Cellular and Molecular Mechanisms of MT1-MMP-Dependent Cancer Cell Invasion.

Metastasis is responsible for most cancer-associated deaths. Accumulating evidence based on 3D migration models has revealed a diversity of invasive migratory schemes reflecting the plasticity of tumor cells to switch between proteolytic and nonproteolytic modes of invasion. Yet, initial stages of localized regional tumor dissemination require proteolytic remodeling of the extracellular matrix to overcome tissue barriers. Recent data indicate that surface-exposed membrane type 1-matrix metalloproteinase (MT1-MMP), belonging to a group of membrane-anchored MMPs, plays a central role in pericellular matrix degradation during basement membrane and interstitial tissue transmigration programs. In addition, a large body of work indicates that MT1-MMP is targeted to specialized actin-rich cell protrusions termed invadopodia, which are responsible for matrix degradation. This review describes the multistep assembly of actin-based invadopodia in molecular details. Mechanisms underlying MT1-MMP traffic to invadopodia through endocytosis/recycling cycles, which are key to the invasive program of carcinoma cells, are discussed.

Centrosome amplification fine tunes tubulin acetylation to differentially control intracellular organization.

Intracellular organelle organization is conserved in eukaryotic cells and is primarily achieved through active transport by motor proteins along the microtubule cytoskeleton. Microtubule post-translational modifications (PTMs) can contribute to microtubule diversity and differentially regulate motor-mediated transport. Here, we show that centrosome amplification, commonly observed in cancer and shown to promote aneuploidy and invasion, induces a global change in organelle positioning towards the cell periphery and facilitates nuclear migration through confined spaces. This reorganization requires kinesin-1 and is analogous to the loss of dynein. Cells with amplified centrosomes display increased levels of acetylated tubulin, a PTM that could enhance kinesin-1-mediated transport. Depletion of α-tubulin acetyltransferase 1 (αTAT1) to block tubulin acetylation rescues the displacement of centrosomes, mitochondria, and vimentin but not Golgi or endosomes. Analyses of the distribution of total and acetylated microtubules indicate that the polarized distribution of modified microtubules, rather than levels alone, plays an important role in the positioning of specific organelles, such as the centrosome. We propose that increased tubulin acetylation differentially impacts kinesin-1-mediated organelle displacement to regulate intracellular organization.

YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis.

YEASTRACT+ (http://yeastract-plus.org/) is a tool for the analysis, prediction and modelling of transcription regulatory data at the gene and genomic levels in yeasts. It incorporates three integrated databases: YEASTRACT (http://yeastract-plus.org/yeastract/), PathoYeastract (http://yeastract-plus.org/pathoyeastract/) and NCYeastract (http://yeastract-plus.org/ncyeastract/), focused on Saccharomyces cerevisiae, pathogenic yeasts of the Candida genus, and non-conventional yeasts of biotechnological relevance. In this release, YEASTRACT+ offers upgraded information on transcription regulation for the ten previously incorporated yeast species, while extending the database to another pathogenic yeast, Candida auris. Since the last release of YEASTRACT+ (January 2020), a fourth database has been integrated. CommunityYeastract (http://yeastract-plus.org/community/) offers a platform for the creation, use, and future update of YEASTRACT-like databases for any yeast of the users' choice. CommunityYeastract currently provides information for two Saccharomyces boulardii strains, Rhodotorula toruloides NP11 oleaginous yeast, and Schizosaccharomyces pombe 972h-. In addition, YEASTRACT+ portal currently gathers 304 547 documented regulatory associations between transcription factors (TF) and target genes and 480 DNA binding sites, considering 2771 TFs from 11 yeast species. A new set of tools, currently implemented for S. cerevisiae and C. albicans, is further offered, combining regulatory information with genome-scale metabolic models to provide predictions on the most promising transcription factors to be exploited in cell factory optimisation or to be used as novel drug targets. The expansion of these new tools to the remaining YEASTRACT+ species is ongoing.

Profiles of interferon-stimulated genes in multiple tissues and circulating pregnancy-associated glycoproteins and their association with pregnancy loss in dairy cows†.

