Microbiota of bovine milk, teat skin, and teat canal: Similarity and variation due to sampling technique and milk fraction.

The aim of this study was to evaluate the effect of sampling technique and milk fraction on bovine milk microbiota data and to compare the microbiota in milk to microbiota on the teat end and in the teat canal. Representative milk samples are highly important for assessment of bacteriological findings and microbiota in milk. Samples were obtained from 5 healthy lactating dairy cows at udder quarter level during 1 milking. Swab samples from the teat end and teat canal, and milk samples collected using different techniques and in different milk fractions were included. Milk was collected by hand stripping and through a teat canal cannula before and after machine milking, through a trans-teat wall needle aspirate after milking, and from udder quarter composite milk. The microbiota of the samples was analyzed with sequencing of the V1-V3 region of the 16S rRNA gene. In addition, somatic cell counts and bacterial cultivability were analyzed in the milk samples. Microbiota data were analyzed using multivariate methods, and differences between samples were tested using analysis of similarity (ANOSIM). Differences between samples were further explored via individual studies of the 10 most abundant genera. The microbiota on the teat end, in the teat canal, and in udder quarter composite milk, collected using a milking machine, differed in composition from the microbiota in milk collected directly from the udder quarter. No differences in milk microbiota composition were detected between hand-stripped milk samples, milk samples taken through a teat canal cannula, or milk samples taken as a trans-teat wall needle aspirate before or after milking. We conclude that for aseptic milk samples collected directly from the lactating udder quarter, sampling technique or milk fraction has minor effect on the microbiota composition.

Evaluating risk factors for re-exploration due to postoperative neck hematoma after thyroid surgery: a nested case-control study.

PURPOSE: Postoperative bleeding after thyroid surgery remains a potentially lethal complication. Outpatient thyroidectomy is an increasing trend in the high volume centers. There is a need to identify risk factors for postoperative bleeding in order to select proper patients for outpatient thyroidectomy. This study aimed to investigate this issue using a national population-based register. MATERIAL AND METHOD: A nested case-control study on patients registered in the Swedish national register for endocrine surgery (SQRTPA) was performed. Patients with postoperative bleeding were matched 1:1 by age and gender to controls. Additional information on cases and controls was obtained from attending surgeons using a questionnaire. Risk factors for postoperative bleeding were evaluated with logistic regression and are presented as odds ratios (ORs) with 95% confidence intervals (CIs). The time of bleeding in relation to surgery was also investigated. RESULTS: There were 9494 operations, and 174 (1.8%) of them involved postoperative bleeding. In the whole cohort, patients with postoperative bleeding were older, 58 (46-69) vs. 49 (37-62) years, than patients without, p < 0.01. Male patients had a higher risk of bleeding, OR 2.18 (95% CI 1.58-2.99). In the case-control cohort, drain was an independent risk factor for bleeding, OR 1.64 (1.05-2.57). Two-thirds of patients bled within 6 h after surgery. The incidence of bleeding after 24 h was 10%. CONCLUSION: High age, male gender, and drain are independent risk factors for bleeding after thyroid surgery. Even with careful patient selection, prolonged observation might be necessary in thyroid surgery.

A Nested Case-Control Study on the Risk of Surgical Site Infection After Thyroid Surgery.

INTRODUCTION: It is unclear if antibiotic prophylaxis reduces the risk of surgical site infection (SSI) in thyroid surgery. This study assessed risk factors for SSI and antibiotic prophylaxis in subgroups of patients. METHOD AND DESIGN: A nested case-control study on patients registered in the Swedish National Register for Endocrine Surgery was performed. Patients with SSI were matched 1:1 by age and gender to controls. Additional information on patients with SSI and controls was queried from attending surgeons using a questionnaire. Risk factors for SSI were evaluated by logistic regression analysis and presented as odds ratio (OR) with 95% confidence interval (CI). RESULTS: There were 9494 operations; 109 (1.2%) patients had SSI. Patients with SSI were older (median 53 vs. 49 years) than patients without SSI p = 0.01 and more often had a cancer diagnosis 23 (21.1%) versus 1137 (12.1%) p = 0.01. In the analysis of patients with SSI versus controls, patients with SSI more often had post-operative drainage 68 (62.4%) versus 46 (42.2%) p = 0.01 and lymph node surgery 40 (36.7%) versus 14 (13.0%) p < 0.01, and both were independent risk factors for SSI, drain OR 1.82 (CI 1.04-3.18) and lymph node dissection, OR 3.22 (95% CI 1.32-7.82). A higher number of 26(62%) patients with independent risk factors for SSI and diagnosed with SSI did not receive antibiotic prophylaxis. Data were missing for 8 (31%) patients. CONCLUSION: Lymph node dissection and drain are independent risk factors for SSI after thyroidectomy. Antibiotic prophylaxis might be considered in patients with these risk factors.

