Exchange mechanism of chromosome loss]

Frequencies of induced losses of autosome 2, free arm of autosome 2 and simultaneous losses of two free arms of autosome 2 were determined as 3.25 x 10(-3), 2.78 x 10(-3), 0.84 x 10(-3), respectively. High frequency of simultaneous losses of two chromosomes may have pointed to the exchange nature of the chromosome losses. The similarity of frequencies of half-translocations in heterochromatin of autosome 2 and frequencies of the losses observed show that the chromosome losses are the consequence of exchanges in chromosomal heterochromatin.     

Random species loss underestimates dilution effects of host diversity on foliar fungal diseases under fertilization

With increasing attention being paid to the consequences of global biodiversity losses, several recent studies have demonstrated that realistic species losses can have larger impacts than random species losses on community productivity and resilience. However, little is known about the effects of the order in which species are lost on biodiversity–disease relationships. Using a multiyear nitrogen addition and artificial warming experiment in natural assemblages of alpine meadow vegetation on the Qinghai‐Tibetan Plateau, we inferred the sequence of plant species losses under fertilization/warming. Then the sequence of species losses under fertilization/warming was used to simulate the species loss orders (both realistic and random) in an adjacently novel removal experiment manipulating plot‐level plant diversity. We explicitly compared the effect sizes of random versus realistic species losses simulated from fertilization/warming on plant foliar fungal diseases. We found that realistic species losses simulated from fertilization had greater effects than random losses on fungal diseases, and that species identity drove the diversity–disease relationship. Moreover, the plant species most prone to foliar fungal diseases were also the least vulnerable to extinction under fertilization, demonstrating the importance of protecting low competence species (the ability to maintain and transmit fungal infections was low) to impede the spread of infectious disease. In contrast, there was no difference between random and realistic species loss scenarios simulated from experimental warming (or the combination of warming and fertilization) on the diversity–disease relationship, indicating that the functional consequences of species losses may vary under different drivers.     

Lactation weight loss influences subsequent reproductive performance of sows

In order to examine the effect of different lactation weight losses of sows of different parity on subsequent reproductive performance, the present trial was performed in German (n = 4) and Slowakian (n = 11) indoor pig breeding units (n = 1677 sows evaluated). Weaning-to-service-intervals, farrowing rates and total-born litter sizes in sows with different lactation weight losses were compared. Sows were categorized according to lactation weight losses of <5%, 5-10%, 11-15%, 16-20%, >20%. Lactation weight losses exerted a quadratic effect (P < 0.01) on weaning-to-service-intervals. When analyzed across parity categories, with parity category included as a fixed effect, the weaning-to-service-intervals appeared to be minimized at lactation weight losses of <5%. Weaning-to-service-intervals increased (P < 0.05) when lactation weight losses increased above 5% for parity 1 sows, but not until lactation weight losses exceeded 10% for animals of parity 2 and more. There was a parity effect observed at lactation weight losses of <10%, P < 0.05, but the difference was not significant any more at lactation weight losses of >10%. Lactation weight losses >10% had a negative (P < 0.05) effect on subsequent farrowing rates to first service. The difference was higher (P < 0.01) in sows with lactation weight losses >20%. Lactation weight losses exerted a negative (P < 0.001) effect on total-born litter sizes in parity 1 versus parity >5 and parity 1 versus parity 2-5 sows at lactation weight losses of >10%. CONCLUSION: As weight loss of sows during lactation increases subsequent reproduction performance decreases.     