Pregnancy loss (PL) in lactating dairy cows disrupts reproductive and productive efficiency. We evaluated the expression of interferon-stimulated genes (ISG) in blood leukocytes, vaginal and cervical epithelial cells, luteolysis-related genes, progesterone, and pregnancy-associated glycoprotein (PAG) profiles in lactating dairy cows (n = 86) to gain insight about PL. Expression of ISG on d17, d19, and d21 was greater in cows that maintained the pregnancy (P33) compared to nonpregnant with no PL (NP). Greater ISG differences between groups were observed in the cervix (96.7-fold) than vagina (31.0-fold), and least in blood leukocytes (5.6-fold). Based on individual profiles of ISG and PAG, PL was determined to occur either before (~13%) or after (~25%) d22. For cows with PL before d22, ISG expression was similar on d17 but by d21 was lower and OXTR was greater than P33 cows and similar to NP; timing of luteolysis was similar compared to NP cows suggesting embryonic failure to promote luteal maintenance and to attach to the endometrium (no increase in PAG). For cows with PL after d22, ISG expression was similar to P33 cows on d17, d19, and d21 and luteolysis, when it occurred, was later than NP cows; delayed increase in PAG suggested later or inadequate embryonic attachment. In conclusion, PL before d22 occurred due to embryonic demise/failure to signal for luteal maintenance, as reflected in reduced ISG expression by d21. Alternatively, embryos with PL between d22 and 33 adequately signaled for luteal maintenance (ISG) but had delayed/inadequate embryonic attachment and/or inappropriate luteolysis causing PL.

Could driving help us to "see better"? A comparative assessment of saccadic efficiency, visual speed, and attention.

BACKGROUND: This study aimed at comparing drivers' and non-drivers' results in the Adult Developmental Eye Movement with Distractors test (ADEMd) and the Useful Field of View test (UFOV). METHODS: One hundred and twenty Spaniards (mean age 50.90 ± 17.32 years) without eye disease voluntarily participated in this cross-sectional descriptive study. Participants in a single experimental session completed a questionnaire on sociodemographic, health, eyesight, and driving information. They also performed the ADEMd and UFOV tests randomly following standardized protocols. The ADEMd is a visual-verbal test that measures saccadic efficiency and visual attention. Brown-Forsythe (B-F) tests with Games-Howell post-hoc adjustments were conducted to assess differences between groups. Groups were formed according to sex, age (young adults, adults, and older adults), and driver/non-driver for further analysis. Additionally, associations between dependent variables were assessed through Spearman's correlations. RESULTS: Drivers obtained significantly better results in the ADEMd compared with non-drivers. Non-significant differences between drivers and non-drivers were encountered in the UFOV. Additionally, significant differences were observed between sexes and age groups. It is worth highlighting that non-driver's age significantly correlated with worse ADEMd performance (rho = .637 to .716). This correlation was non-significant in drivers. Similarly, reading hours significantly correlated with better ADEMd performance in non-drivers (rho = - .291 to - .363), but not in drivers. The only significant correlations between ADEMd and UFOV tests were found in drivers (rho = .307 to .410). CONCLUSION: Considering all the discussed results, it could be hypothesized that the driving task promotes abilities, such as oculomotor and cognitive function, which are relevant for the performance in the ADEMd. However, this hypothesis is based on correlational outcomes and further studies should causally assess this possible relation.

Southern Ocean phytoplankton dynamics and carbon export: insights from a seasonal cycle approach.

Quantifying the strength and efficiency of the Southern Ocean biological carbon pump (BCP) and its response to predicted changes in the Earth's climate is fundamental to our ability to predict long-term changes in the global carbon cycle and, by extension, the impact of continued anthropogenic perturbation of atmospheric CO2. There is little agreement, however, in climate model projections of the sensitivity of the Southern Ocean BCP to climate change, with a lack of consensus in even the direction of predicted change, highlighting a gap in our understanding of a major planetary carbon flux. In this review, we summarize relevant research that highlights the important role of fine-scale dynamics (both temporal and spatial) that link physical forcing mechanisms to biogeochemical responses that impact the characteristics of the seasonal cycle of phytoplankton and by extension the BCP. This approach highlights the potential for integrating autonomous and remote sensing observations of fine scale dynamics to derive regionally optimized biogeochemical parameterizations for Southern Ocean models. Ongoing development in both the observational and modelling fields will generate new insights into Southern Ocean ecosystem function for improved predictions of the sensitivity of the Southern Ocean BCP to climate change. This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.

