formaldehyde-fixed spermatozoa, revealed the presence of multiple particles attached to the surface of spermatozoa counted as dead cells at fixation. Transmission electron microscopy revealed these were multivesicular and multilamellar vesicles, built up by phospholipid membranes. The case is classified as a post-epididymal multivesicular sperm defect with a favorable prognosis.
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http://dx.doi.org/10.1186/s13028-018-0375-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870522PMC
March 2018
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