Apparent trends of amino Acid gain and loss in protein evolution due to nearly neutral variation

It has recently been claimed that certain amino acids have been increasing in frequency in all living organisms for most of the history of life on earth, while other amino acids have been decreasing in frequency. Three lines of evidence have been offered for this assertion, but each has a more plausible alternative interpretation. Here I show that unequal patterns of gains and losses for particular pairs of amino acids (such as more leucine --> phenylalanine than phenylalanine --> leucine substitutions in humans and chimpanzees since they split from a common ancestor) are consistent with a simple neutral model at equilibrium amino acid frequencies. Unequal numbers of gains and losses for particular amino acids (such as more gains than losses of cysteine) are shown by simulations to be consistent with a model of nearly neutral evolution. Unequal numbers of gains and losses for particular amino acids in human polymorphism data are shown by simulations to be explainable by the nearly neutral model as well. In a comparison of protein sequences from four strains of Escherichia coli, polarized by one outgroup strain of Salmonella, the disparity in number of gains and losses for particular amino acids is strong in terminal branches but weaker or nonexistent in internal branches, which is inconsistent with the universal trend model but as expected under the nearly neutral model.     

Global declines in human‐driven mangrove loss

Global mangrove loss has been attributed primarily to human activity. Anthropogenic loss hotspots across Southeast Asia and around the world have characterized the ecosystem as highly threatened, though natural processes such as erosion can also play a significant role in forest vulnerability. However, the extent of human and natural threats has not been fully quantified at the global scale. Here, using a Random Forest‐based analysis of over one million Landsat images, we present the first 30 m resolution global maps of the drivers of mangrove loss from 2000 to 2016, capturing both human‐driven and natural stressors. We estimate that 62% of global losses between 2000 and 2016 resulted from land‐use change, primarily through conversion to aquaculture and agriculture. Up to 80% of these human‐driven losses occurred within six Southeast Asian nations, reflecting the regional emphasis on enhancing aquaculture for export to support economic development. Both anthropogenic and natural losses declined between 2000 and 2016, though slower declines in natural loss caused an increase in their relative contribution to total global loss area. We attribute the decline in anthropogenic losses to the regionally dependent combination of increased emphasis on conservation efforts and a lack of remaining mangroves viable for conversion. While efforts to restore and protect mangroves appear to be effective over decadal timescales, the emergence of natural drivers of loss presents an immediate challenge for coastal adaptation. We anticipate that our results will inform decision‐making within conservation and restoration initiatives by providing a locally relevant understanding of the causes of mangrove loss.     

Looking for loss in all the wrong places: loss avoidance does not explain cheater detection

The ability to detect cheaters has been proposed as an adaptive design feature of psychological adaptations for cooperation. This proposal has been tested with studies on the Wason selection task, which purportedly demonstrate that humans possess a specific competence for detecting cheaters in cooperative interactions. An alternative set of theories suggests that people are not looking for cheaters per se, but are looking for losses in an effort to maximize their utility. In previous investigations of cheater detection, cheating has been confounded with someone suffering a loss. We sought to test rival accounts of cheater detection by devising versions of the selection task in which cheating is unconfounded with losses. The results suggest that people are competent at detecting cheaters even when no losses are involved, lending support to the view that cheater detection is a specific design feature of psychological adaptations for cooperation.     

Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra

In protein identification through tandem mass spectrometry, it is critical to accurately predict the theoretical spectrum for a peptide sequence. The widely used prediction models, such as SEQUEST and MASCOT, ignore the intensity of the ions with important neutral losses, including water loss and ammonia loss. However, ignoring these neutral losses results in a significant deviation between the predicted theoretical spectrum and its experimental counterpart. Here, based on the "one peak, multiple explanations" observation, we proposed an expectation-maximization (EM) method to automatically learn the probabilities of water loss and ammonia loss for each amino acid. Then we employed these probabilities to design an improved statistical model for theoretical spectrum prediction. We implemented these methods and tested them on practical data. On a training set containing 1803 spectra, the experimental results show a good agreement with some known knowledge about neutral losses, such as the tendency of water loss from Asp, Glu, Ser, and Thr. Furthermore, on a testing set containing 941 spectra, the improved similarity between the experimental and predicted spectra demonstrates that this method can generate more reasonable predictions relative to the model that ignores neutral losses. As an application of the derived probabilities, we implemented a database searching method adopting the improved theoretical spectrum model with neutral loss ions estimated. Experimental results on Keller's data set demonstrate that this method can identify peptides more accurately than SEQUEST. In another application to validate SEQUEST's results, the reported peptide-spectrum pairs are reranked with respect to the similarity between experimental and predicted spectra. Experimental results on both LTQ and QSTAR data sets suggest that this reranking strategy can effectively distinguish the false negative predictions reported by SEQUEST.     