Mode of delivery and the probability of subsequent childbearing: a population-based register study.

OBJECTIVE: To investigate the relationship between mode of first delivery and probability of subsequent childbearing. DESIGN: Population-based study. SETTING: Nationwide study in Sweden. POPULATION: A cohort of 771 690 women who delivered their first singleton infant in Sweden between 1992 and 2010. METHODS: Using Cox's proportional-hazards regression models, risks of subsequent childbearing were compared across four modes of delivery. Hazard ratios (HRs) were calculated, using 95% confidence intervals (95% CIs). MAIN OUTCOME MEASURES: Probability of having a second and third child; interpregnancy interval. RESULTS: Compared with women who had a spontaneous vaginal first delivery, women who delivered by vacuum extraction were less likely to have a second pregnancy (HR 0.96, 95% CI 0.95-0.97), and the probabilities of a second childbirth were substantially lower among women with a previous emergency caesarean section (HR 0.85, 95% CI 0.84-0.86) or an elective caesarean section (HR 0.82, 95% CI 0.80-0.83). There were no clinically important differences in the median time between first and second pregnancy by mode of first delivery. Compared with women younger than 30 years of age, older women were more negatively affected by a vacuum extraction with respect to the probability of having a second child. A primary vacuum extraction decreased the probability of having a third child by 4%, but having two consecutive vacuum extraction deliveries did not further alter the probability. CONCLUSIONS: A first delivery by vacuum extraction does not reduce the probability of subsequent childbearing to the same extent as a first delivery by emergency or elective caesarean section.

Functions of the GTPase Ran in RNA export from the nucleus.

Significant and exciting advances in the field of RNA and protein export have been made recently, due in large part to discovery of the roles played by Ran, a small, soluble GTPase present in both the nucleus and cytoplasm of all eukaryotic cells. Ran is thought to be primarily bound to GTP in the nucleus and to GDP in the cytoplasm, as a result of the assymetric distribution of factors that interact with Ran to promote guanine nucleotide exchange (in the nucleus) and GTP hydrolysis (in the cytoplasm). A key function of the nuclear Ran.GTP is to support formation of complexes containing an export receptor (an exportin) and cargos such as RNAs, RNPs or proteins that are destined for export. In the cytoplasm, removal of the Ran.GTP from the complex results in its destabilization and release of the export cargo. Although Ran.GTP is required for formation of the export complex, GTP hydrolysis does not appear to be necessary for translocation through the nuclear pore complex or cytoplasmic release. Nevertheless, the GTPase of Ran does appear to be required in as yet unidentified intranuclear steps prior to export of some, but not all, RNAs.

Analysis of conformational variations of the cricoid cartilages in Thoroughbred horses using computed tomography.