The Southern Ocean mixed layer and its boundary fluxes: fine-scale observational progress and future research priorities.

Interactions between the upper ocean and air-ice-ocean fluxes in the Southern Ocean play a critical role in global climate by impacting the overturning circulation and oceanic heat and carbon uptake. Remote and challenging conditions have led to sparse observational coverage, while ongoing field programmes often fail to collect sufficient information in the right place or at the time-space scales required to constrain the variability occurring in the coupled ocean-atmosphere system. Only within the last 10 years have we been able to directly observe and assess the role of the fine-scale ocean and rapidly evolving atmospheric marine boundary layer on the upper limb of the Southern Ocean's overturning circulation. This review summarizes advances in mechanistic understanding, arising in part from observational programmes using autonomous platforms, of the fine-scale processes (1-100 km, hours-seasons) influencing the Southern Ocean mixed layer and its variability. We also review progress in observing the ocean interior connections and the coupled interactions between the ocean, atmosphere and cryosphere that moderate air-sea fluxes of heat and carbon. Most examples provided are for the ice-free Southern Ocean, while major challenges remain for observing the ice-covered ocean. We attempt to elucidate contemporary research gaps and ongoing/future efforts needed to address them. This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.

Rhizobacterial Isolates from Prosopis limensis Promote the Growth of Raphanus sativus L. Under Salt Stress.

Microbial biotechnology employes techniques that rely based on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing agricultural crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments. In this study, bacterial isolates were obtained from soil and roots of Prosopis limensis Bentham from the department of Lambayeque, Peru. This region has high salinity levels, therefore, the collected samples were used to isolate plant growth-promoting rhizobacteria (PGPR), which were identified through morphological, and physical-biochemical characteristics. These salt tolerant bacteria were screened phosphate solubilization, indole acetic acid, deaminase activity and molecular characterization by 16S rDNA sequencing. Eighteen samples from saline soils of the Prosopis limensis plants in the northern coastal desert of San Jose district, Lambayeque, Peru. The bacterial isolates were screened for salt tolerance ranging from 2 to 10%, a total of 78 isolates were found. Isolates 03, 13 and 31 showed maximum salt tolerance at 10%, in vitro ACC production, phosphate solubilization and IAA production. The three isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Pseudomonas sp. 03 (MW604823), Pseudomonas sp. 13 (MW604824) and Bordetella sp. 31 (MW604826). These microorganisms promoted the germination of radish plants and increased the germination rates for treatments T2, T3 and T4 by 129, 124 and 118% respectively. The beneficial effects of salt tolerant PGPR isolates isolated from saline environments can be new species, used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of using these strains as a source of products that can be employed for the development of new compounds proving their potential as biofertilizers for saline environments.

Effects of feeding rumen-protected methionine pre- and postpartum in multiparous Holstein cows: Health disorders and interactions with production and reproduction.