Firm-level economic effects of HABS: A tool for business loss assessment

While the economic consequences of HABs may seem obvious, there is little empirical evidence to support the assertion or its magnitude relative to other environmental effects. As scientists learn more about the effectiveness of alternative HAB prevention, mitigation, and control strategies and agencies prepare for a suite of environmental events, information on potential economic losses are needed at the firm level to evaluate and justify continued HAB-related expenditures. To determine the extent of monetary losses that some firms may have incurred due to blooms of Karenia brevis (red tides) in Southwest Florida, 7 years of daily proprietary data were obtained from three beachfront restaurants and supplemented with environmental data from nearby weather stations. The statistical models revealed that reductions in daily sales ranged from $868 to $3734 (13.7%–15.3% on average) when red tide conditions were present. Estimated losses are compared to other environmental events and were found to coincide with those from other studies. The incidence of red tide events (as noted by each restaurant manager) corresponded with cell counts that averaged 180,853 cells/l as measured within 6 miles. Collectively this information supports the hypothesis of localized economic losses and provides a threshold cell count for future loss projections.     

On the incidence of intron loss and gain in paralogous gene families

Understanding gene duplication and gene structure evolution are fundamental goals of molecular evolutionary biology. A previous study by Babenko et al. (2004. Prevalence of intron gain over intron loss in the evolution of paralogous gene families. Nucleic Acids Res. 32:3724-3733) employed Dollo parsimony to infer spliceosomal intron losses and gains in paralogous gene families and concluded that there was a general excess of gains over losses. This result contrasts with patterns in orthologous genes, in which most lineages show an excess of intron losses over gains, suggesting the possibility of fundamentally different modes of intron evolution between orthologous and paralogous genes. We further studied the data and found a low level of intron position conservation with outgroups, and this led to problems with using Dollo parsimony to analyze the data. Statistical reanalysis of the data suggests, instead, that intron losses have outnumbered intron gains in paralogous gene families.     

Four separate regions on chromosome 17 show loss of heterozygosity in familial breast carcinomas

Two genes predisposing females to autosomal dominant breast cancer are located on chromosome 17. Mutations in the p53-gene on the short arm have been shown to predispose females to early onset breast cancer in families with the rare Li-Fraumeni syndrome. Another locus on 17q (BRCA1), was found to be linked to the disease in a subset of families with breast cancer. In order to determine the involvement of tumour suppressor genes at these loci in tumour development, we studied allele losses for markers on chromosome 17 in 78 familial breast carcinomas. The analysis used six polymorphic DNA markers, three on each arm. We found support for at least four separate regions displaying allele losses on chromosome 17: the p53-region, the distal part of 17p, the BRCA1 region and the distal part of 17q. The frequency of allele losses on distal 17p (16%) is low in these familial tumours compared with the previously reported incidence in sporadic tumours (>50%), whereas the frequency of losses at the p53 locus and on 17q was similar to sporadic tumours (5%–40%). These data suggest that several regions on chromosomal 17 can harbour tumour suppressor genes involved in tumour development of familial breast cancer.     