REASONS FOR PERFORMING STUDY: Loss of arytenoid abduction is a common post operative complication of laryngoplasty without a definitive cause. It has been a clinical impression during laryngoplasty surgery that there is great conformational variability along the caudal edge of the Thoroughbred cricoid cartilage that could impact post operative retention of suture position. A change in suture position would probably lead to some loss of abduction. Defining any structural variability of the cricoid would be an initial step in determining whether this variability could impact on the retention of suture position. HYPOTHESIS: Anatomical variations in the larynx of Thoroughbred horses may be detected and measured using objective analysis and computed tomography. METHODS: Larynges were harvested from 15 mature Thoroughbred horses. Helical CT scans were performed on each specimen. Three independent observers performed a series of measurements on 2D and 3D reconstruction images using digital software. Measurements included the lateral cricoid angle, the caudal cricoid prominences, the distance to the cricoid slope, the angle of the cricoarytenoid joints (CAJ), the cricoid thickness and the suture angle. Mean, standard deviation, coefficient of variation and linear regression analysis were performed among all observers and all measurements. RESULTS: Notable conformational differences were evident on the 3D reconstructions. The highest degree of variability was found in 3 measurements: the distance to the lateral cricoid slope, the lateral cricoid angle and the cricoid thickness. A larger left CAJ angle directly and significantly correlated with a larger suture angle. CONCLUSIONS: There are notable conformational differences among cricoid specimens in the Thoroughbred larynx. POTENTIAL RELEVANCE: The morphometric differences identified may impact on optimal prosthesis placement and long-term retention. Since a larger lateral cricoid angle may facilitate abduction loss secondary to a displaced and loosened suture, alternative techniques for suture placement may be of value to prevent arytenoid abduction loss.

Incidence, detection and outcome of differentiated thyroid cancer in Western Sweden.

BACKGROUND: It is unclear whether the increasing incidence of thyroid cancer (TC) due to increased diagnosis of small and indolent tumours might mask a real increase of clinically significant cancers. The aim of this study was to correlate surgery, pathology and outcome data of individual patients to the mode of primary detection (palpation, by imaging or incidental) to assess if TC incidence has increased. METHODS: The Swedish Cancer Registry identified all patients with TC in Västra Götaland County representing approximately 1.6 million inhabitants. Clinical information was retrieved from medical records of patient cohorts from three study intervals (2001-2002, 2006-2007 and 2011-2014) comprising 60 per cent of all TC patients. Data were also obtained from the NORDCAN registry to compare of TC incidence with other Nordic countries. RESULTS: Between 2001 and 2014, the annualized standard incidence rate/100 000 population (ASR) of TC increased from 3.14 to 10.71 in women and from 1.12 to 3.77 in men. This was higher than the mean incidence for Sweden but similar to that in Norway and Finland. Differentiated TC (DTC) increased more than threefold. The majority of tumours (64 per cent) were detected by palpation. Larger tumours (10-20, 21-40 and greater than 40 mm) increased as much as microcarcinomas (less than 10 mm). Only 5 per cent of the tumours were detected by imaging. All disease-specific deaths (8.5 per cent of DTC in the first two cohorts) and most patients with recurrent or persistent disease (6.6 per cent of DTC cases) were diagnosed due to tumour-related symptoms. CONCLUSION: DTC in Western Sweden gradually increased between 2001 and 2014. The majority of tumours were detected by palpation suggesting a real increase in the incidence of clinically significant thyroid malignancies.

The vertebrate GLFG nucleoporin, Nup98, is an essential component of multiple RNA export pathways.

The 97-kD O-linked glycoprotein, Nup98, is a component of the Xenopus laevis nuclear pore complex and the only vertebrate GLFG nucleoporin identified (Powers, M.A., C. Macauley, F. Masiarz, and D.J. Forbes. 1995. J. Cell Biol. 128:721-736). We have investigated possible roles of xNup98 in the nucleocytoplasmic transport of proteins and RNAs by analyzing the consequences of injecting monospecific polyclonal antibodies to xNup98 into X. laevis oocytes. We show here that nuclear injection of anti-xNup98 inhibited the export of multiple classes of RNAs, including snRNAs, 5S RNA, large ribosomal RNAs, and mRNA. In contrast, the export of tRNA was unaffected. Injection of anti-xNup98 into the oocyte cytoplasm had no effect on export of any of the RNAs. Significantly, nuclear injection of anti-xNup98 antibodies did not inhibit import of either karyophilic proteins or snRNPs. This latter result is in agreement with our previous finding that Nup98 is not an essential element of the protein import pathway. Thus, Nup98 plays a role specifically in RNA export from the nucleus, and it appears to be an essential component of multiple RNA export pathways.

Single strands, triple strands, and kinks in H-DNA.