Study objectives were to evaluate the effects of feeding rumen-protected Met (RPM) in pre- and postpartum total mixed rations (TMR) on health disorders and the interactions of health disorders with lactation and reproductive performance. Multiparous Holstein cows [470; 235 cows at University of Wisconsin (UW) and 235 cows at Cornell University (CU)] were enrolled at approximately 4 wk before parturition and housed in close-up dry cow (n = 6) and replicated lactation pens (n = 16). Pens were randomly assigned to treatment diets (pre- and postpartum, respectively): (1) control (CON): basal diet = 2.30% and 2.09% Met as % of metabolizable protein (MP) (UW) or 2.22% and 2.19% Met as % of MP (CU); (2) RPM: basal diet fed with RPM with 2.83% and 2.58% Met (Smartamine M, Adisseo Inc.; 12 g prepartum and 27 g postpartum), as % of MP (UW) or 2.85% and 2.65% Met (Smartamine M; 13 g prepartum and 28 g postpartum), as % of MP (CU). Total serum Ca was evaluated at the time of parturition and on d 3 ± 1 postpartum. Daily rumination was monitored from 7 d before parturition until 28 d postpartum. Health disorders were recorded during the experimental period until the time of first pregnancy diagnosis (32 d after timed artificial insemination; 112 ± 3 d in milk). Uterine health was evaluated on d 35 ± 3 postpartum. Time to pregnancy and herd exit were evaluated up to 350 d in milk. Treatment had no effect on the incidence of most health disorders and did not alter daily rumination. Cows fed RPM had reduced subclinical hypocalcemia (13.6 vs. 22%; UW only) on day of parturition relative to CON. Percentage of cows culled (13.1 vs. 19.3%) and hazard of herd exit due to culling [hazard ratio = 0.65, 95% confidence interval (CI): 0.42-1.02] tended to be reduced for cows fed RPM compared with CON. Moreover, cows fed RPM had greater milk protein concentration and protein yield overall, although retrospective analysis indicated that RPM only significantly increased protein yield in the group of cows with one or more health disorders (1.47 vs. 1.40 kg/d), not in cows without health disorders (1.49 vs. 1.46 kg/d) compared with CON. Overall, treatment had no effect on pregnancy per timed artificial insemination; however, among cows with health disorders, those fed RPM had reduced time to pregnancy compared with CON (hazard ratio = 0.71, 95% CI: 0.53-0.96). Thus, except for subclinical hypocalcemia on the day of parturition, feeding RPM in pre- and postpartum TMR did not reduce the incidence of health disorders, but our retrospective analysis indicated that it lessened the negative effects of health disorders on milk protein production and time to pregnancy.

A rare case of skin metastasis from a chordoma.

Chordoma is an uncommon, indolent malignant tumor arising from notochordal remnants. The incidence of distant metastasis varies between 30 and 40% in different series. Even though local involvement of the skin by direct invasion of chordoma is common, distant skin metastasis are rare, with less than 30 cases reported in the literature. The present clinical case illustrates the slow-growing natural history of a sacral chordoma, which evolved with lung metastasis, followed three years later by skin metastasis, thus giving us the opportunity to review the diagnostic approach, as well as the clinical and histopathological characteristics of this rare tumor.

Boolean function metrics can assist modelers to check and choose logical rules.

Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and interpretation of those systems. Defining rules that determine how the output activity of biological entities is regulated by their respective inputs has proven to be challenging. Partly this is because of the inherent noise in data that allows multiple model parameterizations to fit the experimental observations, but some of it is also due to the fact that models become increasingly larger, making the use of automated tools to assemble the underlying rules indispensable. We present several Boolean function metrics that provide modelers with the appropriate framework to analyze the impact of a particular model parameterization. We demonstrate the link between a semantic characterization of a Boolean function and its consistency with the model's underlying regulatory structure. We further define the properties that outline such consistency and show that several of the Boolean functions under study violate them, questioning their biological plausibility and subsequent use. We also illustrate that regulatory functions can have major differences with regard to their asymptotic output behavior, with some of them being biased towards specific Boolean outcomes when others are dependent on the ratio between activating and inhibitory regulators. Application results show that in a specific signaling cancer network, the function bias can be used to guide the choice of logical operators for a model that matches data observations. Moreover, graph analysis indicates that commonly used Boolean functions become more biased with increasing numbers of regulators, supporting the idea that rule specification can effectively determine regulatory outcome despite the complex dynamics of biological networks.

YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts.

The YEASTRACT+ information system (http://YEASTRACT-PLUS.org/) is a wide-scope tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in yeasts of biotechnological or human health relevance. YEASTRACT+ is a new portal that integrates the previously existing YEASTRACT (http://www.yeastract.com/) and PathoYeastract (http://pathoyeastract.org/) databases and introduces the NCYeastract (Non-Conventional Yeastract) database (http://ncyeastract.org/), focused on the so-called non-conventional yeasts. The information in the YEASTRACT database, focused on Saccharomyces cerevisiae, was updated. PathoYeastract was extended to include two additional pathogenic yeast species: Candida parapsilosis and Candida tropicalis. Furthermore, the NCYeastract database was created, including five biotechnologically relevant yeast species: Zygosaccharomyces baillii, Kluyveromyces lactis, Kluyveromyces marxianus, Yarrowia lipolytica and Komagataella phaffii. The YEASTRACT+ portal gathers 289 706 unique documented regulatory associations between transcription factors (TF) and target genes and 420 DNA binding sites, considering 247 TFs from 10 yeast species. YEASTRACT+ continues to make available tools for the prediction of the TFs involved in the regulation of gene/genomic expression. In this release, these tools were upgraded to enable predictions based on orthologous regulatory associations described for other yeast species, including two new tools for cross-species transcription regulation comparison, based on multi-species promoter and TF regulatory network analyses.