Differential loss of cytochrome-c oxidase subunits in ischemia-reperfusion injury: exacerbation of COI subunit loss by PKC-epsilon inhibition

We have previously described a PKC-epsilon interaction with cytochrome oxidase subunit IV (COIV) that correlates with enhanced CO activity and cardiac ischemic preconditioning (PC). We therefore investigated the effects of PC and ischemia-reperfusion (I/R) injury on CO subunit levels in an anesthetized rat coronary ligation model. Homogenates prepared from the left ventricular regions at risk (RAR) and not at risk (RNAR) for I/R injury were fractionated into cell-soluble (S), 600 g low-speed centrifugation (L), gradient-purified mitochondrial (M), and 100,000 g particulate (P) fractions. In RAR tissue, PC (2 cycles of 5-min ischemia and 5-min reperfusion) decreased the COI in the P fraction ( approximately 29% of total cellular COI), suggesting changes in interfibrillar mitochondria. After 30 min of ischemia and 120 min of reperfusion, total COI levels decreased in the RAR by 72%. Subunit Va was also downregulated by 42% following prolonged I/R in the RAR. PC administered before I/R reduced the loss of COI in the M and P fractions approximately 30% and prevented COVa losses completely. We observed no losses in subunits Vb and VIIa following I/R alone; however, significant losses occurred when PC was administered before prolonged I/R. Delivery of a cell-permeable PKC-epsilon translocation inhibitor (epsilonV1-2) to isolated rat hearts before prolonged I/R dramatically increased COI loss, suggesting that PKC-epsilon protects COI levels. We propose that additional measures to protect CO subunits when coadministered with PC may improve its cardioprotection against I/R injury.     

Future hotspots of terrestrial mammal loss

Current levels of endangerment and historical trends of species and habitats are the main criteria used to direct conservation efforts globally. Estimates of future declines, which might indicate different priorities than past declines, have been limited by the lack of appropriate data and models. Given that much of conservation is about anticipating and responding to future threats, our inability to look forward at a global scale has been a major constraint on effective action. Here, we assess the geography and extent of projected future changes in suitable habitat for terrestrial mammals within their present ranges. We used a global earth-system model, IMAGE, coupled with fine-scale habitat suitability models and parametrized according to four global scenarios of human development. We identified the most affected countries by 2050 for each scenario, assuming that no additional conservation actions other than those described in the scenarios take place. We found that, with some exceptions, most of the countries with the largest predicted losses of suitable habitat for mammals are in Africa and the Americas. African and North American countries were also predicted to host the most species with large proportional global declines. Most of the countries we identified as future hotspots of terrestrial mammal loss have little or no overlap with the present global conservation priorities, thus confirming the need for forward-looking analyses in conservation priority setting. The expected growth in human populations and consumption in hotspots of future mammal loss mean that local conservation actions such as protected areas might not be sufficient to mitigate losses. Other policies, directed towards the root causes of biodiversity loss, are required, both in Africa and other parts of the world.     

The frequency of endemic fetal loss in dairy cattle: a review

Estimates of the frequency of endemic fetal loss range from 0.4 to 10.6%, a 26-fold difference, in 26 studies of dairy herds over 5 decades. Sources of this difference include breed, geographic, study population, case definition and procedural differences. The definition of fetal loss was inconsistent among the studies and was often not clearly stated. Twelve of the studies cited only visually observed losses, while the remainder reported losses of all known pregnancies but using different gestational at-risk periods. Definitions of the resulting frequency measure and methods of computation varied widely among the studies. Fetal loss frequencies have been reported as ratios, proportions, incidence rates and cumulative incidence rates. Denominators used in frequency calculations have included the number of pregnant cows, number of cows in the breeding herd, number of cows that calved before or after the risk period and number of calves born. These procedural differences make comparisons among studies and an overall estimate of an expected frequency of endemic fetal loss in dairy cattle difficult at best. Procedural and definition differences aside, the median frequency of fetal loss from studies enumerating only observed abortions was 1.95% and from the studies that included both observed and unobserved abortions 6.5%. Based on this difference, approximately only 30% of endemic fetal losses are observed visually.     