A naturally occurring (dT-dC)18:(dA-dG)18 repeat in the H conformation of DNA was shown to contain single-stranded nucleotides in the center of the TC18 repeat and on one half of the AG18 repeat. These results support the model that H-DNA is a structure containing both triple-stranded and single-stranded regions. The stability of this structure was affected by both pH and the degree of negative supercoiling: at pH 7.6 to 7.7, a high level of supercoiling was needed to keep about half of the molecules in the H conformation; at pH 6 and pH 5, normal levels of supercoiling supported H-DNA; and at pH 4, no supercoiling was required. At mildly alkaline pH, the TC/AG18 repeat assumed a novel conformation called J-DNA that differed from both the B and H forms. A three-dimensional model for the structure of H-DNA is proposed that accounts both for the single-strandedness of the nucleotides and for the influence of supercoiling on H-DNA formation. This model predicts and evidence is presented that H-DNA introduces a sharp kink in the DNA. Moreover, the angle of this kink appears not to be fixed, so that H-DNA is also a hinged-DNA.

Cyclic 2',3'-phosphates and nontemplated nucleotides at the 3' end of spliceosomal U6 small nuclear RNA's.

Spliceosomal U6 small nuclear RNA (U6 RNA) in species as diverse as man, frog, fruitfly, and soybean have at their 3' ends a cyclic 2',3'-phosphate (greater than p) apparently derived from uridylic acid residues that were added post-transcriptionally. The 3' ends of U6 RNA's from various sources may be processed in different ways, or to different extents, depending on the organism or stage of development. The presence of a greater than p terminus on U6 RNA may influence the activity of U6 RNA either directly during splicing or indirectly by ensuring that the RNA has a defined length or proper conformation (or both).

Proofreading and aminoacylation of tRNAs before export from the nucleus.

After synthesis and processing in the nucleus, mature transfer RNAs (tRNAs) are exported to the cytoplasm in a Ran.guanosine triphosphate-dependent manner. Export of defective or immature tRNAs is avoided by monitoring both structure and function of tRNAs in the nucleus, and only tRNAs with mature 5' and 3' ends are exported. All tRNAs examined can be aminoacylated in nuclei of Xenopus oocytes, thereby providing a possible mechanism for functional proofreading of newly made tRNAs. Inhibition of aminoacylation of a specific tRNA retards its appearance in the cytoplasm, indicating that nuclear aminoacylation promotes efficient export.

Topology and formation of triple-stranded H-DNA.

Repeating copolymers of (dT-dC)n.(dA-dG)n sequences (TC.AGn) can assume a hinged DNA structure (H-DNA) which is composed of triple-stranded and single-stranded regions. A model for the formation of H-DNA is proposed, based on two-dimensional gel electrophoretic analysis of DNA's with different lengths of (TC.AG)n copolymers. In this model, H-DNA formation is initiated at a small denaturation bubble in the interior of the copolymer, which allows the duplexes on either side to rotate slightly and to fold back, in order to make the first base triplet. This nucleation establishes which of several nonequivalent H-DNA conformations is to be assumed by any DNA molecule, thereby trapping each molecule in one of several metastable conformers that are not freely interconvertible. Subsequently, the acceptor region spools up single-stranded polypyrimidines as they are released by progressive denaturation of the donor region; both the spooling and the denaturation result in relaxation of negative supercoils in the rest of the DNA molecule. From the model, it can be predicted that the levels of supercoiling of the DNA determine which half of the (dT-dC)n repeat is to become the donated third strand.

Inhibition of Ran guanosine triphosphatase-dependent nuclear transport by the matrix protein of vesicular stomatitis virus.

Transport of macromolecules into and out of nuclei, essential steps in gene expression, are potential points of control. The matrix protein (M protein) of vesicular stomatitis virus (VSV) was shown to block transport of RNAs and proteins between the nucleus and cytoplasm of Xenopus laevis oocytes. The pattern of inhibition indicated that M protein interfered with transport that is dependent on the ras-like nuclear guanosine triphosphatase (GTPase) Ran-TC4 and its associated factors. This inhibition of nuclear transport by M protein explains several observations about the effects of VSV infection on host cell gene expression and suggests that RNA export is closely coupled to protein import.