Call the Eckols: Present and Future Potential Cancer Therapies.

In recent years, an increased interest in marine macroalgae bioactive compounds has been recorded due to their benefits to human health and welfare. Several of their bioactivities have been demonstrated, such as anti-inflammatory, antioxidant, anticarcinogenic, antibacterial and antiviral behavior. However, there still lacks a clear definition regarding how these compounds exert their bioactive properties. Of all the bioactive compounds derived from marine macroalgae, attention has been focused on phenolic compounds, specifically in phlorotannins, due to their potential for biomedical applications. Phlorotannins are a diverse and wide group of phenolic compounds, with several structural variations based on the monomer phloroglucinol. Among the diverse phlorotannin structures, the eckol-family of phlorotannins demonstrates remarkable bioactivity, notably their anti-tumoral properties. However, the molecular mechanisms by which this activity is achieved remain elusive and sparse. This review focuses on the described molecular mechanisms of anti-tumoral effects by the eckol family of compounds and the future prospects of these molecules for potential application in oncology therapies.

Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: Clues on host survival and probiotic activity based on promoter sequence variability.

Although Saccharomyces cerevisiae and S. cerevisiae var. boulardii share more than 95% genome sequence homology, only S. cerevisiae var. boulardii displays probiotic activity. In this study, the transcriptomic differences exhibited by S. cerevisiae and S. cerevisiae var. boulardii in intestinal like medium were evaluated. S. cerevisiae was found to display stress response overexpression, consistent with higher ability of S. cerevisiae var. boulardii to survive within the human host, while S. cerevisiae var. boulardii exhibited transcriptional patterns associated with probiotic activity, suggesting increased acetate biosynthesis. Resorting to the creation of a S. cerevisiae var. boulardii genomic database within Yeastract+, a possible correlation between loss or gain of transcription factor binding sites in S. cerevisiae var. boulardii promoters and the transcriptomic pattern is discussed. This study suggests that S. cerevisiae var. boulardii probiotic activity, when compared to S. cerevisiae, relies, at least partially, on differential expression regulation, based on promoter variability.

Cultural and environmental aspects influence lateral preferences.

Transcultural approaches comparing the distribution of lateral preference between countries focused primarily on handedness. However, other laterality dimensions may also be susceptible to cultural variations. The present study compared lateral preference in five dimensions (hand, foot, trunk, hearing, and visual) of young adults from Brazil and Mozambique. Two hundred and two undergraduate students participated in the study, of which 101 were Brazilian (21.7 ± 1.66 years old) and 101 Mozambican (25.6 ± 6.2 years old). The participants' lateral preference direction and degree were assessed using the global lateral preference inventory. Most Brazilians were classified in the moderate preference category, while Mozambicans had a higher frequency of individuals with strong preferences. Hence, Mozambicans presented a higher lateralization degree for all dimensions. A subsequent analysis considering only preference direction (right, left or indifferent), and not degree, did not show the same outcomes, revealing similarities in preference distribution between the two groups. This finding highlights the necessity to incorporate preference degrees in future analysis to not overlook potential differences. We also conclude lateral preference investigations with transcultural approaches should analyse beyond handedness, as other dimensions can also be modulated by cultural characteristics.

From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon.