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss

Dollo’s law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic causes. The genomes of budding yeasts have been shaped by extensive reductive evolution, such as reduced genome sizes and the losses of metabolic capabilities. However, the extent and mechanisms of trait reacquisition after gene loss in yeasts have not been thoroughly studied. Here, through phylogenomic analyses, we reconstructed the evolutionary history of the yeast galactose utilization pathway and observed widespread and repeated losses of the ability to utilize galactose, which occurred concurrently with the losses of GALactose (GAL) utilization genes. Unexpectedly, we detected multiple galactose-utilizing lineages that were deeply embedded within clades that underwent ancient losses of galactose utilization. We show that at least two, and possibly three, lineages reacquired the GAL pathway via yeast-to-yeast horizontal gene transfer. Our results show how trait reacquisition can occur tens of millions of years after an initial loss via horizontal gene transfer from distant relatives. These findings demonstrate that the losses of complex traits and even whole pathways are not always evolutionary dead-ends, highlighting how reversals to ancestral states can occur.     

The irreversible loss of a decomposition pathway marks the single origin of an ectomycorrhizal symbiosis

Microbial symbioses have evolved repeatedly across the tree of life, but the genetic changes underlying transitions to symbiosis are largely unknown, especially for eukaryotic microbial symbionts. We used the genus Amanita, an iconic group of mushroom-forming fungi engaged in ectomycorrhizal symbioses with plants, to identify both the origins and potential genetic changes maintaining the stability of this mutualism. A multi-gene phylogeny reveals one origin of the symbiosis within Amanita, with a single transition from saprotrophic decomposition of dead organic matter to biotrophic dependence on host plants for carbon. Associated with this transition are the losses of two cellulase genes, each of which plays a critical role in extracellular decomposition of organic matter. However a third gene, which acts at later stages in cellulose decomposition, is retained by many, but not all, ectomycorrhizal species. Experiments confirm that symbiotic Amanita species have lost the ability to grow on complex organic matter and have therefore lost the capacity to live in forest soils without carbon supplied by a host plant. Irreversible losses of decomposition pathways are likely to play key roles in the evolutionary stability of these ubiquitous mutualisms.     

Analysis of several factors of variation of gestation loss in breeding mares

The files for ultrasound diagnosis of gestating mares belonging to the French equine herd recorded for 3 consecutive years were joined with the files for foal birth of these same mares, allowing the statistical analysis of factors of pregnancy loss. For 28 872 positive diagnoses of gestation, 2898 losses were recorded, that is, a global rate of gestation interruption of 9.12%. The etiology of these interruptions is mainly extrinsic: the year and month of insemination, as well as region for climatic reasons. The intrinsic causes that are implicated are breed of the father (heavy breeds except the hypermetric ones lose fewer pregnancies than warm-blooded breeds), age of the mother (losses are lower in mares of 7 to 10 years of age) and status (mares with foals have fewer pregnancy losses than mares not having foaled the previous year), as well as fetuses with consanguinity (when this increases, the pregnancy losses increase as well). However, the additive genetic effect is extremely low; it corresponds to heritability below 5% and few effects of the environment, common to the offspring of the same mare, were identified. This therefore gives little hope of being able to select against the ‘gestation loss’ trait.     

Human footprints in the Global South accelerate biomass carbon loss in ecologically sensitive regions

Human activities have placed significant pressure on the terrestrial biosphere, leading to ecosystem degradation and carbon losses. However, the full impact of these activities on terrestrial biomass carbon remains unexplored. In this study, we examined changes in global human footprint (HFP) and human-induced aboveground biomass carbon (AGBC) losses from 2000 to 2018. Our findings show an increasing trend in HFP globally, resulting in the conversion of wilderness areas to highly modified regions. These changes have altered global biomes' habitats, particularly in tropical and subtropical regions. We also found accelerated AGBC loss driven by HFP expansion, with a total loss of 19.99 ± 0.196 PgC from 2000 to 2018, especially in tropical regions. Additionally, AGBC is more vulnerable in the Global South than in the Global North. Human activities threaten natural habitats, resulting in increasing AGBC loss even in strictly protected areas. Therefore, scientifically guided planning of future human activities is crucial to protect half of Earth through mitigation and adaptation under future risks of climate change and global urbanization.     