Differential control of U1 small nuclear RNA expression during mouse development.

During normal mouse development the relative amounts of two types of U1 small nuclear RNA's (U1 RNA) change significantly. Fetal tissues have comparable levels of the two major types of mouse U1 RNA's, mU1a and mU1b, whereas most differentiated adult tissues contain only mU1a RNA's. Those adult tissues that also accumulate detectable amounts of embryonic (mU1b) RNA's (for example, testis, spleen, and thymus) contain a significant proportion of stem cells capable of further differentiation. Several strains of mice express minor sequence variants of U1 RNA's that are subject to the same developmental controls as the major types of adult and embryonic U1 RNA. The differential accumulation of embryonic U1 RNA's may influence the pattern of gene expression during early development and differentiation.

Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases.

Previously known 5' exonucleases of several eubacterial DNA polymerases have now been shown to be structure-specific endonucleases that cleave single-stranded DNA or RNA at the bifurcated end of a base-paired duplex. Cleavage was not coupled to synthesis, although primers accelerated the rate of cleavage considerably. The enzyme appeared to gain access to the cleavage site by moving from the free end of a 5' extension to the bifurcation of the duplex, where cleavage took place. Single-stranded 5' arms up to 200 nucleotides long were cleaved from such a duplex. Essentially any linear single-stranded nucleic acid can be targeted for specific cleavage by the 5' nuclease of DNA polymerase through hybridization with an oligonucleotide that converts the desired cleavage site into a substrate.

Diverse effects of the guanine nucleotide exchange factor RCC1 on RNA transport.

Transport of RNAs within nuclei and through nuclear pore complexes (NPCs) are essential, but poorly understood, steps in gene expression. In experiments with mammalian cells, RCC1, the abundant nuclear guanine nucleotide exchange factor for the guanosine triphosphatase Ran/TC4, was shown to be required for nucleocytoplasmic transport of precursors of spliceosomal small nuclear RNAs (snRNAs), intranuclear transport of U3 snRNA, and processing of ribosomal RNAs, but not for export of transfer RNAs. It is proposed that guanosine triphosphate (GTP)-bound Ran/TC4 associates with ribonucleoprotein particles (RNPs) during intranuclear movement, and that GTP hydrolysis promotes deposition of RNPs at targeted sites such as NPCs or nucleoli.

Retention and 5' cap trimethylation of U3 snRNA in the nucleus.

It is shown here that maturation of the m7G-capped precursors of U3 small nuclear RNA (snRNA) occurs by a previously unknown pathway. In contrast to the 5' m7G-capped precursors of other snRNAs, this RNA is not exported to the cytoplasm but is retained in the nuclei of Xenopus laevis oocytes, where it undergoes trimethylation of its 5' cap. The m7G caps of most snRNA precursors are trimethylated only after transport of the RNAs to the cytoplasm. The nuclear retention and maturation of this nucleolar RNA raises the possibility that other m7G-capped RNAs are also retained and modified in the nucleus.

Changing seasonal variation in births by sociodemographic factors: a population-based register study.