Numerous genomes are sequenced and made available to the community through the NCBI portal. However, and, unlike what happens for gene function annotation, annotation of promoter sequences and the underlying prediction of regulatory associations is mostly unavailable, severely limiting the ability to interpret genome sequences in a functional genomics perspective. Here we present an approach where one can download a genome of interest from NCBI in the GenBank Flat File (.gbff) format and, with a minimum set of commands, have all the information parsed, organized and made available through the platform web interface. Also, the new genomes are compared with a given genome of reference in search of homologous genes, shared regulatory elements and predicted transcription associations. We present this approach within the context of Community YEASTRACT of the YEASTRACT + portal, thus benefiting from immediate access to all the comparative genomics queries offered in the YEASTRACT + portal. Besides the yeast community, other communities can install the platform independently, without any constraints. In this work, we exemplify the usefulness of the presented tool, within Community YEASTRACT, in constructing a dedicated database and analysing the genome of the highly promising oleaginous red yeast species Rhodotorula toruloides currently poorly studied at the genome and transcriptome levels and with limited genome editing tools. Regulatory prediction is based on the conservation of promoter sequences and available regulatory networks. The case-study examined is focused on the Haa1 transcription factor-a key regulator of yeast resistance to acetic acid, an important inhibitor of industrial bioconversion of lignocellulosic hydrolysates. The new tool described here led to the prediction of a RtHaa1 regulon with expected impact in the optimization of R. toruloides robustness for lignocellulosic and pectin-rich residue biorefinery processes.

Accessory corpus luteum regression during pregnancy II: reproductive outcomes.

The objective of this study was to evaluate the effect of accessory corpus luteum (CL) induction on fertility in dairy cows. On day 5 after artificial insemination (AI), lactating Holstein cows were assigned unequally to receive gonadotrophin-releasing hormone treatment (GnRH) (n = 641) or no treatment (control; n = 289). Cows had their blood sampled for progesterone (P4), and ovaries were scanned by ultrasound on days 5, 12, 19, 26, 33, 47, and 61 after AI. Pregnancy diagnosis was performed on days 26, 33, 47, and 61. On day 12, cows treated with GnRH were allocated to ipsilateral (n = 239) or contralateral (n = 241) groups based on the side of accessory CL formation relative to previous ovulation. Accessory CL cows had greater P4 than controls. In total, 52.7% (78/148) of pregnant cows in contralateral group had accessory CL regression earlier (

Accessory corpus luteum regression during pregnancy I: timing, physiology, and P4 profiles.

Inappropriate corpus luteum (CL) regression can produce pregnancy loss. An experimental model was utilized to investigate regression of accessory CL during pregnancy in dairy cows. Cows were bred (day 0) and treated with gonadotrophin-releasing hormone 6 days later to form accessory CL. Transrectal ultrasound (every other days) and blood samples for progesterone (P4; daily) were performed until day 56 of pregnancy. On day 28, 13 cows were confirmed pregnant, and accessory CL were found contralateral (n = 9) or ipsilateral (n = 4) to previous ovulation. On day 18, CL biopsy was performed to analyze mRNA expression for interferon-stimulated genes (ISGs). Luteolysis occurred more frequently in cows that had contralateral accessory CL (88.9% (8/9)) than in cows with ipsilateral accessory CL (0% (0/4)). Luteolysis of contralateral accessory CL occurred either earlier (days 19-23; 2/8) or later (days 48-53; 6/8) in pregnancy and occurred rapidly (24 h), based on daily P4. After onset of earlier or later accessory CL regression, circulating P4 decreased by 41.2%. There was no difference in luteal tissue mRNA expression for ISGs on day 18 between accessory and original CL and between CL that subsequently regressed or did not regress. On day 56, an oxytocin challenge dramatically increased prostaglandin F2α metabolite (PGFM) in all cows but produced no pregnancy losses, although cows with previous accessory CL regression had greater PGFM. In summary, ipsilateral accessory CL did not regress during pregnancy, whereas most contralateral CL regressed by 63 days of pregnancy, providing evidence for local mechanisms in regression of accessory CL and protection of CL during pregnancy.

The N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts.