Infectious causes of reproductive loss in camelids

Reproductive losses in camelids are due to infertility, pregnancy loss, udder diseases and neonatal mortality caused by a variety of infectious diseases. Uterine infection and abortion represent the major complaint in camelid veterinary practice. The major infectious organisms in endometritis and metritis are E. coli and Streptococcus equi subspecies zooepidemicus. Abortion rates due to infectious diseases vary from 10% to more than 70% in some areas. Leptospirosis, toxoplasmosis and chlamydiosis have been diagnosed as the major causes of abortion in llamas and alpacas. In camels, brucellosis and trypanosomiasis represent the major causes of infectious abortion in the Middle East and Africa. Mastitis is rare in South American camelids. The prevalence of subclinical udder infection in camels can reach very high proportions in dairy camels. Udder infections are primarily due to Streptococcus agalactiae and Staphylococcus aureus. Neonatal mortality is primarily due to diarrhea following failure of passive transfer and exposure to E. coli, rotavirus, coronavirus, Coccidia and Salmonella. This paper reviews the etio-pathogenesis of these causes of reproductive losses, as well as the major risk factors and strategies to prevent their occurrence.     

The genetics of vitamin C loss in vertebrates

Vitamin C (ascorbic acid) plays important roles as an anti-oxidant and in collagen synthesis. These important roles, and the relatively large amounts of vitamin C required daily, likely explain why most vertebrate species are able to synthesize this compound. Surprisingly, many species, such as teleost fishes, anthropoid primates, guinea pigs, as well as some bat and Passeriformes bird species, have lost the capacity to synthesize it. Here, we review the genetic bases behind the repeated losses in the ability to synthesize vitamin C as well as their implications. In all cases so far studied, the inability to synthesize vitamin C is due to mutations in the L-gulono-γ-lactone oxidase (GLO) gene which codes for the enzyme responsible for catalyzing the last step of vitamin C biosynthesis. The bias for mutations in this particular gene is likely due to the fact that losing it only affects vitamin C production. Whereas the GLO gene mutations in fish, anthropoid primates and guinea pigs are irreversible, some of the GLO pseudogenes found in bat species have been shown to be reactivated during evolution. The same phenomenon is thought to have occurred in some Passeriformes bird species. Interestingly, these GLO gene losses and reactivations are unrelated to the diet of the species involved. This suggests that losing the ability to make vitamin C is a neutral trait.     

Analysis of ammonia loss mechanisms in microbial fuel cells treating animal wastewater

Ammonia losses during swine wastewater treatment were examined using single- and two-chambered microbial fuel cells (MFCs). Ammonia removal was 60% over 5 days for a single-chamber MFC with the cathode exposed to air (air-cathode), versus 69% over 13 days from the anode chamber in a two-chamber MFC with a ferricyanide catholyte. In both types of systems, ammonia losses were accelerated with electricity generation. For the air-cathode system, our results suggest that nitrogen losses during electricity generation were increased due to ammonia volatilization with conversion of ammonium ion to the more volatile ammonia species as a result of an elevated pH near the cathode (where protons are consumed). This loss mechanism was supported by abiotic tests (applied voltage of 1.1 V). In a two-chamber MFC, nitrogen losses were primarily due to ammonium ion diffusion through the membrane connecting the anode and cathode chambers. This loss was higher with electricity generation as the rate of ammonium transport was increased by charge transfer across the membrane. Ammonia was not found to be used as a substrate for electricity generation, as intermittent ammonia injections did not produce power. The ammonia-oxidizing bacterium Nitrosomonas europaea was found on the cathode electrode of the single-chamber system, supporting evidence of biological nitrification, but anaerobic ammonia-oxidizing bacteria were not detected by molecular analyses. It is concluded that ammonia losses from the anode chamber were driven primarily by physical-chemical factors that are increased with electricity generation, although some losses may occur through biological nitrification and denitrification.