STUDY QUESTION: Have seasonal variations in births by factors related to maternal education, age, parity and re-partnering changed over a 72-year period? SUMMARY ANSWER: Seasonal variation in births has been reduced overall but also changed its pattern over the last seven decades. WHAT IS KNOWN ALREADY: The number of births varies markedly by season, but the causes of this variation are not fully understood. Seasonality of births is, in some populations, strongly influenced by sociodemographic factors. STUDY DESIGN SIZE DURATION: A longitudinal study design was used by analysing the seasonal variation in live births between 1940 and 2012, and relating it to mothers' sociodemographic characteristics at the time of childbirth (maternal education, age, parity and re-partnering). PARTICIPANTS/MATERIALS SETTING METHODS: Register data on 6 768 810 live births in Sweden between 1940 and 2012 were used. Information on biological parents are available for more than 95% of all births. Multinomial logistic regressions were used to calculate predicted probabilities of giving birth for each calendar month. MAIN RESULTS AND THE ROLE OF CHANCE: Between 1940 and 1999, Swedish birth rates showed the typical seasonal variation with high numbers of births during the spring, and low numbers of births during the last quarter of the year. However, during the 21st century, the seasonal variation in fertility declined so that only minor variation in birth rates between February and September now remains. Still, the pattern of low birth rates at the end of the year remains and has even become more pronounced from the 1980s onwards. The characteristic 'Christmas effect' that used to be visible in September has vanished over the last 30 years. The roles in seasonal variation of maternal education, the mother's age, parity and instances where the mother has re-partnered between subsequent births changed during the second half of the 20th century. From 1980s onwards, the decline in birth rates during the last quarter of the year became particularly pronounced among highly educated mothers. Over the 72 years studied, the seasonal variation among first-time mothers declined steadily and has almost disappeared at the end of the study period. Using data that cover ~180 000 births in each month, all meaningful results are statistically significant. LIMITATIONS REASONS FOR CAUTION: The study uses data from one Nordic country only, making it difficult to draw conclusions that may hold for other countries. WIDER IMPLICATIONS OF THE FINDINGS: The typical seasonal variation reported for Sweden between 1940 and 1999, with high numbers of births during the spring and low numbers of births during the last quarter of the year, is in line with results from most other European countries during the same time period. However, the significant decline in seasonal variation in the early 21st century is a novel development. The study underlines that in a society with low fertility and efficient birth control, active choices and behaviours associated with an individual's sociodemographic characteristics tend to matter more for the seasonal timing of childbearing than environmental factors related to the physiological ability to reproduce and cultural-behavioural factors related to the frequency of intercourse. STUDY FUNDING/COMPETING INTERESTS: The study was funded by the Swedish Research Council (Vetenskapsrådet) via the Swedish Initiative for Research on Microdata in the Social and Medical Sciences (SIMSAM): Stockholm University SIMSAM Node for Demographic Research (grant registration number 340-2013-5164). The authors declare no conflicts of interest. TRIAL REGISTRATION NUMBER: Not applicable.

3'-end-dependent formation of U6 small nuclear ribonucleoprotein particles in Xenopus laevis oocyte nuclei.

We have identified and characterized a U6 small nuclear (sn) ribonucleoprotein particle (RNP) present in the nuclei of Xenopus laevis oocytes. The structure of this U6 snRNP was investigated by native gel shift analysis and a combination of RNA-protein UV cross-linking, RNase T1 fingerprinting, and immunoprecipitation assays. These analyses demonstrate that certain forms of U6 snRNA associate with the 50-kDa nuclear antigen La both in vivo and in vitro. The La protein binds the stretch of uridylates at the 3' hydroxyl end of newly synthesized U6 snRNA. La does not bind to mature U6 snRNAs that have 2',3'-cyclic phosphate (greater than p) groups at their 3' ends (E. Lund and J. E. Dahlberg, Science 255:327-330, 1992) or to U6 snRNAs in anti-Sm-precipitable U4/U6 snRNPs. We propose that 3'-end modification, including posttranscriptional UMP addition, modulates the binding of La protein to U6 snRNA which, in turn, may affect the function of this RNA.

Nucleocytoplasmic transport and processing of small nuclear RNA precursors.

We have analyzed the structures and locations of small nuclear RNA (snRNA) precursors at various stages in their synthesis and maturation. In the nuclei of pulse-labeled Xenopus laevis oocytes, we detected snRNAs that were longer than their mature forms at their 3' ends by up to 10 nucleotides. Analysis of the 5' caps of these RNAs and pulse-chase experiments showed that these nuclear snRNAs were precursors of the cytoplasmic pre-snRNAs that have been observed in the past. Synthesis of pre-snRNAs was not abolished by wheat germ agglutinin, which inhibits export of the pre-snRNAs from the nucleus, indicating that synthesis of these RNAs is not obligatorily coupled to their export. Newly synthesized U1 RNAs could be exported from the nucleus regardless of the length of the 3' extension, but pre-U1 RNAs that were elongated at their 3' ends by more than about 10 nucleotides were poor substrates for trimming in the cytoplasm. The structure at the 3' end was critical for subsequent transport of the RNA back to the nucleus. This requirement ensures that truncated and incompletely processed U1 RNAs are excluded from the nucleus.