Responding to the recent interest of the yeast research community in non-Saccharomyces cerevisiae species of biotechnological relevance, the N.C.Yeastract (http://yeastract-plus.org/ncyeastract/) was associated to YEASTRACT + (http://yeastract-plus.org/). The YEASTRACT + portal is a curated repository of known regulatory associations between transcription factors (TFs) and target genes in yeasts. N.C.Yeastract gathers all published regulatory associations and TF-binding sites for Komagataellaphaffii (formerly Pichia pastoris), the oleaginous yeast Yarrowia lipolytica, the lactose fermenting species Kluyveromyces lactis and Kluyveromyces marxianus, and the remarkably weak acid-tolerant food spoilage yeast Zygosaccharomyces bailii. The objective of this review paper is to advertise the update of the existing information since the release of N.C.Yeastract in 2019, and to raise awareness in the community about its potential to help the day-to-day work on these species, exploring all the information available in the global YEASTRACT + portal. Using simple and widely used examples, a guided exploitation is offered for several tools: (i) inference of orthologous genes; (ii) search for putative TF binding sites and (iii) inter-species comparison of transcription regulatory networks and prediction of TF-regulated networks based on documented regulatory associations available in YEASTRACT + for well-studied species. The usage potentialities of the new CommunityYeastract platform by the yeast community are also discussed.

Effects of feeding rumen-protected methionine pre- and postpartum on reproductive outcomes of multiparous Holstein cows.

Our primary objective was to evaluate the effect of feeding rumen-protected Met (RPM) in the pre- and postpartum total mixed ration (TMR) on pregnancy per artificial insemination (AI) and pregnancy loss in multiparous Holstein cows. We also evaluated multiple secondary reproductive physiological outcomes before and after AI, including uterine health, ovarian cyclicity, response to synchronization of ovulation, and markers of embryo development and size. A total of 470 multiparous Holstein cows [235 at the University of Wisconsin (UW) and 235 at Cornell University (CU)] were used for this experiment. Experimental treatment diets were applied at the pen level (2 and 4 close-up pens at CU and UW, respectively, and 12 and 6 postfresh pens at CU and UW, respectively); thus, pen was the experimental unit, and cow was the observational unit. Cows were enrolled and randomly assigned to be fed the experimental treatment diets at approximately 4 wk before parturition until 67 d of gestation [147 d in milk (DIM)] after their first service. Close-up dry cow and replicated lactation pens were randomly assigned to treatment diets: RPM, prepartum = 2.83% (UW) and 2.85% (CU), postpartum = 2.58% (UW) and 2.65% (CU); and control (CON), prepartum = 2.30% (UW) and 2.22% (CU), postpartum = 2.09% (UW) and 2.19% (CU; Met as percentage of metabolizable protein). Vaginal discharge and uterine cytology (percentage of polymorphonuclear leucocytes) were evaluated at 35 ± 3 DIM. Cows received timed AI (TAI) at 80 ± 3 DIM after synchronization of ovulation with the Double-Ovsynch protocol. Ovarian cyclicity status, response to synchronization of ovulation, and luteal function were determined by measuring circulating concentrations of progesterone at 35 and 49 ± 3 DIM, 48 and 24 h before TAI, and 8, 18, 22, 25, and 29 d after TAI. Interferon-stimulated gene expression in white blood cells were compared on 18 d after TAI (CU only) and pregnancy-specific protein B concentrations at 22, 25, 29, 32, and 67 d after TAI. Pregnancy status was determined using pregnancy-specific protein B at 25 and 29 d after TAI, and by transrectal ultrasonography at 32, 39, and 67 d after TAI. Embryo and amniotic vesicle size were determined at 32 and 39 d after TAI. Pregnancy per AI (25 d: 64.7 vs. 64.0%, 32 d: 54.3 vs. 55.1% for CON and RPM, respectively) and pregnancy loss (25 to 67 d: 22.6 vs. 19.2% for CON and RPM, respectively) for synchronized cows did not differ. The proportion of cows with purulent vaginal discharge (CON = 7.7 vs. RPM = 4.6%) and cytological endometritis (CON = 20.8 vs. RPM = 23.6%) did not differ. Cyclicity status, ovarian responses to the synchronization protocol, and synchronization rate also did not differ. In addition, fold change for interferon-stimulated genes, concentrations of pregnancy-specific protein B, and embryo size were not affected by treatments. In conclusion, feeding RPM in the pre- and postpartum TMR at the amounts used in this experiment did not affect uterine health, cyclicity, embryo development, or reproductive efficiency in dairy cows.